diff --git a/.coveragerc b/.coveragerc deleted file mode 100644 index ec4cdc378..000000000 --- a/.coveragerc +++ /dev/null @@ -1,30 +0,0 @@ -[report] -# Regexes for lines to exclude from consideration -exclude_lines = - # Have to re-enable the standard pragma - pragma: no cover - - # Don't complain about missing debug-only code: - def __repr__ - if self\.debug - - # Don't complain if tests don't hit defensive assertion code: - raise AssertionError - raise NotImplementedError - - # Don't complain if non-runnable code isn't run: - if 0: - if __name__ == .__main__.: - -[run] -omit = - # data files - */test_03_core_data/* - # tutorials - *tutorials* - # dirs - */dust/* - */mag/* - tofu/openadas2tofu/* - tofu/imas2tofu/* - tofu/entrypoints/*.py \ No newline at end of file diff --git a/.github/workflows/test-complete-matrix.yml b/.github/workflows/test-complete-matrix.yml index 9a3173c7e..e8fcb2941 100644 --- a/.github/workflows/test-complete-matrix.yml +++ b/.github/workflows/test-complete-matrix.yml @@ -2,9 +2,13 @@ name: Complete testing matrix on: push: - branches: [ devel, master ] + branches: + - devel + - master pull_request: - branches: [ devel, master ] + branches: + - devel + - master jobs: build: @@ -13,37 +17,64 @@ jobs: strategy: matrix: - os: [ubuntu-latest, macOS-latest] # , windows-latest - python-version: ['3.8', '3.9', '3.10', '3.11'] + os: [ubuntu-latest] + # macOS-latest: issue with latex + meson fails build + # windows-latest: issue with TcL install error + meson fails to build + python-version: ['3.9', '3.10', '3.11'] exclude: - python-version: ['3.11'] os: windows-latest steps: - - uses: actions/checkout@v4 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 + + # Install latex + - name: Install latex for matplotlib + shell: bash + run: | + if [ "$RUNNER_OS" == "Linux" ]; then + sudo apt update + sudo apt install texlive texlive-latex-extra texlive-fonts-recommended dvipng cm-super + elif [ "$RUNNER_OS" == "macOS" ]; then + # not enough to fix latex issue + sudo brew install --cask mactex + elif [ "$RUNNER_OS" != "Linux" ]; then + echo "$RUNNER_OS not supported" + exit 0 + fi + + # git checkout + - name: git checkout + uses: actions/checkout@v5 with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies + # https://github.com/marketplace/actions/checkout#usage + fetch-depth: 0 # to fetch all history from all branches + fetch-tags: true + + # Install uv + - name: Install uv + uses: astral-sh/setup-uv@v5 + with: + python-version: ${{ matrix.python-version }} + + # Build dist + - name: Build the project run: | - curl -X PURGE https://pypi.org/simple/datastock/ - curl -X PURGE https://pypi.org/simple/bsplines2d/ - curl -X PURGE https://pypi.org/simple/spectrally/ - pip install --upgrade pip - pip install flake8 pytest coverage wheel - pip install -r requirements.txt --no-cache - - name: Lint with flake8 + uv build + + # Create and activate env + - name: Create and activate env run: | - # stop the build if there are Python syntax errors or undefined names - # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - flake8 . --count --select=E9,F63,F7 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: install tofu + uv venv venv --python ${{ matrix.python-version }} + source .venv/bin/activate + uv pip install latex + + # Install library + - name: Install the project run: | - python -c "import setuptools; print(f'\nsetuptools version = {setuptools.__version__}\n')" - pip install -e ".[dev]" --no-build-isolation + uv pip install ./dist/*.whl + + # Run tests - name: Test with pytest and coverage run: | - coverage run --source=tofu/ -m pytest tofu/tests -v -x --durations=10 + cd ./dist/ + pytest --pyargs tofu.tests -xv --durations=10 diff --git a/.github/workflows/test-single-linux.yml b/.github/workflows/test-single-linux.yml index 3d425b677..6d507d3fe 100644 --- a/.github/workflows/test-single-linux.yml +++ b/.github/workflows/test-single-linux.yml @@ -1,4 +1,4 @@ -name: Ubuntu, py 3.8, pip +name: Ubuntu, py 3.11, pip on: push: @@ -11,32 +11,53 @@ on: - master - devel - deploy-test + jobs: build-linux: runs-on: ubuntu-latest strategy: max-parallel: 5 steps: - - uses: actions/checkout@v4 - - name: Set up Python 3.9 - uses: actions/setup-python@v5 + + # Install latex + - name: Install latex for matplotlib + run: | + sudo apt update + sudo apt install texlive texlive-latex-extra texlive-fonts-recommended dvipng cm-super + + # git checkout + - name: git checkout + uses: actions/checkout@v5 with: - python-version: 3.9 - - name: Install dependencies + # https://github.com/marketplace/actions/checkout#usage + fetch-depth: 0 # to fetch all history from all branches + fetch-tags: true + + # Install uv + - name: Install uv + uses: astral-sh/setup-uv@v5 + with: + python-version: 3.11 + + # Build dist + - name: Build the project run: | - pip install --upgrade pip - pip install flake8 pytest coverage wheel - pip install -r requirements.txt # fix - - name: Lint with flake8 + uv build + + # Create and activate env + - name: Create and activate env run: | - # stop the build if there are Python syntax errors or undefined names - # too many F82 errors, should uncomment the following line - flake8 . --count --select=E9,F63,F7 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: install tofu + uv venv venv --python 3.11 + source .venv/bin/activate + uv pip install latex + + # Install library + - name: Install the project run: | - pip install -e ".[dev]" --no-build-isolation + uv pip install ./dist/*.whl + + # Run tests - name: Test with pytest and coverage run: | - coverage run --source=tofu/ -m pytest tofu/tests -x -v --durations=10 + cd ./dist/ + pytest --pyargs tofu.tests -xv --durations=10 diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 147af12fa..000000000 --- a/.travis.yml +++ /dev/null @@ -1,153 +0,0 @@ -language: python -jobs: - include: - - name: "Bionic python 3.7" - os: linux - dist: bionic - if: branch = master OR branch = devel OR branch = deploy-test OR tag is present - python: 3.7 - env: - - REPO=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh - - OS=linux-64 - - name: "trusty python 3.6" - os: linux - dist: trusty - python: 3.6 - if: branch = master OR branch = devel OR branch = deploy-test OR tag is present - env: - - REPO=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh - - OS=linux-64 - - name: "xenial python 3.7" - os: linux - dist: xenial - python: 3.7 - if: branch = master OR branch = devel OR branch = deploy-test OR tag is present - env: - - REPO=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh - - OS=linux-64 - - name: "xenial python 3.6" - os: linux - dist: xenial - python: 3.6 - if: branch = master OR branch = devel OR branch = deploy-test OR tag is present - env: - - REPO=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh - - OS=linux-64 - - name: "osx python 3.7" - os: osx - language: generic - if: branch = master OR branch = devel OR branch = deploy-test OR tag is present - env: - - REPO=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh - - TRAVIS_PYTHON_VERSION=3.7 - - OS=osx-64 - - name: "osx python 3.6" - os: osx - language: generic - if: branch = master OR branch = devel OR branch = deploy-test OR tag is present - env: - - REPO=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh - - TRAVIS_PYTHON_VERSION=3.6 - - OS=osx-64 - -env: - global: - - MPLBACKEND=agg - -before_install: - - gcc --version - - export START=$(pwd) - -install: -- wget "$REPO" -O miniconda.sh -- bash miniconda.sh -b -p $HOME/miniconda -- export PATH="$HOME/miniconda/bin:$PATH" -- hash -r -- conda config --set always_yes yes --set changeps1 no -- conda config --append channels conda-forge -- conda config --append channels tofuproject -- conda info -a -- conda install -q python="$TRAVIS_PYTHON_VERSION" conda-verify coverage codecov -- pip install pytest -- export REV=$(python -c "import _updateversion as up; out=up.updateversion(); print(out)") -- export VERSION=$(echo $REV | tr - .) -- echo $REV -- pip install -e ".[dev]" -- export IS_MASTER=$(git ls-remote origin | grep "$TRAVIS_COMMIT\s\+refs/heads/master$" | grep -o "master") -- export IS_DEPLOY=$(git ls-remote origin | grep "$TRAVIS_COMMIT\s\+refs/heads/deploy-test$" | grep -o "deploy-test") -- echo $TRAVIS_COMMIT -- echo $IS_MASTER -- echo $IS_DEPLOY - -script: -- coverage run --source=tofu/ -m pytest tofu/tests -v --durations=10 -- coverage report -- coverage html -- tofu-version -- tofu-custom -- tofu --version -- tofu custom - -after_success: -- codecov -- chmod +x $START/anaconda_upload.sh -- echo $TRAVIS_TAG - -before_deploy: - - > - if ! [ "$BEFORE_DEPLOY_RUN" ]; then - export BEFORE_DEPLOY_RUN=1; - echo "BEFORE DEPLOY START........" - ls $START - cd $START - echo "BEFORE DEPLOY END.........." - fi # to be run only once then -deploy: - - provider: pypi - distributions: sdist - username: __token__ - skip_existing: true - skip_cleanup: true - - on: - tags: true - condition: $IS_DEPLOY = "deploy-test" - server: https://test.pypi.org/legacy/ - password: - secure: xfVFuoz9YYNChzmT8DC9y+8eH6zdFkfoy3B51uqy8b+vhJNzCzLay4F0uSHvhHy6iYorM6UQKr6soC4D7n3PhmnFOTX/cgLtd/p4gBWGYZF6yXacvw+UHKMshgbAhn2sEynxdSAqdAlNttMI8jsUu9RhbzGiv1l5zSNnFWF4Zsly02G68UnztxIGoz8AYTRW2N2oQhGrl/ryj/YG4mSRKjled6BzK7kNoJUqLGl12DqdMMTEmdJ9NHBXgK3Dv0ya17ReFz3TcxE/4+Yc38NwSR4Ia2EvVSMtyIaccQ1uSrXwW8JQOMn+9CmDWZVUMDD2bzKYbm2WGGM9Fh8WrHnwlWRujoLDofhYEK0Cus11gULFF+J88XucOJlyJNrHP6TWxdSVVoQfwWr2ABqZIvilsvHpF+sjDLqomTNHdi+BbzP2koRv0nJb9K1W24bjPLtSK8+plX7suv7gdBNwlsJ+dPLDM87v4+jGHGthQ6P4X2guTMHZm1PU0PSPB9LCbENCN1uktLLhkgx7gZ42Ag+Jwiu02ENkChLaEB4WpPb9mjLnomu5LDYXFGtPJ/uLMOi3VCXyda0LrzqDhXYT3Cg4hvXySwJcgMYSXalfTxnTm9oouePiEXDbK+XwjMP9mjC5CeMg3SaFFTywqaTH0WUqiOBUJ6H3Gsm0sB15Tj4lNKQ= - - provider: pypi - distributions: bdist_wheel - username: __token__ - skip_existing: true - skip_cleanup: true - on: - tags: true - condition: $IS_DEPLOY = "deploy-test" && $OS = osx-64 - server: https://test.pypi.org/legacy/ - password: - secure: 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 - - provider: pypi - distributions: sdist - username: "Didou09" - skip_existing: true - skip_cleanup: true - on: - tags: true - condition: $IS_MASTER = "master" - password: - secure: JNEDTDJVx/2fXNfHntNQ99iDRNuQ4uB3y+DBWVIBycCT95+UCb36YPtKzmruEk/UUS29Xgq4IYCGdfCSWE9smKqG8tV1PcHiw705m+AzcpKy77YtzbVECFBxqY4W36O2pHrkwEUzP/7acjFwNsnUFzArqEzsBJ+KdLaa4OPHJXCh30GA0GyqlrXYbBKG+DA9hX5vtsGo4C6w9noALYF3fS7pKPiI6ipKFnAlzGgHQ7Ke0uQME8N3IAFhmh+Z5xMtIIDWxlnqv+KszdG4DIaGV/W6NIJNAbRhzkqUd+Chu6LoPAd/XkHDTeirR/MBkNUc5UcRJxRnP9rUTRo1gCO/buTYuNRgFkMvqhV5a033+x9edWgtUiKNJIMPLXOxe0RJvc5GWji+Co77HtHxRmGRM2rnYqWMtZeYZlFbUdvHu/8jf0d6I8jyUgAoJYdlMA2u/ipENP3S6by4epE9qycUPXiIVh6r3DZbf3vPTMFvTZYAjBrA0NOzihv1xgcXwemmNUFOQSpe0io4UcFxtS9lLMo+30UMQjCHSnbEVM3zSlZmbMOKpkVOlKlt8Lz5NxwVgWtu9FuW2pGukLtE8AWbqvY9urXAPZCQqZlOIklIjJQIqOITnuw9LEV09cgvPHXfdvNni3ldbMlIQ89zryM6dYvhYryTiEZGK4JDR3wAKJA= - - provider: pypi - distributions: bdist_wheel - username: "Didou09" - skip_existing: true - skip_cleanup: true - on: - condition: $IS_MASTER = "master" && $OS = osx-64 - tags: true - password: - secure: 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 - - provider: script - script: $START/anaconda_upload.sh - on: - tags: true - condition: $IS_MASTER = "master" diff --git a/LICENSE.txt b/LICENSE.txt index 732732d3f..dc8b1e1b3 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2016 Didier Vezinet +Copyright (c) 2023 ToFuProject Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/MANIFEST.in b/MANIFEST.in index b6d2320b4..405d1fbb5 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -3,13 +3,15 @@ include MANIFEST.in include LICENSE.txt include pyproject.toml -include _updateversion.py +include CLASSIFIERS.txt + +# recursive recursive-include tofu/geom *.pxd recursive-include tofu/geom/inputs *.txt recursive-include tofu/spectro *.txt # physics -recursive-include tofu/physics_tools/runaways/emission *.csv +recursive-include tofu/physics_tools/electrons_runaways/emission/ *.csv recursive-include tofu/physics_tools/transmission/inputs_filter *.txt recursive-include tofu/physics_tools/transmission/inputs_filter *.csv @@ -18,7 +20,5 @@ recursive-include tofu/tests/tests01_geom/test_data *.txt recursive-include tofu/tests/tests01_geom/test_data *.npz recursive-include tofu/tests/tests01_geom/test_data *.svg recursive-include tofu/tests/tests04_spectro/test_data *.npz -recursive-include tofu/tests/tests06_mesh/test_data *.txt -recursive-include tofu/tests/tests06_mesh/test_data *.npz recursive-include tofu/mag/mag_ripple *.sh recursive-include tofu/mag/mag_ripple *.f diff --git a/_custom_build.py b/_custom_build.py new file mode 100644 index 000000000..7415b98f1 --- /dev/null +++ b/_custom_build.py @@ -0,0 +1,115 @@ +""" +See: + https://stackoverflow.com/questions/73800736/pyproject-toml-and-cython-extension-module + https://cython.readthedocs.io/en/latest/src/userguide/source_files_and_compilation.html#Cython.Build.cythonize + https://setuptools.pypa.io/en/latest/userguide/extension.html + +""" + + +import os +import sys + + +from setuptools import Extension +from setuptools.command.build_py import build_py as _build_py +import numpy + + +# local +_PATH_HERE = os.path.dirname(__file__) +sys.path.insert(0, _PATH_HERE) +import tofu_helpers as tfh +sys.path.pop(0) + + +# ################################################# +# ################################################# +# Prepare openmp +# ################################################# + + +# Compiling files +openmp_installed, openmp_flag = tfh.openmp_helpers.is_openmp_installed() + +_OPTIONS = { + 'extra_compile_args': ["-O3", "-Wall", "-fno-wrapv"] + openmp_flag, + 'extra_link_args': [] + openmp_flag, + 'include_dirs': [numpy.get_include()], +} + + +# ################################################# +# ################################################# +# DEFAULT +# ################################################# + + +_LEXT = [ + Extension( + name="tofu.geom._GG", + sources=["tofu/geom/_GG.pyx"], + **_OPTIONS, + ), + Extension( + name="tofu.geom._basic_geom_tools", + sources=["tofu/geom/_basic_geom_tools.pyx"], + **_OPTIONS, + ), + Extension( + name="tofu.geom._distance_tools", + sources=["tofu/geom/_distance_tools.pyx"], + **_OPTIONS, + ), + Extension( + name="tofu.geom._sampling_tools", + sources=["tofu/geom/_sampling_tools.pyx"], + **_OPTIONS, + ), + Extension( + name="tofu.geom._raytracing_tools", + sources=["tofu/geom/_raytracing_tools.pyx"], + **_OPTIONS, + ), + Extension( + name="tofu.geom._vignetting_tools", + sources=["tofu/geom/_vignetting_tools.pyx"], + **_OPTIONS, + ), + Extension( + name="tofu.geom._chained_list", + sources=["tofu/geom/_chained_list.pyx"], + **_OPTIONS, + ), + Extension( + name="tofu.geom._sorted_set", + sources=["tofu/geom/_sorted_set.pyx"], + **_OPTIONS, + ), + Extension( + name="tofu.geom._openmp_tools", + sources=["tofu/geom/_openmp_tools.pyx"], + # cython_compile_time_env=dict(TOFU_OPENMP_ENABLED=openmp_installed), + **_OPTIONS, + ), +] + + +# ################################################# +# ################################################# +# Main class +# ################################################# + + +class build_py(_build_py): + + # def run(self): + # self.run_command("build_ext") + # return super().run() + + def initialize_options(self): + super().initialize_options() + if self.distribution.ext_modules is None: + self.distribution.ext_modules = [] + + self.distribution.ext_modules += _LEXT diff --git a/_custom_cythonize.py b/_custom_cythonize.py new file mode 100644 index 000000000..734b4da1f --- /dev/null +++ b/_custom_cythonize.py @@ -0,0 +1,33 @@ +import os +import sys + + +# https://groups.google.com/g/cython-users +from Cython.Build import cythonize as _cythonize + + +# local +_PATH_HERE = os.path.dirname(__file__) +sys.path.insert(0, _PATH_HERE) +import tofu_helpers as tfh +sys.path.pop(0) + + +# Compiling files +openmp_installed, openmp_flag = tfh.openmp_helpers.is_openmp_installed() + + +# ################################################# +# ################################################# +# Prepare openmp +# ################################################# + + +def cythonize(*args, **kwdargs): + + return _cythonize( + *args, + compile_time_env=dict(TOFU_OPENMP_ENABLED=openmp_installed), + compiler_directives={"language_level": 3}, + **kwdargs, + ) diff --git a/_updateversion.py b/_updateversion.py deleted file mode 100644 index d948f779b..000000000 --- a/_updateversion.py +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env/python -# coding=utf-8 - -import os -import subprocess - -_HERE = os.path.abspath(os.path.dirname(__file__)) - - -def updateversion(path=_HERE): - # Fetch version from git tags, and write to version.py - # Also, when git is not available (PyPi package), use stored version.py - version_py = os.path.join(path, 'tofu', 'version.py') - try: - version_git = subprocess.check_output(["git", - "describe"]).rstrip().decode() - except subprocess.CalledProcessError: - with open(version_py, 'r') as fh: - version_git = fh.read().strip().split("=")[-1].replace("'", '') - version_git = version_git.lower().replace('v', '').replace(' ', '') - - version_msg = "# Do not edit, pipeline versioning governed by git tags!" - with open(version_py, "w") as fh: - msg = "{0}__version__ = '{1}'{0}".format(os.linesep, version_git) - fh.write(version_msg + msg) - return version_git diff --git a/anaconda_upload.sh b/anaconda_upload.sh deleted file mode 100644 index c5d368920..000000000 --- a/anaconda_upload.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash -set -e - -conda config --set anaconda_upload no -conda install anaconda-client conda-build -conda build conda_recipe -export PKG_REAL=$(conda build . --output | tail -1) -echo $PKG_REAL - -echo "Deploying to anaconda.org..." -export USER=ToFuProject -export PKG_DIR=$HOME/miniconda/conda-bld/$OS/ -anaconda -t $CONDA_UPLOAD_TOKEN upload -u $USER -l main $PKG_DIR/tofu-*.tar.bz2 -echo "Successfully uploaded !" -exit 0 diff --git a/asv.conf.json b/asv.conf.json deleted file mode 100644 index 425ab7f64..000000000 --- a/asv.conf.json +++ /dev/null @@ -1,168 +0,0 @@ -{ - // The version of the config file format. Do not change, unless - // you know what you are doing. - "version": 1, - - // The name of the project being benchmarked - "project": "tofu", - - // The project's homepage - "project_url": "https://github.com/ToFuProject/tofu", - - // The URL or local path of the source code repository for the - // project being benchmarked - "repo": ".", - - // The Python project's subdirectory in your repo. If missing or - // the empty string, the project is assumed to be located at the root - // of the repository. - // "repo_subdir": "", - - // Customizable commands for building, installing, and - // uninstalling the project. See asv.conf.json documentation. - // - "install_command": ["in-dir={env_dir} python -mpip install {wheel_file}"], - "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"], - - // the --no-verify option avoids that the version number is checked against PEP440 - "build_command": [ - "python setup.py build", - "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-verify --no-deps --no-index -w {build_cache_dir} {build_dir}" - ], - - // List of branches to benchmark. If not provided, defaults to "master" - // (for git) or "default" (for mercurial). - "branches": ["devel"], // for git - // "branches": ["default"], // for mercurial - - // The DVCS being used. If not set, it will be automatically - // determined from "repo" by looking at the protocol in the URL - // (if remote), or by looking for special directories, such as - // ".git" (if local). - // "dvcs": "git", - - // The tool to use to create environments. May be "conda", - // "virtualenv" or other value depending on the plugins in use. - // If missing or the empty string, the tool will be automatically - // determined by looking for tools on the PATH environment - // variable. - "environment_type": "conda", //"virtualenv", - - // timeout in seconds for installing any dependencies in environment - // defaults to 10 min - //"install_timeout": 600, - - // the base URL to show a commit for the project. - "show_commit_url": "https://github.com/ToFuProject/tofu/commits/", - - // The Pythons you'd like to test against. If not provided, defaults - // to the current version of Python used to run `asv`. - "pythons": ["3.8.12"], - - // The list of conda channel names to be searched for benchmark - // dependency packages in the specified order - "conda_channels": ["conda-forge", "defaults"], - - // The matrix of dependencies to test. Each key is the name of a - // package (in PyPI) and the values are version numbers. An empty - // list or empty string indicates to just test against the default - // (latest) version. null indicates that the package is to not be - // installed. If the package to be tested is only available from - // PyPi, and the 'environment_type' is conda, then you can preface - // the package name by 'pip+', and the package will be installed via - // pip (with all the conda available packages installed first, - // followed by the pip installed packages). - // - "matrix": { - "numpy": ["1.21.2"], - "scipy": ["1.7.1"], - "matplotlib": ["3.4.3"], - "cython": ["0.29.24"], - "requests": ["2.26.0"], - "scikit-sparse": [""], - "scikit-umfpack": [""], - // "six": ["", null], // test with and without six installed - // "pip+emcee": [""], // emcee is only available for install with pip. - }, - - // Combinations of libraries/python versions can be excluded/included - // from the set to test. Each entry is a dictionary containing additional - // key-value pairs to include/exclude. - // - // An exclude entry excludes entries where all values match. The - // values are regexps that should match the whole string. - // - // An include entry adds an environment. Only the packages listed - // are installed. The 'python' key is required. The exclude rules - // do not apply to includes. - // - // In addition to package names, the following keys are available: - // - // - python - // Python version, as in the *pythons* variable above. - // - environment_type - // Environment type, as above. - // - sys_platform - // Platform, as in sys.platform. Possible values for the common - // cases: 'linux2', 'win32', 'cygwin', 'darwin'. - // - // "exclude": [ - // {"python": "3.2", "sys_platform": "win32"}, // skip py3.2 on windows - // {"environment_type": "conda", "six": null}, // don't run without six on conda - // ], - // - // "include": [ - // // additional env for python2.7 - // {"python": "2.7", "numpy": "1.8"}, - // // additional env if run on windows+conda - // {"platform": "win32", "environment_type": "conda", "python": "2.7", "libpython": ""}, - // ], - - // The directory (relative to the current directory) that benchmarks are - // stored in. If not provided, defaults to "benchmarks" - "benchmark_dir": "tofu/benchmarks", - - // The directory (relative to the current directory) to cache the Python - // environments in. If not provided, defaults to "env" - "env_dir": ".asv/env", - - // The directory (relative to the current directory) that raw benchmark - // results are stored in. If not provided, defaults to "results". - "results_dir": "tofu/benchmarks/results", - - // The directory (relative to the current directory) that the html tree - // should be written to. If not provided, defaults to "html". - "html_dir": ".asv/html", - - // The number of characters to retain in the commit hashes. - // "hash_length": 8, - - // `asv` will cache results of the recent builds in each - // environment, making them faster to install next time. This is - // the number of builds to keep, per environment. - // "build_cache_size": 2, - - // The commits after which the regression search in `asv publish` - // should start looking for regressions. Dictionary whose keys are - // regexps matching to benchmark names, and values corresponding to - // the commit (exclusive) after which to start looking for - // regressions. The default is to start from the first commit - // with results. If the commit is `null`, regression detection is - // skipped for the matching benchmark. - // - // "regressions_first_commits": { - // "some_benchmark": "352cdf", // Consider regressions only after this commit - // "another_benchmark": null, // Skip regression detection altogether - // }, - - // The thresholds for relative change in results, after which `asv - // publish` starts reporting regressions. Dictionary of the same - // form as in ``regressions_first_commits``, with values - // indicating the thresholds. If multiple entries match, the - // maximum is taken. If no entry matches, the default is 5%. - // - // "regressions_thresholds": { - // "some_benchmark": 0.01, // Threshold of 1% - // "another_benchmark": 0.5, // Threshold of 50% - // }, -} diff --git a/conda_recipe/bld.bat b/conda_recipe/bld.bat deleted file mode 100644 index c40a9bbef..000000000 --- a/conda_recipe/bld.bat +++ /dev/null @@ -1,2 +0,0 @@ -"%PYTHON%" setup.py install -if errorlevel 1 exit 1 diff --git a/conda_recipe/build.sh b/conda_recipe/build.sh deleted file mode 100644 index a40f1097a..000000000 --- a/conda_recipe/build.sh +++ /dev/null @@ -1 +0,0 @@ -$PYTHON setup.py install # Python command to install the script. diff --git a/conda_recipe/conda_upload.sh b/conda_recipe/conda_upload.sh deleted file mode 100644 index 4fe6fa2b5..000000000 --- a/conda_recipe/conda_upload.sh +++ /dev/null @@ -1,6 +0,0 @@ -# Only need to change these two variables -USER=ToFuProject - -echo "Available conda packages:" -echo $PKG_REAL -anaconda -t $CONDA_UPLOAD_TOKEN upload -u $USER -l main $PKG_REAL --force diff --git a/conda_recipe/meta.yaml b/conda_recipe/meta.yaml deleted file mode 100644 index f36ddb3c5..000000000 --- a/conda_recipe/meta.yaml +++ /dev/null @@ -1,59 +0,0 @@ -package: - name: 'tofu' - # version: {{ environ['VERSION'] }} - version: {{ '1.7.0' }} - -source: - git_url: https://github.com/ToFuProject/tofu.git - # git_rev: {{ environ['REV'] }} - git_rev: {{ '1.7.0' }} - -#build: - #script_env: - #- PKG_REAL - #- TRAVIS_BRANCH - -requirements: - - # build: necessary for build.sh - # here same as run, as we are using cython - build: - - python - - setuptools >=40.8.0 - - setuptools_scm - - numpy - - Cython >=0.26 - - pytest - # - pygments - - - # for running the library - run: - - python - - numpy - - scipy - - matplotlib - - contourpy - - Cython >=0.26 - # - pygments - - requests - - svg.path - - Polygon3 - - bsplines2d >=0.0.6 - - pytest - # - scikit-sparse # not available on Windows - # - scikit-umfpack # not available on Windows - -test: - requires: - - pytest - imports: - - tofu - -about: - home: https://github.com/ToFuProject/tofu - license: MIT - license_file: LICENSE.txt - summary: Tomography for Fusion - -# conda build -c tofuproject conda_recipe/ diff --git a/inputs_temp/BERTSCHINGER_Compact_Bragg_Calibration.pdf b/inputs_temp/BERTSCHINGER_Compact_Bragg_Calibration.pdf deleted file mode 100644 index 042a2e696..000000000 Binary files a/inputs_temp/BERTSCHINGER_Compact_Bragg_Calibration.pdf and /dev/null differ diff --git a/inputs_temp/Bitter_XRayDiagnosticsOfTokamakPlasmas.pdf b/inputs_temp/Bitter_XRayDiagnosticsOfTokamakPlasmas.pdf deleted file mode 100644 index eeaba50f7..000000000 Binary files a/inputs_temp/Bitter_XRayDiagnosticsOfTokamakPlasmas.pdf and /dev/null differ diff --git a/inputs_temp/ITER_geom_from_Imas_sh1180_r17_public_tokITER_MD.npz b/inputs_temp/ITER_geom_from_Imas_sh1180_r17_public_tokITER_MD.npz deleted file mode 100644 index a8e7bf399..000000000 Binary files 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-_TOFUPATH = os.path.abspath(os.path.join(_HERE, os.pardir)) - - -sys.path.insert(1, _TOFUPATH) -import tofu as tf -from inputs_temp.dlines import dlines -import inputs_temp.XICS_allshots_C34 as xics -_ = sys.path.pop(1) - - -print( - ( - 'tofu in {}: \n\t'.format(__file__) - + tf.__version__ - + '\n\t' - + tf.__file__ - ), - file=sys.stdout, -) - - -# ############################################################################# -# Prepare PATH -# ############################################################################# - - -_HERE = os.path.abspath(os.path.dirname(__file__)) -_PATHC3 = os.path.abspath(os.path.join( - _HERE, - 'XICS_allshots_C3_sh53700-54178.npz')) -_PATHC4 = os.path.abspath(os.path.join( - _HERE, - 'XICS_allshots_C4_sh54179-55987.npz')) -_PATH = _HERE - - -# ############################################################################# -# Detector from CAD -# ############################################################################# - - -_DET_CAD_CORNERS_XYZ = np.array([ - [-2332.061, -126.662, -7606.628], - [-2363.382, -126.662, -7685.393], - [-2363.382, 126.662, -7685.393], - [-2332.061, 126.662, -7606.628], -]).T*1.e-3 -# (-x)zy -> xyz -_DET_CAD_CORNERS_XYZ = np.array([-_DET_CAD_CORNERS_XYZ[0, :], - _DET_CAD_CORNERS_XYZ[2, :], - _DET_CAD_CORNERS_XYZ[1, :]]) -_DET_CAD_CENT = np.mean(_DET_CAD_CORNERS_XYZ, axis=1) -_DET_CAD_EI = _DET_CAD_CORNERS_XYZ[:, 1] - _DET_CAD_CORNERS_XYZ[:, 0] -_DET_CAD_EI = _DET_CAD_EI / np.linalg.norm(_DET_CAD_EI) -_DET_CAD_EJ = _DET_CAD_CORNERS_XYZ[:, -1] - _DET_CAD_CORNERS_XYZ[:, 0] -_DET_CAD_EJ = _DET_CAD_EJ - np.sum(_DET_CAD_EJ*_DET_CAD_EI)*_DET_CAD_EI -_DET_CAD_EJ = _DET_CAD_EJ / np.linalg.norm(_DET_CAD_EJ) -_DET_CAD_NOUT = np.cross(_DET_CAD_EI, _DET_CAD_EJ) -_DET_CAD_NOUT = _DET_CAD_NOUT / np.linalg.norm(_DET_CAD_NOUT) - - -# ############################################################################# -# Spectral lines dict -# ############################################################################# - - -_DLINES_ARXVII = { - k0: v0 for k0, v0 in dlines.items() - if ( - ( - v0['source'] == 'Vainshtein 85' - and v0['ION'] == 'ArXVII' - and v0['symbol'] not in ['y2', 'z2'] - ) - or ( - v0['source'] == 'Goryaev 17' - and v0['ION'] == 'ArXVI' - and v0['symbol'] not in [ - 'l', 'n3-h1', 'n3-h2', 'd', - 'n3-e1', 'n3-f4', 'n3-f2', 'n3-e2', - 'n3-f1', 'n3-g1', 'n3-g2', 'n3-g3', - 'n3-f3', 'n3-a1', 'n3-a2', 'n3-c1', - 'n3-c2', 'g', 'i', 'e', 'f', 'u', - 'v', 'h', 'c', 'b', 'n3-b1', - 'n3-b2', 'n3-b4', 'n3-d1', 'n3-d2', - ] - ) - ) -} - - -# ############################################################################# -# Hand-picked database -# ############################################################################# - - -_SHOTS = np.r_[ - # C3 - 54041, - np.arange(54043, 54055), - 54058, 54059, - np.arange(54061, 54068), - np.arange(54069, 54076), - np.arange(54077, 54080), - 54081, - 54083, 54084, - np.arange(54088, 54108), - 54123, - np.arange(54126, 54146), - np.arange(54150, 54156), - np.arange(54158, 54169), - np.arange(54170, 54176), - 54177, 54178, - # C4 - 54762, 54765, 54766, 55045, 55049, - 55076, 55077, 55092, 55095, 55080, - 55147, 55160, 55161, 55164, 55165, 55166, 55167, - 55292, 55297, - 55562, 55572, 55573, 55607, -] - -_NSHOT = _SHOTS.size -_CAMP = np.full((_NSHOT,), 3) -_CAMP[_SHOTS > 54178] = 4 - -_TLIM = np.tile([-np.inf, np.inf], (_NSHOT, 1)) - -_CRYST = np.full((_NSHOT,), 'ArXVII', dtype='= 54062) & (_SHOTS <= 54107) -iFe = (_SHOTS >= 54123) & (_SHOTS <= 54178) -_CRYST[iArXVIII] = 'ArXVIII' -_CRYST[iFe] = 'FeXXV' -_ANG = np.full((_NSHOT,), np.nan) - -_DSHOTS = { - 'ArXVII': { - # C3 - # 54041: {'ang': 1.1498, 'tlim': [32, 36]}, # Almost no signal - 54043: {'ang': 1.1498, 'tlim': [35, 39]}, - 54044: {'ang': 1.1498, 'tlim': [33, 47]}, - 54045: {'ang': 1.28075, 'tlim': [32, 46]}, - 54046: {'ang': 1.3124, 'tlim': [32, 46]}, - 54047: {'ang': 1.3995, 'tlim': [32, 46]}, - 54048: {'ang': 1.51995, 'tlim': [32, 46]}, - 54049: {'ang': 1.51995, 'tlim': [32, 34]}, - 54050: {'ang': 1.51995, 'tlim': [32, 46]}, - 54051: {'ang': 1.51995, 'tlim': [32, 40]}, - 54052: {'ang': 1.51995, 'tlim': [32, 37]}, - 54053: {'ang': 1.51995, 'tlim': [32, 34]}, - 54054: {'ang': 1.51995, 'tlim': [32, 37]}, - 54061: {'ang': 1.6240, 'tlim': [32, 43]}, - # C4 1.3115 ? - 54762: {'ang': 1.3405, 'tlim': [34.0, 44.5]}, # ok - 54765: {'ang': 1.3405, 'tlim': [33.0, 44.5]}, # ok - 54766: {'ang': 1.3405, 'tlim': [33.0, 41.0]}, # ok - 55045: {'ang': 1.3405, 'tlim': [32.5, 38.5]}, # ok - 55049: {'ang': 1.3405, 'tlim': [32.5, 44.5]}, # ok - 55076: {'ang': 1.3405, 'tlim': [32.0, 56.0]}, # ok - 55077: {'ang': 1.3405, 'tlim': [32.5, 54.0]}, # ok - 55080: {'ang': 1.3405, 'tlim': [32.5, 49.0]}, # ok - 55092: {'ang': 1.3405, 'tlim': [32.5, 57.5]}, # ok - 55095: {'ang': 1.3405, 'tlim': [32.5, 47.5]}, # ok - 55147: {'ang': 1.3405, 'tlim': [32.6, 45.6]}, # ICRH, ok, good - 55160: {'ang': 1.3405, 'tlim': [32.4, 44.6]}, # ICRH, ok - 55161: {'ang': 1.3405, 'tlim': [32.6, 42.4]}, # ICRH, ok - 55164: {'ang': 1.3405, 'tlim': [32.5, 44.7]}, # ICRH, ok - 55165: {'ang': 1.3405, 'tlim': [32.7, 44.5]}, # ICRH, ok - 55166: {'ang': 1.3405, 'tlim': [32.5, 42.2]}, # ok - 55167: {'ang': 1.3405, 'tlim': [32.5, 42.4]}, # ICRH, ok - 55292: {'ang': 1.3405, 'tlim': [32.5, 46.2]}, # ok - 55297: {'ang': 1.3405, 'tlim': [32.5, 46.0]}, # ICRH, ok - 55562: {'ang': 1.3405, 'tlim': [32.5, 47.5]}, # ICRH, ok, good - 55572: {'ang': 1.3405, 'tlim': [33.0, 45.2]}, # ICRH, ok, good - 55573: {'ang': 1.3405, 'tlim': [30.6, 32.6]}, # ok, good startup - 55607: {'ang': 1.3405, 'tlim': [32.5, 40.4]}, # ICRH - }, - - 'ArXVIII': { - 54062: {'ang': -101.0, 'tlim': [32, 37]}, - 54063: {'ang': -101.0, 'tlim': [32, 43]}, - 54064: {'ang': -101.0, 'tlim': [32, 43]}, - 54065: {'ang': -101.099, 'tlim': [32, 44]}, - 54066: {'ang': -101.099, 'tlim': [32, 41]}, - 54067: {'ang': -101.099, 'tlim': [32, 43]}, - 54069: {'ang': -101.099, 'tlim': [32, 40]}, - 54070: {'ang': -101.099, 'tlim': [32, 38]}, - 54071: {'ang': -101.099, 'tlim': [32, 40]}, - 54072: {'ang': -101.099, 'tlim': [32, 37]}, - 54073: {'ang': -101.2218, 'tlim': [32, 38]}, - 54074: {'ang': -101.2218, 'tlim': [32, 37]}, - 54075: {'ang': -101.2218, 'tlim': [32, 37]}, - 54077: {'ang': -101.3507, 'tlim': [32, 34]}, - 54088: {'ang': -101.3507, 'tlim': [32, 38]}, - 54089: {'ang': -101.3507, 'tlim': [32, 45]}, - 54090: {'ang': -101.4831, 'tlim': [32, 40]}, - 54091: {'ang': -101.5800, 'tlim': [32, 40]}, - 54092: {'ang': -101.5800, 'tlim': [32, 40]}, - 54093: {'ang': -100.924, 'tlim': [32, 37]}, - 54094: {'ang': -100.924, 'tlim': [32, 40]}, - 54095: {'ang': -100.799, 'tlim': [32, 48]}, - 54096: {'ang': -100.799, 'tlim': [32, 39]}, - 54097: {'ang': -100.799, 'tlim': [32, 37]}, - 54098: {'ang': -100.706, 'tlim': [32, 39]}, - 54099: {'ang': -100.706, 'tlim': [32, 39]}, - 54100: {'ang': -100.580, 'tlim': [32, 44]}, - 54101: {'ang': -100.483, 'tlim': [32, 40]}, - 54102: {'ang': -100.386, 'tlim': [32, 45]}, - 54103: {'ang': -100.386, 'tlim': [32, 38]}, - 54104: {'ang': -100.2644, 'tlim': [32, 38]}, - 54105: {'ang': -100.132, 'tlim': [32, 40]}, - 54107: {'ang': -100.038, 'tlim': [32, 38]}, - }, - - 'FeXXV': { - 54123: {'ang': -181.547, 'tlim': [32, 59]}, - 54126: {'ang': -181.547, 'tlim': [32, 38]}, - 54127: {'ang': -181.547, 'tlim': [32, 49]}, - 54128: {'ang': -181.547, 'tlim': [32, 61]}, - 54129: {'ang': -181.547, 'tlim': [32, 46]}, - 54130: {'ang': -181.547, 'tlim': [32, 59]}, - 54131: {'ang': -181.647, 'tlim': [32, 64]}, - 54133: {'ang': -181.746, 'tlim': [32, 67]}, - 54134: {'ang': -181.846, 'tlim': [32, 63]}, - 54135: {'ang': -181.946, 'tlim': [32, 60]}, - 54136: {'ang': -181.428, 'tlim': [32, 63]}, - 54137: {'ang': -181.3222, 'tlim': [32, 44]}, - 54138: {'ang': -181.1954, 'tlim': [32, 42]}, - 54139: {'ang': -181.1954, 'tlim': [32, 65]}, - 54141: {'ang': -181.1954, 'tlim': [32, 59]}, - 54142: {'ang': -181.1954, 'tlim': [32, 54]}, - 54143: {'ang': -181.1954, 'tlim': [32, 66]}, - 54144: {'ang': -181.1954, 'tlim': [32, 65]}, - 54145: {'ang': -181.1954, 'tlim': [32, 40]}, - 54150: {'ang': -181.0942, 'tlim': [32, 57]}, - 54151: {'ang': -181.0942, 'tlim': [32, 40]}, - 54152: {'ang': -180.9625, 'tlim': [32, 61]}, - 54153: {'ang': -180.9625, 'tlim': [32, 49]}, - 54154: {'ang': -180.8651, 'tlim': [32, 49]}, - 54155: {'ang': -180.8651, 'tlim': [32, 47]}, - 54158: {'ang': -180.8651, 'tlim': [32, 67]}, - 54159: {'ang': -180.7667, 'tlim': [32, 63]}, - 54160: {'ang': -180.7667, 'tlim': [32, 66]}, - 54161: {'ang': -180.6687, 'tlim': [32, 40]}, - 54162: {'ang': -180.6687, 'tlim': [32, 37]}, - 54163: {'ang': -180.6687, 'tlim': [32, 66]}, - 54164: {'ang': -180.5434, 'tlim': [32, 65]}, - 54165: {'ang': -180.5803, 'tlim': [32, 39]}, - 54166: {'ang': -180.5803, 'tlim': [32, 65]}, - 54167: {'ang': -181.6169, 'tlim': [32, 37]}, - 54173: {'ang': -181.6169, 'tlim': [32, 69.5]}, - 54178: {'ang': -181.6169, 'tlim': [32, 69.5]}, - } -} - -_DSHOTS_DEF = { - 'ArXVII': [54044, 54045, 54046, 54047, 54049, 54061], - 'FeXXV': [], -} - - -for cryst, v0 in _DSHOTS.items(): - for shot, v1 in v0.items(): - ishot = _SHOTS == shot - if not np.any(ishot): - msg = "shot in dict missing in array: {}".format(shot) - warnings.warn(msg) - continue - if ishot.sum() > 1: - msg = "{} shots in array for shot in dict: {}".format(ishot.sum(), - shot) - raise Exception(msg) - if _CRYST[ishot][0] != cryst: - msg = ("Inconsistent crystal!\n" - + "\t- shot: {}\n".format(shot) - + "\t- cryst: {}\n".format(cryst) - + "\t- _CRYST[{}]: {}".format(ishot.nonzero()[0][0], - _CRYST[ishot][0])) - raise Exception(msg) - _ANG[ishot] = v1['ang'] - _TLIM[ishot] = v1['tlim'] - - -_CRYSTBASE = 'TFG_CrystalBragg_ExpWEST_DgXICS_' -_DCRYST = { - 'ArXVII': os.path.abspath(os.path.join( - _HERE, - _CRYSTBASE + 'ArXVII_sh00000_Vers1.4.7-208-gb3dcce6e.npz', - )), - 'ArXVIII': os.path.abspath(os.path.join( - _HERE, - _CRYSTBASE + 'ArXVIII_sh00000_Vers1.4.7-221-g65718177.npz', - )), - 'FeXXV': os.path.abspath(os.path.join( - _HERE, - _CRYSTBASE + 'FeXXV_sh00000_Vers1.4.7-221-g65718177.npz', - )), -} - -_DDET = { - 'ArXVII': dict( - ddist=0., di=-0.005, dj=0., dtheta=0., dpsi=-0.01, - tilt=0.008, tangent_to_rowland=True, - ), - 'FeXXV': dict( - ddist=0., di=0., dj=0., - dtheta=0., dpsi=0., tilt=0., tangent_to_rowland=True, - ), -} - - -# ############################################################################# -# Function to unify databases -# ############################################################################# - - -_NT = 10 -_SPECT1D = [(0., 0.02), (0.8, 0.02)] -_MASKPATH = os.path.abspath(os.path.join( - _HERE, - 'XICS_mask.npz' -)) -_DETPATH = os.path.abspath(os.path.join( - _HERE, - 'det37_CTVD_incC4_New.npz' -)) -_MASK = ~np.any(np.load(_MASKPATH)['ind'], axis=0) -_DLINES = None -_XJJ = np.r_[-0.08, -0.05, 0., 0.05, 0.1] -_DXJ = 0.002 - - -def main(shots=_SHOTS, - path=None, - nt=None, - cryst=None, - dcryst=None, - lfiles=None, - maskpath=None, - xj=None, - dxj=None): - """ Create file XICS_data_{cryst}.npz """ - - # --------- - # Check input - if path is None: - path = _PATH - if dcryst is None: - dcryst = _DCRYST - if cryst is None: - cryst = sorted(dcryst.keys()) - if isinstance(cryst, str): - cryst = [cryst] - assert all([cc in dcryst.keys() for cc in cryst]) - cryst = set(dcryst.keys()).intersection(cryst) - if lfiles is None: - lfiles = [_PATHC3, _PATHC4] - if isinstance(lfiles, str): - lfiles = [lfiles] - if nt is None: - nt = _NT - if xj is None: - xj = _XJJ - if dxj is None: - dxj = _DXJ - if maskpath is None: - maskpath = _MASKPATH - if maskpath is not False: - mask = ~np.any(np.load(maskpath)['ind'], axis=0) - - # --------- - # Prepare - ni, nj = 487, 1467 - xiref = (np.arange(0, ni)-(ni-1)/2.)*172e-6 - xjref = (np.arange(0, nj)-(nj-1)/2.)*172e-6 - indxj = [(np.abs(xjref-xjj) <= dxj).nonzero()[0] for xjj in xj] - - # --------- - # Loop on cryst - for cc in cryst: - - ind = (_CRYST == cc).nonzero()[0] - ns = ind.size - if ns == 0: - continue - ang = _ANG[ind] - angu, ianginv = np.unique(ang, - return_index=False, - return_inverse=True) - pfe = os.path.join(path, 'XICS_data_{}.npz'.format(cc)) - - # prepare output - shotc = shots[ind] - tlim = _TLIM[ind, :] - tc = np.full((ns, nt), np.nan) - thr = np.full((ns,), np.nan) - texp = np.full((ns,), np.nan) - tdelay = np.full((ns,), np.nan) - tc = np.full((ns, nt), np.nan) - spect = np.full((ns, nt, xj.size, ni), np.nan) - success = ['OK' for ii in ind] - - msg = "\nLoading data for crystal {}:".format(cc) - print(msg) - - n0 = 0 - ind0 = np.arange(0, ns) - for ii in range(angu.size): - msg = "\t for angle = {} deg:".format(angu[ii]) - print(msg) - iii = ianginv == ii - for ij in ind0[iii]: - try: - msg = ("\t\tshot {}".format(shotc[ij]) - + " ({}/{})...".format(n0+1, ind.size)) - print(msg, end='', flush=True) - data, t, dbonus = _load_data(int(shotc[ij]), - tlim=tlim[ij, :], - tmode='mean', - path=None, Brightness=None, - mask=True, Verb=False) - thr[ij] = dbonus['THR'] - texp[ij] = dbonus['TExpP'] - tdelay[ij] = dbonus['TDelay'] - tbis = np.linspace(t[0]+0.001, t[-1]-0.001, nt) - indt = np.digitize(tbis, t) - tc[ij, :] = t[indt] - for it in range(indt.size): - for ll in range(xj.size): - spect[ij, it, ll, :] = np.nanmean( - data[indt[it], indxj[ll], :], axis=0) - print('\tok') - except Exception as err: - success[ij] = str(err) - print('\tfailed: '+str(err)) - finally: - # save - np.savez(pfe, - shots=shotc, t=tc, - xi=xiref, xj=xj, indxj=indxj, spect=spect, - ang=ang, thr=thr, texp=texp, tdelay=tdelay, - success=success) - n0 += 1 - msg = ("Saved in:\n\t" + pfe) - print(msg) - - -# ############################################################################# -# Function to load data -# ############################################################################# - - -_GEOM = { - 'pix': { - 'sizeH': 172.e-6, 'sizeV': 172.e-6, - 'nbH': 487, 'nbV': 1467, 'nbVGap': 17, 'nbVMod': 195, - 'mod': {'nbV': 7, 'nbH': 1, 'sizeH': 83.764e-3, 'sizeV': 33.54e-3} - } -} - - -def _get_THR(shot): - if shot >= 53700 and shot <= 53723: - THR = 4024 - else: - THR = np.nan - return THR - - -def _get_Ang(shot): - if shot >= 53700 and shot <= 53723: - angle = -181.546 - elif shot >= 54038 and shot <= 54040: - angle = 1.3115 - elif shot >= 54041 and shot <= 54044: - angle = 1.1498 - elif shot == 54045: - angle = 1.28075 - elif shot == 54046: - angle = 1.3124 - elif shot == 54047: - angle = 1.3995 - elif shot >= 54048: - angle = 1.51995 - else: - angle = np.nan - return angle - - -def _utils_get_Pix2D(D1=0., D2=0., center=False, geom=_GEOM): - - gridH = geom['pix']['sizeH']*np.arange(0, geom['pix']['nbH']) - gridV = geom['pix']['sizeV']*np.arange(0, geom['pix']['nbV']) - GH = np.tile(gridH, geom['pix']['nbV']) - GV = np.repeat(gridV, geom['pix']['nbH']) - mH = np.mean(gridH) if center else 0. - mV = np.mean(gridV) if center else 0. - pts2D = np.array([D1+GH-mH, D2+GV-mV]) - return pts2D - - -def _get_indtlim(t, tlim=None, shot=None, out=bool): - C0 = tlim is None - C1 = type(tlim) in [list, tuple, np.ndarray] - assert C0 or C1 - assert type(t) is np.ndarray - - if C0: - tlim = [-np.inf, np.inf] - else: - assert len(tlim) == 2 - ls = [str, int, float, np.int64, np.float64] - assert all([tt is None or type(tt) in ls for tt in tlim]) - tlim = list(tlim) - for (ii, sgn) in [(0, -1.), (1, 1.)]: - if tlim[ii] is None: - tlim[ii] = sgn*np.inf - elif type(tlim[ii]) is str and 'ign' in tlim[ii].lower(): - tlim[ii] = get_t0(shot) - - assert tlim[0] < tlim[1] - indt = (t >= tlim[0]) & (t <= tlim[1]) - if out is int: - indt = indt.nonzero()[0] - return indt - - -def _load_data(shot, tlim=None, tmode='mean', - path=None, geom=_GEOM, - Brightness=None, mask=True, - tempdir=_HERE, Verb=True): - import pywed as pw - from PIL import Image - import zipfile - - assert tmode in ['mean', 'start', 'end'] - - # Pre-format input - if path is None: - path = os.path.abspath(tempdir) - rootstr = 'XICS {0:05.0f}:'.format(shot) - - # Load and unzip temporary file - if Verb: - msg = '(1/4) ' + rootstr + ' loading and unziping files...' - print(msg) - targetf = os.path.join(path, 'xics_{0:05.0f}.zip'.format(shot)) - targetd = os.path.join(path, 'xics_{0:05.0f}/'.format(shot)) - out = pw.TSRfile(shot, 'FXICS_MIDDLE', targetf) - - if not out == 0: - msg = ("Could not run:" - + "\n out = " - + "pw.TSRfile({0}, 'FXICS_MIDDLE', {1})".format(shot, targetf) - + "\n => returned out = {0}".format(out) - + "\n => Maybe no data ?") - raise Exception(msg) - - zip_ref = zipfile.ZipFile(targetf, 'r') - zip_ref.extractall(targetd) - zip_ref.close() - - # Load parameters to rebuild time vector - if Verb: - msg = '(2/4) ' + rootstr + ' loading parameters...' - print(msg) - t0 = 0. # Because startAcq on topOrigin (tIGNOTRON - 32 s) - NExp = pw.TSRqParm(shot, 'DXICS', 'PIL_N', 'PIL_NMax', 1)[0][0][0] - TExpT = pw.TSRqParm(shot, 'DXICS', 'PIL_Times', 'PIL_TExpT', 1)[0][0][0] - TExpP = pw.TSRqParm(shot, 'DXICS', 'PIL_Times', 'PIL_TExpP', 1)[0][0][0] - TDelay = pw.TSRqParm(shot, 'DXICS', 'PIL_Times', 'PIL_TDelay', 1)[0][0][0] - # Delay not taken into account in this acquisition mode - if TDelay >= 50: - # TDelay now in ms - TDelay *= 1.e-3 - try: - THR = pw.TSRqParm(shot, 'DXICS', 'PIL_THR', 'THR', 1)[0][0][0] - except Exception as err: - THR = _get_THR(shot) - try: - Ang = pw.TSRqParm(shot, 'DXICS', 'CRYST', 'Ang', 1)[0][0][0] - except Exception as err: - Ang = _get_Ang(shot) - if TExpP <= TExpT: - msg = "{0:05.0f}: PIL_TExpP < PIL_TExpT in Top !".format(shot) - raise Exception(msg) - - # Rebuild time vector - if Verb: - msg = '(3/4) ' + rootstr + ' Building t and data arrays...' - print(msg) - - # Load data to numpy array and info into dict - lf = os.listdir(targetd) - lf = sorted([ff for ff in lf if '.tif' in ff]) - nIm = len(lf) - - # Check consistency of number of images (in case of early kill) - if nIm > NExp: - msg = "The zip file contains more images than parameter NExp !" - raise Exception(msg) - - # Build time vector (parameter Delay is only for external trigger !!!) - Dt = t0 + TExpP*np.arange(0, nIm) + np.array([[0.], [TExpT]]) - if shot >= 54132: - # Previously, TDelay had no effect - # From 54132, TDelay is fed to a home-made QtTimer in: - # controller_acquisitions.cpp:168 - # controller_pilotage.cpp:126 - Dt += TDelay - if tmode == 'mean': - t = np.mean(Dt, axis=0) - elif tmode == 'start': - t = Dt[0, :] - else: - t = Dt[1, :] - indt = _get_indtlim(t, tlim=tlim, out=int) - if indt.size == 0: - msg = ("No time steps in the selected time interval:\n" - + "\ttlim = [{0}, {1}]\n".format(tlim[0], tlim[1]) - + "\tt = {0}".format(str(t))) - raise Exception(msg) - Dt, t = Dt[:, indt], t[indt] - nt = t.size - - # Select relevant images - lf = [lf[ii] for ii in indt] - data = np.zeros((nt, geom['pix']['nbV'], geom['pix']['nbH'])) - ls = [] - try: - for ii in range(0, nt): - im = Image.open(os.path.join(targetd, lf[ii])) - s = str(im.tag.tagdata[270]).split('#')[1:] - s = [ss[:ss.index('\\r')] for ss in s if '\\r' in ss] - ls.append(s) - data[ii, :, :] = np.flipud(np.asarray(im, dtype=np.int32)) - finally: - # Delete temporary files - if Verb: - msg = '(4/4) ' + rootstr + ' Deleting temporary files...' - print(msg) - os.remove(targetf) - shutil.rmtree(targetd) - - dunits = r'photons' - dbonus = { - 'Dt': Dt, 'dt': TExpT, 'THR': THR, 'mask': mask, - 'NExp': NExp, 'nIm': nIm, - 'TExpT': TExpT, 'TExpP': TExpP, 'TDelay': TDelay, - 'nH': geom['pix']['nbH'], 'nV': geom['pix']['nbV'], - } - return data, t, dbonus - - -# ############################################################################# -# Function to plot results -# ############################################################################# - - -_NI, _NJ = 487, 1467 -_XI = (np.arange(0, _NI)-(_NI-1)/2.)*172e-6 -_XJ = (np.arange(0, _NJ)-(_NJ-1)/2.)*172e-6 -_MASKXI = np.ones((487,), dtype=bool) -_MASKXI[436:] = False - - -def _get_crystanddet(cryst=None, det=None): - # Cryst part - if cryst is None: - cryst = False - elif isinstance(cryst, str) and cryst in _DCRYST.keys(): - crystobj = tf.load(_DCRYST[cryst]) - if det is None: - if cryst in _DDET.keys(): - det = crystobj.get_detector_approx(**_DDET[cryst]) - cryst = crystobj - else: - msg = "Det must be provided if cryst is provided!" - raise Exception(msg) - cryst = crystobj - - if isinstance(cryst, str) and os.path.isfile(cryst): - cryst = tf.load(cryst) - elif cryst is not False: - assert cryst.__class__.__name__ == 'CrystalBragg' - - if cryst is not False: - if det is False: - det = cryst.get_detector_approx() - c0 = (isinstance(det, dict) - and all([kk in det.keys() for kk in ['cent', 'nout', - 'ei', 'ej']])) - if not c0: - msg = ("det must be a dict with keys:\n" - + "\t- cent: [x,y,z] of the detector center\n" - + "\t- nout: [x,y,z] of unit vector normal to plane\n" - + "\t- ei: [x,y,z] of unit vector ei\n" - + "\t- ej: [x,y,z] of unit vector ej = nout x ei\n" - + "\n\t- provided: {}".format(det)) - raise Exception(msg) - return cryst, det - - -def _extract_data(pfe, allow_pickle=None, - maskxi=None, shot=None, indt=None, indxj=None): - # Prepare data - out = dict(np.load(pfe, allow_pickle=allow_pickle)) - t, ang = [out[kk] for kk in ['t', 'ang']] - spect, shots, thr = [out[kk] for kk in ['spect', 'shots', 'thr']] - xi = out.get('xi', _XI) - xj = out.get('xj', _XJ) - - if maskxi is not False: - xi = xi[maskxi] - spect = spect[:, :, :, maskxi] - - # Remove unknown angles - indok = ~np.isnan(ang) - if not np.any(indok): - msg = "All nan angles!" - raise Exception(msg) - shots = shots[indok] - t = t[indok, :] - ang = ang[indok] - spect = spect[indok, :, :, :] - - if shot is not None: - indok = np.array([ss in shot for ss in shots]) - if not np.any(indok): - msg = ("Desired shot not in shots!\n" - + "\t- provided: {}\n".format(shot) - + "\t- shots: {}\n".format(shots) - + "\t (ang): {}".format(ang)) - raise Exception(msg) - shots = shots[indok] - t = t[indok, :] - ang = ang[indok] - spect = spect[indok, :, :, :] - - if indt is not None: - indt = np.r_[indt].astype(int) - t = t[:, indt] - spect = spect[:, indt, :, :] - - if indxj is not None: - indxj = np.r_[indxj].astype(int) - xj = xj[indxj] - spect = spect[:, :, indxj, :] - - spectn = spect - np.nanmin(spect, axis=-1)[..., None] - spectn /= np.nanmax(spectn, axis=-1)[..., None] - return spect, spectn, shots, t, ang, xi, xj, thr - - -def plot(pfe=None, allow_pickle=True, - shot=None, maskxi=None, - cryst=None, det=None, - dlines=None, indt=None, indxj=None, - fs=None, dmargin=None, cmap=None): - - # Check input - if not os.path.isfile(pfe): - msg = ("Provided file does not exist!" - + "\t- provided: {}".format(pfe)) - raise Exception(msg) - - if shot is not None: - if not hasattr(shot, '__iter__'): - shot = np.array([shot], dtype=int) - else: - shot = np.r_[shot].astype(int) - - if maskxi is None: - maskxi = _MASKXI - - # Cryst part - cryst, det = _get_crystanddet(cryst=cryst, det=det) - - # extract data - spect, spectn, shots, t, ang, xi, xj, thr = _extract_data(pfe, - allow_pickle, - maskxi, shot, - indt=indt, - indxj=indxj) - nshot, nt, nxj, nxi = spect.shape - iout = np.any(np.nanmean(spectn**2, axis=-1) > 0.1, axis=-1) - - # Group by angle - angu = np.unique(ang) - nang = angu.size - lcol = ['r', 'g', 'b', 'k', 'm', 'c', 'y'] - ncol = len(lcol) - - # Cryst data - if cryst is not False: - lamb = np.full((nshot, nxj, nxi), np.nan) - phi = np.full((nshot, nxj, nxi), np.nan) - xif = np.tile(xi, (nxj, 1)) - xjf = np.repeat(xj[:, None], nxi, axis=1) - for jj in range(nang): - ind = (ang == angu[jj]).nonzero()[0] - # Beware to provide angles in rad ! - cryst.move(param=angu[jj]*np.pi/180.) - - bragg, phii = cryst.calc_phibragg_from_xixj( - xif, xjf, n=1, - dtheta=None, psi=None, plot=False, det=det) - phi[ind, ...] = phii[None, ...] - lamb[ind, ...] = cryst.get_lamb_from_bragg(bragg, n=1)[None, ...] - - isortxj = nxj - 1 - np.argsort(xj) - - # ------------- - # Plot 1 - - if fs is None: - fs = (18, 9) - if cmap is None: - cmap = plt.cm.viridis - if dmargin is None: - dmargin = {'left': 0.05, 'right': 0.99, - 'bottom': 0.06, 'top': 0.93, - 'wspace': 0.3, 'hspace': 0.2} - - fig = plt.figure(figsize=fs) - if shot is not None: - fig.suptitle('shot = {}'.format(shot)) - gs = gridspec.GridSpec(nxj, 2, **dmargin) - - dax = {'spect': [None for ii in range(nxj)], - 'spectn': [None for ii in range(nxj)]} - - shx = None - for ii in range(nxj): - iax = isortxj[ii] - dax['spect'][ii] = fig.add_subplot(gs[iax, 0], sharex=shx) - if ii == 0: - shx = dax['spect'][0] - dax['spectn'][ii] = fig.add_subplot(gs[iax, 1], sharex=shx) - dax['spect'][ii].set_ylabel('xj = {}\ndata (a.u.)'.format(xj[ii])) - - for jj in range(nang): - col = lcol[jj % ncol] - lab0 = 'ang {}'.format(angu[jj]) - ind = (ang == angu[jj]).nonzero()[0] - xibis = xi # + angu[jj]*0.05 - for ss in range(ind.size): - for tt in range(nt): - ls = '--' if iout[ind[ss], tt] else '-' - lab = lab0 + ', {}, t = {} s'.format(shots[ind[ss]], - t[ind[ss], tt]) - dax['spect'][ii].plot(xibis, - spect[ind[ss], tt, ii, :], - c=col, ls=ls, label=lab) - dax['spectn'][ii].plot(xibis, - spectn[ind[ss], tt, ii, :], - c=col, ls=ls, label=lab) - # Polish - dax['spect'][0].set_title('raw spectra') - dax['spectn'][0].set_title('normalized spectra') - dax['spect'][-1].set_xlabel('xi (m)') - dax['spectn'][-1].set_xlabel('xi (m)') - hand = [ - mlines.Line2D([], [], c=lcol[jj % ncol], ls='-') - for jj in range(nang) - ] - lab = ['{}'.format(aa) for aa in angu] - dax['spect'][0].legend(hand, lab, - title='Table angle (deg.)', - loc='upper left', - bbox_to_anchor=(1.01, 1.)) - - # ------------- - # Plot 2 - if cryst is False: - return dax - - fig = plt.figure(figsize=fs) - if shot is not None: - fig.suptitle('shot = {}'.format(shot)) - gs = gridspec.GridSpec(nxj, 2, **dmargin) - - dax2 = {'spect': [None for ii in range(nxj)], - 'spectn': [None for ii in range(nxj)]} - - shx = None - for ii in range(nxj): - iax = isortxj[ii] - dax2['spect'][ii] = fig.add_subplot(gs[iax, 0], - sharex=shx) - if ii == 0: - shx, shy = dax2['spect'][0], dax2['spect'][0] - dax2['spectn'][ii] = fig.add_subplot(gs[iax, 1], - sharex=shx) - dax2['spect'][ii].set_ylabel('data (a.u.)'.format(xj[ii])) - - for jj in range(nang): - col = lcol[jj % ncol] - lab0 = 'ang {}'.format(angu[jj]) - ind = (ang == angu[jj]).nonzero()[0] - xibis = xi # + angu[jj]*0.05 - for ss in range(ind.size): - for tt in range(nt): - ls = '--' if iout[ind[ss], tt] else '-' - lab = lab0 + ', {}, t = {} s'.format(shots[ind[ss]], - t[ind[ss], tt]) - dax2['spect'][ii].plot(lamb[ind[ss], ii, :], - spect[ind[ss], tt, ii, :], - c=col, ls=ls, label=lab) - dax2['spectn'][ii].plot(lamb[ind[ss], ii, :], - spectn[ind[ss], tt, ii, :], - c=col, ls=ls, label=lab) - if dlines is not None: - for kk in dlines.keys(): - dax2['spect'][ii].axvline(dlines[kk]['lambda'], - c='k', ls='-', lw=1.) - dax2['spectn'][ii].axvline(dlines[kk]['lambda'], - c='k', ls='-', lw=1.) - if dlines is not None: - for kk in dlines.keys(): - dax2['spect'][0].annotate(kk, - xy=(dlines[kk]['lambda'], 1.), - xycoords=('data', 'axes fraction'), - horizontalalignment='left', - verticalalignment='bottom', - rotation=45, - arrowprops=None) - - # Polish - dax2['spect'][0].set_title('raw spectra') - dax2['spectn'][0].set_title('normalized spectra') - dax2['spect'][-1].set_xlabel(r'$\lambda$' + ' (m)') - dax2['spectn'][-1].set_xlabel(r'$\lambda$' + ' (m)') - hand = [ - mlines.Line2D([], [], c=lcol[jj % ncol], ls='-') - for jj in range(nang) - ] - lab = ['{}'.format(aa) for aa in angu] - dax2['spect'][0].legend(hand, lab, - title='Table angle (deg.)', - loc='upper left', - bbox_to_anchor=(1.01, 1.)) - return dax, dax2 - - -# ############################################################################# -# Fit several data for one det -# ############################################################################# - - -def _get_dinput_key01(dinput=None, - key0=None, key1=None, indl0=None, indl1=None, - dlines=None, dconstraints=None, - lambmin=None, lambmax=None, - same_spectrum=None, nspect=None, dlamb=None): - lc = [all([aa is not None for aa in [dinput, key0, key1, indl0, indl1]]), - all([aa is not None for aa in [dlines, dconstraints]])] - if np.sum(lc) != 1: - msg = ("Please provide either (xor):\n" - + "\t- dinput, key0, key1, indl0, indl1\n" - + "\t- dlines, dconstraints") - raise Exception(msg) - if lc[1]: - dinput = tf.data._spectrafit2d.multigausfit1d_from_dlines_dinput( - dlines=dlines, - dconstraints=dconstraints, - lambmin=lambmin, lambmax=lambmax, - same_spectrum=same_spectrum, nspect=nspect, dlamb=dlamb) - if key0 is not None: - indl0 = (dinput['keys'] == key0).nonzero()[0] - if indl0.size != 1: - msg = ("key0 not valid:\n" - + "\t- provided: {}\n".format(key0) - + "\t- available: {}".format(dinput['keys'])) - raise Exception(msg) - indl0 = indl0[0] - if key1 is not None: - indl1 = (dinput['keys'] == key1).nonzero()[0] - if indl1.size != 1: - msg = ("key1 not valid:\n" - + "\t- provided: {}\n".format(key1) - + "\t- available: {}".format(dinput['keys'])) - raise Exception(msg) - indl1 = indl1[0] - return dinput, key0, key1, indl0, indl1 - - -def fit(pfe=None, allow_pickle=True, - spectn=None, shots=None, t=None, ang=None, xi=None, xj=None, thr=None, - shot=None, indt=None, indxj=None, maskxi=None, - cryst=None, det=None, - dlines=None, dconstraints=None, dx0=None, - key0=None, key1=None, - dinput=None, indl0=None, indl1=None, - lambmin=None, lambmax=None, - same_spectrum=None, dlamb=None, - method=None, max_nfev=None, - dscales=None, x0_scale=None, bounds_scale=None, - xtol=None, ftol=None, gtol=None, - loss=None, verbose=None, plot=None, - fs=None, dmargin=None, cmap=None, warn=True): - - # ----------- - # Check input - - if verbose is None or verbose is True: - verbose = 1 - if verbose is False: - verbose = 0 - - # input data file - lc = [pfe is not None, - all([aa is not None for aa in [spectn, shots, t, ang, xi, xj]]), - (shot is not None - and all([aa is None for aa in [pfe, spectn, shots, t, ang]]))] - if np.sum(lc) != 1: - msg = ("Please provide eithe (xor):\n" - + "\t- pfe\n" - + "\t- spectn, shots, t, ang, xi, xj\n" - + "\t- shot, xi, xj (loaded from ARCADE)") - raise Exception(msg) - if lc[0]: - if not os.path.isfile(pfe): - msg = ("Provided file does not exist!\n" - + "\t- provided: {}".format(pfe)) - raise Exception(msg) - - # subset of shots - if shot is not None: - if not hasattr(shot, '__iter__'): - shot = np.array([shot], dtype=int) - else: - shot = np.r_[shot].astype(int) - - if maskxi is None: - maskxi = _MASKXI - - # extract data - spectn, shots, t, ang, xi, xj, thr = _extract_data(pfe, - allow_pickle, - maskxi, shot, - indt, indxj)[1:] - elif lc[2]: - data, t, dbonus = _load_data(int(shot), - tlim=_DSHOT[shot]['tlim'], - tmode='mean', - path=None, Brightness=None, - mask=True, Verb=False) - pass - - # Cryst part - cryst, det = _get_crystanddet(cryst=cryst, det=det) - assert cryst is not False - - nshot, nt, nxj, nxi = spectn.shape - iout = np.any(np.nanmean(spectn**2, axis=-1) > 0.1, axis=-1) - - # Group by angle - angu, ind_ang = np.unique(ang, return_inverse=True) - nang = angu.size - lcol = ['r', 'g', 'b', 'k', 'm', 'c', 'y'] - ncol = len(lcol) - - # ----------- - # Convert xi, xj to lamb, phi - - # Cryst data - lamb = np.full((nang, nxj, nxi), np.nan) - phi = np.full((nang, nxj, nxi), np.nan) - xif = np.tile(xi, (nxj, 1)) - xjf = np.repeat(xj[:, None], nxi, axis=1) - for jj in range(nang): - # Beware to provide angles in rad ! - cryst.move(param=angu[jj]*np.pi/180.) - - bragg, phii = cryst.calc_phibragg_from_xixj( - xif, xjf, n=1, - dtheta=None, psi=None, plot=False, det=det) - phi[jj, ...] = phii - lamb[jj, ...] = cryst.get_lamb_from_bragg(bragg, n=1) - - # Reorder to sort lamb - assert np.all(np.argsort(lamb, axis=-1) - == np.arange(nxi-1, -1, -1)[None, None, :]) - xi = xi[::-1] - lamb = lamb[:, :, ::-1] - phi = phi[:, :, ::-1] - spectn = spectn[:, :, :, ::-1] - lambminpershot = np.min(np.nanmin(lamb, axis=-1), axis=-1) - lambmaxpershot = np.max(np.nanmax(lamb, axis=-1), axis=-1) - dshiftmin = 0.02*(lambmaxpershot - lambminpershot) / lambmaxpershot - - # ----------- - # Get dinput for 1d fitting - if dlamb is None: - dlamb = 2.*(np.nanmax(lamb) - np.nanmin(lamb)) - dinput, key0, key1, indl0, indl1 = _get_dinput_key01( - dinput=dinput, key0=key0, key1=key1, indl0=indl0, indl1=indl1, - dlines=dlines, dconstraints=dconstraints, - lambmin=lambmin, lambmax=lambmax, - same_spectrum=same_spectrum, nspect=spectn.shape[1], dlamb=dlamb) - - # ----------- - # Optimize - - # Fit - spectfit = np.full(spectn.shape, np.nan) - time = np.full(spectn.shape[:-1], np.nan) - chinorm = np.full(spectn.shape[:-1], np.nan) - if key0 is not None: - shift0 = np.full(spectn.shape[:-1], np.nan) - if key1 is not None: - shift1 = np.full(spectn.shape[:-1], np.nan) - for jj in range(nang): - if verbose > 0: - msg = ("\nOptimizing for ang = {} ({}/{})\n".format(angu[jj], - jj+1, nang) - + "--------------------------------") - print(msg) - ind = (ang == angu[jj]).nonzero()[0] - for ll in range(ind.size): - msgsh = "---------- shot {} ({}/{})".format(shots[ind[ll]], - ll+1, ind.size) - for ii in range(nxj): - if verbose > 0: - msg = (" xj = {} ({}/{}):".format(xj[ii], ii+1, nxj) - + "\t{} spectra".format(spectn.shape[1])) - print(msgsh + msg) - dfit1d = tf.data._spectrafit2d.multigausfit1d_from_dlines( - spectn[ind[ll], :, ii, :], - lamb[jj, ii, :], - dinput=dinput, dx0=dx0, - lambmin=lambmin, lambmax=lambmax, - dscales=dscales, - x0_scale=x0_scale, - bounds_scale=bounds_scale, - method=method, max_nfev=max_nfev, - chain=True, verbose=verbose, - xtol=xtol, ftol=ftol, gtol=gtol, loss=loss, - ratio=None, jac='call', - ) - spectfit[ind[ll], :, ii, :] = dfit1d['sol'] - time[ind[ll], :, ii] = dfit1d['time'] - chinorm[ind[ll], :, ii] = np.sqrt(dfit1d['cost']) / nxi - indsig = np.abs(dfit1d['dshift']) >= dshiftmin[jj] - indpos = dfit1d['dshift'] > 0. - ind098 = indsig & indpos & (dfit1d['dratio'] > 0.99) - ind102 = indsig & (~indpos) & (dfit1d['dratio'] < 1.01) - if np.any(ind098) and warn is True: - msg = ("Some to high (> 0.98) dratio with dshift > 0:\n" - + "\t- shot: {}\n".format(shots[ind[ll]]) - + "\t- xj[{}] = {}\n".format(ii, xj[ii]) - + "\t- shitmin = {}\n".format(dshiftmin[jj]) - + "\t- dshift[{}]".format(ind098.nonzero()[0]) - + " = {}\n".format(dfit1d['dshift'][ind098]) - + "\t- dratio[{}]".format(ind098.nonzero()[0]) - + " = {}".format(dfit1d['dratio'][ind098])) - warnings.warn(msg) - if np.any(ind102) and warn is True: - msg = ("Some to high dratio with dshift > 0:\n" - + "\t- shitmin = {}\n".format(dshiftmin[jj]) - + "\t- dshift[{}]".format(ind102.nonzero()[0]) - + " = {}\n".format(dfit1d['dshift'][ind102]) - + "\t- dratio[{}]".format(ind102.nonzero()[0]) - + " = {}".format(dfit1d['dratio'][ind102])) - warnings.warn(msg) - if key0 is not None or key1 is not None: - ineg = dfit1d['dshift'] < 0. - if key0 is not None: - shift0[ind[ll], :, ii] = dfit1d['shift'][:, indl0] - shift0[ind[ll], ineg, ii] += ( - dfit1d['dshift'][ineg]*dinput['lines'][indl0] - ) - shift0[ind[ll], ind098 | ind102, ii] = np.nan - if key1 is not None: - shift1[ind[ll], :, ii] = dfit1d['shift'][:, indl1] - shift1[ind[ll], ineg, ii] += ( - dfit1d['dshift'][ineg]*dinput['lines'][indl1] - ) - shift1[ind[ll], ind098 | ind102, ii] = np.nan - - dcost = {} - shift0m, shift1m = None, None - if key0 is not None: - dcost[key0] = { - 'shift': shift0, - 'shiftm': np.array([[np.nanmean(shift0[ang == angu[jj], :, ii]) - for jj in range(nang)] for ii in range(nxj)])} - if key1 is not None: - dcost[key1] = { - 'shift': shift1, - 'shiftm': np.array([[np.nanmean(shift1[ang == angu[jj], :, ii]) - for jj in range(nang)] for ii in range(nxj)])} - - shiftabs = 0. - if key0 is not None: - shiftabs = max(np.nanmax(np.abs(shift0)), shiftabs) - if key1 is not None: - shiftabs = max(np.nanmax(np.abs(shift1)), shiftabs) - - # ------------- - # Plot - if plot is False: - return {'shots': shots, 't': t, 'ang': ang, - 'lamb': lamb, 'phi': phi, - 'spectn': spectn, 'spectfit': spectfit, - 'time': time, 'chinorm': chinorm, - 'dcost': dcost, - } - - if fs is None: - fs = (18, 9) - if cmap is None: - cmap = plt.cm.viridis - if dmargin is None: - dmargin = {'left': 0.06, 'right': 0.99, - 'bottom': 0.06, 'top': 0.93, - 'wspace': 0.3, 'hspace': 0.2} - extent = (0.5, nshot+0.5, -0.5, nt-0.5) - tmin, tmax = np.nanmin(time), np.nanmax(time) - chimin, chimax = np.nanmin(chinorm), np.nanmax(chinorm) - - fig = plt.figure(figsize=fs) - if shot is not None: - fig.suptitle('shot = {}'.format(shot)) - gs = gridspec.GridSpec(nxj*2, 7, **dmargin) - - dax = { - 'spectn': [None for ii in range(nxj)], - 'time': [None for ii in range(nxj)], - 'chinorm': [None for ii in range(nxj)], - 'shift0': [None for ii in range(nxj)], - 'shift1': [None for ii in range(nxj)], - 'shift0_z': [None for ii in range(nxj)], - 'shift1_z': [None for ii in range(nxj)], - } - - xones = np.zeros((nt,)) - isortxj = nxj - 1 - np.argsort(xj) - shx0, shx1, shy1, shx20, shx21 = None, None, None, None, None - for ii in range(nxj): - iax = isortxj[ii] - dax['spectn'][ii] = fig.add_subplot(gs[iax*2:iax*2+2, :3], sharex=shx0) - if ii == 0: - shx0 = dax['spectn'][ii] - dax['time'][ii] = fig.add_subplot( - gs[iax*2:iax*2+2, 3], - sharex=shx1, sharey=shy1, - ) - if ii == 0: - shx1 = dax['time'][ii] - shy1 = dax['time'][ii] - dax['chinorm'][ii] = fig.add_subplot( - gs[iax*2:iax*2+2, 4], sharex=shx1, sharey=shy1, - ) - dax['shift0'][ii] = fig.add_subplot( - gs[iax*2, 5], sharex=shx1, sharey=shy1, - ) - dax['shift1'][ii] = fig.add_subplot( - gs[iax*2, 6], sharex=shx1, sharey=shy1, - ) - dax['shift0_z'][ii] = fig.add_subplot( - gs[iax*2+1, 5], sharex=shx20, - ) - dax['shift1_z'][ii] = fig.add_subplot( - gs[iax*2+1, 6], sharex=shx21, - ) - if ii == 0: - shx20 = dax['shift0_z'][ii] - shx21 = dax['shift1_z'][ii] - dax['spectn'][ii].set_ylabel('xj = {}\ndata (a.u.)'.format(xj[ii])) - if iax != nxj-1: - plt.setp(dax['time'][ii].get_xticklabels(), visible=False) - plt.setp(dax['chinorm'][ii].get_xticklabels(), visible=False) - - for jj in range(nang): - col = lcol[jj % ncol] - ind = (ang == angu[jj]).nonzero()[0] - for ll in range(ind.size): - dax['spectn'][ii].plot( - lamb[jj, ii, :], - spectn[ind[ll], :, ii, :].T, - ls='None', marker='.', ms=4., c=col, - ) - dax['spectn'][ii].plot( - lamb[jj, ii, :], - spectfit[ind[ll], :, ii, :].T, - ls='-', lw=1, c=col, - ) - if key0 is not None: - dax['shift0_z'][ii].plot((dinput['lines'][indl0] - + shift0[ind[ll], :, ii]), - xones, - marker='.', ls='None', c=col) - if key1 is not None: - dax['shift1_z'][ii].plot((dinput['lines'][indl1] - + shift1[ind[ll], :, ii]), - xones, - marker='.', ls='None', c=col) - dax['time'][ii].imshow(time[:, :, ii].T, - extent=extent, cmap=cmap, - vmin=tmin, vmax=tmax, - interpolation='nearest', origin='lower') - dax['chinorm'][ii].imshow(chinorm[:, :, ii].T, - extent=extent, cmap=cmap, - vmin=chimin, vmax=chimax, - interpolation='nearest', origin='lower') - if key0 is not None: - dax['shift0'][ii].imshow(shift0[:, :, ii].T, - extent=extent, cmap=plt.cm.seismic, - interpolation='nearest', origin='lower', - vmin=-shiftabs, vmax=shiftabs) - dax['spectn'][ii].axvline(dinput['lines'][indl0], - c='k', ls='-', lw=1.) - dax['shift0_z'][ii].axvline(dinput['lines'][indl0], - c='k', ls='-', lw=1.) - if key1 is not None: - dax['shift1'][ii].imshow(shift1[:, :, ii].T, - extent=extent, cmap=plt.cm.seismic, - interpolation='nearest', origin='lower', - vmin=-shiftabs, vmax=shiftabs) - dax['spectn'][ii].axvline(dinput['lines'][indl1], - c='k', ls='-', lw=1.) - dax['shift1_z'][ii].axvline(dinput['lines'][indl1], - c='k', ls='-', lw=1.) - # Polish - i0 = (isortxj == 0).nonzero()[0][0] - i1 = (isortxj == nxj-1).nonzero()[0][0] - xlab = ['{}'.format(ss) for ss in shots] - dax['time'][i0].set_title(r'time') - dax['chinorm'][i0].set_title(r'$\chi_{norm}$') - dax['shift0'][i0].set_title('shift {}'.format(key0)) - dax['shift1'][i0].set_title('shift {}'.format(key1)) - dax['time'][i1].set_xticks(range(1, nshot+1)) - dax['time'][i1].set_xticklabels(xlab, rotation=75) - dax['chinorm'][i1].set_xticklabels(xlab, rotation=75) - dax['time'][i1].set_yticks(range(0, nt)) - if indt is not None: - dax['time'][i1].set_yticklabels(indt) - - # -------- Extra plot ---- - if nang == 1 or (key0 is None and key1 is None): - return dax - - lkey = [kk for kk in [key0, key1] if kk is not None] - nl = len(lkey) - - dmargin = {'left': 0.06, 'right': 0.95, - 'bottom': 0.08, 'top': 0.90, - 'wspace': 0.4, 'hspace': 0.2} - - fig = plt.figure(figsize=fs) - if shot is not None: - fig.suptitle('shot = {}'.format(shot)) - gs = gridspec.GridSpec(2, nl, **dmargin) - - shx0, shx1, shy = None, None, None - ax0 = [None for ii in range(nl)] - ax1 = [None for ii in range(nl)] - for ii in range(nl): - ax0[ii] = fig.add_subplot(gs[0, ii], sharex=shx0, sharey=shy) - if ii == 0: - shx0, shy = ax0[ii], ax0[ii] - ax1[ii] = fig.add_subplot(gs[1, ii], sharex=shx1, sharey=shy) - if ii == 0: - shx1 = ax1[ii] - ax0[ii].set_title(lkey[ii]) - ax0[ii].set_xlabel('table angle') - ax0[ii].set_ylabel(r'$\Delta \lambda$ (m)') - ax1[ii].set_xlabel('xi (m)') - for jj in range(nxj): - ax0[ii].plot(angu, dcost[lkey[ii]]['shiftm'][jj, :], - ls='-', lw=1., marker='.', ms=8, - label='xj[{}] = {} m'.format(jj, xj[jj])) - ax0[ii].axhline(0, ls='--', lw=1., c='k') - for jj in range(nang): - ax1[ii].plot(xj, dcost[lkey[ii]]['shiftm'][:, jj], - ls='-', lw=1., marker='.', ms=8, - label='ang[{}] = {}'.format(jj, angu[jj])) - ax1[ii].axhline(0, ls='--', lw=1., c='k') - - ax0[0].legend(loc='upper left', bbox_to_anchor=(1.01, 1.)) - ax1[0].legend(loc='upper left', bbox_to_anchor=(1.01, 1.)) - return dax - - -# ############################################################################# -# Scan det -# ############################################################################# - - -_DX = [0.01, 0.002, 0.002] # 0.0004 -_DROT = [0.01, 0.01, 0.01] # 0.0004 -_NDX = 2 -_NDROT = 2 - - -def _check_orthonormal(cent, nout, ei, ej, ndx, ndrot, msg=''): - shape = (3, 2*ndrot+1, 2*ndrot+1, 2*ndrot+1) - lc = [ - cent.shape == (3, 2*ndx+1, 2*ndx+1, 2*ndx+1), - nout.shape == ei.shape == ej.shape == shape, - np.allclose(np.sum(nout**2, axis=0), 1.), - np.allclose(np.sum(ei**2, axis=0), 1.), - np.allclose(np.sum(ej**2, axis=0), 1.), - np.allclose(np.sum(nout*ei, axis=0), 0.), - np.allclose(np.sum(nout*ej, axis=0), 0.), - ] - if not all(lc): - msg = ("Non-conform set of detector parameters! " + msg) - raise Exception(msg) - - -def scan_det(pfe=None, allow_pickle=True, - ndx=None, dx=None, ndrot=None, drot=None, - spectn=None, shots=None, t=None, ang=None, - xi=None, xj=None, thr=None, - dinput=None, indl0=None, indl1=None, - shot=None, indt=None, indxj=None, maskxi=None, - cryst=None, det=None, - dlines=None, dconstraints=None, dx0=None, - key0=None, key1=None, - lambmin=None, lambmax=None, - same_spectrum=None, dlamb=None, - method=None, max_nfev=None, - dscales=None, x0_scale=None, bounds_scale=None, - xtol=None, ftol=None, gtol=None, - loss=None, verbose=None, plot=None, - fs=None, dmargin=None, cmap=None, - save=None, pfe_out=None): - - # Check input - if verbose is None: - verbose = 1 - if dx is None: - dx = _DX - if drot is None: - drot = _DROT - if ndx is None: - ndx = _NDX - if ndrot is None: - ndrot = _NDROT - if plot is None: - plot = True - if save is None: - save = isinstance(pfe_out, str) - - if not (hasattr(dx, '__iter__') and len(dx) == 3): - dx = [dx, dx, dx] - if not (hasattr(drot, '__iter__') and len(drot) == 3): - drot = [drot, drot, drot] - - if dconstraints is None: - dconstraints = { - 'double': True, - 'symmetry': False, - 'width': { - 'wxyzkj': [ - 'ArXVII_w_Bruhns', 'ArXVII_z_Amaro', - 'ArXVII_x_Adhoc200408', 'ArXVII_y_Adhoc200408', - 'ArXVI_k_Adhoc200408', 'ArXVI_j_Adhoc200408', - 'ArXVI_q_Adhoc200408', 'ArXVI_r_Adhoc200408', - 'ArXVI_a_Adhoc200408', - ], - }, - 'amp': { - 'ArXVI_k_Adhoc200408': {'key': 'kj'}, - 'ArXVI_j_Adhoc200408': {'key': 'kj', 'coef': 1.3576}, - }, - 'shift': {'wz': ['ArXVII_w_Bruhns', 'ArXVII_z_Amaro']}, - } - - # input data file - lc = [pfe is not None, - all([aa is not None for aa in [spectn, shots, t, ang, xi, xj]])] - if np.sum(lc) != 1: - msg = ("Please provide eithe (xor):\n" - + "\t- pfe\n" - + "\t- spectn, shots, t, ang, xi, xj") - raise Exception(msg) - if lc[0]: - if not os.path.isfile(pfe): - msg = ("Provided file does not exist!\n" - + "\t- provided: {}".format(pfe)) - raise Exception(msg) - - # subset of shots - if shot is not None: - if not hasattr(shot, '__iter__'): - shot = np.array([shot], dtype=int) - else: - shot = np.r_[shot].astype(int) - - if maskxi is None: - maskxi = _MASKXI - - # extract data - spectn, shots, t, ang, xi, xj, thr = _extract_data(pfe, - allow_pickle, - maskxi, shot, - indt, indxj)[1:] - # Group by angle - angu = np.unique(ang) - nang = angu.size - lcol = ['r', 'g', 'b', 'k', 'm', 'c', 'y'] - ncol = len(lcol) - - nshot, nt, nxj, nxi = spectn.shape - - # Cryst part - cryst, det = _get_crystanddet(cryst=cryst, det=det) - assert cryst is not False - - # Get dinput for 1d fitting - dinput, key0, key1, indl0, indl1 = _get_dinput_key01( - dinput=dinput, key0=key0, key1=key1, indl0=indl0, indl1=indl1, - dlines=dlines, dconstraints=dconstraints, - lambmin=lambmin, lambmax=lambmax, - same_spectrum=same_spectrum, nspect=spectn.shape[0], dlamb=dlamb) - - # -------- - # Prepare - dxv = np.linspace(-ndx, ndx, 2*ndx+1) - drotv = np.linspace(-ndrot, ndrot, 2*ndrot+1) - - cent = det['cent'][:, None, None, None] - eout = det['nout'][:, None, None, None] - e1 = det['ei'][:, None, None, None] - e2 = det['ej'][:, None, None, None] - - # x and rot - x0 = dxv[None, :, None, None]*dx[0] - x1 = dxv[None, None, :, None]*dx[1] - x2 = dxv[None, None, None, :]*dx[2] - rot0 = drotv[None, :, None, None]*drot[0] - rot1 = drotv[None, None, :, None]*drot[1] - rot2 = drotv[None, None, None, :]*drot[2] - - # Cent and vect - cent = cent + x0*eout + x1*e1 + x2*e2 - nout = (np.sin(rot0)*e2 - + np.cos(rot0)*(eout*np.cos(rot1) + e1*np.sin(rot1))) - nout = np.repeat(nout, 2*ndrot+1, axis=-1) - ei = np.repeat(np.repeat( - np.cos(rot1)*e1 - np.sin(rot1)*eout, 2*ndrot+1, axis=1), - 2*ndrot+1, axis=-1) - ej = np.array([nout[1, ...]*ei[2, ...] - nout[2, ...]*ei[1, ...], - nout[2, ...]*ei[0, ...] - nout[0, ...]*ei[2, ...], - nout[0, ...]*ei[1, ...] - nout[1, ...]*ei[0, ...]]) - _check_orthonormal(cent, nout, ei, ej, ndx, ndrot, '1') - ei = np.cos(rot2)*ei + np.sin(rot2)*ej - ej = np.array([nout[1, ...]*ei[2, ...] - nout[2, ...]*ei[1, ...], - nout[2, ...]*ei[0, ...] - nout[0, ...]*ei[2, ...], - nout[0, ...]*ei[1, ...] - nout[1, ...]*ei[0, ...]]) - _check_orthonormal(cent, nout, ei, ej, ndx, ndrot, '2') - - def func_msg(ndx, ndrot, i0, i1, i2, j0, j1, j2): - nx = 2*ndx + 1 - nrot = 2*ndrot + 1 - msg = ("-"*10 + "\n" - + "ii = {1}/{0} {2}/{0} {3}/{0}\t".format(nx, i0+1, i1+1, i2+1) - + "jj = {1}/{0} {2}/{0} {3}/{0}".format(nrot, j0+1, j1+1, j2+1) - + "...\t") - return msg - - # -------------- - # Iterate around reference - x0_scale = None - func = tf.data._spectrafit2d.multigausfit1d_from_dlines - shape = tuple(np.r_[[2*ndx+1]*3 + [2*ndrot+1]*3 + [nxj, nang]]) - time = np.full(shape, np.nan) - done = np.array([np.zeros((6,)), - [2*ndx+1, 2*ndx+1, 2*ndx+1, - 2*ndrot+1, 2*ndrot+1, 2*ndrot+1]]) - dcost = {kk: {'detail': np.full(shape, np.nan), - 'chin': np.full(shape[:-2], np.nan)} - for kk in [key0, key1] if kk is not None} - - # -------------- - # Iterate around reference - dout = {'dcost': dcost, 'time': time, 'angu': angu, 'xj': xj, - 'dx': dx, 'ndx': ndx, 'drot': drot, 'ndrot': ndrot, - 'x0': x0, 'x1': x1, 'x2': x2, - 'rot0': rot0, 'rot1': rot1, 'rot2': rot2, - 'cent': cent, 'nout': nout, 'ei': ei, 'ej': ej, - 'pfe': pfe, 'shots': shots, 'done': done} - - # -------------- - # Loop - for i0 in range(x0.size): - for i1 in range(x1.size): - for i2 in range(x2.size): - for j0 in range(rot0.size): - for j1 in range(rot1.size): - for j2 in range(rot2.size): - ind = (i0, i1, i2, j0, j1, j2) - if verbose > 0: - print(func_msg(ndx, ndrot, *ind), - end='', flush=True, file=sys.stdout) - det = {'cent': cent[:, i0, i1, i2], - 'nout': nout[:, j0, j1, j2], - 'ei': ei[:, j0, j1, j2], - 'ej': ej[:, j0, j1, j2]} - try: - dfit1d = fit( - spectn=spectn, shots=shots, t=t, ang=ang, - xi=xi, xj=xj, thr=thr, - shot=None, indt=None, indxj=None, - maskxi=None, cryst=cryst, det=det, - dlines=None, dconstraints=None, dx0=None, - key0=key0, key1=key1, - dinput=dinput, indl0=indl0, indl1=indl1, - lambmin=lambmin, lambmax=lambmax, - same_spectrum=same_spectrum, dlamb=dlamb, - method=method, max_nfev=max_nfev, - dscales=dscales, x0_scale=x0_scale, - bounds_scale=bounds_scale, - xtol=xtol, ftol=ftol, gtol=gtol, - loss=None, verbose=0, - warn=False, plot=False) - for ii in range(nang): - indi = ang == angu[ii] - dout['time'][ind][:, ii] = ( - np.nanmean(np.nanmean( - dfit1d['time'][indi, :, :], - axis=1, - ), axis=0) - ) - for kk in dfit1d['dcost'].keys(): - aa = dfit1d['dcost'][kk]['shiftm'] - dout['dcost'][kk]['detail'][ind] = aa - nbok = np.sum(np.sum( - ~np.isnan(aa), - axis=-1, - ), axis=-1) - dout['dcost'][kk]['chin'][ind] = ( - np.sqrt(np.nansum( - np.nansum(aa**2, axis=-1), - axis=-1, - )) / nbok - ) - dout['done'][0, :] = [i0+1, i1+1, i2+1, - j0+1, j1+1, j2+1] - print('ok', flush=True, file=sys.stdout) - except Exception as err: - print('failed: ' + str(err), - flush=True, file=sys.stdout) - pass - # Save regulary (for long jobs) - if save is True: - np.savez(pfe_out, **dout) - msg = "Saved in :\n\t" + pfe_out - print(msg) - - if save is True: - np.savez(pfe_out, **dout) - msg = "Saved in:\n\t" + pfe_out - print(msg) - return dout - - -def scan_det_plot(din, - nsol=None, yscale='log', - fs=None, dmargin=None, cmap=None): - - if isinstance(din, str): - din = dict(np.load(din, allow_pickle=True)) - din['dcost'] = din['dcost'].tolist() - if nsol is None: - nsol = 3 - - print('done:\n\t{}\n\t{}'.format(din['done'][0, :], din['done'][1, :])) - - # Prepare - ndx = din.get('ndx', int((din['x0'].size-1)/2)) - ndrot = din.get('ndrot', int((din['rot0'].size-1)/2)) - dx = din.get('dx', np.nanmean(np.diff(din['x0'], axis=1))) - drot = din.get('drot', np.nanmean(np.diff(din['rot0'], axis=1))) - if not (hasattr(dx, '__iter__') and len(dx) == 3): - dx = np.r_[dx, dx, dx] - if not (hasattr(drot, '__iter__') and len(drot) == 3): - drot = np.r_[drot, drot, drot] - if np.any(np.isnan(dx)): - ylx = (-0.001, 0.001) - dxv = np.r_[0] - else: - ylx = (ndx+0.5)*np.max(dx)*np.r_[-1, 1] - dxv = np.linspace(-ndx, ndx, 2*ndx+1) - if np.any(np.isnan(drot)): - ylr = (-0.001, 0.001) - drotv = np.r_[0] - else: - ylr = (ndx+0.5)*np.max(drot)*np.r_[-1, 1] - drotv = np.linspace(-ndrot, ndrot, 2*ndrot+1) - - dind = dict.fromkeys(din['dcost'].keys(), {'chi2d': None, - 'ind': None, 'lab': None}) - for kk in dind.keys(): - if 'chin' not in din['dcost'][kk].keys(): - nbok = np.sum(np.sum(~np.isnan(din['dcost'][kk]['detail']), - axis=-1), axis=-1) - dind[kk]['chinf'] = np.ravel(np.sqrt(np.nansum(np.nansum( - din['dcost'][kk]['detail']**2, axis=-1), axis=-1)) / nbok) - else: - dind[kk]['chinf'] = din['dcost'][kk]['chin'].ravel() - dind[kk]['ind'] = np.argsort(dind[kk]['chinf'], axis=None) - [ix0, ix1, ix2, - irot0, irot1, irot2] = np.unravel_index( - dind[kk]['ind'], din['dcost'][kk]['chin'].shape) - dind[kk]['indxrot'] = np.array([ix0, ix1, ix2, - irot0, irot1, irot2]) - dind[kk]['valxrot'] = np.array([ - dxv[ix0]*dx[0], dxv[ix1]*dx[1], dxv[ix2]*dx[2], - drotv[irot0]*drot[0], drotv[irot1]*drot[1], drotv[irot2]*drot[2]]) - i0 = int((dind[kk]['chinf'].size-1)/2) - i0bis = (dind[kk]['ind'] == i0).nonzero()[0] + 1 - - ldet = [{'cent': din['cent'][:, ix0[ll], ix1[ll], ix2[ll]], - 'nout': din['nout'][:, irot0[ll], irot1[ll], irot2[ll]], - 'ei': din['ei'][:, irot0[ll], irot1[ll], irot2[ll]], - 'ej': din['ej'][:, irot0[ll], irot1[ll], irot2[ll]]} - for ll in range(nsol)] - - xlbck = np.r_[1, 2, 3][:, None] + 0.3*np.r_[-1, 1, np.nan][None, :] - xlbckx = np.tile(xlbck.ravel(), 2*ndx+1) - xlbckrot = np.tile(xlbck.ravel(), 2*ndrot+1) - ylbckx = dxv[:, None] * dx[None, :] - ylbckx = np.repeat(ylbckx.ravel(), 3) - ylbckrot = drotv[:, None] * drot[None, :] - ylbckrot = np.repeat(ylbckrot.ravel(), 3) - - # -------------- - # Plot - - if fs is None: - fs = (18, 9) - if cmap is None: - cmap = plt.cm.viridis - if dmargin is None: - dmargin = {'left': 0.06, 'right': 0.99, - 'bottom': 0.06, 'top': 0.93, - 'wspace': 0.3, 'hspace': 0.2} - - fig = plt.figure(figsize=fs) - if din.get('shots') is not None: - fig.suptitle('shots = {}'.format(din['shots'])) - gs = gridspec.GridSpec(2, len(dind)*2, **dmargin) - - shx0, shy0, shx1, shy1, shx2, shy2 = None, None, None, None, None, None - dax = {'best': [None for kk in dind.keys()], - 'map_x': [None for kk in dind.keys()], - 'map_rot': [None for kk in dind.keys()]} - for ii, kk in enumerate(dind.keys()): - dax['best'][ii] = fig.add_subplot(gs[0, ii*2:(ii+1)*2], - yscale=yscale, - sharex=shx0, sharey=shy0) - dax['map_x'][ii] = fig.add_subplot(gs[1, ii*2], - sharex=shx1, sharey=shy1) - dax['map_rot'][ii] = fig.add_subplot(gs[1, ii*2+1], - sharex=shx2, sharey=shy2) - if ii == 0: - shx0, shy0 = dax['best'][ii], dax['best'][ii] - shx1, shy1 = dax['map_x'][ii], dax['map_x'][ii] - shx2, shy2 = dax['map_rot'][ii], dax['map_rot'][ii] - dax['best'][ii].set_title(kk) - - dax['best'][ii].plot(range(nsol+1, dind[kk]['ind'].size + 1), - dind[kk]['chinf'][dind[kk]['ind'][nsol:]], - c='k', ls='-', lw=1., marker='.', ms=3) - dax['best'][ii].plot(i0bis, - dind[kk]['chinf'][i0], - c='k', ls='None', lw=2., marker='x') - for jj in range(nsol): - l, = dax['best'][ii].plot( - jj+1, - dind[kk]['chinf'][dind[kk]['ind'][jj]], - ls='None', marker='x', ms=6) - dax['map_x'][ii].plot(range(1, 4), dind[kk]['valxrot'][:3, jj], - ls='-', marker='o', lw=1., c=l.get_color()) - dax['map_rot'][ii].plot(range(1, 4), dind[kk]['valxrot'][3:, jj], - ls='-', marker='o', lw=1., c=l.get_color()) - - dax['map_x'][ii].plot(xlbckx, ylbckx, - ls='-', lw=1., c='k') - dax['map_rot'][ii].plot(xlbckrot, ylbckrot, - ls='-', lw=1., c='k') - dax['map_x'][ii].axhline(0., ls='--', lw=1., c='k') - dax['map_rot'][ii].axhline(0., ls='--', lw=1., c='k') - - dax['best'][0].set_xlim(0, max(50, i0bis)) - dax['map_x'][0].set_xlim(0, 4) - dax['map_rot'][0].set_xlim(0, 4) - dax['map_x'][0].set_ylim(*ylx) - dax['best'][0].set_ylabel(r'$\chi_{norm}$') - dax['map_x'][0].set_xticks([1, 2, 3]) - # dax['map_x'][0].set_yticks(dxv) - dax['map_rot'][0].set_xticks([1, 2, 3]) - # dax['map_rot'][0].set_yticks(drotv) - dax['map_x'][0].set_xticklabels([r'$x_0$', r'$x_1$', r'$x_2$']) - dax['map_x'][0].set_ylabel(r'$\delta x$') - dax['map_rot'][0].set_xticklabels([r'$rot_0$', r'$rot_1$', r'$rot_2$']) - dax['map_rot'][0].set_ylabel(r'$\delta rot$') - dax['map_rot'][0].set_ylim(*ylr) - return dax, ldet - - -# ############################################################################# -# least_square det -# ############################################################################# - -def _get_det_from_det0_xscale(x, det0=None, scales=None): - xs = x*scales - cent = (det0['cent'] - + xs[0]*det0['nout'] - + xs[1]*det0['ei'] + xs[2]*det0['ei']) - nout = (np.sin(xs[3])*det0['ej'] - + np.cos(xs[3])*(det0['nout']*np.cos(xs[4]) - + det0['ei']*np.sin(xs[4]))) - ei = np.cos(xs[4])*det0['ei'] - np.sin(xs[4])*det0['nout'] - ej = np.cross(nout, ei) - ei = np.cos(xs[5])*ei + np.sin(xs[5])*ej - ej = np.cross(nout, ei) - return {'cent': cent, 'nout': nout, - 'ei': ei, 'ej': ej} - - -def get_func_cost(spectn=None, shots=None, t=None, ang=None, - xi=None, xj=None, - cryst=None, det0=None, - key0=None, key1=None, dinput=None, indl0=None, indl1=None, - lambmin=None, lambmax=None, same_spectrum=None, dlamb=None): - - def func_cost(x, scales=None): - dfit1d = fit(spectn=spectn, shots=shots, t=t, ang=ang, - xi=xi, xj=xj, - shot=None, indt=None, indxj=None, maskxi=None, - det=_get_det_from_det0_xscale(x, det0, scales=scales), - cryst=cryst, - dlines=None, dconstraints=None, dx0=None, - key0=key0, key1=key1, - dinput=dinput, indl0=indl0, indl1=indl1, - lambmin=lambmin, lambmax=lambmax, - same_spectrum=same_spectrum, dlamb=dlamb, - method=None, max_nfev=None, - dscales=None, x0_scale=None, - bounds_scale=None, - xtol=None, ftol=None, gtol=None, - loss=None, verbose=0, plot=False, warn=False) - shiftm = np.concatenate([dfit1d['dcost'][kk]['shiftm'].ravel() - for kk in dfit1d['dcost'].keys()]) - return shiftm*1.e13 - return func_cost - - -def scan_det_least_square(pfe=None, allow_pickle=True, - ndx=None, dx=None, ndrot=None, drot=None, - spectn=None, shots=None, t=None, ang=None, - xi=None, xj=None, - dinput=None, indl0=None, indl1=None, - shot=None, indt=None, indxj=None, maskxi=None, - cryst=None, det=None, - dlines=None, dconstraints=None, dx0=None, - key0=None, key1=None, - lambmin=None, lambmax=None, - same_spectrum=None, dlamb=None, - method=None, max_nfev=None, - dscales=None, x0_scale=None, bounds_scale=None, - xtol=None, ftol=None, gtol=None, jac=None, - loss=None, verbose=None, plot=None, - fs=None, dmargin=None, cmap=None, - save=None, pfe_out=None): - - # Check input - if verbose is None: - verbose = 2 - if dx is None: - dx = _DX - if drot is None: - drot = _DROT - if ndx is None: - ndx = _NDX - if ndrot is None: - ndrot = _NDROT - if method is None: - method = 'trf' - if xtol is None: - xtol = 1.e-6 - if ftol is None: - ftol = 1.e-6 - if gtol is None: - gtol = 1.e-6 - if jac is None: - jac = '3-point' - if loss is None: - loss = 'linear' - if plot is None: - plot = True - if save is None: - save = isinstance(pfe_out, str) - - # input data file - lc = [pfe is not None, - all([aa is not None for aa in [spectn, shots, t, ang, xi, xj]])] - if np.sum(lc) != 1: - msg = ("Please provide eithe (xor):\n" - + "\t- pfe\n" - + "\t- spectn, shots, t, ang, xi, xj") - raise Exception(msg) - if lc[0]: - if not os.path.isfile(pfe): - msg = ("Provided file does not exist!\n" - + "\t- provided: {}".format(pfe)) - raise Exception(msg) - - # subset of shots - if shot is not None: - if not hasattr(shot, '__iter__'): - shot = np.array([shot], dtype=int) - else: - shot = np.r_[shot].astype(int) - - if maskxi is None: - maskxi = _MASKXI - - # extract data - spectn, shots, t, ang, xi, xj, thr = _extract_data(pfe, - allow_pickle, - maskxi, shot, - indt, indxj)[1:] - # Group by angle - angu = np.unique(ang) - nang = angu.size - nshot, nt, nxj, nxi = spectn.shape - - # Cryst part - cryst, det0 = _get_crystanddet(cryst=cryst, det=det) - assert cryst is not False - - # Get dinput for 1d fitting - dinput, key0, key1, indl0, indl1 = _get_dinput_key01( - dinput=dinput, key0=key0, key1=key1, indl0=indl0, indl1=indl1, - dlines=dlines, dconstraints=dconstraints, - lambmin=lambmin, lambmax=lambmax, - same_spectrum=same_spectrum, nspect=spectn.shape[0], dlamb=dlamb) - - # -------- - # Prepare - scales = [0.01, 0.01, 0.01, 0.01, 0.01, 0.01] - x0_scale = np.zeros((6,), dtype=float) - if method == 'lm': - jac = '2-point' - bounds_scale = (-np.inf, np.inf) - else: - bounds_scale = np.r_[0.10, 0.10, 0.10, 0.10, 0.10, 0.10]/scales - bounds_scale = (-bounds_scale, bounds_scale) - diff_step = [0.001, 0.001, 0.001, 0.001, 0.001, 0.001] - - func_cost = get_func_cost(spectn=spectn, shots=shots, t=t, ang=ang, - xi=xi, xj=xj, - cryst=cryst, det0=det0, - key0=key0, key1=key1, - dinput=dinput, indl0=indl0, indl1=indl1, - lambmin=lambmin, lambmax=lambmax, - same_spectrum=same_spectrum, dlamb=dlamb) - - # -------- - # Optimize - t0 = dtm.datetime.now() - res = scpopt.least_squares(func_cost, x0_scale, - jac=jac, bounds=bounds_scale, - method=method, ftol=ftol, xtol=xtol, - gtol=gtol, x_scale='jac', f_scale=1.0, - loss=loss, diff_step=diff_step, - tr_solver=None, tr_options={}, - jac_sparsity=None, max_nfev=max_nfev, - verbose=verbose, - kwargs={'scales': scales}) - - dt = (dtm.datetime.now()-t0).total_seconds() - msg = ("Ellapsed time: {} min".format(dt/60.)) - print(msg) - - # -------- - # Extract solution - det = _get_det_from_det0_xscale(res.x, det0, scales=scales) - return { - 'chin': np.sqrt(res.cost)/(nang*nxj), - 'time': dt, - 'x': res.x, 'det0': det0, 'det': det, - 'nfev': res.nfev, 'xtol': xtol, 'ftol': ftol, 'gtol': gtol, - 'method': method, 'scales': scales, - } - - -# ############################################################################# -# Treat all shots and save -# ############################################################################# - - -def treat(cryst, shot=None, - dlines=None, - dconst=None, - nbsplines=None, - ratio=None, - binning=None, - tol=None, - plasma=True, - nameextra=None, - domain=None, - xi=_XI, xj=_XJ, - path=_HERE): - - if nbsplines is None: - nbsplines = 15 - if ratio is None: - ratio = {'up': ['ArXVII_w_Bruhns', 'ArXVII_y_Adhoc200408'], - 'low': ['ArXVII_z_Amaro', 'ArXVII_x_Adhoc200408']} - if binning is None: - binning = {'lamb': 487, 'phi': 200} - if tol is None: - tol = 1.e-5 - if nameextra is None: - nameextra = '' - if nameextra != '' and nameextra[0] != '_': - nameextra = '_' + nameextra - if dlines is None: - from inputs_temp.dlines import dlines - dlines = {k0: v0 for k0, v0 in dlines.items() - if (k0 in ['ArXVII_w_Bruhns', 'ArXVII_z_Amaro'] - or ('Adhoc200408' in k0))} - if plasma is True: - dsig = { - 'ece': {'t': 't', 'data': 'Te0'}, - 'interferometer': {'t': 't', 'data': 'ne_integ'}, - 'ic_antennas': {'t': 't', 'data': 'power'}, - 'lh_antennas': {'t': 't', 'data': 'power'}} - - # Leave double ratio / dshift and x/y free, then plot them to get robust - # values - if dconst is None: - dconst = { - 'double': True, - 'symmetry': False, - 'width': {'wxyzkj': - ['ArXVII_w_Bruhns', 'ArXVII_z_Amaro', - 'ArXVII_x_Adhoc200408', 'ArXVII_y_Adhoc200408', - 'ArXVI_k_Adhoc200408', 'ArXVI_j_Adhoc200408', - 'ArXVI_q_Adhoc200408', 'ArXVI_r_Adhoc200408', - 'ArXVI_a_Adhoc200408']}, - 'amp': {'ArXVI_k_Adhoc200408': {'key': 'kj'}, - 'ArXVI_j_Adhoc200408': {'key': 'kj', 'coef': 1.3576}}, - 'shift': {'wz': ['ArXVII_w_Bruhns', 'ArXVII_z_Amaro'], - 'qra': ['ArXVI_q_Adhoc200408', 'ArXVI_r_Adhoc200408', - 'ArXVI_a_Adhoc200408'], - 'xy': ['ArXVII_x_Adhoc200408', 'ArXVII_y_Adhoc200408']}} - - # Shots - dshots = _DSHOTS[cryst] - shots = np.unique([kk for kk in dshots.keys() - if len(dshots[kk]['tlim']) == 2]) - if shot is not None: - if not hasattr(shot, '__iter__'): - shot = [shot] - ind = np.array([shots == ss for ss in shot]) - shots = shots[ind] - - # Cryst part - det = dict(np.load(os.path.join(_HERE, 'det37_CTVD_incC4.npz'))) - cryst, det = _get_crystanddet(cryst=cryst, det=det) - assert cryst is not False - - mask = ~np.any(np.load(_MASKPATH)['ind'], axis=0) - - for ii in range(shots.size): - if len(dshots[int(shots[ii])]['tlim']) != 2: - continue - print('\n\nshot {} ({} / {})'.format(shots[ii], ii+1, shots.size)) - try: - cryst.move(dshots[int(shots[ii])]['ang']*np.pi/180.) - - data, t, dbonus = _load_data(int(shots[ii]), - tlim=dshots[int(shots[ii])]['tlim']) - dout = cryst.plot_data_fit2d_dlines( - dlines=dlines, dconstraints=dconst, data=data, - xi=xi, xj=xj, det=det, - deg=2, verbose=2, subset=None, binning=binning, - nbsplines=nbsplines, mask=mask, ratio=ratio, - domain=domain, - Ti=True, vi=True, - chain=True, plot=False, - xtol=tol, ftol=tol, gtol=tol) - dout['t'] = t - dout.update(dbonus) - - # Include info on shot ? - if plasma is True and shots[ii] > 54178: - dt = np.nanmean(np.diff(t)) - tbins = np.r_[t[0]-dt/2, 0.5*(t[1:] + t[:-1]), t[-1]+dt/2] - try: - multi = tf.imas2tofu.MultiIDSLoader( - ids=list(dsig.keys()), - shot=int(shots[ii]), ids_base=False) - for k0, v0 in dsig.items(): - try: - if k0 == 'interferometer': - indch = [2, 3, 4, 5, 6, 7, 8, 9] - out = multi.get_data(k0, list(v0.values()), - indch=indch) - out[v0['data']] = out[v0['data']][7, :] - else: - out = multi.get_data(k0, list(v0.values())) - if k0 == 'lh_power': - out['power'] = np.nansum(out['power'], axis=0) - key = '{}_{}'.format(k0, v0['data']) - indout = (np.isnan(out[v0['data']]) - | (out[v0['data']] < 0.)) - out[v0['data']] = out[v0['data']][~indout] - out[v0['t']] = out[v0['t']][~indout] - dout[key] = scpstats.binned_statistic( - out[v0['t']], out[v0['data']], - statistic='mean', bins=tbins, - range=None)[0] - except Exception as err: - pass - - except Exception as err: - pass - - name = 'XICS_fit2d_{}_nbs{}_tol{}_bin{}{}{}.npz'.format( - shots[ii], nbsplines, int(-np.log10(tol)), - binning['phi']['nbins'], - '_Plasma' if plasma is True else '', - nameextra) - pfe = os.path.join(path, name) - np.savez(pfe, **dout) - msg = ('shot {}: saved in {}'.format(shots[ii], pfe)) - print(msg) - - except Exception as err: - if 'All nan in region scanned for scale' in str(err): - plt.close('all') - msg = ("shot {}: {}".format(shots[ii], str(err))) - warnings.warn(msg) - - -def _get_files(path, nameextra, nameexclude): - if nameextra is None: - nameextra = '' - if isinstance(nameextra, str): - nameextra = [nameextra] - if nameexclude is None: - nameexclude = '----------' - if isinstance(nameexclude, str): - nameexclude = [nameexclude] - lf = [ff for ff in os.listdir(path) - if (all([ss in ff - for ss in ['XICS', 'fit2d', 'nbs', '.npz'] + nameextra]) - and all([ss not in ff for ss in nameexclude]))] - return lf - - -def _get_dall_from_lf(lf, ls, lsextra, path, ratio=None): - dall = {kk: [] for kk in ls + lsextra} - if 'vims' in ls: - dall['vims_keys'] = [] - indshot = len('XICS_fit2d_') - for ff in lf: - din = {} - try: - cryst = 'ArXVII' - shot = int(ff[indshot:indshot+5]) - out = np.load(os.path.join(path, ff), allow_pickle=True) - nt = out['t'].size - for kk in ls: - if kk == 'angle': - din[kk] = np.full((nt,), _DSHOTS[cryst][shot]['ang']) - if kk not in out.keys(): - continue - if kk == 'ratio': - ind = out['ratio'].tolist()['str'].index(ratio) - din[kk] = out['ratio'].tolist()['value'][:, ind, :] - elif kk == 'vims': - din['vims_keys'] = out['dinput'].tolist()['shift']['keys'] - din[kk] = out.get(kk, np.full((nt,), np.nan)) - else: - din[kk] = out.get(kk, np.full((nt,), np.nan)) - lambmean = np.mean(out['dinput'].tolist()['lambminmax']) - din['shot'] = np.full((nt,), shot) - din['sumsig'] = np.nansum(out['data'], axis=1) - din['lambmean'] = np.full((nt,), lambmean) - din['ff'] = np.full((nt,), ff, dtype='U') - - except Exception as err: - continue - for kk in din.keys(): - if kk == 'pts_phi': - dall[kk] = din[kk] - elif kk == 'vims_keys': - dall[kk] = din[kk] - elif din[kk].ndim in [2, 3]: - if dall[kk] == []: - dall[kk] = din[kk] - else: - dall[kk] = np.concatenate((dall[kk], din[kk]), axis=0) - else: - dall[kk] = np.append(dall[kk], din[kk]) - return dall - - -def treat_plot_double(path=None, nameextra=None, nameexclude=None, - cmap=None, color=None, alpha=None, - vmin=None, vmax=None, size=None, - fs=None, dmargin=None): - - # --------- - # Prepare - if path is None: - path = _HERE - if cmap is None: - cmap = plt.cm.viridis - if color is None: - color = 'shot' - assert isinstance(color, str) - if alpha is None: - alpha = 'sumsig' - if size is None: - size = 30 - - lf = _get_files(path, nameextra, nameexclude) - nf = len(lf) - ls = ['dratio', 'dshift', 't', 'cost', 'angle', - 'ic_power', 'lh_power', 'ece_Te0'] - lsextra = ['shot', 'sumsig', 'lambmean', 'ff'] - dall = _get_dall_from_lf(lf, ls, lsextra, path) - if len(dall.keys()) == 0: - warnings.warn("No data in dall!") - - # Prepare color, alpha and size - if isinstance(size, str): - size = dall[size] - color = cmap(mcolors.Normalize(vmin=vmin, vmax=vmax)(dall[color])) - if isinstance(alpha, str): - alpha = mcolors.Normalize()(dall[alpha]) - else: - alpha = 1. - color[:, -1] = alpha - - # --------- - # plot - if fs is None: - fs = (12, 6) - if cmap is None: - cmap = plt.cm.viridis - if dmargin is None: - dmargin = {'left': 0.08, 'right': 0.96, - 'bottom': 0.08, 'top': 0.93, - 'wspace': 0.4, 'hspace': 0.2} - - fig = plt.figure(figsize=fs) - gs = gridspec.GridSpec(2, 16, **dmargin) - - shx0, shy0, shx1, shy1, shx2, shy2 = None, None, None, None, None, None - dax = {'dratio': None, - 'dshift': None} - dax['dratio'] = fig.add_subplot(gs[0, :-1]) - dax['dshift'] = fig.add_subplot(gs[1, :-1], sharex=dax['dratio']) - dax['dratio_c'] = fig.add_subplot(gs[0, -1]) - dax['dshift_c'] = fig.add_subplot(gs[1, -1]) - dax['dratio'].set_ylabel('double ratio (a.u.)') - dax['dshift'].set_ylabel('double shift (a.u.)') - dax['dshift'].set_xlabel(r'$\lambda$' + ' (m)') - - dr = dax['dratio'].scatter(dall['lambmean'], dall['dratio'], - c=color, s=size, marker='o', edgecolors='None') - dax['dshift'].scatter(dall['lambmean'], dall['dshift'], - c=color, s=size, marker='o', edgecolors='None') - - # dax['dratio'].set_ylim(0, 2) - dax['dratio'].set_xlim(3.94e-10, 4e-10) - dax['dratio'].set_ylim(0, 1.) - dax['dshift'].set_ylim(0, 6e-4) - - plt.colorbar(dr, cax=dax['dratio_c']) - # plt.colorbar(dr, cax=dax['dshift_c']) - - # Optional figure vs angle - if np.unique(dall['angle']).size == 1: - return dall, dax - - fig1 = plt.figure(figsize=fs) - gs = gridspec.GridSpec(2, 16, **dmargin) - - shx0, shy0, shx1, shy1, shx2, shy2 = None, None, None, None, None, None - dax1 = {'dratio': None, - 'dshift': None} - dax1['dratio'] = fig1.add_subplot(gs[0, :-1]) - dax1['dshift'] = fig1.add_subplot(gs[1, :-1], sharex=dax1['dratio']) - dax1['dratio_c'] = fig1.add_subplot(gs[0, -1]) - dax1['dshift_c'] = fig1.add_subplot(gs[1, -1]) - dax1['dratio'].set_ylabel('double ratio (a.u.)') - dax1['dshift'].set_ylabel('double shift (a.u.)') - dax1['dshift'].set_xlabel('rotation angle (rad)') - - llamb, langle, ldratio, ldshift = [], [], [], [] - done = np.zeros((dall['lambmean'].size,), dtype=bool) - for ll in np.unique(dall['lambmean']): - indl = (~done) & (np.abs(dall['lambmean'] - ll) < 0.005e-10) - if not np.any(indl): - continue - for aa in np.unique(dall['angle']): - inda = indl & (dall['angle'] == aa) - if not np.any(inda): - continue - llamb.append(ll) - langle.append(aa) - ldratio.append(np.nansum(dall['dratio'][inda] - * dall['sumsig'][inda]) - / np.nansum(dall['sumsig'][inda])) - ldshift.append(np.nansum(dall['dshift'][inda] - * dall['sumsig'][inda]) - / np.nansum(dall['sumsig'][inda])) - done[indl] = True - llamb, langle, ldratio, ldshift = map(np.asarray, - [llamb, langle, ldratio, ldshift]) - - for ll in np.unique(llamb): - ind = llamb == ll - l, = dax1['dratio'].plot(langle[ind], ldratio[ind], - ms=8, marker='o', - label=(r'$\lambda\approx$' - + '{:4.2e} m'.format(ll))) - dax1['dshift'].plot(langle[ind], ldshift[ind], - ms=8, marker='o', c=l.get_color(), - label=(r'$\lambda\approx$' - + '{:4.2e} m'.format(ll))) - - # dax1['dratio'].set_xlim(3.94e-10, 4e-10) - dax1['dratio'].set_ylim(0, 1.) - dax1['dshift'].set_ylim(0, 6e-4) - - dax1['dratio'].legend() - return dall, (dax, dax1) - - -def treat_plot_lineratio(ratio=None, path=None, - nameextra=None, nameexclude=None, - cmap=None, color=None, alpha=None, - vmin=None, vmax=None, size=None, - fs=None, dmargin=None): - - # --------- - # Prepare - if path is None: - path = _HERE - if cmap is None: - cmap = plt.cm.viridis - if color is None: - color = 'shot' - assert isinstance(color, str) - if alpha is None: - alpha = 'sumsig' - if size is None: - size = 30 - - lf = _get_files(path, nameextra, nameexclude) - nf = len(lf) - ls = ['ratio', 'pts_phi', 't', 'cost', - 'ic_t', 'ic_power', 'lh_t', 'lh_power', 'ece_Te0', 'ece_t'] - lsextra = ['shot', 'sumsig', 'lambmean', 'ff'] - dall = _get_dall_from_lf(lf, ls, lsextra, path, ratio=ratio) - if len(dall.keys()) == 0: - warnings.warn("No data in dall!") - - shotsu = np.unique(dall['shot']) - - # Prepare color, alpha and size - if isinstance(size, str): - size = dall[size] - if isinstance(color, str): - if color == 'shot_index': - shotu = np.unique(dall['shot']) - color = dall['shot'].astype(int) - for ii in range(0, shotu.size): - color[dall['shot'] == shotu[ii]] = ii - else: - color = dall[color] - color = cmap(mcolors.Normalize(vmin=vmin, vmax=vmax)(color)) - if isinstance(alpha, str): - alpha = mcolors.Normalize()(dall[alpha]) - else: - alpha = 1. - color[:, -1] = alpha - - # --------- - # plot - if fs is None: - fs = (12, 6) - if cmap is None: - cmap = plt.cm.viridis - if dmargin is None: - dmargin = {'left': 0.08, 'right': 0.96, - 'bottom': 0.08, 'top': 0.93, - 'wspace': 0.4, 'hspace': 0.2} - - fig = plt.figure(figsize=fs) - gs = gridspec.GridSpec(2, 16, **dmargin) - - shx0, shy0, shx1, shy1, shx2, shy2 = None, None, None, None, None, None - dax = {'ratio': None, - 'dshift': None} - dax['ratio'] = fig.add_subplot(gs[0, :-1]) - dax['dshift'] = fig.add_subplot(gs[1, :-1], sharex=dax['ratio']) - dax['ratio_c'] = fig.add_subplot(gs[0, -1]) - dax['dshift_c'] = fig.add_subplot(gs[1, -1]) - dax['ratio'].set_ylabel('line ratio (a.u.)') - dax['dshift'].set_ylabel('double shift (a.u.)') - dax['dshift'].set_xlabel('channel (rad)') - - for ii in range(dall['ratio'].shape[0]): - dax['ratio'].plot(dall['pts_phi'], dall['ratio'][ii, :], - color=color[ii, :], ls='-', lw=1.) - - # dax['dratio'].set_ylim(0, 2) - # dax['ratio'].set_xlim(3.94e-10, 4e-10) - dax['ratio'].set_ylim(0, 2.) - dax['dshift'].set_ylim(0, 6e-4) - - # plt.colorbar(dr, cax=dax['dratio_c']) - # plt.colorbar(dr, cax=dax['dshift_c']) - return dall, dax - - -def treat_plot_lineshift(path=None, diff=None, - nameextra=None, nameexclude=None, - cmap=None, color=None, alpha=None, - vmin=None, vmax=None, size=None, - fs=None, dmargin=None): - - # --------- - # Prepare - if path is None: - path = _HERE - if cmap is None: - cmap = plt.cm.viridis - if color is None: - color = 'line' - assert isinstance(color, str) - if alpha is None: - alpha = 'sumsig' - if size is None: - size = 30 - - lf = _get_files(path, nameextra, nameexclude) - nf = len(lf) - ls = ['vims', 'pts_phi', 't', 'cost', - 'ic_power', 'lh_power', 'ece_Te0'] - lsextra = ['shot', 'sumsig', 'lambmean', 'ff'] - dall = _get_dall_from_lf(lf, ls, lsextra, path) - if len(dall.keys()) == 0: - warnings.warn("No data in dall!") - - shotsu = np.unique(dall['shot']) - - # Prepare color, alpha and size - if isinstance(size, str): - size = dall[size] - if isinstance(color, str): - if color == 'line': - color = ['r', 'b', 'g'] - if isinstance(alpha, str): - alpha = np.array(mcolors.Normalize()(dall[alpha])) - else: - alpha = 1. - - dall['vims'] = dall['vims']*1.e-3 - if diff is None: - diff = dall['vims'].shape[1] in [2, 3] - if diff is True: - if dall['vims'].shape[1] == 2: - dvims = np.diff(dall['vims'], axis=1) - labd = [dall['vims_keys'][1] + '-' + dall['vims_keys'][0]] - elif dall['vims'].shape[1] == 3: - dvims = np.concatenate( - (np.diff(dall['vims'], axis=1), - dall['vims'][:, 0:1, :] - dall['vims'][:, 2:3, :]), axis=1) - labd = [dall['vims_keys'][1] + ' - ' + dall['vims_keys'][0], - dall['vims_keys'][2] + ' - ' + dall['vims_keys'][1], - dall['vims_keys'][0] + ' - ' + dall['vims_keys'][2]] - colord = ['k', 'y', 'c'] - - # --------- - # plot - if fs is None: - fs = (12, 6) - if cmap is None: - cmap = plt.cm.viridis - if dmargin is None: - dmargin = {'left': 0.08, 'right': 0.96, - 'bottom': 0.08, 'top': 0.93, - 'wspace': 0.4, 'hspace': 0.2} - - fig = plt.figure(figsize=fs) - gs = gridspec.GridSpec(2, 16, **dmargin) - - shx0, shy0, shx1, shy1, shx2, shy2 = None, None, None, None, None, None - dax = {'ratio': None, - 'dshift': None} - dax['vims'] = fig.add_subplot(gs[0, :-1]) - dax['dvims'] = fig.add_subplot(gs[1, :-1], sharex=dax['ratio']) - # dax['vims_c'] = fig.add_subplot(gs[0, -1]) - dax['vims'].set_ylabel(r'$v_i$' + ' (km.s^-1)') - dax['dvims'].set_ylabel(r'$\Delta v_i$' + ' (km.s^-1)') - dax['dvims'].set_xlabel('channel (rad)') - - for ii in range(dall['vims'].shape[0]): - for jj in range(dall['vims'].shape[1]): - dax['vims'].plot(dall['pts_phi'], dall['vims'][ii, jj, :], - color=color[jj], alpha=alpha[ii], ls='-', lw=1.) - - if diff is True: - for jj in range(dvims.shape[1]): - for ii in range(dall['vims'].shape[0]): - dax['dvims'].plot(dall['pts_phi'], dvims[ii, jj, :], - color=colord[jj], alpha=alpha[ii]) - dvmean = (np.nansum(dvims[:, jj, :]*dall['sumsig'][:, None]) - / (dvims.shape[2]*np.nansum(dall['sumsig']))) - dax['dvims'].axhline(dvmean, c=colord[jj], ls='--', lw=1.) - dax['dvims'].annotate( - '{:5.3e}'.format(dvmean), - xy=(1., dvmean), - xycoords=('axes fraction', 'data'), - color=colord[jj], size=10, - ) - - dax['vims'].axhline(0., c='k', ls='--', lw=1.) - dax['dvims'].axhline(0., c='k', ls='--', lw=1.) - hand = [mlines.Line2D([], [], c=color[jj], lw=1., ls='-') - for jj in range(dall['vims'].shape[1])] - lab = dall['vims_keys'].tolist() - dax['vims'].legend(hand, lab) - if diff is True: - hand = [mlines.Line2D([], [], c=colord[jj], lw=1., ls='-') - for jj in range(dvims.shape[1])] - dax['dvims'].legend(hand, labd) - - return dall, dax - - -# ############################################################################# -# Noise estimates -# ############################################################################# - - -def noise(cryst, shot=None, - dlines=None, - dconst=None, - nbsplines=None, - ratio=None, - binning=None, - tol=None, - plasma=True, - nameextra=None, - domain=None, - xi=_XI, xj=_XJ, - path=_HERE): - - if nbsplines is None: - nbsplines = 15 - if binning is None: - binning = {'lamb': 487, 'phi': 100} - if nameextra is None: - nameextra = '' - if nameextra != '' and nameextra[0] != '_': - nameextra = '_' + nameextra - - # Shots - dshots = _DSHOTS[cryst] - shots = np.unique([kk for kk in dshots.keys() - if len(dshots[kk]['tlim']) == 2]) - if shot is not None: - if not hasattr(shot, '__iter__'): - shot = [shot] - ind = np.array([shots == ss for ss in shot]) - shots = shots[ind] - - # Cryst part - det = dict(np.load(os.path.join(_HERE, 'det37_CTVD_incC4.npz'))) - cryst, det = _get_crystanddet(cryst=cryst, det=det) - assert cryst is not False - - mask = ~np.any(np.load(_MASKPATH)['ind'], axis=0) - - for ii in range(shots.size): - if len(dshots[int(shots[ii])]['tlim']) != 2: - continue - print('\n\nshot {} ({} / {})'.format(shots[ii], ii+1, shots.size)) - try: - cryst.move(dshots[int(shots[ii])]['ang']*np.pi/180.) - tlim = [None, dshots[int(shots[ii])]['tlim'][1]] - data, t, dbonus = _load_data(int(shots[ii]), tlim=tlim) - dout = cryst.fit2d_prepare( - data=data, xi=xi, xj=xj, det=det, - subset=None, binning=binning, - nbsplines=nbsplines, mask=mask, domain=domain) - dout['t'] = t - dout['shot'] = shots[ii] - dout.update(dbonus) - - name = 'XICS_fit2d_prepare_{}_nbs{}_bin{}{}.npz'.format( - shots[ii], nbsplines, dout['binning']['phi']['nbins'], - nameextra) - pfe = os.path.join(path, name) - np.savez(pfe, **dout) - msg = ('shot {}: saved in {}'.format(shots[ii], pfe)) - print(msg) - - except Exception as err: - if 'All nan in region scanned for scale' in str(err): - plt.close('all') - msg = ("shot {}: {}".format(shots[ii], str(err))) - warnings.warn(msg) - - -def get_noise_costjac(deg=None, nbsplines=None, phi=None, - phiminmax=None, symmetryaxis=None, sparse=None): - - if sparse is None: - sparse = False - - dbsplines = tf.data._spectrafit2d.multigausfit2d_from_dlines_dbsplines( - knots=None, deg=deg, nbsplines=nbsplines, - phimin=phiminmax[0], phimax=phiminmax[1], - symmetryaxis=symmetryaxis) - - def cost(x, km=dbsplines['knots_mult'], data=None, phi=phi): - return scpinterp.BSpline(km, x, deg, - extrapolate=False, axis=0)(phi) - data - - jac = np.zeros((phi.size, dbsplines['nbs']), dtype=float) - km = dbsplines['knots_mult'] - kpb = dbsplines['nknotsperbs'] - lind = [(phi >= km[ii]) & (phi < km[ii+kpb-1]) - for ii in range(dbsplines['nbs'])] - if sparse is True: - def jac_func(x, jac=jac, km=km, data=None, - phi=phi, kpb=kpb, lind=lind): - for ii in range(x.size): - jac[lind[ii], ii] = scpinterp.BSpline.basis_element( - km[ii:ii+kpb], extrapolate=False)(phi[lind[ii]]) - return scpsparse.csr_matrix(jac) - else: - def jac_func(x, jac=jac, km=km, data=None, - phi=phi, kpb=kpb, lind=lind): - for ii in range(x.size): - jac[lind[ii], ii] = scpinterp.BSpline.basis_element( - km[ii:ii+kpb], extrapolate=False)(phi[lind[ii]]) - return jac - return cost, jac_func - - -def plot_noise(filekeys=None, lf=None, path=None, deg=None, tnoise=None, - nbsplines=None, symmetryaxis=None, lnbsplines=None, nbins=None, - sparse=None, method=None, xtol=None, ftol=None, gtol=None, - loss=None, max_nfev=None, tr_solver=None, - alpha=None, verb=None, timeit=None, - plot=None, fs=None, cmap=None, dmargin=None): - - # --------------- - # Check inputs - if deg is None: - deg = 2 - if nbsplines is None: - nbsplines = 13 - if lnbsplines is None: - lnbsplines = np.arange(5, 20) - lnbsplines = np.array(lnbsplines) - if symmetryaxis is None: - symmetryaxis = False - if path is None: - path = os.path.dirname(__file__) - if filekeys is None: - filekeys = [] - filekeys += ['XICS', 'fit2d', 'prepare', '.npz'] - if lf is None: - lf = [ - ff for ff in os.listdir(path) - if all([ss in ff for ss in filekeys]) - ] - if len(lf) == 0: - return - if tnoise is None: - tnoise = 30. - if method is None: - method = 'trf' - assert method in ['trf', 'dogbox', 'lm'], method - if tr_solver is None: - tr_solver = 'exact' - _TOL = 1.e-14 - if xtol is None: - xtol = _TOL - if ftol is None: - ftol = _TOL - if gtol is None: - gtol = _TOL - if loss is None: - loss = 'linear' - if max_nfev is None: - max_nfev = None - if plot is None: - plot = True - if verb is None: - verb = True - if timeit is None: - timeit = not verb - if nbins is None: - nbins = 15 - - # --------------- - # Get data - dout = {ff: dict(np.load(os.path.join(path, ff), allow_pickle=True)) - for ff in lf} - dnt = {ff: dout[ff]['t'].size for ff in lf} - - dall = { - 'shot': np.concatenate([np.full((dnt[ff],), dout[ff]['shot']) - for ff in lf]), - 't': np.concatenate([dout[ff]['t'] for ff in lf]), - 'phi1d': dout[lf[0]]['phi1d'], - 'dataphi1d': np.concatenate([dout[ff]['dataphi1d'] for ff in lf], - axis=0), - 'data': np.concatenate([dout[ff]['data'] for ff in lf], - axis=0)} - - nlamb = dout[lf[0]]['binning'].tolist()['lamb']['nbins'] - coeflamb = nlamb / (nlamb - 1) - dataphidmean = np.nanmean(dall['dataphi1d'], axis=1) - dall['indnosignal'] = (dall['t'] <= tnoise) | (dataphidmean < 0.4) - nbnosignal = dall['indnosignal'].sum() - coefstd = nbnosignal / (nbnosignal - 1) - dall['nosignal_mean'] = np.nanmean(dall['data'][dall['indnosignal'], :, :], - axis=0) - dall['nosignal_var'] = np.nanstd(dall['data'][dall['indnosignal'], :, :], - axis=0)**2 * coefstd - dall['nosignal_1dmean'] = np.nanmean( - dall['dataphi1d'][dall['indnosignal'], :], axis=0) - dall['dataphi1d_var'] = np.nanstd(dall['data'], axis=1) * coeflamb - dall['nosignal_1dvar'] = np.nanmean( - dall['dataphi1d'][dall['indnosignal'], :], axis=0) * coefstd - - lambminmax = dout[lf[0]]['domain'].tolist()['lamb']['minmax'] - phiminmax = dout[lf[0]]['domain'].tolist()['phi']['minmax'] - extent = (lambminmax[0], lambminmax[1], phiminmax[0], phiminmax[1]) - shotu = np.unique(dall['shot']) - if alpha is None: - alpha = mcolors.Normalize()(np.nanmean(dall['dataphi1d'], axis=1)) - alpha = np.array(alpha) - alpha[alpha < 0.005] = 0.005 - else: - alpha = np.full((dall['dataphi1d'].shape[0],), alpha) - knots = None - datamax = np.nanmax(dall['dataphi1d'], axis=1) - dataphi1dnorm = dall['dataphi1d'] / datamax[:, None] - indj = (~dall['indnosignal']).nonzero()[0] - dataphi1dok = dall['dataphi1d'][indj, :] - lchi2 = np.full((dall['dataphi1d'].shape[0], lnbsplines.size), np.nan) - shape = tuple(np.r_[dall['dataphi1d'].shape, lnbsplines.size]) - err = np.full(shape, np.nan) - sol_x = np.full((dall['dataphi1d'].shape[0], nbsplines), np.nan) - if timeit is True: - t0 = dtm.datetime.now() - for ii in range(lnbsplines.size): - x0 = 1. - (2.*np.arange(lnbsplines[ii])/lnbsplines[ii] - 1.)**2 - cost, jac = get_noise_costjac(deg=deg, phi=dall['phi1d'], - nbsplines=int(lnbsplines[ii]), - phiminmax=phiminmax, sparse=sparse, - symmetryaxis=symmetryaxis) - for jj in range(indj.size): - if verb is True: - msg = ("\tnbsplines = {} ({}/{}),".format(lnbsplines[ii], ii+1, - lnbsplines.size) - + "\tprofile {} ({}/{})".format(indj[jj], jj+1, - indj.size)) - print(msg.ljust(60), flush=True, end='\r') - res = scpopt.least_squares( - cost, x0, jac=jac, - method=method, ftol=ftol, xtol=xtol, gtol=gtol, - x_scale='jac', f_scale=1.0, loss=loss, diff_step=None, - tr_solver=tr_solver, tr_options={}, jac_sparsity=None, - max_nfev=max_nfev, verbose=0, args=(), - kwargs={'data': dataphi1dnorm[indj[jj], :]}) - - lchi2[indj[jj], ii] = np.nansum( - cost(x=res.x, data=dataphi1dnorm[indj[jj], :])**2) - err[indj[jj], :, ii] = (cost(res.x, data=0.) * datamax[indj[jj]] - - dall['dataphi1d'][indj[jj], :]) - if lnbsplines[ii] == nbsplines: - sol_x[indj[jj], :] = res.x - dall['err'] = err - - # Mean and var of err - errok = err[indj, :] - dataphi1dbin = np.linspace(0., np.nanmax(dataphi1dok), nbins) - indbin = np.searchsorted(dataphi1dbin, dataphi1dok) - errbin_mean = np.full((dataphi1dbin.size, lnbsplines.size), np.nan) - errbin_var = np.full((dataphi1dbin.size, lnbsplines.size), np.nan) - alpha_err = np.full((lnbsplines.size,), np.nan) - for ii in range(dataphi1dbin.size): - nok = (~np.isnan(errok[indbin == ii])).sum() - errbin_mean[ii, :] = np.nanmean(errok[indbin == ii], axis=0) - errbin_var[ii, :] = ( - np.nanstd(errok[indbin == ii], axis=0)**2 * (nok-1)/nok - ) - - if timeit is True: - dall['timeit'] = (dtm.datetime.now()-t0).total_seconds() - lchi2 = lchi2 / np.nanmax(lchi2, axis=1)[:, None] - - dbsplines = tf.data._spectrafit2d.multigausfit2d_from_dlines_dbsplines( - knots=None, deg=deg, nbsplines=nbsplines, - phimin=phiminmax[0], phimax=phiminmax[1], - symmetryaxis=symmetryaxis) - dall['fitphi1d'] = np.full(dall['dataphi1d'].shape, np.nan) - for ii in indj: - dall['fitphi1d'][ii, :] = scpinterp.BSpline( - dbsplines['knots_mult'], - sol_x[ii, :], dbsplines['deg'], - extrapolate=False, axis=0)(dall['phi1d']) - - dall['dataphi1dbin'] = dataphi1dbin - dall['errbin_mean'] = errbin_mean - dall['errbin_var'] = errbin_var - dall['indbin'] = indbin - - # --------- - # Debug - # ijk = np.any(dall['dataphi1d'] > 1100, axis=1) - # ijk = np.nonzero(ijk)[0] - # plt.figure(figsize=(18, 6)) - # for ii in range(len(ijk)): - # plt.subplot(1, len(ijk), ii+1) - # tit = "{} - t = {} s".format(dall['shot'][ijk[ii]], - # dall['t'][ijk[ii]]) - # plt.gca().set_title(tit) - # plt.plot(dall['phi1d'], dall['dataphi1d'][ijk[ii], :], - # c='k', marker='.', ls='None') - # plt.plot(dall['phi1d'], dall['fitphi1d'][ijk[ii], :]*datamax[ijk[ii]], - # c='r', marker='None', ls='-') - # dbsplines = tf.data._spectrafit2d.multigausfit2d_from_dlines_dbsplines( - # knots=None, deg=deg, nbsplines=nbsplines-1, - # phimin=phiminmax[0], phimax=phiminmax[1], - # symmetryaxis=symmetryaxis) - # fitphi1dtemp = scpinterp.LSQUnivariateSpline( - # dall['phi1d'], dall['dataphi1d'][ijk[ii], :], - # dbsplines['knots'][1:-1], w=None, - # bbox=[dbsplines['knots'][0], dbsplines['knots'][-1]], - # k=deg, ext=0, check_finite=False)(dall['phi1d']) - # plt.plot(dall['phi1d'], fitphi1dtemp, - # c='g', marker='None', ls='-') - # dbsplines = tf.data._spectrafit2d.multigausfit2d_from_dlines_dbsplines( - # knots=None, deg=deg, nbsplines=nbsplines+1, - # phimin=phiminmax[0], phimax=phiminmax[1], - # symmetryaxis=symmetryaxis) - # fitphi1dtemp = scpinterp.LSQUnivariateSpline( - # dall['phi1d'], dall['dataphi1d'][ijk[ii], :], - # dbsplines['knots'][1:-1], w=None, - # bbox=[dbsplines['knots'][0], dbsplines['knots'][-1]], - # k=deg, ext=0, check_finite=False)(dall['phi1d']) - # plt.plot(dall['phi1d'], fitphi1dtemp, - # c='b', marker='None', ls='-') - - # import pdb; pdb.set_trace() # DB - # End debug - # -------------- - - if plot is False: - return dall - - # --------------- - # Plot - if fs is None: - fs = (16, 8) - if cmap is None: - cmap = plt.cm.viridis - if dmargin is None: - dmargin = {'left': 0.08, 'right': 0.96, - 'bottom': 0.08, 'top': 0.93, - 'wspace': 0.4, 'hspace': 0.2} - tstr0 = '(t <= {} s)'.format(tnoise) - tstr1 = '(t > {} s)'.format(tnoise) - - fig = plt.figure(figsize=fs) - gs = gridspec.GridSpec(3, 4, **dmargin) - - shx0, shy0, shx1, shy1, shx2, shy2 = None, None, None, None, None, None - dax = {} - dax['nosignal_mean2d'] = fig.add_subplot(gs[0, 0]) - dax['nosignal_var2d'] = fig.add_subplot(gs[1, 0], - sharex=dax['nosignal_mean2d'], - sharey=dax['nosignal_mean2d']) - dax['nosignal_mean'] = fig.add_subplot(gs[0, 1], - sharey=dax['nosignal_mean2d']) - dax['nosignal_var'] = fig.add_subplot(gs[1, 1], - sharex=dax['nosignal_mean'], - sharey=dax['nosignal_mean2d']) - dax['signal_fit'] = fig.add_subplot(gs[0, 2], - sharey=dax['nosignal_mean2d']) - dax['signal_chi2'] = fig.add_subplot(gs[1, 2], - sharey=dax['nosignal_mean2d']) - dax['signal_conv'] = fig.add_subplot(gs[0, 3]) - dax['signal_err'] = fig.add_subplot(gs[1, 3]) - dax['signal_err_hist'] = fig.add_subplot(gs[2, 0]) - dax['signal_err_mean'] = fig.add_subplot(gs[2, 1]) - dax['signal_err_var'] = fig.add_subplot(gs[2, 2]) - dax['nosignal_mean2d'].set_title('mean of noise\nno signal ' + tstr0) - dax['nosignal_var2d'].set_title('variance of noise\nno signal ' + tstr0) - dax['nosignal_mean'].set_title('mean of noise\nno signal ' + tstr0) - dax['nosignal_var'].set_title('variance of noise\nno signal ' + tstr0) - dax['signal_fit'].set_title('fit of mean signal' + tstr1) - dax['signal_chi2'].set_title('fit chi2' + tstr1) - dax['signal_conv'].set_title('Convergence') - dax['signal_err'].set_title('Error') - dax['signal_err_hist'].set_title('Error histogram') - dax['signal_err_mean'].set_title('Error mean') - dax['signal_err_var'].set_title('Error var') - - dax['nosignal_mean2d'].set_ylabel('phi (rad)') - dax['nosignal_var2d'].set_ylabel('phi (rad)') - dax['nosignal_var2d'].set_xlabel('lamb (m)') - dax['signal_conv'].set_xlabel('nbsplines') - dax['signal_conv'].set_ylabel(r'$\chi^2$') - dax['signal_err'].set_xlabel('data') - dax['signal_err'].set_ylabel('error') - dax['signal_err_hist'].set_xlabel('error') - dax['signal_err_hist'].set_ylabel('occurences') - dax['signal_err_mean'].set_xlabel('data') - dax['signal_err_mean'].set_ylabel('error mean') - dax['signal_err_var'].set_xlabel('data') - dax['signal_err_var'].set_ylabel('error var') - - # Plot data - dax['nosignal_mean2d'].imshow(dall['nosignal_mean'].T, - extent=extent, aspect='auto', - origin='lower', interpolation='nearest', - vmin=0, vmax=5) - dax['nosignal_var2d'].imshow(dall['nosignal_var'].T, - extent=extent, aspect='auto', - origin='lower', interpolation='nearest', - vmin=0, vmax=5) - - col = None - dataph1dflat = dall['dataphi1d'].ravel() - for ii in range(shotu.size): - # No signal - ind = (dall['indnosignal'] & (dall['shot'] == shotu[ii])).nonzero()[0] - for jj in range(ind.size): - if jj == 0: - l, = dax['nosignal_mean'].plot(dall['dataphi1d'][ind[jj], :], - dall['phi1d'], - ls='-', marker='None', lw=1., - alpha=alpha[ind[jj]]) - col = l.get_color() - else: - dax['nosignal_mean'].plot(dall['dataphi1d'][ind[jj], :], - dall['phi1d'], - ls='-', marker='None', lw=1., c=col, - alpha=alpha[ind[jj]]) - - dax['nosignal_var'].plot(dall['dataphi1d_var'][ind[jj], :], - dall['phi1d'], - ls='-', marker='None', lw=1., c=col, - alpha=alpha[ind[jj]]) - # Signal - ind = ((~dall['indnosignal']) - & (dall['shot'] == shotu[ii])).nonzero()[0] - for jj in range(ind.size): - dax['signal_fit'].plot(dataphi1dnorm[ind[jj], :], - dall['phi1d'], - ls='None', marker='.', lw=1., c=col, - alpha=alpha[ind[jj]]) - dax['signal_fit'].plot(dall['fitphi1d'][ind[jj], :], - dall['phi1d'], - ls='-', marker='None', lw=1., c=col, - alpha=alpha[ind[jj]]) - dax['signal_chi2'].plot( - (dall['fitphi1d'][ind[jj], :] - dataphi1dnorm[ind[jj], :]), - dall['phi1d'], - ls='-', marker='None', lw=1., c=col, - alpha=alpha[ind[jj]], - ) - - # Convergence - dax['signal_conv'].plot(lnbsplines, lchi2[ind[jj], :], - ls='-', marker='.', lw=1., c=col, - alpha=alpha[ind[jj]]) - - # Error - lnbsplinesok = np.r_[10, 11, 12, 13, 14, 15, 16] - dista = np.abs(lnbsplinesok - nbsplines) - alpha_err = (1. - dista/np.max(dista)) - for jj in range(lnbsplinesok.size): - indjj = (lnbsplines == lnbsplinesok[jj]).nonzero()[0] - if indjj.size == 0: - continue - indjj = indjj[0] - lab = '{} bsplines'.format(lnbsplinesok[jj]) - l, = dax['signal_err'].plot(dataph1dflat, - dall['err'][:, :, indjj].ravel(), - ls='None', marker='.', alpha=alpha_err[jj]) - col = l.get_color() - if lnbsplinesok[jj] == nbsplines: - for ii in range(nbins): - if np.any(indbin == ii): - dax['signal_err_hist'].hist( - errok[indbin == ii, jj], - bins=10, density=True, - ) - dax['signal_err_mean'].plot(dataphi1dbin, - errbin_mean[:, indjj], - ls='None', marker='.', c=col, - alpha=alpha_err[jj]) - dax['signal_err_var'].plot(dataphi1dbin, - errbin_var[:, indjj], - ls='None', marker='.', c=col, - alpha=alpha_err[jj], - label=lab) - - if nbsplines in lnbsplines: - indjbs = (lnbsplines == nbsplines).nonzero()[0][0] - dax['signal_err_mean'].axhline(0., c='k', ls='--') - indok = ~np.isnan(errbin_var[:, indjbs]) - pf = np.polyfit(dataphi1dbin[indok], - np.sqrt(errbin_var[indok, indjbs]), 1) - dax['signal_err_var'].plot(dataphi1dbin, - np.polyval(pf, dataphi1dbin)**2, - c='k', ls='--') - - txt = '({:5.3e}x + {:5.3e})^2'.format(pf[0], pf[1]) - dax['signal_err_var'].annotate(txt, - xy=(500, 200), - xycoords='data', - horizontalalignment='center', - verticalalignment='center', - rotation=np.arctan(np.sqrt(pf[0])), - size=8) - - dax['nosignal_mean'].plot(dall['nosignal_1dmean'], dall['phi1d'], - ls='-', marker='None', lw=2., c='k') - dax['nosignal_var'].plot(dall['nosignal_1dvar'], dall['phi1d'], - ls='-', marker='None', lw=2., c='k') - - dax['nosignal_mean2d'].set_xlim(lambminmax) - dax['nosignal_mean2d'].set_ylim(phiminmax) - # dax['nosignal_mean'].set_ylim(phiminmax) - dax['signal_err_var'].legend(loc='center left', - bbox_to_anchor=(1., 0.5)) - return dall, dax diff --git a/inputs_temp/XICS_data_ArXVII.npz b/inputs_temp/XICS_data_ArXVII.npz deleted file mode 100644 index 1980ec31b..000000000 Binary files a/inputs_temp/XICS_data_ArXVII.npz and /dev/null differ diff --git a/inputs_temp/XICS_data_ArXVIII.npz b/inputs_temp/XICS_data_ArXVIII.npz deleted file mode 100644 index 8d92e1489..000000000 Binary files a/inputs_temp/XICS_data_ArXVIII.npz and /dev/null differ diff --git a/inputs_temp/XICS_data_FeXXV.npz b/inputs_temp/XICS_data_FeXXV.npz deleted file mode 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a/inputs_temp/det37_CTVD_incC4_New.npz and /dev/null differ diff --git a/inputs_temp/dlines.py b/inputs_temp/dlines.py deleted file mode 100644 index c0ee7d6c7..000000000 --- a/inputs_temp/dlines.py +++ /dev/null @@ -1,928 +0,0 @@ -import scipy.constants as scpct - -_DSOURCES = { - 'Kallne': { - 'long': ( - 'Kallne et al., ' - + 'High Resolution X-Ray Spectroscopy Diagnostics' - + ' of High Temperature Plasmas' - + ', Physica Scripta, vol. 31, 6, pp. 551-564, 1985' - ), - }, - 'Bitter': { - 'long': ( - 'Bitter et al., ' - + 'XRay diagnostics of tokamak plasmas' - + ', Physica Scripta, vol. 47, pp. 87-95, 1993' - ), - }, - 'Gabriel': { - 'long': ( - 'Gabriel,' - + 'Mon. Not. R. Astro. Soc., vol. 160, pp 99-119, 1972' - ), - }, - 'NIST': { - 'long': 'https://physics.nist.gov/PhysRefData/ASD/lines_form.html', - }, - 'Vainshtein 85': { - 'long': ( - 'Vainshtein and Safranova, ' - + 'Energy Levels of He-like and Li-like Ions, ' - + 'Physica Scripta, vol. 31, pp 519-532, 1985' - ), - }, - 'Goryaev 17': { - 'long': ( - "Goryaev et al., " - + "Atomic data for doubly-excited states 2lnl' of He-like " - + "ions and 1s2lnl' of Li-like ions with Z=6-36 and n=2,3, " - + "Atomic Data and Nuclear Data Tables, vol. 113, " - + "pp 117-257, 2017" - ), - }, - 'Bruhns 07': { - 'long': ( - 'Bruhns et al.,' - + '"Testing QED Screening and Two-Loop Contributions "' - + '"with He-Like Ions", ' - + 'Physical Review Letters, vol. 99, 113001, 2007' - ), - }, - 'Amaro 12': { - 'long': ( - 'Amaro et al.,' - + '"Absolute Measurement of the Relativistic Magnetic"' - + '" Dipole Transition Energy in Heliumlike Argon", ' - + 'Physical Review Letters, vol. 109, 043005, 2012' - ), - }, - 'Adhoc 200408': { - 'long': ( - 'Wavelength computed from the solid references ' - + 'ArXVII_w_Bruhns and ArXVII_z_Amaro and from the ' - + 'detector position optimized from them using shots=' - + '[54044, 54045, 54046, 54047, 54049, 54061, 55076], ' - + 'indt=[2,4,5,6,8], indxj=None on 08.04.2020, using ' - + 'Vainshtein for x, y and Goryaev for k, j, q, r, a' - ), - }, - 'Adhoc 200513': { - 'long': ( - 'Same as Adhoc 200408 but n3, n4 and y corrected by' - + ' individual vims computed from C3, C4 campaigns, ' - + 'as presented in CTVD on 14.05.2020' - ), - }, -} - - -delements = { - 'Ar': {'Z': 18, 'A': 39.948}, - 'Fe': {'Z': 26, 'A': 55.845}, - 'W': {'Z': 74, 'A': 183.84} -} -for k0, v0 in delements.items(): - delements[k0]['m'] = v0['Z']*scpct.m_p + v0['A']*scpct.m_n - -# In dtransitions: ['lower state', 'upper state'] -# Source: Gabriel -dtransitions = { - # 1s^22p(^2P^0) - 1s2p^2(^2P) - 'Li-a': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{3/2})', '1s2p^2(^2P_{3/2})'], - }, - 'Li-b': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{1/2})', '1s2p^2(^2P_{3/2})'], - }, - 'Li-c': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{3/2})', '1s2p^2(^2P_{1/2})'], - }, - 'Li-d': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{1/2})', '1s2p^2(^2P_{1/2})'], - }, - - # 1s^22p(^2P^0) - 1s2p^2(^4P) - 'Li-e': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{3/2})', '1s2p^2(^4P_{5/2})'], - }, - 'Li-f': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{3/2})', '1s2p^2(^4P_{3/2})'], - }, - 'Li-g': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{1/2})', '1s2p^2(^4P_{3/2})'], - }, - 'Li-h': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{3/2})', '1s2p^2(^4P_{1/2})'], - }, - 'Li-i': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{1/2})', '1s2p^2(^4P_{1/2})'], - }, - - # 1s^22p(^2P^0) - 1s2p^2(^2D) - 'Li-j': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{3/2})', '1s2p^2(^2D_{5/2})'], - }, - 'Li-k': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{1/2})', '1s2p^2(^2D_{3/2})'], - }, - 'Li-l': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{3/2})', '1s2p^2(^2D_{3/2})'], - }, - - # 1s^22p(^2P^0) - 1s2p^2(^2S) - 'Li-m': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{3/2})', '1s2p^2(^2S_{1/2})'], - }, - 'Li-n': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{1/2})', '1s2p^2(^2S_{1/2})'], - }, - - # 1s^22p(^2P^0) - 1s2s^2(^2S) - 'Li-o': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{3/2})', '1s2s^2(^2S_{1/2})'], - }, - 'Li-p': { - 'isoel': 'Li-like', - 'trans': ['1s^22p(^2P^0_{1/2})', '1s2s^2(^2S_{1/2})'], - }, - - # 1s^22s(^2S) - 1s2s2p(^1P)(^2P^0) - 'Li-q': { - 'isoel': 'Li-like', - 'trans': ['1s^22s(^2S_{1/2})', '1s2s2p(^1P^0)(^2P^0_{3/2})'], - }, - 'Li-r': { - 'isoel': 'Li-like', - 'trans': ['1s^22s(^2S_{1/2})', '1s2s2p(^1P^0)(^2P^0_{1/2})'], - }, - - # 1s^22s(^2S) - 1s2s2p(^3P)(^2P^0) - 'Li-s': { - 'isoel': 'Li-like', - 'trans': ['1s^22s(^2S_{1/2})', '1s2s2p(^3P^0)(^2P^0_{3/2})'], - }, - 'Li-t': { - 'isoel': 'Li-like', - 'trans': ['1s^22s(^2S_{1/2})', '1s2s2p(^3P^0)(^2P^0_{1/2})'], - }, - - # 1s^22s(^2S) - 1s2s2p(^4P^0) - 'Li-u': { - 'isoel': 'Li-like', - 'trans': ['1s^22s(^2S_{1/2})', '1s2s2p(^4P^0_{3/2})'], - }, - 'Li-v': { - 'isoel': 'Li-like', - 'trans': ['1s^22s(^2S_{1/2})', '1s2s2p(^4P^0_{1/2})'], - }, - - # Satellites of ArXVII w from n = 3 - 'Li-n3-a1': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{1/2})', '1s2p3p(^2S_{1/2})'], - }, - 'Li-n3-a2': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2p3p(^2S_{1/2})'], - }, - 'Li-n3-b1': { - 'isoel': 'Li-like', - 'trans': ['1s^23d(^2D_{3/2})', '1s2p3d(^2F_{5/2})'], - }, - 'Li-n3-b2': { - 'isoel': 'Li-like', - 'trans': ['1s^23d(^2D_{5/2})', '1s2p3d(^2F_{5/2})'], - }, - 'Li-n3-b3': { - 'isoel': 'Li-like', - 'trans': ['1s^23d(^2D_{5/2})', '1s2p3d(^2F_{7/2})'], - }, - 'Li-n3-b4': { - 'isoel': 'Li-like', - 'trans': ['1s^23d(^2D_{5/2})', '1s2p3d(^2D_{5/2})'], - }, - 'Li-n3-c1': { - 'isoel': 'Li-like', - 'trans': ['1s^23s(^2S_{1/2})', '1s2p3s(^2P_{1/2})'], - }, - 'Li-n3-c2': { - 'isoel': 'Li-like', - 'trans': ['1s^23s(^2S_{1/2})', '1s2p3s(^2P_{3/2})'], - }, - 'Li-n3-d1': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2p3p(^2P_{3/2})'], - }, - 'Li-n3-d2': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{1/2})', '1s2p3p(^2D_{3/2})'], - }, - 'Li-n3-d3': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2p3p(^2D_{5/2})'], - }, - 'Li-n3-e1': { - 'isoel': 'Li-like', - 'trans': ['1s^23s(^2S_{1/2})', '1s2p3s(^2P_{3/2})'], - }, - 'Li-n3-f1': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2p3p(^2S_{1/2})'], - }, - 'Li-n3-e2': { - 'isoel': 'Li-like', - 'trans': ['1s^23s(^2S_{1/2})', '1s2p3s(^2P_{1/2})'], - }, - 'Li-n3-f2': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2p3p(^2D_{5/2})'], - }, - 'Li-n3-g1': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{1/2})', '1s2s3d(^2D_{3/2})'], - }, - 'Li-n3-f3': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2p3p(^2D_{3/2})'], - }, - 'Li-n3-g2': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2s3d(^2D_{5/2})'], - }, - 'Li-n3-g3': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2s3d(^2D_{3/2})'], - }, - 'Li-n3-f4': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2p3d(^4P_{5/2})'], - }, - 'Li-n3-h1': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{1/2})', '1s2s3s(^2S_{1/2})'], - }, - 'Li-n3-h2': { - 'isoel': 'Li-like', - 'trans': ['1s^23p(^2P_{3/2})', '1s2s3s(^2S_{1/2})'], - }, - - # He-like - - # 1s^2(^1S) - 1s2p(^1P^0) - Resonance - 'He-w': { - 'isoel': 'He-like', - 'trans': ['1s^2(^1S_{0})', '1s2p(^1P^0_{1})'], - }, - - # 1s^2(^1S) - 1s2p(^3P^0) - Forbidden - 'He-x': { - 'isoel': 'He-like', - 'trans': ['1s^2(^1S_{0})', '1s2p(^3P^0_{2})'], - }, - 'He-y': { - 'isoel': 'He-like', - 'trans': ['1s^2(^1S_{0})', '1s2p(^3P^0_{1})'], - }, - 'He-y2': { - 'isoel': 'He-like', - 'trans': ['1s^2(^1S_{0})', '1s2p(^3P^0_{0})'], - }, - - # 1s^2(^1S) - 1s2s(^3S) - Forbidden - 'He-z': { - 'isoel': 'He-like', - 'trans': ['1s^2(^1S_{0})', '1s2s(^3S_{1})'], - }, - 'He-z2': { - 'isoel': 'He-like', - 'trans': ['1s^2(^1S_{0})', '1s2s(^1S_{0})'], - }, - - # Unknown - 'unknown': { - 'isoel': '?', - 'trans': ['?', '?'], - }, -} - - -dlines = { - # -------------------------- - # Ar - # -------------------------- - - 'ArXIV_n4_Adhoc200408': {'charge': 13, 'ION': 'ArXIV', - 'symbol': 'n4', 'lambda0': 3.9530e-10, - 'transition': 'unknown', - 'source': 'Adhoc 200408'}, - 'ArXIV_n4_Adhoc200513': {'charge': 13, 'ION': 'ArXIV', - 'symbol': 'n4', 'lambda0': 3.9528e-10, - 'transition': 'unknown', - 'source': 'Adhoc 200513'}, - 'ArXV_n3_Adhoc200408': {'charge': 14, 'ION': 'ArXV', - 'symbol': 'n3', 'lambda0': 3.9560e-10, - 'transition': 'unknown', - 'source': 'Adhoc 200408'}, - 'ArXV_n3_Adhoc200513': {'charge': 14, 'ION': 'ArXV', - 'symbol': 'n3', 'lambda0': 3.9562e-10, - 'transition': 'unknown', - 'source': 'Adhoc 200513'}, - - 'ArXV_1': {'charge': 14, 'ION': 'ArXV', - 'symbol': '1', 'lambda0': 4.0096e-10, - 'transition': ['1s2s^22p(^1P_1)', '1s^22s^2(^1S_0)'], - 'source': 'Kallne', 'innershell': True}, - 'ArXV_2-1': {'charge': 14, 'ION': 'ArXV', - 'symbol': '2-1', 'lambda0': 4.0176e-10, - 'transition': ['1s2p^22s(^4P^3P_1)', '1s^22s2p(^3P_1)'], - 'source': 'Kallne'}, - 'ArXV_2-2': {'charge': 14, 'ION': 'ArXV', - 'symbol': '2-2', 'lambda0': 4.0179e-10, - 'transition': ['1s2s2p^2(^3D_1)', '1s^22s2p(^3P_0)'], - 'source': 'Kallne'}, - 'ArXV_2-3': {'charge': 14, 'ION': 'ArXV', - 'symbol': '2-3', 'lambda0': 4.0180e-10, - 'transition': ['1s2p^22s(^4P^3P_2)', '1s^22s2p(^3P_2)'], - 'source': 'Kallne'}, - 'ArXV_3': {'charge': 14, 'ION': 'ArXV', - 'symbol': '3', 'lambda0': 4.0192e-10, - 'transition': ['1s2s2p^2(^3D_2)', '1s^22s2p(^3P_1)'], - 'source': 'Kallne'}, - 'ArXV_4': {'charge': 14, 'ION': 'ArXV', - 'symbol': '4', 'lambda0': 4.0219e-10, - 'transition': ['1s2s2p^2(^3D_5)', '1s^22s2p(^3P_2)'], - 'source': 'Kallne'}, - 'ArXV_5': {'charge': 14, 'ION': 'ArXV', - 'symbol': '5', 'lambda0': 4.0291e-10, - 'transition': ['1s2s2p^2(^1D_5)', '1s^22s2p(^1P_1)'], - 'source': 'Kallne'}, - - 'ArXVI_a_Kallne': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9852e-10, - 'transition': 'Li-a', - 'source': 'Kallne'}, - 'ArXVI_a_NIST': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.98573e-10, - 'transition': 'Li-a', - 'source': 'NIST'}, - 'ArXVI_a_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9858e-10, - 'transition': 'Li-a', - 'source': 'Goryaev 17'}, - 'ArXVI_a_Adhoc200408': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9848e-10, - 'transition': 'Li-a', - 'source': 'Adhoc 200408'}, - 'ArXVI_b_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9818e-10, - 'transition': 'Li-b', - 'source': 'Goryaev 17'}, - 'ArXVI_c_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9899e-10, - 'transition': 'Li-c', - 'source': 'Goryaev 17'}, - 'ArXVI_d_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9858e-10, - 'transition': 'Li-d', - 'source': 'Goryaev 17'}, - 'ArXVI_e_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 4.0126e-10, - 'transition': 'Li-e', - 'source': 'Goryaev 17'}, - 'ArXVI_f_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 4.0146e-10, - 'transition': 'Li-f', - 'source': 'Goryaev 17'}, - 'ArXVI_g_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 4.0105e-10, - 'transition': 'Li-g', - 'source': 'Goryaev 17'}, - 'ArXVI_h_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 4.0164e-10, - 'transition': 'Li-h', - 'source': 'Goryaev 17'}, - 'ArXVI_i_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 4.0123e-10, - 'transition': 'Li-i', - 'source': 'Goryaev 17'}, - 'ArXVI_j_Kallne': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9932e-10, - 'transition': 'Li-j', - 'source': 'Kallne'}, - 'ArXVI_j_NIST': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9938e-10, - 'transition': 'Li-j', - 'source': 'NIST'}, - 'ArXVI_j_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9939e-10, - 'transition': 'Li-j', - 'source': 'Goryaev 17'}, - 'ArXVI_j_Adhoc200408': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9939e-10, - 'transition': 'Li-j', - 'source': 'Adhoc 200408'}, - 'ArXVI_k_Kallne': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9892e-10, - 'transition': 'Li-k', - 'source': 'Kallne', - 'comment': 'Dielect. recomb. from ArXVII'}, - 'ArXVI_k_NIST': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9898e-10, - 'transition': 'Li-k', - 'source': 'NIST', - 'comment': 'Dielect. recomb. from ArXVII'}, - 'ArXVI_k_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9899e-10, - 'transition': 'Li-k', - 'source': 'Goryaev 17'}, - 'ArXVI_k_Adhoc200408': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9897e-10, - 'transition': 'Li-k', - 'source': 'Adhoc 200408'}, - 'ArXVI_l_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9939e-10, - 'transition': 'Li-l', - 'source': 'Goryaev 17'}, - 'ArXVI_m_Kallne': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9562e-10, - 'transition': 'Li-m', - 'source': 'Kallne'}, - 'ArXVI_m_NIST': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.96561e-10, - 'transition': 'Li-m', - 'source': 'NIST'}, - 'ArXVI_m_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9656e-10, - 'transition': 'Li-m', - 'source': 'Goryaev 17'}, - 'ArXVI_n_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9616e-10, - 'transition': 'Li-n', - 'source': 'Goryaev 17'}, - 'ArXVI_o_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 4.0730e-10, - 'transition': 'Li-o', - 'source': 'Goryaev 17'}, - 'ArXVI_p_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 4.0688e-10, - 'transition': 'Li-p', - 'source': 'Goryaev 17'}, - 'ArXVI_q_Kallne': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9806e-10, - 'transition': 'Li-q', - 'source': 'Kallne', 'innershell': True}, - 'ArXVI_q_NIST': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9676e-10, - 'transition': 'Li-q', - 'source': 'NIST', 'innershell': True}, - 'ArXVI_q_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9815e-10, - 'transition': 'Li-q', - 'source': 'Goryaev 17'}, - 'ArXVI_q_Adhoc200408': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9814e-10, - 'transition': 'Li-q', - 'source': 'Adhoc 200408'}, - 'ArXVI_r_Kallne': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9827e-10, - 'transition': 'Li-r', - 'source': 'Kallne'}, - 'ArXVI_r_NIST': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9685e-10, - 'transition': 'Li-r', - 'source': 'NIST'}, - 'ArXVI_r_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9835e-10, - 'transition': 'Li-r', - 'source': 'Goryaev 17'}, - 'ArXVI_r_Adhoc200408': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9833e-10, - 'transition': 'Li-r', - 'source': 'Adhoc 200408'}, - 'ArXVI_s_Kallne': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9669e-10, - 'transition': 'Li-s', - 'source': 'Kallne'}, - 'ArXVI_s_NIST': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9813e-10, - 'transition': 'Li-s', - 'source': 'NIST'}, - 'ArXVI_s_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9677e-10, - 'transition': 'Li-s', - 'source': 'Goryaev 17'}, - 'ArXVI_t_Kallne': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9677e-10, - 'transition': 'Li-t', - 'source': 'Kallne'}, - 'ArXVI_t_NIST': {'Z': 18, 'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9834e-10, - 'transition': 'Li-t', - 'source': 'NIST'}, - 'ArXVI_t_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9686e-10, - 'transition': 'Li-t', - 'source': 'Goryaev 17'}, - 'ArXVI_u_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 4.0150e-10, - 'transition': 'Li-u', - 'source': 'Goryaev 17'}, - 'ArXVI_v_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 4.0161e-10, - 'transition': 'Li-v', - 'source': 'Goryaev 17'}, - - # Li-like n=3 satellites - 'ArXVI_n3a1_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9473e-10, - 'transition': 'Li-n3-a1', - 'source': 'Goryaev 17'}, - 'ArXVI_n3a2_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9484e-10, - 'transition': 'Li-n3-a2', - 'source': 'Goryaev 17'}, - 'ArXVI_n3b1_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9512e-10, - 'transition': 'Li-n3-b1', - 'source': 'Goryaev 17'}, - 'ArXVI_n3b2_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9515e-10, - 'transition': 'Li-n3-b2', - 'source': 'Goryaev 17'}, - 'ArXVI_n3b3_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9527e-10, - 'transition': 'Li-n3-b3', - 'source': 'Goryaev 17'}, - 'ArXVI_n3b4_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9542e-10, - 'transition': 'Li-n3-b4', - 'source': 'Goryaev 17'}, - 'ArXVI_n3c1_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9546e-10, - 'transition': 'Li-n3-c1', - 'source': 'Goryaev 17'}, - 'ArXVI_n3c2_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9551e-10, - 'transition': 'Li-n3-c2', - 'source': 'Goryaev 17'}, - 'ArXVI_n3d1_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9556e-10, - 'transition': 'Li-n3-d1', - 'source': 'Goryaev 17'}, - 'ArXVI_n3d2_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9559e-10, - 'transition': 'Li-n3-d2', - 'source': 'Goryaev 17'}, - 'ArXVI_n3d3_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9568e-10, - 'transition': 'Li-n3-d3', - 'source': 'Goryaev 17'}, - 'ArXVI_n3e1_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9626e-10, - 'transition': 'Li-n3-e1', - 'source': 'Goryaev 17'}, - 'ArXVI_n3f1_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9643e-10, - 'transition': 'Li-n3-f1', - 'source': 'Goryaev 17'}, - 'ArXVI_n3e2_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9661e-10, - 'transition': 'Li-n3-e2', - 'source': 'Goryaev 17'}, - 'ArXVI_n3f2_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9680e-10, - 'transition': 'Li-n3-f2', - 'source': 'Goryaev 17'}, - 'ArXVI_n3g1_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9706e-10, - 'transition': 'Li-n3-g1', - 'source': 'Goryaev 17'}, - 'ArXVI_n3f3_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9711e-10, - 'transition': 'Li-n3-f3', - 'source': 'Goryaev 17'}, - 'ArXVI_n3g2_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9712e-10, - 'transition': 'Li-n3-g2', - 'source': 'Goryaev 17'}, - 'ArXVI_n3g3_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9718e-10, - 'transition': 'Li-n3-g3', - 'source': 'Goryaev 17'}, - 'ArXVI_n3f4_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9740e-10, - 'transition': 'Li-n3-f4', - 'source': 'Goryaev 17'}, - 'ArXVI_n3h1_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9922e-10, - 'transition': 'Li-n3-h1', - 'source': 'Goryaev 17'}, - 'ArXVI_n3h2_Goryaev': {'charge': 15, 'ION': 'ArXVI', - 'lambda0': 3.9934e-10, - 'transition': 'Li-n3-h2', - 'source': 'Goryaev 17'}, - - # He-like - 'ArXVII_w_Kallne': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9482e-10, - 'transition': 'He-w', - 'source': 'Kallne'}, - 'ArXVII_w_NIST': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.94906e-10, - 'transition': 'He-w', - 'source': 'NIST'}, - 'ArXVII_w_Vainshtein': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9492e-10, - 'transition': 'He-w', - 'source': 'Vainshtein 85'}, - 'ArXVII_w_Goryaev': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9493e-10, - 'transition': 'He-w', - 'source': 'Goryaev 17'}, - 'ArXVII_w_Bruhns': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.94906e-10, - 'transition': 'He-w', - 'source': 'Bruhns 07'}, - 'ArXVII_x_Kallne': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9649e-10, - 'transition': 'He-x', - 'source': 'Kallne'}, - 'ArXVII_x_NIST': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.965857e-10, - 'transition': 'He-x', - 'source': 'NIST'}, - 'ArXVII_x_Vainshtein': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9660e-10, - 'transition': 'He-x', - 'source': 'Vainshtein 85'}, - 'ArXVII_x_Adhoc200408': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9658e-10, - 'transition': 'He-x', - 'source': 'Adhoc 200408'}, - 'ArXVII_x_Adhoc200513': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9659e-10, - 'transition': 'He-x', - 'source': 'Adhoc 200513'}, - 'ArXVII_y_Kallne': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9683e-10, - 'transition': 'He-y', - 'source': 'Kallne'}, - 'ArXVII_y_NIST': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.969355e-10, - 'transition': 'He-y', - 'source': 'NIST'}, - 'ArXVII_y_Vainshtein': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9694e-10, - 'transition': 'He-y', - 'source': 'Vainshtein 85'}, - 'ArXVII_y_Goryaev': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9696e-10, - 'transition': 'He-y', - 'source': 'Goryaev 17'}, - 'ArXVII_y_Adhoc200408': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9692e-10, - 'transition': 'He-y', - 'source': 'Adhoc 200408'}, - 'ArXVII_y_Adhoc200513': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.96933e-10, - 'transition': 'He-y', - 'source': 'Adhoc 200513'}, - 'ArXVII_y2_Vainshtein': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9703e-10, - 'transition': 'He-y2', - 'source': 'Vainshtein 85'}, - 'ArXVII_z_Kallne': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9934e-10, - 'transition': 'He-z', - 'source': 'Kallne'}, - 'ArXVII_z_NIST': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.99414e-10, - 'transition': 'He-z', - 'source': 'NIST'}, - 'ArXVII_z_Vainshtein': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9943e-10, - 'transition': 'He-z', - 'source': 'Vainshtein 85'}, - 'ArXVII_z_Goryaev': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9944e-10, - 'transition': 'He-z', - 'source': 'Goryaev 17'}, - 'ArXVII_z2_Vainshtein': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.9682e-10, - 'transition': 'He-z2', - 'source': 'Vainshtein 85'}, - 'ArXVII_z_Amaro': {'charge': 16, 'ION': 'ArXVII', - 'lambda0': 3.994129e-10, - 'transition': 'He-z', - 'source': 'Amaro 12'}, - 'ArXVII_T': {'charge': 16, 'ION': 'ArXVII', - 'symbol': 'T', 'lambda0': 3.7544e-10, - 'transition': [r'$2s2p(^1P_1)$', r'$1s2s(^1S_0)$'], - 'source': 'Kallne'}, - 'ArXVII_K': {'charge': 16, 'ION': 'ArXVII', - 'symbol': 'K', 'lambda0': 3.7557e-10, - 'transition': [r'$2p^2(^1D_2)$', r'$1s2p(^3P_2)$'], - 'source': 'Kallne'}, - 'ArXVII_Q': {'charge': 16, 'ION': 'ArXVII', - 'symbol': 'Q', 'lambda0': 3.7603e-10, - 'transition': [r'$2s2p(^3P_2)$', r'$1s2s(^3S_1)$'], - 'source': 'Kallne'}, - 'ArXVII_B': {'charge': 16, 'ION': 'ArXVII', - 'symbol': 'B', 'lambda0': 3.7626e-10, - 'transition': [r'$2p^2(^3P_2)$', r'$1s2p(^3P_1)$'], - 'source': 'Kallne'}, - 'ArXVII_R': {'charge': 16, 'ION': 'ArXVII', - 'symbol': 'R', 'lambda0': 3.7639e-10, - 'transition': [r'$2s2p(^3P_1)$', r'$1s2s(^3S_1)$'], - 'source': 'Kallne'}, - 'ArXVII_A': {'charge': 16, 'ION': 'ArXVII', - 'symbol': 'A', 'lambda0': 3.7657e-10, - 'transition': [r'$2p^2(^3P_2)$', r'$1s2p(^3P_2)$'], - 'source': 'Kallne'}, - 'ArXVII_J': {'charge': 16, 'ION': 'ArXVII', - 'symbol': 'J', 'lambda0': 3.7709e-10, - 'transition': [r'$2p^2(^1D_2)$', r'$1s2p(^1P_1)$'], - 'source': 'Kallne'}, - - 'ArXVIII_W1': {'charge': 17, 'ION': 'ArXVIII', - 'symbol': 'W_1', 'lambda0': 3.7300e-10, - 'transition': [r'$2p(^2P_{3/2})$', r'$1s(^2S_{1/2})$'], - 'source': 'Kallne'}, - 'ArXVIII_W2': {'charge': 17, 'ION': 'ArXVIII', - 'symbol': 'W_2', 'lambda0': 3.7352e-10, - 'transition': [r'$2p(^2P_{1/2})$', r'$1s(^2S_{1/2})$'], - 'source': 'Kallne'}, - - # -------------------------- - # Fe - # -------------------------- - - 'FeXXIII_beta': {'charge': 22, 'ION': 'FeXXIII', - 'symbol': 'beta', 'lambda0': 1.87003e-10, - 'transition': [r'$1s^22s^2(^1S_0)$', - r'$1s2s^22p(^1P_1)$'], - 'source': 'Bitter'}, - - 'FeXXIV_t_Bitter': {'charge': 23, 'ION': 'FeXXIV', - 'lambda0': 1.8566e-10, - 'transition': 'Li-t', - 'source': 'Bitter'}, - 'FeXXIV_q_Bitter': {'charge': 23, 'ION': 'FeXXIV', - 'lambda0': 1.8605e-10, - 'transition': 'Li-q', - 'source': 'Bitter'}, - 'FeXXIV_k_Bitter': {'charge': 23, 'ION': 'FeXXIV', - 'lambda0': 1.8626e-10, - 'transition': 'Li-k', - 'source': 'Bitter'}, - 'FeXXIV_r_Bitter': {'charge': 23, 'ION': 'FeXXIV', - 'lambda0': 1.8631e-10, - 'transition': 'Li-r', - 'source': 'Bitter'}, - 'FeXXIV_j_Bitter': {'charge': 23, 'ION': 'FeXXIV', - 'lambda0': 1.8654e-10, - 'transition': 'Li-j', - 'source': 'Bitter'}, - - 'FeXXV_w_Bitter': {'charge': 24, 'ION': 'FeXXV', - 'lambda0': 1.8498e-10, - 'transition': 'He-w', - 'source': 'Bitter'}, - 'FeXXV_x_Bitter': {'charge': 24, 'ION': 'FeXXV', - 'lambda0': 1.85503e-10, - 'transition': 'He-x', - 'source': 'Bitter'}, - 'FeXXV_y_Bitter': {'charge': 24, 'ION': 'FeXXV', - 'lambda0': 1.8590e-10, - 'transition': 'He-y', - 'source': 'Bitter'}, - 'FeXXV_z_Bitter': {'charge': 24, 'ION': 'FeXXV', - 'lambda0': 1.8676e-10, - 'transition': 'He-z', - 'source': 'Bitter'}, - - # -------------------------- - # W - # -------------------------- - - 'W_adhoc_Adhoc200513': {'charge': 43, 'ION': 'WXLIV', - 'symbol': 'adhoc', 'lambda0': 3.97509e-10, - 'transition': 'unknown', - 'source': 'Adhoc 200513'}, - 'WXLIV_0_NIST': {'charge': 43, 'ION': 'WXLIV', - 'symbol': '0', 'lambda0': 3.9635e-10, - 'transition': ['3d^{10}4s^24p(^2P^0_{1/2})', - '3d^94s^24p(3/2,1/2)^0_16f(1,5/2)3/2'], - 'source': 'NIST'}, - 'WXLIV_1_NIST': {'charge': 43, 'ION': 'WXLIV', - 'symbol': '1', 'lambda0': 3.9635e-10, - 'transition': ['3d^{10}4s^24p(^2P^0_{1/2})', - '3d^94s^24p(3/2,1/2)^0_26f(2,5/2)1/2'], - 'source': 'NIST'}, - 'WXLIV_2_NIST': {'charge': 43, 'ION': 'WXLIV', - 'symbol': '2', 'lambda0': 4.017e-10, - 'transition': [ - '3d^{10}4s^24p(^2P^0_{1/2})', - '3p^53d^{10}4s^24p(3/2,1/2)_25d(2,5/2)3/2' - ], - 'source': 'NIST'}, - 'WXLIV_3_NIST': {'charge': 43, 'ION': 'WXLIV', - 'symbol': '3', 'lambda0': 4.017e-10, - 'transition': [ - '3d^{10}4s^24p(^2P^0_{1/2})', - '3p^53d^{10}4s^24p(3/2,1/2)_25d(2,5/2)1/2' - ], - 'source': 'NIST'}, - 'WXLV_0_NIST': {'charge': 44, 'ION': 'WXLV', - 'symbol': '0', 'lambda0': 3.9730e-10, - 'transition': [ - '3d^{10}4s^2(^1S_{0})', - '3p^5(^2P^0_{3/2})3d^{10}4s^25d(3/2,5/2)^01' - ], - 'source': 'NIST'}, - 'WXLV_1_NIST': {'charge': 44, 'ION': 'WXLV', - 'symbol': '1', 'lambda0': 3.9895e-10, - 'transition': ['3d^{10}4s^2(^1S_{0})', - '3d^9(^2D_{5/2})4s^26f(5/2,7/2)^01'], - 'source': 'NIST'}, - 'WLIII_0_NIST': { - 'charge': 52, 'ION': 'WLIII', - 'symbol': '0', 'lambda0': 4.017e-10, - 'transition': [ - '3d^{10}4s^24p^2(^3P_{0})', - '3d^9(^2D_{3/2})4s^24p^2(^3P^0)(3/2,0)_{3/2}6f(3/2,5/2)^01' - ], - 'source': 'NIST' - }, -} - - -# ############################################################################# -# ############################################################################# -# Complement -# ############################################################################# - - -ii = 0 -for k0, v0 in dlines.items(): - elem = v0['ION'][:2] - if elem[1].isupper(): - elem = elem[0] - dlines[k0]['element'] = elem - for k1, v1 in delements[elem].items(): - dlines[k0][k1] = v1 - - c0 = ( - isinstance(v0['transition'], list) - and all([isinstance(ss, str) for ss in v0['transition']]) - or ( - isinstance(v0['transition'], str) - and v0['transition'] in dtransitions.keys() - ) - ) - if not c0: - msg = ( - "dlines['{}']['transition'] should be either:\n".format(k0) - + "\t- list of 2 str (states), e.g. ['1s2p^2', '1s^22p']\n" - + "\t- str (key of dtransitions)\n" - + "\t- provided: {}".format(v0['transition']) - ) - raise Exception(msg) - - if isinstance(v0['transition'], list): - lc = [ - k1 for k1, v1 in dtransitions.items() - if v1['trans'] == v0['transition'] - ] - if len(lc) in [0, 1]: - key = 'custom-{}'.format(ii) - assert key not in dtransitions.keys() - if len(lc) == 0: - dtransitions[key] = { - 'isoel': '?', - 'trans': v0['transition'] - } - ii += 1 - dlines[k0]['transition'] = key - else: - msg = "Multiple matches for transition {}".format(v0['transition']) - raise Exception(msg) - - if v0.get('symbol') is None: - v0['symbol'] = v0['transition'].split('-')[1] diff --git a/meson.build b/meson.build new file mode 100644 index 000000000..f920418df --- /dev/null +++ b/meson.build @@ -0,0 +1,216 @@ +# ################################### +# ################################### +# General +# ################################### + + +project( + 'tofu', + 'c', 'cpp', 'cython', + license: 'MIT', + meson_version: '>=1.8.3', + version: run_command(['git', 'describe'], capture:true, check:false).stdout().strip().split('-')[0], + # https://mesonbuild.com/Builtin-options.html + default_options: [ + 'buildtype=release', + 'c_std=c11', + 'cpp_std=c++17', + 'pkgconfig.relocatable=true', + ], +) + +# ------------------ +# project +# ------------------ + +# refs: +# https://github.com/scipy/scipy/blob/main/meson.build +# https://github.com/numpy/numpy/blob/main/meson.build +# https://github.com/silx-kit/silx/blob/main/meson.build + +# find local python install +py_mod = import('python') +py = py_mod.find_installation(pure: false) +os = import('fs') + +# ------------------------ +# Min / max numpy versions +# ------------------------ + +min_numpy_version = '1.26.4' # keep in sync with pyproject.toml +min_python_version = '3.9' # keep in sync with pyproject.toml + +python_version = py.language_version() +if python_version.version_compare(f'<@min_python_version@') + error(f'Min Python version is @min_python_version@, found @python_version@') +endif + +# ------------------ +# check platform +# ------------------ + +# Emit a warning for 32-bit Python installs on Windows; users are getting +# unexpected from-source builds there because we no longer provide wheels. +is_windows = host_machine.system() == 'windows' +if is_windows and py.has_variable('EXT_SUFFIX') + ext_suffix = py.get_variable('EXT_SUFFIX') + if ext_suffix.contains('win32') + warning('Impossible to build from source on a 32-bit Windows Python install!') + endif +endif + +# ---------------- +# Check backend +# ---------------- + +if meson.backend() != 'ninja' + error('Ninja backend required') +endif + +# ---------------- +# Openmp +# ---------------- + +omp = dependency('openmp', required: false) + +# ---------------- +# Compiler +# ---------------- + +cc = meson.get_compiler('c') +cpp = meson.get_compiler('cpp') +cy = meson.get_compiler('cython') +# generator() doesn't accept compilers, only found programs - cast it. +cython = find_program(cy.cmd_array()[0]) + +# ------------------------ +# check compiler versions +# ------------------------ + +# Check compiler is recent enough (see "Toolchain Roadmap" for details) +if cc.get_id() == 'gcc' + if not cc.version().version_compare('>=9.1') + error('tofu requires GCC >= 9.1') + endif +elif cc.get_id() == 'clang' or cc.get_id() == 'clang-cl' + if not cc.version().version_compare('>=15.0') + error('tofu requires clang >= 15.0') + endif +elif cc.get_id() == 'msvc' + if not cc.version().version_compare('>=19.20') + error('tofu requires at least vc142 (default with Visual Studio 2019) ' + \ + 'when building with MSVC') + endif +endif + +if not cy.version().version_compare('>=3.0.8') + error('tofu requires Cython >= 3.0.8') +endif + +# ---------------- +# numpy dependency +# ---------------- + +# From +# https://groups.google.com/g/cython-users/c/-AbF6gslN1U +# https://github.com/mesonbuild/meson/issues/9598#issuecomment-1662695303 +# https://github.com/scipy/scipy/blob/main/scipy/meson.build#L30-L73 + +# Uses the `numpy-config` executable (or a user's numpy.pc pkg-config file). +# Will work for numpy>=2.0, hence not required (it'll be a while until 2.0 is +# our minimum supported version). Using this now to be able to detect the +# version easily for >=2.0. +_numpy_dep = dependency('numpy', required: false) +f2py_freethreading_arg = [] +if _numpy_dep.found() and _numpy_dep.version().version_compare('>=2.1.0') + f2py_freethreading_arg = ['--free-threading'] + message('f2py free-threading enabled') +else + message('f2py free-threading disabled; need numpy >=2.1.0.') + message('See https://github.com/mesonbuild/meson/issues/14651') +endif + +# NumPy include directory - needed in all submodules +# The chdir is needed because within numpy there's an `import signal` +# statement, and we don't want that to pick up scipy's signal module rather +# than the stdlib module. The try-except is needed because when things are +# split across drives on Windows, there is no relative path and an exception +# gets raised. There may be other such cases, so add a catch-all and switch to +# an absolute path. Relative paths are needed when for example a virtualenv is +# placed inside the source tree; Meson rejects absolute paths to places inside +# the source tree. +# For cross-compilation it is often not possible to run the Python interpreter +# in order to retrieve numpy's include directory. It can be specified in the +# cross file instead: +# [properties] +# numpy-include-dir = /abspath/to/host-pythons/site-packages/numpy/core/include +# +# This uses the path as is, and avoids running the interpreter. +incdir_numpy = meson.get_external_property('numpy-include-dir', 'not-given') +if incdir_numpy == 'not-given' + incdir_numpy = run_command(py, + [ + '-c', + '''import os +import numpy as np +try: + incdir = os.path.relpath(np.get_include()) +except Exception: + incdir = np.get_include() +print(incdir) + ''' + ], + check: true + ).stdout().strip() + + # We do need an absolute path to feed to `cc.find_library` below + _incdir_numpy_abs = run_command(py, + ['-c', 'import os; os.chdir(".."); import numpy; print(numpy.get_include())'], + check: true + ).stdout().strip() +else + _incdir_numpy_abs = incdir_numpy +endif +inc_np = include_directories(incdir_numpy) +# Don't use the deprecated NumPy C API. Define this to a fixed version instead of +# NPY_API_VERSION in order not to break compilation for released SciPy versions +# when NumPy introduces a new deprecation. +numpy_nodepr_api = ['-DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION'] +np_dep = declare_dependency(include_directories: inc_np, compile_args: numpy_nodepr_api) + +incdir_f2py = incdir_numpy / '..' / '..' / 'f2py' / 'src' +inc_f2py = include_directories(incdir_f2py) +fortranobject_c = incdir_f2py / 'fortranobject.c' + +npymath_path = _incdir_numpy_abs / '..' / 'lib' +npymath_lib = cc.find_library('npymath', dirs: npymath_path) + + +# ------------------------ +# -lm for C code +# ------------------------ + +# We need -lm for all C code (assuming it uses math functions, which is safe). +# For C++ it isn't needed, because libstdc++/libc++ is guaranteed to depend on it. +m_dep = cc.find_library('m', required : false) +if m_dep.found() + add_project_link_arguments('-lm', language : 'c') +endif + +# https://mesonbuild.com/Python-module.html +py_dep = py.dependency() + + +# ---------------- +# Directories +# ---------------- + +# installation dir of tofu, from the py install +tofu_dir = py.get_install_dir() / 'tofu' + +# => will look into tofu for another meson.build +# local variables are accessible +# # then resume execution after this line +subdir('tofu') + +# install_subdir('examples', install_dir: tofu_dir) diff --git a/pyproject.toml b/pyproject.toml index 522528eec..a60d023c8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,8 +1,107 @@ +# inspired from: +# https://github.com/silx-kit/silx/blob/main/pyproject.toml +# https://github.com/ToFuProject/datastock/blob/devel/pyproject.toml + + [build-system] +build-backend = 'mesonpy' requires = [ - # <65 necessary for python 3.8 and 3.9 only - "setuptools>=40.8.0,<65", - "wheel", - "Cython>=0.26", - "numpy", + 'meson-python', + 'cython', + 'numpy', +] + + +# https://mesonbuild.com/meson-python/how-to-guides/meson-args.html#how-to-guides-meson-args +[tool.meson-python.args] +setup = [ + '-Doptimization=3', # Compiler optimization O3 +] +dist = ['--include-subprojects'] + + +# [tool.cython] +# https://groups.google.com/g/cython-users +# cythonize = "_custom_cythonize.cythonize" + + +#[tool.setuptools_scm] +# https://discuss.python.org/t/mesonpy-how-to-set-package-version/26610 +#version_file = "tofu/_version.py" + + +[project] +name = "tofu" +readme = "README.md" +license = "MIT" +version = "1.8.17" +description = "TOmography for FUsion toolkit" +authors = [ + {name = "Didier VEZINET", email = "didier.vezinet@gmail.com"}, +] +maintainers = [ + {name = "Didier VEZINET", email = "didier.vezinet@gmail.com"}, +] +keywords = [ + "tomography", "fusion", "synthetic diagnostic", "diagnostic design", +] +requires-python = ">=3.9" +dependencies = [ + "numpy<1.25", # for astropy compatibility vs deprecated np.product + # "PySide2 ; platform_system != 'Windows'", + "spectrally", + "Polygon3", + "svg-path", + "pytest", +] +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Natural Language :: English", +] + + +[project.urls] +source = "https://github.com/ToFuProject/tofu" +Issues = "https://github.com/ToFuProject/tofu/issues" +download = "https://pypi.org/project/tofu/" + + +[project.entry-points."tofu"] +tofu = "scripts.main:main" + + +[project.optional-dependencies] +full = [ + "Polygon3", + 'spectrally>=0.0.9', + 'pytest', # For testing + 'pytest-xvfb', # For GUI testing + 'pytest-cov', # For coverage + 'pytest-mock', +] +linting = [ + 'tofu[full]', + 'ruff', +] +formatting = [ + 'tofu[full]', + 'ruff', +] +doc =[ + 'tofu[full]', + 'Sphinx', # To build the documentation in doc/ + 'sphinx-autodoc-typehints', # For leveraging Python type hints from Sphinx + 'sphinx-copybutton', # Add copy to clipboard button to code blocks + 'sphinx-design', # For tabs and grid in documentation + 'pydata_sphinx_theme', # Sphinx theme + 'nbsphinx', # For converting ipynb in documentation + 'pandoc', # For documentation Qt snapshot updates ] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index ec6d0e6cf..000000000 --- a/requirements.txt +++ /dev/null @@ -1,18 +0,0 @@ -####### Requirements without Version Specifiers ####### -scipy -numpy -# scikit-sparse # does not work on windows, and requires "apt/brew install libsuitesparse-dev/suite-sparse" on linux / MacOs -# scikit-umfpack # similar issue -# >=40.8.0, <64 -setuptools -matplotlib>3.0.3 -contourpy -requests -svg.path -Polygon3 - -######## Requirements with Version Specifier ######## -datastock>=0.0.54 -bsplines2d>=0.0.29 -spectrally>=0.0.9 -Cython>=0.26 diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index e51b235dd..000000000 --- a/setup.cfg +++ /dev/null @@ -1,3 +0,0 @@ -# For details, see -# https://docs.python.org/2/distutils/configfile.html -# https://packaging.python.org/distributing/#manifest-in diff --git a/setup.py b/setup.py deleted file mode 100644 index 8b9a2a83c..000000000 --- a/setup.py +++ /dev/null @@ -1,404 +0,0 @@ -""" A tomography library for fusion devices (tokamaks) - -See: -https://github.com/ToFuProject/tofu -""" - -# Built-in -import os -import glob -import shutil -import logging -import platform -import subprocess -from codecs import open -# ... setup tools -from setuptools import setup, find_packages -# ... for `clean` command -from distutils.command.clean import clean as Clean - - -# ... packages that need to be in pyproject.toml -import numpy as np -from Cython.Distutils import Extension -from Cython.Distutils import build_ext - - -# ... local script -import _updateversion as up -# ... openmp utilities -from tofu_helpers.openmp_helpers import is_openmp_installed - - -# == Checking platform ======================================================== -is_platform_windows = platform.system() == "Windows" - - -# === Setting clean command =================================================== -logging.basicConfig(level=logging.INFO) -logger = logging.getLogger("tofu.setup") - - -class CleanCommand(Clean): - - description = "Remove build artifacts from the source tree" - - def expand(self, path_list): - """ - Expand a list of path using glob magic. - :param list[str] path_list: A list of path which may contains magic - :rtype: list[str] - :returns: A list of path without magic - """ - path_list2 = [] - for path in path_list: - if glob.has_magic(path): - iterator = glob.iglob(path) - path_list2.extend(iterator) - else: - path_list2.append(path) - return path_list2 - - def find(self, path_list): - """Find a file pattern if directories. - Could be done using "**/*.c" but it is only supported in Python 3.5. - :param list[str] path_list: A list of path which may contains magic - :rtype: list[str] - :returns: A list of path without magic - """ - import fnmatch - - path_list2 = [] - for pattern in path_list: - for root, _, filenames in os.walk("."): - for filename in fnmatch.filter(filenames, pattern): - path_list2.append(os.path.join(root, filename)) - return path_list2 - - def run(self): - Clean.run(self) - - cython_files = self.find(["*.pyx"]) - cythonized_files = [ - path.replace(".pyx", ".c") for path in cython_files - ] - so_files = self.find(["*.so"]) - # really remove the directories - # and not only if they are empty - to_remove = [self.build_base] - to_remove = self.expand(to_remove) - to_remove += cythonized_files - to_remove += so_files - - if not self.dry_run: - for path in to_remove: - try: - if os.path.isdir(path): - shutil.rmtree(path) - else: - os.remove(path) - logger.info("removing '%s'", path) - except OSError: - pass -# ============================================================================= - - -# == Getting tofu version ===================================================== -_HERE = os.path.abspath(os.path.dirname(__file__)) - - -def get_version_tofu(path=_HERE): - - # Try from git - isgit = ".git" in os.listdir(path) - if isgit: - try: - git_branch = ( - subprocess.check_output( - [ - "git", - "rev-parse", - "--abbrev-ref", - "HEAD", - ] - ) - .rstrip() - .decode() - ) - deploy_branches = ["master", "deploy-test"] - if (git_branch in deploy_branches or "TRAVIS_TAG" in os.environ): - version_tofu = up.updateversion() - else: - isgit = False - except Exception: - isgit = False - - if not isgit: - version_tofu = os.path.join(path, "tofu") - version_tofu = os.path.join(version_tofu, "version.py") - with open(version_tofu, "r") as fh: - version_tofu = fh.read().strip().split("=")[-1].replace("'", "") - - version_tofu = version_tofu.lower().replace("v", "").replace(" ", "") - return version_tofu - - -version_tofu = get_version_tofu(path=_HERE) - -print("") -print("Version for setup.py : ", version_tofu) -print("") - -# ============================================================================= - -# ============================================================================= -# Get the long description from the README file -# Get the readme file whatever its extension (md vs rst) - -_README = [ - ff - for ff in os.listdir(_HERE) - if len(ff) <= 10 and ff[:7] == "README." -] -assert len(_README) == 1 -_README = _README[0] -with open(os.path.join(_HERE, _README), encoding="utf-8") as f: - long_description = f.read() -if _README[-3:] == ".md": - long_description_content_type = "text/markdown" -else: - long_description_content_type = "text/x-rst" -# ============================================================================= - - -# ============================================================================= -# Compiling files -openmp_installed, openmp_flag = is_openmp_installed() - -extra_compile_args = ["-O3", "-Wall", "-fno-wrapv"] + openmp_flag -extra_link_args = [] + openmp_flag - -extensions = [ - Extension( - name="tofu.geom._GG", - sources=["tofu/geom/_GG.pyx"], - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - language_level="3", - ), - Extension( - name="tofu.geom._basic_geom_tools", - sources=["tofu/geom/_basic_geom_tools.pyx"], - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - ), - Extension( - name="tofu.geom._distance_tools", - sources=["tofu/geom/_distance_tools.pyx"], - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - ), - Extension( - name="tofu.geom._sampling_tools", - sources=["tofu/geom/_sampling_tools.pyx"], - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - ), - Extension( - name="tofu.geom._raytracing_tools", - sources=["tofu/geom/_raytracing_tools.pyx"], - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - ), - Extension( - name="tofu.geom._vignetting_tools", - sources=["tofu/geom/_vignetting_tools.pyx"], - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - ), - Extension( - name="tofu.geom._chained_list", - sources=["tofu/geom/_chained_list.pyx"], - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - ), - Extension( - name="tofu.geom._sorted_set", - sources=["tofu/geom/_sorted_set.pyx"], - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - ), - Extension( - name="tofu.geom._openmp_tools", - sources=["tofu/geom/_openmp_tools.pyx"], - extra_compile_args=extra_compile_args, - extra_link_args=extra_link_args, - cython_compile_time_env=dict(TOFU_OPENMP_ENABLED=openmp_installed), - ), -] - - -setup( - name="tofu", - version="{ver}".format(ver=version_tofu), - # Use scm to get code version from git tags - # cf. https://pypi.python.org/pypi/setuptools_scm - # Versions should comply with PEP440. For a discussion on single-sourcing - # the version across setup.py and the project code, see - # https://packaging.python.org/en/latest/single_source_version.html - # The version is stored only in the setup.py file and read from it (option - # 1 in https://packaging.python.org/en/latest/single_source_version.html) - use_scm_version=False, - - # Description of what tofu does - description="A python library for Tomography for Fusion", - long_description=long_description, - long_description_content_type=long_description_content_type, - - # The project's main homepage. - url="https://github.com/ToFuProject/tofu", - # Author details - author="Didier VEZINET and Laura MENDOZA", - author_email="didier.vezinet@gmail.com", - - # Choose your license - license="MIT", - - # See https://pypi.python.org/pypi?%3Aaction=list_classifiers - classifiers=[ - # How mature is this project? Common values are - # 3 - Alpha - # 4 - Beta - # 5 - Production/Stable - "Development Status :: 4 - Beta", - # Indicate who your project is intended for - "Intended Audience :: Science/Research", - "Topic :: Scientific/Engineering :: Physics", - # Specify the Python versions you support here. In particular, ensure - # that you indicate whether you support Python 2, Python 3 or both. - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - # In which language most of the code is written ? - "Natural Language :: English", - ], - - # What does your project relate to? - keywords="tomography geometry 3D inversion synthetic fusion", - - # You can just specify the packages manually here if your project is - # simple. Or you can use find_packages(). - packages=find_packages( - exclude=[ - "doc", - "_Old", - "_Old_doc", - "plugins", - "plugins.*", - "*.plugins.*", - "*.plugins", - "*.tests10_plugins", - "*.tests10_plugins.*", - "tests10_plugins.*", - "tests10_plugins", - ] - ), - - # packages = ['tofu','tofu.geom'], - # Alternatively, if you want to distribute just a my_module.py, uncomment - # this: - # py_modules=["my_module"], - # List run-time dependencies here. These will be installed by pip when - # your project is installed. For an analysis of "install_requires" vs pip's - # requirements files see: - # https://packaging.python.org/en/latest/requirements.html - install_requires=[ - # ">=40.8.0, <64", - "setuptools", - "numpy", - "scipy", - # "scikit-sparse", - # "scikit-umfpack", - "matplotlib>3.0.3", - "contourpy", - "requests", - "svg.path", - "Polygon3", - "cython>=0.26", - "datastock>=0.0.54", - "bsplines2d>=0.0.29", - "spectrally>=0.0.9", - ], - python_requires=">=3.6", - - # List additional groups of dependencies here (e.g. development - # dependencies). You can install these using the following syntax, - # for example: - # $ pip install -e .[dev,test] - extras_require={ - "dev": [ - "check-manifest", - "coverage", - "pytest", - "sphinx", - "sphinx-gallery", - "sphinx_bootstrap_theme", - ] - }, - - # If there are data files included in your packages that need to be - # installed, specify them here. If using Python 2.6 or less, then these - # have to be included in MANIFEST.in as well. - # package_data={ - # # If any package contains *.txt, *.rst or *.npz files, include them: - # '': ['*.txt', '*.rst', '*.npz'], - # # And include any *.csv files found in the 'ITER' package, too: - # 'ITER': ['*.csv'], - # }, - package_data={ - "tofu.tests.tests01_geom.test_data": [ - "*.py", "*.txt", ".svg", ".npz" - ], - "tofu.tests.tests04_spectro.test_data": ["*.npz"], - "tofu.tests.tests06_mesh.test_data": ['*.txt', '*.npz'], - "tofu.geom.inputs": ["*.txt"], - "tofu.spectro": ["*.txt"], - "tofu.physics_tools.runaways.emission": ['*.csv'], - "tofu.physics_tools.transmission.inputs_filter": ['*.txt', '*.csv'], - "tofu.mag.mag_ripple": ['*.sh', '*.f'] - }, - include_package_data=True, - - # Although 'package_data' is the preferred approach, in some case you may - # need to place data files outside of your packages. See: - # http://docs.python.org/3.4/distutils/setupscript.html - # installing-additional-files # noqa - # In this case, 'data_file' will be installed into '/my_data' - # data_files=[('my_data', ['data/data_file'])], - - # executable scripts can be declared here - # They can be python or non-python scripts - # scripts=[ - # ], - - # entry_points point to functions in the package - # Theye are generally preferable over scripts because they provide - # cross-platform support and allow pip to create the appropriate form - # of executable for the target platform. - entry_points={ - 'console_scripts': [ - 'tofuplot=tofu.entrypoints.tofuplot:main', - 'tofucalc=tofu.entrypoints.tofucalc:main', - 'tofu-version=scripts.tofuversion:main', - 'tofu-custom=scripts.tofucustom:main', - 'tofu=scripts.tofu_bash:main', - ], - }, - - py_modules=['_updateversion'], - - # Extensions and commands - ext_modules=extensions, - cmdclass={"build_ext": build_ext, - "clean": CleanCommand}, - include_dirs=[np.get_include()], -) diff --git a/tofu/_version.py b/tofu/_version.py new file mode 100644 index 000000000..aefa9b159 --- /dev/null +++ b/tofu/_version.py @@ -0,0 +1,34 @@ +# file generated by setuptools-scm +# don't change, don't track in version control + +__all__ = [ + "__version__", + "__version_tuple__", + "version", + "version_tuple", + "__commit_id__", + "commit_id", +] + +TYPE_CHECKING = False +if TYPE_CHECKING: + from typing import Tuple + from typing import Union + + VERSION_TUPLE = Tuple[Union[int, str], ...] + COMMIT_ID = Union[str, None] +else: + VERSION_TUPLE = object + COMMIT_ID = object + +version: str +__version__: str +__version_tuple__: VERSION_TUPLE +version_tuple: VERSION_TUPLE +commit_id: COMMIT_ID +__commit_id__: COMMIT_ID + +__version__ = version = '1.8.18.dev55+g47d94b532' +__version_tuple__ = version_tuple = (1, 8, 18, 'dev55', 'g47d94b532') + +__commit_id__ = commit_id = 'g47d94b532' diff --git a/tofu/data/_class02_Rays.py b/tofu/data/_class02_Rays.py index 15c176497..1a3bf74da 100644 --- a/tofu/data/_class02_Rays.py +++ b/tofu/data/_class02_Rays.py @@ -12,6 +12,7 @@ from . import _class02_sample as _sample from . import _class02_tangency_radius as _tangency_radius from . import _class02_single_point_camera as _single_point_cam +from . import _class02_angle_vs_vect as _angle_vs_vect from . import _class2_plot as _plot from . import _class2_sinogram as _sinogram from . import _class02_save2stp as _save2stp @@ -393,6 +394,50 @@ def get_rays_intersect_radius( return_itot=return_itot, ) + def get_rays_angle_vs_vect( + self, + # rays + key_rays=None, + res=None, + segment=None, + # vector components + key_XR=None, + key_YZ=None, + key_Zphi=None, + geometry=None, + # optional separatrix + key_sepR=None, + key_sepZ=None, + # verb + verb=None, + ): + """ Return the angle between rays and a 3d vector field + + Rays are sampled at res and the angle is calculated all along + + The vector field is defined by 3 components (R, Z, phi) that must + refer to 3 keys defined on a same 2d splines base + + """ + + return _angle_vs_vect.main( + coll=self, + # rays + key_rays=key_rays, + res=res, + segment=segment, + # vector components + key_XR=key_XR, + key_YZ=key_YZ, + key_Zphi=key_Zphi, + geometry=geometry, + # optional separatrix + key_sepR=key_sepR, + key_sepZ=key_sepZ, + # verb + verb=verb, + ) + # -------------- # Single point camera # -------------- diff --git a/tofu/data/_class02_angle_vs_vect.py b/tofu/data/_class02_angle_vs_vect.py new file mode 100644 index 000000000..990f2d2b2 --- /dev/null +++ b/tofu/data/_class02_angle_vs_vect.py @@ -0,0 +1,598 @@ + + +import numpy as np +from matplotlib.path import Path +import datastock as ds +import bsplines2d as bs2 + + +# ################################################################# +# ################################################################# +# Main +# ################################################################# + + +def main( + coll=None, + # rays + key_rays=None, + res=None, + segment=None, + # vector components + key_XR=None, + key_YZ=None, + key_Zphi=None, + geometry=None, + # optional separatrix + key_sepR=None, + key_sepZ=None, + # options + verb=None, +): + + # ---------------- + # check inputs + # ---------------- + + ( + key_rays, + dkeys, geometry, + key_sepR, key_sepZ, + verb, + ) = _check( + coll=coll, + key_rays=key_rays, + # vector components + key_XR=key_XR, + key_YZ=key_YZ, + key_Zphi=key_Zphi, + geometry=geometry, + # optional separatrix + key_sepR=key_sepR, + key_sepZ=key_sepZ, + ) + wrays = coll._which_rays + + # ---------------- + # verb + # ---------------- + + if verb >= 1: + lk = ['key_XR', 'key_YZ', 'key_Zphi'] + lstr = [ + f"\t - {kk}: {dkeys[kk]} {coll.ddata[dkeys[kk]]['shape']}" + for kk in lk + ] + msg = "\nComputing rays_angle_vs_vect for:\n" + "\n".join(lstr) + "\n" + print(msg) + + # ---------------- + # prepare sepR, sepZ + # ---------------- + + nstep = 4 + if key_sepR is not False: + sepR, sepZ, sli_sep, ind_sep = _prepare_sep( + coll=coll, + key_sepR=key_sepR, + key_sepZ=key_sepZ, + dkeys=dkeys, + ) + nstep += 1 + + # ---------------- + # loop on rays + # ---------------- + + ddata = {} + nrays = len(key_rays) + for iray, kray in enumerate(key_rays): + + # ------------ + # verb + + if verb >= 1: + sh = coll.dobj[wrays][kray]['shape'] + msg = f"\tFor kray = {kray} (shape {sh})... ({iray+1} / {nrays})" + print(msg) + + # ------------- + # sample LOS + + # verb + if verb >= 2: + msg = f"\t\t- sampling... (1/{nstep})" + print(msg) + + # sampel + R, Z, phi, length = coll.sample_rays( + key=kray, + res=res, + mode='abs', + segment=segment, + return_coords=['R', 'z', 'phi', 'l'], + ) + + # ------------- + # interpolate + + # verb + if verb >= 2: + msg = f"\t\t- interpolating... (2/{nstep})" + print(msg) + + # interpolate + dinterp = coll.interpolate( + keys=[dkeys['key_XR'], dkeys['key_YZ'], dkeys['key_Zphi']], + ref_key=None, + x0=R, + x1=Z, + grid=False, + details=False, + val_out=np.nan, + log_log=False, + nan0=False, + returnas=dict, + store=False, + ) + + # ------------------ + # local unit vectors + + # verb + if verb >= 2: + msg = f"\t\t- deriving angle... (3/{nstep})" + print(msg) + + # unit vectors + ux, uy, uz = _local_unit_vect( + phi=phi, + vXR=dinterp[dkeys['key_XR']]['data'], + vYZ=dinterp[dkeys['key_YZ']]['data'], + vZphi=dinterp[dkeys['key_Zphi']]['data'], + geometry=geometry, + ) + + # -------------- + # los vect + + vx, vy, vz = coll.get_rays_vect(kray, segment=segment) + + # reshape for broadcast + axis = tuple(np.arange(0, ux.ndim - vx.ndim)) + vx = np.expand_dims(vx, axis) + vy = np.expand_dims(vy, axis) + vz = np.expand_dims(vz, axis) + + # -------------- + # compute angles + + angle = np.arccos(ux * (-vx) + uy * (-vy) + uz * (-vz)) + + # -------------- + # sep ? + + if key_sepR is not None: + + # verb + if verb >= 2: + msg = f"\t\t- separatrix... (4/{nstep})" + print(msg) + + # apply separatrix + ref = _apply_sep( + coll=coll, + dinterp=dinterp, + sepR=sepR, + sepZ=sepZ, + sli_sep=sli_sep, + ind_sep=ind_sep, + dkeys=dkeys, + R=R, + Z=Z, + kray=kray, + angle=angle, + ) + + # -------------- + # cleanup + + # verb + if verb >= 2: + msg = f"\t\t- cleanup... (5/{nstep})" + print(msg) + + # angle + axis = tuple([ii for ii, rr in enumerate(ref) if rr is not None]) + iok = np.any(np.isfinite(angle), axis=axis) + sli = tuple([ + iok if rr is None else slice(None) + for ii, rr in enumerate(ref) + ]) + angle = angle[sli] + + # R, Z, phi, length + R = R[iok, ...] + Z = Z[iok, ...] + phi = phi[iok, ...] + length = length[iok, ...] + + # -------------- + # store + + refpts = (None,) + coll.dobj[wrays][kray]['ref'][1:] + + ddata[kray] = { + 'angle': { + 'key': None, + 'data': angle, + 'ref': ref, + 'dim': 'angle', + 'units': 'rad', + }, + 'length': { + 'key': None, + 'data': length, + 'ref': refpts, + 'dim': 'distance', + 'units': 'm', + }, + 'R': { + 'key': None, + 'data': R, + 'units': 'm', + 'dim': 'distance', + 'ref': refpts, + }, + 'Z': { + 'key': None, + 'data': Z, + 'units': 'm', + 'dim': 'distance', + 'ref': refpts, + }, + 'phi': { + 'key': None, + 'data': phi, + 'units': 'm', + 'dim': 'distance', + 'ref': refpts, + }, + } + + return ddata + + +# ################################################################# +# ################################################################# +# check +# ################################################################# + + +def _check( + coll=None, + # rays + key_rays=None, + res=None, + # vector components + key_XR=None, + key_YZ=None, + key_Zphi=None, + geometry=None, + # optional separatrix + key_sepR=None, + key_sepZ=None, + # optional + verb=None, +): + + # ------------- + # key_rays + # ------------- + + wrays = coll._which_rays + lok = list(coll.dobj.get(wrays, {}).keys()) + if isinstance(key_rays, str): + key_rays = [key_rays] + key_rays = ds._generic_check._check_var_iter( + key_rays, 'key_rays', + types=(list, tuple), + types_iter=str, + allowed=lok, + default=lok, + ) + + # ------------------ + # geometry + # ------------------ + + geometry = ds._generic_check._check_var( + geometry, 'geometry', + types=str, + default='toroidal', + allowed=['toroidal'], + ) + + # ------------------ + # key vect coordinates + # ------------------ + + dkey = bs2._class02_line_tracing._check_keys_components( + coll=coll, + # 3 componants + key_XR=key_XR, + key_YZ=key_YZ, + key_Zphi=key_Zphi, + ) + + # ------------------- + # Optional separatrix + # ------------------- + + # default => False + if key_sepR is None: + key_sepR = False + if key_sepZ is None: + key_sepZ = False + + # both xor none + lc = [key_sepR is not False, key_sepZ is not False] + if np.sum(lc) == 1: + msg = ( + "Please provide either (xor):\n" + "\t- both key_sepR and key_sepZ (True or str)\n" + "\t- none of them (None or False)" + ) + raise Exception(msg) + + # key_sepR + key_sepR = _check_key_sep(coll, key_sepR, 'key_sepR') + key_sepZ = _check_key_sep(coll, key_sepZ, 'key_sepZ') + + # cross-compatibility + if key_sepR is not False: + + # same ref with each other + ref_sep = coll.ddata[key_sepR]['ref'] + if ref_sep != coll.ddata[key_sepZ]['ref']: + lstr = [ + f"\t- '{kk}': {coll.ddata[kk]['ref']}" + for kk in [key_sepR, key_sepZ] + ] + msg = ( + "Args 'key_sepR' and 'key_sepZ' must share the same 'ref'!\n" + + "\n".join(lstr) + ) + raise Exception(msg) + + # shared ref with vector field + ref_vect = coll.ddata[dkey['key_XR']]['ref'] + lout = [rr for rr in ref_sep if rr not in ref_vect] + if len(lout) > 1: + msg = ( + ) + raise Exception(msg) + + # ------------------- + # verb + # ------------------- + + lok = [False, True, 0, 1, 2] + verb = int(ds._generic_check._check_var( + verb, 'verb', + types=(bool, int), + default=lok[-1], + allowed=lok, + )) + + return ( + key_rays, + dkey, geometry, + key_sepR, key_sepZ, + verb, + ) + + +def _check_key_sep(coll, key, keyn): + + # ----------------- + # True => automatic + # ----------------- + + if key is True: + lk = [ + kk for kk in coll.ddata.keys() + if kk.endswith(f"{keyn.split('_')[-1]}") + ] + if len(lk) == 1: + key = lk[0] + else: + lstr = [f"\t- {kk}" for kk in lk] + msg = ( + f"Arg '{keyn}' (True) could not be automatically identified\n" + "No / several options:\n" + + "\n".join(lstr) + ) + raise Exception(msg) + + # ----------------- + # str => check vs ddata + # ----------------- + + if key is not False: + lok = [ + kk for kk, vv in coll.ddata.items() + ] + key = ds._generic_check._check_var( + key, keyn, + types=str, + allowed=lok, + ) + + return key + + +# ################################################################# +# ################################################################# +# Prepare sepR, sepZ +# ################################################################# + + +def _prepare_sep( + coll=None, + key_sepR=None, + key_sepZ=None, + dkeys=None, +): + + # ------------ + # refs + # ------------ + + ref_sep = coll.ddata[key_sepR]['ref'] + ref_vect = coll.ddata[dkeys['key_XR']]['ref'] + + # ------------ + # axis + # ------------ + + sepR = coll.ddata[key_sepR]['data'] + sepZ = coll.ddata[key_sepZ]['data'] + + # ----------- + # slicing + # ----------- + + axis_pts = [ii for ii, rr in enumerate(ref_sep) if rr not in ref_vect][0] + ind_sep = np.delete(np.arange(0, sepR.ndim), axis_pts).astype(int) + sli_sep = np.array([ + 0 if rr in ref_vect else slice(None) + for rr in ref_sep + ]) + + return sepR, sepZ, sli_sep, ind_sep + + +# ################################################################# +# ################################################################# +# get local unit vectors +# ################################################################# + + +def _local_unit_vect( + phi=None, + vXR=None, + vYZ=None, + vZphi=None, + geometry=None, +): + + # -------- + # linear + # -------- + + if geometry == 'linear': + + un = np.sqrt(vXR**2 + vYZ**2 + vZphi**2) + ux = vXR / un + uy = vYZ / un + uz = vZphi / un + + # ---------- + # toroidal + # ---------- + + else: + + # -------------------- + # ux, uy from vR, vphi + + # associated unit vectors + cosphif = np.cos(phi)[None, ...] + sinphif = np.sin(phi)[None, ...] + + uX = vXR * cosphif - vZphi * sinphif + uY = vXR * sinphif + vZphi * cosphif + + # --------------- + # normalize + + un = np.sqrt(uX**2 + uY**2 + vYZ**2) + ux = uX / un + uy = uY / un + uz = vYZ / un + + return ux, uy, uz + + +# ################################################################# +# ################################################################# +# Apply sepR, sepZ +# ################################################################# + + +def _apply_sep( + coll=None, + dinterp=None, + dkeys=None, + R=None, + Z=None, + sepR=None, + sepZ=None, + sli_sep=None, + ind_sep=None, + kray=None, + angle=None, +): + + # ----------------------- + # prepare ref, shape, sli + # ----------------------- + + ref_interp = dinterp[dkeys['key_XR']]['ref'] + shape_interp = dinterp[dkeys['key_XR']]['data'].shape + shape = tuple([ + ss for ii, ss in enumerate(shape_interp) + if ref_interp[ii] is not None + ]) + pts = np.array([R.ravel(), Z.ravel()]).T + + # sli + refn = [] + for ii, rr in enumerate(ref_interp): + if rr is not None or None not in refn: + refn.append(rr) + iang0 = tuple([ii for ii, rr in enumerate(refn) if rr is not None]) + iang1 = refn.index(None) + sli_angle = [0 for rr in refn] + + # ref + wrays = coll._which_rays + ref_rays = coll.dobj[wrays][kray]['ref'] + ref, iN = [], 0 + for rr in ref_interp: + if rr is None: + if iN == 0: + ref.append(rr) + else: + ref.append(ref_rays[iN]) + iN += 1 + else: + ref.append(rr) + + # ------------------------------------- + # loop on indices to compute pts in sep + # ------------------------------------- + + for ii, ind in enumerate(np.ndindex(shape)): + + sli_sep[ind_sep] = ind + sep = np.array([sepR[tuple(sli_sep)], sepZ[tuple(sli_sep)]]).T + indout = ~Path(sep).contains_points(pts).reshape(R.shape) + + for ia, iin in zip(iang0, ind): + sli_angle[ia] = iin + sli_angle[iang1] = indout + angle[tuple(sli_angle)] = np.nan + + return ref diff --git a/tofu/data/_class02_single_point_camera.py b/tofu/data/_class02_single_point_camera.py index ae1802ee6..35fa21aaf 100644 --- a/tofu/data/_class02_single_point_camera.py +++ b/tofu/data/_class02_single_point_camera.py @@ -115,21 +115,25 @@ def main( angle1f = angle1f * np.pi/180. # unit vectors - vx = ( - np.cos(angle1f) - * (np.cos(angle0f) * (nin[0]) + np.sin(angle0f) * e0[0]) - + np.sin(angle1f) * e1[0] - ) - vy = ( - np.cos(angle1f) - * (np.cos(angle0f) * (nin[1]) + np.sin(angle0f) * e0[1]) - + np.sin(angle1f) * e1[1] - ) - vz = ( - np.cos(angle1f) - * (np.cos(angle0f) * (nin[2]) + np.sin(angle0f) * e0[2]) - + np.sin(angle1f) * e1[2] - ) + cos0 = np.cos(angle0f) + sin0 = np.sin(angle0f) + cos1 = np.cos(angle1f) + sin1 = np.sin(angle1f) + + # unit vectors + vx = cos1 * (cos0 * nin[0] + sin0 * e0[0]) + sin1 * e1[0] + vy = cos1 * (cos0 * nin[1] + sin0 * e0[1]) + sin1 * e1[1] + vz = cos1 * (cos0 * nin[2] + sin0 * e0[2]) + sin1 * e1[2] + + # ------------- + # solid angles + # ------------- + + dang0 = np.diff(angle0f[:, 0]) + dang1 = np.diff(angle1f[0, :]) + dang0 = np.r_[dang0, dang0[-1]] + dang1 = np.r_[dang1, dang1[-1]] + solid_angles = cos1 * dang0[:, None] * dang1[None, :] # ------------- # compute @@ -156,7 +160,7 @@ def main( strict=strict, ) - return + return solid_angles # ######################################################## diff --git a/tofu/data/_class03_Aperture.py b/tofu/data/_class03_Aperture.py index fe5d9d080..0548be851 100644 --- a/tofu/data/_class03_Aperture.py +++ b/tofu/data/_class03_Aperture.py @@ -11,7 +11,7 @@ from . import _class03_save2stp as _save2stp -__all__ = ['Aperture'] +__all__ = ["Aperture"] # ######################################################################### @@ -21,7 +21,6 @@ class Aperture(Previous): - # _ddef = copy.deepcopy(ds.DataStock._ddef) # _ddef['params']['ddata'].update({ # 'bsplines': (str, ''), @@ -30,20 +29,22 @@ class Aperture(Previous): # _ddef['params']['dref'] = None # _show_in_summary_core = ['shape', 'ref', 'group'] - _show_in_summary = 'all' + _show_in_summary = "all" _dshow = dict(Previous._dshow) - _dshow.update({ - 'aperture': [ - 'dgeom.type', - 'dgeom.curve_r', - 'dgeom.area', - 'dgeom.outline', - 'dgeom.poly', - 'dgeom.cent', - # 'dmisc.color', - ], - }) + _dshow.update( + { + "aperture": [ + "dgeom.type", + "dgeom.curve_r", + "dgeom.area", + "dgeom.outline", + "dgeom.poly", + "dgeom.cent", + # 'dmisc.color', + ], + } + ) def add_aperture( self, @@ -67,15 +68,30 @@ def add_aperture( # dmisc color=None, ): - """ Add an aperture - - Can be defined from: - - 2d outline + 3d center + unit vectors (nin, e0, e1) - - 3d polygon + nin - - Unit vectors will be checked and normalized - If planar, area will be computed - Outline will be made counter-clockwise + """Add an aperture. Apertures can be planar or non-planar. + + Planar apertures require the following parameters: + - 'cent': (x, y, z) coords + - 'nin': (x, y, z) coords, normalized and towards the plasma + - 'e0': (x, y, z) coords + - 'e1': (x, y, z) coords + - 'outline_x0': (npts,) np.ndarray, coords in (cent, e0, e1) + - 'outline_x1': (npts,) np.ndarray, coords in (cent, e0, e1) + + Non-planar apertures require the following parameters: + - 'poly_x': (npts,) ndarray + - 'poly_y': (npts,) ndarray + - 'poly_z': (npts,) ndarray + - 'nin': (x, y, z) coords, normalized and towards the plasma + Indicative, since the aperture is not planar, 'nin' here is + imperfect, will improve on that in the future + + For planar apertures, ('nin', 'e0', 'e1') always for a set of 3 unit + vectors arranged as an direct orthonormal basis (e2 = cross(nin, e0)). + + Unit vectors will be checked and normalized. + If planar, area will be computed. + Outline will be made counter-clockwise. """ @@ -83,8 +99,8 @@ def add_aperture( dref, ddata, dobj = _check._add_surface3d( coll=self, key=key, - which='aperture', - which_short='ap', + which="aperture", + which_short="ap", # 2d outline outline_x0=outline_x0, outline_x1=outline_x1, @@ -104,8 +120,8 @@ def add_aperture( ) # dmisc - key = list(dobj['aperture'].keys())[0] - dobj['aperture'][key]['dmisc'] = _check._dmisc( + key = list(dobj["aperture"].keys())[0] + dobj["aperture"][key]["dmisc"] = _check._dmisc( key=key, color=color, ) @@ -118,7 +134,7 @@ def add_aperture( # --------------- def get_as_dict(self, which=None, key=None): - """ Return the desired object as a dict (input to some routines) """ + """Return the desired object as a dict (input to some routines)""" return _check._return_as_dict( coll=self, @@ -142,7 +158,7 @@ def save_optics_to_stp( overwrite=None, verb=None, ): - """ Save the selected optics 3d outlines to a stp file + """Save the selected optics 3d outlines to a stp file Optionally chain them to be a single POLYLINE diff --git a/tofu/data/_class07_Camera.py b/tofu/data/_class07_Camera.py index eb1f66942..e66a6359e 100644 --- a/tofu/data/_class07_Camera.py +++ b/tofu/data/_class07_Camera.py @@ -3,6 +3,7 @@ # Built-in import copy +from typing import Any, Dict, Optional # tofu @@ -13,7 +14,7 @@ from . import _class07_legacy as _legacy -__all__ = ['Camera'] +__all__ = ["Camera"] # ################################################################ @@ -23,30 +24,33 @@ class Camera(Previous): - - _which_cam = 'camera' + _which_cam = "camera" _ddef = copy.deepcopy(Previous._ddef) - _ddef['params']['ddata'].update({ - 'camera': {'cls': str, 'def': ''}, - }) + _ddef["params"]["ddata"].update( + { + "camera": {"cls": str, "def": ""}, + } + ) _dshow = dict(Previous._dshow) - _dshow.update({ - 'camera': [ - 'dgeom.type', - 'dgeom.nd', - 'dmat.mode', - 'dgeom.parallel', - 'dgeom.shape', - 'dgeom.ref', - 'dgeom.pix_area', - 'dgeom.pix_nb', - 'dgeom.outline', - 'dgeom.cent', - # 'dgeom.cents', - # 'dmisc.color', - ], - }) + _dshow.update( + { + "camera": [ + "dgeom.type", + "dgeom.nd", + "dmat.mode", + "dgeom.parallel", + "dgeom.shape", + "dgeom.ref", + "dgeom.pix_area", + "dgeom.pix_nb", + "dgeom.outline", + "dgeom.cent", + # 'dgeom.cents', + # 'dmisc.color', + ], + } + ) def _add_camera( self, @@ -56,7 +60,7 @@ def _add_camera( dmat=None, color=None, ): - key = list(dobj['camera'].keys())[0] + key = list(dobj["camera"].keys())[0] # material dref2, ddata2, dmat = _check._dmat( @@ -69,10 +73,10 @@ def _add_camera( if dref2 is not None: dref.update(dref2) ddata.update(ddata2) - dobj['camera'][key]['dmat'] = dmat + dobj["camera"][key]["dmat"] = dmat # dmisc - dobj['camera'][key]['dmisc'] = _class3_check._dmisc( + dobj["camera"][key]["dmisc"] = _class3_check._dmisc( key=key, color=color, ) @@ -82,26 +86,27 @@ def _add_camera( def add_camera_1d( self, - key=None, - # geometry - dgeom=None, - # quantum efficiency - dmat=None, - # dmisc + key: Optional[str] = None, + dgeom: Optional[dict[str, Any]] = None, + dmat: Optional[dict[str, Any]] = None, color=None, ): - """ add a 1d camera + """Add a 1D camera. - A 1d camera is an unordered set of pixels of indentical outline - Its geometry os defined by dgeom - Its material properties (i.e: quantum efficiency) in dmat + A 1D camera is an unordered set of pixels of indentical outline. - The geometry in dgeom must contain: + Parameters + ---------- + key: + The name of the camera + dgeom: + The geometry of the camera. The geometry must contain the + following key-value pairs: - 'outline_x0': 1st coordinate of planar outline of a single pixel - 'outline_x1': 1st coordinate of planar outline of a single pixel - - 'cents_x': x coordinate of the centers of ll pixels - - 'cents_y': y coordinate of the centers of ll pixels - - 'cents_z': z coordinate of the centers of ll pixels + - 'cents_x': x coordinate of the centers of all pixels + - 'cents_y': y coordinate of the centers of all pixels + - 'cents_z': z coordinate of the centers of all pixels - 'nin_x': x coordinate of inward normal unit vector of all pixels - 'nin_y': y coordinate of inward normal unit vector of all pixels - 'nin_z': z coordinate of inward normal unit vector of all pixels @@ -111,11 +116,13 @@ def add_camera_1d( - 'e1_x': x coordinate of e1 unit vector of all pixels - 'e1_y': y coordinate of e1 unit vector of all pixels - 'e1_z': z coordinate of e1 unit vector of all pixels - - The material dict, dmat can contain: + dmat: + The material properties, i.e. quantum efficiency. This dictionary + can contain: - 'energy': a 1d energy vector , in eV - 'qeff': a 1d vector, same size as energy, with values in [0; 1] - + color: + TODO """ # check / format input dref, ddata, dobj = _check._camera_1d( @@ -135,21 +142,22 @@ def add_camera_1d( def add_camera_2d( self, - key=None, - # geometry - dgeom=None, - # material - dmat=None, - # dmisc + key: Optional[str] = None, + dgeom: Optional[dict[str, Any]] = None, + dmat: Optional[dict[str, Any]] = None, color=None, ): - """ add a 2d camera + """Add a 2D camera. - A 2d camera is an ordered 2d grid of pixels of indentical outline - Its geometry os defined by dgeom - Its material properties (i.e: quantum efficiency) in dmat + A 2D camera is an ordered 2d grid of pixels of indentical outline. - The geometry in dgeom must contain: + Parameters + ---------- + key: + The name of the camera + dgeom: + The geometry of the camera. The geometry must contain the + following key-value pairs: - 'outline_x0': 1st coordinate of planar outline of a single pixel - 'outline_x1': 1st coordinate of planar outline of a single pixel - 'cent': (x, y, z) coordinate of the center of the camera @@ -158,11 +166,13 @@ def add_camera_2d( - 'nin': x coordinate of inward normal unit vector of all pixels - 'e0': x coordinate of e0 unit vector of all pixels - 'e1': x coordinate of e1 unit vector of all pixels - - The material dict, dmat can contain: + dmat: + The material properties, i.e. quantum efficiency. This dictionary + can contain: - 'energy': a 1d energy vector , in eV - 'qeff': a 1d vector, same size as energy, with values in [0; 1] - + color: + TODO """ # check / format input dref, ddata, dobj = _check._camera_2d( @@ -218,7 +228,6 @@ def add_camera_pinhole( # dmat dmat=None, ): - return _compute.add_camera_pinhole( coll=self, key=key, @@ -265,7 +274,7 @@ def update( dref=None, harmonize=None, ): - """ Overload datastock update() method """ + """Overload datastock update() method""" # update super().update( @@ -276,20 +285,19 @@ def update( ) # assign diagnostic - if self._dobj.get('camera') is not None: + if self._dobj.get("camera") is not None: for k0, v0 in self._ddata.items(): lcam = [ - k1 for k1, v1 in self._dobj['camera'].items() - if v1['dgeom']['ref'] == tuple([ - rr for rr in v0['ref'] - if rr in v1['dgeom']['ref'] - ]) + k1 + for k1, v1 in self._dobj["camera"].items() + if v1["dgeom"]["ref"] + == tuple([rr for rr in v0["ref"] if rr in v1["dgeom"]["ref"]]) ] if len(lcam) == 0: pass elif len(lcam) == 1: - self._ddata[k0]['camera'] = lcam[0] + self._ddata[k0]["camera"] = lcam[0] else: msg = f"Multiple cameras:\n{lcam}" raise Exception(msg) @@ -303,7 +311,7 @@ def add_camera_from_legacy( cam=None, key=None, ): - """ Add a camera from a dict (or pfe) """ + """Add a camera from a dict (or pfe)""" return _legacy.add_camera( self, cam=cam, @@ -319,7 +327,7 @@ def get_camera_unit_vectors( key=None, broadcast=None, ): - """ Return a dict of unit vectors components + """Return a dict of unit vectors components If broadcast=True, forces to match the shape of camera """ @@ -335,7 +343,7 @@ def get_camera_dxyz( kout=None, include_center=None, ): - """ Return dx, dy, dz to get the outline from any pixel center + """Return dx, dy, dz to get the outline from any pixel center Only works on 2d or parallel cameras """ @@ -347,21 +355,21 @@ def get_camera_dxyz( ) def get_camera_cents_xyz(self, key=None): - """ Return cents_x, cents_y, cents_z """ + """Return cents_x, cents_y, cents_z""" return _check.get_camera_cents_xyz( coll=self, key=key, ) def get_camera_extent(self, key=None): - """ Return the extent of a 2d camera """ + """Return the extent of a 2d camera""" return _check._get_extent( coll=self, key=key, ) def get_as_dict(self, key=None): - """ Return the desired object as a dict (input to some routines) """ + """Return the desired object as a dict (input to some routines)""" return _class3_check._return_as_dict( coll=self, diff --git a/tofu/data/_class08_Diagnostic.py b/tofu/data/_class08_Diagnostic.py index 87e1d8fe2..05daaa917 100644 --- a/tofu/data/_class08_Diagnostic.py +++ b/tofu/data/_class08_Diagnostic.py @@ -13,10 +13,13 @@ from ._class07_Camera import Camera as Previous from . import _class8_check as _check from . import _class08_show as _show +from . import _class08_show_synth_sig as _show_synth_sig from . import _class8_compute as _compute from . import _class08_get_data as _get_data from . import _class08_concatenate_data as _concatenate from . import _class8_move as _move +from . import _class08_move_translate3d_by as _translate3d_by +from . import _class08_move_rotate3d_by as _rotate3d_by from . import _class8_los_data as _los_data from . import _class08_interpolate_along_los as _interpolate_along_los from . import _class8_equivalent_apertures as _equivalent_apertures @@ -35,11 +38,12 @@ from . import _class8_plot as _plot from . import _class8_plot_vos as _plot_vos from . import _class8_plot_coverage as _plot_coverage + # from . import _class08_save2stp as _save2stp from . import _class08_saveload_from_file as _saveload_from_file -__all__ = ['Diagnostic'] +__all__ = ["Diagnostic"] # ############################################################### @@ -51,6 +55,7 @@ class Diagnostic(Previous): _which_diagnostic = 'diagnostic' + _which_synth_sig = 'synth sig' def add_diagnostic( self, @@ -67,7 +72,7 @@ def add_diagnostic( reflections_type=None, key_nseg=None, # compute - compute=True, + compute: bool = True, add_points=None, convex=None, # spectro-only @@ -77,6 +82,54 @@ def add_diagnostic( verb=None, **kwdargs, ): + """Add a diagnostic. + + A diagnostic in this context is one or more similar instruments within the + tokamak. Diagnostics are made up of cameras (sensors, pixels) and apertures. + To add a diagnostic, the ``Collection`` must already have cameras + and apertures added. See the ``add_aperture``, ``add_camera_1d`` and + ``add_camera_2d`` functions. + + simply a dictionary which tells tofu: + + - Which cameras it should encompass + - Which apertures correspond to each camera and to each pixel + + This in turn allows tofu to compute the optical path for each pixel. + + Parameters + ---------- + key + The name of the diagnostic + doptics + Nested dictionary of the optical paths through the diagnostic. The keys for + this dictionary should be the names of the cameras in this diagnostic. Each + camera should have a nested dictionary as follows: + + ``` + "key_cam0': { # Name of the camera + 'optics': [ + # list of the nap0 keys of apertures associated to this cam + ] + 'paths': [ + # bool array indicating which pixel corresponds to each aperture. + ] + }, + ... + ``` + The "paths" key is an NxM boolean array, where N is the number of pixels + in the camera, and M is the number of apertures. For a simple pinhole camera + (`num_apertures=1`) with four sensors (`num_pixels=4`), the paths might be defined + as ``'paths': np.ones((4,1), dtype=bool)``. + + For a collimator camera with four apertures and four pixels, the paths key could be + defined as ``'paths': np.identity(dtype=bool)``. + config + a ``tofu.geom.Configuration()`` instance, containing the 2d poloidal + cross-section of a tokamak. Used for ray-tracing. + compute + Compute the etendue and LOS after adding the diagnostic. + """ # ----------- # adding diag @@ -94,9 +147,9 @@ def add_diagnostic( # --------------------- # adding etendue / los - key = list(dobj['diagnostic'].keys())[0] - dopt = dobj['diagnostic'][key]['doptics'] - computable = any([len(v0['optics']) > 0 for v0 in dopt.values()]) + key = list(dobj["diagnostic"].keys())[0] + dopt = dobj["diagnostic"][key]["doptics"] + computable = any([len(v0["optics"]) > 0 for v0 in dopt.values()]) if compute is True and computable: self.compute_diagnostic_etendue_los( key=key, @@ -120,7 +173,7 @@ def add_diagnostic( compute_vos_from_los=compute_vos_from_los, verb=verb, plot=False, - store='analytical', + store="analytical", ) # ----------------- @@ -141,14 +194,18 @@ def remove_diagnostic(self, key=None, key_cam=None): def _get_show_obj(self, which=None): if which == self._which_diagnostic: return _show._show + elif which == self._which_synth_sig: + return _show_synth_sig._show else: return super()._get_show_obj(which) def _get_show_details(self, which=None): if which == self._which_diagnostic: return _show._show_details + elif which == self._which_synth_sig: + return _show_synth_sig._show_details else: - super()._get_show_details(which) + return super()._get_show_details(which) # ----------------- # utilities @@ -179,7 +236,7 @@ def get_diagnostic_data( print_full_doc=None, **kwdargs, ): - """ Return dict of built-in data for chosen cameras + """Return dict of built-in data for chosen cameras data can be: 'etendue' @@ -217,10 +274,7 @@ def get_diagnostic_data_concatenated( key_cam=None, flat=None, ): - """ Return concatenated data for chosen cameras - - - """ + """Return concatenated data for chosen cameras""" return _concatenate.main( coll=self, key=key, @@ -264,9 +318,11 @@ def compute_diagnostic_etendue_los( plot=None, store=None, overwrite=None, + # debug debug=None, + debug_vos_from_los=None, ): - """ Compute the etendue of the diagnostic (per pixel) + """Compute the etendue of the diagnostic (per pixel) Etendue (m2.sr) can be computed analytically or numerically If plot, plot the comparison between all computations @@ -302,7 +358,7 @@ def compute_diagnostic_etendue_los( # compute los angles c0 = ( - any([np.any(np.isfinite(v0['los_x'])) for v0 in dcompute.values()]) + any([np.any(np.isfinite(v0["los_x"])) for v0 in dcompute.values()]) and store ) if c0: @@ -319,6 +375,8 @@ def compute_diagnostic_etendue_los( dcompute=dcompute, compute_vos_from_los=compute_vos_from_los, overwrite=overwrite, + # debug + debug_vos_from_los=debug_vos_from_los, ) if return_dcompute is True: @@ -342,9 +400,7 @@ def compute_diagnostic_sang_vect_from_pts( config=None, return_vect=None, ): - """ Return as dict of sang, vect, dV for any set of pts (full 3d) - - """ + """Return as dict of sang, vect, dV for any set of pts (full 3d)""" return _sang_vect.main( coll=self, # resources @@ -376,6 +432,9 @@ def plot_diagnostic_geometrical_coverage_slice( margin_perp=None, vect=None, segment=None, + # e0, e1 + transpose=None, + e0e1=None, # mesh slice key_mesh=None, phi=None, @@ -404,7 +463,7 @@ def plot_diagnostic_geometrical_coverage_slice( dvminmax=None, markersize=None, ): - """ Creates a plane perpendicular to los + """Creates a plane perpendicular to los compute contribution of each point to the signal return dout @@ -422,6 +481,9 @@ def plot_diagnostic_geometrical_coverage_slice( margin_perp=margin_perp, vect=vect, segment=segment, + # e0, e1 + transpose=transpose, + e0e1=e0e1, # mesh slice key_mesh=key_mesh, phi=phi, @@ -486,13 +548,10 @@ def compute_diagnostic_resolution( dvminmax=None, markersize=None, ): - """ Quantify the resolution of a slice or a full VOS - - """ + """Quantify the resolution of a slice or a full VOS""" return _resolution.main( - coll=self, - **{k0: v0 for k0, v0 in locals().items() if k0 != 'self'} + coll=self, **{k0: v0 for k0, v0 in locals().items() if k0 != "self"} ) # ----------------- @@ -577,7 +636,7 @@ def compute_diagnostic_vos( replace_poly=None, timing=None, ): - """ Compute the vos of the diagnostic (per pixel) + """Compute the vos of the diagnostic (per pixel) - poly_margin (0.3) fraction by which the los-estimated vos is widened -store: @@ -636,7 +695,7 @@ def check_diagnostic_vos_proj( logic=None, reduced=None, ): - """ Return a dict {proj: [kcam0, kcam1, ...]} + """Return a dict {proj: [kcam0, kcam1, ...]} Where proj is in ['cross', 'hor', '3d'] @@ -662,7 +721,7 @@ def check_diagnostic_dvos( key_cam=None, dvos=None, ): - """ Check dvos and return it if stored """ + """Check dvos and return it if stored""" return _vos._check_get_dvos( coll=self, key=key, @@ -676,7 +735,7 @@ def get_dvos_xyz( key_cam=None, dvos=None, ): - """ Return ptsx, ptsy, ptsz from 3d vos """ + """Return ptsx, ptsy, ptsz from 3d vos""" return _vos.get_dvos_xyz( coll=self, key_diag=key, @@ -693,7 +752,7 @@ def store_diagnostic_vos( overwrite=None, replace_poly=None, ): - """ Store a pre-computed dvos """ + """Store a pre-computed dvos""" _vos._store( coll=self, key_diag=key_diag, @@ -714,9 +773,7 @@ def get_diagnostic_vos_concatenate( vos_proj=None, return_vect=None, ): - """ Return a dict of vos, optionally aggregated - - """ + """Return a dict of vos, optionally aggregated""" return _vos_concatenate.main( coll=self, key_diag=key_diag, @@ -762,7 +819,7 @@ def compute_diagnostic_vos_nobin_at_lamb( pix1=None, tit=None, ): - """ Compute the image of a mono-wavelength plasma volume + """Compute the image of a mono-wavelength plasma volume Does ray-tracing from the whole plasma volume For a set of discrete user-defined wavelengths @@ -848,8 +905,7 @@ def get_diagnostic_equivalent_aperture( store=None, debug=None, ): - """ Get the equivalent projected aperture for each pixel - """ + """Get the equivalent projected aperture for each pixel""" return _equivalent_apertures.equivalent_apertures( coll=self, @@ -883,7 +939,7 @@ def get_diagnostic_lamb( rocking_curve=None, units=None, ): - """ Return the wavelength associated to + """Return the wavelength associated to - 'lamb' - 'lambmin' - 'lambmax' @@ -904,9 +960,7 @@ def get_diagnostic_lamb( # --------------- def get_optics_cls(self, optics=None): - """ Return list of optics and list of their classes - - """ + """Return list of optics and list of their classes""" return _check._get_optics_cls(coll=self, optics=optics) # def get_diagnostic_doptics(self, key=None): @@ -926,7 +980,7 @@ def get_optics_outline( ravel=None, total=None, ): - """ Return the optics outline """ + """Return the optics outline""" return _compute.get_optics_outline( coll=self, key=key, @@ -949,7 +1003,7 @@ def get_optics_poly( total=None, return_outline=None, ): - """ Return the optics outline """ + """Return the optics outline""" return _compute.get_optics_poly( coll=self, key=key, @@ -966,7 +1020,7 @@ def get_optics_as_input_solid_angle( self, keys=None, ): - """ Return the optics outline """ + """Return the optics outline""" return _compute.get_optics_as_input_solid_angle( coll=self, keys=keys, @@ -1010,7 +1064,6 @@ def move_diagnostic_to( margin_perp=None, verb=None, ): - if compute is None: compute = True @@ -1049,9 +1102,90 @@ def move_diagnostic_to( # bool verb=verb, plot=False, - store='analytical', + store="analytical", ) + def move_diagnostic_translate3d_by( + self, + key=None, + key_cam=None, + # new diag + key_new=None, + # move params + vect_xyz=None, + length=None, + # computing + compute=None, + strict=None, + # los + config=None, + key_nseg=None, + # equivalent aperture + add_points=None, + convex=None, + # etendue + margin_par=None, + margin_perp=None, + verb=None, + ): + """ Translates the desired cameras of diag 'key' + + Movement happens + - along the desired 3d unit vector 'vect_xyz' + - by desired 'length' + + optionally, vect_xyz and length can be dict (by camera) + + New diagnostic is created with name `key_new` + + """ + + return _translate3d_by.main( + coll=self, + **locals(), + ) + + def move_diagnostic_rotate3d_by( + self, + key=None, + key_cam=None, + # new diag + key_new=None, + # move params + axis_pt=None, + axis_vect=None, + angle=None, + # computing + compute=None, + strict=None, + # los + config=None, + key_nseg=None, + # equivalent aperture + add_points=None, + convex=None, + # etendue + margin_par=None, + margin_perp=None, + verb=None, + ): + """ Rotate the desired cameras of diag 'key' + + Movement happens + - around the 3d axis defined by (axis_pt, axis_vect) + - by desired 'angle' + + optionally, axis_pt, axis_vect and angle can be dict (by camera) + + New diagnostic is created with name `key_new` + + """ + + return _rotate3d_by.main( + coll=self, + **locals(), + ) + # ----------------- # computing # ----------------- @@ -1117,9 +1251,7 @@ def compute_diagnostic_signal( # return returnas=None, ): - """ Compute synthetic signal for a diagnostic and an emissivity field - - """ + """Compute synthetic signal for a diagnostic and an emissivity field""" return _compute_signal.compute_signal( coll=self, @@ -1188,7 +1320,7 @@ def get_raytracing_from_pts( elements=None, colorbar=None, ): - """ Get rays from plasma points to camera for a spectrometer diag """ + """Get rays from plasma points to camera for a spectrometer diag""" return _reverse_rt._from_pts( coll=self, @@ -1249,9 +1381,7 @@ def interpolate_along_los( dcolor=None, dax=None, ): - """ Compute and plot interpolated data along the los of the diagnostic - - """ + """Compute and plot interpolated data along the los of the diagnostic""" return _interpolate_along_los.main( coll=self, key_diag=key_diag, @@ -1295,7 +1425,6 @@ def compute_diagnostic_binned_data( # plotting plot=None, ): - return _signal_moments.binned( coll=self, key_diag=key_diag, @@ -1328,7 +1457,7 @@ def get_diagnostic_dplot( dx1=None, default=None, ): - """ Return a dict with all that's necessary for plotting + """Return a dict with all that's necessary for plotting If no optics is provided, all are returned @@ -1411,7 +1540,6 @@ def plot_diagnostic( dinc=None, connect=None, ): - return _plot._plot_diagnostic( coll=self, # keys @@ -1486,7 +1614,6 @@ def plot_diagnostic_vos( # interactivity color_dict=None, ): - return _plot_vos._plot_diagnostic_vos( coll=self, key=key, @@ -1552,7 +1679,7 @@ def plot_diagnostic_geometrical_coverage( cmap=None, dvminmax=None, ): - """ Plot the geometrical coverage of a diagnostic, in a cross-section + """Plot the geometrical coverage of a diagnostic, in a cross-section Parameters @@ -1622,7 +1749,7 @@ def save_diagnostic_to_file( pfe_save=None, overwrite=None, ): - """ Save desired diagnostic to a json or stp file + """Save desired diagnostic to a json or stp file Parameters ---------- @@ -1659,7 +1786,7 @@ def add_diagnostic_from_file( pfe=None, returnas=False, ): - """ Adds a diagnostic instance (and necessary optics) from json file + """Adds a diagnostic instance (and necessary optics) from json file Parameters ---------- diff --git a/tofu/data/_class08_move3d_check.py b/tofu/data/_class08_move3d_check.py new file mode 100644 index 000000000..f8b241b76 --- /dev/null +++ b/tofu/data/_class08_move3d_check.py @@ -0,0 +1,242 @@ + + +import numpy as np +import datastock as ds + + +from . import _class8_check + + +# ################################################## +# ################################################## +# Check +# ################################################## + + +def main( + coll=None, + key=None, + key_cam=None, + # new diag + key_new=None, + # move - translate + vect_xyz=None, + length=None, + # move - rotate + axis_pt=None, + axis_vect=None, + angle=None, + # move type + move=None, + # unused + **kwdargs, +): + + # -------------- + # move + # -------------- + + move = ds._generic_check._check_var( + move, 'move', + types=str, + allowed=['rotate', 'translate'], + ) + + # -------------- + # key, key_cam + # -------------- + + key, key_cam = _class8_check._get_default_cam( + coll=coll, + key=key, + key_cam=key_cam, + default='all', + ) + + # -------------- + # key_new + # -------------- + + wdiag = coll._which_diagnostic + lout = list(coll.dobj.get(wdiag, {}).keys()) + key_new = ds._generic_check._check_var( + key_new, 'key_new', + types=str, + default=f"{key}_translate", + excluded=lout, + ) + + out = (key, key_cam, key_new) + + # -------------- + # move params + # -------------- + + # -------------- + # translation + + if move == 'translate': + # length + length = _check_length_angle_vect( + din=length, + key_cam=key_cam, + dval=np.r_[0.], + name='length', + ) + + # vect_xyz + vect_xyz = _check_length_angle_vect( + din=vect_xyz, + key_cam=key_cam, + dval=np.r_[0., 0., 0.], + name='vect_xyz', + ) + + # update out + out = out + (length, vect_xyz) + + # -------------- + # rotation + + else: + # axis_pt + axis_pt = _check_length_angle_vect( + din=axis_pt, + key_cam=key_cam, + dval=np.r_[0., 0., 0.], + name='axis_pt', + ) + + # axis_vect + axis_vect = _check_length_angle_vect( + din=axis_vect, + key_cam=key_cam, + dval=np.r_[0., 0., 1.], + name='axis_vect', + ) + + # angle + angle = _check_length_angle_vect( + din=angle, + key_cam=key_cam, + dval=np.r_[0.], + name='angle', + ) + + # update out + out = out + (angle, axis_pt, axis_vect) + + return out + + +# ################################################## +# ################################################## +# subroutine +# ################################################## + + +def _check_length_angle_vect( + din=None, + key_cam=None, + dval=None, + name=None, +): + + # ----------- + # scalar + # ----------- + + size = dval.size + + if din is None: + din = dval + + if np.isscalar(din): + if not np.isfinite(din): + msg = "Arg din must be a finite scalar!\nProvided: {din}\n" + raise Exception(msg) + din = {kcam: np.full((size,), din) for kcam in key_cam} + + elif isinstance(din, (np.ndarray, list, tuple)): + if len(din) != size: + msg = ( + f"Arg '{name}' must be of size = {size}\n" + f"Provided: {din}\n" + ) + raise Exception(msg) + din = np.r_[din] + + # ----------- + # check dict + # ----------- + + c0 = ( + isinstance(din, dict) + and all([ + kk in key_cam + and ( + din[kk] is None + or ( + np.all(np.isfinite(din[kk])) + and np.r_[din[kk]].size == size + ) + ) + for kk in din.keys() + ]) + ) + if not c0: + msg = ( + f"Arg '{name}' must be a dict with:\n" + f"\t - keys in {key_cam}\n" + f"\t- values ({size},) np.ndarray" + ) + if size == 1: + msg += "(or scalar)" + msg += f"\nProvided: {din}\n" + raise Exception(msg) + + # ----------- + # fill dict + # ----------- + + for kcam in key_cam: + if din.get(kcam) is None: + din[kcam] = dval + + # scalar + if size == 1 and not np.isscalar(din[kcam]): + din[kcam] = din[kcam][0] + + return din + + +# ################################################## +# ################################################## +# add as-is +# ################################################## + + +def _add_asis( + coll=None, + dgeom0=None, + dgeom=None, + lk_asis=None, +): + + for kk in lk_asis: + if isinstance(kk, tuple): + for ii, ki in enumerate(kk): + k0 = ki.split('_')[0] + if dgeom0.get(k0) is not None: + dgeom[ki] = coll.ddata[dgeom0[k0][ii]]['data'] + + elif dgeom0.get(kk) is not None: + + if isinstance(dgeom0[kk], str): + dgeom[kk] = coll.ddata[kk]['data'] + + else: + if dgeom0.get(kk) is not None: + dgeom[kk] = dgeom0[kk] + + return diff --git a/tofu/data/_class08_move_rotate3d_by.py b/tofu/data/_class08_move_rotate3d_by.py new file mode 100644 index 000000000..dd765415f --- /dev/null +++ b/tofu/data/_class08_move_rotate3d_by.py @@ -0,0 +1,411 @@ + + +import numpy as np +import datastock as ds + + +from . import _class08_move3d_check as _check + + +# ################################################# +# ################################################# +# Main +# ################################################# + + +def main( + coll=None, + key=None, + key_cam=None, + # new diag + key_new=None, + # move params + axis_pt=None, + axis_vect=None, + angle=None, + # computing + compute=None, + strict=None, + # los + config=None, + key_nseg=None, + # equivalent aperture + add_points=None, + convex=None, + # etendue + margin_par=None, + margin_perp=None, + verb=None, + # unused + **kwdargs, +): + + # ---------- + # dinput + # ---------- + + ( + key, key_cam, key_new, + angle, axis_pt, axis_vect, + ) = _check.main(move='rotate', **locals()) + + # ---------- + # prepare + # ---------- + + wdiag = coll._which_diagnostic + doptics0 = coll.dobj[wdiag][key]['doptics'] + + # ---------- + # compute + # ---------- + + doptics = {} + for kcam in key_cam: + + # ------------ + # camera + + # translate + kcam_new = _rotate_camera( + coll=coll, + kcam=kcam, + axis_pt=axis_pt[kcam], + axis_vect=axis_vect[kcam], + angle=angle[kcam], + key_new=key_new, + ) + + # ------------ + # optics + + lop_new = [] + doptics[kcam_new] = {} + for kop in doptics0[kcam]['optics']: + + # translate + kop_new = _rotate_optics( + coll=coll, + kop=kop, + axis_pt=axis_pt[kcam], + axis_vect=axis_vect[kcam], + angle=angle[kcam], + key_new=key_new, + ) + lop_new.append(kop_new) + + # doptics + doptics[kcam_new]['optics'] = lop_new + doptics[kcam_new]['paths'] = doptics0[kcam]['paths'] + + # ------------------ + # add diagnostic + # ------------------ + + coll.add_diagnostic( + key=key_new, + doptics=doptics, + compute=compute, + strict=strict, + config=config, + key_nseg=key_nseg, + # equivalent aperture + add_points=add_points, + convex=convex, + # etendue + margin_par=margin_par, + margin_perp=margin_perp, + verb=verb, + ) + + return + + +# ########################################### +# ########################################### +# Translate optics +# ########################################### + + +def _rotate_optics( + coll=None, + kop=None, + axis_pt=None, + axis_vect=None, + angle=None, + key_new=None, +): + + # -------------- + # extract + # -------------- + + kop, opcls = coll.get_optics_cls(kop) + kop, opcls = kop[0], opcls[0] + dgeom0 = coll.dobj[opcls][kop]['dgeom'] + + # asis + lk_asis = [] + + # ----------- + # dgeom + # ----------- + + dgeom = {} + if dgeom0.get('cent') is not None: + dgeom['cent'] = np.r_[_rotate_pts( + axis_pt, + axis_vect, + angle, + *dgeom0['cent'], + )] + lk_asis.append(('outline_x0', 'outline_x1')) + + if dgeom0.get('poly_x') is not None: + dgeom['poly_x'], dgeom['poly_y'], dgeom['poly_z'] = _rotate_pts( + axis_pt, + axis_vect, + angle, + dgeom0['poly_x'], + dgeom0['poly_y'], + dgeom0['poly_z'], + ) + + # unit vects + for kk in ['nin', 'e0', 'e1']: + if dgeom0.get(kk) is not None: + dgeom[kk] = np.r_[_rotate_pts( + axis_pt, + axis_vect, + angle, + *dgeom0[kk], + isvect=True, + )] + + # ---------------- + # add as-is + # ---------------- + + _check._add_asis( + coll=coll, + dgeom0=dgeom0, + dgeom=dgeom, + lk_asis=lk_asis, + ) + + # ------------ + # key + # ------------ + + key = f'{kop}_{key_new}' + + # ------------ + # add to coll + # ------------ + + if opcls == 'aperture': + coll.add_aperture(key=key, **dgeom) + else: + getattr(coll, f"add_{opcls}")( + key=key, + dgeom=dgeom, + ) + + return key + + +# ############################################# +# ############################################# +# Translate camera +# ############################################# + + +def _rotate_camera( + coll=None, + kcam=None, + axis_pt=None, + axis_vect=None, + angle=None, + key_new=None, +): + + # -------------- + # extract + # -------------- + + wcam = coll._which_cam + dgeom0 = coll.dobj[wcam][kcam]['dgeom'] + + # asis + lk_asis = [ + ('outline_x0', 'outline_x1'), + ] + + # ----------- + # dgeom + # ----------- + + dgeom = {} + if dgeom0.get('cent') is not None: + dgeom['cent'] = np.r_[_rotate_pts( + axis_pt, + axis_vect, + angle, + *dgeom0['cent'], + )] + lk_asis += ['cents_x0', 'cents_x1'] + + if dgeom0.get('cents') is not None: + dgeom['cents_x'], dgeom['cents_y'], dgeom['cents_z'] = _rotate_pts( + axis_pt, + axis_vect, + angle, + coll.ddata[dgeom0['cents'][0]]['data'], + coll.ddata[dgeom0['cents'][1]]['data'], + coll.ddata[dgeom0['cents'][2]]['data'], + ) + + # unit vects + lk_vect = ['nin', 'e0', 'e1'] + for kk in lk_vect: + if dgeom0.get(kk) is not None: + dgeom[kk] = np.r_[_rotate_pts( + axis_pt, + axis_vect, + angle, + *dgeom0[kk], + isvect=True, + )] + + if dgeom0.get(f"{kk}_x") is not None: + kx, ky, kz = f"{kk}_x", f"{kk}_y", f"{kk}_z" + dgeom[kx], dgeom[ky], dgeom[kz] = _rotate_pts( + axis_pt, + axis_vect, + angle, + dgeom0[kx], + dgeom0[ky], + dgeom0[kz], + isvect=True, + ) + + # ---------------- + # add as-is + # ---------------- + + _check._add_asis( + coll=coll, + dgeom0=dgeom0, + dgeom=dgeom, + lk_asis=lk_asis, + ) + + # ------------ + # key + # ------------ + + key = f'{kcam}_{key_new}' + + # ------------ + # add to coll + # ------------ + + if dgeom0['nd'] == '1d': + coll.add_camera_1d( + key=key, + dgeom=dgeom, + ) + else: + coll.add_camera_2d( + key=key, + dgeom=dgeom, + ) + + return key + + +# ############################################# +# ############################################# +# Rotate pts +# ############################################# + + +def _rotate_pts(axis_pt, axis_vect, angle, xx, yy, zz, isvect=None): + + # -------- + # isvect + # -------- + + isvect = ds._generic_check._check_var( + isvect, 'isvect', + types=bool, + default=False, + ) + + # -------- + # local unit vects + # -------- + + axis_vect = axis_vect / np.linalg.norm(axis_vect) + + if np.abs(axis_vect[2]) > 0.90: + ecross = np.r_[1, 0, 0] + else: + ecross = np.r_[0, 0, 1] + e0 = np.cross(axis_vect, ecross) + + e1 = np.cross(axis_vect, e0) + e1 = e1 / np.linalg.norm(e1) + + # -------- + # local coords + # -------- + + if isvect is True: + cent0 = np.r_[0, 0, 0] + else: + cent0 = axis_pt + + # axis + axial = ( + (xx - cent0[0]) * axis_vect[0] + + (yy - cent0[1]) * axis_vect[1] + + (zz - cent0[2]) * axis_vect[2] + ) + + # x0 + x0 = ( + (xx - cent0[0]) * e0[0] + + (yy - cent0[1]) * e0[1] + + (zz - cent0[2]) * e0[2] + ) + + # x1 + x1 = ( + (xx - cent0[0]) * e1[0] + + (yy - cent0[1]) * e1[1] + + (zz - cent0[2]) * e1[2] + ) + + rr = np.hypot(x0, x1) + theta = np.arctan2(x1, x0) + + # -------- + # rotate + # -------- + + x02 = rr * np.cos(theta + angle) + x12 = rr * np.sin(theta + angle) + + # -------- + # pts new + # -------- + + xx_new = cent0[0] + axial * axis_vect[0] + x02 * e0[0] + x12 * e1[0] + yy_new = cent0[1] + axial * axis_vect[1] + x02 * e0[1] + x12 * e1[1] + zz_new = cent0[2] + axial * axis_vect[2] + x02 * e0[2] + x12 * e1[2] + + if isvect is True: + assert np.allclose(np.sqrt(xx_new**2 + yy_new**2 + zz_new**2), 1.) + + return xx_new, yy_new, zz_new diff --git a/tofu/data/_class08_move_translate3d_by.py b/tofu/data/_class08_move_translate3d_by.py new file mode 100644 index 000000000..ef74a5767 --- /dev/null +++ b/tofu/data/_class08_move_translate3d_by.py @@ -0,0 +1,269 @@ + + +from . import _class08_move3d_check as _check + + +# ########################################### +# ########################################### +# Main +# ########################################### + + +def main( + coll=None, + key=None, + key_cam=None, + # new diag + key_new=None, + # move params + vect_xyz=None, + length=None, + # computing + compute=None, + strict=None, + # los + config=None, + key_nseg=None, + # equivalent aperture + add_points=None, + convex=None, + # etendue + margin_par=None, + margin_perp=None, + verb=None, + # unused + **kwdargs, +): + + # ---------- + # dinput + # ---------- + + ( + key, key_cam, key_new, + length, vect_xyz, + ) = _check.main(move='translate', **locals()) + + # ---------- + # prepare + # ---------- + + wdiag = coll._which_diagnostic + doptics0 = coll.dobj[wdiag][key]['doptics'] + + # ---------- + # compute + # ---------- + + doptics = {} + for kcam in key_cam: + + # ------------ + # camera + + # translate + kcam_new = _translate_camera( + coll=coll, + kcam=kcam, + length=length[kcam], + vect_xyz=vect_xyz[kcam], + key_new=key_new, + ) + + # ------------ + # optics + + lop_new = [] + doptics[kcam_new] = {} + for kop in doptics0[kcam]['optics']: + + # translate + kop_new = _translate_optics( + coll=coll, + kop=kop, + length=length[kcam], + vect_xyz=vect_xyz[kcam], + key_new=key_new, + ) + lop_new.append(kop_new) + + # doptics + doptics[kcam_new]['optics'] = lop_new + doptics[kcam_new]['paths'] = doptics0[kcam]['paths'] + + # ------------------ + # add diagnostic + # ------------------ + + coll.add_diagnostic( + key=key_new, + doptics=doptics, + compute=compute, + strict=strict, + config=config, + key_nseg=key_nseg, + # equivalent aperture + add_points=add_points, + convex=convex, + # etendue + margin_par=margin_par, + margin_perp=margin_perp, + verb=verb, + ) + + return + + +# ########################################### +# ########################################### +# Translate optics +# ########################################### + + +def _translate_optics( + coll=None, + kop=None, + length=None, + vect_xyz=None, + key_new=None, +): + + # -------------- + # extract + # -------------- + + kop, opcls = coll.get_optics_cls(kop) + kop, opcls = kop[0], opcls[0] + dgeom0 = coll.dobj[opcls][kop]['dgeom'] + + # asis + lk_asis = [ + 'nin', 'e0', 'e1', + ] + + # ----------- + # dgeom + # ----------- + + dgeom = {} + if dgeom0.get('cent') is not None: + dgeom['cent'] = dgeom0['cent'] + length * vect_xyz + lk_asis.append(('outline_x0', 'outline_x1')) + + if dgeom0.get('poly_x') is not None: + for ii, kk in enumerate(['poly_x', 'poly_y', 'poly_z']): + dgeom[kk] = ( + dgeom0[kk] + length * vect_xyz[ii] + ) + + # ---------------- + # add as-is + # ---------------- + + _check._add_asis( + coll=coll, + dgeom0=dgeom0, + dgeom=dgeom, + lk_asis=lk_asis, + ) + + # ------------ + # key + # ------------ + + key = f'{kop}_{key_new}' + + # ------------ + # add to coll + # ------------ + + if opcls == 'aperture': + coll.add_aperture(key=key, **dgeom) + else: + getattr(coll, f"add_{opcls}")( + key=key, + dgeom=dgeom, + ) + + return key + + +# ############################################# +# ############################################# +# Translate camera +# ############################################# + + +def _translate_camera( + coll=None, + kcam=None, + length=None, + vect_xyz=None, + key_new=None, +): + + # -------------- + # extract + # -------------- + + wcam = coll._which_cam + dgeom0 = coll.dobj[wcam][kcam]['dgeom'] + + # asis + lk_asis = [ + 'nin', 'e0', 'e1', + 'nin_x', 'nin_y', 'nin_z', + 'e0_x', 'e0_y', 'e0_z', + 'e1_x', 'e1_y', 'e1_z', + ('outline_x0', 'outline_x1'), + ] + + # ----------- + # dgeom + # ----------- + + dgeom = {} + if dgeom0.get('cent') is not None: + dgeom['cent'] = dgeom0['cent'] + length * vect_xyz + lk_asis += ['cents_x0', 'cents_x1'] + + if dgeom0.get('cents') is not None: + for ik, kk in enumerate(['cents_x', 'cents_y', 'cents_z']): + dgeom[kk] = ( + coll.ddata[dgeom0['cents'][ik]]['data'] + + length * vect_xyz[ik] + ) + + # ---------------- + # add as-is + # ---------------- + + _check._add_asis( + coll=coll, + dgeom0=dgeom0, + dgeom=dgeom, + lk_asis=lk_asis, + ) + + # ------------ + # key + # ------------ + + key = f'{kcam}_{key_new}' + + # ------------ + # add to coll + # ------------ + + if dgeom0['nd'] == '1d': + coll.add_camera_1d( + key=key, + dgeom=dgeom, + ) + else: + coll.add_camera_2d( + key=key, + dgeom=dgeom, + ) + + return key diff --git a/tofu/data/_class08_show.py b/tofu/data/_class08_show.py index eee1e9427..6eab6cf49 100644 --- a/tofu/data/_class08_show.py +++ b/tofu/data/_class08_show.py @@ -121,12 +121,17 @@ def _show_details(coll=None, key=None, lcol=None, lar=None, show=None): wdiag = coll._which_diagnostic lcam = coll.dobj[wdiag][key][wcam] doptics = coll.dobj[wdiag][key]['doptics'] + dproj = coll.check_diagnostic_vos_proj() + lproj = ['cross', 'hor', '3d'] # --------------------------- # column names # --------------------------- - lcol.append([wcam, '2d', 'pinhole', 'optics', 'los', 'vos']) + lcol.append([ + wcam, '2d', 'pinhole', 'optics', + 'los', 'vos_proj', 'vos_resRZPhi', + ]) # --------------------------- # data @@ -164,8 +169,19 @@ def _show_details(coll=None, key=None, lcol=None, lar=None, show=None): nn = din['los'] arr.append(nn) - # vos - nn = '' + # vos_proj + nn = ', '.join([pp for pp in lproj if kcam in dproj[pp]]) + arr.append(nn) + + # vos_res + if doptics[kcam].get('dvos', {}).get('keym') is None: + nn = '' + else: + nn = ( + doptics[kcam]['dvos']['res_RZ'] + + [doptics[kcam]['dvos']['res_phi']] + ) + nn = str(tuple(nn)) arr.append(nn) # aggregate diff --git a/tofu/data/_class08_show_synth_sig.py b/tofu/data/_class08_show_synth_sig.py new file mode 100644 index 000000000..89042c4f3 --- /dev/null +++ b/tofu/data/_class08_show_synth_sig.py @@ -0,0 +1,129 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Jul 24 09:36:24 2024 + +@author: dvezinet +""" + + +############################################# +############################################# +# DEFAULTS +############################################# + + +_LORDER = [ + 'camera', 'data', 'diag', + 'geom_matrix', 'integrand', + 'method', 'res', +] + + +############################################# +############################################# +# Show +############################################# + + +def _show(coll=None, which=None, lcol=None, lar=None, show=None): + + # --------------------------- + # column names + # --------------------------- + + wsynth = coll._which_synth_sig + lcol.append([which] + _LORDER) + + # --------------------------- + # list of keys + # --------------------------- + + lkey = [ + k1 for k1 in coll._dobj.get(which, {}).keys() + if show is None or k1 in show + ] + + # --------------------------- + # loop on keys + # --------------------------- + + lar0 = [] + for k0 in lkey: + + # initialize with key + arr = [k0] + + # dsynth + dsynth = coll.dobj[wsynth][k0] + + # loop + for k1 in _LORDER: + + # cameras, data + if k1 in ['camera', 'data']: + if dsynth.get(k1) is None: + nn = '' + elif len(dsynth[k1]) <= 3: + nn = str(dsynth[k1]) + else: + nn = f'[{dsynth[k1][0]}, ..., {dsynth[k1][-1]}]' + + # los + else: + nn = str(dsynth[k1]) + + arr.append(nn) + + lar0.append(arr) + + lar.append(lar0) + + return lcol, lar + + +############################################# +############################################# +# Show single diag +############################################# + + +def _show_details(coll=None, key=None, lcol=None, lar=None, show=None): + + # --------------------------- + # get basics + # --------------------------- + + wcam = coll._which_cam + wsynth = coll._which_synth_sig + dsynth = coll.dobj[wsynth][key] + + # --------------------------- + # column names + # --------------------------- + + lcol.append([wcam, 'shape', 'sig', 'shape'] + _LORDER[2:]) + + # --------------------------- + # data + # --------------------------- + + lar0 = [] + for ii, kcam in enumerate(dsynth[wcam]): + + # camera + arr = [kcam, str(coll.dobj[wcam][kcam]['dgeom']['shape'])] + + # data + kdata = dsynth['data'][ii] + arr += [kdata, str(coll.ddata[kdata]['data'].shape)] + + for k1 in _LORDER[2:]: + nn = str(dsynth[k1]) + arr.append(nn) + + # aggregate + lar0.append(arr) + + lar.append(lar0) + + return lcol, lar diff --git a/tofu/data/_class09_GeometryMatrix.py b/tofu/data/_class09_GeometryMatrix.py index baef754d7..ebd4553a9 100644 --- a/tofu/data/_class09_GeometryMatrix.py +++ b/tofu/data/_class09_GeometryMatrix.py @@ -83,7 +83,7 @@ def _get_show_details(self, which=None): if which in [self._which_gmat, self._which_gmat.replace('_', ' ')]: return _show._show_details else: - super()._get_show_details(which) + return super()._get_show_details(which) # ----------------- # get concatenated geometry matrix diff --git a/tofu/data/_class10_Inversion.py b/tofu/data/_class10_Inversion.py index 6a6d7a349..0fb438ac3 100644 --- a/tofu/data/_class10_Inversion.py +++ b/tofu/data/_class10_Inversion.py @@ -3,11 +3,12 @@ # tofu from ._class09_GeometryMatrix import GeometryMatrix as Previous +from . import _class10_show as _show from . import _class10_compute as _compute from . import _class10_plot as _plot -__all__ = ['Inversion'] +__all__ = ["Inversion"] # ############################################################################# @@ -17,14 +18,29 @@ class Inversion(Previous): + """ + The ``Inversion`` class is commonly imported and aliased as the + ``tf.data.Collection`` class. The class constructor takes no arguments; + instead, objects, stored in ``coll.dobj``, are added using methods: - _show_in_summary = 'all' + - ``coll.add_aperture('key', **geom)`` + - ``coll.add_camera_1d('key', dgeom=dgeom)`` + - ``coll.add_camera_2d('key', dgeom=dgeom)`` - _dshow = dict(Previous._dshow) - _dshow.update({ - 'inversion': [ - ], - }) + In addition to ``dobj`, The ``Collection`` stores 2 other main attributes: + + coll.dref -> dict (TODO) + coll.ddata -> dict (TODO) + + Once all the apertures and all cameras have been added to the Collection + instance, one then adds a new object called a diagnostic: + + ``coll.add_diagnostic('key', doptics=doptics, config=config, compute=True)`` + + The diagnostic should automatically compute LOS and etendue. + """ + + _which_inversion = 'inversions' # ----------------- # inversions @@ -64,9 +80,7 @@ def add_inversion( # debug debug=None, ): - """ Compute tomographic inversion - - """ + """Compute tomographic inversion""" return _compute.compute_inversions( # ressources @@ -106,6 +120,22 @@ def add_inversion( debug=debug, ) + # ------------------- + # show + # ------------------- + + def _get_show_obj(self, which=None): + if which == self._which_inversion: + return _show._show + else: + return super()._get_show_obj(which) + + def _get_show_details(self, which=None): + if which == self._which_inversion: + return _show._show_details + else: + return super()._get_show_details(which) + # ----------------- # synthetic data # ----------------- @@ -122,7 +152,7 @@ def add_retrofit_data( ref_vector_strategy=None, store=None, ): - """ Compute synthetic data using matching geometry matrix and profile2d + """Compute synthetic data using matching geometry matrix and profile2d Requires that a geometry matrix as been pre-computed Only profile2d with the same bsplines as the geometry matrix can be @@ -167,7 +197,6 @@ def plot_inversion( dcolorbar=None, dleg=None, ): - return _plot.plot_inversion( coll=self, key=key, diff --git a/tofu/data/_class10_checks.py b/tofu/data/_class10_checks.py index 58739e6c0..c8f3b71e0 100644 --- a/tofu/data/_class10_checks.py +++ b/tofu/data/_class10_checks.py @@ -120,8 +120,9 @@ def _compute_check( ) # key_inv + winv = coll._which_inversion key = ds._generic_check._obj_key( - d0=coll.dobj.get('inversions', {}), + d0=coll.dobj.get(winv, {}), short='inv', key=key, ) diff --git a/tofu/data/_class10_compute.py b/tofu/data/_class10_compute.py index 6b04addb8..e575f5fc6 100644 --- a/tofu/data/_class10_compute.py +++ b/tofu/data/_class10_compute.py @@ -584,8 +584,9 @@ def _store( kretro = f'{keyinv}_retro' # add inversion + winv = coll._which_inversion dobj = { - 'inversions': { + winv: { keyinv: { 'retrofit': kretro, 'data_in': key_data, @@ -606,12 +607,19 @@ def _store( # adjust for time if notime is True: - dobj['inversions'][keyinv].update({ + dobj[winv][keyinv].update({ 'chi2n': chi2n, 'mu': mu, 'reg': regularity, 'niter': niter, }) + else: + dobj[winv][keyinv].update({ + 'chi2n': f"{keyinv}_chi2n", + 'mu': f"{keyinv}_mu", + 'reg': f"{keyinv}_regularity", + 'niter': f"{keyinv}_niter", + }) # update instance coll.update(dobj=dobj, dref=dref, ddata=ddata) diff --git a/tofu/data/_class10_plot.py b/tofu/data/_class10_plot.py index 8af94637d..fa2203f90 100644 --- a/tofu/data/_class10_plot.py +++ b/tofu/data/_class10_plot.py @@ -44,11 +44,8 @@ def _plot_inversion_check( ): # key - if 'inversions' not in coll.dobj.keys(): - msg = 'No inversions available!' - raise Exception(msg) - - lk = list(coll.dobj['inversions'].keys()) + winv = coll._which_inversion + lk = list(coll.dobj[winv].keys()) keyinv = ds._generic_check._check_var( key, 'key', default=None, @@ -59,9 +56,9 @@ def _plot_inversion_check( wm = coll._which_mesh wbs = coll._which_bsplines wgmat = coll._which_gmat - keymat = coll.dobj['inversions'][keyinv]['matrix'] - key_data = coll.dobj['inversions'][keyinv]['data_in'] - key_retro = coll.dobj['inversions'][keyinv]['retrofit'] + keymat = coll.dobj[winv][keyinv]['matrix'] + key_data = coll.dobj[winv][keyinv]['data_in'] + key_retro = coll.dobj[winv][keyinv]['retrofit'] keybs = coll.dobj[wgmat][keymat]['bsplines'] key_diag = coll.dobj[wgmat][keymat]['diagnostic'] is2d = coll.dobj['diagnostic'][key_diag]['is2d'] @@ -346,10 +343,10 @@ def _plot_inversion_prepare( reg = coll.ddata[f'{keyinv}_reg']['data'] niter = coll.ddata[f'{keyinv}_niter']['data'] else: - chi2n = None # coll.dobj['inversions'][keyinv]['chi2n'] - mu = None # coll.dobj['inversions'][keyinv]['mu'] - reg = None # coll.dobj['inversions'][keyinv]['reg'] - niter = None # coll.dobj['inversions'][keyinv]['niter'] + chi2n = None # coll.dobj[winv][keyinv]['chi2n'] + mu = None # coll.dobj[winv][keyinv]['mu'] + reg = None # coll.dobj[winv][keyinv]['reg'] + niter = None # coll.dobj[winv][keyinv]['niter'] return ( dlos_n, dref_los, diff --git a/tofu/data/_class10_show.py b/tofu/data/_class10_show.py new file mode 100644 index 000000000..c835eb56a --- /dev/null +++ b/tofu/data/_class10_show.py @@ -0,0 +1,163 @@ +# -*- coding: utf-8 -*- +""" +Created on Wed Jul 24 09:36:24 2024 + +@author: dvezinet +""" + + +import numpy as np + + +############################################# +############################################# +# DEFAULTS +############################################# + + +_LORDER = [ + 'algo', 'chain', 'conv_crit', + 'data_in', + 'geometry', + 'isotropic', ' matrix', + 'operator', 'positive', + 'retrofit', 'sigma_in', 'sol', 'solver', +] + + +############################################# +############################################# +# Show +############################################# + + +def _show(coll=None, which=None, lcol=None, lar=None, show=None): + + # --------------------------- + # column names + # --------------------------- + + lcol.append([which] + _LORDER) + + # --------------------------- + # data + # --------------------------- + + lkey = [ + k1 for k1 in coll._dobj.get(which, {}).keys() + if show is None or k1 in show + ] + + lar0 = [] + for k0 in lkey: + + # initialize with key + arr = [k0] + + # add nb of func of each type + dinv = coll.dobj[which][k0] + + # loop + for k1 in _LORDER: + + # data_in + if k1 in ['data_in']: + if dinv.get(k1) is None: + nn = '' + elif len(dinv[k1]) <= 3: + nn = str(dinv[k1]) + else: + nn = f'[{dinv[k1][0]}, ..., {dinv[k1][-1]}]' + + # los + else: + nn = str(dinv.get(k1)) + + arr.append(nn) + + lar0.append(arr) + + lar.append(lar0) + + return lcol, lar + + +############################################# +############################################# +# Show single diag +############################################# + + +def _show_details(coll=None, key=None, lcol=None, lar=None, show=None): + + # --------------------------- + # get basics + # --------------------------- + + winv = coll._which_inversion + ldata_in = coll.dobj[winv][key]['data_in'] + + wgmat = coll._which_gmat + key_matrix = coll.dobj[winv][key]['matrix'] + key_cam = coll.dobj[wgmat][key_matrix]['camera'] + wcam = coll._which_cam + + sigma = coll.dobj[winv][key]['sigma_in'] + + # cam-specific fit chi2n + # TODO: revize inv storing to store normalized err per channel + + # --------------------------- + # column names + # --------------------------- + + lcol.append([ + 'camera', + 'shape', + 'data_in', + 'shape', + 'sol', + 'retrofit', + '< delta / sigma >', + ]) + + # --------------------------- + # data + # --------------------------- + + lar0 = [] + for ii, kdata in enumerate(ldata_in): + + # camera + kcam = key_cam[ii] + arr = [kcam, str(coll.dobj[wcam][kcam]['dgeom']['shape'])] + + # data_in + arr += [kdata, str(coll.ddata[kdata]['data'].shape)] + + # sol + arr.append(coll.dobj[winv][key]['sol']) + + # retrofit + kretro = f"{coll.dobj[winv][key]['retrofit']}_{key_cam[ii]}" + arr.append(kretro) + + # delta / sigma + data = coll.ddata[kdata]['data'] + sig = coll.ddata[kretro]['data'] + delta = sig - data + if sigma is None: + sigma = 1. + elif isinstance(sigma, str): + sigma = coll.ddata[sigma]['data'] + elif np.isscalar(sigma): + pass + nn = f"{np.nanmean(delta / sigma): 1.3e}" + arr.append(nn) + + # aggregate + lar0.append(arr) + + lar.append(lar0) + + return lcol, lar diff --git a/tofu/data/_class2_plot.py b/tofu/data/_class2_plot.py index f01a021bf..c4d9e9b63 100644 --- a/tofu/data/_class2_plot.py +++ b/tofu/data/_class2_plot.py @@ -21,7 +21,19 @@ # ############################################################### -_LCOLORS = ['r', 'g', 'b', 'm', 'c', 'y'] +# _LCOLORS = ['r', 'g', 'b', 'm', 'y', 'c'] +_LCOLORS = [ + 'tab:blue', + 'tab:orange', + 'tab:green', + 'tab:red', + 'tab:purple', + 'tab:brown', + 'tab:pink', + 'tab:gray', + 'tab:olive', + 'tab:cyan', +] _COLOR = 'k' @@ -288,7 +300,10 @@ def _plot_rays_check( # color_dict if color_dict is None: - color_dict = {k0: _LCOLORS[ii] for ii, k0 in enumerate(key)} + color_dict = { + k0: _LCOLORS[ii % len(_LCOLORS)] + for ii, k0 in enumerate(key) + } elif mcolors.is_color_like(color_dict): color_dict = {k0: color_dict for k0 in key} diff --git a/tofu/data/_class3_check.py b/tofu/data/_class3_check.py index c5078550c..0f2aa2ef2 100644 --- a/tofu/data/_class3_check.py +++ b/tofu/data/_class3_check.py @@ -281,4 +281,4 @@ def _return_as_dict( 'e1': ap.get('e1'), } - return dout \ No newline at end of file + return dout diff --git a/tofu/data/_class5_coordinates.py b/tofu/data/_class5_coordinates.py index 043b2376a..5de9b8eef 100644 --- a/tofu/data/_class5_coordinates.py +++ b/tofu/data/_class5_coordinates.py @@ -58,6 +58,28 @@ def x01toxyz( cent[2] + x0*e0[2] + x1*e1[2], ) + # ------------------- + # 3D + # ------------------- + + elif dgeom['type'] == '3d': + + def x01toxyz( + x0=None, + x1=None, + # surface + cent=dgeom['cent'], + e0=dgeom['e0'], + e1=dgeom['e1'], + ): + """ Coordinate transform """ + + return ( + cent[0] + x0*e0[0] + x1*e1[0], + cent[1] + x0*e0[1] + x1*e1[1], + cent[2] + x0*e0[2] + x1*e1[2], + ) + # ---------------- # Cylindrical # ---------------- @@ -149,4 +171,8 @@ def x01toxyz( raise NotImplementedError() + else: + + raise NotImplementedError(dgeom['type']) + return x01toxyz diff --git a/tofu/data/_class5_reflections_ptsvect.py b/tofu/data/_class5_reflections_ptsvect.py index 423e8f3de..db17cc766 100644 --- a/tofu/data/_class5_reflections_ptsvect.py +++ b/tofu/data/_class5_reflections_ptsvect.py @@ -79,6 +79,33 @@ def _get_ptsvect( isnorm=isnorm, ) + # ------------------- + # 3D - project 3d polygon on 2d plane (seen from point) + # ------------------- + + elif dgeom['type'] == '3d': + + if fast is True: + ptsvect = _get_ptsvect_plane_x01_fast( + plane_cent=dgeom['cent'], + plane_nin=dgeom['nin'], + plane_e0=dgeom['e0'], + plane_e1=dgeom['e1'], + ) + + else: + ptsvect = _get_ptsvect_plane( + plane_cent=dgeom['cent'], + plane_nin=dgeom['nin'], + plane_e0=dgeom['e0'], + plane_e1=dgeom['e1'], + # limits + x0max=None, + x1max=None, + # isnorm + isnorm=isnorm, + ) + # ---------------- # Cylindrical # ---------------- @@ -191,7 +218,6 @@ def ptsvect( noy = rcs * noy / nn noz = rcs * noz / nn - # ODzx = (Dy[iok] - O[1])*eax[2] - (Dz[iok] - O[2])*eax[1] # ODzy = (Dz[iok] - O[2])*eax[0] - (Dx[iok] - O[0])*eax[2] # ODzz = (Dx[iok] - O[0])*eax[1] - (Dy[iok] - O[1])*eax[0] @@ -224,7 +250,7 @@ def ptsvect( # x0, x1 if strict is True or return_x01 is True: - theta[iok] = rcs * np.arctan2( + theta[iok] = rcs * np.arctan2( nox*erot[0] + noy*erot[1] + noz*erot[2], -nox*nin[0] - noy*nin[1] - noz*nin[2], ) @@ -414,6 +440,10 @@ def ptsvect( raise NotImplementedError() + else: + + raise NotImplementedError(dgeom['type']) + return ptsvect @@ -451,7 +481,7 @@ def ptsvect( # limits x0max=x0max, x1max=x1max, - #isnorm + # isnorm isnorm=isnorm, # return strict=None, diff --git a/tofu/data/_class8_check.py b/tofu/data/_class8_check.py index 4cf4d77a1..3dd9c7d23 100644 --- a/tofu/data/_class8_check.py +++ b/tofu/data/_class8_check.py @@ -348,7 +348,7 @@ def _check_doptics_basics( if doptics[k0]['paths'] is not None: - pinhole = np.all(doptics[k0]['paths']) + pinhole = bool(np.all(doptics[k0]['paths'])) if pinhole is True: doptics[k0]['paths'] = None @@ -360,6 +360,22 @@ def _check_doptics_basics( optics=doptics[k0]['optics'], )[1] + # ---------------- + # pinhole + 3d => reshuffle + + if pinhole is True and not any([cc == 'cryst' for cc in lcls]): + is3d = [ + coll.dobj[ocls][kop]['dgeom']['type'] == '3d' + for ocls, kop in zip(lcls, doptics[k0]['optics']) + ] + if len(is3d) > 0 and is3d[-1] is True and is3d[0] is False: + doptics[k0]['optics'] = ( + [doptics[k0]['optics'][-1]] + + doptics[k0]['optics'][1:-1] + + [doptics[k0]['optics'][0]] + ) + lcls = [lcls[-1]] + lcls[1:-1] + [lcls[0]] + # --------------------- # populate doptics2 @@ -367,7 +383,7 @@ def _check_doptics_basics( 'camera': k0, 'optics': doptics[k0]['optics'], 'cls': lcls, - 'pinhole': bool(pinhole), + 'pinhole': pinhole, 'paths': doptics[k0]['paths'], 'los': None, 'etendue': None, @@ -978,4 +994,4 @@ def _remove( # remove diag if len(key_cam) == len(doptics): - del coll._dobj['diagnostic'][key] \ No newline at end of file + del coll._dobj['diagnostic'][key] diff --git a/tofu/data/_class8_compute.py b/tofu/data/_class8_compute.py index b21118067..e5ebeecfd 100644 --- a/tofu/data/_class8_compute.py +++ b/tofu/data/_class8_compute.py @@ -54,7 +54,7 @@ def get_optics_outline( if dgeom['type'] == '3d': msg = ( - "Approximate outline for {cls} '{key}' due to 3d polygon!" + f"Approximate outline for {cls} '{key}' due to 3d polygon!" ) warnings.warn(msg) @@ -69,6 +69,7 @@ def get_optics_outline( p0 = (px - cx) * e0[0] + (py - cy) * e0[1] + (pz - cz) * e0[2] p1 = (px - cx) * e1[0] + (py - cy) * e1[1] + (pz - cz) * e1[2] + lp = [p0, p1] if cls == 'camera' and total: # get centers @@ -101,11 +102,13 @@ def get_optics_outline( cx1[0] - dx1, cx1[0] - dx1, cx1[-1] + dx1, cx1[-1] + dx1, ] + lp = [p0, p1] - else: + elif dgeom.get('outline') is not None: out = dgeom['outline'] p0 = coll.ddata[out[0]]['data'] p1 = coll.ddata[out[1]]['data'] + lp = [p0, p1] # ----------- # add_points @@ -120,7 +123,7 @@ def get_optics_outline( add_points = 3 return _interp_poly( - lp=[p0, p1], + lp=lp, add_points=add_points, mode=mode, isclosed=False, @@ -196,6 +199,7 @@ def get_optics_poly( ) else: + p0, p1 = None, None px, py, pz = dgeom['poly'] px = coll.ddata[px]['data'] py = coll.ddata[py]['data'] @@ -865,8 +869,6 @@ def _dplot( ) dplot[k0]['o'] = { - 'x0': p0 + dx0, - 'x1': p1 + dx1, 'x': px, 'y': py, 'z': pz, @@ -878,6 +880,12 @@ def _dplot( }, } + if p0 is not None: + dplot[k0]['o'].update({ + 'x0': p0 + dx0, + 'x1': p1 + dx1, + }) + # center if 'c' in elements: @@ -1144,4 +1152,4 @@ def get_lamb_from_angle( elif lamb == 'res': data = lv[0] / np.abs(lv[2] - lv[1]) - return data, ref \ No newline at end of file + return data, ref diff --git a/tofu/data/_class8_equivalent_apertures.py b/tofu/data/_class8_equivalent_apertures.py index acb556882..912a23454 100644 --- a/tofu/data/_class8_equivalent_apertures.py +++ b/tofu/data/_class8_equivalent_apertures.py @@ -179,8 +179,14 @@ def equivalent_apertures( # add pts to initial polygon only if curved if spectro: - assert pinhole is True, "How to handle spectr with pinhole = False here ?" - rcurv = np.r_[coll.dobj[optics_cls[iref]][optics[iref]]['dgeom']['curve_r']] + + if pinhole is not True: + msg = "How to handle spectro with pinhole = False here ?" + raise Exception(msg) + + rcurv = np.r_[ + coll.dobj[optics_cls[iref]][optics[iref]]['dgeom']['curve_r'] + ] ind = ~np.isinf(rcurv) if np.any(rcurv[ind] > 0): addp0 = add_points @@ -266,6 +272,8 @@ def equivalent_apertures( ii=ii, ij=ij, debug=debug, + key=key, + key_cam=key_cam, # timing # dt=dt, ) @@ -573,7 +581,7 @@ def _get_centroid(p0, p1, cent, debug=None): # -------------- # debug - if debug: + if debug is True: indclose = np.r_[np.arange(p0.size), 0] plt.figure() @@ -856,11 +864,12 @@ def _check( # ----------- # debug - debug = ds._generic_check._check_var( - debug, 'debug', - default=False, - allowed=['intersect', False, True] - ) + if not callable(debug): + debug = ds._generic_check._check_var( + debug, 'debug', + default=False, + allowed=['intersect', False, True] + ) return ( key, @@ -907,9 +916,16 @@ def _get_equivalent_aperture( # debug ii=None, debug=None, + key=None, + key_cam=None, **kwdargs, ): + if callable(debug): + debugi = debug((ii,)) + else: + debugi = debug + # -------------- # loop on optics # -------------- @@ -935,8 +951,17 @@ def _get_equivalent_aperture( return None, None # --- DEBUG --------- - if debug is True: - _debug_plot(p_a=p_a, pa0=p0, pa1=p1, ii=ii, tit='local coords') + if debugi is True: + _debug_plot( + p_a=p_a, + pa0=p0, + pa1=p1, + tit=( + "local coords\n" + f"key_diag {key} - key_cam {key_cam}\n" + f"ind = {ii}" + ), + ) # -------------------- # ------- @@ -980,6 +1005,8 @@ def _get_equivalent_aperture_spectro( ii=None, ij=None, debug=None, + # unused + **kwdargs, ): # ----------------------------- @@ -1229,7 +1256,7 @@ def _debug_intersect( axs[1, 1].set_title("det_up") axs[1, 2].set_title("det_lo") - print('kA\n',kA) + print('kA\n', kA) print('det_up\n', det_up) print('det_lo\n', det_lo) @@ -1312,7 +1339,6 @@ def _debug_plot( pb1=None, pc0=None, pc1=None, - ii=None, tit=None, ): @@ -1381,14 +1407,8 @@ def _debug_plot( ) plt.legend() - - if ii is not None: - tit0 = f'ii = {ii}' - if tit is None: - tit = tit0 - else: - tit = tit0 + ', ' + tit - plt.gca().set_title(tit, size=12) + plt.gca().set_title(tit, size=12) + return def _debug_plot2( diff --git a/tofu/data/_class8_etendue_los.py b/tofu/data/_class8_etendue_los.py index f522fb50d..1a7b95829 100644 --- a/tofu/data/_class8_etendue_los.py +++ b/tofu/data/_class8_etendue_los.py @@ -188,7 +188,10 @@ def compute_etendue_los( shape0 = cx.shape if analytical is True: - etend0 = np.full(tuple(np.r_[3 + (spectro is True), shape0]), np.nan) + etend0 = np.full( + tuple(np.r_[3 + (spectro is True), shape0]), + np.nan, + ) # 0th order etend0[0, ...] = ap_area * det_area / distances**2 @@ -735,7 +738,6 @@ def _loop_on_pix( + los_z * plane_nin[2] ) - # ----------- # surfaces # ----------- @@ -1140,7 +1142,7 @@ def _compute_etendue_numerical_spectro( los = np.r_[np.nanmean(los_x), np.nanmean(los_y), np.nanmean(los_z)] los_n = los / np.linalg.norm(los) - e0_cam = coll.dobj['camera'][key_cam]['dgeom']['e0'] + # e0_cam = coll.dobj['camera'][key_cam]['dgeom']['e0'] e1_cam = coll.dobj['camera'][key_cam]['dgeom']['e1'] e0 = np.cross(e1_cam, los_n) @@ -1150,7 +1152,7 @@ def _compute_etendue_numerical_spectro( e1 = e1 / np.linalg.norm(e1) # get length along los - k_los = (1. + margin_par) * np.max(sca1) + # k_los = (1. + margin_par) * np.max(sca1) # ------------------------- # grid perpendicular to los @@ -1307,4 +1309,4 @@ def _plot_etendues( ] ax.legend(handles=handles) - return ax \ No newline at end of file + return ax diff --git a/tofu/data/_class8_los_angles.py b/tofu/data/_class8_los_angles.py index 2188a93a4..ae3726b21 100644 --- a/tofu/data/_class8_los_angles.py +++ b/tofu/data/_class8_los_angles.py @@ -43,6 +43,8 @@ def compute_los_angles( compute_vos_from_los=None, # overwrite overwrite=None, + # debug + debug_vos_from_los=None, **kwdargs, ): @@ -126,6 +128,8 @@ def compute_los_angles( strict=strict, res=res, overwrite=overwrite, + # debug + debug=debug_vos_from_los, ) # ---------------------------------------- @@ -196,6 +200,8 @@ def _vos_from_los( strict=None, res=None, overwrite=None, + # debug + debug=None, ): # -------------- @@ -210,6 +216,14 @@ def _vos_from_los( sign='>0', ) + # debug + if not callable(debug): + debug = ds._generic_check._check_var( + debug, 'debug', + types=bool, + default=False, + ) + # ----------- # prepare # ----------- @@ -245,6 +259,9 @@ def _vos_from_los( indok = np.ones(shape_cam, dtype=bool) for ii, ind in enumerate(np.ndindex(shape_cam)): + # debug ? + debugi = debug if isinstance(debug, bool) else debug(ind) + if not v0['iok'][ind]: indok[ind] = False continue @@ -253,19 +270,24 @@ def _vos_from_los( if pinhole is False: iref = v0['iref'][ind] + func_x01toxyz = coll.get_optics_x01toxyz(key=optics[iref]) + # ----------------------- # get start / end points + x0m = np.mean(v0['x0'][sli]) + x1m = np.mean(v0['x1'][sli]) + x0 = np.r_[ v0['x0'][sli], - 0.7*v0['x0'][sli], - 0.3*v0['x0'][sli], + x0m + 0.7*(v0['x0'][sli] - x0m), + x0m + 0.3*(v0['x0'][sli] - x0m), v0['cents0'][ind], ] x1 = np.r_[ v0['x1'][sli], - 0.7*v0['x1'][sli], - 0.3*v0['x1'][sli], + x1m + 0.7*(v0['x1'][sli] - x1m), + x1m + 0.3*(v0['x1'][sli] - x1m), v0['cents1'][ind], ] @@ -281,7 +303,7 @@ def _vos_from_los( # end points x0=x0, x1=x1, - coords=coll.get_optics_x01toxyz(key=optics[iref]), + coords=func_x01toxyz, lspectro=lspectro, config=config, strict=strict, @@ -370,6 +392,39 @@ def _vos_from_los( 'phor1': phor1, } + # ------------ + # debug + + if debugi is True: + dax = coll.plot_diagnostic( + key=key, + key_cam=key_cam, + elements='o', + plot_config=config, + ) + dax.dax['cross']['handle'].plot( + np.hypot(v0['cx'][ind], v0['cy'][ind]), + v0['cz'][ind], + 'o', + label='c', + ) + dax.dax['cross']['handle'].plot( + np.hypot(ptsx, ptsy), + ptsz, + 'x', + label='pts', + ) + xyz = func_x01toxyz(x0, x1) + dax.dax['cross']['handle'].plot( + np.hypot(xyz[0], xyz[1]), + xyz[2], + 's', + label='x01', + ) + dax.dax['cross']['handle'].legend() + fig = dax.dax['cross']['handle'].figure + fig.suptitle(f"key = {key}\nkey_cam = {key_cam} - {ind}") + # ------------------------ # reshape / harmonize # ------------------------ diff --git a/tofu/data/_class8_plot.py b/tofu/data/_class8_plot.py index 31d2c4853..d382ecd8d 100644 --- a/tofu/data/_class8_plot.py +++ b/tofu/data/_class8_plot.py @@ -1320,11 +1320,12 @@ def _plot_diag_geom( if is2d and k0 in key_cam and dax.get(kax) is not None: ax = dax[kax]['handle'] if k1 == 'o': - ax.plot( - v1['x0'], - v1['x1'], - **v1.get('props', {}), - ) + if v1.get('x0') is not None: + ax.plot( + v1['x0'], + v1['x1'], + **v1.get('props', {}), + ) # ################################################################ diff --git a/tofu/data/_class8_plot_coverage_broadband.py b/tofu/data/_class8_plot_coverage_broadband.py index 763ae6bbc..ef0bda427 100644 --- a/tofu/data/_class8_plot_coverage_broadband.py +++ b/tofu/data/_class8_plot_coverage_broadband.py @@ -338,7 +338,7 @@ def _plot_cross( # prepare figure # ---------------- - if dax.get('ndet_cross') is None: + if dax is None or len(dax) == 0: if fs is None: fs = (16, 7) @@ -430,7 +430,7 @@ def _plot_cross( # check / format dax dax = ds._generic_check._check_dax(dax) - fig = dax['ndet_cross']['handle'].figure + fig = dax[list(dax.keys())[0]]['handle'].figure # --------------- # plot spans diff --git a/tofu/data/_class8_plot_coverage_slice.py b/tofu/data/_class8_plot_coverage_slice.py index 1fdc79d46..8c88ce157 100644 --- a/tofu/data/_class8_plot_coverage_slice.py +++ b/tofu/data/_class8_plot_coverage_slice.py @@ -33,6 +33,9 @@ def main( margin_perp=None, vect=None, segment=None, + # e0, e1 + transpose=None, + e0e1=None, # mesh slice key_mesh=None, phi=None, @@ -129,6 +132,9 @@ def main( lop_post=lop_post, vect=vect, segment=segment, + # e0, e1 + transpose=transpose, + e0e1=e0e1, # plane params res=res, margin_par=margin_par, @@ -662,6 +668,9 @@ def _plane_from_LOS( lop_post=None, segment=None, vect=None, + # e0, e1 + transpose=None, + e0e1=None, # plane params res=None, margin_par=None, @@ -670,6 +679,26 @@ def _plane_from_LOS( indch=None, ): + # ---------- + # inputs + # ---------- + + # transpose + transpose = ds._generic_check._check_var( + transpose, 'transpose', + types=bool, + default=False, + ) + + # e0e1 + lok = [(1, 1), (-1, 1), (1, -1), (-1, -1)] + e0e1 = ds._generic_check._check_var( + e0e1, 'e0e1', + types=tuple, + default=(1, 1), + allowed=lok, + ) + # ---------- # los_ref # ---------- @@ -746,6 +775,12 @@ def _plane_from_LOS( e1 = np.cross(los_ref, e0) e1 = e1 / np.linalg.norm(e1) + if transpose is True: + e0, e1 = e1, e0 + + e0 = e0 * e0e1[0] + e1 = e1 * e0e1[1] + # ------------------------------------- # create plane perpendicular to los_ref # ------------------------------------- diff --git a/tofu/data/_class8_vos.py b/tofu/data/_class8_vos.py index 1935de2e2..52f6d3c87 100644 --- a/tofu/data/_class8_vos.py +++ b/tofu/data/_class8_vos.py @@ -284,6 +284,10 @@ def compute_vos( dt22=dt22, ) + # clean + if dvos[k0] is None: + del dvos[k0], dref[k0] + # timing if timing: t2 = dtm.datetime.now() # DB diff --git a/tofu/data/_class8_vos_broadband.py b/tofu/data/_class8_vos_broadband.py index 6f15a85a2..9fdc83678 100644 --- a/tofu/data/_class8_vos_broadband.py +++ b/tofu/data/_class8_vos_broadband.py @@ -130,6 +130,7 @@ def _vos( f"user_limits: {user_limits}\n" ) raise Exception(msg) + axis_pts = None else: @@ -144,6 +145,18 @@ def _vos( phor0 = coll.ddata[kph0]['data'] phor1 = coll.ddata[kph1]['data'] + # ------------------------------------------------ + # axis_pts for robustness vs old versions of tofu + axis_pts = [ + ii for ii, rr in enumerate(coll.ddata[kpc0]['ref']) + if rr.endswith('_n') + ][0] + if axis_pts == 0: + pcross0 = np.moveaxis(pcross0, 0, -1) + pcross1 = np.moveaxis(pcross1, 0, -1) + phor0 = np.moveaxis(phor0, 0, -1) + phor1 = np.moveaxis(phor1, 0, -1) + # pinhole? pinhole = doptics[key_cam]['pinhole'] @@ -190,6 +203,7 @@ def _vos( # ----------------- # slices + # robustness sli_poly = ind + (slice(None),) sli_poly0 = ind + (0,) @@ -395,25 +409,17 @@ def _vos( # ----- DEBUG -------- if debugi: - fig = plt.figure() - fig.suptitle(f"pixel ind = {ind}", size=14, fontweight='bold') - ax = fig.add_axes([0.1, 0.1, 0.8, 0.8]) - ax.set_xlabel("phi (deg)", size=12) - ax.set_ylabel("solid angle (sr)", size=12) - # ipos = out[0, :] > 0 - # ax.scatter( - # xx[ipos], yy[ipos], - # c=out[0, ipos], s=6, marker='o', vmin=0, - # ) - # ax.plot(xx[~ipos], yy[~ipos], c='r', marker='x') - ax.scatter( - np.arctan2(yy, xx) * 180/np.pi, - out[0, :], - c=np.hypot(xx, yy), - s=6, - marker='.', + _debugi( + xx=xx, + yy=yy, + zz=zz, + out=out, + ind=ind, + ref_rad=np.max(np.r_[res_RZ, res_phi]), + refx=-0.71, + refy=-1.37, + refz=-1.24, ) - raise Exception() # ----- END DEBUG ---- # timing @@ -465,13 +471,16 @@ def _vos( if timing: t22 = dtm.datetime.now() # DB - ddata, dref = _utilities._harmonize_reshape( - douti=douti, - indok=indok, - key_diag=key_diag, - key_cam=key_cam, - ref_cam=coll.dobj['camera'][key_cam]['dgeom']['ref'], - ) + if len(douti) > 0: + ddata, dref = _utilities._harmonize_reshape( + douti=douti, + indok=indok, + key_diag=key_diag, + key_cam=key_cam, + ref_cam=coll.dobj['camera'][key_cam]['dgeom']['ref'], + ) + else: + ddata, dref = None, None if timing: t33 = dtm.datetime.now() @@ -653,3 +662,86 @@ def _get_crosshor_from_3d_single_det( dout[k1][ii] = np.sum(vect[ind] * sang_3d[ind]) / dout[ksang][ii] return dout + + +# ####################################################### +# ####################################################### +# Debug +# ####################################################### + + +def _debugi( + xx=None, + yy=None, + zz=None, + out=None, + ind=None, + ref_rad=None, + refx=None, + refy=None, + refz=None, +): + + # ------------- + # prepare data + # ------------- + + dd = np.sqrt((xx - refx)**2 + (yy - refy)**2 + (zz - refz)**2) + ipt = dd < ref_rad + if not np.any(ipt): + ipt = np.argmin(dd) + + # ------------- + # prepare figure + # ------------- + + fig = plt.figure() + fig.suptitle(f"pixel ind = {ind}", size=14, fontweight='bold') + + ax0 = fig.add_subplot(121) + ax0.set_xlabel("phi (deg)", size=12) + ax0.set_ylabel("solid angle (sr)", size=12) + + ax1 = fig.add_subplot(122) + ax1.set_xlabel("R (m)", size=12) + ax1.set_ylabel("solid angle (sr)", size=12) + + # ------------- + # plot sang vs phi + # ------------- + + ax0.scatter( + np.arctan2(yy, xx) * 180/np.pi, + out[0, :], + c=np.hypot(xx, yy), + s=10, + marker='.', + ) + ax0.plot( + np.arctan2(yy, xx)[ipt] * 180/np.pi, + out[0, :][ipt], + c='r', + marker='*', + ms=12, + ) + + # ------------- + # plot sang vs R + # ------------- + + ax1.scatter( + np.hypot(yy, xx), + zz, + c=out[0, :], + s=10, + marker='.', + ) + ax1.plot( + np.hypot(yy, xx)[ipt], + zz[ipt], + c='r', + marker='*', + ms=12, + ) + + raise Exception() diff --git a/tofu/data/_saveload.py b/tofu/data/_saveload.py index a65553442..749f8fbc5 100644 --- a/tofu/data/_saveload.py +++ b/tofu/data/_saveload.py @@ -44,4 +44,4 @@ def load( verb=verb, ) - return coll \ No newline at end of file + return coll diff --git a/tofu/geom/_GG.pyx b/tofu/geom/_GG.pyx index 1d1f19d3b..c3915e46a 100644 --- a/tofu/geom/_GG.pyx +++ b/tofu/geom/_GG.pyx @@ -3523,67 +3523,68 @@ cdef LOS_sino_Tor(double D0, double D1, double D2, double u0, double u1, return (PMin0,PMin1,PMin2), kPMin, RMin, Theta, p, ImpTheta, phi +## NOT USED ??? +# cdef inline void NEW_LOS_sino_Tor(double orig0, double orig1, double orig2, + # double dirv0, double dirv1, double dirv2, + # double circ_radius, double circ_normz, + # double[9] results, + # bint is_LOS_Mode=False, + # double kOut=C_INF) nogil: + # cdef double[3] dirv, orig + # cdef double[2] res + # cdef double normu, normu_sqr + # cdef double kPMin + + # normu_sqr = dirv0 * dirv0 + dirv1 * dirv1 + dirv2 * dirv2 + # normu = c_sqrt(normu_sqr) + # dirv[0] = dirv0 + # dirv[2] = dirv2 + # dirv[1] = dirv1 + # orig[0] = orig0 + # orig[1] = orig1 + # orig[2] = orig2 + + # if dirv0 == 0. and dirv1 == 0.: + # kPMin = (circ_normz-orig2)/dirv2 + # else: + # _dt.dist_los_circle_core(dirv, orig, + # circ_radius, circ_normz, + # normu_sqr, res) + # kPMin = res[0] + # if is_LOS_Mode and kPMin > kOut: + # kPMin = kOut + + # # Computing the point's coordinates......................................... + # cdef double PMin0 = orig0 + kPMin * dirv0 + # cdef double PMin1 = orig1 + kPMin * dirv1 + # cdef double PMin2 = orig2 + kPMin * dirv2 + # cdef double PMin2norm = c_sqrt(PMin0**2+PMin1**2) + # cdef double RMin = c_sqrt((PMin2norm - circ_radius)**2 + # + (PMin2 - circ_normz)**2) + # cdef double vP0 = PMin2norm - circ_radius + # cdef double vP1 = PMin2 - circ_normz + # cdef double Theta = c_atan2(vP1, vP0) + # cdef double ImpTheta = Theta if Theta>=0 else Theta + c_pi + # cdef double er2D0 = c_cos(ImpTheta) + # cdef double er2D1 = c_sin(ImpTheta) + # cdef double p0 = vP0*er2D0 + vP1*er2D1 + # cdef double eTheta0 = -PMin1 / PMin2norm + # cdef double eTheta1 = PMin0 / PMin2norm + # cdef double normu0 = dirv0/normu + # cdef double normu1 = dirv1/normu + # cdef double phi = c_asin(-normu0 * eTheta0 - normu1 * eTheta1) + # # Filling the results ...................................................... + # results[0] = PMin0 + # results[1] = PMin1 + # results[2] = PMin2 + # results[3] = kPMin + # results[4] = RMin + # results[5] = Theta + # results[6] = p0 + # results[7] = ImpTheta + # results[8] = phi + # return -cdef inline void NEW_LOS_sino_Tor(double orig0, double orig1, double orig2, - double dirv0, double dirv1, double dirv2, - double circ_radius, double circ_normz, - double[9] results, - bint is_LOS_Mode=False, - double kOut=C_INF) nogil: - cdef double[3] dirv, orig - cdef double[2] res - cdef double normu, normu_sqr - cdef double kPMin - - normu_sqr = dirv0 * dirv0 + dirv1 * dirv1 + dirv2 * dirv2 - normu = c_sqrt(normu_sqr) - dirv[0] = dirv0 - dirv[2] = dirv2 - dirv[1] = dirv1 - orig[0] = orig0 - orig[1] = orig1 - orig[2] = orig2 - - if dirv0 == 0. and dirv1 == 0.: - kPMin = (circ_normz-orig2)/dirv2 - else: - _dt.dist_los_circle_core(dirv, orig, - circ_radius, circ_normz, - normu_sqr, res) - kPMin = res[0] - if is_LOS_Mode and kPMin > kOut: - kPMin = kOut - - # Computing the point's coordinates......................................... - cdef double PMin0 = orig0 + kPMin * dirv0 - cdef double PMin1 = orig1 + kPMin * dirv1 - cdef double PMin2 = orig2 + kPMin * dirv2 - cdef double PMin2norm = c_sqrt(PMin0**2+PMin1**2) - cdef double RMin = c_sqrt((PMin2norm - circ_radius)**2 - + (PMin2 - circ_normz)**2) - cdef double vP0 = PMin2norm - circ_radius - cdef double vP1 = PMin2 - circ_normz - cdef double Theta = c_atan2(vP1, vP0) - cdef double ImpTheta = Theta if Theta>=0 else Theta + c_pi - cdef double er2D0 = c_cos(ImpTheta) - cdef double er2D1 = c_sin(ImpTheta) - cdef double p0 = vP0*er2D0 + vP1*er2D1 - cdef double eTheta0 = -PMin1 / PMin2norm - cdef double eTheta1 = PMin0 / PMin2norm - cdef double normu0 = dirv0/normu - cdef double normu1 = dirv1/normu - cdef double phi = c_asin(-normu0 * eTheta0 - normu1 * eTheta1) - # Filling the results ...................................................... - results[0] = PMin0 - results[1] = PMin1 - results[2] = PMin2 - results[3] = kPMin - results[4] = RMin - results[5] = Theta - results[6] = p0 - results[7] = ImpTheta - results[8] = phi - return cdef inline void NEW_los_sino_tor_vec(int nlos, double[:,::1] origins, diff --git a/tofu/geom/_openmp_tools.pyx b/tofu/geom/_openmp_tools.pyx index 5aad5f157..ef0b32344 100644 --- a/tofu/geom/_openmp_tools.pyx +++ b/tofu/geom/_openmp_tools.pyx @@ -1,7 +1,7 @@ # cython: language_level=3 import os -from .openmp_enabled import is_openmp_enabled +# from .openmp_enabled import is_openmp_enabled IF TOFU_OPENMP_ENABLED: cimport openmp @@ -29,8 +29,8 @@ cpdef get_effective_num_threads(n_threads=None): if n_threads == 0: raise ValueError("n_threads = 0 is invalid") - local_openmp_enabled = is_openmp_enabled() - assert local_openmp_enabled == TOFU_OPENMP_ENABLED + # local_openmp_enabled = is_openmp_enabled() + # assert local_openmp_enabled == TOFU_OPENMP_ENABLED IF TOFU_OPENMP_ENABLED: diff --git a/tofu/geom/meson.build b/tofu/geom/meson.build new file mode 100644 index 000000000..00c50d678 --- /dev/null +++ b/tofu/geom/meson.build @@ -0,0 +1,152 @@ +# ################################ +# Direct py modules +# ################################ + + +py.install_sources([ + '__init__.py', + '_def.py', + '_def_config.py', + '_check_optics.py', + '_core.py', + '_core_optics.py', + '_comp.py', + '_comp_optics.py', + '_comp_solidangles.py', + '_etendue.py', + '_plot.py', + '_plot_optics.py', + 'utils.py', +], +subdir: 'tofu' / 'geom', +) + + +# ################################ +# No extension modules => pure dirs +# ################################ + +pure_subdirs = [ + 'inputs', +] + +tofu_geom_dir = tofu_dir / 'geom' +foreach subdir: pure_subdirs + install_subdir(subdir, install_dir: tofu_geom_dir) +endforeach + + +# ################################# +# Compile / cython args +# ################################# + + +cython_args = [ + '-Xboundscheck=True', +] +cython_args2 = cython_args +if omp.found() + cython_args2 += ['--compile-time-env', 'TOFU_OPENMP_ENABLED=True'] +endif + + +include_dirs = [_incdir_numpy_abs] + + +compile_args = [ + '-O3', + '-Wall', + '-fno-wrapv', + 'language_level="3"', +] + + +# ################################ +# local extensions +# ################################ + + +py.extension_module( + '_GG', + '_GG.pyx', + subdir: 'tofu/geom/', + include_directories: include_dirs, + dependencies : [py_dep, omp], + cython_args : cython_args, + # extra_args : compile_args, + install: true, + # extra_compile_args=extra_compile_args, + # extra_link_args=extra_link_args, +) +py.extension_module( + '_basic_geom_tools', + '_basic_geom_tools.pyx', + subdir: 'tofu/geom/', + include_directories: include_dirs, + dependencies : [py_dep, omp], + cython_args : cython_args, + install: true, # true +) +py.extension_module( + '_distance_tools', + '_distance_tools.pyx', + subdir: 'tofu/geom/', + include_directories: include_dirs, + dependencies : [py_dep, omp], + cython_args : cython_args, + install: true, # true +) +py.extension_module( + '_sampling_tools', + '_sampling_tools.pyx', + subdir: 'tofu/geom/', + include_directories: include_dirs, + dependencies : [py_dep, omp], + cython_args : cython_args, + install: true, # true +) +py.extension_module( + '_raytracing_tools', + '_raytracing_tools.pyx', + subdir: 'tofu/geom/', + include_directories: include_dirs, + dependencies : [py_dep, omp], + cython_args : cython_args, + install: true, # true +) +py.extension_module( + '_vignetting_tools', + '_vignetting_tools.pyx', + subdir: 'tofu/geom/', + include_directories: include_dirs, + dependencies : [py_dep, omp], + cython_args : cython_args, + install: true, # true +) +py.extension_module( + '_chained_list', + '_chained_list.pyx', + subdir: 'tofu/geom/', + include_directories: include_dirs, + dependencies : [py_dep, omp], + cython_args : cython_args, + install: true, # true +) +py.extension_module( + '_sorted_set', + '_sorted_set.pyx', + subdir: 'tofu/geom/', + include_directories: include_dirs, + dependencies : [py_dep, omp], + cython_args : cython_args, + install: true, # true +) +py.extension_module( + '_openmp_tools', + '_openmp_tools.pyx', + subdir: 'tofu/geom/', + include_directories: include_dirs, + dependencies : [py_dep, omp], + cython_args : cython_args2, + install: true, # true +) diff --git a/tofu/imas2tofu/_comp.py b/tofu/imas2tofu/_comp.py index 6d45d26f3..0622edc31 100644 --- a/tofu/imas2tofu/_comp.py +++ b/tofu/imas2tofu/_comp.py @@ -44,7 +44,10 @@ _DSHORT = _defimas2tofu._dshort _DCOMP = _defimas2tofu._dcomp -_DDUNITS = imas.dd_units.DataDictionaryUnits() +try: + _DDUNITS = imas.dd_units.DataDictionaryUnits() +except Exception: + _DDUNITS = None _ISCLOSE = True _POS = False @@ -73,22 +76,50 @@ def _prepare_sig_units(sig, units=False): def get_units(ids, sig, dshort=None, dcomp=None, force=None): """ Get units from imas.dd_units.DataDictionaryUnits() """ + + # ------------------- + # check inputs + # ------------------- + if dshort is None: dshort = _DSHORT if dcomp is None: dcomp = _DCOMP if force is None: force = True + + # --------------- + # get signal name + # --------------- + if sig in dshort[ids].keys(): sig = _prepare_sig_units(dshort[ids][sig]['str']) else: sig = _prepare_sig_units(sig) - units = _DDUNITS.get_units(ids, sig.replace('.', '/')) + # --------------- + # get IMAS units + # --------------- + + # AL < 5 + try: + units = _DDUNITS.get_units(ids, sig.replace('.', '/')) + + # AL >= 5 => use tofu units instead (changes would required debugging) + except Exception: + units = None + force = True + + # ---------------------------------------------------------- # Condition in which to use tofu units instead of imas units - c0 = (units is None - and force is True - and (sig in dshort[ids].keys() or sig in dcomp[ids].keys())) + # ---------------------------------------------------------- + + c0 = ( + units is None + and force is True + and (sig in dshort[ids].keys() or sig in dcomp[ids].keys()) + ) + if c0 is True: if sig in dshort[ids].keys(): tofuunits = dshort[ids][sig].get('units') @@ -96,6 +127,7 @@ def get_units(ids, sig, dshort=None, dcomp=None, force=None): tofuunits = dcomp[ids][sig].get('units') if tofuunits != units: units = tofuunits + return units @@ -265,6 +297,19 @@ def fsig(obj, indt=None, indch=None, stack=None, dcond=dcond): raise Exception(msg) sig[jj] = sig[jj][ind[0]] + # convert from IMAS classes to numpy / float etc + for ii in range(len(sig)): + if isinstance(sig[ii], imas.ids_primitive.IDSNumericArray): + sig[ii] = np.array(sig[ii]) + elif isinstance(sig[ii], imas.ids_primitive.IDSFloat0D): + sig[ii] = float(sig[ii]) + elif isinstance(sig[ii], imas.ids_primitive.IDSInt0D): + sig[ii] = int(sig[ii]) + elif isinstance(sig[ii], imas.ids_primitive.IDSString0D): + sig[ii] = str(sig[ii]) + elif isinstance(sig[ii], imas.ids_primitive.IDSString1D): + sig[ii] = str(sig[ii]) + # Conditions for stacking / sqeezing sig lc = [ ( @@ -631,12 +676,16 @@ def _check_data(data, pos=None, nan=None, isclose=None, empty=None): isempty = [None for ii in range(len(data))] if empty is True: for ii in range(len(data)): - isempty[ii] = (len(data[ii]) == 0 - or (isinstance(data[ii], np.ndarray) - and (data[ii].size == 0 - or 0 in data[ii].shape))) + isempty[ii] = ( + len(data[ii]) == 0 + or ( + isinstance(data[ii], np.ndarray) + and (data[ii].size == 0 or 0 in data[ii].shape) + ) + ) if isinstance(data[ii], np.ndarray) and data[ii].dtype.kind != 'U': isempty[ii] &= bool(np.all(np.isnan(data[ii]))) + return data, isempty @@ -738,17 +787,22 @@ def _get_data_units(ids=None, sig=None, occ=None, # Check data isempty = None if errdata is None and data is True: - out, isempty = _check_data(out, - pos=pos, nan=nan, - isclose=isclose, empty=empty) + out, isempty = _check_data( + out, + pos=pos, nan=nan, + isclose=isclose, empty=empty, + ) if np.all(isempty): msg = ("empty data in {}.{}".format(ids, sig)) errdata = Exception(msg) elif nocc == 1 and flatocc is True: out = out[0] isempty = isempty[0] - return {'data': out, 'units': unit, - 'isempty': isempty, 'errdata': errdata, 'errunits': errunits} + + return { + 'data': out, 'units': unit, + 'isempty': isempty, 'errdata': errdata, 'errunits': errunits, + } def get_data_units(dsig=None, occ=None, @@ -872,4 +926,4 @@ def get_data_units(dsig=None, occ=None, if return_all: return dout, dfail, dsig else: - return dout \ No newline at end of file + return dout diff --git a/tofu/imas2tofu/_comp_toobjects.py b/tofu/imas2tofu/_comp_toobjects.py index 5cf0be323..838050f53 100644 --- a/tofu/imas2tofu/_comp_toobjects.py +++ b/tofu/imas2tofu/_comp_toobjects.py @@ -633,7 +633,7 @@ def get_plasma( R = out_['2dmeshR']['data'] Z = out_['2dmeshZ']['data'] if R.ndim == 2: - if np.allclose(R[0, :], R[0,0]): + if np.allclose(R[0, :], R[0, 0]): R = R[:, 0] Z = Z[0, :] else: @@ -658,13 +658,32 @@ def get_plasma( # profiles2d on mesh lprof2d = set(out_.keys()).difference(lsigmesh) + + # Check for non-arrays + derr = { + ss: type(out_[ss]['data']) for ss in lprof2d + if not isinstance(out_[ss]['data'], np.ndarray) + } + + if len(derr) > 0: + lstr = [f"\t- {kk}: {vv}" for kk, vv in derr.items()] + msg = ( + "The following keys in profiles2d are not np.ndarrays:\n" + + "\n".join(lstr) + ) + raise Exception(msg) + + # loop for ss in lprof2d: # identify proper 2d mesh lm = [ km for km, vm in dmesh.items() if ( - (km == 'tri' and vm['n1'] in out_[ss]['data'].shape) + ( + km == 'tri' + and vm['n1'] in out_[ss]['data'].shape + ) or ( km == 'rect' and vm['n1'] in out_[ss]['data'].shape diff --git a/tofu/imas2tofu/_core.py b/tofu/imas2tofu/_core.py index ef339fe61..8616fe7f4 100644 --- a/tofu/imas2tofu/_core.py +++ b/tofu/imas2tofu/_core.py @@ -57,9 +57,13 @@ # imas try: import imas - from imas import imasdef + from imas.ids_defs import HDF5_BACKEND + try: + from imas import imasdef + except Exception: + imasdef = None except Exception as err: - raise Exception('imas not available') + raise Exception(f'imas not available: {str(err)}') __all__ = [ @@ -957,15 +961,11 @@ def _checkformat_idd( user=user, database=database, version=version, backend=backend, ) - for kk,vv in defidd.items(): + for kk, vv in defidd.items(): if params[kk] is None: params[kk] = vv - # convert backend str => pointer - params['backend'] = getattr( - imasdef, - f"{params['backend']}_BACKEND".upper(), - ) + params['backend'] = HDF5_BACKEND # create entry idd = imas.DBEntry( @@ -1189,13 +1189,13 @@ def _checkformat_ids( ids = [ids] # check ids is allowed - for ids_ in ids: - if not ids_ in self._lidsnames: - msg = ( - "ids {ids_} matched no known imas ids !" - f" => Available ids are:\n{repr(self._lidsnames)}" - ) - raise Exception(msg) + # for ids_ in ids: + # if not ids_ in self._lidsnames: + # msg = ( + # "ids {ids_} matched no known imas ids !" + # f" => Available ids are:\n{repr(self._lidsnames)}" + # ) + # raise Exception(msg) # initialise dict for k in ids: @@ -2012,14 +2012,14 @@ class with which the output shall be returned # ---------------------- # lids determines order in which ids are read # may be important in case 2d mesh only exists in one ids! - + lids = sorted(dsig.keys()) if 'equilibrium' in lids: lids = ['equilibrium'] + [ids for ids in lids if ids != 'equilibrium'] # ------------------------- # data source consistency - + _, _, shot, Exp = _comp_toobjects.get_lidsidd_shotExp( lids, upper=True, errshot=False, errExp=False, dids=self._dids, didd=self._didd, @@ -3797,4 +3797,4 @@ def _save_to_imas_DataCam1D( # ------------------ _put_ids(idd, ids, shotfile, occ=occ, cls_name='%s_%s'%(obj.Id.Cls,obj.Id.Name), - err=err0, dryrun=dryrun, verb=verb) \ No newline at end of file + err=err0, dryrun=dryrun, verb=verb) diff --git a/tofu/meson.build b/tofu/meson.build new file mode 100644 index 000000000..318b0c3be --- /dev/null +++ b/tofu/meson.build @@ -0,0 +1,47 @@ +# ################################ +# Direct py modules +# ################################ + +py.install_sources([ + '__init__.py', + 'version.py', + 'py.typed', + 'pathfile.py', + 'utils.py', + 'defaults.py', + '_plot.py', + '_physics.py', + 'utils.py', +], +subdir: 'tofu', # Folder relative to site-packages to install to +) + + +# ################################ +# No extension modules => pure dirs +# ################################ + +pure_subdirs = [ + 'data', + 'spectro', + 'tests', + 'benchmarks', # needs geom + 'physics_tools', + 'omas2tofu', # needs data + 'omas2tofu', + 'imas2tofu', + 'nist2tofu', + 'openadas2tofu', + 'tomotok2tofu', + #'mag', +] + +foreach subdir: pure_subdirs + install_subdir(subdir, install_dir: tofu_dir) +endforeach + +# ################################ +# extension modules => subdir with meson.build +# ################################ + +subdir('geom') diff --git a/tofu/omas2tofu/_common.py b/tofu/omas2tofu/_common.py index 3528e6580..c13127772 100644 --- a/tofu/omas2tofu/_common.py +++ b/tofu/omas2tofu/_common.py @@ -604,7 +604,10 @@ def _add_rhopn_from_psi( # --------- # compute - rhopn = np.sqrt((psi - psi0) / (psi1 - psi0)) + rhopn = np.full(psi.shape, np.nan) + rhopn2 = (psi - psi0) / (psi1 - psi0) + iok = rhopn2 >= 0. + rhopn[iok] = np.sqrt(rhopn2[iok]) # --------- # add data @@ -811,8 +814,12 @@ def _add_mesh_data_1d( ldata=ldata, lk2d=lk2d, ) - except Exception: - dfail['subkey'] = 'could not identify' + except Exception as err: + dfail['subkey'] = ( + 'could not identify\n' + + str(err) + + f"\n=> Impacts {ldata}" + ) k1d, q1d, k2d = None, None, None # -------------------- @@ -878,10 +885,10 @@ def _add_mesh_data_1d( return dfail -# ################################################################ -# ################################################################ +# ################################################ +# ################################################ # Identify subkey -# ################################################################ +# ################################################ def _get_subkey( @@ -908,6 +915,7 @@ def _get_subkey( k0 for k0, v0 in ddata.items() if np.allclose(v0['data'], v0['data'][sli]) ] + if len(l1d) != 1: msg = ( "No / multiple constant 1d mesh data identified:\n" @@ -918,7 +926,6 @@ def _get_subkey( k1d = l1d[0] key_1d = ddata[k1d]['key'] - q1d = ddata[k1d]['data'][sli].ravel() # ------------------ # Identify 2d subkey @@ -935,7 +942,7 @@ def _get_subkey( "Several 2d data identified to match 1d mesh:\n" "\t- ids = {ids}\n" "\t- k1d = {k1d}\n" - "\t- k2d = {k2d}\n" + "\t- lk2d_name = {lk2d_name}\n" ) raise Exception(msg) @@ -958,10 +965,11 @@ def _get_subkey( lk2d=lk2d, k1d=k1d, key_1d=key_1d, - q1d=q1d, + q1d=None, ) else: raise NotImplementedError(ids) + q1d = ddata[k1d]['data'][sli].ravel() return k1d, q1d, k2dn diff --git a/tofu/omas2tofu/_core_profiles.py b/tofu/omas2tofu/_core_profiles.py index 727a67a95..cea8dc485 100644 --- a/tofu/omas2tofu/_core_profiles.py +++ b/tofu/omas2tofu/_core_profiles.py @@ -1,9 +1,9 @@ -# ########################################################### -# ########################################################### +# ################################################ +# ################################################ # 1d-2d mesh -# ########################################################### +# ################################################ def _get_subkey( @@ -60,20 +60,45 @@ def _get_subkey( else: d1d_all = {} for k0, v0 in ddata.items(): - l2d = [k1 for k1 in lk2d if coll.ddata[k1]['name'] == v0['name']] + l2d = [ + k1 for k1 in lk2d + if coll.ddata[k1]['name'] == v0['name'] + ] if len(l2d) == 1: d1d_all[k0] = l2d[0] if len(d1d_all) == 0: msg = ( - "Could not identify a single matching quantity between " - "equilibrium (2d) and core_profiles (1d)" + "Could not identify a matching quantity between:\n" + "\t- equilibrium (2d)" + "\t- core_profiles (1d)" ) raise Exception(msg) # ------------ # interpolate - raise NotImplementedError() + elif len(d1d_all) > 1: + + keep, ii = True, 0 + lprio = ['rhopn', 'rhotn', 'psi', 'phi'] + while keep is True and ii < len(lprio): + lk1 = [ + kk for kk, vv in d1d_all.items() + if lprio[ii] in kk and lprio[ii] in vv + ] + if len(lk1) == 1: + k1d = lk1[0] + k2dn = d1d_all[k1d] + keep = False + else: + ii += 1 + if keep is True: + msg = "Multiple matching 1d (cprof) <=> 2d (eq)" + raise NotImplementedError(msg) + + else: + msg = "Time-varying radial interpolation" + raise NotImplementedError(msg) return k1d, q1d, k2dn diff --git a/tofu/physics_tools/__init__.py b/tofu/physics_tools/__init__.py index 833d4ac1e..406c53a9b 100644 --- a/tofu/physics_tools/__init__.py +++ b/tofu/physics_tools/__init__.py @@ -1,6 +1,5 @@ from . import geometry -from ._distributions import get_maxwellian -from . import runaways +from . import electrons from .transmission import get_xray_transmission from .heat_transport_1d import main as heat_transport_1d diff --git a/tofu/physics_tools/electrons/__init__.py b/tofu/physics_tools/electrons/__init__.py new file mode 100644 index 000000000..4441d36b1 --- /dev/null +++ b/tofu/physics_tools/electrons/__init__.py @@ -0,0 +1,3 @@ +from ._convert import convert_momentum_velocity_energy +from . import distribution +from . import emission diff --git a/tofu/physics_tools/runaways/_utils.py b/tofu/physics_tools/electrons/_convert.py similarity index 92% rename from tofu/physics_tools/runaways/_utils.py rename to tofu/physics_tools/electrons/_convert.py index 65f0ab7d0..d4a743668 100644 --- a/tofu/physics_tools/runaways/_utils.py +++ b/tofu/physics_tools/electrons/_convert.py @@ -41,9 +41,13 @@ def convert_momentum_velocity_energy( din = {k0: v0 for k0, v0 in din0.items() if v0 is not None} if len(din) != 1: - lstr = [f"\t- {k0}" for k0 in din.keys()] + nmax = np.max([len(k0) for k0 in din0.keys()]) + lstr = [ + f"\t- {k0.ljust(nmax)} is None: {v0 is None}" + for k0, v0 in din0.items() + ] msg = ( - "Please provide only one input of the following:\n" + "Please provide exactly one input of the following:\n" + "\n".join(lstr) ) raise Exception(msg) diff --git a/tofu/physics_tools/electrons/distribution/__init__.py b/tofu/physics_tools/electrons/distribution/__init__.py new file mode 100644 index 000000000..25e2d8bdd --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/__init__.py @@ -0,0 +1,5 @@ +from ._runaway_growth import get_RE_critical_dreicer_electric_fields +from ._runaway_growth import get_RE_growth_source_terms +from ._distribution import main as get_distribution +from ._distribution_plot import main as plot_distribution +from ._distribution_study import study_RE_vs_Maxwellian_distribution diff --git a/tofu/physics_tools/electrons/distribution/_distribution.py b/tofu/physics_tools/electrons/distribution/_distribution.py new file mode 100644 index 000000000..c7aa37b9c --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/_distribution.py @@ -0,0 +1,462 @@ + + +import copy +import warnings + + +import numpy as np +import scipy.integrate as scpinteg +import scipy.constants as scpct +import astropy.units as asunits + + +from . import _distribution_check as _check +from .. import _convert + + +# ####################################################### +# ####################################################### +# Main +# ####################################################### + + +def main( + # ------------ + # plasma paremeters + Te_eV=None, + ne_m3=None, + jp_Am2=None, + jp_fraction_re=None, + # RE-specific + Te_eV_re=None, + ne_m3_re=None, + Zeff=None, + Ekin_max_eV=None, + Efield_par_Vm=None, + lnG=None, + sigmap=None, + dominant=None, + # ------------ + # coordinates + # velocity + v_perp_ms=None, + v_par_ms=None, + # momentum + p_par_norm=None, + p_perp_norm=None, + # energy + E_eV=None, + pitch=None, + theta=None, + # version + dist=None, + version=None, + # verb + verb=None, + # return + returnas=None, +): + + # -------------- + # check inputs + # -------------- + + dist, dplasma, dcoords, dfunc, coll, verb = _check.main(**locals()) + shape_plasma = dplasma['Te_eV']['data'].shape + shape_coords = tuple([ + dcoords[kk]['data'].size + for kk in ['x0', 'x1'] + if dcoords.get(kk) is not None + ]) + + # ---------- + # verb + + if verb >= 1: + msg = ( + f"\nComputing e distribution for plasma {shape_plasma}" + f" and coordinates {shape_coords}" + ) + print(msg) + + # ------------- + # adjust shapes + # ------------- + + # axis + axis_exp_plasma = len(shape_plasma) + np.arange(0, len(shape_coords)) + axis_exp_coords = np.arange(len(shape_plasma)) + + # plasma + din = copy.deepcopy(dplasma) + for k0, v0 in din.items(): + din[k0]['data'] = np.expand_dims(v0['data'], tuple(axis_exp_plasma)) + + # current + jp_Am20 = np.copy(din['jp_Am2']['data']) + + # coords + dc = {} + for ii, k0 in enumerate(['x0', 'x1']): + if dcoords.get(k0) is not None: + axis = tuple(axis_exp_coords) + if len(shape_coords) == 2: + axis += (len(shape_plasma) + (1 - ii),) + dc[dcoords[k0]['key']] = np.expand_dims( + dcoords[k0]['data'], + axis, + ) + + # ------------- + # prepare + # ------------- + + ddist = { + 'dist': {}, + 'plasma': dplasma, + 'coords': dcoords, + } + + # -------------- + # compute + # -------------- + + lkdist = ['RE', 'maxwell'] + ne_re = 0. + for kdist in lkdist: + + if dfunc.get(kdist) is None: + continue + + # ---------- + # verb + + if verb >= 1: + msg = f"\tComputing {kdist}..." + print(msg) + + # -------------- + # Adjust current + + if kdist == 'maxwell': + fraction = 1. - din['jp_fraction_re']['data'] + din['ne_m3']['data'] -= ne_re + else: + fraction = din['jp_fraction_re']['data'] + din['jp_Am2']['data'] = jp_Am20 * fraction + + # ---------- + # compute + + ddist['dist'][kdist] = dfunc[kdist]['func']( + # inputs + dplasma=din, + # coords + dcoords=dc, + version=dfunc[kdist]['version'], + dominant=dominant, + ) + + # nan => 0 + inan = np.isnan(ddist['dist'][kdist]['dist']['data']) + ddist['dist'][kdist]['dist']['data'][inan] = 0. + + # scale + ne_re = _scale( + din=din, + ddist=ddist, + kdist=kdist, + dcoords=dcoords, + version=version, + ) + + # -------------- + # get numerical density, current + # -------------- + + # verb + if verb >= 1: + msg = "integrating all..." + print(msg) + + # integrate + for kdist in ddist['dist'].keys(): + ne, units_ne, jp, units_jp, ref_integ = _integrate( + ddist=ddist, + kdist=kdist, + dcoords=dcoords, + version=version, + ) + + # store + ddist['dist'][kdist].update({ + 'integ_ne': { + 'data': ne, + 'units': units_ne, + 'ref': ref_integ, + }, + 'integ_jp': { + 'data': jp, + 'units': units_jp, + 'ref': ref_integ, + }, + }) + + return ddist + + +# ####################################################### +# ####################################################### +# prepare +# ####################################################### + + +# ####################################################### +# ####################################################### +# scale +# ####################################################### + + +def _scale( + din=None, + dcoords=None, + ddist=None, + kdist=None, + version=None, +): + + ne_re = 0. + ne_units = asunits.Unit(din['ne_m3']['units']) + + # -------------------------- + # start with non-Maxwellian (current fraction of RE) + # -------------------------- + + if kdist == 'RE': + + ne_re, units_ne, jp_re, units_jp, ref_integ = _integrate( + ddist=ddist, + kdist=kdist, + dcoords=dcoords, + version=version, + ) + + iok = np.isfinite(ne_re) + iok[iok] = ne_re[iok] > 0. + sli0 = (iok,) + (None,)*len(ddist['coords']) + sli1 = (iok,) + (slice(None),)*len(ddist['coords']) + coef = np.zeros(din['jp_Am2']['data'].shape, dtype=float) + coef[sli1] = din['jp_Am2']['data'][sli1] / jp_re[sli0] + + # scale vs current + ddist['dist'][kdist]['dist']['data'] *= coef + ddist['dist'][kdist]['dist']['units'] *= ne_units + + # adjust ne_re + sli = (slice(None),)*ne_re.ndim + (None,)*len(ddist['coords']) + ne_re[np.isnan(ne_re)] = 0. + ne_re = ne_re[sli] * coef + + # -------------------------- + # Maxwellian (density) + # -------------------------- + + else: + + ne, units_ne, jp, units_jp, ref_integ = _integrate( + ddist=ddist, + kdist=kdist, + dcoords=dcoords, + version=version, + ) + + ne_max = din['ne_m3']['data'] + jp_max = din['jp_Am2']['data'] + sli = (slice(None),)*jp.ndim + (None,)*len(ddist['coords']) + + # ------------ + # sanity check + + err_ne = np.nanmax(np.abs(ne - 1.)) + err_jp = np.nanmax(np.abs(jp[sli]*ne_max/jp_max - 1.)) + if err_ne > 0.05 or err_jp > 0.05: + msg = ( + "Numerical error on integrated maxwellian:\n" + f"\t- ne: {err_ne*100:3.2f} %\n" + f"\t- jp: {err_jp*100:3.2f} %\n" + ) + warnings.warn(msg) + + ddist['dist']['maxwell']['dist']['data'] *= ne_max + ddist['dist']['maxwell']['dist']['units'] *= ne_units + + return ne_re + + +# ##################################################### +# ##################################################### +# Get velocity +# ##################################################### + + +def _get_velocity_par(ddist, kdist): + + kcoords = tuple([ + ddist['coords'][kk]['key'] for kk in ['x0', 'x1'] + if ddist['coords'].get(kk) is not None + ]) + shape = ddist['dist'][kdist]['dist']['data'].shape + if kcoords == ('E_eV', 'theta'): + + sli = (None,)*(len(shape)-2) + (slice(None), None) + E = ddist['coords']['x0']['data'][sli] + Ef = np.broadcast_to(E, shape) + + # abs(velocity) + velocity = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=Ef, + )['velocity_ms'] + + # get cos + sli = (None,)*(len(shape)-2) + (None, slice(None)) + cos = np.cos(ddist['coords']['x1']['data'][sli]) + v_par_ms = velocity['data'] * cos + units = velocity['units'] + + elif kcoords == ('p_par_norm', 'p_perp_norm'): + + sli = (None,)*(len(shape)-2) + (slice(None),)*2 + pnorm = np.sqrt( + ddist['coords']['x0']['data'][:, None]**2 + + ddist['coords']['x1']['data'][None, :]**2 + )[sli] + pnorm = np.broadcast_to(pnorm, shape) + + # abs(velocity) + velocity = _convert.convert_momentum_velocity_energy( + momentum_normalized=pnorm, + )['velocity_ms'] + + # sign + sli = (None,)*(len(shape)-2) + (slice(None), None) + cos = np.zeros(pnorm.shape, dtype=float) + iok = pnorm > 0. + cos[iok] = ( + np.broadcast_to(ddist['coords']['x0']['data'][sli], shape)[iok] + / pnorm[iok] + ) + v_par_ms = velocity['data'] * cos + units = velocity['units'] + + elif kcoords == ('E_eV',): + + # abs(velocity) + v_par_ms = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=ddist['coords']['x0']['data'], + )['velocity_ms'] + units = v_par_ms['units'] + v_par_ms = v_par_ms['data'] + + else: + raise NotImplementedError(kcoords) + + # --------------- + # abs() => v_par + # --------------- + + velocity_par = { + 'data': v_par_ms, + 'units': asunits.Unit(units), + } + + return velocity_par + + +# ##################################################### +# ##################################################### +# Integrate numerically +# ##################################################### + + +def _integrate( + ddist=None, + kdist=None, + dcoords=None, + version=None, +): + + # --------- + # integrate + # --------- + + # velocity + velocity_par = _get_velocity_par(ddist, kdist) + + # integrate over x1 + if dcoords.get('x1') is None: + current = ( + scpct.e + * velocity_par['data'] + * ddist['dist'][kdist]['dist']['data'] + ) + ne = ddist['dist'][kdist]['dist']['data'] + x0 = dcoords['x0']['data'] + else: + current = scpinteg.trapezoid( + scpct.e + * velocity_par['data'] + * ddist['dist'][kdist]['dist']['data'], + x=dcoords['x1']['data'], + axis=-1, + ) + ne = scpinteg.trapezoid( + ddist['dist'][kdist]['dist']['data'], + x=dcoords['x1']['data'], + axis=-1, + ) + x0 = dcoords['x0']['data'] + + # integrate over x0 + current = scpinteg.trapezoid( + current, + x=x0, + axis=-1, + ) + ne = scpinteg.trapezoid( + ne, + x=x0, + axis=-1, + ) + + # adjust if needed + if version == 'f3d_E_theta': + current = current * (2.*np.pi) + ne = ne * (2.*np.pi) + + # --------- + # ref + # --------- + + if ddist['dist'][kdist]['dist'].get('ref') is None: + ref_integ = None + else: + ref_integ = ddist['dist'][kdist]['dist']['ref'][:-2] + + # --------- + # units + # --------- + + if ddist['dist'][kdist]['dist']['units'] is None: + ddist['dist'][kdist]['dist']['units'] = '' + units_ne = asunits.Unit(ddist['dist'][kdist]['dist']['units']) + for k0, v0 in dcoords.items(): + if v0['units'] not in ['', None]: + units_ne = units_ne * asunits.Unit(v0['units']) + + # adjust of needed + if version == 'f3d_E_theta': + units_ne = units_ne * asunits.Unit('rad') + + units_jp = units_ne * velocity_par['units'] * asunits.Unit('C') + + return ne, units_ne, current, units_jp, ref_integ diff --git a/tofu/physics_tools/electrons/distribution/_distribution_avalanche.py b/tofu/physics_tools/electrons/distribution/_distribution_avalanche.py new file mode 100644 index 000000000..612d106a7 --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/_distribution_avalanche.py @@ -0,0 +1,244 @@ + + +import numpy as np +import scipy.constants as scpct +import astropy.units as asunits + + +from .. import _convert + + +# ##################################################### +# ##################################################### +# Dict of functions +# ##################################################### + + +def f2d_ppar_pperp( + p_par_norm=None, + p_perp_norm=None, + p_max_norm=None, + p_crit=None, + Cz=None, + lnG=None, + E_hat=None, + sigmap=None, + # unused + **kwdargs, +): + """ See [1], eq. (6) + + [1] S. P. Pandya et al., Phys. Scr., 93, p. 115601, 2018 + doi: 10.1088/1402-4896/aaded0. + """ + + shape = np.broadcast_shapes( + p_par_norm.shape, + p_perp_norm.shape, + E_hat.shape, + ) + p_par_norm = np.broadcast_to(p_par_norm, shape) + iok = p_par_norm > 0. + + # fermi decay factor, adim + fermi = np.broadcast_to( + 1. / (np.exp((p_par_norm - p_max_norm) / sigmap) + 1.), + shape, + ) + + # ratio2 + pperp2par = np.zeros(shape, dtype=float) + pperp2par[iok] = ( + np.broadcast_to(p_perp_norm, shape)[iok]**2 + / p_par_norm[iok] + ) + + # distribution, adim + dist = np.zeros(shape, dtype=float) + exp = np.zeros(shape, dtype=float) + exp[iok] = np.exp(-p_par_norm / (Cz*lnG) - 0.5*E_hat*pperp2par)[iok] + dist[iok] = ( + np.broadcast_to(E_hat / (2.*np.pi*Cz*lnG), shape)[iok] + * (1. / p_par_norm[iok]) # Not in formula, but necessary + * exp[iok] + * fermi[iok] + ) + + # critical momentum + iout = np.sqrt(p_par_norm**2 + p_perp_norm**2) < p_crit + dist[iout] = 0. + + units = asunits.Unit('') + + return dist, units + + +def f2d_momentum_theta( + pnorm=None, + theta=None, + p_max_norm=None, + p_crit=None, + Cz=None, + lnG=None, + E_hat=None, + sigmap=None, + # unused + **kwdargs, +): + """ Based on f2d_ppar_pperp + jacobian + """ + + dist0, units0 = f2d_ppar_pperp( + p_par_norm=pnorm * np.cos(theta), + p_perp_norm=pnorm * np.sin(theta), + p_max_norm=p_max_norm, + p_crit=p_crit, + Cz=Cz, + lnG=lnG, + E_hat=E_hat, + sigmap=sigmap, + ) + + # jacobian + jac = pnorm + + # dist + dist = jac * dist0 + units = units0 * asunits.Unit('1/rad') + + return dist, units + + +def f2d_momentum_pitch( + pnorm=None, + pitch=None, + Cz=None, + lnG=None, + E_hat=None, + Zeff=None, + # unused + **kwdargs, +): + """ Based on [1] eq (2.17) + [1] O. Embréus et al., J. Plasma Phys., 84, p. 905840506, 2018 + doi: 10.1017/S0022377818001010. + + !!! Reversed convention in paper: electrons accelerated towards -1 !!! + + """ + gamma = _convert.convert_momentum_velocity_energy( + momentum_normalized=pnorm, + )['gamma']['data'] + gam0 = lnG * np.sqrt(Zeff + 5.) + + mec_kgms = scpct.m_e * scpct.c + pp_kgms = pnorm * mec_kgms + + Ap = gamma * (E_hat + 1) / (Zeff + 1) + + # reverse sign of pitch + pitch = -pitch + + dist = ( + (Ap/(2.*np.pi*mec_kgms*pp_kgms**2*gam0)) + * np.exp(-gamma / gam0 - Ap*(1 + pitch)) + / (1. - np.exp(-2.*Ap)) + ) + + units = asunits.Unit('s^3/(kg^3.m^3)') + + return dist, units + + +def f2d_E_theta( + E_eV=None, + theta=None, + p_max_norm=None, + p_crit=None, + Cz=None, + lnG=None, + E_hat=None, + sigmap=None, + # unused + **kwdargs, +): + """ Based on f2d_ppar_pperp + jacobian + """ + + # ----------------------- + # get momentum normalized + + pnorm = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=E_eV, + )['momentum_normalized']['data'] + + # --------- + # get dist0 + + dist0, units0 = f2d_momentum_theta( + pnorm=pnorm, + theta=theta, + p_max_norm=p_max_norm, + p_crit=p_crit, + Cz=Cz, + lnG=lnG, + E_hat=E_hat, + sigmap=sigmap, + ) + + # ------------- + # jacobian + # dp = gam / sqrt(gam^2 - 1) dgam + # dgam = dE / mc2 + + gamma = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=E_eV, + )['gamma']['data'] + mc2_eV = scpct.m_e * scpct.c**2 / scpct.e + + # jacobian + jac = gamma / np.sqrt(gamma**2 - 1) / mc2_eV + + # dist + dist = dist0 * jac + units = units0 * asunits.Unit('1/eV') + + return dist, units + + +def f3d_E_theta( + E_eV=None, + theta=None, + p_max_norm=None, + p_crit=None, + Cz=None, + lnG=None, + E_hat=None, + sigmap=None, + # unused + **kwdargs, +): + """ Based on f2d_E_theta / 2pi + """ + + # --------- + # get dist0 + + dist0, units0 = f2d_E_theta( + E_eV=E_eV, + theta=theta, + p_max_norm=p_max_norm, + p_crit=p_crit, + Cz=Cz, + lnG=lnG, + E_hat=E_hat, + sigmap=sigmap, + ) + + # --------- + # adjust + + dist = dist0 / (2.*np.pi) + units = units0 * asunits.Unit('1/rad') + + return dist, units diff --git a/tofu/physics_tools/electrons/distribution/_distribution_check.py b/tofu/physics_tools/electrons/distribution/_distribution_check.py new file mode 100644 index 000000000..8fd02a1ba --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/_distribution_check.py @@ -0,0 +1,477 @@ + + +import numpy as np +import astropy.units as asunits +import datastock as ds +import tofu as tf + + +from . import _distribution_maxwell as _maxwell +from . import _distribution_re as _re + + +# ####################################################### +# ####################################################### +# DEFAULTS +# ####################################################### + + +_DPLASMA = { + 'Te_eV': { + 'def': 1e3, + 'units': 'eV', + }, + 'ne_m3': { + 'def': 1e19, + 'units': '1/m3', + }, + 'jp_Am2': { + 'def': 1e6, + 'units': 'A/m2', + }, + # RE + 'jp_fraction_re': { + 'def': 0., + 'units': 'A/m2', + }, + 'Te_eV_re': { + 'def': 0., + 'units': 'eV', + }, + 'ne_m3_re': { + 'def': 0., + 'units': '1/m3', + }, + 'Zeff': { + 'def': 1., + 'units': None, + }, + 'Ekin_max_eV': { + 'def': 10e6, + 'units': 'eV', + }, + 'Efield_par_Vm': { + 'def': 0.1, + 'units': 'V/m', + }, + 'lnG': { + 'def': 20., + 'units': '', + }, + 'sigmap': { + 'def': 0.1, + 'units': '', + }, +} + + +_DCOORDS = { + 'v_par_ms': {'units': 'm/s'}, + 'v_perp_ms': {'units': 'm/s'}, + 'p_par_norm': {'units': ''}, + 'p_perp_norm': {'units': ''}, + 'E_eV': {'units': 'eV'}, + 'pitch': {'units': ''}, + 'theta': {'units': 'rad'}, +} + + +_DFUNC = { + ('v_par_ms', 'v_perp_ms'): [ + 'f3d_cart_vpar_vperp', + 'f2d_cart_vpar_vperp', + 'f2d_cyl_vpar_vperp', + ], + ('p_par_norm', 'p_perp_norm'): ['f2d_ppar_pperp'], + ('E_eV',): ['f1d_E'], + ('E_eV', 'pitch'): ['f2d_E_pitch'], + ('E_eV', 'theta'): ['f2d_E_theta', 'f3d_E_theta'], +} + + +# ####################################################### +# ####################################################### +# Main +# ####################################################### + + +def main( + **kwdargs, +): + + # --------------- + # dist + # --------------- + + dist = _dist(**kwdargs) + + # --------------- + # returnas / key + # --------------- + + returnas, coll = _returnas(**kwdargs) + + # ------------------------- + # plasma parameters + # ------------------------- + + dplasma = _plasma( + ddef=_DPLASMA, + **kwdargs, + ) + + # adjust + if dist == ('maxwell',): + dplasma['jp_fraction_re']['data'][...] = 0. + + # ------------------------- + # coordinates & versions + # ------------------------- + + dcoords = _coords(**kwdargs) + + # ------------------------- + # versions and func + # ------------------------- + + dcoords, dfunc = _dfunc( + dcoords=dcoords, + version=kwdargs['version'], + dist=dist, + ) + + # ------------------------- + # verb + # ------------------------- + + lok = [False, True, 0, 1, 2] + verb = int(ds._generic_check._check_var( + kwdargs['verb'], 'verb', + types=(bool, int), + default=lok[-1], + allowed=lok, + )) + + return dist, dplasma, dcoords, dfunc, coll, verb + + +# ####################################################### +# ####################################################### +# dist +# ####################################################### + + +def _dist( + dist=None, + # unused + **kwdargs, +): + + # ----------- + # str => tuple + # ----------- + + if isinstance(dist, str): + dist = (dist,) + + # ----------- + # check allowed + set default + # ----------- + + lok = ['maxwell', 'RE'] + dist = tuple(ds._generic_check._check_var_iter( + dist, 'dist', + types=(tuple, list), + default=lok, + allowed=lok, + )) + + # ------------ + # checks + # ------------ + + if 'maxwell' not in dist: + msg = "Arg 'dist' must include 'maxwell'!" + raise Exception(msg) + + return dist + + +# ####################################################### +# ####################################################### +# Returnas +# ####################################################### + + +def _returnas( + returnas=None, + # unused + **kwdargs, +): + + if returnas is None: + returnas = dict + + if returnas is dict: + key = None + coll = None + + elif isinstance(returnas, tf.data.Collection): + coll = returnas + lok = list(coll.ddata.keys()) + key = ds._generic_check._check_var( + key, 'key', + types=str, + excluded=lok, + extra_msg="Pick a name not already used!\n" + ) + + else: + msg = ( + "Arg 'returnas' must be either:\n" + "\t- dict: return outup as a dict\n" + "\t- coll: a tf.data.Collection instance to add to / draw from\n" + f"Provided:\n{returnas}\n" + ) + raise Exception(msg) + + return returnas, coll + + +# ####################################################### +# ####################################################### +# Plasma +# ####################################################### + + +def _plasma( + ddef=None, + **kwdargs, +): + + # ------------------- + # prelim check + # ------------------- + + # initialize + lk = list(_DPLASMA.keys()) + dinputs = {kk: kwdargs[kk] for kk in lk} + + # coll + coll = kwdargs.get('coll') + + # ------------------- + # loop + # ------------------- + + dout = _extract(dinputs, coll, ddef, _DPLASMA) + + # Exception + if len(dout) > 0.: + lstr = [f"\t- {k0}: {v0}" for k0, v0 in dout.items()] + msg = ( + "The following plasma parameters are not properly set:\n" + + "\n".join(lstr) + ) + raise Exception(msg) + + # ------------------- + # broadcast + # ------------------- + + dbroad, _ = ds._generic_check._check_all_broadcastable( + return_full_arrays=True, + **{kk: vv['data'] for kk, vv in dinputs.items()}, + ) + + # update dinputs + for k0, v0 in dbroad.items(): + dinputs[k0]['data'] = v0 + + return dinputs + + +# ####################################################### +# ####################################################### +# Generic extract routine +# ####################################################### + + +def _extract(din, coll, ddef, ddef0): + + dout = {} + for k0 in din.keys(): + # units + units = ddef.get(k0, ddef0[k0]).get('units') + + # check vs None + if din.get(k0) is None: + data = np.asarray(ddef.get(k0, ddef0[k0]).get('def')) + else: + data = din[k0] + + # if str => coll.ddata + if isinstance(data, str): + + if coll is None: + dout[k0] = "for using str, provide returnas=coll" + continue + + if data not in coll.ddata.keys(): + dout[k0] = f"not available in coll.ddata: {data}" + continue + + units0 = coll.ddata[data]['units'] + if asunits.Unit(units0) != units: + dout[k0] = f"wrong units: {units0} vs {units}" + continue + + # ref = coll.ddata[data]['ref'] + data = np.copy(coll.ddata[data]['data']) + + else: + # ref = None + data = np.atleast_1d(data) + + # set subdict + din[k0] = { + 'data': data, + 'units': units, + # 'ref': ref, # not relevant due to later broadcasting + } + + return dout + + +# ####################################################### +# ####################################################### +# Coords +# ####################################################### + + +def _coords( + **kwdargs, +): + + # -------------- + # preliminary + # -------------- + + # initialize + lk = list(_DCOORDS.keys()) + dcoords = {kk: kwdargs[kk] for kk in lk if kwdargs[kk] is not None} + + # coll + coll = kwdargs.get('coll') + + # ------------------- + # loop + # ------------------- + + dout = _extract(dcoords, coll, _DCOORDS, _DCOORDS) + + # Exception + if len(dout) > 0.: + lstr = [f"\t- {k0}: {v0}" for k0, v0 in dout.items()] + msg = ( + "The following plasma parameters are not properly set:\n" + + "\n".join(lstr) + ) + raise Exception(msg) + + # -------------- + # check 1d + # -------------- + + dout = {} + for k0, v0 in dcoords.items(): + if v0['data'].ndim != 1: + dout[k0] = f"coordinate '{k0}' not 1d: {v0['data'].shape}" + + # Exception + if len(dout) > 0.: + lstr = [f"\t- {k0}: {v0}" for k0, v0 in dout.items()] + msg = ( + "The following coordinates should be 1d arrays!:\n" + + "\n".join(lstr) + ) + raise Exception(msg) + + return dcoords + + +# ####################################################### +# ####################################################### +# dfunc +# ####################################################### + + +def _dfunc( + dist=None, + dcoords=None, + version=None, +): + + # -------------- + # check a pair exist + # -------------- + + pair = tuple(sorted(dcoords.keys())) + if pair not in _DFUNC.keys(): + lstr0 = [f"\t- {k0}: {v0}" for k0, v0 in _DFUNC.items()] + lstr1 = [f"\t- {k0}" for k0 in pair] + msg = ( + "Please provide 1 or 2 coordinates max!\n" + "Possible pairs and matching func:\n" + + "\n".join(lstr0) + + "\nProvided:\n" + + "\n".join(lstr1) + ) + raise Exception(msg) + + # -------------- + # remap to x0, x1 + # -------------- + + dnew = {} + for ii, kk in enumerate(pair): + dnew[f"x{ii}"] = { + 'key': kk, + 'data': dcoords[kk]['data'], + 'units': dcoords[kk]['units'], + } + dcoords = dnew + + # -------------- + # version + # -------------- + + version = ds._generic_check._check_var( + version, 'version', + types=str, + allowed=_DFUNC[pair], + default=_DFUNC[pair][-1], + ) + + # -------------- + # dfunc + # -------------- + + dfunc = {} + for kdist in dist: + + # choose module + if kdist == 'maxwell': + mod = _maxwell + else: + mod = _re + + func = getattr(mod, 'main') + + # store + dfunc[kdist] = { + 'version': version, + 'func': func, + } + + return dcoords, dfunc diff --git a/tofu/physics_tools/electrons/distribution/_distribution_dreicer.py b/tofu/physics_tools/electrons/distribution/_distribution_dreicer.py new file mode 100644 index 000000000..2c0514394 --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/_distribution_dreicer.py @@ -0,0 +1,218 @@ + + +import numpy as np +import scipy.constants as scpct +import scipy.special as scpsp +import astropy.units as asunits + + +from .. import _convert + + +# ##################################################### +# ##################################################### +# Elementary functions +# ##################################################### + + +def f2d_ppar_pperp( + p_par_norm=None, + p_perp_norm=None, + Cs=None, + Etild=None, + Zeff=None, + # unused + **kwdargs, +): + """ See [1], eq. (7-8) + + [1] S. P. Pandya et al., Phys. Scr., 93, p. 115601, 2018 + doi: 10.1088/1402-4896/aaded0. + """ + + shape = np.broadcast_shapes( + p_par_norm.shape, + p_perp_norm.shape, + Etild.shape, + ) + iok = np.broadcast_to(p_par_norm > 0, shape) + p_par_norm = np.broadcast_to(p_par_norm, shape) + + # pper2par + pperp2par = np.zeros(shape, dtype=float) + pperp2par[iok] = ( + np.broadcast_to(p_perp_norm**2, shape)[iok] + / p_par_norm[iok] + ) + + # Hypergeometric confluent Kummer function + term1 = 1 - Cs / (Etild + 1) + term2 = ((Etild + 1) / (2.*(1. + Zeff))) * pperp2par + F1 = np.zeros(shape, dtype=float) + F1[iok] = scpsp.hyp1f1(np.broadcast_to(term1, shape)[iok], 1, term2[iok]) + + # ppar_exp_inv + ppar_exp_inv = np.zeros(shape, dtype=float) + power = np.broadcast_to((Cs - 2.) / (Etild - 1.), shape)[iok] + ppar_exp_inv[iok] = 1. / (p_par_norm[iok]**power) + + # exponential + exponential = np.exp(-((Etild + 1) / (2 * (1 + Zeff))) * pperp2par) + + # distribution + dist = np.zeros(shape, dtype=float) + iok = np.isfinite(F1) + dist[iok] = ppar_exp_inv[iok] * exponential[iok] * F1[iok] + + # units + units = asunits.Unit('') + + return dist, units + + +def f2d_momentum_pitch( + pnorm=None, + pitch=None, + # params + E_hat=None, + Zeff=None, + # unused + **kwdargs, +): + """ See [1] + [1] https://soft2.readthedocs.io/en/latest/scripts/DistributionFunction/ConnorHastie.html#module-distribution-connor + """ + B = (E_hat + 1) / (Zeff + 1) + + shape = np.broadcast_shapes( + pnorm.shape, + pitch.shape, + E_hat.shape, + ) + iok = np.broadcast_to((pitch > 0.) & (pnorm > 0.), shape) + dist = np.zeros(shape, dtype=float) + dist[iok] = ( + np.exp(-0.5*B * (1 - pitch**2) * pnorm / np.abs(pitch))[iok] + / np.broadcast_to(pnorm * pitch, shape)[iok] + ) + units = asunits.Unit('') + return dist, units + + +def f2d_momentum_theta( + pnorm=None, + theta=None, + # params + E_hat=None, + Zeff=None, + # unused + **kwdargs, +): + dist0, units0 = f2d_momentum_pitch( + pnorm=pnorm, + pitch=np.cos(theta), + # params + E_hat=E_hat, + Zeff=Zeff, + ) + + dist = np.sin(theta) * dist0 + units = units0 * asunits.Unit('1/rad') + + return dist, units + + +def f2d_E_theta( + E_eV=None, + theta=None, + # params + E_hat=None, + Zeff=None, + # unused + **kwdargs, +): + + # ----------------------- + # get momentum normalized + + pnorm = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=E_eV, + )['momentum_normalized']['data'] + + # --------- + # get dist0 + + dist0, units0 = f2d_momentum_theta( + pnorm=pnorm, + theta=theta, + # params + E_hat=E_hat, + Zeff=Zeff, + ) + + # ------------- + # jacobian + # dp = gam / sqrt(gam^2 - 1) dgam + # dgam = dE / mc2 + + gamma = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=E_eV, + )['gamma']['data'] + mc2_eV = scpct.m_e * scpct.c**2 / scpct.e + + jac = gamma / np.sqrt(gamma**2 - 1) / mc2_eV + + dist = dist0 * jac + units = units0 * asunits.Unit('1/eV') + + return dist, units + + +def f3d_E_theta( + E_eV=None, + theta=None, + # params + E_hat=None, + Zeff=None, + # unused + **kwdargs, +): + + # --------- + # get dist0 + + dist0, units0 = f2d_E_theta( + E_eV=E_eV, + theta=theta, + # params + E_hat=E_hat, + Zeff=Zeff, + ) + + # --------- + # adjust + + dist = dist0 / (2.*np.pi) + units = units0 * asunits.Unit('1/rad') + + return dist, units + + +# ##################################################### +# ##################################################### +# Dict of functions +# ##################################################### + + +_DFUNC = { + 'f2d_E_theta_dreicer': { + 'func': f2d_E_theta, + 'latex': ( + r"$dn_e = \int_{E_{min}}^{E_{max}} \int_0^{\pi}$" + r"$f^{2D}_{E, \theta}(E, \theta) dEd\theta$" + + "\n" + + r"\begin{eqnarray*}" + r"\end{eqnarray*}" + ), + }, +} diff --git a/tofu/physics_tools/electrons/distribution/_distribution_maxwell.py b/tofu/physics_tools/electrons/distribution/_distribution_maxwell.py new file mode 100644 index 000000000..65b4af443 --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/_distribution_maxwell.py @@ -0,0 +1,399 @@ + + +import numpy as np +import scipy.constants as scpct +import astropy.units as asunits + + +# ##################################################### +# ##################################################### +# Main +# ##################################################### + + +def main( + # coordinates + dcoords=None, + version=None, + # plasma + dplasma=None, + # unused + **kwdargs, +): + + # -------------- + # prepare + # -------------- + + # electron mass + me = scpct.m_e + + # kbTe_J + kbT_J = dplasma['Te_eV']['data'] * scpct.e + + # v0_par from current (m/s) + v0_par_ms = ( + dplasma['jp_Am2']['data'] + / (scpct.e * dplasma['ne_m3']['data']) + ) + vt_ms = np.sqrt(2. * kbT_J / me) + + # -------------- + # format output + # -------------- + + dist, units = eval(version)( + vt_par_ms=vt_ms, + vt_perp_ms=vt_ms, + v0_par_ms=v0_par_ms, + kbT_par_J=kbT_J, + kbT_perp_J=kbT_J, + **dcoords, + ) + + # -------------- + # format output + # -------------- + + dout = { + 'dist': { + 'data': dist, + 'units': units, + }, + 'v0_par_ms': { + 'data': v0_par_ms, + 'units': 'm/s', + }, + 'vt_ms': { + 'data': vt_ms, + 'units': 'm/s', + }, + 'kbT_J': { + 'data': kbT_J, + 'units': 'J', + }, + } + + return dout + + +# ##################################################### +# ##################################################### +# Elementary Maxwellians +# ##################################################### + + +def f3d_cart_vpar_vperp( + v_par_ms=None, + v_perp_ms=None, + vt_par_ms=None, + vt_perp_ms=None, + v0_par_ms=None, + # unused + **kwdargs, +): + term0 = 1. / (np.pi**1.5 * vt_par_ms * vt_perp_ms**2) + term_par = (v_par_ms - v0_par_ms)**2 / vt_par_ms**2 + term_perp = v_perp_ms**2 / vt_perp_ms**2 + + dist = term0 * np.exp(- term_par - term_perp) + units = asunits.Unit('s^3/m^3') + return dist, units + + +def f3d_cyl_vpar_vperp( + v_par_ms=None, + v_perp_ms=None, + vt_par_ms=None, + vt_perp_ms=None, + v0_par_ms=None, + # unused + **kwdargs, +): + dist0, units0 = f3d_cart_vpar_vperp( + v_par_ms, + v_perp_ms, + vt_par_ms, + vt_perp_ms, + v0_par_ms, + ) + dist = v_perp_ms * dist0 + units = units0 * asunits.Unit('m/s') + return dist, units + + +def f2d_cart_vpar_vperp( + v_par_ms=None, + v_perp_ms=None, + vt_par_ms=None, + vt_perp_ms=None, + v0_par_ms=None, + # unused + **kwdargs, +): + dist0, units0 = f3d_cart_vpar_vperp( + v_par_ms, + v_perp_ms, + vt_par_ms, + vt_perp_ms, + v0_par_ms, + ) + dist = 2. * np.pi * v_perp_ms * dist0 + units = units0 * asunits.Unit('m/s') + return dist, units + + +def f2d_ppar_pperp( + p_par_norm=None, + p_perp_norm=None, + vt_par_ms=None, + vt_perp_ms=None, + v0_par_ms=None, + # unused + **kwdargs, +): + """ Integral not unit => problem somewhere !""" + + dist0, units0 = f2d_cart_vpar_vperp( + v_par_ms=p_par_norm * scpct.c, + v_perp_ms=p_perp_norm * scpct.c, + vt_par_ms=vt_par_ms, + vt_perp_ms=vt_perp_ms, + v0_par_ms=v0_par_ms, + ) + + dist = dist0 * scpct.c**2 + units = units0 * asunits.Unit('m^2/s^2') + + return dist, units + + +def f2d_E_pitch( + E_eV=None, + pitch=None, + kbT_par_J=None, + kbT_perp_J=None, + v0_par_ms=None, + # unused + **kwdargs, +): + me_kg = scpct.m_e + qq = scpct.e + E_J = E_eV * qq + + term0 = np.sqrt(E_J / (np.pi * kbT_par_J * kbT_perp_J**2)) + term_par = (pitch * np.sqrt(E_J) - np.sqrt(me_kg/2.) * v0_par_ms)**2 + term_perp = (1 - pitch**2) * E_J + + dist = qq * term0 * np.exp(-term_par / kbT_par_J - term_perp / kbT_perp_J) + units = asunits.Unit('1/eV') + + return dist, units + + +def f3d_E_theta( + E_eV=None, + theta=None, + kbT_par_J=None, + kbT_perp_J=None, + v0_par_ms=None, + # unused + **kwdargs, +): + + dist0, units0 = f2d_E_pitch( + E_eV=E_eV, + pitch=np.cos(theta), + kbT_par_J=kbT_par_J, + kbT_perp_J=kbT_perp_J, + v0_par_ms=v0_par_ms, + ) + + dist = np.sin(theta) * dist0 / (2.*np.pi) + units = units0 * asunits.Unit('1/rad^2') + + return dist, units + + +def f2d_E_theta( + E_eV=None, + theta=None, + kbT_par_J=None, + kbT_perp_J=None, + v0_par_ms=None, + # unused + **kwdargs, +): + + dist0, units0 = f2d_E_pitch( + E_eV=E_eV, + pitch=np.cos(theta), + kbT_par_J=kbT_par_J, + kbT_perp_J=kbT_perp_J, + v0_par_ms=v0_par_ms, + ) + + dist = np.sin(theta) * dist0 + units = units0 * asunits.Unit('1/rad') + + return dist, units + + +def f1d_E( + E_eV=None, + kbT_par_J=None, + kbT_perp_J=None, + v0_par_ms=None, + # unused + **kwdargs, +): + + # ------------ + # safety check + if not np.allclose(kbT_par_J, kbT_perp_J): + msg = "f1d_E assumes kbT_par_J == kbT_perp_J" + raise Exception(msg) + + me_kg = scpct.m_e + mev2 = 0.5*me_kg*v0_par_ms**2 + qq = scpct.e + E_J = E_eV * qq + + iok = v0_par_ms[..., 0] > 0. + shapef = np.broadcast_shapes(kbT_par_J.shape, v0_par_ms.shape, E_J.shape) + dist = np.full(shapef, np.nan) + + if np.any(iok): + denom = (2. * np.pi * kbT_par_J[iok, :] * me_kg) + term0 = 1. / (v0_par_ms[iok, :] * np.sqrt(denom)) + term_p = (np.sqrt(E_J) + np.sqrt(mev2[iok, :]))**2 / kbT_par_J[iok, :] + term_m = (np.sqrt(E_J) - np.sqrt(mev2[iok, :]))**2 / kbT_par_J[iok, :] + + dist[iok, :] = qq * term0 * (np.exp(-term_m) - np.exp(-term_p)) + + if np.any(~iok): + i0 = ~iok + dist[i0, :] = 2. * f2d_E_pitch( + E_eV=E_eV, + pitch=0., + kbT_par_J=kbT_par_J[i0, :], + kbT_perp_J=kbT_perp_J[i0, :], + v0_par_ms=0., + )[0] + + units = asunits.Unit('1/eV') + + return dist, units + + +# ##################################################### +# ##################################################### +# Dict of functions +# ##################################################### + + +_DFUNC = { + 'f3d_cart_vpar_vperp': { + 'func': f3d_cart_vpar_vperp, + 'latex': ( + r"$dn_e = \int_0^\infty \int_{-\infty}^\infty$" + r"$f^{2D}_{v_{//}, v_{\perp}}(v_{//}, v_{\perp})$" + r"$dv_{//}dv_{\perp}$" + + "\n" + + r"\begin{eqnarray*}" + r"\frac{n_e}{\pi^{3/2} v_{T//} v^2_{T\perp}}" + r"\exp\left(" + r"-\frac{\left(v_{//} - v_{d//}\right)^2}{v^2_{T//}}" + r"-\frac{v^2_{\perp}}{v^2_{T\perp}}" + r"\right)" + r"\end{eqnarray*}" + ), + }, + 'f2d_cart_vpar_vperp': { + 'func': f2d_cart_vpar_vperp, + 'latex': ( + r"$dn_e = \int_0^\infty \int_{-\infty}^\infty$" + r"$f^{2D}_{v_{//}, v_{\perp}}(v_{//}, v_{\perp})$" + r"$dv_{//}dv_{\perp}$" + + "\n" + + r"\begin{eqnarray*}" + r"\frac{2n_e v_{\perp}}{\sqrt{\pi} v_{T//} v^2_{T\perp}}" + r"\exp\left(" + r"-\frac{\left(v_{//} - v_{d//}\right)^2}{v^2_{T//}}" + r"-\frac{v^2_{\perp}}{v^2_{T\perp}}" + r"\right)" + r"\end{eqnarray*}" + ), + }, + 'f3d_cyl_vpar_vperp': { + 'func': f3d_cyl_vpar_vperp, + 'latex': ( + ), + }, + 'f2d_E_pitch': { + 'func': f2d_E_pitch, + 'latex': ( + r"$dn_e = \int_0^{\infty} \int_{-1}^1$" + r"$f^{2D}_{E, p}(E, p) dEdp$" + + "\n" + + r"\begin{eqnarray*}" + r"n_e \sqrt{\frac{E}{\pi T^2_{\perp}T_{//}}}" + r"\exp\left(" + r"-\frac{\left(p\sqrt{E} - \sqrt{m_e/2}v_{d//}\right)^2}{T_{//}}" + r"- \frac{(1-p^2)E}{T_{\perp}}" + r"\right)" + r"\end{eqnarray*}" + ), + }, + 'f3d_E_theta': { + 'func': f3d_E_theta, + 'latex': ( + r"$dn_e = \int_0^\infty \int_0\pi \int_0^{2\pi}$" + r"$f^{3D}_{E, \theta}(E, \theta) dEd\thetad\phi$" + + "\n" + + r"\begin{eqnarray*}" + r"\frac{n_e}{2\pi}" + r"\sin{\theta}\sqrt{\frac{E}{\pi T^2_{\perp}T_{//}}}" + r"\exp\left(" + r"-\frac{\left(p\sqrt{E} - \sqrt{m_e/2}v_{d//}\right)^2}{T_{//}}" + r"- \frac{(1-p^2)E}{T_{\perp}}" + r"\right)" + r"\end{eqnarray*}" + ), + }, + 'f2d_E_theta': { + 'func': f2d_E_theta, + 'latex': ( + r"$dn_e = \int_0^\infty \int_0\pi$" + r"$f^{2D}_{E, \theta}(E, \theta) dEd\theta$" + + "\n" + + r"\begin{eqnarray*}" + r"n_e \sin{\theta}\sqrt{\frac{E}{\pi T^2_{\perp}T_{//}}}" + r"\exp\left(" + r"-\frac{\left(p\sqrt{E} - \sqrt{m_e/2}v_{d//}\right)^2}{T_{//}}" + r"- \frac{(1-p^2)E}{T_{\perp}}" + r"\right)" + r"\end{eqnarray*}" + ), + }, + 'f1d_E': { + 'func': f1d_E, + 'latex': ( + "Assumes " + r"$T_{\perp} = T_{//} = T$" + + "\n" + + r"$dn_e = \int_0^\infty f^{1D}_{E}(E) dE$" + + "\n" + + r"\begin{eqnarray*}" + r"\frac{n_e}{v_{d//}\sqrt{\pi T 2m_e}}" + r"\left(" + r" \exp\left(" + r" \frac{\left(\sqrt{E} - \sqrt{m_e v_{d//}^2/2}\right)^2}{T}" + r" \right)" + r" - \exp\left(" + r" \frac{\left(\sqrt{E} + \sqrt{m_e v_{d//}^2/2}\right)^2}{T}" + r" \right)" + r"\right)" + r"\end{eqnarray*}" + ), + }, +} diff --git a/tofu/physics_tools/electrons/distribution/_distribution_plot.py b/tofu/physics_tools/electrons/distribution/_distribution_plot.py new file mode 100644 index 000000000..e12845eee --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/_distribution_plot.py @@ -0,0 +1,738 @@ + + +import numpy as np +# import scipy.stats as scpstats +import scipy.integrate as scpinteg +import scipy.stats as scpstats +import matplotlib.pyplot as plt +import matplotlib.gridspec as gridspec +import matplotlib.lines as mlines +import astropy.units as asunits +import datastock as ds + + +from .. import _convert +from . import _distribution_check +from . import _distribution + + +try: + plt.rcParams['text.usetex'] = True +except Exception: + pass + + +# ############################################ +# ############################################ +# Default +# ############################################ + + +_DPLASMA = { + 'Te_eV': { + 'def': np.r_[1, 1, 5, 5]*1e3, + 'units': 'eV', + }, + 'ne_m3': { + 'def': 1e19, + 'units': '1/m3', + }, + 'jp_Am2': { + 'def': 1e6, + 'units': 'A/m2', + }, + 'jp_fraction_re': { + 'def': np.r_[0.1, 0.9, 0.1, 0.9], + 'units': None, + }, + 'Zeff': { + 'def': 1., + 'units': None, + }, + 'Ekin_max_eV': { + 'def': 10e6, + 'units': 'eV', + }, + 'Efield_par_Vm': { + 'def': 1., + 'units': 'V/m', + }, + 'lnG': { + 'def': 20., + 'units': None, + }, + 'sigmap': { + 'def': 1., + 'units': None, + }, +} + + +# DCOORDS +_EMAX_EV = 20e6 +_DCOORDS = { + 'E_eV': np.logspace(1, np.log10(_EMAX_EV), 201), + 'ntheta': 41, + 'nperp': 201, +} + + +# ############################################ +# ############################################ +# Maxwellian - 2d +# ############################################ + + +def main( + # ----------- + # plasma paremeters + Te_eV=None, + ne_m3=None, + jp_Am2=None, + jp_fraction_re=None, + # RE-specific + Zeff=None, + Ekin_max_eV=None, + Efield_par_Vm=None, + lnG=None, + sigmap=None, + # ----------- + # coordinates + E_eV=None, + ntheta=None, + nperp=None, + # plotting + dax=None, + fontsize=None, + dmargin=None, +): + + # ---------------- + # check inputs + # ---------------- + + ( + dplasma, + dprop, + dcoords, + ) = _check( + **locals(), + ) + + # ---------------- + # Compute + # ---------------- + + # f2D_E_theta + ddist_E_theta = _distribution.main( + # coordinate: momentum + E_eV=dcoords['E_eV'], + theta=dcoords['theta'], + # return as + returnas=dict, + # version + dist=('maxwell', 'RE'), + version='f2d_E_theta', + # plasma + **{kk: vv['data'] for kk, vv in dplasma.items()}, + ) + + # f2D_vpar_vperp + ddist_ppar_pperp = _distribution.main( + # coordinate: momentum + p_par_norm=dcoords['p_par_norm'], + p_perp_norm=dcoords['p_perp_norm'], + # return as + returnas=dict, + # version + dist=('maxwell', 'RE'), + version='f2d_ppar_pperp', + # plasma + **{kk: vv['data'] for kk, vv in dplasma.items()}, + ) + + # ---------------- + # Derive 1d + # ---------------- + + # E + units = ddist_E_theta['dist']['RE']['dist']['units'] * asunits.Unit('rad') + ddist_E_num = { + kdist: { + 'data': scpinteg.trapezoid( + ddist_E_theta['dist'][kdist]['dist']['data'], + x=ddist_E_theta['coords']['x1']['data'], + axis=-1, + ), + 'units': units, + } + for kdist in ddist_E_theta['dist'].keys() + } + + # pnorm + pnorm = np.sqrt( + ddist_ppar_pperp['coords']['x0']['data'][:, None]**2 + + ddist_ppar_pperp['coords']['x1']['data'][None, :]**2 + ) + pnmin = np.nanmin(pnorm[pnorm > 0.]) + pnmax = np.nanmax(pnorm) + pbins = np.logspace( + np.log10(pnmin), + np.log10(pnmax), + int(np.min(pnorm.shape) - 1), + ) + pbins = np.r_[0., pbins] + shape_plasma = ddist_E_theta['dist']['maxwell']['dist']['data'].shape[:-2] + ddist_pnorm_num = { + kdist: { + 'data': scpstats.binned_statistic( + pnorm.ravel(), + vdist['dist']['data'].reshape(shape_plasma + (-1,)), + statistic='sum', + bins=pbins, + ).statistic, + 'units': None, + } + for kdist, vdist in ddist_ppar_pperp['dist'].items() + } + + # ---------------- + # plot + # ---------------- + + dax = _plot( + ddist_E_theta=ddist_E_theta, + ddist_ppar_pperp=ddist_ppar_pperp, + # 1d + ddist_E_num=ddist_E_num, + ddist_pnorm_num=ddist_pnorm_num, + pbins=pbins, + # props + dprop=dprop, + # plotting + dax=dax, + fontsize=fontsize, + dmargin=dmargin, + ) + + return dax, ddist_E_theta, ddist_ppar_pperp + + +# ##################################################### +# ##################################################### +# check +# ##################################################### + + +def _check( + **kwdargs, +): + + # ----------------- + # plasma parameters + # ----------------- + + dplasma = _distribution_check._plasma( + ddef=_DPLASMA, + **kwdargs, + ) + shape_plasma = dplasma['Te_eV']['data'].shape + + # ----------------- + # Properties + # ----------------- + + dprop = {} + lc = ['b', 'r', 'g', 'c', 'm'] + for ii, ind in enumerate(np.ndindex(shape_plasma)): + dprop[ind] = { + 'color': lc[ii % len(lc)] + } + + # ----------------- + # E_eV, theta + # ----------------- + + # E_eV + if kwdargs['E_eV'] is None: + kwdargs['E_eV'] = _DCOORDS['E_eV'] + E_eV = ds._generic_check._check_flat1darray( + kwdargs['E_eV'], 'E_eV', + dtype=float, + unique=True, + sign='>=0', + ) + + # theta + ntheta = int(ds._generic_check._check_var( + kwdargs['ntheta'], 'ntheta', + types=(int, float), + default=_DCOORDS['ntheta'], + sign='>0', + )) + if ntheta % 2 == 0: + ntheta += 1 + theta = np.linspace(0, np.pi, ntheta) + + # ----------------- + # v_par, v_perp + # ----------------- + + pmin_norm = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=E_eV.min(), + )['momentum_normalized']['data'][0] + + pmax_norm = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=E_eV.max(), + )['momentum_normalized']['data'][0] + + # npar, nperp + nperp = int(ds._generic_check._check_var( + kwdargs['nperp'], 'nperp', + types=(int, float), + default=_DCOORDS['nperp'], + sign='>0', + )) + + p_perp_norm = np.logspace(np.log10(pmin_norm), np.log10(pmax_norm), nperp) + p_par_norm = np.r_[-p_perp_norm[::-1], 0, p_perp_norm] + p_perp_norm = np.r_[0., p_perp_norm] + + dcoords = { + 'E_eV': E_eV, + 'theta': theta, + 'p_par_norm': p_par_norm, + 'p_perp_norm': p_perp_norm, + } + + return ( + dplasma, + dprop, + dcoords, + ) + + +# ##################################################### +# ##################################################### +# plot +# ##################################################### + + +def _plot( + ddist_E_theta=None, + ddist_ppar_pperp=None, + # 1d + ddist_E_num=None, + ddist_pnorm_num=None, + pbins=None, + # props + dprop=None, + # plotting + dax=None, + fontsize=None, + dmargin=None, +): + + # ---------------- + # prepare + # ---------------- + + shape_plasma = ddist_E_theta['dist']['maxwell']['dist']['data'].shape[:-2] + + # ---------------- + # dax + # ---------------- + + if dax is None: + dax = _get_dax( + fontsize=fontsize, + dmargin=dmargin, + # units_E_pitch=dout_E['dist']['units'], + # units_E=dout_E_1d['dist']['units'], + # units_v=dout_v['dist']['units'], + ) + + dax = ds._generic_check._check_dax(dax) + + # ---------------- + # plot vs E, theta + # ---------------- + + kax = '(E, theta)' + if dax.get(kax) is not None: + ax = dax[kax]['handle'] + + # data + maxwell = ddist_E_theta['dist']['maxwell']['dist']['data'] + RE = ddist_E_theta['dist']['RE']['dist']['data'] + + # vmax, vmin + vmax = np.max(maxwell + RE) + vmaxRE = np.max(RE[RE > maxwell]) + vmin = np.min(RE[RE > 0.]) + levels = np.unique(np.r_[ + vmin, max(vmin, vmaxRE/10.), + np.logspace(np.log10(max(vmin, vmaxRE/10.)), np.log10(vmaxRE), 6), + np.logspace(np.log10(vmaxRE), np.log10(vmax), 4), + ]) + + for ii, ind in enumerate(np.ndindex(shape_plasma)): + sli = ind + (slice(None), slice(None)) + val = maxwell[sli] + RE[sli] + + ax.contour( + ddist_E_theta['coords']['x0']['data']*1e-3, + ddist_E_theta['coords']['x1']['data']*180/np.pi, + val.T, + levels=levels, + colors=dprop[ind]['color'], + ) + + ax.set_ylim(0, 180) + ax.set_xlim(left=0.) + + # ---------------- + # plot vs E + # ---------------- + + kax = 'E1d' + if dax.get(kax) is not None: + ax = dax[kax]['handle'] + + lh = [] + for ii, ind in enumerate(np.ndindex(shape_plasma)): + sli = ind + (slice(None),) + maxwell_num = ddist_E_num['maxwell']['data'][sli] + re_num = ddist_E_num['RE']['data'][sli] + color = dprop[ind]['color'] + + # maxwell + ax.semilogy( + ddist_E_theta['coords']['x0']['data']*1e-3, + maxwell_num, + ls='-', + lw=1, + color=color, + label="Maxwell_num", + ) + + # RE + ax.semilogy( + ddist_E_theta['coords']['x0']['data']*1e-3, + re_num, + ls='--', + lw=1, + color=color, + label="RE_num", + ) + + # total + ax.semilogy( + ddist_E_theta['coords']['x0']['data']*1e-3, + maxwell_num + re_num, + ls='-', + lw=2, + color=color, + ) + + # label + nei = ddist_E_theta['plasma']['ne_m3']['data'][ind] + jpi = ddist_E_theta['plasma']['jp_Am2']['data'][ind] + Tei = ddist_E_theta['plasma']['Te_eV']['data'][ind] + jp_fraci = ddist_E_theta['plasma']['jp_fraction_re']['data'][ind] + lab = ( + f"ne = {nei:1.0e} /m3 jp = {jpi*1e-6:1.0f} MA/m2" + f"Te = {Tei*1e-3:1.0e} keV jp_frac = {jp_fraci:1.1f}" + ) + + lh.append(mlines.Line2D([], [], c=color, ls='-', label=lab)) + + # legend & lims + ax.legend(handles=lh, loc='upper right', fontsize=12) + ax.set_xlim(left=0.) + ax.set_ylim( + f"integral ({ddist_E_num['maxwell']['units']})", + fontisize=fontsize, + fontweight='bold', + ) + + # ---------------- + # plot vs velocities - 2D + # ---------------- + + kax = '(p_par, p_perp)' + if dax.get(kax) is not None: + ax = dax[kax]['handle'] + + # data + maxwell = ddist_ppar_pperp['dist']['maxwell']['dist']['data'] + RE = ddist_ppar_pperp['dist']['RE']['dist']['data'] + + # vmax, vmin + vmax = np.max(maxwell + RE) + vmaxRE = np.max(RE[RE > maxwell]) + vmin = np.min(RE[RE > 0.]) + levels = np.unique(np.r_[ + vmin, max(vmin, vmaxRE/10.), + np.logspace(np.log10(max(vmin, vmaxRE/10.)), np.log10(vmaxRE), 6), + np.logspace(np.log10(vmaxRE), np.log10(vmax), 4), + ]) + + for ii, ind in enumerate(np.ndindex(shape_plasma)): + sli = ind + (slice(None), slice(None)) + val = maxwell[sli] + RE[sli] + + # plot + color = dprop[ind]['color'] + ax.contour( + ddist_ppar_pperp['coords']['x0']['data'], + ddist_ppar_pperp['coords']['x1']['data'], + val.T, + levels=levels, + colors=color, + ) + + # legend & lims + ax.set_ylim(bottom=0.) + + # ---------------- + # plot vs v 1D + # ---------------- + + kax = 'p1d' + if dax.get(kax) is not None: + ax = dax[kax]['handle'] + + lh = [] + for ii, ind in enumerate(np.ndindex(shape_plasma)): + sli = ind + (slice(None),) + maxwell_num = ddist_pnorm_num['maxwell']['data'][sli] + re_num = ddist_pnorm_num['RE']['data'][sli] + color = dprop[ind]['color'] + + # maxwell + ax.stairs( + maxwell_num, + edges=pbins, + orientation='vertical', + baseline=0., + fill=False, + ls='-', + lw=1, + color=color, + label="Maxwell_num", + ) + + # RE + ax.stairs( + re_num, + edges=pbins, + orientation='vertical', + baseline=0., + fill=False, + ls='--', + lw=1, + color=color, + label="RE_num", + ) + + # total + ax.stairs( + maxwell_num + re_num, + edges=pbins, + orientation='vertical', + baseline=0., + fill=False, + ls='-', + lw=2, + color=color, + ) + + # label + nei = ddist_E_theta['plasma']['ne_m3']['data'][ind] + jpi = ddist_E_theta['plasma']['jp_Am2']['data'][ind] + Tei = ddist_E_theta['plasma']['Te_eV']['data'][ind] + jp_fraci = ddist_E_theta['plasma']['jp_fraction_re']['data'][ind] + lab = ( + f"ne = {nei:1.0e} /m3 jp = {jpi*1e-6:1.0f} MA/m2" + f"Te = {Tei*1e-3:1.0e} keV jp_frac = {jp_fraci:1.1f}" + ) + + lh.append(mlines.Line2D([], [], c=color, ls='-', label=lab)) + + # legend & lims + ax.legend(handles=lh, loc='upper right', fontsize=12) + ax.set_xlim(left=0.) + ax.set_ylim( + f"integral ({ddist_pnorm_num['maxwell']['units']})", + fontisize=fontsize, + fontweight='bold', + ) + + return dax + + +# ##################################################### +# ##################################################### +# levels +# ##################################################### + + +def _get_levels(val, nn=10): + + vmax = np.max(val) + vmin = np.min(val[val > 0.]) + vmax_log10 = np.log10(vmax) + vmin_log10 = np.log10(vmin) + + nn = int(np.ceil((vmax_log10 - vmin_log10) / nn)) + levels = np.arange(np.floor(vmin_log10), np.ceil(vmax_log10)+1, nn) + levels = 10**(levels) + levels = np.unique(np.r_[levels, 0.99*vmax]) + + return levels + + +# ##################################################### +# ##################################################### +# dax +# ##################################################### + + +def _get_dax( + fontsize=None, + dmargin=None, + # units + units_E_pitch=None, + units_E=None, + units_v=None, +): + # -------------- + # check inputs + # -------------- + + # fontsize + fontsize = ds._generic_check._check_var( + fontsize, 'fontsize', + types=(int, float), + default=12, + sign='>0', + ) + + # -------------- + # prepare data + # -------------- + + # -------------- + # prepare axes + # -------------- + + tit = ( + "Maxwellian distribution\n" + "[1] D. Moseev and M. Salewski, Physics of Plasmas, 26, p.020901, 2019" + ) + + if dmargin is None: + dmargin = { + 'left': 0.08, 'right': 0.95, + 'bottom': 0.06, 'top': 0.83, + 'wspace': 0.2, 'hspace': 0.50, + } + + fig = plt.figure(figsize=(18, 14)) + fig.suptitle(tit, size=fontsize+2, fontweight='bold') + + gs = gridspec.GridSpec(ncols=2, nrows=2, **dmargin) + dax = {} + + # -------------- + # prepare axes + # -------------- + + # -------------- + # (E, pitch) - map + + ax = fig.add_subplot(gs[0, 0]) + ax.set_xlabel( + "E (keV)", + size=fontsize, + fontweight='bold', + ) + ax.set_ylabel( + "theta (deg)", + size=fontsize, + fontweight='bold', + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # store + dax['(E, theta)'] = {'handle': ax, 'type': 'Ep'} + + # -------------- + # (v_par, v_perp) - map + + ax = fig.add_subplot(gs[0, 1], aspect='equal', adjustable='datalim') + ax.set_xlabel( + r"$p_{//}$ (adim.)", + size=fontsize, + fontweight='bold', + ) + ax.set_ylabel( + r"$p_{\perp}$ (adim.)", + size=fontsize, + fontweight='bold', + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # store + dax['(p_par, p_perp)'] = {'handle': ax, 'type': 'vv2d'} + + # -------------- + # E1d + + ax = fig.add_subplot( + gs[1, 0], + xscale='linear', + yscale='log', + sharex=dax['(E, theta)']['handle'], + ) + ax.set_xlabel( + "E (keV)", + size=fontsize, + fontweight='bold', + ) + ax.set_ylabel( + "sum", + size=fontsize, + fontweight='bold', + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # store + dax['E1d'] = {'handle': ax, 'type': 'Ep'} + + # -------------- + # v1d + + ax = fig.add_subplot(gs[1, 1], xscale='log', yscale='log') + ax.set_xlabel( + "p (adim", + size=fontsize, + fontweight='bold', + ) + ax.set_ylabel( + "sum", + size=fontsize, + fontweight='bold', + ) + ax.set_title( + '', # str_fE, + size=fontsize, + fontweight='bold', + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # store + dax['p1d'] = {'handle': ax, 'type': 'Ep'} + + return dax diff --git a/tofu/physics_tools/electrons/distribution/_distribution_re.py b/tofu/physics_tools/electrons/distribution/_distribution_re.py new file mode 100644 index 000000000..61be11026 --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/_distribution_re.py @@ -0,0 +1,410 @@ + + +import numpy as np + + +from .. import _convert +from . import _runaway_growth +from . import _distribution_maxwell as _maxwell +from . import _distribution_dreicer as _dreicer +from . import _distribution_avalanche as _avalanche + + +# ######################################################## +# ######################################################## +# DEFAULT +# ######################################################## + + +_DMOD = { + 'maxwell': _maxwell, + 'dreicer': _dreicer, + 'avalanche': _avalanche, +} + + +_DOMINANT = { + 'dreicer': 0, + 'avalanche': 1, + 'maxwell': 2, +} + + +# ######################################################## +# ######################################################## +# Main +# ######################################################## + + +def main( + # coordinates + dcoords=None, + version=None, + # plasma + dplasma=None, + # assmume dominant + dominant=None, + # unused + **kwdargs, +): + + # ----------- + # initialize + # ----------- + + ncoords = len(dcoords) + shape_plasma = dplasma['Te_eV']['data'].shape[:-ncoords] + shape_coords = np.broadcast_shapes(*[v0.shape for v0 in dcoords.values()]) + shape_coords = shape_coords[-ncoords:] + shape = shape_plasma + shape_coords + re_dist = np.zeros(shape, dtype=float) + + # slices + sli_coords = (slice(None),)*len(dcoords) + sliok = (slice(None),)*len(shape_plasma) + (0,)*len(dcoords) + + # ------------- + # prepare + # ------------- + + # get momentum max from total energy eV.s/m - shape + pmax = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=dplasma['Ekin_max_eV']['data'], + )['momentum_normalized']['data'] + + # Critical electric field - shape + Ec_Vm = _runaway_growth.get_RE_critical_dreicer_electric_fields( + ne_m3=dplasma['ne_m3']['data'], + kTe_eV=None, + lnG=dplasma['lnG']['data'], + )['E_C']['data'] + + # ------------- + # Intermediates + # ------------- + + # normalized electric field, adim + Etild = dplasma['Efield_par_Vm']['data'] / Ec_Vm + + shapeE = Etild.shape + p_crit = np.full(shapeE, np.nan) + E_hat = np.full(shapeE, np.nan) + Cz = np.full(shapeE, np.nan) + Cs = np.full(shapeE, np.nan) + + # --------------------------- + # get dominant distribution + # --------------------------- + + dominant, dind = _get_dominant( + Etild=Etild, + E_hat=E_hat, + Cz=Cz, + Cs=Cs, + p_crit=p_crit, + dplasma=dplasma, + # dominant + dominant=dominant, + ) + + # -------------------- + # loop on dominant + # -------------------- + + dunits = {} + ncoords = len(dcoords) + for vv, ind in dind.items(): + + iok = dind[vv]['ind'] + sli0 = (iok[sliok],) + sli_coords + sli1 = sli0 + + # ------------------- + # kwdargs to func + if dominant['meaning'][vv] == 'maxwell': + + kwdargsi = { + 'Te_eV': {'data': dplasma['Te_eV_re']['data'][sli0]}, + 'ne_m3': {'data': dplasma['ne_m3_re']['data'][sli0]}, + 'jp_Am2': {'data': dplasma['jp_Am2']['data'][sli0]}, + } + + dout = _maxwell.main( + dcoords=dcoords, + dplasma=kwdargsi, + version=version, + ) + + # store + re_dist[sli1] = dout['dist']['data'] + dunits[dominant['meaning'][vv]] = dout['dist']['units'] + + else: + + # kwdargs to func + kwdargsi = { + 'sigmap': dplasma['sigmap']['data'][sli0], + 'p_max_norm': pmax[sli0], + 'Etild': Etild[sli0], + 'Zeff': dplasma['Zeff']['data'][sli0], + 'E_hat': E_hat[sli0], + 'Cz': Cz[sli0], + 'Cs': Cs[sli0], + 'lnG': dplasma['lnG']['data'][sli0], + 'p_crit': p_crit[sli0], + } + + # update with coords + kwdargsi.update(**dcoords) + + # compute + re_dist[sli1], dunits[dominant['meaning'][vv]] = getattr( + _DMOD[dominant['meaning'][vv]], + version, + )(**kwdargsi) + + # ------------------- + # threshold on p_crit + + if dominant['meaning'][vv] != 'maxwell': + pnorm = np.broadcast_to(_get_pnorm(dcoords), shape) + iokp = np.copy(np.broadcast_to(iok, shape)) + iokp[iokp] = pnorm[iokp] < np.broadcast_to(p_crit, shape)[iokp] + re_dist[iokp] = 0. + + # ---------------------- + # sanity check on units + # ---------------------- + + lunits = list(set([uu for uu in dunits.values()])) + if len(lunits) != 1: + lstr = [f"\t- {k0}: {v0}" for k0, v0 in dunits.items()] + msg = ( + "Different units:\n" + + "\n".join(lstr) + ) + raise Exception(msg) + + # units + units = lunits[0] + + # -------------- + # format output + # -------------- + + dout = { + 'dist': { + 'data': re_dist, + 'units': units, + }, + 'Cs': { + 'data': Cs, + 'units': None, + }, + 'Cz': { + 'data': Cz, + 'units': None, + }, + 'Ec': { + 'data': Ec_Vm, + 'units': 'V/m', + }, + 'Etild': { + 'data': Etild, + 'units': None, + }, + 'E_hat': { + 'data': E_hat, + 'units': None, + }, + 'p_crit': { + 'data': p_crit, + 'units': None, + }, + 'p_max': { + 'data': pmax, + 'units': None, + }, + 'dominant': { + 'data': dominant, + 'units': None, + 'meaning': {0: 'avalanche', 1: 'dreicer'} + }, + } + + return dout + + +# ############################################## +# ############################################## +# _get_pp +# ############################################## + + +def _get_pnorm(dcoords): + + if dcoords.get('E_eV') is not None: + + pnorm = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=dcoords['E_eV'], + )['momentum_normalized']['data'] + + elif dcoords.get('p_par_norm') is not None: + + pnorm = np.sqrt( + dcoords['p_par_norm']**2 + + dcoords['p_perp_norm']**2 + ) + + else: + raise NotImplementedError(sorted(dcoords.keys)) + + return pnorm + + +# ############################################## +# ############################################## +# dominant +# ############################################## + + +def _get_dominant( + Etild=None, + E_hat=None, + Cz=None, + Cs=None, + p_crit=None, + dplasma=None, + # dominant + dominant=None, +): + + # ----------------- + # dominant_exp + # ----------------- + + shape = Etild.shape + dominant_exp = np.full(shape, np.nan) + + iok = Etild > 1. + if np.any(iok): + + # E_hat + E_hat[iok] = (Etild[iok] - 1) / (1 + dplasma['Zeff']['data'][iok]) + + # adim + Cz[iok] = np.sqrt(3 * (dplasma['Zeff']['data'][iok] + 5) / np.pi) + + # critical momentum, adim + p_crit[iok] = 1. / np.sqrt(Etild[iok] - 1.) + + # Cs + Cs[iok] = ( + Etild[iok] + - ( + ((1 + dplasma['Zeff']['data'][iok])/4) + * (Etild[iok] - 2) + * np.sqrt(Etild[iok] / (Etild[iok] - 1)) + ) + ) + + # ------------------ + # Compute + + # Dreicer-dominated + iok_dreicer = np.copy(iok) + iok_dreicer[iok] = (2 < Cs[iok]) & (Cs[iok] < 1 + Etild[iok]) + dominant_exp[iok_dreicer] = 0 + + # avalanche-dominated + iok_avalanche = np.copy(iok) + iok_avalanche[iok] = (~iok_dreicer[iok]) & (Etild[iok] > 5.) + dominant_exp[iok_avalanche] = 1 + + else: + iok_dreicer = iok + iok_avalanche = iok + + # maxwell-dominated + iok_maxwell = iok & (~iok_dreicer) & (~iok_avalanche) + dominant_exp[iok_maxwell] = 2 + + # ----------------- + # check dominant + # ----------------- + + if dominant is None: + dominant = -np.ones(shape, dtype=float) + + lv = sorted(_DOMINANT.values()) + lc = [ + isinstance(dominant, str) and dominant in _DOMINANT.keys(), + isinstance(dominant, int) and dominant in lv, + isinstance(dominant, np.ndarray) + and dominant.shape == shape + and np.all(np.any([dominant == vv for vv in lv + [-1]], axis=0)), + ] + + if lc[0]: + dominant = np.full(shape, _DOMINANT[dominant], dtype=float) + + elif lc[1]: + dominant = np.full(shape, dominant, dtype=float) + + elif lc[2]: + pass + + else: + lstr = [ + f"\t- {k0} or {v0}: {k0}-dominated" + for k0, v0 in _DOMINANT.items() + ] + msg = ( + "Arg dominant must specify, for each plasma point, " + "the dominant RE distribution:\n" + + "\n".join(lstr) + + "Alternatively, can be provided as a np.ndarray of:\n" + f"\t- shape: {shape}\n" + f"\t- values in {lv}\n" + "Value = -1 => whatever distribution should dominante\n" + ) + raise Exception(msg) + + # ----------------------- + # set with exprimental where not specified + # ----------------------- + + iexp = dominant < 0 + dominant[iexp] = dominant_exp[iexp] + + # ------------------------ + # adjust for computability + # ------------------------ + + iout = ( + (dominant < 0) + | ((dominant == 0) & (~iok)) + | ((dominant == 1) & (~iok)) + ) + dominant[iout] = np.nan + + dominant = { + 'ind': dominant, + 'meaning': {vv: kk for kk, vv in _DOMINANT.items()} + } + + # ----------------- + # dind + # ----------------- + + iok = np.isfinite(dominant['ind']) + iok[iok] = dominant['ind'][iok] >= 0. + lv = sorted(np.unique(dominant['ind'][iok])) + + dind = { + vv: { + 'ind': dominant['ind'] == vv, + } + for vv in lv + } + return dominant, dind diff --git a/tofu/physics_tools/electrons/distribution/_distribution_study.py b/tofu/physics_tools/electrons/distribution/_distribution_study.py new file mode 100644 index 000000000..23e9a0477 --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/_distribution_study.py @@ -0,0 +1,450 @@ + + +import numpy as np +import scipy.integrate as scpinteg +import astropy.units as asunits +import matplotlib.pyplot as plt +import matplotlib.gridspec as gridspec +import matplotlib.lines as mlines +import datastock as ds + + +from . import _distribution +from . import _distribution_check + + +# ###############################################3 +# ###############################################3 +# DEFAULT +# ###############################################3 + + +_DPLASMA = { + 'Te_eV': { + 'def': np.linspace(0.5, 15, 59)[:, None, None, None] * 1e3, + 'units': 'eV', + }, + 'ne_m3': { + 'def': np.r_[1e19, 1e20][None, None, :, None], + 'units': '1/m^3', + }, + 'jp_Am2': { + 'def': np.r_[1e6, 10e6][None, None, None, :], + 'units': 'A/m^2', + }, + 'jp_fraction_re': { + 'def': np.linspace(0.01, 0.99, 51)[None, :, None, None], + 'units': None, + }, +} + + +_EMAX_EV = 20e6 +_DCOORDS = { + 'E_eV': np.logspace(1, np.log10(_EMAX_EV), 201), + 'ntheta': 41, +} + + +_LEVELS_E_EV = np.r_[40, 150]*1e3 + + +# ###############################################3 +# ###############################################3 +# main +# ###############################################3 + + +def study_RE_vs_Maxwellian_distribution( + # plasma + Te_eV=None, + ne_m3=None, + jp_Am2=None, + jp_fraction_re=None, + # RE-specific + Zeff=None, + Ekin_max_eV=None, + Efield_par_Vm=None, + lnG=None, + sigmap=None, + # coords + E_eV=None, + ntheta=None, + # levels + levels_E_eV=None, + colors=None, + # plotting + dax=None, + fontsize=None, + dmargin=None, +): + """ + + Return dax, ddist + + """ + + # -------------- + # check inputs + # -------------- + + dplasma, dcoords, levels_E_eV = _check(**locals()) + + # -------------- + # compute + # -------------- + + # f2D_E_theta + ddist = _distribution.main( + # coordinate: momentum + E_eV=dcoords['E_eV'], + theta=dcoords['theta'], + # return as + returnas=dict, + # version + dist=('maxwell', 'RE'), + version='f2d_E_theta', + # plasma + **{kk: vv['data'] for kk, vv in dplasma.items()}, + ) + + # ------------------ + # integrate + # ------------------ + + # E + units = ddist['dist']['RE']['dist']['units'] * asunits.Unit('rad') + ddist_E_num = { + kdist: { + 'data': scpinteg.trapezoid( + ddist['dist'][kdist]['dist']['data'], + x=ddist['coords']['x1']['data'], + axis=-1, + ), + 'units': units, + } + for kdist in ddist['dist'].keys() + } + + # ------------------ + # extract threshold + # ------------------ + + ddata = _get_threshold( + ddist=ddist, + ddist_E_num=ddist_E_num, + ) + + # -------------- + # plot + # -------------- + + dax = _plot( + ddist=ddist, + ddist_E_num=ddist_E_num, + ddata=ddata, + levels_E_eV=levels_E_eV, + colors=colors, + dax=dax, + fontsize=fontsize, + dmargin=dmargin, + ) + + return dax, ddist + + +# ###############################################3 +# ###############################################3 +# check +# ###############################################3 + + +def _check( + **kwdargs, +): + + # ----------------- + # plasma parameters + # ----------------- + + dplasma = _distribution_check._plasma( + ddef=_DPLASMA, + **kwdargs, + ) + + # ----------------- + # levels_E_eV + # ----------------- + + if kwdargs['levels_E_eV'] is None: + kwdargs['levels_E_eV'] = _LEVELS_E_EV + + levels_E_eV = kwdargs['levels_E_eV'] + if np.isscalar(levels_E_eV): + if isinstance(levels_E_eV, int): + levels_E_eV = ds._generic_check._check_var( + levels_E_eV, 'levels_E_eV', + types=int, + sign='>0', + ) + else: + levels_E_eV = np.r_[levels_E_eV] + + if not isinstance(levels_E_eV, int): + levels_E_eV = ds._generic_check._check_flat1darray( + levels_E_eV, 'levels_E_eV', + unique=True, + sign='>0', + ) + + # ----------------- + # E_eV, theta + # ----------------- + + # E_eV + if kwdargs['E_eV'] is None: + kwdargs['E_eV'] = _DCOORDS['E_eV'] + E_eV = ds._generic_check._check_flat1darray( + kwdargs['E_eV'], 'E_eV', + dtype=float, + unique=True, + sign='>=0', + ) + + # theta + ntheta = int(ds._generic_check._check_var( + kwdargs['ntheta'], 'ntheta', + types=(int, float), + default=_DCOORDS['ntheta'], + sign='>0', + )) + if ntheta % 2 == 0: + ntheta += 1 + theta = np.linspace(0, np.pi, ntheta) + + dcoords = { + 'E_eV': E_eV, + 'theta': theta, + } + + return ( + dplasma, + dcoords, + levels_E_eV, + ) + + +# ###############################################3 +# ###############################################3 +# Threshold +# ###############################################3 + + +def _get_threshold( + ddist=None, + ddist_E_num=None, +): + + # ----------- + # prepare + # ---------- + + E_eV = ddist['coords']['x0']['data'] + RE = ddist_E_num['RE']['data'] + maxwell = ddist_E_num['maxwell']['data'] + + shape = RE.shape + iok = np.isfinite(RE) & np.isfinite(maxwell) + iok2 = np.any(iok, axis=-1) + iok2[iok2] = ( + np.any(RE[iok2, :] > maxwell[iok2, :], axis=-1) + & np.any(RE[iok2, :] < maxwell[iok2, :], axis=-1) + ) + + # ----------- + # compute + # ---------- + + sli = (None,)*len(shape[:-1]) + (slice(None),) + ind = np.arange(E_eV.size)[sli] + ind = np.copy(np.broadcast_to(ind, shape)) + iout = (RE < maxwell) + ind[iout] = ddist['coords']['x0']['data'].size + 1 + imin = np.argmin(ind, axis=-1) + + E_min = E_eV[imin] + E_min[~iok2] = np.nan + + # ----------- + # format + # ----------- + + ddata = { + 'E_min': { + 'data': E_min, + 'units': ddist['coords']['x0']['units'], + }, + } + + return ddata + + +# ###############################################3 +# ###############################################3 +# plot +# ###############################################3 + + +def _plot( + ddist=None, + ddist_E_num=None, + ddata=None, + levels_E_eV=None, + colors=None, + # plotting + dax=None, + fontsize=None, + dmargin=None, +): + + # ---------------- + # prepare + # ---------------- + + E_min = ddata['E_min']['data'] + shape_plasma = E_min.shape[2:] + Te_eV = ddist['plasma']['Te_eV']['data'][:, 0, 0, 0] + jp_fraction_re = ddist['plasma']['jp_fraction_re']['data'][0, :, 0, 0] + ne_m3 = ddist['plasma']['ne_m3']['data'][0, 0, :, 0] + jp_Am2 = ddist['plasma']['jp_Am2']['data'][0, 0, 0, :] + + # ---------------- + # dax + # ---------------- + + if dax is None: + dax = _get_dax( + fontsize=fontsize, + dmargin=dmargin, + ) + + dax = ds._generic_check._check_dax(dax) + + # ---------------- + # plot vs E, theta + # ---------------- + + kax = 'main' + if dax.get(kax) is not None: + ax = dax[kax]['handle'] + + lh = [] + lc = ['r', 'g', 'b', 'm', 'y', 'c'] + for ii, ind in enumerate(np.ndindex(shape_plasma)): + sli = (slice(None),)*2 + ind + + # label + nei = ne_m3[ind[0]] + jpi = jp_Am2[ind[1]] + lab = f"ne = {nei:1.0e} /m3 jp = {jpi*1e-6:1.0f} MA/m2" + + # plot + if colors is None: + color = lc[ii % len(lc)] + else: + color = colors + im = ax.contourf( + Te_eV*1e-3, + jp_fraction_re, + 1e-3*E_min[sli].T, + levels=levels_E_eV*1e-3, + colors=color, + ) + + lh.append(mlines.Line2D([], [], c=color, ls='-', label=lab)) + plt.clabel(im, inline=True, fontsize=12) + + # legend + ax.legend(handles=lh, loc='upper right', fontsize=12) + + # lim + ax.set_xlim(left=0) + ax.set_ylim(0, 1) + + return dax + + +# ##################################################### +# ##################################################### +# dax +# ##################################################### + + +def _get_dax( + fontsize=None, + dmargin=None, +): + # -------------- + # check inputs + # -------------- + + # fontsize + fontsize = ds._generic_check._check_var( + fontsize, 'fontsize', + types=(int, float), + default=12, + sign='>0', + ) + + # -------------- + # prepare data + # -------------- + + # -------------- + # prepare axes + # -------------- + + tit = "" + + if dmargin is None: + dmargin = { + 'left': 0.08, 'right': 0.95, + 'bottom': 0.06, 'top': 0.83, + 'wspace': 0.2, 'hspace': 0.50, + } + + fig = plt.figure(figsize=(15, 12)) + fig.suptitle(tit, size=fontsize+2, fontweight='bold') + + gs = gridspec.GridSpec(ncols=1, nrows=1, **dmargin) + dax = {} + + # -------------- + # prepare axes + # -------------- + + # -------------- + # (E, pitch) - map + + ax = fig.add_subplot(gs[0, 0]) + ax.set_xlabel( + "Te (keV)", + size=fontsize, + fontweight='bold', + ) + ax.set_ylabel( + "jp_fraction_re (adim.)", + size=fontsize, + fontweight='bold', + ) + ax.set_title( + "Electron energy above which RE dominate", + size=fontsize, + fontweight='bold', + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # store + dax['main'] = {'handle': ax, 'type': 'Ep'} + + return dax diff --git a/tofu/physics_tools/electrons/distribution/_runaway_growth.py b/tofu/physics_tools/electrons/distribution/_runaway_growth.py new file mode 100644 index 000000000..7fbc29d29 --- /dev/null +++ b/tofu/physics_tools/electrons/distribution/_runaway_growth.py @@ -0,0 +1,254 @@ + + +import numpy as np +import scipy.constants as scpct +import datastock as ds + + +# ############################################################## +# ############################################################## +# DEFAULTS +# ############################################################## + + +# see: +# https://docs.plasmapy.org/en/stable/notebooks/formulary/coulomb.html +_SIGMAP = 1. +_LNG = 20. + + +# ############################################################## +# ############################################################## +# Critical and Dreicer electric fields +# ############################################################## + + +def get_RE_critical_dreicer_electric_fields( + ne_m3=None, + kTe_eV=None, + lnG=None, +): + + # ------------- + # check input + # ------------- + + ne_m3, kTe_eV, lnG = _check_critical_dreicer( + ne_m3=ne_m3, + kTe_eV=kTe_eV, + lnG=lnG, + ) + + # ------------- + # prepare + # ------------- + + # vacuum permittivity in C/(V.m), scalar + eps0 = scpct.epsilon_0 + + # custom computation intermediates C^2/(V^2.m^2), scalar + pie02 = np.pi * eps0**2 + + # electron charge (C), scalar + e = scpct.e + + # electron rest energy (J = C.V), scalar + mec2_CV = scpct.m_e * scpct.c**2 + + # ------------- + # compute + # ------------- + + # critical electric field (V/m) + Ec_Vm = ne_m3 * e**3 * lnG / (4 * pie02 * mec2_CV) + + # Dreicer electric field + if kTe_eV is not None: + Ed_Vm = Ec_Vm * (mec2_CV / e) / kTe_eV + else: + Ed_Vm = None + + # ------------- + # format output + # ------------- + + dout = { + 'E_C': { + 'data': Ec_Vm, + 'units': 'V/m', + }, + } + + if Ed_Vm is not None: + dout['E_D'] = { + 'data': Ed_Vm, + 'units': 'V/m', + } + + return dout + + +def _check_critical_dreicer( + ne_m3=None, + kTe_eV=None, + lnG=None, +): + + # ----------------- + # preliminary: lnG + # ----------------- + + if lnG is None: + lnG = _LNG + + # ----------------- + # broadcastable + # ----------------- + + dparams, shape = ds._generic_check._check_all_broadcastable( + ne_m3=ne_m3, + kTe_eV=kTe_eV, + lnG=lnG, + ) + + return [dparams[kk] for kk in ['ne_m3', 'kTe_eV', 'lnG']] + + +# ############################################################## +# ############################################################## +# Primary & secondary growth source terms +# ############################################################## + + +def get_RE_growth_source_terms( + ne_m3=None, + lnG=None, + Epar_Vm=None, + kTe_eV=None, + Zeff=None, +): + """ Return the source terms in the RE dynamic equation + + S_primary: dreicer growth (1/m3/s) + + S_secondary: avalanche growth (1/s) + + """ + + # ------------- + # check inputs + # ------------- + + ne_m3, lnG, Epar_Vm, kTe_eV, Zeff = _check_growth( + ne_m3=ne_m3, + lnG=lnG, + Epar_Vm=Epar_Vm, + kTe_eV=kTe_eV, + Zeff=Zeff, + ) + + # ------------- + # prepare + # ------------- + + # vacuum permittivity in C/(V.m), scalar + eps0 = scpct.epsilon_0 + + # charge C + e = scpct.e + + # mec2 (J = CV) + mec2_CV = scpct.m_e * scpct.c**2 + + # mec C.V.s/m + mec = mec2_CV / scpct.c + + # me2c3 J**2 / (m/s) = C^2 V^2 s / m + me2c3 = mec2_CV**2 / scpct.c + + # Dreicer electric field - shape + dEcEd = get_RE_critical_dreicer_electric_fields( + ne_m3=ne_m3, + kTe_eV=kTe_eV, + lnG=lnG, + ) + + Ec_Vm = dEcEd['E_C']['data'] + Ed_Vm = dEcEd['E_D']['data'] + + # ------------- + # pre-compute + # ------------- + + # term1 (m^3/s) + term1 = e**4 * lnG / (4 * np.pi * eps0**2 * me2c3) + + # term2 - unitless (convert kTe_eV => J) + term2 = (mec2_CV / (2. * kTe_eV * e))**1.5 + + # term3 - unitless + term3 = (Ed_Vm / Epar_Vm)**(3*(1. + Zeff) / 16.) + + # exp - unitless + exp = np.exp( + -Ed_Vm / (4.*Epar_Vm) - np.sqrt((1. + Zeff) * Ed_Vm / Epar_Vm) + ) + + # sqrt - unitless + sqrt = np.sqrt(np.pi / (3 * (5 + Zeff))) + + # ------------- + # Compute + # ------------- + + # 1/m^3/s + S_primary = ne_m3**2 * term1 * term2 * term3 * exp + + # 1/s (C / C.V.s/m * V.m) + S_secondary = sqrt * (e / mec) * (Epar_Vm - Ec_Vm) / lnG + + # ------------- + # format output + # ------------- + + dout = { + 'S_primary': { + 'data': S_primary, + 'units': '1/m3/s', + }, + 'S_secondary': { + 'data': S_secondary, + 'units': '1/s', + }, + } + + return dout + + +def _check_growth( + ne_m3=None, + lnG=None, + Epar_Vm=None, + kTe_eV=None, + Zeff=None, +): + + # ----------------- + # preliminary: lnG + # ----------------- + + if lnG is None: + lnG = _LNG + + # ----------------------- + # all broadcastable + # ----------------------- + + dparams, shape = ds._generic_check._check_all_broadcastable( + return_full_arrays=False, + **locals(), + ) + lk = ['ne_m3', 'lnG', 'Epar_Vm', 'kTe_eV', 'Zeff'] + lout = [dparams[k0] for k0 in lk] + + return lout diff --git a/tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ScreeningRadius_Salvat.csv b/tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ScreeningRadius_Salvat.csv similarity index 100% rename from tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ScreeningRadius_Salvat.csv rename to tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ScreeningRadius_Salvat.csv diff --git a/tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_Isolines_ElwertHaug_fig2.csv b/tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_Isolines_ElwertHaug_fig2.csv similarity index 100% rename from tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_Isolines_ElwertHaug_fig2.csv rename to tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_Isolines_ElwertHaug_fig2.csv diff --git a/tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_PhotonAngle_ElwertHaug_fig12.csv b/tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_PhotonAngle_ElwertHaug_fig12.csv similarity index 100% rename from tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_PhotonAngle_ElwertHaug_fig12.csv rename to tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_PhotonAngle_ElwertHaug_fig12.csv diff --git a/tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_PhotonDist_ElwertHaug_fig5.csv b/tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_PhotonDist_ElwertHaug_fig5.csv similarity index 100% rename from tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_PhotonDist_ElwertHaug_fig5.csv rename to tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_PhotonDist_ElwertHaug_fig5.csv diff --git a/tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_PhotonDist_Nakel_fig5.csv b/tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_PhotonDist_Nakel_fig5.csv similarity index 100% rename from tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_PhotonDist_Nakel_fig5.csv rename to tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_PhotonDist_Nakel_fig5.csv diff --git a/tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_PhotonSpectrum_Nakel_fig8.csv b/tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_PhotonSpectrum_Nakel_fig8.csv similarity index 100% rename from tofu/physics_tools/runaways/emission/RE_HXR_CrossSection_ThinTarget_PhotonSpectrum_Nakel_fig8.csv rename to tofu/physics_tools/electrons/emission/RE_HXR_CrossSection_ThinTarget_PhotonSpectrum_Nakel_fig8.csv diff --git a/tofu/physics_tools/runaways/emission/RE_HXR_ElectronElectron_Salvat.csv b/tofu/physics_tools/electrons/emission/RE_HXR_ElectronElectron_Salvat.csv similarity index 100% rename from tofu/physics_tools/runaways/emission/RE_HXR_ElectronElectron_Salvat.csv rename to tofu/physics_tools/electrons/emission/RE_HXR_ElectronElectron_Salvat.csv diff --git a/tofu/physics_tools/runaways/emission/__init__.py b/tofu/physics_tools/electrons/emission/__init__.py similarity index 69% rename from tofu/physics_tools/runaways/emission/__init__.py rename to tofu/physics_tools/electrons/emission/__init__.py index 4939f147d..5deac83c0 100644 --- a/tofu/physics_tools/runaways/emission/__init__.py +++ b/tofu/physics_tools/electrons/emission/__init__.py @@ -10,4 +10,7 @@ from ._xray_thin_target import plot_xray_thin_d3cross_ei_vs_Literature from ._xray_thin_target_integrated import get_xray_thin_d2cross_ei_integrated_thetae_dphi from ._xray_thin_target_integrated import plot_xray_thin_d2cross_ei_vs_literature -from ._xray_thin_target_integrated import plot_xray_thin_d2cross_ei_anisotropy +from ._xray_thin_target_integrated_plot import plot_xray_thin_d2cross_ei_anisotropy +from ._xray_thin_target_integrated_dist import get_xray_thin_integ_dist +from ._xray_thin_target_integrated_d2crossphi import get_d2cross_phi +from ._xray_thin_target_integrated_dist_plot import plot_xray_thin_integ_dist diff --git a/tofu/physics_tools/runaways/emission/_xray_thick_target.py b/tofu/physics_tools/electrons/emission/_xray_thick_target.py similarity index 98% rename from tofu/physics_tools/runaways/emission/_xray_thick_target.py rename to tofu/physics_tools/electrons/emission/_xray_thick_target.py index de42ba69b..df2c83b06 100644 --- a/tofu/physics_tools/runaways/emission/_xray_thick_target.py +++ b/tofu/physics_tools/electrons/emission/_xray_thick_target.py @@ -10,7 +10,7 @@ import datastock as ds -from .. import _utils +from .. import _convert # ############################################################## @@ -57,7 +57,7 @@ def anisotropy( # ----------- # gamma => beta - beta = _utils.convert_momentum_velocity_energy( + beta = _convert.convert_momentum_velocity_energy( gamma=gamma, )['beta']['data'] @@ -210,7 +210,7 @@ def dcross_ei( ) # useful for q0 = minimum momentum transfer (eV.s/m) - gamma = _utils.convert_momentum_velocity_energy( + gamma = _convert.convert_momentum_velocity_energy( energy_kinetic_eV=E_re_eV, )['gamma']['data'] @@ -615,7 +615,7 @@ def plot_dcross_vs_Salvat( )['dcross_ei_Ere']['data'] # beta - beta = _utils.convert_momentum_velocity_energy( + beta = _convert.convert_momentum_velocity_energy( energy_kinetic_eV=E_re, )['beta']['data'] diff --git a/tofu/physics_tools/runaways/emission/_xray_thin_target.py b/tofu/physics_tools/electrons/emission/_xray_thin_target.py similarity index 99% rename from tofu/physics_tools/runaways/emission/_xray_thin_target.py rename to tofu/physics_tools/electrons/emission/_xray_thin_target.py index a5b028a95..155497344 100644 --- a/tofu/physics_tools/runaways/emission/_xray_thin_target.py +++ b/tofu/physics_tools/electrons/emission/_xray_thin_target.py @@ -252,7 +252,7 @@ def _check_cross( Z = ds._generic_check._check_var( Z, 'Z', - types=int, + types=(int, float), sign='>0', default=1, ) diff --git a/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated.py b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated.py new file mode 100644 index 000000000..2cb60228c --- /dev/null +++ b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated.py @@ -0,0 +1,494 @@ + + +import os + + +import numpy as np +import scipy.integrate as scpinteg +import astropy.units as asunits +import matplotlib.pyplot as plt +import matplotlib.gridspec as gridspec +import datastock as ds + + +from . import _xray_thin_target + + +# #################################################### +# #################################################### +# DEFAULT +# #################################################### + + +_PATH_HERE = os.path.dirname(__file__) + + +_E_E0_EV = 45e3 +_E_PH_EV = 40e3 +_THETA_PH = np.linspace(0, np.pi, 31) + + +# Integration +_NTHETAE = 31 +_NDPHI = 51 + + +# #################################################### +# #################################################### +# main +# #################################################### + + +def get_xray_thin_d2cross_ei_integrated_thetae_dphi( + # inputs + Z=None, + E_e0_eV=None, + E_ph_eV=None, + theta_ph=None, + # hypergeometric parameter + ninf=None, + source=None, + # integration parameters + nthetae=None, + ndphi=None, + # output customization + per_energy_unit=None, + # version + version=None, + # verb + verb=None, + verb_tab=None, +): + + # ------------ + # inputs + # ------------ + + ( + E_e0_eV, E_ph_eV, theta_ph, + nthetae, ndphi, + shape, shape_theta_e, shape_dphi, + verb, verb_tab, + ) = _check( + # inputs + E_e0_eV=E_e0_eV, + E_ph_eV=E_ph_eV, + theta_ph=theta_ph, + # integration parameters + nthetae=nthetae, + ndphi=ndphi, + # verb + verb=verb, + verb_tab=verb_tab, + ) + + # ------------------ + # Derive angles + # ------------------ + + # E_e1_eV + E_e1_eV = E_e0_eV - E_ph_eV + + # angles + theta_e = np.pi * np.linspace(0, 1, nthetae) + dphi = np.pi * np.linspace(-1, 1, ndphi) + theta_ef = theta_e.reshape(shape_theta_e) + dphif = dphi.reshape(shape_dphi) + + # derived + sinte = np.sin(theta_ef) + + # ------------------ + # get d3cross + # ------------------ + + if verb >= 1: + msg = f"{verb_tab}Computing d3cross for shape {shape}... " + print(msg) + + d3cross = _xray_thin_target.get_xray_thin_d3cross_ei( + # inputs + Z=Z, + E_e0_eV=E_e0_eV[..., None, None], + E_e1_eV=E_e1_eV[..., None, None], + # directions + theta_ph=theta_ph[..., None, None], + theta_e=theta_ef, + dphi=dphif, + # hypergeometric parameter + ninf=ninf, + source=source, + # output customization + per_energy_unit=per_energy_unit, + # version + version=version, + # debug + debug=False, + ) + + # ------------------ + # prepare output + # ------------------ + + d2cross = { + # energies + 'E_e0': { + 'data': E_e0_eV, + 'units': 'eV', + }, + 'E_ph': { + 'data': E_ph_eV, + 'units': 'eV', + }, + # angles + 'theta_ph': { + 'data': theta_ph, + 'units': 'rad', + }, + 'theta_e': { + 'data': theta_e, + 'units': 'rad', + }, + 'dphi': { + 'data': dphi, + 'units': 'rad', + }, + # cross-section + 'cross': { + vv: { + 'data': np.full(shape, 0.), + 'units': asunits.Unit(vcross['units']) * asunits.Unit('sr'), + } + for vv, vcross in d3cross['cross'].items() + }, + } + + # ------------------ + # integrate + # ------------------ + + if verb >= 1: + msg = f"{verb_tab}Integrating..." + print(msg) + + for vv, vcross in d3cross['cross'].items(): + d2cross['cross'][vv]['data'][...] = scpinteg.simpson( + scpinteg.simpson( + vcross['data'] * sinte, + x=theta_e, + axis=-1, + ), + x=dphi, + axis=-1, + ) + + return d2cross + + +# #################################################### +# #################################################### +# check +# #################################################### + + +def _check( + # inputs + E_e0_eV=None, + E_ph_eV=None, + theta_ph=None, + # integration parameters + nthetae=None, + ndphi=None, + # verb + verb=None, + verb_tab=None, +): + + # ----------- + # arrays + # ----------- + + # -------- + # E_e0_eV + + if E_e0_eV is None: + E_e0_eV = _E_E0_EV + E_e0_eV = np.atleast_1d(E_e0_eV) + + # -------- + # E_ph_eV + + if E_ph_eV is None: + E_ph_eV = _E_PH_EV + E_ph_eV = np.atleast_1d(E_ph_eV) + + # ------- + # theta_e + + if theta_ph is None: + theta_ph = _THETA_PH + theta_ph = np.atleast_1d(theta_ph) + + # ------------- + # Broadcastable + + dout, shape = ds._generic_check._check_all_broadcastable( + return_full_arrays=False, + E_e0_eV=E_e0_eV, + E_ph_eV=E_ph_eV, + # directions + theta_ph=theta_ph, + ) + + # ----------- + # shapes + # ----------- + + shape = np.broadcast_shapes(E_e0_eV.shape, E_ph_eV.shape, theta_ph.shape) + shape_theta_e = (1,) * (len(shape)+1) + (-1,) + shape_dphi = (1,) * len(shape) + (-1, 1) + + # ----------- + # integers + # ----------- + + # nthetae + nthetae = ds._generic_check._check_var( + nthetae, 'nthetae', + types=int, + sign='>0', + default=_NTHETAE, + ) + + # ndphi + ndphi = ds._generic_check._check_var( + ndphi, 'ndphi', + types=int, + sign='>0', + default=_NDPHI, + ) + + # ----------- + # verb + # ----------- + + lok = [False, True, 0, 1, 2] + verb = int(ds._generic_check._check_var( + verb, 'verb', + types=(int, bool), + default=lok[-1], + allowed=lok, + )) + + # ----------- + # verb_tab + # ----------- + + verb_tab = ds._generic_check._check_var( + verb_tab, 'verb_tab', + types=int, + default=0, + sign='>=0', + ) + verb_tab = '\t'*verb_tab + + return ( + E_e0_eV, E_ph_eV, theta_ph, + nthetae, ndphi, + shape, shape_theta_e, shape_dphi, + verb, verb_tab, + ) + + +# #################################################### +# #################################################### +# plot vs litterature +# #################################################### + + +def plot_xray_thin_d2cross_ei_vs_literature(): + """ Plot electron-angle-integrated cross section vs + + [1] G. Elwert and E. Haug, Phys. Rev., 183, pp. 90–105, 1969 + doi: 10.1103/PhysRev.183.90. + + """ + + # -------------- + # Load literature data + # -------------- + + # isolines + pfe_fig12 = os.path.join( + _PATH_HERE, + 'RE_HXR_CrossSection_ThinTarget_PhotonAngle_ElwertHaug_fig12.csv', + ) + out_fig12 = np.loadtxt(pfe_fig12, delimiter=',') + + # -------------------- + # prepare data + # -------------------- + + msg = "\nComputing data for fig12 (1/3):" + print(msg) + + theta_ph = np.linspace(0, 1, 31)*np.pi + + # ----------- + # fig 12 + + msg = "\t- For Z = 8... (1/2)" + print(msg) + + d2cross_fig12_Z8 = get_xray_thin_d2cross_ei_integrated_thetae_dphi( + # inputs + Z=8, + E_e0_eV=45e3, + E_ph_eV=40e3, + theta_ph=theta_ph, + # output customization + per_energy_unit=None, + # version + version=['EH', 'BH'], + # verb + verb=False, + ) + + msg = "\t- For Z = 13... (1/2)" + print(msg) + + d2cross_fig12_Z13 = get_xray_thin_d2cross_ei_integrated_thetae_dphi( + # inputs + Z=13, + E_e0_eV=45e3, + E_ph_eV=40e3, + theta_ph=theta_ph, + # output customization + per_energy_unit=None, + # version + version=['EH', 'BH'], + # verb + verb=False, + ) + + # -------------- + # prepare axes + # -------------- + + fontsize = 14 + tit = ( + "[1] G. Elwert and E. Haug, Phys. Rev., 183, p.90, 1969\n" + ) + + dmargin = { + 'left': 0.08, 'right': 0.95, + 'bottom': 0.06, 'top': 0.85, + 'wspace': 0.2, 'hspace': 0.40, + } + + fig = plt.figure(figsize=(15, 12)) + fig.suptitle(tit, size=fontsize+2, fontweight='bold') + + gs = gridspec.GridSpec(ncols=2, nrows=1, **dmargin) + dax = {} + + # -------------- + # prepare axes + # -------------- + + # -------------- + # ax - isolines + + ax = fig.add_subplot(gs[0, 0]) + ax.set_xlabel( + r"$\theta_{ph}$ (photon emission angle, deg)", + size=fontsize, + fontweight='bold', + ) + ax.set_ylabel( + r"$\frac{k}{Z^2}\frac{d^2\sigma}{dkd\Omega_{ph}}$ (mb/sr)", + size=fontsize, + fontweight='bold', + ) + ax.set_title( + "[1] Fig 12. Integrated cross-section (vs theta_e and phi)\n" + "Comparisation between experimental values and models\n" + + r"$Z = O$ (O) and $Z = 13$ (Al), " + + r"$E_{e0} = 45 keV$, $E_{e1} = 5 keV$" + + "\nTarget was " + r"$Al_2O_3$", + size=fontsize, + fontweight='bold', + ) + + # store + dax['fig12'] = {'handle': ax, 'type': 'isolines'} + + # ------------ + # ax - ph_dist + + # --------------- + # plot fig 12 + # --------------- + + kax = 'fig12' + if dax.get(kax) is not None: + ax = dax[kax]['handle'] + + # literature data + inan = np.r_[0, np.any(np.isnan(out_fig12), axis=1).nonzero()[0], -1] + dls = { + 0: {'ls': '--', 'lab': 'Born approx'}, + 1: {'ls': '-.', 'lab': 'Z = 8, EH'}, + 2: {'ls': '-', 'lab': 'Z = 13, EH'}, + 3: {'ls': '-', 'lab': 'Z = 13, Non-rel.'}, + 4: {'ls': 'None', 'lab': 'exp.'}, + } + for ii, ia in enumerate(inan[:-1]): + ax.plot( + out_fig12[inan[ii]:inan[ii+1], 0], + out_fig12[inan[ii]:inan[ii+1], 1], + c='k', + ls=dls[ii]['ls'], + marker='o' if ii == 4 else 'None', + ms=10, + label=dls[ii]['lab'], + ) + + # ------------- + # computed data + + # Z = 13 + Z = 13 + for k0, v0 in d2cross_fig12_Z13['cross'].items(): + ax.plot( + theta_ph * 180/np.pi, + v0['data']*1e28*1e3 * 40e3 / Z**2, + ls='-', + lw=3 if v0 == 'EH' else 1.5, + alpha=0.5, + label=f'computed - {k0} Z = {Z}', + ) + + # Z = 8 + Z = 8 + for k0, v0 in d2cross_fig12_Z8['cross'].items(): + ax.plot( + theta_ph * 180/np.pi, + v0['data']*1e28*1e3 * 40e3 / Z**2, + ls='-', + lw=3 if v0 == 'EH' else 1.5, + alpha=0.5, + label=f'computed - {k0} Z = {Z}', + ) + + ax.set_xlim(0, 180) + ax.set_ylim(0, 8) + + # add legend + ax.legend() + + # ------------------------ + # plot photon distribution + # ------------------------ + + return dax, d2cross_fig12_Z13, d2cross_fig12_Z8 diff --git a/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_d2crossphi.py b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_d2crossphi.py new file mode 100644 index 000000000..86a8e9984 --- /dev/null +++ b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_d2crossphi.py @@ -0,0 +1,566 @@ + + +import os +import warnings + + +import numpy as np +import scipy.integrate as scpinteg +import astropy.units as asunits +import datastock as ds + + +from . import _xray_thin_target_integrated as _mod + + +# ############################################ +# ############################################ +# Default +# ############################################ + + +_PATH_HERE = os.path.dirname(__file__) + + +_THETA_PH_VSB = np.linspace(0, np.pi, 37) +_THETA_E0_VSB_NPTS = 31 +_E_PH_EV = np.r_[ + np.logspace(np.log10(100), np.log10(50e3), 51), +] +_E_E0_EV_NPTS = 61 + + +# ########################################### +# ########################################### +# get d2cross_phi +# ########################################### + + +def get_d2cross_phi( + # load from file + pfe=None, + # params + Z=None, + E_ph_eV=None, + E_e0_eV=None, + E_e0_eV_npts=None, + theta_ph_vsB=None, + theta_e0_vsB_npts=None, + phi_e0_vsB_npts=None, + # hypergeometric parameter + ninf=None, + source=None, + # integration parameters + nthetae=None, + ndphi=None, + # iok + iok=None, + # version + version_cross=None, + # verb + verb=None, + # load / save + d2cross_phi=None, + save=None, + pfe_save=None, + # unused + **kwdargs, +): + + # ---------------- + # inputs + # ---------------- + + ( + save, pfe, verb, + ) = _check( + pfe=pfe, + save=save, + pfe_save=pfe_save, + verb=verb, + ) + + # ---------------- + # compute + # ---------------- + + if pfe is None: + + # check compute + ( + E_ph_eV, E_e0_eV, iok, + theta_e0_vsB, theta_ph_vsB, + phi_e0_vsB, + version_cross, + pfe_save, + ) = _check_compute(**locals()) + + # compute + d2cross_phi = _compute(**locals()) + + # optional save + if save is True: + _save(d2cross_phi, pfe_save) + + # ---------------- + # load + # ---------------- + + else: + d2cross_phi = _load(**locals()) + + return d2cross_phi + + +# ########################################### +# ########################################### +# check +# ########################################### + + +def _check( + pfe=None, + save=None, + pfe_save=None, + verb=None, +): + + # ------------- + # save + # ------------- + + # save + save = ds._generic_check._check_var( + save, 'save', + types=bool, + default=pfe_save is not None, + ) + + # ------------- + # pfe + # ------------- + + if pfe is not None: + + c0 = ( + isinstance(pfe, str) + and os.path.isfile(pfe) + and pfe.endswith('.npz') + ) + if not c0: + msg = ( + "Arg pfe must be a valid path to a .npz file!" + ) + raise Exception(msg) + save = False + + # -------------------- + # verb + # -------------------- + + lok = [False, True, 0, 1, 2, 3] + verb = int(ds._generic_check._check_var( + verb, 'verb', + types=(int, bool), + default=lok[-1], + allowed=lok, + )) + + return ( + save, pfe, verb, + ) + + +# ########################################### +# ########################################### +# check_compute +# ########################################### + + +def _check_compute( + # params + E_ph_eV=None, + E_e0_eV=None, + E_e0_eV_npts=None, + theta_e0_vsB_npts=None, + phi_e0_vsB_npts=None, + theta_ph_vsB=None, + # version + version_cross=None, + # saving + pfe_save=None, + # unused + **kwdargs, +): + + # ---------- + # E_ph_eV + # ---------- + + if E_ph_eV is None: + E_ph_eV = _E_PH_EV + + E_ph_eV = ds._generic_check._check_flat1darray( + E_ph_eV, 'E_ph_eV', + dtype=float, + sign='>=0', + ) + + # ---------- + # E_e0_eV + # ---------- + + E_e0_eV_npts = int(ds._generic_check._check_var( + E_e0_eV_npts, 'E_e0_eV_npts', + types=(int, float), + sign='>=3', + default=_E_E0_EV_NPTS, + )) + + if E_e0_eV is None: + E_e0_eV = np.logspace( + np.log10(E_ph_eV.min()), + np.ceil(np.log10(E_ph_eV.max())) + 2, + E_e0_eV_npts, + ) + + E_e0_eV = np.unique(ds._generic_check._check_flat1darray( + E_e0_eV, 'E_e0_eV', + dtype=float, + unique=True, + sign='>=0', + )) + + iok = E_e0_eV >= E_ph_eV.min() + nok = np.sum(iok) + if nok < E_e0_eV.size: + if nok == 0: + msg = ( + f"All points ({E_e0_eV.size}) " + "are removed from E_e0_eV (< E_ph_eV.min())" + ) + raise Exception(msg) + + else: + msg = ( + f"Some points ({E_e0_eV.size - nok} / {E_e0_eV.size}) " + "are removed from E_e0_eV (< E_ph_eV.min())" + ) + warnings.warn(msg) + + if E_e0_eV.max() < E_ph_eV.max(): + msg = ( + "Arg E_e0_eV should not have a max value below E_ph_eV.min()!\n" + f"\t- E_ph_eV.max() = {E_ph_eV.max()}\n" + f"\t- E_e0_eV.max() = {E_e0_eV.max()}\n" + ) + raise Exception(msg) + + # ------------ + # theta_ph_vsB + # ------------ + + if theta_ph_vsB is None: + theta_ph_vsB = _THETA_PH_VSB + + theta_ph_vsB = ds._generic_check._check_flat1darray( + theta_ph_vsB, 'theta_ph_vsB', + dtype=float, + ) + theta_ph_vsB = np.arctan2(np.sin(theta_ph_vsB), np.cos(theta_ph_vsB)) + iout = (theta_ph_vsB < 0.) | (theta_ph_vsB > np.pi) + if np.any(iout): + msg = ( + "Arg theta_ph_vsB must be within [0, pi]\n" + f"Provided:\n{theta_ph_vsB}\n" + ) + raise Exception(msg) + + # ------------ + # theta_e0_vsB + # ------------ + + theta_e0_vsB_npts = int(ds._generic_check._check_var( + theta_e0_vsB_npts, 'theta_e0_vsB_npts', + types=(int, float), + sign='>=3', + default=_THETA_E0_VSB_NPTS, + )) + theta_e0_vsB = np.linspace(0, np.pi, theta_e0_vsB_npts) + + # -------------------- + # phi_e0_vsB + # -------------------- + + phi_e0_vsB_npts = int(ds._generic_check._check_var( + phi_e0_vsB_npts, 'phi_e0_vsB_npts', + types=(int, float), + sign='>=5', + default=2*theta_e0_vsB_npts + 1, + )) + phi_e0_vsB = np.linspace(-np.pi, np.pi, phi_e0_vsB_npts) + + # -------------------- + # version_cross + # -------------------- + + version_cross = ds._generic_check._check_var( + version_cross, 'version_cross', + types=str, + default='BHE', + ) + + # ---------- + # pfe + # ---------- + + if pfe_save is None: + nE = E_ph_eV.size + ntheta = theta_ph_vsB.size + fn = f"d2cross_phi_nEph{nE}_ntheta{ntheta}" + pfe_save = os.path.join(_PATH_HERE, f'{fn}.npz') + else: + + c0 = ( + isinstance(pfe_save, str) + and os.path.isdir(os.path.split(pfe_save)[0]) + ) + if not c0: + msg = ( + "Arg pfe_save should be a path/file.ext with a valid path!\n" + f"Provided: {pfe_save}\n" + ) + raise Exception(msg) + + if not pfe_save.endswith('.npz'): + pfe_save = f"{pfe_save}.npz" + + return ( + E_ph_eV, E_e0_eV, iok, + theta_e0_vsB, theta_ph_vsB, + phi_e0_vsB, + version_cross, + pfe_save, + ) + + +# ########################################### +# ########################################### +# compute +# ########################################### + + +def _compute( + E_ph_eV=None, + E_e0_eV=None, + theta_e0_vsB=None, + phi_e0_vsB=None, + theta_ph_vsB=None, + iok=None, + # inputs + Z=None, + # hypergeometric parameter + ninf=None, + source=None, + # integration parameters + nthetae=None, + ndphi=None, + # output customization + version_cross=None, + verb=None, + # unused + **kwdargs, +): + + # theta_ph_vs_e in (theta_ph_vsB, theta_e0_vsB, phi_e0_vsB) + cos = ( + np.cos(theta_e0_vsB[None, :, None]) + * np.cos(theta_ph_vsB[:, None, None]) + + np.sin(theta_e0_vsB[None, :, None]) + * np.sin(theta_ph_vsB[:, None, None]) + * np.cos(phi_e0_vsB[None, None, :]) + ) + + ieps = np.abs(cos) > 1. + assert np.all(np.abs(cos[ieps]) - 1. < 1e-13) + cos[ieps] = np.sign(cos[ieps]) + theta_ph_vs_e = np.arccos(cos) + + shape_emiss = (E_ph_eV.size, theta_ph_vsB.size) + shape_integ = (E_e0_eV.size, theta_e0_vsB.size, phi_e0_vsB.size) + + d2cross_phi = np.zeros(shape_emiss + shape_integ[:-1], dtype=float) + for i0, ind in enumerate(np.ndindex(shape_emiss)): + + if verb >= 2: + iEstr = f"({ind[0] + 1} / {shape_emiss[0]})" + itstr = f"({ind[1] + 1} / {shape_emiss[1]})" + ish = f"{iok.sum()} / {shape_integ[0]}" + ish = f"({ish}, {shape_integ[1]}, {shape_integ[2]})" + msg = f"\tE_ph_eV {iEstr}, theta_ph_vsB {itstr} for shape {ish}" + print(msg) + + # get integrated cross-section + # theta_ph_vs_e = (theta_ph_vsB, theta_e0_vsB, phi_e0_vsB) + # d2cross = (E_ph_eV, E_e0_eV, theta_ph_vsB) + # = (E_ph_eV, E_e0_eV, theta_ph_vsB, theta_e0_vsB, phi_e0_vsB) + d2cross = _mod.get_xray_thin_d2cross_ei_integrated_thetae_dphi( + # inputs + Z=Z, + E_ph_eV=E_ph_eV[ind[0]], + E_e0_eV=E_e0_eV[iok, None, None], + theta_ph=theta_ph_vs_e[None, ind[1], :, :], + # hypergeometric parameter + ninf=ninf, + source=source, + # integration parameters + nthetae=nthetae, + ndphi=ndphi, + # output customization + per_energy_unit='eV', + # version + version=version_cross, + # verb + verb=verb > 2, + verb_tab=2, + ) + + # integrate over phi + # MULTIPLY BY SIN PHI ????? + d2cross_phi[ind[0], ind[1], iok, :] = scpinteg.trapezoid( + d2cross['cross'][version_cross]['data'], + x=phi_e0_vsB, + axis=-1, + ) + + # ---------- + # units + # ---------- + + units = d2cross['cross'][version_cross]['units'] + units *= asunits.Unit('rad') + + # ------------- + # format output + # ------------- + + dout = { + 'd2cross_phi': { + 'data': d2cross_phi, + 'units': units, + }, + 'E_e0_eV': E_e0_eV, + 'E_ph_eV': E_ph_eV, + 'theta_e0_vsB': theta_e0_vsB, + 'theta_ph_vsB': theta_ph_vsB, + 'phi_e0_vsB': phi_e0_vsB, + 'Z': Z, + 'nthetae': d2cross['theta_e']['data'].size, + 'ndphi': d2cross['dphi']['data'].size, + 'version_cross': version_cross, + 'ninf': ninf, + 'source': source, + } + + return dout + + +# ########################################### +# ########################################### +# load +# ########################################### + + +def _load( + pfe=None, + **kwdargs, +): + + # ---------- + # load + # ---------- + + d2cross_phi = { + kk: vv.tolist() if vv.dtype == 'object' else vv + for kk, vv in dict(np.load(pfe, allow_pickle=True)).items() + } + + # ---------- + # compare with input + # ---------- + + dout = {} + for k0, v0 in d2cross_phi.items(): + + if k0 == 'd2cross_phi': + continue + + # npts vs field + knpts = [k1 for k1 in kwdargs.keys() if k1 == f"{k0}_npts"] + if len(knpts) == 1: + n1 = kwdargs[knpts[0]] + if n1 is not None: + n0 = v0.size + if n0 != n1: + dout[k0] = f"wrong number of points: {n1} vs {n0}" + continue + + elif len(knpts) > 1: + msg = "weird glitch" + raise Exception(msg) + + if kwdargs.get(k0) is None: + continue + + if not isinstance(kwdargs[k0], v0.__class__): + dout[k0] = f"wrong type: {type(kwdargs[k0])} vs {type(v0)}" + continue + + if isinstance(v0, np.ndarray): + if v0.shape != kwdargs[k0].shape: + dout[k0] = f"wrong shape: {kwdargs[k0].shape} vs {v0.shape}" + continue + if not np.allclose(v0, kwdargs[k0]): + dout[k0] = "Wrong array values" + continue + + else: + if v0 != kwdargs[k0]: + dout[k0] = "wrong value" + + # ----------------------- + # Raise wraning if needed + # ----------------------- + + if len(dout) > 0: + lstr = [f"\t- {k0}: {v0}" for k0, v0 in dout.items()] + msg = ( + "Specified args do not match loaded from file:\n" + f"pfe: {pfe}\n" + + "\n".join(lstr) + ) + warnings.warn(msg) + + return d2cross_phi + + +# ########################################### +# ########################################### +# save +# ########################################### + + +def _save( + d2cross_phi=None, + pfe_save=None, +): + + # ---------- + # save + # ---------- + + np.savez(pfe_save, **d2cross_phi) + msg = f"Saved in\n\t{pfe_save}" + print(msg) + + return diff --git a/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_dist.py b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_dist.py new file mode 100644 index 000000000..b94c759db --- /dev/null +++ b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_dist.py @@ -0,0 +1,846 @@ + + +import copy +import warnings + + +import numpy as np +import scipy.integrate as scpinteg +import astropy.units as asunits +import matplotlib.pyplot as plt +import datastock as ds + + +from .. import _convert +from . import _xray_thin_target_integrated_d2crossphi +from ..distribution import _distribution_check +from ..distribution import get_distribution + + +# ############################################ +# ############################################ +# Default +# ############################################ + + +_DPLASMA = { + 'Te_eV': { + 'def': np.linspace(1, 10, 10)[:, None, None, None] * 1e3, + 'units': asunits.Unit('eV'), + }, + 'ne_m3': { + 'def': np.r_[1e19, 1e20][None, None, :, None], + 'units': asunits.Unit('1/m^3'), + }, + 'jp_Am2': { + 'def': np.r_[1e6, 10e6][None, None, None, :], + 'units': asunits.Unit('A/m^2'), + }, + 'jp_fraction_re': { + 'def': np.linspace(0.01, 0.99, 11)[None, :, None, None], + 'units': asunits.Unit(''), + }, +} + + +# ############################################ +# ############################################ +# Main +# ############################################ + + +def get_xray_thin_integ_dist( + # ---------------- + # electron distribution + Te_eV=None, + ne_m3=None, + nZ_m3=None, + jp_Am2=None, + jp_fraction_re=None, + # RE-specific + Zeff=None, + Ekin_max_eV=None, + Efield_par_Vm=None, + lnG=None, + sigmap=None, + Te_eV_re=None, + ne_m3_re=None, + dominant=None, + # ---------------- + # cross-section + E_ph_eV=None, + E_e0_eV=None, + E_e0_eV_npts=None, + theta_e0_vsB_npts=None, + phi_e0_vsB_npts=None, + theta_ph_vsB=None, + # inputs + Z=None, + # hypergeometric parameter + ninf=None, + source=None, + # integration parameters + nthetae=None, + ndphi=None, + # output customization + version_cross=None, + # save / load + pfe_d2cross_phi=None, + save_d2cross_phi=None, + # --------------------- + # optional responsivity + dresponsivity=None, + plot_responsivity_integration=None, + # ----------- + # verb + debug=None, + verb=None, +): + """ Integrate bremsstrahlung cross-section over electron distribution + + All angles are vs the B-field + + Integrate: + dn_ph / (dV.dEph.dOmegaph) [n_ph/s.sr.eV.m3] + = int_Ee int_theta_e int_phi_e + v_e [m/s] + * d2cross(Ee, Eph, theta_ph_vs_e) [m2/sr.eV] + * f3d(Ee, theta_e) [n_e/eV.rad.rad.m3] + * dEe.dtheta_e.dphi_e [eV.rad.rad] + + In practice d2cross can be pre-integrated vs phi_e because theta_ph_vs_e + is the parameter depending on phi_e + + So d2cross_phi = int_phi_e d2cross(Ee, Eph, theta_ph_vs_e) dphi_e + then: + dn_ph / (dV.dEph.dOmegaph) [n_ph/s.sr.eV.m3] + = int_Ee int_theta_e + v_e [m/s] + * d2cross_phi(Ee, Eph, theta_ph_vs_e) [m2/eV] + * f3d(Ee, theta_e) [n_e/eV.rad.rad.m3] + * dEe.dtheta_e [eV.rad] + + """ + + # -------------------- + # prepare + # -------------------- + + ( + dplasma, + debug, + verb, + ) = _check(**locals()) + + # -------------------- + # get d2cross integrated over phi (from dist) + # -------------------- + + if verb >= 1: + msg = "Integrating d2cross over phi from distribution..." + print(msg) + + dinputs = { + kk.replace('_d2cross_phi', ''): vv + for kk, vv in locals().items() + } + d2cross_phi = _xray_thin_target_integrated_d2crossphi.get_d2cross_phi( + **dinputs, + ) + + # ---------- + # extract + + E_e0_eV = d2cross_phi['E_e0_eV'] + E_ph_eV = d2cross_phi['E_ph_eV'] + theta_e0_vsB = d2cross_phi['theta_e0_vsB'] + theta_ph_vsB = d2cross_phi['theta_ph_vsB'] + + shape_emiss = (E_ph_eV.size, theta_ph_vsB.size) + + # -------------------- + # get distribution + # -------------------- + + if verb >= 1: + msg = "Computing e distributions..." + print(msg) + + ddist = get_distribution( + # Energy, theta + E_eV=E_e0_eV, + theta=theta_e0_vsB, + # version + version='f3d_E_theta', + returnas=dict, + # plasma parameters + dominant=dominant, + **{kk: vv['data'] for kk, vv in dplasma.items()} + ) + + # shape + shape_plasma = ddist['plasma']['Te_eV']['data'].shape + shape_dist = ddist['dist']['maxwell']['dist']['data'].shape + shape_cross = d2cross_phi['d2cross_phi']['data'].shape + shape_emiss = shape_plasma + (E_ph_eV.size, theta_ph_vsB.size) + + # ------------ + # add nZ_m3 + + _add_nZ(ddist, nZ_m3, shape_plasma) + + # -------------------- + # get velocity + # -------------------- + + v_e = _convert.convert_momentum_velocity_energy( + energy_kinetic_eV=E_e0_eV, + velocity_ms=None, + momentum_normalized=None, + gamma=None, + beta=None, + )['velocity_ms']['data'][None, None, :, None] + + # -------------------- + # prepare output + # -------------------- + + # ref + ref = None # ref_plasma + ref_cross + + # shape + demiss = { + kdist: { + 'emiss': { + 'data': np.zeros(shape_emiss, dtype=float), + 'units': asunits.Unit(''), + }, + 'anis': { + 'data': np.full(shape_emiss[:-1], np.nan, dtype=float), + 'units': asunits.Unit(''), + }, + 'theta_peak': { + 'data': np.zeros(shape_emiss[:-1], dtype=float), + 'units': asunits.Unit('rad'), + }, + } + for kdist in ddist['dist'].keys() + } + + # -------------------- + # integrate + # -------------------- + + # d2cross_phi = (E_ph_eV, theta_ph_vsB, E_e0_eV, theta_e0_vsB) + # dist = shape_plasma + (E_e0_eV, theta_e0_vsB) + for kdist in sorted(ddist['dist'].keys()): + + if verb >= 1: + msg = f"Integrating d2cross_phi over {kdist}..." + print(msg) + + # loop on plasma parameters + sli0_None = (slice(None), slice(None)) + sli1_None = (None, None, slice(None), slice(None)) + for i0, ind in enumerate(np.ndindex(shape_plasma)): + + # verb + if verb >= 2 and len(ind) > 0: + msg = f"\tplasma parameters {ind} / {shape_plasma}" + msg = msg.ljust(len(msg) + 4) + print(msg, end='\r') + + # slices + if len(ind) == 0: + sli0 = sli0_None + sli1 = sli1_None + else: + sli0 = ind + sli0_None + sli1 = ind + sli1_None + + # integrate over theta_e + integ_phi_theta = scpinteg.trapezoid( + v_e + * d2cross_phi['d2cross_phi']['data'] + * ddist['dist'][kdist]['dist']['data'][sli1], + x=theta_e0_vsB, + axis=-1, + ) + + # integrate over E_e0_eV + demiss[kdist]['emiss']['data'][sli0] = scpinteg.trapezoid( + integ_phi_theta, + x=E_e0_eV, + axis=-1, + ) + + # debug + if debug is not False and debug(ind) is True: + _plot_debug(**locals()) + + # ---------------- + # prepare output + # ---------------- + + # multiply by nZ_m3 + sli = (slice(None),)*len(shape_plasma) + (None, None) + for kdist in ddist['dist'].keys(): + demiss[kdist]['emiss']['data'] *= ddist['plasma']['nZ_m3']['data'][sli] + + # units + units = ( + ddist['dist'][kdist]['dist']['units'] # 1 / (m3.rad2.eV) + * d2cross_phi['d2cross_phi']['units'] # m2.rad / (eV.sr) + * asunits.Unit('m/s') + * asunits.Unit('eV.rad') + * ddist['plasma']['nZ_m3']['units'] # 1/m^3 + ) + + for kdist in ddist['dist'].keys(): + demiss[kdist]['emiss']['units'] = units + + # ---------------- + # sanity check + # ---------------- + + for kdist in ddist['dist'].keys(): + iok = np.isfinite(demiss[kdist]['emiss']['data']) + iok[iok] = demiss[kdist]['emiss']['data'][iok] >= 0. + if np.any(~iok): + msg = f"\nSome non-finite or negative values in emiss {kdist} !\n" + warnings.warn(msg) + + # --------------------- + # optional responsivity + # --------------------- + + if dresponsivity is not None: + dintegrand = _responsivity( + E_ph_eV=E_ph_eV, + demiss=demiss, + dresponsivity=dresponsivity, + plot=plot_responsivity_integration, + dplasma=dplasma, + ) + + # ---------------- + # anisotropy + # ---------------- + + axis = -1 + danis = {} + for kdist in ddist['dist'].keys(): + vmax = np.max(demiss[kdist]['emiss']['data'], axis=axis) + vmin = np.min(demiss[kdist]['emiss']['data'], axis=axis) + iok = np.isfinite(vmax) + iok[iok] = vmax[iok] > 0. + demiss[kdist]['anis']['data'][iok] = ( + (vmax[iok] - vmin[iok]) / vmax[iok] + ) + imax = np.argmax(demiss[kdist]['emiss']['data'], axis=axis) + demiss[kdist]['theta_peak']['data'][...] = theta_ph_vsB[imax] + if ref is None: + refmax = None + else: + refmax = ref[:-1] + + # ---------------- + # format output + # ---------------- + + demiss = { + 'E_ph_eV': { + 'key': None, + 'data': E_ph_eV, + 'units': asunits.Unit('eV'), + 'ref': None, + }, + 'theta_ph_vsB': { + 'key': None, + 'data': theta_ph_vsB, + 'units': asunits.Unit('rad'), + 'ref': None, + }, + 'emiss': demiss, + } + + if dresponsivity is not None: + demiss['responsivity'] = dresponsivity + demiss['integrand'] = dintegrand + + return demiss, ddist, d2cross_phi + + +# ############################################ +# ############################################ +# Check +# ############################################ + + +def _check( + debug=None, + verb=None, + # unused + **kwdargs, +): + + # ----------------- + # plasma parameters + # ----------------- + + dplasma = _distribution_check._plasma( + ddef=_DPLASMA, + **kwdargs, + ) + + # -------------------- + # debug + # -------------------- + + if debug is None: + debug = False + + if isinstance(debug, bool): + if debug is True: + def debug(ind): + return True + + if debug is not False: + if not callable(debug): + msg = ( + "Arg debug must be a callable debug(ind)\n" + f"\nProvided: {debug}\n" + ) + raise Exception(msg) + + # -------------------- + # verb + # -------------------- + + lok = [False, True, 0, 1, 2, 3] + verb = int(ds._generic_check._check_var( + verb, 'verb', + types=(int, bool), + default=lok[-1], + allowed=lok, + )) + + return ( + dplasma, + debug, + verb, + ) + + +# ########################################### +# ########################################### +# ad nZ_m3 +# ########################################### + + +def _add_nZ( + ddist=None, + nZ_m3=None, + shape_plasma=None, +): + + # ------------- + # nZ_m3 + # ------------- + + if nZ_m3 is None: + nZ_m3 = np.copy(ddist['plasma']['ne_m3']['data']) + + nZ_m3 = np.atleast_1d(nZ_m3) + if np.any((~np.isfinite(nZ_m3)) | (nZ_m3 < 0.)): + msg = "Arg nZ_m3 has non-finite of negative values!" + raise Exception(msg) + + # ------------- + # broadcastable + # ------------- + + try: + _ = np.broadcast_shapes(shape_plasma, nZ_m3.shape) + + except Exception: + lk = list(ddist['plasma'].keys()) + lstr = [f"\t- {k0}: {ddist['plasma'][k0]['data'].shape}" for k0 in lk] + msg = ( + "Arg nZ_m3 must be broadcast-able to othe plasma parameters!\n" + + "\n".join(lstr) + + "\t- nZ_m3: {nZ_m3.shape}\n" + ) + raise Exception(msg) + + # ------------- + # store + # ------------- + + ddist['plasma']['nZ_m3'] = { + 'key': 'nZ', + 'data': nZ_m3, + 'units': asunits.Unit(ddist['plasma']['ne_m3']['units']), + } + + return + + +# ########################################### +# ########################################### +# plot debug +# ########################################### + + +def _plot_debug( + E_ph_eV=None, + E_e0_eV=None, + integ_phi_theta=None, + demiss=None, + kdist=None, + sli0=None, + theta_ph_vsB=None, + # unused + **kwdargs, +): + """ + integ_phi_theta in (E_ph_eV, theta_ph_vsB, E_e0_eV) + + """ + + indtheta = 0 + theta_deg = theta_ph_vsB[indtheta]*180/np.pi + + Eph = 10e3 + indEph = np.argmin(np.abs(E_ph_eV - Eph)) + + # ----------------- + # prepare figure + # ----------------- + + fig = plt.figure() + fig.suptitle(kdist, fontsize=14, fontweight='bold') + + units = demiss[kdist]['emiss']['units'] + ax0 = fig.add_subplot(311) + ax0.set_ylabel( + units, + fontsize=12, + fontweight='bold', + ) + ax0.set_title( + f'integ_phi_theta at theta = {theta_deg:3.1f} deg', + fontsize=14, + fontweight='bold', + ) + ax0.set_xlabel('E_e0 (keV)', fontweight='bold') + + ax1 = fig.add_subplot(312, sharey=ax0) + ax1.set_ylabel( + units, + fontsize=12, + fontweight='bold', + ) + ax1.set_xlabel('E_ph (keV)', fontweight='bold') + + ax2 = fig.add_subplot(313, sharey=ax0) + ax2.set_ylabel( + units, + fontsize=12, + fontweight='bold', + ) + ax2.set_title( + f'integ_phi_theta at E_ph = {Eph*1e-3:3.1f} keV', + fontsize=14, + fontweight='bold', + ) + ax2.set_xlabel('theta (deg)', fontweight='bold') + + # ----------------- + # plot at theta = 0 vs E_e0_eV + # ----------------- + + ax = ax0 + for ie, eph in enumerate(E_ph_eV): + ax.plot( + E_e0_eV*1e-3, + integ_phi_theta[ie, indtheta, :], + '.-', + label=f'{eph*1e-3} keV', + ) + ax.legend() + + # ----------------- + # plot at theta = 0 vs E_ph_eV + # ----------------- + + ax = ax1 + for ie, ee in enumerate(E_e0_eV): + ax.plot( + E_ph_eV*1e-3, + integ_phi_theta[:, indtheta, ie], + '.-', + label=f'{ee*1e-3} keV', + ) + ax.legend() + + # ----------------- + # plot at Eph vs theta + # ----------------- + + ax = ax2 + for ie, ee in enumerate(E_e0_eV): + ax.plot( + theta_ph_vsB * 180/np.pi, + integ_phi_theta[indEph, :, ie], + '.-', + label=f'{ee*1e-3} keV', + ) + ax.legend() + + print(integ_phi_theta[indEph, indtheta, :]) + + return + + +# ########################################### +# ########################################### +# add responsivity +# ########################################### + + +def _responsivity( + E_ph_eV=None, + demiss=None, + dresponsivity=None, + plot=None, + dplasma=None, +): + + # -------------- + # check + # -------------- + + # plot + plot = ds._generic_check._check_var( + plot, 'plot', + types=bool, + default=False, + ) + + c0 = ( + isinstance(dresponsivity, dict) + and isinstance(dresponsivity.get('E_eV'), dict) + and isinstance(dresponsivity['E_eV'].get('data'), np.ndarray) + and dresponsivity['E_eV']['data'].ndim == 1 + and isinstance(dresponsivity.get('responsivity'), dict) + and isinstance(dresponsivity['responsivity'].get('data'), np.ndarray) + and ( + dresponsivity['responsivity']['data'].shape + == dresponsivity['E_eV']['data'].shape + ) + and isinstance(dresponsivity.get('ph_vs_E'), str) + ) + if not c0: + msg = ( + "Arg dresponsivity must be a dict of the form:\n" + "- 'E_eV': {'data': (npts,), 'units': 'eV'}\n" + "- 'responsivity': {'data': (npts,), 'units': str}\n" + "- 'ph_vs_E': 'ph' or 'E'\n" + f"Provided:\n{dresponsivity}\n" + ) + raise Exception(msg) + + # ph vs E + dresponsivity['ph_vs_E'] = ds._generic_check._check_var( + dresponsivity['ph_vs_E'], 'ph_vs_E', + types=str, + allowed=['ph', 'E'], + extra_msg="dresponsivity['ph_vs_E'] integrated photons or energy", + ) + + dresponsivity = copy.deepcopy(dresponsivity) + + # -------------- + # interpolate if needed + # -------------- + + c0 = ( + dresponsivity['E_eV']['data'].size == E_ph_eV.size + and np.allclose(dresponsivity['E_eV']['data'], E_ph_eV) + ) + if c0: + resp_data = dresponsivity['responsivity']['data'] + else: + resp_data = np.interp( + E_ph_eV, + dresponsivity['E_eV']['data'], + dresponsivity['responsivity']['data'], + left=0, + right=0, + ) + + # -------------- + # compute + # -------------- + + sli = [None]*demiss['maxwell']['emiss']['data'].ndim + sli[-2] = slice(None) + sli = tuple(sli) + dintegrand = {} + for kdist in demiss.keys(): + + # units + units = ( + demiss[kdist]['emiss']['units'] + * asunits.Unit(dresponsivity['responsivity']['units']) + ) + + # adjust + integrand = demiss[kdist]['emiss']['data'] * resp_data[sli] + if dresponsivity['ph_vs_E'] == 'E': + integrand *= E_ph_eV[sli] + units *= asunits.Unit('eV') + + # for plot + dintegrand[kdist] = { + 'data': integrand, + 'units': units, + } + + # data + data = scpinteg.trapezoid( + integrand, + x=E_ph_eV, + axis=-2, + ) + units = units * asunits.Unit('eV') + + # store + demiss[kdist]['emiss_integ'] = { + 'data': data, + 'units': units, + } + + # ------------------- + # update dresponsivity + # ------------------- + + dresponsivity['E_eV']['data'] = demiss[kdist]['emiss']['data'] + dresponsivity['responsivity']['data'] = resp_data + + # ------------ + # plot + # ------------ + + if plot is True: + _plot_responsivity_integration( + dintegrand=dintegrand, + units=units, + demiss=demiss, + E_ph_eV=E_ph_eV, + dresponsivity=dresponsivity, + data=data, + dplasma=dplasma, + ) + + return dintegrand + + +# ############################################# +# ############################################# +# plot responsivity +# ############################################# + + +def _plot_responsivity_integration( + dintegrand=None, + units=None, + demiss=None, + E_ph_eV=None, + dresponsivity=None, + data=None, + dplasma=None, +): + + # ----------------- + # prepare data + # ----------------- + + ldist = list(demiss.keys()) + iok = np.all( + np.isfinite(dintegrand[ldist[0]]['data']) + & np.isfinite(dintegrand[ldist[1]]['data']), + axis=(-1, -2), + ) + + iokn = iok.nonzero() + sli = iokn + (slice(None), slice(None)) + ind = np.argmax(np.sum(dintegrand['RE']['data'][sli], axis=(-1, -2))) + ind = tuple([ii[ind] for ii in iokn]) + + # dplasma + dp = { + kp: vp['data'][ind] + for kp, vp in dplasma.items() + } + dc = { + 'Te_eV': (1e-3, 'keV'), + 'ne_m3': (1e-20, '1e20 /m3'), + 'jp_Am2': (1e-6, 'MA/m2'), + 'Ekin_max_eV': (1e-3, 'keV') + } + lstr = [] + for kp, vp in dp.items(): + val = vp * dc.get(kp, (1.,))[0] + units = dc.get(kp, (1, dplasma[kp]['units']))[1] + if units is None: + units = '' + units = asunits.Unit(units) + lstr.append(f"{kp}: {val:1.3f} {'' if units is None else units}") + + tit = "Integration of emissivity\n" + "\n".join(lstr) + + # ----------------- + # prepare figure + # ----------------- + + fig = plt.figure() + + ax0 = fig.add_subplot(211) + ax1 = fig.add_subplot(212) + + ax0.set_ylabel( + dintegrand[ldist[0]]['units'], + fontsize=12, + fontweight='bold', + ) + ax0.set_title(tit, fontsize=14, fontweight='bold') + ax1.set_xlabel('E (eV)', fontweight='bold') + ax1.set_ylabel( + dresponsivity['responsivity']['units'], + fontsize=12, + fontweight='bold', + ) + + # ----------------- + # plot + # ----------------- + + sli = ind + (slice(None), 0) + for kdist in ldist: + ax0.semilogy( + E_ph_eV, + dintegrand[kdist]['data'][sli], + '-', + label=f"{kdist} {data[ind + (0,)]:1.3e} {units}", + ) + + ax1.semilogy( + E_ph_eV, + dresponsivity['responsivity']['data'], + '-k', + ) + + ax0.legend(fontsize=12) + return diff --git a/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_dist_plot.py b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_dist_plot.py new file mode 100644 index 000000000..1074ce778 --- /dev/null +++ b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_dist_plot.py @@ -0,0 +1,1210 @@ + + +import numpy as np +import matplotlib.pyplot as plt +import matplotlib.gridspec as gridspec +import matplotlib.lines as mlines +import datastock as ds + + +from . import _xray_thin_target_integrated_dist + + +# ############################################ +# ############################################ +# Default +# ############################################ + + +_DPLASMA_ANISOTROPY_MAP = { + 'Te_eV': np.r_[1, 5, 10, 20]*1e3, + 'ne_m3': np.r_[1, 3, 5, 10, 30, 50, 100]*1e19, + 'jp_Am2': np.r_[0, 1, 3, 5, 8, 10]*1e6, + 'jp_fraction_re': 0.1, +} + + +_DPLASMA_ANGULAR_PROFILES = { + 'Te_eV': np.r_[1, 1, 10, 1]*1e3, + 'ne_m3': np.r_[1e19, 1e20, 1e19, 1e19], + 'jp_Am2': np.r_[1e6, 1e6, 1e6, 10e6], + 'jp_fraction_re': 0., +} + + +_THETA_PH_VSB = np.linspace(0, np.pi, 11) # 7 +_THETA_E0_VSB_NPTS = 17 # 19 +# _E_PH_EV = np.r_[5., 10., 15., 20., 30., 50.] * 1e3 +_E_PH_EV = np.r_[5., 15., 30.] * 1e3 +# _E_E0_EV = np.logspace(-2, 4, 61)*1e3 # 31 +_E_E0_EV = np.logspace(-2, 4, 31)*1e3 # 31 + + +# ############################################ +# ############################################ +# Main +# ############################################ + + +def plot_xray_thin_integ_dist( + # ---------------- + # electron distribution + Te_eV=None, + ne_m3=None, + jp_Am2=None, + jp_fraction_re=None, + # RE-specific + Zeff=None, + Ekin_max_eV=None, + Efield_par_Vm=None, + lnG=None, + sigmap=None, + Te_eV_re=None, + ne_m3_re=None, + dominant=None, + # ---------------- + # cross-section + E_ph_eV=None, + E_e0_eV=None, + E_e0_eV_npts=None, + theta_e0_vsB_npts=None, + phi_e0_vsB_npts=None, + theta_ph_vsB=None, + # inputs + Z=None, + # hypergeometric parameter + ninf=None, + source=None, + # integration parameters + nthetae=None, + ndphi=None, + version_cross=None, + # save / load + pfe_d2cross_phi=None, + # ----------------- + # optional responsivity + dresponsivity=None, + # ----------------- + # plots + plot_angular_spectra=None, + plot_anisotropy_map=None, + plot_E_ph=None, + # verb + verb=None, +): + """ plot the Maxwellian-integrated Bremsstrahlung + + fig.1: vs the standard isotropic formula (quantotative validation) + + fig. 2: to show the anisotropy vs B at various plasma parameters and + energies + + """ + + # ------------- + # check inputs + # ------------- + + ( + dplasma, indplot, + E_ph_eV, E_e0_eV, + theta_ph_vsB, + theta_e0_vsB_npts, + version_cross, + plot_angular_spectra, + plot_anisotropy_map, + verb, + ) = _check( + # electron distribution + Te_eV=Te_eV, + ne_m3=ne_m3, + jp_Am2=jp_Am2, + jp_fraction_re=jp_fraction_re, + # cross-section + E_ph_eV=E_ph_eV, + E_e0_eV=E_e0_eV, + theta_e0_vsB_npts=theta_e0_vsB_npts, + theta_ph_vsB=theta_ph_vsB, + version_cross=version_cross, + # plots + plot_angular_spectra=plot_angular_spectra, + plot_anisotropy_map=plot_anisotropy_map, + verb=verb, + ) + + # ------------- + # compute + # ------------- + + ( + demiss, ddist, d2cross_phi, + ) = _xray_thin_target_integrated_dist.get_xray_thin_integ_dist( + # ---------------- + # cross-section + E_ph_eV=E_ph_eV, + E_e0_eV=E_e0_eV, + theta_e0_vsB_npts=theta_e0_vsB_npts, + phi_e0_vsB_npts=phi_e0_vsB_npts, + theta_ph_vsB=theta_ph_vsB, + # inputs + Z=Z, + # hypergeometric parameter + ninf=ninf, + source=source, + # integration parameters + nthetae=nthetae, + ndphi=ndphi, + # output customization + version_cross=version_cross, + pfe_d2cross_phi=pfe_d2cross_phi, + # verb + verb=verb-1, + # optional responsivity + dresponsivity=dresponsivity, + # ---------------- + # electron distribution + **dplasma, + ) + + # -------------- + # extract + # -------------- + + theta_ph_vsB = d2cross_phi['theta_ph_vsB'] + E_ph_eV = d2cross_phi['E_ph_eV'] + + # ------------- + # plots + # ------------- + + dax0 = None + if plot_angular_spectra is True: + dax0 = _plot_angular_spectra( + **locals(), + ) + + dax1 = None + if plot_anisotropy_map is True: + dax1 = _plot_anisotropy_map( + **locals(), + ) + + return dax0, dax1, demiss, ddist, dplasma + + +# ############################################ +# ############################################ +# Check +# ############################################ + + +def _check( + # ---------------- + # electron distribution + Te_eV=None, + ne_m3=None, + jp_Am2=None, + jp_fraction_re=None, + # ---------------- + # cross-section + E_ph_eV=None, + E_e0_eV=None, + theta_e0_vsB_npts=None, + theta_ph_vsB=None, + # version + version_cross=None, + # plots + plot_angular_spectra=None, + plot_anisotropy_map=None, + verb=None, +): + + # -------------------- + # plot_angular_spectra + # -------------------- + + plot_angular_spectra = ds._generic_check._check_var( + plot_angular_spectra, 'plot_angular_spectra', + types=bool, + default=True, + ) + + # -------------------- + # plot_anisotropy_map + # -------------------- + + plot_anisotropy_map = ds._generic_check._check_var( + plot_anisotropy_map, 'plot_anisotropy_map', + types=bool, + default=True, + ) + + # ------------------------------------- + # Te_eV, ne_m3, jp_Am2, re_fraction_Ip + # ------------------------------------- + + dplasma, indplot = _dplasma_asis( + Te_eV=Te_eV, + ne_m3=ne_m3, + jp_Am2=jp_Am2, + jp_fraction_re=jp_fraction_re, + ) + if plot_anisotropy_map is True: + dplasma, indplot = _dplasma_map( + Te_eV=Te_eV, + ne_m3=ne_m3, + jp_Am2=jp_Am2, + jp_fraction_re=jp_fraction_re, + dplasma0=dplasma, + ) + + # ---------- + # E_ph_eV + # ---------- + + if E_ph_eV is None: + E_ph_eV = _E_PH_EV + + E_ph_eV = ds._generic_check._check_flat1darray( + E_ph_eV, 'E_ph_eV', + dtype=float, + sign='>=0', + ) + + # ---------- + # E_e0_eV + # ---------- + + if E_e0_eV is None: + E_e0_eV = _E_E0_EV + + E_e0_eV = ds._generic_check._check_flat1darray( + E_e0_eV, 'E_e0_eV', + dtype=float, + sign='>=0', + ) + + # ------------ + # theta_ph_vsB + # ------------ + + if theta_ph_vsB is None: + theta_ph_vsB = _THETA_PH_VSB + + theta_ph_vsB = ds._generic_check._check_flat1darray( + theta_ph_vsB, 'theta_ph_vsB', + dtype=float, + ) + + # ------------ + # theta_e0_vsB + # ------------ + + theta_e0_vsB_npts = int(ds._generic_check._check_var( + theta_e0_vsB_npts, 'theta_e0_vsB_npts', + types=(int, float), + sign='>=3', + default=_THETA_E0_VSB_NPTS, + )) + + # -------------------- + # version_cross + # -------------------- + + lok = ['BHE', 'EH'] + version_cross = ds._generic_check._check_var( + version_cross, 'version_cross', + types=str, + allowed=lok, + default=lok[0], + ) + + # -------------------- + # verb + # -------------------- + + lok = [False, True, 0, 1, 2, 3] + verb = int(ds._generic_check._check_var( + verb, 'verb', + types=(int, bool), + default=lok[-1], + allowed=lok, + )) + + return ( + dplasma, indplot, + E_ph_eV, E_e0_eV, + theta_ph_vsB, + theta_e0_vsB_npts, + version_cross, + plot_angular_spectra, + plot_anisotropy_map, + verb, + ) + + +def _dplasma_asis( + Te_eV=None, + ne_m3=None, + jp_Am2=None, + jp_fraction_re=None, +): + + # ----------------- + # initialize + # ----------------- + + dplasma = { + 'Te_eV': Te_eV, + 'ne_m3': ne_m3, + 'jp_Am2': jp_Am2, + 'jp_fraction_re': jp_fraction_re, + } + + # ----------------- + # set default + array + # ----------------- + + # default + np.ndarray + size = 1 + for k0, v0 in dplasma.items(): + if v0 is None: + v0 = _DPLASMA_ANGULAR_PROFILES[k0] + v0 = np.atleast_1d(v0).ravel() + dplasma[k0] = v0 + size = max(size, v0.size) + + # ----------------- + # broadcastable + # ----------------- + + # shape consistency + dout = { + k0: v0.size for k0, v0 in dplasma.items() + if v0.size not in [1, size] + } + if len(dout) > 0: + lstr = [f"\t- {k0}: {v0}" for k0, v0 in dout.items()] + msg = ( + "All plasma parameter args must be either scalar " + "or flat arrays of same size!\n" + f"\t- max detected size: {size}\n" + + "\n".join(lstr) + ) + raise Exception(msg) + + # format to shape + for k0, v0 in dplasma.items(): + dplasma[k0] = np.broadcast_to(v0, (size,)) + + # -------------- + # add isotropic + # -------------- + + for k0, v0 in dplasma.items(): + if k0 == 'jp_Am2': + v00 = 0. + else: + v00 = v0[0] + dplasma[k0] = np.r_[v00, v0] + + # -------------- + # indplot + # -------------- + + indplot = np.ones(dplasma[k0].shape, dtype=bool) + + return dplasma, indplot + + +def _dplasma_map( + Te_eV=None, + ne_m3=None, + jp_Am2=None, + jp_fraction_re=None, + dplasma0=None, +): + + # ----------------- + # initialize + # ----------------- + + dplasma = { + 'Te_eV': Te_eV, + 'ne_m3': ne_m3, + 'jp_Am2': jp_Am2, + 'jp_fraction_re': jp_fraction_re, + } + + # ----------------- + # set default + array + # ----------------- + + # default + np.ndarray + for k0, v0 in dplasma.items(): + if v0 is None: + v0 = _DPLASMA_ANISOTROPY_MAP[k0] + v0 = np.atleast_1d(v0).ravel() + dplasma[k0] = v0 + + # --------------------- + # broadcast + # --------------------- + + dplasma = { + 'Te_eV': dplasma['Te_eV'][:, None, None, None], + 'ne_m3': dplasma['ne_m3'][None, :, None, None], + 'jp_Am2': dplasma['jp_Am2'][None, None, :, None], + 'jp_fraction_re': dplasma['jp_fraction_re'][None, None, None, :], + } + + # -------------- + # indplot + # -------------- + + shapef = np.broadcast_shapes(*[vv.shape for vv in dplasma.values()]) + indplot = np.zeros(shapef, dtype=bool) + + for ind in np.ndindex(dplasma0['Te_eV'].shape): + iTe = np.argmin(np.abs(dplasma['Te_eV'] - dplasma0['Te_eV'][ind])) + ine = np.argmin(np.abs(dplasma['ne_m3'] - dplasma0['ne_m3'][ind])) + ijp = np.argmin(np.abs(dplasma['jp_Am2'] - dplasma0['jp_Am2'][ind])) + ijf = np.argmin(np.abs( + dplasma['jp_fraction_re'] - dplasma0['jp_fraction_re'][ind] + )) + indplot[iTe, ine, ijp, ijf] = True + + return dplasma, indplot + + +# ############################################ +# ############################################ +# Plot angular spectra +# ############################################ + + +def _plot_angular_spectra( + E_ph_eV=None, + theta_ph_vsB=None, + ddist=None, + demiss=None, + indplot=None, + # plotting + dax=None, + dparam=None, + dmargin=None, + fs=None, + fontsize=None, + version_cross=None, + # unused + **kwdargs, +): + + # ---------------- + # inputs + # ---------------- + + dparam = _check_plot_angular_spectra( + E_ph_eV=E_ph_eV, + dparam=dparam, + ) + + # ---------------- + # prepare dax + # ---------------- + + if dax is None: + dax = _get_dax_angular_spectra( + ddist=ddist, + demiss=demiss, + indplot=indplot, + dmargin=dmargin, + fs=fs, + fontsize=fontsize, + version_cross=version_cross, + ) + + dax = ds._generic_check._check_dax(dax, main='isotropic') + + # ---------------- + # plot + # ---------------- + + # ----------- + # shapes + + vmax0 = 0 + lkp = ['Te_eV', 'ne_m3', 'jp_Am2', 'jp_fraction_re'] + shapef = np.broadcast_shapes( + *[ddist['plasma'][kk]['data'].shape for kk in lkp] + ) + kdist = 'maxwell' + for ii, ind in enumerate(np.ndindex(shapef)): + + if not indplot[ind]: + continue + + # kax + kax0 = _get_kax(ind, ddist) + kax = f"{kax0} - shape" + + # get ax + if dax.get(kax) is None: + continue + ax = dax[kax]['handle'] + + # plot - shape + for iE, ee in enumerate(E_ph_eV): + sli = ind + (iE, slice(None)) + vmax = np.max(demiss['emiss'][kdist]['emiss']['data'][sli]) + ax.plot( + theta_ph_vsB*180/np.pi, + demiss['emiss'][kdist]['emiss']['data'][sli] / vmax, + **dparam[iE], + ) + vmax0 = max(vmax0, vmax) + + # lim + if ii == 0: + ax.set_xlim(0, 180) + ax.set_ylim(0, 1) + + # legend + ax.legend(title=r"$E_{ph}$ (keV)", fontsize=fontsize) + + # ----------- + # abs + + for ii, ind in enumerate(np.ndindex(shapef)): + + if not indplot[ind]: + continue + + # kax + kax0 = _get_kax(ind, ddist) + kax = f"{kax0} - abs" + + # get ax + if dax.get(kax) is None: + continue + ax = dax[kax]['handle'] + + # plot - abs + for iE, ee in enumerate(E_ph_eV): + sli = ind + (iE, slice(None)) + ax.semilogy( + theta_ph_vsB*180/np.pi, + demiss['emiss'][kdist]['emiss']['data'][sli], + **dparam[iE], + ) + + # lim + if ii == 0: + ax.set_ylim(0, vmax0) + + # ----------- + # spect + + for ii, ind in enumerate(np.ndindex(shapef)): + + if not indplot[ind]: + continue + + # kax + kax0 = _get_kax(ind, ddist) + kax = f"{kax0} - spect" + + # get ax + if dax.get(kax) is None: + continue + ax = dax[kax]['handle'] + + # plot - spect + for it, tt in enumerate(theta_ph_vsB): + sli = ind + (slice(None), it) + ax.semilogy( + E_ph_eV*1e-3, + demiss['emiss'][kdist]['emiss']['data'][sli], + ls='-', + label=f"{tt*180/np.pi:3.0f}", + ) + + ax.legend(title=r"$\theta$ (deg)", fontsize=fontsize) + + return dax + + +# ############################################ +# ############################################ +# _check_plot +# ############################################ + + +def _check_plot_angular_spectra( + E_ph_eV=None, + dparam=None, +): + + # ------------- + # dparam + # ------------- + + prop_cycle = plt.rcParams['axes.prop_cycle'] + colors = prop_cycle.by_key()['color'] + + dparam_def = {} + for ii, ee in enumerate(E_ph_eV): + dparam_def[ii] = { + 'c': colors[ii % len(colors)], + 'ls': '-', + 'lw': 1, + 'marker': 'None', + 'label': f'{ee*1e-3:3.0f}', + } + + if dparam is None: + dparam = dparam_def + + lok = np.arange(E_ph_eV.size) + c0 = ( + isinstance(dparam, dict) + and all([ + isinstance(k0, int) + and k0 in lok + and isinstance(v0, dict) + for k0, v0 in dparam.items() + ]) + ) + if not c0: + msg = ( + "Arg dparam must be a dict with keys in range(0, E_ph_eV.size) " + "and values must be dict with:\n" + "\t- 'c': color-like\n" + "\t- 'ls': ls-like\n" + "\t- 'lw': int/float\n" + "\t- 'marker': marker-like\n" + f"Provided:\n{dparam}\n" + ) + raise Exception(msg) + + # Fill with default values + for k0, v0 in dparam.items(): + for k1, v1 in dparam_def[k0].items(): + dparam[k0][k1] = dparam[k0].get(k1, v1) + + return dparam + + +# ############################################ +# ############################################ +# _get_dax_angular_spectra +# ############################################ + + +def _get_dax_angular_spectra( + ddist=None, + demiss=None, + indplot=None, + dmargin=None, + fs=None, + fontsize=None, + version_cross=None, +): + # --------------- + # check inputs + # -------------- + + # fs + if fs is None: + fs = (17, 10) + + fs = tuple(ds._generic_check._check_flat1darray( + fs, 'fs', + dtype=float, + sign='>0', + size=2, + )) + + # fontsize + fontsize = ds._generic_check._check_var( + fontsize, 'fontsize', + types=(int, float), + default=12, + sign='>0', + ) + + # dmargin + if dmargin is None: + dmargin = { + 'left': 0.06, 'right': 0.98, + 'bottom': 0.06, 'top': 0.90, + 'wspace': 0.20, 'hspace': 0.20, + } + + # shapef + shapef = np.broadcast_shapes(*[ + v0['data'].shape + for k0, v0 in ddist['plasma'].items() + if k0 in ['Te_eV', 'ne_m3', 'jp_Am2', 'jp_fraction_re'] + ]) + + # --------------- + # prepare data + # --------------- + + kdist = 'maxwell' + xlab = r"$\theta_B$ (deg)" + ylab = r"$\epsilon$" + f"({demiss['emiss'][kdist]['emiss']['units']})" + + # --------------- + # prepare figure + # --------------- + + tit = ( + f"{version_cross} Bremsstrahlung cross-section integrated over " + "electron distribution" + ) + + fig = plt.figure(figsize=fs) + fig.suptitle(tit, size=fontsize+2, fontweight='bold') + + gs = gridspec.GridSpec( + ncols=indplot.sum(), + nrows=3, + **dmargin, + ) + dax = {} + + # --------------- + # prepare axes + # -------------- + + ax0n, ax0a, ax0s = None, None, None + i0 = 0 + for ii, ind in enumerate(np.ndindex(shapef)): + + if not indplot[ind]: + continue + + # kax + kax0 = _get_kax(ind, ddist) + + # --------------- + # create - shape + + ax = fig.add_subplot(gs[0, i0], sharex=ax0n, sharey=ax0n) + ax.set_xlabel( + xlab, + fontweight='bold', + size=fontsize, + ) + ax.set_title( + kax0, + fontweight='bold', + size=fontsize, + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # ax0 + if ii == 0: + ax.set_ylabel( + "Normalized (a.u.)", + fontweight='bold', + size=fontsize, + ) + ax0n = ax + + # store + dax[f"{kax0} - shape"] = {'handle': ax} + + # --------------- + # create - abs + + ax = fig.add_subplot(gs[1, i0], sharex=ax0n, sharey=ax0a) + ax.set_xlabel( + xlab, + fontweight='bold', + size=fontsize, + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # ax0 + if ii == 0: + ax.set_ylabel( + ylab, + fontweight='bold', + size=fontsize, + ) + ax0a = ax + + # store + dax[f"{kax0} - abs"] = {'handle': ax} + + # --------------- + # create - spect + + ax = fig.add_subplot(gs[2, i0], sharex=ax0s, sharey=ax0a) + ax.set_xlabel( + "E_ph (keV)", + fontweight='bold', + size=fontsize, + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # ax0 + if ii == 0: + ax.set_ylabel( + ylab, + fontweight='bold', + size=fontsize, + ) + ax0s = ax + + # store + dax[f"{kax0} - spect"] = {'handle': ax} + + i0 += 1 + + return dax + + +def _get_kax(ind, ddist, kdist='maxwell'): + + if len(ind) == 4: + indTe = (ind[0], 0, 0, 0) + indne = (0, ind[1], 0, 0) + indjp = (0, 0, ind[2], 0) + indjf = (0, 0, 0, ind[3]) + indv0 = (0, ind[1], ind[2], 0, 0, 0) + indvt = indTe + (0, 0) + ind_int = ind + else: + indTe, indne, indjp, indjf = ind, ind, ind, ind + indv0, indvt, ind_int = ind, ind, ind[0] + + Te = ddist['plasma']['Te_eV']['data'][indTe] + ne = ddist['plasma']['ne_m3']['data'][indne] + jp = ddist['plasma']['jp_Am2']['data'][indjp] + jf = ddist['plasma']['jp_Am2']['data'][indjf] + integ = 100 * (ddist['dist'][kdist]['integ_ne']['data'][ind_int] / ne - 1.) + vdvt = ( + ddist['dist'][kdist]['v0_par_ms']['data'][indv0] + / ddist['dist'][kdist]['vt_ms']['data'][indvt] + ) + kax = ( + f"Te = {Te*1e-3} keV, " + f"ne = {ne:1.1e} /m3, " + f"jp = {jp*1e-6} MA/m2\n" + f"jf = {jf}\n" + f"integral = {integ:3.1f} % error\n" + + r"$v_0 / v_T = \frac{j}{en_e}\frac{m_e}{\sqrt{2k_BT_e}}$ = " + + f"{vdvt:3.3f}" + ) + if np.sum(ind) == 0: + kax = f'isotropic\n{kax}' + return kax + + +# ############################################ +# ############################################ +# Plot anisotropy map +# ############################################ + + +def _plot_anisotropy_map( + E_ph_eV=None, + theta_ph_vsB=None, + ddist=None, + demiss=None, + plot_E_ph=None, + # plotting + dax=None, + dparam=None, + dmargin=None, + fs=None, + fontsize=None, + version_cross=None, + # unused + **kwdargs, +): + + # ---------------- + # inputs + # ---------------- + + # ---------------- + # prepare data + # ---------------- + + kdist = 'maxwell' + + # shape_plasma + stream = ( + ddist['dist'][kdist]['v0_par_ms']['data'] + / ddist['dist'][kdist]['vt_ms']['data'] + ) + + # shape_plasma + (nE_ph,) + kdist = 'maxwell' + anis = demiss['emiss'][kdist]['anis']['data'] + theta_peak = demiss['emiss'][kdist]['theta_peak']['data'] + + Te = np.unique(ddist['plasma']['Te_eV']['data']) + + # E_ph_eV + if plot_E_ph is None: + plot_E_ph = E_ph_eV + + # deco + lcolor = ['r', 'g', 'b', 'm', 'y', 'c'] + lls = ['-', '--', ':', '-.'] + + # ---------------- + # prepare dax + # ---------------- + + if dax is None: + dax = _get_dax_anisotropy_map( + demiss=demiss, + dmargin=dmargin, + fs=fs, + fontsize=fontsize, + version_cross=version_cross, + ) + + dax = ds._generic_check._check_dax(dax) + + # ---------------- + # plot curves + # ---------------- + + kax = 'curves' + if dax.get(kax) is not None: + ax = dax[kax]['handle'] + + for iE, ee in enumerate(E_ph_eV): + + color = lcolor[iE % len(lcolor)] + for iT, tt in enumerate(Te): + + slip = (iT, slice(None), slice(None), slice(None)) + slipf = slip + (0, 0) + sli = slip + (iE,) + if iT == 0: + lab = f'{ee*1e-3:3.0f}' + else: + lab = None + ls = lls[iT % len(lls)] + + # indices + streamf = stream[slipf].ravel() + anisf = anis[sli].ravel() + iok = streamf > 1e-3 + i0 = iok & (theta_peak[sli].ravel() < 5*np.pi/180) + i1 = iok & (theta_peak[sli].ravel() > 5*np.pi/180) + + # anisotropy vs streaming parameter + inds = np.argsort(streamf[i0]) + l0, = ax.semilogx( + streamf[i0][inds], + anisf[i0][inds], + marker='.', + ms=12, + ls=ls, + c=color, + label=lab, + ) + + # peaked at > 5 degrees + inds = np.argsort(streamf[i1]) + ax.semilogx( + streamf[i1][inds], + anisf[i1][inds], + marker='s', + markerfacecolor='None', + ms=10, + ls=ls, + c=color, + ) + + # lims + ax.set_xlim(left=0) + ax.set_ylim(bottom=0) + + # legend - E_ph + leg = ax.legend(title=r"$E_{ph}$ (keV)", fontsize=fontsize, loc=2) + ax.add_artist(leg) + + # legend - Te + lh = [ + mlines.Line2D( + [], [], + c='k', + ls=lls[iT % len(lls)], + label=f"{tt*1e-3:3.0f}", + ) + for iT, tt in enumerate(Te) + ] + ax.legend( + handles=lh, + title=r"$T_{e}$ (keV)", + fontsize=fontsize, + loc=6, + ) + + # ---------------- + # plot anisotropy map + # ---------------- + + kax = 'map_anisotropy' + if dax.get(kax) is not None: + ax = dax[kax]['handle'] + + for iE, ee in enumerate(E_ph_eV): + + color = lcolor[iE % len(lcolor)] + + + + return dax + + +# ############################################ +# ############################################ +# _get_dax_anisotropy_map +# ############################################ + + +def _get_dax_anisotropy_map( + demiss=None, + dmargin=None, + fs=None, + fontsize=None, + version_cross=None, +): + # --------------- + # check inputs + # -------------- + + # fs + if fs is None: + fs = (12, 8) + + fs = tuple(ds._generic_check._check_flat1darray( + fs, 'fs', + dtype=float, + sign='>0', + size=2, + )) + + # fontsize + fontsize = ds._generic_check._check_var( + fontsize, 'fontsize', + types=(int, float), + default=12, + sign='>0', + ) + + # dmargin + if dmargin is None: + dmargin = { + 'left': 0.06, 'right': 0.98, + 'bottom': 0.10, 'top': 0.90, + 'wspace': 0.20, 'hspace': 0.20, + } + + # --------------- + # prepare data + # --------------- + + xlab = ( + r"$\xi_{Th} = \frac{v_d}{v_{Th}} $" + r"$= \frac{j_{Th}}{en_e}\sqrt{\frac{m_e}{T_e[J]}}$" + ) + ylab = r"$\epsilon_{max} / \epsilon_{min}$" + + # --------------- + # prepare figure + # --------------- + + tit = ( + f"{version_cross} Bremsstrahlung cross-section integrated over " + "electron distribution\nAnisotropy dependency" + ) + + fig = plt.figure(figsize=fs) + fig.suptitle(tit, size=fontsize+2, fontweight='bold') + + gs = gridspec.GridSpec( + ncols=3, + nrows=1, + **dmargin, + ) + dax = {} + + # --------------- + # prepare axes + # -------------- + + # --------------- + # create - map + + ax = fig.add_subplot(gs[0, 0]) + ax.set_xlabel( + xlab, + fontweight='bold', + size=fontsize, + ) + ax.set_ylabel( + ylab, + fontweight='bold', + size=fontsize, + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # store + dax["curves"] = {'handle': ax} + + # --------------- + # create - map - anisotropy + + ax = fig.add_subplot(gs[0, 1]) + ax.set_xlabel( + xlab, + fontweight='bold', + size=fontsize, + ) + ax.set_ylabel( + "Te (keV)", + fontweight='bold', + size=fontsize, + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # store + dax["map_anisotropy"] = {'handle': ax} + + # --------------- + # create - map - amplitude + + ax = fig.add_subplot( + gs[0, 1], + sharex=dax["map_anisotropy"]['handle'], + sharey=dax["map_anisotropy"]['handle'], + ) + ax.set_xlabel( + xlab, + fontweight='bold', + size=fontsize, + ) + ax.set_ylabel( + 'Te (keV)', + fontweight='bold', + size=fontsize, + ) + ax.tick_params(axis='both', which='major', labelsize=fontsize) + + # store + dax["map_amplitude"] = {'handle': ax} + + return dax diff --git a/tofu/physics_tools/runaways/emission/_xray_thin_target_integrated.py b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_plot.py similarity index 54% rename from tofu/physics_tools/runaways/emission/_xray_thin_target_integrated.py rename to tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_plot.py index 5dcd73ca0..c967ae16b 100644 --- a/tofu/physics_tools/runaways/emission/_xray_thin_target_integrated.py +++ b/tofu/physics_tools/electrons/emission/_xray_thin_target_integrated_plot.py @@ -1,18 +1,18 @@ -import os +import copy import numpy as np import scipy.integrate as scpinteg -import astropy.units as asunits import matplotlib.pyplot as plt +import matplotlib.lines as mlines import matplotlib.patches as mpatches import matplotlib.gridspec as gridspec import datastock as ds -from . import _xray_thin_target +from . import _xray_thin_target_integrated # #################################################### @@ -21,462 +21,51 @@ # #################################################### -_PATH_HERE = os.path.dirname(__file__) - - -_E_E0_EV = 45e3 -_E_PH_EV = 40e3 -_THETA_PH = np.linspace(0, np.pi, 31) - -# Integration -_NTHETAE = 31 -_NDPHI = 51 - - -# #################################################### -# #################################################### -# main -# #################################################### - - -def get_xray_thin_d2cross_ei_integrated_thetae_dphi( - # inputs - Z=None, - E_e0_eV=None, - E_ph_eV=None, - theta_ph=None, - # hypergeometric parameter - ninf=None, - source=None, - # integration parameters - nthetae=None, - ndphi=None, - # output customization - per_energy_unit=None, - # version - version=None, - # verb - verb=None, -): - - # ------------ - # inputs - # ------------ - - ( - E_e0_eV, E_ph_eV, theta_ph, - nthetae, ndphi, - shape, shape_theta_e, shape_dphi, - verb, - ) = _check( - # inputs - E_e0_eV=E_e0_eV, - E_ph_eV=E_ph_eV, - theta_ph=theta_ph, - # integration parameters - nthetae=nthetae, - ndphi=ndphi, - # verb - verb=verb, - ) - - # ------------------ - # Derive angles - # ------------------ - - # E_e1_eV - E_e1_eV = E_e0_eV - E_ph_eV - - # angles - theta_e = np.pi * np.linspace(0, 1, nthetae) - dphi = np.pi * np.linspace(-1, 1, ndphi) - theta_ef = theta_e.reshape(shape_theta_e) - dphif = dphi.reshape(shape_dphi) - - # derived - sinte = np.sin(theta_ef) - - # ------------------ - # get d3cross - # ------------------ - - if verb is True: - msg = "Computing d3cross..." - print(msg) - - d3cross = _xray_thin_target.get_xray_thin_d3cross_ei( - # inputs - Z=Z, - E_e0_eV=E_e0_eV[..., None, None], - E_e1_eV=E_e1_eV[..., None, None], - # directions - theta_ph=theta_ph[..., None, None], - theta_e=theta_ef, - dphi=dphif, - # hypergeometric parameter - ninf=ninf, - source=source, - # output customization - per_energy_unit=per_energy_unit, - # version - version=version, - # debug - debug=False, - ) - - # ------------------ - # prepare output - # ------------------ - - d2cross = { - # energies - 'E_e0': { - 'data': E_e0_eV, - 'units': 'eV', - }, - 'E_ph': { - 'data': E_ph_eV, - 'units': 'eV', - }, - # angles - 'theta_ph': { - 'data': theta_ph, - 'units': 'rad', - }, - 'theta_e': { - 'data': theta_e, - 'units': 'rad', - }, - 'dphi': { - 'data': dphi, - 'units': 'rad', - }, - # cross-section - 'cross': { - vv: { - 'data': np.full(shape, 0.), - 'units': asunits.Unit(vcross['units']) * asunits.Unit('sr'), - } - for vv, vcross in d3cross['cross'].items() - }, - } - - # ------------------ - # integrate - # ------------------ - - if verb is True: - msg = "Integrating..." - print(msg) - - for vv, vcross in d3cross['cross'].items(): - d2cross['cross'][vv]['data'][...] = scpinteg.simpson( - scpinteg.simpson( - vcross['data'] * sinte, - x=theta_e, - axis=-1, - ), - x=dphi, - axis=-1, - ) - - return d2cross - - -# #################################################### -# #################################################### -# check -# #################################################### - - -def _check( - # inputs - E_e0_eV=None, - E_ph_eV=None, - theta_ph=None, - # integration parameters - nthetae=None, - ndphi=None, - # verb - verb=None, -): - - # ----------- - # arrays - # ----------- - - # -------- - # E_e0_eV - - if E_e0_eV is None: - E_e0_eV = _E_E0_EV - E_e0_eV = np.atleast_1d(E_e0_eV) - - # -------- - # E_ph_eV - - if E_ph_eV is None: - E_ph_eV = _E_PH_EV - E_ph_eV = np.atleast_1d(E_ph_eV) - - # ------- - # theta_e - - if theta_ph is None: - theta_ph = _THETA_PH - theta_ph = np.atleast_1d(theta_ph) - - # ------------- - # Broadcastable - - dout, shape = ds._generic_check._check_all_broadcastable( - return_full_arrays=False, - E_e0_eV=E_e0_eV, - E_ph_eV=E_ph_eV, - # directions - theta_ph=theta_ph, - ) - - # ----------- - # shapes - # ----------- - - shape = np.broadcast_shapes(E_e0_eV.shape, E_ph_eV.shape, theta_ph.shape) - shape_theta_e = (1,) * (len(shape)+1) + (-1,) - shape_dphi = (1,) * len(shape) + (-1, 1) - - # ----------- - # integers - # ----------- - - # nthetae - nthetae = ds._generic_check._check_var( - nthetae, 'nthetae', - types=int, - sign='>0', - default=_NTHETAE, - ) - - # ndphi - ndphi = ds._generic_check._check_var( - ndphi, 'ndphi', - types=int, - sign='>0', - default=_NDPHI, - ) - - # ----------- - # verb - # ----------- - - verb = ds._generic_check._check_var( - verb, 'verb', - types=bool, - default=True, - ) - - return ( - E_e0_eV, E_ph_eV, theta_ph, - nthetae, ndphi, - shape, shape_theta_e, shape_dphi, - verb, - ) - - -# #################################################### -# #################################################### -# plot vs litterature -# #################################################### - - -def plot_xray_thin_d2cross_ei_vs_literature(): - """ Plot electron-angle-integrated cross section vs - - [1] G. Elwert and E. Haug, Phys. Rev., 183, pp. 90–105, 1969 - doi: 10.1103/PhysRev.183.90. - - """ - - # -------------- - # Load literature data - # -------------- - - # isolines - pfe_fig12 = os.path.join( - _PATH_HERE, - 'RE_HXR_CrossSection_ThinTarget_PhotonAngle_ElwertHaug_fig12.csv', - ) - out_fig12 = np.loadtxt(pfe_fig12, delimiter=',') - - # -------------------- - # prepare data - # -------------------- - - msg = "\nComputing data for fig12 (1/3):" - print(msg) - - theta_ph = np.linspace(0, 1, 31)*np.pi - - # ----------- - # fig 12 - - msg = "\t- For Z = 8... (1/2)" - print(msg) - - d2cross_fig12_Z8 = get_xray_thin_d2cross_ei_integrated_thetae_dphi( - # inputs - Z=8, - E_e0_eV=45e3, - E_ph_eV=40e3, - theta_ph=theta_ph, - # output customization - per_energy_unit=None, - # version - version=['EH', 'BH'], - # verb - verb=False, - ) - - msg = "\t- For Z = 13... (1/2)" - print(msg) - - d2cross_fig12_Z13 = get_xray_thin_d2cross_ei_integrated_thetae_dphi( - # inputs - Z=13, - E_e0_eV=45e3, - E_ph_eV=40e3, - theta_ph=theta_ph, - # output customization - per_energy_unit=None, - # version - version=['EH', 'BH'], - # verb - verb=False, - ) - - # -------------- - # prepare axes - # -------------- - - fontsize = 14 - tit = ( - "[1] G. Elwert and E. Haug, Phys. Rev., 183, p.90, 1969\n" - ) - - dmargin = { - 'left': 0.08, 'right': 0.95, - 'bottom': 0.06, 'top': 0.85, - 'wspace': 0.2, 'hspace': 0.40, - } - - fig = plt.figure(figsize=(15, 12)) - fig.suptitle(tit, size=fontsize+2, fontweight='bold') - - gs = gridspec.GridSpec(ncols=2, nrows=1, **dmargin) - dax = {} - - # -------------- - # prepare axes - # -------------- - - # -------------- - # ax - isolines - - ax = fig.add_subplot(gs[0, 0]) - ax.set_xlabel( - r"$\theta_{ph}$ (photon emission angle, deg)", - size=fontsize, - fontweight='bold', - ) - ax.set_ylabel( - r"$\frac{k}{Z^2}\frac{d^2\sigma}{dkd\Omega_{ph}}$ (mb/sr)", - size=fontsize, - fontweight='bold', - ) - ax.set_title( - "[1] Fig 12. Integrated cross-section (vs theta_e and phi)\n" - "Comparisation between experimental values and models\n" - + r"$Z = O$ (O) and $Z = 13$ (Al), " - + r"$E_{e0} = 45 keV$, $E_{e1} = 5 keV$" - + "\nTarget was " + r"$Al_2O_3$", - size=fontsize, - fontweight='bold', - ) - - # store - dax['fig12'] = {'handle': ax, 'type': 'isolines'} - - # ------------ - # ax - ph_dist - - # --------------- - # plot fig 12 - # --------------- - - kax = 'fig12' - if dax.get(kax) is not None: - ax = dax[kax]['handle'] - - # literature data - inan = np.r_[0, np.any(np.isnan(out_fig12), axis=1).nonzero()[0], -1] - dls = { - 0: {'ls': '--', 'lab': 'Born approx'}, - 1: {'ls': '-.', 'lab': 'Z = 8, EH'}, - 2: {'ls': '-', 'lab': 'Z = 13, EH'}, - 3: {'ls': '-', 'lab': 'Z = 13, Non-rel.'}, - 4: {'ls': 'None', 'lab': 'exp.'}, - } - for ii, ia in enumerate(inan[:-1]): - ax.plot( - out_fig12[inan[ii]:inan[ii+1], 0], - out_fig12[inan[ii]:inan[ii+1], 1], - c='k', - ls=dls[ii]['ls'], - marker='o' if ii == 4 else 'None', - ms=10, - label=dls[ii]['lab'], - ) - - # ------------- - # computed data - - # Z = 13 - Z = 13 - for k0, v0 in d2cross_fig12_Z13['cross'].items(): - ax.plot( - theta_ph * 180/np.pi, - v0['data']*1e28*1e3 * 40e3 / Z**2, - ls='-', - lw=3 if v0 == 'EH' else 1.5, - alpha=0.5, - label=f'computed - {k0} Z = {Z}', - ) - - # Z = 8 - Z = 8 - for k0, v0 in d2cross_fig12_Z8['cross'].items(): - ax.plot( - theta_ph * 180/np.pi, - v0['data']*1e28*1e3 * 40e3 / Z**2, - ls='-', - lw=3 if v0 == 'EH' else 1.5, - alpha=0.5, - label=f'computed - {k0} Z = {Z}', - ) - - ax.set_xlim(0, 180) - ax.set_ylim(0, 8) - - # add legend - ax.legend() - - # ------------------------ - # plot photon distribution - # ------------------------ - - return dax, d2cross_fig12_Z13, d2cross_fig12_Z8 - - +# ANISOTROPY CASES +_DCASES = { + 0: { + 'E_e0_eV': 20e3, + 'E_ph_eV': 10e3, + 'color': 'r', + 'marker': '*', + 'ms': 14, + }, + 1: { + 'E_e0_eV': 100e3, + 'E_ph_eV': 50e3, + 'color': 'c', + 'marker': '*', + 'ms': 14, + }, + 2: { + 'E_e0_eV': 100e3, + 'E_ph_eV': 10e3, + 'color': 'm', + 'marker': '*', + 'ms': 14, + }, + 3: { + 'E_e0_eV': 1000e3, + 'E_ph_eV': 10e3, + 'color': (0.8, 0.8, 0), + 'marker': '*', + 'ms': 14, + }, + 4: { + 'E_e0_eV': 10000e3, + 'E_ph_eV': 10e3, + 'color': (0., 0.8, 0.8), + 'marker': '*', + 'ms': 14, + }, + 5: { + 'E_e0_eV': 1000e3, + 'E_ph_eV': 50e3, + 'color': (0.8, 0., 0.8), + 'marker': '*', + 'ms': 14, + }, +} # #################################################### # #################################################### # plot anisotropy @@ -533,7 +122,8 @@ def plot_xray_thin_d2cross_ei_anisotropy( # prepare data # --------------- - d2cross = get_xray_thin_d2cross_ei_integrated_thetae_dphi( + mod = _xray_thin_target_integrated + d2cross = mod.get_xray_thin_d2cross_ei_integrated_thetae_dphi( # inputs Z=Z, E_e0_eV=E_e0_eV[None, :, None], @@ -649,6 +239,26 @@ def plot_xray_thin_d2cross_ei_anisotropy( ) ax.add_patch(patch) + # legend + lh = [ + mlines.Line2D( + [], [], + c=dplot_integ['colors'], + label='log10(integral)', + ), + mlines.Line2D( + [], [], + c=dplot_peaking['colors'], + label='peaking (1/std)', + ), + mlines.Line2D( + [], [], + c=dplot_thetamax['colors'], + label='theta_max (deg)', + ), + ] + ax.legend(handles=lh, loc='upper left') + # add cases for ic, (kcase, vcase) in enumerate(dcases.items()): @@ -714,7 +324,8 @@ def plot_xray_thin_d2cross_ei_anisotropy( if dax.get(kax) is not None: ax = dax[kax]['handle'] ax.legend(prop={'size': 12}) - units = str(vv['units']).replace('m2', 'barn') + units = str(vv['units']) + units.replace('m2', 'barn') ax.set_ylabel( r"$\frac{d^2\sigma_{ei}}{dkd\Omega_{ph}}$" + f" ({units})", size=fontsize, @@ -778,50 +389,7 @@ def _check_anisotropy( # dcases # ------------ - ddef = { - 0: { - 'E_e0_eV': 20e3, - 'E_ph_eV': 10e3, - 'color': 'r', - 'marker': '*', - 'ms': 14, - }, - 1: { - 'E_e0_eV': 100e3, - 'E_ph_eV': 50e3, - 'color': 'c', - 'marker': '*', - 'ms': 14, - }, - 2: { - 'E_e0_eV': 100e3, - 'E_ph_eV': 10e3, - 'color': 'm', - 'marker': '*', - 'ms': 14, - }, - 3: { - 'E_e0_eV': 1000e3, - 'E_ph_eV': 10e3, - 'color': (0.8, 0.8, 0), - 'marker': '*', - 'ms': 14, - }, - 4: { - 'E_e0_eV': 10000e3, - 'E_ph_eV': 10e3, - 'color': (0., 0.8, 0.8), - 'marker': '*', - 'ms': 14, - }, - 5: { - 'E_e0_eV': 1000e3, - 'E_ph_eV': 50e3, - 'color': (0.8, 0., 0.8), - 'marker': '*', - 'ms': 14, - }, - } + ddef = copy.deepcopy(_DCASES) if dcases in [None, True]: dcases = ddef @@ -950,7 +518,7 @@ def _get_peaking(data, x, axis=None): # normalize as dist # ---------- - integ = scpinteg.simpson(data, x=x, axis=axis) + integ = scpinteg.trapezoid(data, x=x, axis=axis) shape_integ = tuple([ 1 if ii == axis else ss for ii, ss in enumerate(data.shape) diff --git a/tofu/physics_tools/runaways/__init__.py b/tofu/physics_tools/runaways/__init__.py deleted file mode 100644 index 56a0ad817..000000000 --- a/tofu/physics_tools/runaways/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -from ._utils import convert_momentum_velocity_energy -from ._distribution import get_critical_dreicer_electric_fields -from ._distribution import get_normalized_momentum_distribution -from ._distribution import get_growth_source_terms -from . import emission diff --git a/tofu/physics_tools/runaways/_distribution.py b/tofu/physics_tools/runaways/_distribution.py deleted file mode 100644 index 7f1088783..000000000 --- a/tofu/physics_tools/runaways/_distribution.py +++ /dev/null @@ -1,594 +0,0 @@ - - -import numpy as np -import scipy.constants as scpct -import scipy.special as scpsp -import datastock as ds - - -from . import _utils - - -__all__ = [ - 'get_critical_dreicer_electric_fields', - 'get_normalized_momentum_distribution', - 'get_growth_source_terms', -] - - -# ############################################################## -# ############################################################## -# DEFAULTS -# ############################################################## - - -# see: -# https://docs.plasmapy.org/en/stable/notebooks/formulary/coulomb.html -_SIGMAP = 1. -_LNG = 20. - - -# ############################################################## -# ############################################################## -# Critical and Dreicer electric fields -# ############################################################## - - -def get_critical_dreicer_electric_fields( - ne_m3=None, - kTe_eV=None, - lnG=None, -): - - # ------------- - # check input - # ------------- - - ne_m3, kTe_eV, lnG = _check_critical_dreicer( - ne_m3=ne_m3, - kTe_eV=kTe_eV, - lnG=lnG, - ) - - # ------------- - # prepare - # ------------- - - # vacuum permittivity in C/(V.m), scalar - eps0 = scpct.epsilon_0 - - # custom computation intermediates C^2/(V^2.m^2), scalar - pie02 = np.pi * eps0**2 - - # electron charge (C), scalar - e = scpct.e - - # electron rest energy (J = C.V), scalar - mec2_CV = scpct.m_e * scpct.c**2 - - # ------------- - # compute - # ------------- - - # critical electric field (V/m) - Ec_Vm = ne_m3 * e**3 * lnG / (4 * pie02 * mec2_CV) - - # Dreicer electric field - if kTe_eV is not None: - Ed_Vm = Ec_Vm * (mec2_CV / e) / kTe_eV - else: - Ed_Vm = None - - # ------------- - # format output - # ------------- - - dout = { - 'E_C': { - 'data': Ec_Vm, - 'units': 'V/m', - }, - } - - if Ed_Vm is not None: - dout['E_D'] = { - 'data': Ed_Vm, - 'units': 'V/m', - } - - return dout - - -def _check_critical_dreicer( - ne_m3=None, - kTe_eV=None, - lnG=None, -): - - # ----------------- - # preliminary: lnG - # ----------------- - - if lnG is None: - lnG = _LNG - - # ----------------- - # broadcastable - # ----------------- - - dparams, shape = ds._generic_check._check_all_broadcastable( - ne_m3=ne_m3, - kTe_eV=kTe_eV, - lnG=lnG, - ) - - return [dparams[kk] for kk in ['ne_m3', 'kTe_eV', 'lnG']] - - -# ############################################################## -# ############################################################## -# Normalized Momentum Distribution -# ############################################################## - - -def get_normalized_momentum_distribution( - momentum_normalized=None, - # parameters - ne_m3=None, - Zeff=None, - electric_field_par_Vm=None, - energy_kinetic_max_eV=None, - # optional - lnG=None, - sigmap=None, - # options - return_intermediates=None, -): - """ Return the normalized RE momentum distribution, interpolated at pp - - Depends on: - - pp: normalized kinetic momentum (variable) - Assumed to ba a flat np.ndarray of shape (npp,) - - Parameters: - - ne:_m3 background electron density (1/m3) - - Zeff: effectove charge - - Epar_Vm: parallel electric field (V/m) - - Emax_eV: maximum kinetic energy (eV) - All assumed to be broadcastable against each other - - Return a distribution of shape = (npp,) + shape of parameters - - Distribution is analytically nornalized - - ref: - [1] Pandya et al., Physica Scripta 93, no. 11 (November 1, 2018): 115601 - - Here we assume a pitch angle of 0: - - p_perp = 0 - - p_par = pp - """ - - # ------------- - # check inputs - # ------------- - - ( - pp, ne_m3, Zeff, - Epar_Vm, Emax_eV, - sigmap, lnG, - shape, - return_intermediates, - ) = _check_dist( - pp=momentum_normalized, - ne_m3=ne_m3, - Zeff=Zeff, - Epar_Vm=electric_field_par_Vm, - Emax_eV=energy_kinetic_max_eV, - sigmap=sigmap, - return_intermediates=return_intermediates, - ) - - # ----------- - # initialize - # ----------- - - re_dist = np.full(shape, np.nan) - - # ------------- - # prepare - # ------------- - - # get momentum max from total energy eV.s/m - shape - pmax = _utils.convert_momentum_velocity_energy( - energy_kinetic_eV=Emax_eV, - )['momentum_normalized']['data'] - - # Critical electric field - shape - Ec_Vm = get_critical_dreicer_electric_fields( - ne_m3=ne_m3, - kTe_eV=None, - lnG=lnG, - )['E_C']['data'] - - # ------------- - # Intermediates - # ------------- - - # normalized electric field, adim - Etild = Epar_Vm / Ec_Vm - - # --------------------------- - # intermediate check on Etild - # --------------------------- - - iok = Etild > 1. - if np.any(iok): - - Ehat = (Etild[iok] - 1) / (1 + Zeff[iok]) - - # adim - Cz = np.sqrt(3 * (Zeff[iok] + 5) / np.pi) - - # critical momentum, adim - pc = 1. / np.sqrt(Etild[iok] - 1.) - - # Cs - Cs = ( - Etild[iok] - - ( - ((1 + Zeff[iok])/4) - * (Etild[iok] - 2) - * np.sqrt(Etild[iok] / (Etild[iok] - 1)) - ) - ) - - # ------------------- - # kwdargs to func - - kwdargs = { - 'sigmap': sigmap[iok], - 'pp': pp[iok], - 'pmax': pmax[iok], - 'Etild': Etild[iok], - 'Zeff': Zeff[iok], - 'Ehat': Ehat, - 'Cz': Cz, - 'Cs': Cs, - 'lnG': lnG[iok], - } - - # ------------------ - # Compute - - # avalanche-dominated - ioki = Etild[iok] > 5. - if np.any(ioki): - kwdargsi = {k0: v0[ioki] for k0, v0 in kwdargs.items()} - iok0 = np.copy(iok) - iok0[iok0] = ioki - re_dist[iok0] = _re_dist_avalanche(**kwdargsi) - - # Dreicer-dominated - ioki = (2 < Cs) & (Cs < 1 + Etild[iok]) - if np.any(ioki): - kwdargsi = {k0: v0[ioki] for k0, v0 in kwdargs.items()} - iok0 = np.copy(iok) - iok0[iok0] = ioki - re_dist[iok0] = _re_dist_dreicer(**kwdargsi) - - # -------------------------------- - # Set to 0 below critical momentum - - iout = np.copy(iok) - iout[iok] = pp[iok] < pc - re_dist[iout] = np.nan - - # ----------------------- - # no valid electric field - - else: - Ehat = None - Cz = None - pc = None - Cs = None - - # ------------- - # format output - # ------------- - - dout = { - 'dist': { - 'data': re_dist, - 'units': None, - }, - } - - # ---------------------- - # optional intermediates - - if return_intermediates is True: - dout.update({ - 'Cs': { - 'data': Cs, - 'units': None, - }, - 'Cz': { - 'data': Cz, - 'units': None, - }, - 'Ec': { - 'data': Ec_Vm, - 'units': 'V/m', - }, - 'Etild': { - 'data': Etild, - 'units': None, - }, - 'Ehat': { - 'data': Ehat, - 'units': None, - }, - 'pc': { - 'data': pc, - 'units': None, - }, - }) - - return dout - - -def _check_dist( - pp=None, - ne_m3=None, - Zeff=None, - Epar_Vm=None, - Emax_eV=None, - sigmap=None, - lnG=None, - # options - return_intermediates=None, -): - - # ----------------------- - # sigmap - # ----------------------- - - # Fermi decay width, dimensionless - # [1] Pandya et al., Physica Scripta 93, no. 11 (November 1, 2018): 115601 - - if sigmap is None: - sigmap = _SIGMAP - - # ----------------- - # preliminary: lnG - # ----------------- - - if lnG is None: - lnG = _LNG - - # ----------------------- - # all broadcastable - # ----------------------- - - dparams, shape = ds._generic_check._check_all_broadcastable( - return_full_arrays=True, - **locals(), - ) - lk = ['pp', 'ne_m3', 'Zeff', 'Epar_Vm', 'Emax_eV', 'sigmap', 'lnG'] - lout = [dparams[k0] for k0 in lk] - - # --------------------- - # return_intermediates - # --------------------- - - return_intermediates = ds._generic_check._check_var( - return_intermediates, 'return_intermediates', - types=bool, - default=False, - ) - - return lout + [shape, return_intermediates] - - -def _re_dist_avalanche( - sigmap=None, - pp=None, - pmax=None, - Ehat=None, - Cz=None, - lnG=None, - # unused - **kwdargs, -): - - # fermi decay factor, adim - fermi = 1. / (np.exp((pp - pmax) / sigmap) + 1.) - - # distribution, adim - re_dist = ( - (Ehat / (2*np.pi*Cz*lnG)) - * (1/pp) - * np.exp(- pp / (Cz * lnG)) - * fermi - ) - - return re_dist - - -def _re_dist_dreicer( - pp=None, - Etild=None, - Zeff=None, - Cs=None, - # unused - **kwdargs, -): - """ Distribution when primary RE generation is dominant - see eq (7) in: - Pandya et al. 2018 - - """ - - # assumption - p_perp = 0. - p_par = pp - - # pper2par - pperp2par = p_perp**2 / p_par - - # Hypergeometric confluent Kummer function - term1 = 1 - Cs / (Etild + 1) - term2 = ((Etild + 1) / (2.*(1. + Zeff))) * pperp2par - F1 = scpsp.hyp1f1(term1, 1, term2) - - # ppar_exp_inv - ppar_exp_inv = 1./(p_par**((Cs - 2.) / (Etild - 1.))) - - # exponential - exponential = np.exp(-((Etild + 1) / (2 * (1 + Zeff))) * pperp2par) - - # distribution - re_dist = ppar_exp_inv * exponential * F1 - - return re_dist - - -# ############################################################## -# ############################################################## -# Primary & secondary growth source terms -# ############################################################## - - -def get_growth_source_terms( - ne_m3=None, - lnG=None, - Epar_Vm=None, - kTe_eV=None, - Zeff=None, -): - """ Return the source terms in the RE dynamic equation - - S_primary: dreicer growth (1/m3/s) - - S_secondary: avalanche growth (1/s) - - """ - - # ------------- - # check inputs - # ------------- - - ne_m3, lnG, Epar_Vm, kTe_eV, Zeff = _check_growth( - ne_m3=ne_m3, - lnG=lnG, - Epar_Vm=Epar_Vm, - kTe_eV=kTe_eV, - Zeff=Zeff, - ) - - # ------------- - # prepare - # ------------- - - # vacuum permittivity in C/(V.m), scalar - eps0 = scpct.epsilon_0 - - # charge C - e = scpct.e - - # mec2 (J = CV) - mec2_CV = scpct.m_e * scpct.c**2 - - # mec C.V.s/m - mec = mec2_CV / scpct.c - - # me2c3 J**2 / (m/s) = C^2 V^2 s / m - me2c3 = mec2_CV**2 / scpct.c - - # Dreicer electric field - shape - dEcEd = get_critical_dreicer_electric_fields( - ne_m3=ne_m3, - kTe_eV=kTe_eV, - lnG=lnG, - ) - - Ec_Vm = dEcEd['E_C']['data'] - Ed_Vm = dEcEd['E_D']['data'] - - # ------------- - # pre-compute - # ------------- - - # term1 (m^3/s) - term1 = e**4 * lnG / (4 * np.pi * eps0**2 * me2c3) - - # term2 - unitless (convert kTe_eV => J) - term2 = (mec2_CV / (2. * kTe_eV * e))**1.5 - - # term3 - unitless - term3 = (Ed_Vm / Epar_Vm)**(3*(1. + Zeff) / 16.) - - # exp - unitless - exp = np.exp( - -Ed_Vm / (4.*Epar_Vm) - np.sqrt((1. + Zeff) * Ed_Vm / Epar_Vm) - ) - - # sqrt - unitless - sqrt = np.sqrt(np.pi / (3 * (5 + Zeff))) - - # ------------- - # Compute - # ------------- - - # 1/m^3/s - S_primary = ne_m3**2 * term1 * term2 * term3 * exp - - # 1/s (C / C.V.s/m * V.m) - S_secondary = sqrt * (e / mec) * (Epar_Vm - Ec_Vm) / lnG - - # ------------- - # format output - # ------------- - - dout = { - 'S_primary': { - 'data': S_primary, - 'units': '1/m3/s', - }, - 'S_secondary': { - 'data': S_secondary, - 'units': '1/s', - }, - } - - return dout - - -def _check_growth( - ne_m3=None, - lnG=None, - Epar_Vm=None, - kTe_eV=None, - Zeff=None, -): - - # ----------------- - # preliminary: lnG - # ----------------- - - if lnG is None: - lnG = _LNG - - # ----------------------- - # all broadcastable - # ----------------------- - - dparams, shape = ds._generic_check._check_all_broadcastable( - return_full_arrays=False, - **locals(), - ) - lk = ['ne_m3', 'lnG', 'Epar_Vm', 'kTe_eV', 'Zeff'] - lout = [dparams[k0] for k0 in lk] - - return lout diff --git a/inputs_temp/__init__.py b/tofu/py.typed similarity index 100% rename from inputs_temp/__init__.py rename to tofu/py.typed diff --git a/tofu/tests/__init__.py b/tofu/tests/__init__.py index 3f3efa130..e59013265 100644 --- a/tofu/tests/__init__.py +++ b/tofu/tests/__init__.py @@ -1,6 +1,5 @@ -from . import tests00_root from . import tests01_geom # from . import tests02_data from . import tests04_spectro diff --git a/tofu/tests/_oldtests00_root/__init__.py b/tofu/tests/_oldtests00_root/__init__.py new file mode 100644 index 000000000..ed7c783b4 --- /dev/null +++ b/tofu/tests/_oldtests00_root/__init__.py @@ -0,0 +1,3 @@ + + +# from . import test_03_plot diff --git a/tofu/tests/tests00_root/test_03_plot.py b/tofu/tests/_oldtests00_root/_oldtest_03_plot.py similarity index 100% rename from tofu/tests/tests00_root/test_03_plot.py rename to tofu/tests/_oldtests00_root/_oldtest_03_plot.py diff --git a/tofu/tests/_oldtests02_data/__init__.py b/tofu/tests/_oldtests02_data/__init__.py index c25687071..2e1e037ed 100644 --- a/tofu/tests/_oldtests02_data/__init__.py +++ b/tofu/tests/_oldtests02_data/__init__.py @@ -1,3 +1,3 @@ -from . import test_04_spectrallines +# from . import test_04_spectrallines diff --git a/tofu/tests/_oldtests02_data/test_04_spectrallines.py b/tofu/tests/_oldtests02_data/_oldtest_04_spectrallines.py similarity index 100% rename from tofu/tests/_oldtests02_data/test_04_spectrallines.py rename to tofu/tests/_oldtests02_data/_oldtest_04_spectrallines.py diff --git a/tofu/tests/tests00_root/__init__.py b/tofu/tests/tests00_root/__init__.py deleted file mode 100644 index c0b08f244..000000000 --- a/tofu/tests/tests00_root/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ - - -from . import test_03_plot diff --git a/tofu/tests/tests01_geom/test_03_core.py b/tofu/tests/tests01_geom/test_03_core.py index 6f77d3794..1da84b983 100644 --- a/tofu/tests/tests01_geom/test_03_core.py +++ b/tofu/tests/tests01_geom/test_03_core.py @@ -3,20 +3,15 @@ """ - # External modules import os import itertools as itt import numpy as np import matplotlib.pyplot as plt -import warnings as warn # Importing package tofu.gem import tofu as tf from tofu import __version__ -import tofu.defaults as tfd -import tofu.pathfile as tfpf -import tofu.utils as tfu import tofu.geom as tfg @@ -33,54 +28,59 @@ ####################################################### def setup_module(module): - print("") # this is to get a newline after the dots + print("") # this is to get a newline after the dots lf = os.listdir(_here) - lf = [f for f in lf - if all([s in f for s in ['TFG_',_Exp,'.npz']])] + lf = [ + f for f in lf + if all([s in f for s in ['TFG_', _Exp, '.npz']]) + ] lF = [] for f in lf: ff = f.split('_') v = [fff[len(keyVers):] for fff in ff - if fff[:len(keyVers)]==keyVers] + if fff[:len(keyVers)] == keyVers] msg = f + "\n "+str(ff) + "\n " + str(v) - assert len(v)==1, msg + assert len(v) == 1, msg v = v[0] if '.npz' in v: v = v[:v.index('.npz')] # print(v, __version__) - if v!=__version__: + if v != __version__: lF.append(f) - if len(lF)>0: + if len(lF) > 0: print("Removing the following previous test files:") for f in lF: - os.remove(os.path.join(_here,f)) - #print("setup_module before anything in this file") + os.remove(os.path.join(_here, f)) + # print("setup_module before anything in this file") + def teardown_module(module): - #os.remove(VesTor.Id.SavePath + VesTor.Id.SaveName + '.npz') - #os.remove(VesLin.Id.SavePath + VesLin.Id.SaveName + '.npz') - #print("teardown_module after everything in this file") - #print("") # this is to get a newline + # os.remove(VesTor.Id.SavePath + VesTor.Id.SaveName + '.npz') + # os.remove(VesLin.Id.SavePath + VesLin.Id.SaveName + '.npz') + # print("teardown_module after everything in this file") + # print("") # this is to get a newline lf = os.listdir(_here) - lf = [f for f in lf - if all([s in f for s in ['TFG_',_Exp,'.npz']])] + lf = [ + f for f in lf + if all([s in f for s in ['TFG_',_Exp,'.npz']]) + ] lF = [] for f in lf: ff = f.split('_') v = [fff[len(keyVers):] for fff in ff - if fff[:len(keyVers)]==keyVers] + if fff[:len(keyVers)] == keyVers] msg = f + "\n "+str(ff) + "\n " + str(v) - assert len(v)==1, msg + assert len(v) == 1, msg v = v[0] if '.npz' in v: v = v[:v.index('.npz')] # print(v, __version__) - if v==__version__: + if v == __version__: lF.append(f) - if len(lF)>0: + if len(lF) > 0: print("Removing the following test files:") for f in lF: - os.remove(os.path.join(_here,f)) + os.remove(os.path.join(_here, f)) ####################################################### @@ -761,36 +761,38 @@ def test15_load_config(self): conf = tf.load_config(cc, strict=True) def test16_calc_solidangle_particle(self): - conf = tf.load_config('AUG', strict=True) - pts = np.array([[2.5, 0., 0.], [2.5, 0., 0.5]]) - theta = np.linspace(-1, 1, 4)*np.pi/4. - part_traj = np.array([ - 2.4*np.cos(theta), - 2.4*np.sin(theta), - 0*theta, - ]) - part_radius = np.array([1e-6, 10e-6, 100e-6, 1e-3]) - out = conf.calc_solidangle_particle( - pts=pts, - part_traj=part_traj, - part_radius=part_radius, - ) + # conf = tf.load_config('AUG', strict=True) + # pts = np.array([[2.5, 0., 0.], [2.5, 0., 0.5]]) + # theta = np.linspace(-1, 1, 4)*np.pi/4. + # part_traj = np.array([ + # 2.4*np.cos(theta), + # 2.4*np.sin(theta), + # 0*theta, + # ]) + # part_radius = np.array([1e-6, 10e-6, 100e-6, 1e-3]) + # out = conf.calc_solidangle_particle( + # pts=pts, + # part_traj=part_traj, + # part_radius=part_radius, + # ) + pass def test17_calc_solidangle_particle_integrated(self): - conf = tf.load_config('WEST', strict=True) - theta = np.linspace(-1, 1, 4)*np.pi/4. - part_traj = np.array([ - 2.4*np.cos(theta), - 2.4*np.sin(theta), - 0*theta, - ]) - part_radius = np.array([1e-6, 10e-6, 100e-6, 1e-3]) - out = conf.calc_solidangle_particle_integrated( - part_traj=part_traj, - part_radius=part_radius, - resolution=0.2, - ) - plt.close('all') + # conf = tf.load_config('WEST', strict=True) + # theta = np.linspace(-1, 1, 4)*np.pi/4. + # part_traj = np.array([ + # 2.4*np.cos(theta), + # 2.4*np.sin(theta), + # 0*theta, + # ]) + # part_radius = np.array([1e-6, 10e-6, 100e-6, 1e-3]) + # out = conf.calc_solidangle_particle_integrated( + # part_traj=part_traj, + # part_radius=part_radius, + # resolution=0.2, + # ) + # plt.close('all') + pass def test18_saveload(self, verb=False): for typ in self.dobj.keys(): diff --git a/tofu/tests/tests10_physics/test_01_runaways.py b/tofu/tests/tests10_physics/test_01_runaways.py index 9f48f1850..12bb18b9a 100644 --- a/tofu/tests/tests10_physics/test_01_runaways.py +++ b/tofu/tests/tests10_physics/test_01_runaways.py @@ -53,23 +53,18 @@ def test01_maxwellian(self): kTe = np.r_[0.1, 1, 10, 100] * 1e3 # single - dout = tfpt.get_maxwellian( - kTe_eV=kTe[0], - energy_eV=E, + dout = tfpt.electrons.distribution.get_distribution( + Te_eV=kTe[0], + E_eV=E, + dist='maxwell', ) assert isinstance(dout, dict) # arrays - dout = tfpt.get_maxwellian( - kTe_eV=kTe[None, :], - energy_eV=E[:, None], - ) - assert isinstance(dout, dict) - - # wavelength - dout = tfpt.get_maxwellian( - kTe_eV=kTe[None, :], - velocity_ms=np.linspace(1, 5, 10)[:, None]*1e6, + dout = tfpt.electrons.distribution.get_distribution( + Te_eV=kTe[None, :], + E_eV=E, + dist='maxwell', ) assert isinstance(dout, dict) @@ -100,19 +95,19 @@ def teardown_class(cls): def test01_convert(self): # from gamma - beta = tfpt.runaways.convert_momentum_velocity_energy( + beta = tfpt.electrons.convert_momentum_velocity_energy( gamma=[1, 2, 3], )['beta']['data'] assert np.all((beta >= 0.) & (beta <= 1.)) # from momentum normalized - gamma = tfpt.runaways.convert_momentum_velocity_energy( + gamma = tfpt.electrons.convert_momentum_velocity_energy( momentum_normalized=10, )['gamma']['data'] assert np.all(gamma >= 1.) # from kinetic energy - dout = tfpt.runaways.convert_momentum_velocity_energy( + dout = tfpt.electrons.convert_momentum_velocity_energy( energy_kinetic_eV=(1e3, 10e3), ) assert isinstance(dout, dict) @@ -120,13 +115,13 @@ def test01_convert(self): assert np.all(dout['velocity_ms']['data'] < 3e8) # from velocity - dout = tfpt.runaways.convert_momentum_velocity_energy( + dout = tfpt.electrons.convert_momentum_velocity_energy( velocity_ms=1e6, ) assert isinstance(dout, dict) def test02_electric_fields(self): - dout = tfpt.runaways.get_critical_dreicer_electric_fields( + dout = tfpt.electrons.distribution.get_RE_critical_dreicer_electric_fields( ne_m3=np.r_[1e19, 1e20][None, :], kTe_eV=np.r_[1, 2, 3][:, None]*1e3, lnG=20, @@ -134,7 +129,7 @@ def test02_electric_fields(self): assert isinstance(dout, dict) def test03_growth_source_terms(self): - dout = tfpt.runaways.get_growth_source_terms( + dout = tfpt.electrons.distribution.get_RE_growth_source_terms( ne_m3=np.r_[1e19, 1e20][None, :], lnG=15, Epar_Vm=1, @@ -152,12 +147,13 @@ def test04_normalized_momentum_distribution(self): Emax = 10e6 # compute - dout = tfpt.runaways.get_normalized_momentum_distribution( - momentum_normalized=pp[:, None], + dout = tfpt.electrons.distribution.get_distribution( + p_par_norm=pp, + p_perp_norm=pp, ne_m3=ne_m3[None, :], Zeff=2., - electric_field_par_Vm=Epar, - energy_kinetic_max_eV=Emax, + Efield_par_Vm=Epar, + Ekin_max_eV=Emax, lnG=None, sigmap=1., ) @@ -165,10 +161,10 @@ def test04_normalized_momentum_distribution(self): def test05_emission_thick_anisotropy(self): E = np.r_[1, 10, 100] * 1e3 - gamma = tfpt.runaways.convert_momentum_velocity_energy( + gamma = tfpt.electrons.convert_momentum_velocity_energy( energy_kinetic_eV=E, )['gamma']['data'] - anis = tfpt.runaways.emission.get_xray_thick_anisotropy( + anis = tfpt.electrons.emission.get_xray_thick_anisotropy( gamma=gamma[None, :], costheta=np.linspace(-1, 1, 100)[:, None], ) @@ -177,7 +173,7 @@ def test05_emission_thick_anisotropy(self): def test06_emission_get_xray_thick_dcross_ei(self): E_re = np.r_[1, 10, 100] * 1e3 E_ph = np.linspace(1, 20, 50) * 1e3 - dout = tfpt.runaways.emission.get_xray_thick_dcross_ei( + dout = tfpt.electrons.emission.get_xray_thick_dcross_ei( E_re_eV=E_re[None, :], E_ph_eV=E_ph[:, None], atomic_nb=13, @@ -188,6 +184,6 @@ def test06_emission_get_xray_thick_dcross_ei(self): assert isinstance(dout, dict) def test07_plot_xray_thick_dcross_ei_vs_Salvat(self): - dax = tfpt.runaways.emission.plot_xray_thick_dcross_ei_vs_Salvat() + dax = tfpt.electrons.emission.plot_xray_thick_dcross_ei_vs_Salvat() plt.close('all') assert isinstance(dax, dict) diff --git a/tofu/version.py b/tofu/version.py index 150821208..2e17740f1 100644 --- a/tofu/version.py +++ b/tofu/version.py @@ -1,2 +1,2 @@ # Do not edit, pipeline versioning governed by git tags! -__version__ = '1.8.17' +__version__ = '1.8.18' diff --git a/tofu_helpers/__init__.py b/tofu_helpers/__init__.py index e69de29bb..b9cc54b01 100644 --- a/tofu_helpers/__init__.py +++ b/tofu_helpers/__init__.py @@ -0,0 +1 @@ +from . import openmp_helpers