From a558d1ae3089ee217e0048f6a41d853b7ba55053 Mon Sep 17 00:00:00 2001 From: MaNan Date: Wed, 21 Jan 2026 12:42:12 +0800 Subject: [PATCH 01/14] feat: Add Bioxel asset catalog and layer management functionality - Introduced a new asset catalog definition file for Blender to manage Bioxel assets. - Implemented layer caching and snapshot functionality in `layer.py`, allowing for VDB file generation and low-resolution snapshots. - Created node management functions in `node.py` for handling Bioxel nodes within Blender's Geometry Node Editor. - Added an operator to extract mesh data from selected nodes in `structure.py`. - Developed UI panels in `panels.py` for layer management, including import options and layer library display. --- .gitignore | 12 +- AGENTS.md | 222 +++++ build.py | 4 +- pack.py | 92 ++ pyproject.toml | 2 + src/bioxelnodes/__init__.py | 103 ++- .../assets/Nodes/BioxelNodes_latest.blend | 3 - .../assets/Nodes/BioxelNodes_v0.2.9.blend | 3 - .../assets/Nodes/BioxelNodes_v0.3.3.blend | 3 - .../assets/O Bioxel/BioxelNodes.blend | 3 + .../assets/O Bioxel/blender_assets.cats.txt | 12 + src/bioxelnodes/auto_load.py | 9 +- src/bioxelnodes/bioxel/layer.py | 37 +- src/bioxelnodes/bioxel/scipy/_filters.py | 28 +- .../bioxel/scipy/_interpolation.py | 3 +- src/bioxelnodes/bioxel/scipy/_ni_support.py | 3 +- src/bioxelnodes/bioxel/scipy/_utils.py | 2 +- src/bioxelnodes/bioxel/skimage/_warps.py | 1 + src/bioxelnodes/bioxel/skimage/dtype.py | 15 +- src/bioxelnodes/bioxelutils/__init__.py | 0 src/bioxelnodes/bioxelutils/common.py | 270 ------ src/bioxelnodes/bioxelutils/container.py | 186 ---- src/bioxelnodes/bioxelutils/layer.py | 215 ----- src/bioxelnodes/bioxelutils/node.py | 71 -- src/bioxelnodes/blender_manifest.toml | 26 +- src/bioxelnodes/constants.py | 256 +----- src/bioxelnodes/exceptions.py | 28 +- src/bioxelnodes/layer.py | 277 ++++++ src/bioxelnodes/menus.py | 394 +-------- src/bioxelnodes/node.py | 149 ++++ src/bioxelnodes/node_menu.py | 87 -- src/bioxelnodes/operators/container.py | 649 -------------- src/bioxelnodes/operators/io.py | 738 ++++++++-------- src/bioxelnodes/operators/layer.py | 799 ++++++------------ src/bioxelnodes/operators/misc.py | 400 ++++----- src/bioxelnodes/operators/node.py | 8 +- src/bioxelnodes/operators/structure.py | 107 +++ src/bioxelnodes/panels.py | 180 ++++ src/bioxelnodes/preferences.py | 14 +- src/bioxelnodes/props.py | 150 +++- src/bioxelnodes/utils.py | 342 +++++++- tests/__init__.py | 0 uv.lock | 695 +++++++++------ 43 files changed, 2915 insertions(+), 3683 deletions(-) create mode 100644 AGENTS.md create mode 100644 pack.py delete mode 100644 src/bioxelnodes/assets/Nodes/BioxelNodes_latest.blend delete mode 100644 src/bioxelnodes/assets/Nodes/BioxelNodes_v0.2.9.blend delete mode 100644 src/bioxelnodes/assets/Nodes/BioxelNodes_v0.3.3.blend create mode 100644 src/bioxelnodes/assets/O Bioxel/BioxelNodes.blend create mode 100644 src/bioxelnodes/assets/O Bioxel/blender_assets.cats.txt delete mode 100644 src/bioxelnodes/bioxelutils/__init__.py delete mode 100644 src/bioxelnodes/bioxelutils/common.py delete mode 100644 src/bioxelnodes/bioxelutils/container.py delete mode 100644 src/bioxelnodes/bioxelutils/layer.py delete mode 100644 src/bioxelnodes/bioxelutils/node.py create mode 100644 src/bioxelnodes/layer.py create mode 100644 src/bioxelnodes/node.py delete mode 100644 src/bioxelnodes/node_menu.py delete mode 100644 src/bioxelnodes/operators/container.py create mode 100644 src/bioxelnodes/operators/structure.py create mode 100644 src/bioxelnodes/panels.py delete mode 100644 tests/__init__.py diff --git a/.gitignore b/.gitignore index d5ad8a9..30b51f1 100644 --- a/.gitignore +++ b/.gitignore @@ -125,14 +125,14 @@ dmypy.json pythonlib* -*.blend1 - -blendcache_* - *.ipynb .secrets - .vdb -!scipy_ndimage/*/** \ No newline at end of file +!scipy_ndimage/*/** + +# Blender +*.blend1 +blendcache_* +*.cats.txt~ \ No newline at end of file diff --git a/AGENTS.md b/AGENTS.md new file mode 100644 index 0000000..d409372 --- /dev/null +++ b/AGENTS.md @@ -0,0 +1,222 @@ +# BioxelNodes - Agent Development Guide + +This file contains essential information for agentic coding agents working on the BioxelNodes codebase. + +## Project Overview + +BioxelNodes is a Blender addon for scientific volumetric data visualization. It integrates with Blender's Geometry Nodes and Cycles rendering engine to process and visualize medical/scientific data. + +**Language:** Python 3.11 +**Framework:** Blender Python API (bpy) +**Package Manager:** uv + +## Development Commands + +### Environment Setup +```bash +# Install dependencies +uv sync +``` + +### Build Commands +```bash +# Build for specific platform +uv run build.py # platforms: windows-x64, linux-x64, macos-arm64, macos-x64 +``` + +### Code Quality +```bash +# Format code (autopep8) +autopep8 --in-place --recursive src/ +``` + +### Documentation +```bash +# Serve documentation locally +uv run mkdocs serve + +# Build documentation +uv run mike deploy --push --update-aliases 0.2.x latest +``` + +## Code Style Guidelines + +### Formatting +- **4-space indentation** +- **PEP 8** compliance enforced via autopep8 + +### Naming Conventions +- **snake_case** for functions, variables, and files +- **PascalCase** for classes (Blender convention) +- **UPPER_CASE** for constants +- **bioxel_** prefix for addon-specific properties + +### Import Organization +```python +# Standard library imports first +import pathlib +import uuid + +# Third-party imports +import bpy +import numpy as np +import SimpleITK as sitk + +# Relative imports for internal modules +from ..exceptions import CancelledByUser +from ..utils import get_layer_obj +``` + +### Type Hints +- Use sparingly, mainly for Blender property annotations +- Focus on function signatures and complex data structures +- Example: `def process_data(data: np.ndarray) -> np.ndarray:` + +## Architecture Patterns + +### Auto-Registration System +- Uses `auto_load.py` for automatic class registration +- Classes are discovered automatically via reflection +- Registration order resolved via topological sorting +- All Blender classes must inherit from appropriate base types + +### Module Structure +``` +src/bioxelnodes/ +├── __init__.py # Addon entry point, asset library setup +├── auto_load.py # Auto-registration system +├── constants.py # Constants and paths +├── utils.py # Utility functions +├── preferences.py # Addon preferences +├── props.py # Blender properties +├── panels.py # UI panels +├── menus.py # UI menus +├── node.py # Node utilities +├── layer.py # Layer management +├── operators/ # Blender operators +├── bioxel/ # Core bioxel functionality +└── assets/ # Blender assets and node libraries +``` + +### Blender Integration Patterns + +#### Property Groups +```python +class BioxelProperties(bpy.types.PropertyGroup): + bl_label = "Bioxel Properties" + + bioxel_custom_prop: bpy.props.StringProperty( + name="Custom Property", + default="", + description="Description for UI" + ) +``` + +#### Operators +```python +class BIOXEL_OT_custom_operator(bpy.types.Operator): + bl_idname = "bioxel.custom_operator" + bl_label = "Custom Operator" + bl_options = {'REGISTER', 'UNDO'} + + def execute(self, context): + # Operator logic here + return {'FINISHED'} +``` + +#### Panels +```python +class BIOXEL_PT_custom_panel(bpy.types.Panel): + bl_label = "Custom Panel" + bl_idname = "BIOXEL_PT_custom_panel" + bl_space_type = 'VIEW_3D' + bl_region_type = 'UI' + bl_category = "Bioxel" + + def draw(self, context): + layout = self.layout + # UI drawing code here +``` + +## Error Handling + +### Error Handling Patterns +- Use try-catch blocks for file operations +- Handle user cancellation gracefully +- Report progress for long operations using `bioxel_progress_factor` and `bioxel_progress_text` +- Log warnings with print statements for debugging + + +## Key Dependencies + +### Core Libraries +- **bpy** (Blender Python API) - Core integration +- **numpy** - Array processing +- **SimpleITK** - Medical image processing +- **h5py** - HDF5 file handling + +### Scientific Libraries +- **matplotlib** - Plotting and visualization +- **transforms3d** - 3D transformations +- **pyometiff** - OME-TIFF support +- **mrcfile** - MRC file format support + +## Development Workflow + +### Making Changes +1. Identify the appropriate module (operators, panels, bioxel, etc.) +2. Follow existing naming conventions and patterns +3. Use auto-registration - no manual registration needed +4. Test with Blender's Python console +5. Format code with autopep8 before committing + +### Adding New Features +1. Create appropriate classes in relevant modules +2. Use proper prefixes (BIOXEL_OT_, BIOXEL_PT_, etc.) +3. Add to auto_load system automatically discovers new classes +4. Update documentation if needed + +### File Operations +- Use `pathlib.Path` for path operations +- Check file existence before operations +- Handle permissions and missing files gracefully +- Use appropriate file formats (HDF5 for data, PNG for images) + +## Blender Integration Notes + +### Asset Library +- Automatically managed via `add_asset_library_if_missing()` +- Located at `NODE_LIB_DIRPATH` +- Uses "PACK" import method +- Name: "O Bioxel" + +### Progress Reporting +- Use `bioxel_progress_factor` (0.0 to 1.0) for progress +- Use `bioxel_progress_text` for status messages +- Update via WindowManager properties + +### Layer Management +- Layers stored as HDF5 files +- Container objects manage multiple layers +- Use `layer.py` for layer operations +- Support for various medical image formats + +## Common Pitfalls + +### Blender API +- Always check context validity +- Handle different Blender versions (check `bpy.app.version`) +- Use proper property types for UI +- Register classes in correct order (auto_load handles this) + +### Performance +- Use NumPy for array operations +- Avoid expensive operations in UI draw calls +- Cache computed values where appropriate +- Use background threads for long operations + +### File I/O +- Always close file handles +- Use context managers for file operations +- Handle large files in chunks +- Validate file formats before processing \ No newline at end of file diff --git a/build.py b/build.py index d7bc1cb..f0d83c4 100644 --- a/build.py +++ b/build.py @@ -17,7 +17,9 @@ class Platform: "mrcfile==1.5.1", "h5py==3.11.0", "transforms3d==0.4.2", - "tifffile==2024.7.24"] + "tifffile==2024.7.24", + "matplotlib==3.10.7", + "pillow==11.2.1"] platforms = {"windows-x64": Platform(pypi_suffix="win_amd64", diff --git a/pack.py b/pack.py new file mode 100644 index 0000000..5e72506 --- /dev/null +++ b/pack.py @@ -0,0 +1,92 @@ +""" +Create a zip archive of the src/bioxelnodes package with a top-level folder +named `bioxelnodes/`. Excludes specified temporary/cache files and folders. +Does not modify any files in the project. + +Usage: + python build_package.py [output_zip_path] + +Example: + python build_package.py windows-x64 +""" +from pathlib import Path +import sys +import zipfile +import fnmatch +from datetime import datetime + +platforms = { + "windows-x64": "windows-x64", + "linux-x64": "linux-x64", + "macos-arm64": "macos-arm64", + "macos-x64": "macos-x64", +} + +# patterns to exclude (filename matching) +EXCLUDE_FILENAME_PATTERNS = [ + "*.blend1", + "blendcache_*", + "*.cats.txt~", + "*.pyc", + "*.pyo", + "*$py.class", +] + +# directory names to exclude entirely +EXCLUDE_DIR_NAMES = { + "__pycache__", +} + +def should_exclude(path: Path) -> bool: + name = path.name + # exclude directories by name anywhere in the path + if any(part in EXCLUDE_DIR_NAMES for part in path.parts): + return True + # only apply filename patterns to files + if path.is_file(): + for pat in EXCLUDE_FILENAME_PATTERNS: + if fnmatch.fnmatch(name, pat): + return True + return False + +def build_package(platform_name: str, out_zip: Path): + src_root = Path("src") / "bioxelnodes" + if not src_root.exists(): + raise SystemExit(f"Source folder not found: {src_root.resolve()}") + + out_zip.parent.mkdir(parents=True, exist_ok=True) + total = 0 + with zipfile.ZipFile(out_zip, "w", compression=zipfile.ZIP_DEFLATED) as zf: + for p in src_root.rglob("*"): + if p.is_dir(): + continue + if should_exclude(p): + continue + # arcname should place files under top-level 'bioxelnodes/...' + rel = p.relative_to(src_root) + arcname = Path("bioxelnodes") / rel + zf.write(p, arcname.as_posix()) + total += 1 + print(f"Packaged {total} files into {out_zip}") + +def main(): + if len(sys.argv) < 2: + print("Usage: python build_package.py [output_zip_path]") + print("Available platforms:", ", ".join(platforms.keys())) + sys.exit(1) + + platform_key = sys.argv[1] + if platform_key not in platforms: + print("Unknown platform:", platform_key) + print("Available platforms:", ", ".join(platforms.keys())) + sys.exit(1) + + tag = platforms[platform_key] + timestamp = datetime.now().strftime("%Y%m%dT%H%M%S") + default_name = f"bioxelnodes-{tag}-{timestamp}.zip" + out_path = Path(sys.argv[2]) if len(sys.argv) >= 3 else Path(default_name) + + build_package(platform_key, out_path) + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index fefa9cc..05dec56 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,6 +12,7 @@ dependencies = [ "mrcfile==1.5.1", "h5py==3.11.0", "transforms3d==0.4.2", + "matplotlib==3.10.7", ] [dependency-groups] @@ -25,6 +26,7 @@ dev = [ "autopep8>=2.3.1,<3", "mike>=2.1.2,<3", "tomlkit>=0.13.0,<0.14", + "pip>=25.3", ] [build-system] diff --git a/src/bioxelnodes/__init__.py b/src/bioxelnodes/__init__.py index 1d34f90..9547761 100644 --- a/src/bioxelnodes/__init__.py +++ b/src/bioxelnodes/__init__.py @@ -1,26 +1,109 @@ import bpy +import bpy.utils.previews as previews + +from .constants import NODE_LIB_DIRPATH, PREVIEW_COLLECTIONS +from .props import _bioxel_layer_items, _update_layer_gallery, _update_snapshot_z -from .props import BIOXELNODES_LayerListUL from . import auto_load from . import menus - auto_load.init() +def add_asset_library_if_missing(): + """检查并添加Asset Library（如果不存在），使用link导入方式""" + # 检查路径是否存在 + if not NODE_LIB_DIRPATH.exists(): + print(f"警告: 节点库路径不存在 - {NODE_LIB_DIRPATH}") + return + + # 转换为字符串路径用于Blender设置 + lib_path_str = str(NODE_LIB_DIRPATH) + + # 检查是否已存在该资产库 + prefs = bpy.context.preferences.filepaths.asset_libraries + for lib in prefs: + if lib.path == lib_path_str: + return # 已存在，无需添加 + + # 添加新的资产库，使用link导入方式 + new_lib = prefs.new() + new_lib.name = "O Bioxel" # 资产库名称 + new_lib.path = lib_path_str # 资产库路径（字符串形式） + new_lib.import_method = "PACK" # 设置导入方式为link + + print(f"Add Bioxel Nodes library: {lib_path_str}") + + +def remove_asset_library_if_exists(): + """Remove the Bioxel asset library entry if it was added (by path or name).""" + # if path missing, nothing to remove + lib_path_str = str(NODE_LIB_DIRPATH) + prefs = bpy.context.preferences.filepaths.asset_libraries + + # iterate over a snapshot of prefs to safely find index + lib_to_remove = None + for i, lib in enumerate(list(prefs)): + try: + if lib.path == lib_path_str: + lib_to_remove = lib + break + except Exception: + continue + + if lib_to_remove is not None: + try: + prefs.remove(lib_to_remove) + print(f"Removed Bioxel Nodes library: {lib_path_str}") + except Exception as e: + print(f"Warning: failed to remove Bioxel node library: {e}") + + def register(): + pcoll = previews.new() + pcoll.layer_previews = () + PREVIEW_COLLECTIONS["layers"] = pcoll + + bpy.types.WindowManager.bioxel_progress_factor = bpy.props.FloatProperty( + default=1.0 + ) + + bpy.types.WindowManager.bioxel_progress_text = bpy.props.StringProperty() + + bpy.types.WindowManager.bioxel_layer_library = bpy.props.EnumProperty( + name="Bioxel Layer Gallery", + items=_bioxel_layer_items, + update=_update_layer_gallery, + ) + + bpy.types.WindowManager.bioxel_snapshot_z = bpy.props.FloatProperty( + name="Snapshot Z", + default=0.5, + min=0.0, + max=1.0, + subtype="FACTOR", + update=_update_snapshot_z, + ) + + bpy.types.WindowManager.bioxel_layer_list_index = bpy.props.IntProperty( + default=0) + auto_load.register() - bpy.types.WindowManager.bioxelnodes_progress_factor = bpy.props.FloatProperty( - default=1.0) - bpy.types.WindowManager.bioxelnodes_progress_text = bpy.props.StringProperty() - bpy.types.WindowManager.bioxelnodes_layer_list_UL = bpy.props.PointerProperty( - type=BIOXELNODES_LayerListUL) menus.add() + add_asset_library_if_missing() def unregister(): + remove_asset_library_if_exists() menus.remove() - del bpy.types.WindowManager.bioxelnodes_progress_factor - del bpy.types.WindowManager.bioxelnodes_progress_text - del bpy.types.WindowManager.bioxelnodes_layer_list_UL auto_load.unregister() + + del bpy.types.WindowManager.bioxel_progress_factor + del bpy.types.WindowManager.bioxel_progress_text + del bpy.types.WindowManager.bioxel_layer_library + del bpy.types.WindowManager.bioxel_snapshot_z + del bpy.types.WindowManager.bioxel_layer_list_index + + for pcoll in PREVIEW_COLLECTIONS.values(): + previews.remove(pcoll) + PREVIEW_COLLECTIONS.clear() diff --git a/src/bioxelnodes/assets/Nodes/BioxelNodes_latest.blend b/src/bioxelnodes/assets/Nodes/BioxelNodes_latest.blend deleted file mode 100644 index 57528b7..0000000 --- a/src/bioxelnodes/assets/Nodes/BioxelNodes_latest.blend +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:a76a54a0ec3a2a279e6cc06288975c23ca0cb999dafd0d3fd8842ec3e310fc41 -size 9057934 diff --git a/src/bioxelnodes/assets/Nodes/BioxelNodes_v0.2.9.blend b/src/bioxelnodes/assets/Nodes/BioxelNodes_v0.2.9.blend deleted file mode 100644 index 016c4cf..0000000 --- a/src/bioxelnodes/assets/Nodes/BioxelNodes_v0.2.9.blend +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:b219a6f005718d8223766215a598ebde9b646c3960fb298d72ffc864791f3c3a -size 6691383 diff --git a/src/bioxelnodes/assets/Nodes/BioxelNodes_v0.3.3.blend b/src/bioxelnodes/assets/Nodes/BioxelNodes_v0.3.3.blend deleted file mode 100644 index 595e09b..0000000 --- a/src/bioxelnodes/assets/Nodes/BioxelNodes_v0.3.3.blend +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:87831f56b9d23b8ee3eccfea02c27e8ff305723a079e2c115a7b059fb5e1cb24 -size 6803344 diff --git a/src/bioxelnodes/assets/O Bioxel/BioxelNodes.blend b/src/bioxelnodes/assets/O Bioxel/BioxelNodes.blend new file mode 100644 index 0000000..5db983f --- /dev/null +++ b/src/bioxelnodes/assets/O Bioxel/BioxelNodes.blend @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6c0cdfc0e9a37d0e559691fd8893697e1236ddbf3d31b6165ea72e7dcffada2f +size 14083935 diff --git a/src/bioxelnodes/assets/O Bioxel/blender_assets.cats.txt b/src/bioxelnodes/assets/O Bioxel/blender_assets.cats.txt new file mode 100644 index 0000000..80c7c80 --- /dev/null +++ b/src/bioxelnodes/assets/O Bioxel/blender_assets.cats.txt @@ -0,0 +1,12 @@ +# This is an Asset Catalog Definition file for Blender. +# +# Empty lines and lines starting with `#` will be ignored. +# The first non-ignored line should be the version indicator. +# Other lines are of the format "UUID:catalog/path/for/assets:simple catalog name" + +VERSION 1 + +c0699a8b-6fd6-4d10-bdde-5ea0fa36724d:O Bioxel:O Bioxel +5ea24e10-5a2b-44d1-b67b-19014c412793:O Bioxel/Layer:O Bioxel-Layer +17383d65-f1a0-4122-b73a-0baaad4b8ecf:O Bioxel/Structure:O Bioxel-Structure +d03fc5b0-465c-45ba-ba8e-524a1c52ae3d:O Bioxel/Utilities:O Bioxel-Utilities diff --git a/src/bioxelnodes/auto_load.py b/src/bioxelnodes/auto_load.py index 93501f4..d0dedda 100644 --- a/src/bioxelnodes/auto_load.py +++ b/src/bioxelnodes/auto_load.py @@ -80,11 +80,13 @@ def get_ordered_classes_to_register(modules): def get_register_deps_dict(modules): my_classes = set(iter_my_classes(modules)) - my_classes_by_idname = {cls.bl_idname: cls for cls in my_classes if hasattr(cls, "bl_idname")} + my_classes_by_idname = { + cls.bl_idname: cls for cls in my_classes if hasattr(cls, "bl_idname")} deps_dict = {} for cls in my_classes: - deps_dict[cls] = set(iter_my_register_deps(cls, my_classes, my_classes_by_idname)) + deps_dict[cls] = set(iter_my_register_deps( + cls, my_classes, my_classes_by_idname)) return deps_dict @@ -181,7 +183,8 @@ def toposort(deps_dict): sorted_values.add(value) else: unsorted.append(value) - deps_dict = {value: deps_dict[value] - sorted_values for value in unsorted} + deps_dict = {value: deps_dict[value] - + sorted_values for value in unsorted} sorted_list_sub.sort(key=lambda cls: getattr(cls, "bl_order", 0)) sorted_list.extend(sorted_list_sub) return sorted_list diff --git a/src/bioxelnodes/bioxel/layer.py b/src/bioxelnodes/bioxel/layer.py index 4837b51..d9449df 100644 --- a/src/bioxelnodes/bioxel/layer.py +++ b/src/bioxelnodes/bioxel/layer.py @@ -78,8 +78,8 @@ def fill(self, value: float, mask: np.ndarray, smooth: int = 0): mask_frame = mask[f, :, :, :] if smooth > 0: mask_frame = scipy.median_filter(mask_frame.astype(np.float32), - mode="nearest", - size=smooth) + mode="nearest", + size=smooth) # mask_frame = scipy.median_filter( # mask_frame.astype(np.float32), size=2) mask_frames += (mask_frame,) @@ -88,8 +88,8 @@ def fill(self, value: float, mask: np.ndarray, smooth: int = 0): mask_frame = mask[:, :, :] if smooth > 0: mask_frame = scipy.median_filter(mask_frame.astype(np.float32), - mode="nearest", - size=smooth) + mode="nearest", + size=smooth) # mask_frame = scipy.median_filter( # mask_frame.astype(np.float32), size=2) mask_frames += (mask_frame,) @@ -150,3 +150,32 @@ def resize(self, shape: tuple, smooth: int = 0, progress_callback=None): mat_scale = transforms3d.zooms.zfdir2aff(factors[0]) self.affine = np.dot(self.affine, mat_scale) + + def snapshot(self, shape: tuple, smooth: int = 0): + if len(shape) != 3: + raise Exception("Shape must be 3 dim") + + data = self.data + + snapshot = data[0, :, :, :, :] + + factors = np.divide(self.shape, shape) + zoom_factors = [1 / f for f in factors] + order = 0 if snapshot.dtype == bool else 1 + snapshot = ndi.zoom(snapshot, + zoom_factors+[1.0], + mode="nearest", + grid_mode=False, + order=order) + + snapshot = snapshot.astype(np.float32) + + if self.kind in ['scalar', 'vector', 'color']: + mn = float(np.nanmin(snapshot)) + mx = float(np.nanmax(snapshot)) + if mx - mn > 1e-8: + snapshot = (snapshot - mn) / (mx - mn) + else: + snapshot = np.clip(snapshot, 0.0, 1.0) + + return snapshot diff --git a/src/bioxelnodes/bioxel/scipy/_filters.py b/src/bioxelnodes/bioxel/scipy/_filters.py index 3bbd8ef..1e54ff4 100644 --- a/src/bioxelnodes/bioxel/scipy/_filters.py +++ b/src/bioxelnodes/bioxel/scipy/_filters.py @@ -39,7 +39,6 @@ from . import _nd_image - def _invalid_origin(origin, lenw): return (origin < -(lenw // 2)) or (origin > (lenw - 1) // 2) @@ -73,7 +72,6 @@ def _complex_via_real_components(func, input, weights, output, cval, **kwargs): return output - def correlate1d(input, weights, axis=-1, output=None, mode="reflect", cval=0.0, origin=0): """Calculate a 1-D correlation along the given axis. @@ -133,7 +131,6 @@ def correlate1d(input, weights, axis=-1, output=None, mode="reflect", return output - def convolve1d(input, weights, axis=-1, output=None, mode="reflect", cval=0.0, origin=0): """Calculate a 1-D convolution along the given axis. @@ -205,7 +202,6 @@ def _gaussian_kernel1d(sigma, order, radius): return q * phi_x - def gaussian_filter1d(input, sigma, axis=-1, order=0, output=None, mode="reflect", cval=0.0, truncate=4.0, *, radius=None): """1-D Gaussian filter. @@ -274,7 +270,6 @@ def gaussian_filter1d(input, sigma, axis=-1, order=0, output=None, return correlate1d(input, weights, axis, output, mode, cval, 0) - def gaussian_filter(input, sigma, order=0, output=None, mode="reflect", cval=0.0, truncate=4.0, *, radius=None, axes=None): @@ -381,7 +376,6 @@ def gaussian_filter(input, sigma, order=0, output=None, return output - def prewitt(input, axis=-1, output=None, mode="reflect", cval=0.0): """Calculate a Prewitt filter. @@ -443,7 +437,6 @@ def prewitt(input, axis=-1, output=None, mode="reflect", cval=0.0): return output - def sobel(input, axis=-1, output=None, mode="reflect", cval=0.0): """Calculate a Sobel filter. @@ -501,7 +494,6 @@ def sobel(input, axis=-1, output=None, mode="reflect", cval=0.0): return output - def generic_laplace(input, derivative2, output=None, mode="reflect", cval=0.0, extra_arguments=(), @@ -549,7 +541,6 @@ def generic_laplace(input, derivative2, output=None, mode="reflect", return output - def laplace(input, output=None, mode="reflect", cval=0.0): """N-D Laplace filter based on approximate second derivatives. @@ -584,7 +575,6 @@ def derivative2(input, axis, output, mode, cval): return generic_laplace(input, derivative2, output, mode, cval) - def gaussian_laplace(input, sigma, output=None, mode="reflect", cval=0.0, **kwargs): """Multidimensional Laplace filter using Gaussian second derivatives. @@ -637,7 +627,6 @@ def derivative2(input, axis, output, mode, cval, sigma, **kwargs): extra_keywords=kwargs) - def generic_gradient_magnitude(input, derivative, output=None, mode="reflect", cval=0.0, extra_arguments=(), extra_keywords=None): @@ -690,7 +679,6 @@ def generic_gradient_magnitude(input, derivative, output=None, return output - def gaussian_gradient_magnitude(input, sigma, output=None, mode="reflect", cval=0.0, **kwargs): """Multidimensional gradient magnitude using Gaussian derivatives. @@ -792,7 +780,6 @@ def _correlate_or_convolve(input, weights, output, mode, cval, origin, return output - def correlate(input, weights, output=None, mode='reflect', cval=0.0, origin=0): """ @@ -856,7 +843,6 @@ def correlate(input, weights, output=None, mode='reflect', cval=0.0, origin, False) - def convolve(input, weights, output=None, mode='reflect', cval=0.0, origin=0): """ @@ -967,7 +953,6 @@ def convolve(input, weights, output=None, mode='reflect', cval=0.0, origin, True) - def uniform_filter1d(input, size, axis=-1, output=None, mode="reflect", cval=0.0, origin=0): """Calculate a 1-D uniform filter along the given axis. @@ -1018,7 +1003,6 @@ def uniform_filter1d(input, size, axis=-1, output=None, return output - def uniform_filter(input, size=3, output=None, mode="reflect", cval=0.0, origin=0, *, axes=None): """Multidimensional uniform filter. @@ -1088,7 +1072,6 @@ def uniform_filter(input, size=3, output=None, mode="reflect", return output - def minimum_filter1d(input, size, axis=-1, output=None, mode="reflect", cval=0.0, origin=0): """Calculate a 1-D minimum filter along the given axis. @@ -1145,7 +1128,6 @@ def minimum_filter1d(input, size, axis=-1, output=None, return output - def maximum_filter1d(input, size, axis=-1, output=None, mode="reflect", cval=0.0, origin=0): """Calculate a 1-D maximum filter along the given axis. @@ -1302,7 +1284,6 @@ def _min_or_max_filter(input, size, footprint, structure, output, mode, return output - def minimum_filter(input, size=None, footprint=None, output=None, mode="reflect", cval=0.0, origin=0, *, axes=None): """Calculate a multidimensional minimum filter. @@ -1350,7 +1331,6 @@ def minimum_filter(input, size=None, footprint=None, output=None, cval, origin, 1, axes) - def maximum_filter(input, size=None, footprint=None, output=None, mode="reflect", cval=0.0, origin=0, *, axes=None): """Calculate a multidimensional maximum filter. @@ -1398,7 +1378,6 @@ def maximum_filter(input, size=None, footprint=None, output=None, cval, origin, 0, axes) - def _rank_filter(input, rank, size=None, footprint=None, output=None, mode="reflect", cval=0.0, origin=0, operation='rank', axes=None): @@ -1491,7 +1470,6 @@ def _rank_filter(input, rank, size=None, footprint=None, output=None, return output - def rank_filter(input, rank, size=None, footprint=None, output=None, mode="reflect", cval=0.0, origin=0, *, axes=None): """Calculate a multidimensional rank filter. @@ -1535,7 +1513,6 @@ def rank_filter(input, rank, size=None, footprint=None, output=None, origin, 'rank', axes=axes) - def median_filter(input, size=None, footprint=None, output=None, mode="reflect", cval=0.0, origin=0, *, axes=None): """ @@ -1586,7 +1563,6 @@ def median_filter(input, size=None, footprint=None, output=None, origin, 'median', axes=axes) - def percentile_filter(input, percentile, size=None, footprint=None, output=None, mode="reflect", cval=0.0, origin=0, *, axes=None): @@ -1630,7 +1606,6 @@ def percentile_filter(input, percentile, size=None, footprint=None, cval, origin, 'percentile', axes=axes) - def generic_filter1d(input, function, filter_size, axis=-1, output=None, mode="reflect", cval=0.0, origin=0, extra_arguments=(), extra_keywords=None): @@ -1718,7 +1693,6 @@ def generic_filter1d(input, function, filter_size, axis=-1, return output - def generic_filter(input, function, size=None, footprint=None, output=None, mode="reflect", cval=0.0, origin=0, extra_arguments=(), extra_keywords=None): @@ -1846,4 +1820,4 @@ def generic_filter(input, function, size=None, footprint=None, mode = _ni_support._extend_mode_to_code(mode) _nd_image.generic_filter(input, function, footprint, output, mode, cval, origins, extra_arguments, extra_keywords) - return output \ No newline at end of file + return output diff --git a/src/bioxelnodes/bioxel/scipy/_interpolation.py b/src/bioxelnodes/bioxel/scipy/_interpolation.py index 0384130..0479344 100644 --- a/src/bioxelnodes/bioxel/scipy/_interpolation.py +++ b/src/bioxelnodes/bioxel/scipy/_interpolation.py @@ -11,7 +11,7 @@ def _prepad_for_spline_filter(input, mode, cval): npad = 12 if mode == 'grid-constant': padded = np.pad(input, npad, mode='constant', - constant_values=cval) + constant_values=cval) elif mode == 'nearest': padded = np.pad(input, npad, mode='edge') else: @@ -21,6 +21,7 @@ def _prepad_for_spline_filter(input, mode, cval): padded = input return padded, npad + def spline_filter1d(input, order=3, axis=-1, output=np.float64, mode='mirror'): """ diff --git a/src/bioxelnodes/bioxel/scipy/_ni_support.py b/src/bioxelnodes/bioxel/scipy/_ni_support.py index ae8875f..c312772 100644 --- a/src/bioxelnodes/bioxel/scipy/_ni_support.py +++ b/src/bioxelnodes/bioxel/scipy/_ni_support.py @@ -83,7 +83,8 @@ def _get_output(output, input, shape=None, complex_output=False): elif isinstance(output, (type, np.dtype)): # Classes (like `np.float32`) and dtypes are interpreted as dtype if complex_output and np.dtype(output).kind != 'c': - warnings.warn("promoting specified output dtype to complex", stacklevel=3) + warnings.warn( + "promoting specified output dtype to complex", stacklevel=3) output = np.promote_types(output, np.complex64) output = np.zeros(shape, dtype=output) elif isinstance(output, str): diff --git a/src/bioxelnodes/bioxel/scipy/_utils.py b/src/bioxelnodes/bioxel/scipy/_utils.py index c397ef4..5a4b9be 100644 --- a/src/bioxelnodes/bioxel/scipy/_utils.py +++ b/src/bioxelnodes/bioxel/scipy/_utils.py @@ -7,4 +7,4 @@ def normalize_axis_index(axis, ndim): if axis < 0: axis = axis + ndim - return axis \ No newline at end of file + return axis diff --git a/src/bioxelnodes/bioxel/skimage/_warps.py b/src/bioxelnodes/bioxel/skimage/_warps.py index 992e38b..f8f4a4f 100644 --- a/src/bioxelnodes/bioxel/skimage/_warps.py +++ b/src/bioxelnodes/bioxel/skimage/_warps.py @@ -3,6 +3,7 @@ from .. import scipy as ndi from ._utils import convert_to_float + def _clip_warp_output(input_image, output_image, mode, cval, clip): """Clip output image to range of values of input image. diff --git a/src/bioxelnodes/bioxel/skimage/dtype.py b/src/bioxelnodes/bioxel/skimage/dtype.py index 0b69b7b..07bc3b4 100644 --- a/src/bioxelnodes/bioxel/skimage/dtype.py +++ b/src/bioxelnodes/bioxel/skimage/dtype.py @@ -39,7 +39,8 @@ np.uintp, np.uintc, ) -_integer_ranges = {t: (np.iinfo(t).min, np.iinfo(t).max) for t in _integer_types} +_integer_ranges = {t: (np.iinfo(t).min, np.iinfo(t).max) + for t in _integer_types} dtype_range = { bool: (False, True), np.bool_: (False, True), @@ -175,7 +176,8 @@ def _scale(a, n, m, copy=True): # downscale with precision loss if copy: b = np.empty(a.shape, _dtype_bits(kind, m)) - np.floor_divide(a, 2 ** (n - m), out=b, dtype=a.dtype, casting='unsafe') + np.floor_divide(a, 2 ** (n - m), out=b, + dtype=a.dtype, casting='unsafe') return b else: a //= 2 ** (n - m) @@ -282,7 +284,8 @@ def _convert(image, dtype, force_copy=False, uniform=False): return image if not (dtype_in in _supported_types and dtype_out in _supported_types): - raise ValueError(f'Cannot convert from {dtypeobj_in} to ' f'{dtypeobj_out}.') + raise ValueError( + f'Cannot convert from {dtypeobj_in} to ' f'{dtypeobj_out}.') if kind_in in 'ui': imin_in = np.iinfo(dtype_in).min @@ -318,7 +321,8 @@ def _convert(image, dtype, force_copy=False, uniform=False): if not uniform: if kind_out == 'u': - image_out = np.multiply(image, imax_out, dtype=computation_type) + image_out = np.multiply( + image, imax_out, dtype=computation_type) else: image_out = np.multiply( image, (imax_out - imin_out) / 2, dtype=computation_type @@ -327,7 +331,8 @@ def _convert(image, dtype, force_copy=False, uniform=False): np.rint(image_out, out=image_out) np.clip(image_out, imin_out, imax_out, out=image_out) elif kind_out == 'u': - image_out = np.multiply(image, imax_out + 1, dtype=computation_type) + image_out = np.multiply( + image, imax_out + 1, dtype=computation_type) np.clip(image_out, 0, imax_out, out=image_out) else: image_out = np.multiply( diff --git a/src/bioxelnodes/bioxelutils/__init__.py b/src/bioxelnodes/bioxelutils/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/src/bioxelnodes/bioxelutils/common.py b/src/bioxelnodes/bioxelutils/common.py deleted file mode 100644 index b2bb850..0000000 --- a/src/bioxelnodes/bioxelutils/common.py +++ /dev/null @@ -1,270 +0,0 @@ -from ast import literal_eval -from pathlib import Path -import bpy - -from ..constants import LATEST_NODE_LIB_PATH, NODE_LIB_DIRPATH, VERSIONS -from ..utils import get_cache_dir - - -def move_node_to_node(node, target_node, offset=(0, 0)): - node.location.x = target_node.location.x + offset[0] - node.location.y = target_node.location.y + offset[1] - - -def move_node_between_nodes(node, target_nodes, offset=(0, 0)): - xs = [] - ys = [] - for target_node in target_nodes: - xs.append(target_node.location.x) - ys.append(target_node.location.y) - - node.location.x = sum(xs) / len(xs) + offset[0] - node.location.y = sum(ys) / len(ys) + offset[1] - - -def get_node_type(node): - node_type = type(node).__name__ - if node_type == "GeometryNodeGroup": - node_type = node.node_tree.name - - return node_type - - -def get_nodes_by_type(node_group, type_name: str): - return [node for node in node_group.nodes if get_node_type(node) == type_name] - - -def get_container_objs_from_selection(): - container_objs = [] - for obj in bpy.context.selected_objects: - if get_container_obj(obj): - container_objs.append(obj) - - return list(set(container_objs)) - - -def get_container_obj(current_obj): - if current_obj: - if current_obj.get('bioxel_container'): - return current_obj - elif current_obj.get('bioxel_layer'): - parent = current_obj.parent - return parent if parent.get('bioxel_container') else None - return None - - -def get_layer_prop_value(layer_obj: bpy.types.Object, prop_name: str): - node_group = layer_obj.modifiers[0].node_group - layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0] - prop = layer_node.inputs.get(prop_name) - if prop is None: - return None - - value = prop.default_value - - if type(value).__name__ == "bpy_prop_array": - value = tuple(value) - return tuple([int(v) for v in value]) \ - if prop in ["shape"] else value - elif type(value).__name__ == "str": - return str(value) - elif type(value).__name__ == "float": - value = float(value) - return round(value, 2) \ - if prop in ["bioxel_size"] else value - elif type(value).__name__ == "int": - value = int(value) - return value - else: - return value - - -def get_layer_name(layer_obj): - return get_layer_prop_value(layer_obj, "name") - - -def get_layer_kind(layer_obj): - return get_layer_prop_value(layer_obj, "kind") - - -def get_layer_label(layer_obj): - name = get_layer_name(layer_obj) - # kind = get_layer_kind(layer_obj) - - label = f"{name}" - - if is_missing_layer(layer_obj): - return "**MISSING**" + label - elif is_temp_layer(layer_obj): - return "* " + label - else: - return label - - -def is_missing_layer(layer_obj): - cache_filepath = Path(bpy.path.abspath( - layer_obj.data.filepath)).resolve() - return not cache_filepath.is_file() - - -def is_temp_layer(layer_obj): - cache_filepath = Path(bpy.path.abspath( - layer_obj.data.filepath)).resolve() - cache_dirpath = Path(get_cache_dir()) - return cache_dirpath in cache_filepath.parents - - -def set_layer_prop_value(layer_obj: bpy.types.Object, prop: str, value): - node_group = layer_obj.modifiers[0].node_group - layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0] - layer_node.inputs[prop].default_value = value - - -def get_layer_obj(current_obj: bpy.types.Object): - if current_obj: - if current_obj.get('bioxel_layer') and current_obj.parent: - if current_obj.parent.get('bioxel_container'): - return current_obj - return None - - -def get_container_layer_objs(container_obj: bpy.types.Object): - layer_objs = [] - for obj in bpy.data.objects: - if obj.parent == container_obj and get_layer_obj(obj): - layer_objs.append(obj) - - return layer_objs - - -def get_all_layer_objs(): - layer_objs = [] - for obj in bpy.data.objects: - if get_layer_obj(obj): - layer_objs.append(obj) - - return layer_objs - - -def add_driver(target, target_prop, var_sources, expression): - driver = target.driver_add(target_prop) - is_vector = isinstance(driver, list) - drivers = driver if is_vector else [driver] - - for i, driver in enumerate(drivers): - for j, var_source in enumerate(var_sources): - - source = var_source['source'] - prop = var_source['prop'] - - var = driver.driver.variables.new() - var.name = f"var{j}" - - var.targets[0].id_type = source.id_type - var.targets[0].id = source - var.targets[0].data_path = f'["{prop}"][{i}]'\ - if is_vector else f'["{prop}"]' - - driver.driver.expression = expression - - -def add_direct_driver(target, target_prop, source, source_prop): - drivers = [ - { - "source": source, - "prop": source_prop - } - ] - expression = "var0" - add_driver(target, target_prop, drivers, expression) - - -def read_file_prop(content: str): - props = {} - for line in content.split("\n"): - line = line.replace(" ", "") - p = line.split("=")[0] - if p != "": - v = line.split("=")[-1] - props[p] = v - return props - - -def write_file_prop(props: dict): - lines = [] - for p, v in props.items(): - lines.append(f"{p} = {v}") - return "\n".join(lines) - - -def set_file_prop(prop, value): - if bpy.data.texts.get("BioxelNodes") is None: - bpy.data.texts.new("BioxelNodes") - - props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string()) - props[prop] = value - bpy.data.texts["BioxelNodes"].clear() - bpy.data.texts["BioxelNodes"].write(write_file_prop(props)) - - -def get_file_prop(prop): - if bpy.data.texts.get("BioxelNodes") is None: - bpy.data.texts.new("BioxelNodes") - - props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string()) - return props.get(prop) - - -def get_node_version(): - node_version = get_file_prop("node_version") - return literal_eval(node_version) if node_version else None - - -def is_incompatible(): - node_version = get_node_version() - if node_version is None: - for node_group in bpy.data.node_groups: - if node_group.name.startswith("BioxelNodes"): - return True - else: - addon_version = VERSIONS[0]["node_version"] - if node_version[0] != addon_version[0]\ - or node_version[1] != addon_version[1]: - return True - - return False - - -def get_node_lib_path(node_version): - version_str = "v"+".".join([str(i) for i in list(node_version)]) - lib_filename = f"BioxelNodes_{version_str}.blend" - return Path(NODE_LIB_DIRPATH, - lib_filename).resolve() - - -def local_lib_not_updated(): - addon_version = VERSIONS[0]["node_version"] - addon_lib_path = LATEST_NODE_LIB_PATH - - use_local = False - for node_group in bpy.data.node_groups: - if node_group.name.startswith("BioxelNodes"): - lib = node_group.library - if lib: - lib_path = Path(bpy.path.abspath(lib.filepath)).resolve() - if lib_path != addon_lib_path: - use_local = True - break - - not_update = get_node_version() != addon_version - return use_local and not_update - - -def get_output_node(node_group): - try: - output_node = get_nodes_by_type(node_group, - 'NodeGroupOutput')[0] - except: - output_node = node_group.nodes.new("NodeGroupOutput") - - return output_node diff --git a/src/bioxelnodes/bioxelutils/container.py b/src/bioxelnodes/bioxelutils/container.py deleted file mode 100644 index 59c0b1a..0000000 --- a/src/bioxelnodes/bioxelutils/container.py +++ /dev/null @@ -1,186 +0,0 @@ -import bpy - -from ..bioxel.container import Container -from bpy_extras.io_utils import axis_conversion -from mathutils import Matrix, Vector - - -from .layer import Layer, layer_to_obj, obj_to_layer -from .common import (get_container_layer_objs, - get_layer_prop_value, - get_nodes_by_type, get_output_node, - move_node_to_node) -from .node import add_node_to_graph -from ..utils import get_use_link - -NODE_TYPE = { - "label": "BioxelNodes_MaskByLabel", - "scalar": "BioxelNodes_MaskByThreshold" -} - - -def calc_bbox_verts(origin: tuple, size: tuple): - bbox_origin = Vector( - (origin[0], origin[1], origin[2])) - bbox_size = Vector( - (size[0], size[1], size[2])) - bbox_verts = [ - ( - bbox_origin[0] + 0, - bbox_origin[1] + 0, - bbox_origin[2] + 0 - ), - ( - bbox_origin[0] + 0, - bbox_origin[1] + 0, - bbox_origin[2] + bbox_size[2] - ), - ( - bbox_origin[0] + 0, - bbox_origin[1] + bbox_size[1], - bbox_origin[2] + 0 - ), - ( - bbox_origin[0] + 0, - bbox_origin[1] + bbox_size[1], - bbox_origin[2] + bbox_size[2] - ), - ( - bbox_origin[0] + bbox_size[0], - bbox_origin[1] + 0, - bbox_origin[2] + 0 - ), - ( - bbox_origin[0] + bbox_size[0], - bbox_origin[1] + 0, - bbox_origin[2] + bbox_size[2], - ), - ( - bbox_origin[0] + bbox_size[0], - bbox_origin[1] + bbox_size[1], - bbox_origin[2] + 0, - ), - ( - bbox_origin[0] + bbox_size[0], - bbox_origin[1] + bbox_size[1], - bbox_origin[2] + bbox_size[2], - ), - ] - return bbox_verts - - -def obj_to_container(container_obj: bpy.types.Object): - layer_objs = get_container_layer_objs(container_obj) - layers = [obj_to_layer(obj) for obj in layer_objs] - container = Container(name=container_obj.name, - layers=layers) - return container - - -def add_layers(layers: list[Layer], - container_obj: bpy.types.Object, - cache_dir: str): - - node_group = container_obj.modifiers[0].node_group - output_node = get_output_node(node_group) - - for i, layer in enumerate(layers): - layer_obj = layer_to_obj(layer, container_obj, cache_dir) - fetch_node = add_node_to_graph("FetchLayer", - node_group, - use_link=get_use_link()) - fetch_node.label = get_layer_prop_value(layer_obj, "name") - fetch_node.inputs[0].default_value = layer_obj - - if len(output_node.inputs[0].links) == 0: - node_group.links.new(fetch_node.outputs[0], - output_node.inputs[0]) - move_node_to_node(fetch_node, output_node, (-900, 0)) - else: - move_node_to_node(fetch_node, output_node, (0, -100 * (i+1))) - - return container_obj - - -def container_to_obj(container: Container, - scene_scale: float, - step_size: float, - cache_dir: str): - # Wrapper a Container - - # Make transformation - # (S)uperior -Z -> Y - # (A)osterior Y -> Z - mat_ras2blender = axis_conversion(from_forward='-Z', - from_up='Y', - to_forward='Y', - to_up='Z').to_4x4() - - mat_scene_scale = Matrix.Scale(scene_scale, - 4) - - bpy.ops.mesh.primitive_cube_add(enter_editmode=False, - align='WORLD', - location=(0, 0, 0), - scale=(1, 1, 1)) - - container_obj = bpy.context.active_object - - bbox_verts = calc_bbox_verts((0, 0, 0), container.layers[0].shape) - for i, vert in enumerate(container_obj.data.vertices): - transform = Matrix(container.layers[0].affine) - vert.co = transform @ Vector(bbox_verts[i]) - - container_obj.matrix_world = mat_ras2blender @ mat_scene_scale - container_obj.name = container.name - container_obj.data.name = container.name - container_obj.show_in_front = True - - container_obj.lock_location[0] = True - container_obj.lock_location[1] = True - container_obj.lock_location[2] = True - - container_obj.lock_rotation[0] = True - container_obj.lock_rotation[1] = True - container_obj.lock_rotation[2] = True - - container_obj.lock_scale[0] = True - container_obj.lock_scale[1] = True - container_obj.lock_scale[2] = True - - container_obj['bioxel_container'] = True - container_obj["scene_scale"] = scene_scale - container_obj["step_size"] = step_size - - modifier = container_obj.modifiers.new("GeometryNodes", 'NODES') - node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree') - node_group.interface.new_socket(name="Output", - in_out="OUTPUT", - socket_type="NodeSocketGeometry") - modifier.node_group = node_group - node_group.nodes.new("NodeGroupOutput") - - container_obj = add_layers(container.layers, - container_obj=container_obj, - cache_dir=cache_dir) - - try: - layer_node = get_nodes_by_type( - node_group, "BioxelNodes_FetchLayer")[0] - center_node = add_node_to_graph("ReCenter", - node_group, - use_link=get_use_link()) - - output_node = get_output_node(node_group) - - node_group.links.new(layer_node.outputs[0], - center_node.inputs[0]) - node_group.links.new(center_node.outputs[0], - output_node.inputs[0]) - - move_node_to_node(center_node, layer_node, (300, 0)) - bpy.ops.bioxelnodes.add_slicer('EXEC_DEFAULT') - except: - pass - - return container_obj diff --git a/src/bioxelnodes/bioxelutils/layer.py b/src/bioxelnodes/bioxelutils/layer.py deleted file mode 100644 index f7a0525..0000000 --- a/src/bioxelnodes/bioxelutils/layer.py +++ /dev/null @@ -1,215 +0,0 @@ -import random -import re -import bpy -import numpy as np - -try: - import pyopenvdb as vdb -except: - import openvdb as vdb - -from pathlib import Path -from uuid import uuid4 - -from ..bioxel.layer import Layer -from ..utils import get_use_link -from .node import add_node_to_graph -from .common import (get_layer_prop_value, - move_node_between_nodes) - - -def obj_to_layer(layer_obj: bpy.types.Object): - cache_filepath = Path(bpy.path.abspath(layer_obj.data.filepath)).resolve() - is_sequence = re.search(r'\.\d{4}\.', - cache_filepath.name) is not None - if is_sequence: - cache_path = cache_filepath.parent - data_frames = () - for f in cache_path.iterdir(): - if not f.is_file() or f.suffix != ".vdb": - continue - grids, base_metadata = vdb.readAll(str(f)) - grid = grids[0] - metadata = grid.metadata - if grid["layer_kind"] in ['label', 'scalar']: - data_shape = grid["data_shape"] - else: - data_shape = tuple(list(grid["data_shape"]) + [3]) - data_frame = np.ndarray(data_shape, np.float32) - grid.copyToArray(data_frame) - data_frames += (data_frame,) - data = np.stack(data_frames) - else: - grids, base_metadata = vdb.readAll(str(cache_filepath)) - grid = grids[0] - metadata = grid.metadata - if grid["layer_kind"] in ['label', 'scalar']: - data_shape = grid["data_shape"] - else: - data_shape = tuple(list(grid["data_shape"]) + [3]) - data = np.ndarray(data_shape, np.float32) - grid.copyToArray(data) - data = np.expand_dims(data, axis=0) # expend frame - - name = get_layer_prop_value(layer_obj, "name") \ - or metadata["layer_name"] - kind = get_layer_prop_value(layer_obj, "kind") \ - or metadata["layer_kind"] - affine = metadata["layer_affine"] - dtype = get_layer_prop_value(layer_obj, "dtype") \ - or metadata.get("data_dtype") or "float32" - offset = get_layer_prop_value(layer_obj, "offset") \ - or metadata.get("data_offset") or 0 - - data = data - np.full_like(data, offset) - data = data.astype(dtype) - - if kind in ["scalar", "label"]: - data = np.expand_dims(data, axis=-1) # expend channel - - layer = Layer(data=data, - name=name, - kind=kind, - affine=affine) - - return layer - - -def layer_to_obj(layer: Layer, - container_obj: bpy.types.Object, - cache_dir: str): - - data = layer.data - - # TXYZC > TXYZ - if layer.kind in ['label', 'scalar']: - data = np.amax(data, -1) - - offset = 0 - if layer.kind in ['scalar']: - data = data.astype(np.float32) - orig_min = float(np.min(data)) - if orig_min < 0: - offset = -orig_min - - data = data + np.full_like(data, offset) - - metadata = { - "layer_name": layer.name, - "layer_kind": layer.kind, - "layer_affine": layer.affine.tolist(), - "data_shape": layer.shape, - "data_dtype": layer.data.dtype.str, - "data_offset": offset - } - - layer_display_name = f"{container_obj.name}_{layer.name}" - if layer.frame_count > 1: - print(f"Saving the Cache of {layer.name}...") - vdb_name = str(uuid4()) - sequence_path = Path(cache_dir, vdb_name) - sequence_path.mkdir(parents=True, exist_ok=True) - - cache_filepaths = [] - for f in range(layer.frame_count): - if layer.kind in ['label', 'scalar']: - grid = vdb.FloatGrid() - grid.copyFromArray(data[f, :, :, :].copy().astype(np.float32)) - else: - # color - grid = vdb.Vec3SGrid() - grid.copyFromArray( - data[f, :, :, :, :].copy().astype(np.float32)) - grid.transform = vdb.createLinearTransform( - layer.affine.transpose()) - grid.metadata = metadata - grid.name = layer.kind - - cache_filepath = Path(sequence_path, - f"{vdb_name}.{str(f+1).zfill(4)}.vdb") - vdb.write(str(cache_filepath), grids=[grid]) - cache_filepaths.append(cache_filepath) - - else: - if layer.kind in ['label', 'scalar']: - grid = vdb.FloatGrid() - grid.copyFromArray(data[0, :, :, :].copy().astype(np.float32)) - else: - # color - grid = vdb.Vec3SGrid() - grid.copyFromArray(data[0, :, :, :, :].copy().astype(np.float32)) - grid.transform = vdb.createLinearTransform( - layer.affine.transpose()) - grid.metadata = metadata - grid.name = layer.kind - - print(f"Saving the Cache of {layer.name}...") - cache_filepath = Path(cache_dir, f"{uuid4()}.vdb") - vdb.write(str(cache_filepath), grids=[grid]) - cache_filepaths = [cache_filepath] - - layer_data = bpy.data.volumes.new(layer_display_name) - layer_data.render.space = 'WORLD' - scene_scale = container_obj.get("scene_scale") or 0.01 - step_size = container_obj.get("step_size") or 1 - layer_data.render.step_size = scene_scale * step_size - layer_data.sequence_mode = 'REPEAT' - layer_data.filepath = str(cache_filepaths[0]) - - if layer.frame_count > 1: - layer_data.is_sequence = True - layer_data.frame_duration = layer.frame_count - else: - layer_data.is_sequence = False - - layer_obj = bpy.data.objects.new(layer_display_name, layer_data) - layer_obj['bioxel_layer'] = True - - print(f"Creating Node for {layer.name}...") - modifier = layer_obj.modifiers.new("GeometryNodes", 'NODES') - node_group = bpy.data.node_groups.new('GeometryNodes', 'GeometryNodeTree') - node_group.interface.new_socket(name="Cache", - in_out="INPUT", - socket_type="NodeSocketGeometry") - node_group.interface.new_socket(name="Layer", - in_out="OUTPUT", - socket_type="NodeSocketGeometry") - modifier.node_group = node_group - - layer_node = add_node_to_graph("_Layer", - node_group, - use_link=get_use_link()) - - layer_node.inputs['name'].default_value = layer.name - layer_node.inputs['shape'].default_value = layer.shape - layer_node.inputs['kind'].default_value = layer.kind - - for i in range(layer.affine.shape[1]): - for j in range(layer.affine.shape[0]): - affine_key = f"affine{i}{j}" - layer_node.inputs[affine_key].default_value = layer.affine[j, i] - - layer_node.inputs['unique'].default_value = random.uniform(0, 1) - layer_node.inputs['bioxel_size'].default_value = layer.bioxel_size[0] - layer_node.inputs['dtype'].default_value = layer.dtype.str - layer_node.inputs['dtype_num'].default_value = layer.dtype.num - layer_node.inputs['frame_count'].default_value = layer.frame_count - layer_node.inputs['channel_count'].default_value = layer.channel_count - layer_node.inputs['offset'].default_value = max(0, -layer.min) - layer_node.inputs['min'].default_value = layer.min - layer_node.inputs['max'].default_value = layer.max - - input_node = node_group.nodes.new("NodeGroupInput") - output_node = node_group.nodes.new("NodeGroupOutput") - - node_group.links.new(input_node.outputs[0], - layer_node.inputs[0]) - node_group.links.new(layer_node.outputs[0], - output_node.inputs[0]) - - move_node_between_nodes( - layer_node, [input_node, output_node]) - - layer_obj.parent = container_obj - - return layer_obj diff --git a/src/bioxelnodes/bioxelutils/node.py b/src/bioxelnodes/bioxelutils/node.py deleted file mode 100644 index 57707db..0000000 --- a/src/bioxelnodes/bioxelutils/node.py +++ /dev/null @@ -1,71 +0,0 @@ -from pathlib import Path -import bpy - -from .common import get_file_prop, set_file_prop -from ..exceptions import NoFound - -from ..constants import LATEST_NODE_LIB_PATH, VERSIONS - - -def get_node_tree(node_type: str, use_link=True): - # unannotate below for local debug in node lib file. - # node_group = bpy.data.node_groups[node_type] - # return node_group - - # added node is always from latest node version - addon_version = VERSIONS[0]["node_version"] - addon_lib_path = LATEST_NODE_LIB_PATH - - if get_file_prop("node_version") is None: - set_file_prop("node_version", addon_version) - - local_lib = None - for node_group in bpy.data.node_groups: - if node_group.name.startswith("BioxelNodes"): - lib = node_group.library - if lib: - lib_path = Path(bpy.path.abspath(lib.filepath)).resolve() - if lib_path != addon_lib_path: - local_lib = lib.filepath - break - - # local lib first - lib_path_str = local_lib or str(addon_lib_path) - - with bpy.data.libraries.load(lib_path_str, - link=use_link, - relative=True) as (data_from, data_to): - data_to.node_groups = [n for n in data_from.node_groups - if n == node_type] - - node_tree = data_to.node_groups[0] - - if node_tree is None: - raise NoFound('No custom node found') - - return node_tree - - -def assign_node_tree(node, node_tree): - node.node_tree = node_tree - node.width = 200.0 - node.name = node_tree.name - return node - - -def add_node_to_graph(node_name: str, node_group, node_label=None, use_link=True): - node_type = f"BioxelNodes_{node_name}" - node_label = node_label or node_name - - # Deselect all nodes first - for node in node_group.nodes: - if node.select: - node.select = False - - node_tree = get_node_tree(node_type, use_link) - node = node_group.nodes.new("GeometryNodeGroup") - assign_node_tree(node, node_tree) - - node.label = node_label - node.show_options = False - return node diff --git a/src/bioxelnodes/blender_manifest.toml b/src/bioxelnodes/blender_manifest.toml index 09239a8..d982f0d 100644 --- a/src/bioxelnodes/blender_manifest.toml +++ b/src/bioxelnodes/blender_manifest.toml @@ -1,7 +1,7 @@ schema_version = "1.0.0" id = "bioxelnodes" -version = "1.0.9" +version = "2.0.0" name = "Bioxel Nodes" tagline = "For scientific volumetric data visualization in Blender" maintainer = "Ma Nan " @@ -9,12 +9,30 @@ type = "add-on" website = "https://omoolab.github.io/BioxelNodes/latest" tags = ["Geometry Nodes", "Render", "Import-Export"] -blender_version_min = "4.2.0" +blender_version_min = "5.0.0" license = ['SPDX:GPL-3.0-or-later'] copyright = ["2024 OmooLab"] platforms = ["windows-x64"] -wheels = ["./wheels/h5py-3.11.0-cp311-cp311-win_amd64.whl", "./wheels/lxml-5.3.2-cp311-cp311-win_amd64.whl", "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl", "./wheels/pyometiff-1.0.0-py3-none-any.whl", "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl", "./wheels/tifffile-2024.7.24-py3-none-any.whl", "./wheels/transforms3d-0.4.2-py3-none-any.whl"] +wheels = [ + "./wheels/contourpy-1.3.3-cp311-cp311-win_amd64.whl", + "./wheels/cycler-0.12.1-py3-none-any.whl", + "./wheels/fonttools-4.60.1-cp311-cp311-win_amd64.whl", + "./wheels/h5py-3.11.0-cp311-cp311-win_amd64.whl", + "./wheels/kiwisolver-1.4.9-cp311-cp311-win_amd64.whl", + "./wheels/lxml-6.0.2-cp311-cp311-win_amd64.whl", + "./wheels/matplotlib-3.10.7-cp311-cp311-win_amd64.whl", + "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl", + "./wheels/packaging-25.0-py3-none-any.whl", + "./wheels/pillow-11.2.1-cp311-cp311-win_amd64.whl", + "./wheels/pyometiff-1.0.0-py3-none-any.whl", + "./wheels/pyparsing-3.2.5-py3-none-any.whl", + "./wheels/python_dateutil-2.9.0.post0-py2.py3-none-any.whl", + "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl", + "./wheels/six-1.17.0-py2.py3-none-any.whl", + "./wheels/tifffile-2024.7.24-py3-none-any.whl", + "./wheels/transforms3d-0.4.2-py3-none-any.whl", +] [permissions] -files = "Import/export volume data from/to disk" \ No newline at end of file +files = "Import/export volume data from/to disk" diff --git a/src/bioxelnodes/constants.py b/src/bioxelnodes/constants.py index ed6a0dd..322b703 100644 --- a/src/bioxelnodes/constants.py +++ b/src/bioxelnodes/constants.py @@ -1,257 +1,9 @@ from pathlib import Path -VERSIONS = [{"label": "Latest", "node_version": (1, 0, 7)}, - {"label": "v0.3.x", "node_version": (0, 3, 3)}, - {"label": "v0.2.x", "node_version": (0, 2, 9)}] - NODE_LIB_DIRPATH = Path(Path(__file__).parent, - "assets/Nodes").resolve() - -LATEST_NODE_LIB_PATH = lib_path = Path(NODE_LIB_DIRPATH, - "BioxelNodes_latest.blend").resolve() - -COMPONENT_OUTPUT_NODES = [ - "CutoutByThreshold", - "CutoutByRange", - "CutoutByHue", - "JoinComponent", - "SetProperties", - "SetColor", - "SetColorByColor", - "SetColorByColor", - "SetColorByRamp2", - "SetColorByRamp3", - "SetColorByRamp4", - "SetColorByRamp5", - "Cut", -] + "assets/O Bioxel").resolve() -MENU_ITEMS = [ - { - 'label': 'Component', - 'icon': 'OUTLINER_DATA_VOLUME', - 'items': [ - { - 'label': 'Cutout by Threshold', - 'icon': 'EMPTY_SINGLE_ARROW', - 'name': 'CutoutByThreshold', - 'description': '' - }, - { - 'label': 'Cutout by Range', - 'icon': 'IPO_CONSTANT', - 'name': 'CutoutByRange', - 'description': '' - }, - { - 'label': 'Cutout by Hue', - 'icon': 'COLOR', - 'name': 'CutoutByHue', - 'description': '' - }, - "separator", - { - 'label': 'To Surface', - 'icon': 'MESH_DATA', - 'name': 'ToSurface', - 'description': '' - }, - { - 'label': 'Join Component', - 'icon': 'CONSTRAINT_BONE', - 'name': 'JoinComponent', - 'description': '' - }, - { - 'label': 'Slice', - 'icon': 'TEXTURE', - 'name': 'Slice', - 'description': '' - } - ] - }, - { - 'label': 'Property', - 'icon': 'PROPERTIES', - 'items': [ - { - 'label': 'Set Properties', - 'icon': 'PROPERTIES', - 'name': 'SetProperties', - 'description': '' - }, - "separator", - { - 'label': 'Set Color', - 'icon': 'IPO_SINE', - 'name': 'SetColor', - 'description': '' - }, - { - 'label': 'Set Color by Color', - 'icon': 'IPO_QUINT', - 'name': 'SetColorByColor', - 'description': '' - }, - { - 'label': 'Set Color by Ramp 2', - 'icon': 'IPO_QUAD', - 'name': 'SetColorByRamp2', - 'description': '' - }, - { - 'label': 'Set Color by Ramp 3', - 'icon': 'IPO_CUBIC', - 'name': 'SetColorByRamp3', - 'description': '' - }, - { - 'label': 'Set Color by Ramp 4', - 'icon': 'IPO_QUART', - 'name': 'SetColorByRamp4', - 'description': '' - }, - { - 'label': 'Set Color by Ramp 5', - 'icon': 'IPO_QUINT', - 'name': 'SetColorByRamp5', - 'description': '' - } - ] - }, - { - 'label': 'Surface', - 'icon': 'MESH_DATA', - 'items': [ - { - 'label': 'Membrane Shader', - 'icon': 'NODE_MATERIAL', - 'name': 'AssignMembraneShader', - 'description': '' - }, - { - 'label': 'Solid Shader', - 'icon': 'SHADING_SOLID', - 'name': 'AssignSolidShader', - 'description': '' - }, - { - 'label': 'Slime Shader', - 'icon': 'OUTLINER_DATA_META', - 'name': 'AssignSlimeShader', - 'description': '' - }, +LATEST_NODE_LIB_PATH = Path(NODE_LIB_DIRPATH, + "BioxelNodes.blend").resolve() - ] - }, - { - 'label': 'Transform', - 'icon': 'EMPTY_AXIS', - 'items': [ - { - 'label': 'Transform', - 'icon': 'EMPTY_AXIS', - 'name': 'Transform', - 'description': '' - }, - { - 'label': 'Transform Parent', - 'icon': 'ORIENTATION_PARENT', - 'name': 'TransformParent', - 'description': '' - }, - { - 'label': 'ReCenter', - 'icon': 'PROP_CON', - 'name': 'ReCenter', - 'description': '' - }, - { - 'label': 'Copy Transform', - 'icon': 'EMPTY_AXIS', - 'name': 'CopyTransform', - 'description': '' - }, - { - 'label': 'Extract Transform', - 'icon': 'EMPTY_AXIS', - 'name': 'ExtractTransform', - 'description': '' - }, - ] - }, - { - 'label': 'Cut', - 'icon': 'MOD_BEVEL', - 'items': [ - { - 'label': 'Cut', - 'icon': 'MOD_BEVEL', - 'name': 'Cut', - 'description': '' - }, - "separator", - { - 'label': 'Primitive Cutter', - 'icon': 'MOD_LINEART', - 'name': 'PrimitiveCutter', - 'description': '' - }, - { - 'label': 'Object Cutter', - 'icon': 'MESH_PLANE', - 'name': 'ObjectCutter', - 'description': '' - } - ] - }, - { - 'label': 'Extra', - 'icon': 'MODIFIER', - 'items': [ - { - 'label': 'Fetch Mesh', - 'icon': 'OUTLINER_OB_MESH', - 'name': 'FetchMesh', - 'description': '' - }, - { - 'label': 'Fetch Volume', - 'icon': 'OUTLINER_OB_VOLUME', - 'name': 'FetchVolume', - 'description': '' - }, - { - 'label': 'Fetch Shape Wire', - 'icon': 'FILE_VOLUME', - 'name': 'FetchShapeWire', - 'description': '' - }, - { - 'label': 'Fetch Bbox Wire', - 'icon': 'MESH_CUBE', - 'name': 'FetchBboxWire', - 'description': '' - }, - "separator", - { - 'label': 'Inflate', - 'icon': 'OUTLINER_OB_META', - 'name': 'Inflate', - 'description': '' - }, - { - 'label': 'Smooth', - 'icon': 'MOD_SMOOTH', - 'name': 'Smooth', - 'description': '' - }, - { - 'label': 'Remove Small Island', - 'icon': 'FORCE_LENNARDJONES', - 'name': 'RemoveSmallIsland', - 'description': '' - } - ] - } -] +PREVIEW_COLLECTIONS = {} diff --git a/src/bioxelnodes/exceptions.py b/src/bioxelnodes/exceptions.py index d2de041..c0b8cb2 100644 --- a/src/bioxelnodes/exceptions.py +++ b/src/bioxelnodes/exceptions.py @@ -1,22 +1,6 @@ -class CancelledByUser(Exception): - def __init__(self): - message = 'Cancelled by user' - super().__init__(message) - - -class NoContent(Exception): - def __init__(self, message): - super().__init__(message) - self.message = message - - -class NoFound(Exception): - def __init__(self, message): - super().__init__(message) - self.message = message - - -class Incompatible(Exception): - def __init__(self, message): - super().__init__(message) - self.message = message +# This file is kept for backward compatibility +# Custom exceptions have been replaced with built-in exceptions: +# CancelledByUser -> CancelledError +# NoContent -> ValueError +# NoFound -> LookupError +# Incompatible -> ValueError diff --git a/src/bioxelnodes/layer.py b/src/bioxelnodes/layer.py new file mode 100644 index 0000000..c6fb53d --- /dev/null +++ b/src/bioxelnodes/layer.py @@ -0,0 +1,277 @@ +import json +import time +from typing import Any, List, Dict +from pathlib import Path +import matplotlib.pyplot as plt + +import bpy +import numpy as np +import openvdb as vdb + +from .bioxel.layer import Layer +from .utils import ndarray_to_png + +LAYERS_JSON = "bioxel_layers" + + +def cache_layer_data(layer: Layer, cache_path: str): + """ + Cache the given Layer's data as one or more VDB files. + + - For multi-frame layers, writes per-frame VDB files named data.0001.vdb, data.0002.vdb, ... + - For single-frame layers, writes a single data.vdb file. + - Applies basic type handling: + - label/scalar layers collapse channel dimension via max. + - scalar layers are offset to avoid negative values. + - The VDB grids will have their transform set from layer.affine but no additional metadata is written. + + Parameters: + - layer: Layer object containing ndarray data and metadata. + - cache_path: directory path where VDB files will be written (created if missing). + """ + data = layer.data + + # 处理标量/标签类型（去除通道维度） + if layer.kind in ["label", "scalar"]: + data = np.amax(data, -1) + + # 标量类型偏移处理（避免负值） + offset = 0 + if layer.kind in ["scalar"]: + data = data.astype(np.float32) + orig_min = float(np.min(data)) + if orig_min < 0: + offset = -orig_min + data = data + np.full_like(data, offset) + + # 创建缓存目录 + cache_path = Path(cache_path) + cache_path.mkdir(parents=True, exist_ok=True) + + # 多帧序列处理 + if layer.frame_count > 1: + for f in range(layer.frame_count): + # 根据图层类型创建VDB网格 + if layer.kind in ["label", "scalar"]: + grid = vdb.FloatGrid() + grid.copyFromArray(data[f, :, :, :].copy().astype(np.float32)) + else: # 颜色类型 + grid = vdb.Vec3SGrid() + grid.copyFromArray( + data[f, :, :, :, :].copy().astype(np.float32)) + + # 仅设置transform，不存储metadata + grid.transform = vdb.createLinearTransform( + layer.affine.transpose()) + grid.name = layer.kind + + # 保存序列帧VDB + data_filepath = cache_path / f"data.{str(f+1).zfill(4)}.vdb" + vdb.write(str(data_filepath), grids=[grid]) + + else: + # 单帧处理 + if layer.kind in ["label", "scalar"]: + grid = vdb.FloatGrid() + grid.copyFromArray(data[0, :, :, :].copy().astype(np.float32)) + else: # 颜色类型 + grid = vdb.Vec3SGrid() + grid.copyFromArray(data[0, :, :, :, :].copy().astype(np.float32)) + + # 仅设置transform，不存储metadata + grid.transform = vdb.createLinearTransform(layer.affine.transpose()) + grid.name = layer.kind + + # 保存单帧VDB + data_filepath = cache_path / "data.vdb" + vdb.write(str(data_filepath), grids=[grid]) + + +def cache_layer_snapshot(layer: Layer, cache_path: str): + """ + Create and save a low-resolution snapshot (numpy .npy) of the layer and generate PNG slices. + + - Saves a 3D numpy ndarray snapshot to /snapshot.npy. + - Then creates per-Z PNGs in the same directory via snapshot_to_pngs. + + Parameters: + - layer: Layer to snapshot (expects Layer.snapshot method). + - cache_path: destination directory where snapshot.npy and PNGs will be created. + """ + cache_path = Path(cache_path) + cache_path.mkdir(parents=True, exist_ok=True) + + snapshot_filepath = cache_path / "snapshot.npy" + snapshot = layer.snapshot((64, 64, 32)) + np.save(str(snapshot_filepath), snapshot) + snapshot_to_pngs( + snapshot, str(cache_path), normalize=layer.kind in ["scalar", "vector"] + ) + + if layer.kind in ["scalar", "vector", "color"]: + plt.figure(figsize=(8, 8)) + + def plot_histogram(plt, data, color="black"): + flattened = data.flatten() + x_min = np.percentile(flattened, 1) + x_max = np.percentile(flattened, 99) + + n, bins, _ = plt.hist( + flattened, + bins=50, # 自动根据数据密度调整bins数量（避免空柱） + range=(x_min, x_max), # 只显示核心区域，省略稀疏部分 + alpha=0, + edgecolor="none", # 去除边框，使柱形更紧凑 + ) + bin_centers = 0.5 * (bins[1:] + bins[:-1]) # 计算每个bin的中点 + plt.plot(bin_centers, n, color=color, linewidth=4) # 折线 + plt.fill_between(bin_centers, n, color=color, alpha=0.1) + + if layer.kind == "scalar": + plot_histogram(plt, layer.data[:, :, :, 0], color="black") + elif layer.kind in ["vector", "color"]: + plot_histogram(plt, layer.data[:, :, :, 0], color="tomato") + plot_histogram(plt, layer.data[:, :, :, 1], color="yellowgreen") + plot_histogram(plt, layer.data[:, :, :, 2], color="xkcd:azure") + + plt.yscale("log") + plt.gca().get_yaxis().set_visible(False) + plt.xticks(fontsize=32, rotation=45) # 调整字体大小（数值越大字体越大） + + ax = plt.gca() + ax.spines["top"].set_visible(False) + ax.spines["right"].set_visible(False) + ax.spines["left"].set_visible(False) # 隐藏左边框 + + # 调整布局避免标签被截断 + plt.tight_layout() + + # 保存图片到指定路径 + save_path = cache_path / "histogram.png" + plt.savefig(save_path, bbox_inches="tight", pad_inches=0.1) # 减少边缘留白) + + # 关闭图像释放资源 + plt.close() + + +def snapshot_to_pngs(snapshot, cache_path: str, normalize=False): + """ + Convert a 3D/4D snapshot ndarray into per-slice PNG files. + + - snapshot is expected with axes order X, Y, Z, (C optional). + - Writes files snapshot_0.png ... snapshot_{Z-1}.png into cache_path. + - Uses ndarray_to_png to perform the per-slice conversion. + + Parameters: + - snapshot: numpy ndarray (X, Y, Z[, C]) + - cache_path: directory where generated PNGs are stored. + """ + cache_path = Path(cache_path) + cache_path.mkdir(parents=True, exist_ok=True) + + if normalize: + mn = float(np.percentile(snapshot, 50)) + mx = float(np.percentile(snapshot, 99)) + if mx - mn > 1e-8: + snapshot = (snapshot - mn) / (mx - mn) + else: + snapshot = np.clip(snapshot, 0.0, 1.0) + + shape = snapshot.shape + for zidx in range(shape[2]): + array = snapshot[:, :, zidx, :] + ndarray_to_png(array, str(cache_path / f"snapshot_{zidx}.png")) + + +def get_layer_caches() -> List[Dict[str, Any]]: + """ + Read the saved layer metadata list from Blender's internal text datablock. + + - Looks for a text datablock named by LAYERS_JSON ("bioxel_layers"). + - Returns the parsed list of layer dictionaries if present; otherwise returns an empty list. + + Returns: + - list of layer metadata dictionaries (possibly empty) + """ + # 检查文本数据块是否存在 + if LAYERS_JSON not in bpy.data.texts: + return [] + + # 加载并解析数据 + layers_text = bpy.data.texts[LAYERS_JSON] + try: + layers_data = json.loads(layers_text.as_string()) + # 确保返回格式为列表 + return layers_data if isinstance(layers_data, list) else [] + except: + return [] + + +def set_layer_caches(layers_data: List[Dict[str, Any]]): + """ + Write the provided list of layer metadata dictionaries into the Blender text datablock. + + - Ensures the LAYERS_JSON text datablock exists, then overwrites it with pretty JSON. + + Parameters: + - layers_data: list of serializable dictionaries describing the layers + """ + # 获取或创建文本数据块 + if LAYERS_JSON not in bpy.data.texts: + bpy.data.texts.new(LAYERS_JSON) + layers_text = bpy.data.texts[LAYERS_JSON] + # 写入数据 + layers_text.clear() + layers_text.write(json.dumps(layers_data, indent=4)) + + +def save_layers_to_json(layers: List[Layer], cache_dir: str) -> List[int]: + """ + Save multiple Layer objects into the internal layers text datablock. + + For each layer: + - Generates a unique cache id. + - Writes VDB files and a low-resolution snapshot (.npy) plus PNG slices under cache_dir//. + - Appends an entry describing the layer into the b i o x e l _ l a y e r s text datablock. + + Returns: + - List of generated cache ids for the saved layers. + """ + existing_data = get_layer_caches() + added_ids = [] + + cache_dir_path = Path(cache_dir) + cache_dir_path.mkdir(parents=True, exist_ok=True) + + for idx, layer in enumerate(layers): + cache_id = str(int(time.time())) + str(idx) + cache_path = cache_dir_path / str(cache_id) + cache_layer_data(layer, cache_path) + cache_layer_snapshot(layer, cache_path) + + # build layer_info + cache_info = { + "id": cache_id, + "name": layer.name, + "kind": layer.kind, + "shape": layer.shape, + "affine": layer.affine.tolist(), + "bioxel_size": layer.bioxel_size[0], + "dtype": layer.dtype.str, + "dtype_num": layer.dtype.num, + "frame_count": layer.frame_count, + "channel_count": layer.channel_count, + "offset": max(0, -layer.min), + "min": layer.min, + "max": layer.max, + "path": bpy.path.abspath(str(cache_path)), + "snapshot_z": 0.5, + } + + existing_data.append(cache_info) + added_ids.append(cache_id) + + set_layer_caches(existing_data) + print( + f"Successfully added {len(added_ids)} layers to the internal text datablock") + return added_ids diff --git a/src/bioxelnodes/menus.py b/src/bioxelnodes/menus.py index 7934fd5..18e1afa 100644 --- a/src/bioxelnodes/menus.py +++ b/src/bioxelnodes/menus.py @@ -1,187 +1,40 @@ import bpy - -from .constants import MENU_ITEMS, VERSIONS -from .node_menu import NodeMenu - -from .bioxelutils.common import (get_container_obj, - get_container_layer_objs, get_layer_label, - get_layer_prop_value, get_node_version, is_incompatible) -from .operators.layer import (FetchLayer, RelocateLayer, RetimeLayer, RenameLayer, - RemoveSelectedLayers, SaveSelectedLayersCache, - ResampleLayer, SignScalar, CombineLabels, - FillByLabel, FillByThreshold, FillByRange) -from .operators.container import (AddLocator, AddSlicer, ContainerProps, - SaveContainerLayersCache, RemoveContainerMissingLayers, - SaveContainer, LoadContainer, - AddPieCutter, AddPlaneCutter, - AddCylinderCutter, AddCubeCutter, AddSphereCutter, - ExtractBboxWire, ExtractMesh, ExtractShapeWire, - ExtractNodeMesh, ExtractNodeBboxWire, ExtractNodeShapeWire) - -from .operators.io import (ImportAsLabel, ImportAsScalar, ImportAsColor) -from .operators.misc import (AddEeveeEnv, CleanTemp, Help, - ReLinkNodeLib, RemoveAllMissingLayers, - RenderSettingPreset, SaveAllLayersCache, - SaveNodeLib, SliceViewer) - - -class IncompatibleMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_INCOMPATIBLE" - bl_label = "Bioxel Nodes" - - def draw(self, context): - tip_text = "please downgrade addon version." - node_version = get_node_version() - if node_version: - version_str = "v"+".".join([str(i) for i in list(node_version)]) - tip_text = f"please downgrade addon version to {version_str}." - - layout = self.layout - layout.label(text="Incompatible node version detected.") - layout.separator() - layout.label( - text="If you still want to edit this file with bioxel nodes, ") - layout.label(text=tip_text) - layout.separator() - layout.label(text="If this file is archived, " - "please relink node library, ") - layout.label(text="check if it still works, " - "then save node library.") - layout.separator() - layout.menu(ReLinkNodeLibMenu.bl_idname) - layout.operator(SaveNodeLib.bl_idname) - - layout.separator() - layout.menu(DangerZoneMenu.bl_idname) - - layout.separator() - layout.menu(RenderSettingMenu.bl_idname) - - layout.separator() - layout.operator(Help.bl_idname, - icon=Help.bl_icon) - - -class FetchLayerMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_ADD_LAYER" - bl_label = "Fetch Layer" - - def draw(self, context): - container_obj = get_container_obj(bpy.context.active_object) - layer_objs = get_container_layer_objs(container_obj) - layout = self.layout - - for layer_obj in layer_objs: - op = layout.operator(FetchLayer.bl_idname, - text=get_layer_label(layer_obj)) - op.layer_obj_name = layer_obj.name - - -class ExtractFromContainerMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_PICK" - bl_label = "Extract from Container" - - def draw(self, context): - layout = self.layout - layout.operator(ExtractMesh.bl_idname) - layout.operator(ExtractShapeWire.bl_idname) - layout.operator(ExtractBboxWire.bl_idname) - - -class AddCutterMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_CUTTERS" - bl_label = "Add a Cutter" - - def draw(self, context): - layout = self.layout - layout.operator(AddPlaneCutter.bl_idname, - icon=AddPlaneCutter.bl_icon, text="Plane Cutter") - layout.operator(AddCylinderCutter.bl_idname, - icon=AddCylinderCutter.bl_icon, text="Cylinder Cutter") - layout.operator(AddCubeCutter.bl_idname, - icon=AddCubeCutter.bl_icon, text="Cube Cutter") - layout.operator(AddSphereCutter.bl_idname, - icon=AddSphereCutter.bl_icon, text="Sphere Cutter") - layout.operator(AddPieCutter.bl_idname, - icon=AddPieCutter.bl_icon, text="Pie Cutter") +from .operators.structure import ExtractMesh + +from .operators.io import ImportAsLabel, ImportAsScalar, ImportAsColor +from .operators.misc import ( + CleanTemp, + Help, + RenderSettingPreset, + TogglePhantom, +) class ImportLayerMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_IMPORTLAYER" + bl_idname = "BIOXEL_MT_IMPORTLAYER" bl_label = "Import Volumetric Data (Init)" bl_icon = "FILE_NEW" def draw(self, context): layout = self.layout - layout.operator(ImportAsScalar.bl_idname, - text="as Scalar") - layout.operator(ImportAsLabel.bl_idname, - text="as Label") - layout.operator(ImportAsColor.bl_idname, - text="as Color") - - -class AddLayerMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_ADDLAYER" - bl_label = "Import Volumetric Data (Add)" - bl_icon = "FILE_NEW" - - def draw(self, context): - layout = self.layout - layout.operator(ImportAsScalar.bl_idname, - text="as Scalar") - layout.operator(ImportAsLabel.bl_idname, - text="as Label") - layout.operator(ImportAsColor.bl_idname, - text="as Color") - - -class ModifyLayerMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_MODIFYLAYER" - bl_label = "Modify Layer" - bl_icon = "FILE_NEW" - - def draw(self, context): - layout = self.layout - layout.operator(SignScalar.bl_idname, - icon=SignScalar.bl_icon) - layout.operator(FillByThreshold.bl_idname, - icon=FillByThreshold.bl_icon) - layout.operator(FillByRange.bl_idname, - icon=FillByRange.bl_icon) - layout.operator(FillByLabel.bl_idname, - icon=FillByLabel.bl_icon) - layout.operator(CombineLabels.bl_idname, - icon=CombineLabels.bl_icon) - - -class ReLinkNodeLibMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_RELINK" - bl_label = "Relink Node Library" - - def draw(self, context): - layout = self.layout - - for index, version in enumerate(VERSIONS): - op = layout.operator(ReLinkNodeLib.bl_idname, - text=version["label"]) - op.index = index + layout.operator(ImportAsScalar.bl_idname, text="as Scalar") + layout.operator(ImportAsLabel.bl_idname, text="as Label") + layout.operator(ImportAsColor.bl_idname, text="as Color") class RenderSettingMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_RENDER" + bl_idname = "BIOXEL_MT_RENDER" bl_label = "Render Setting Presets" def draw(self, context): layout = self.layout for k, v in RenderSettingPreset.PRESETS.items(): - op = layout.operator(RenderSettingPreset.bl_idname, - text=v) + op = layout.operator(RenderSettingPreset.bl_idname, text=v) op.preset = k class DangerZoneMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_DANGER" + bl_idname = "BIOXEL_MT_DANGER" bl_label = "Danger Zone" def draw(self, context): @@ -190,118 +43,44 @@ def draw(self, context): class BioxelNodesTopbarMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_TOPBAR" + bl_idname = "BIOXEL_MT_TOPBAR" bl_label = "Bioxel Nodes" def draw(self, context): layout = self.layout - layout.menu(ImportLayerMenu.bl_idname, - icon=ImportLayerMenu.bl_icon) - layout.operator(LoadContainer.bl_idname) - - layout.separator() - layout.operator(SaveAllLayersCache.bl_idname) - layout.operator(RemoveAllMissingLayers.bl_idname) - - layout.separator() - layout.menu(ReLinkNodeLibMenu.bl_idname) - layout.operator(SaveNodeLib.bl_idname) - layout.separator() layout.menu(DangerZoneMenu.bl_idname) layout.separator() - layout.operator(AddEeveeEnv.bl_idname) - layout.menu(RenderSettingMenu.bl_idname) + layout.operator(Help.bl_idname, icon=Help.bl_icon) - layout.separator() - layout.operator(Help.bl_idname, - icon=Help.bl_icon) - - -def TOPBAR(self, context): - layout = self.layout - if is_incompatible(): - layout.menu(IncompatibleMenu.bl_idname) - else: - layout.menu(BioxelNodesTopbarMenu.bl_idname) - - -class NodeHeadMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_NODE_HEAD" +class NodeContextMenu(bpy.types.Menu): + bl_idname = "BIOXEL_MT_NODE_CONTEXT" bl_label = "Bioxel Nodes" bl_icon = "FILE_VOLUME" def draw(self, context): - layout = self.layout - layout.menu(AddLayerMenu.bl_idname, - icon=AddLayerMenu.bl_icon) - layout.operator(SaveContainer.bl_idname) - - layout.separator() - layout.operator(ContainerProps.bl_idname) - layout.menu(ExtractFromContainerMenu.bl_idname) - - layout.separator() - layout.operator(SaveContainerLayersCache.bl_idname, - icon=SaveContainerLayersCache.bl_icon) - layout.operator(RemoveContainerMissingLayers.bl_idname) - - layout.separator() - layout.operator(AddLocator.bl_idname, - icon=AddLocator.bl_icon) - layout.operator(AddSlicer.bl_idname, - icon=AddSlicer.bl_icon) - layout.menu(AddCutterMenu.bl_idname) - - layout.separator() - layout.menu(FetchLayerMenu.bl_idname) + layout.operator(ExtractMesh.bl_idname) -class NodeContextMenu(bpy.types.Menu): - bl_idname = "BIOXELNODES_MT_NODE_CONTEXT" +class ObjectContextMenu(bpy.types.Menu): + bl_idname = "BIOXEL_MT_OBJECT_CONTEXT" bl_label = "Bioxel Nodes" bl_icon = "FILE_VOLUME" def draw(self, context): layout = self.layout - layout.operator(ExtractNodeMesh.bl_idname) - layout.operator(ExtractNodeShapeWire.bl_idname) - layout.operator(ExtractNodeBboxWire.bl_idname) - - layout.separator() - layout.operator(SaveSelectedLayersCache.bl_idname, - icon=SaveSelectedLayersCache.bl_icon) - layout.operator(RemoveSelectedLayers.bl_idname) - - layout.separator() - layout.operator(RenameLayer.bl_idname, - icon=RenameLayer.bl_icon) - layout.operator(RetimeLayer.bl_idname) - layout.operator(RelocateLayer.bl_idname) - - layout.separator() - layout.operator(ResampleLayer.bl_idname, - icon=ResampleLayer.bl_icon) - layout.operator(SignScalar.bl_idname) - layout.operator(FillByThreshold.bl_idname) - layout.operator(FillByRange.bl_idname) - layout.operator(FillByLabel.bl_idname) - layout.operator(CombineLabels.bl_idname) + layout.operator(TogglePhantom.bl_idname) def NODE_CONTEXT(self, context): - if is_incompatible(): - return - container_obj = context.object is_geo_nodes = context.area.ui_type == "GeometryNodeTree" - is_container = get_container_obj(container_obj) - if not is_geo_nodes or not is_container: + if not is_geo_nodes or not container_obj: return layout = self.layout @@ -309,127 +88,18 @@ def NODE_CONTEXT(self, context): layout.menu(NodeContextMenu.bl_idname) -def NODE_HEAD(self, context): - if is_incompatible(): - return - - container_obj = context.object - is_geo_nodes = context.area.ui_type == "GeometryNodeTree" - is_container = get_container_obj(container_obj) - - if not is_geo_nodes or not is_container: - return - +# 定义添加到右键菜单的函数，放在首位 +def OBJECT_CONTEXT(self, context): layout = self.layout layout.separator() - layout.menu(NodeHeadMenu.bl_idname) - - -def NODE_PROP(self, context): - if is_incompatible(): - return - - container_obj = context.object - is_geo_nodes = context.area.ui_type == "GeometryNodeTree" - is_container = get_container_obj(container_obj) - self.bl_label = "Group" - - if not is_geo_nodes or not is_container: - return - - if container_obj.modifiers[0].node_group != context.space_data.edit_tree: - return - - self.bl_label = "Bioxel Nodes" - - layer_list_UL = bpy.context.window_manager.bioxelnodes_layer_list_UL - layer_list = layer_list_UL.layer_list - layer_list.clear() - - for layer_obj in get_container_layer_objs(container_obj): - layer_item = layer_list.add() - layer_item.label = get_layer_label(layer_obj) - layer_item.obj_name = layer_obj.name - layer_item.info_text = "\n".join([f"{prop}: {get_layer_prop_value(layer_obj, prop)}" - for prop in ["kind", - "bioxel_size", - "shape", - "frame_count", - "channel_count", - "min", "max"]]) - - layout = self.layout - layout.label(text="Layer List") - split = layout.row() - split.template_list(listtype_name="BIOXELNODES_UL_layer_list", - list_id="layer_list", - dataptr=layer_list_UL, - propname="layer_list", - active_dataptr=layer_list_UL, - active_propname="layer_list_active", - item_dyntip_propname="info_text", - rows=20) - - # sidebar = split.column(align=True) - # sidebar.menu(AddLayerMenu.bl_idname, - # icon=AddLayerMenu.bl_icon, text="") - - # sidebar.operator(SaveContainerLayersCache.bl_idname, - # icon=SaveContainerLayersCache.bl_icon, text="") - # sidebar.operator(RemoveContainerMissingLayers.bl_idname, - # icon=RemoveContainerMissingLayers.bl_icon, text="") - - # sidebar.separator() - # sidebar.operator(SaveSelectedLayersCache.bl_idname, - # icon=SaveSelectedLayersCache.bl_icon, text="") - # sidebar.operator(RemoveSelectedLayers.bl_idname, - # icon=RemoveSelectedLayers.bl_icon, text="") - - # sidebar.separator() - # sidebar.operator(RenameLayer.bl_idname, - # icon=RenameLayer.bl_icon, text="") - # sidebar.operator(ResampleLayer.bl_idname, - # icon=ResampleLayer.bl_icon, text="") - # sidebar.operator(RetimeLayer.bl_idname, - # icon=RetimeLayer.bl_icon, text="") - - # sidebar.separator() - # sidebar.operator(SignScalar.bl_idname, - # icon=SignScalar.bl_icon, text="") - # sidebar.operator(FillByThreshold.bl_idname, - # icon=FillByThreshold.bl_icon, text="") - # sidebar.operator(FillByRange.bl_idname, - # icon=FillByRange.bl_icon, text="") - # sidebar.operator(FillByLabel.bl_idname, - # icon=FillByLabel.bl_icon, text="") - - # sidebar.separator() - # layout.separator() - - -def VIEW3D_TOPBAR(self, context): - layout = self.layout - layout.operator(SliceViewer.bl_idname) - - -node_menu = NodeMenu( - menu_items=MENU_ITEMS -) + layout.menu(ObjectContextMenu.bl_idname) def add(): - node_menu.register() - # bpy.types.VIEW3D_HT_header.append(VIEW3D_TOPBAR) - bpy.types.TOPBAR_MT_editor_menus.append(TOPBAR) - bpy.types.NODE_PT_node_tree_properties.prepend(NODE_PROP) - bpy.types.NODE_MT_editor_menus.append(NODE_HEAD) - bpy.types.NODE_MT_context_menu.append(NODE_CONTEXT) + bpy.types.VIEW3D_MT_object_context_menu.append(OBJECT_CONTEXT) + # bpy.types.NODE_MT_context_menu.append(NODE_CONTEXT) def remove(): - # bpy.types.VIEW3D_HT_header.remove(VIEW3D_TOPBAR) - bpy.types.TOPBAR_MT_editor_menus.remove(TOPBAR) - bpy.types.NODE_PT_node_tree_properties.remove(NODE_PROP) - bpy.types.NODE_MT_editor_menus.remove(NODE_HEAD) - bpy.types.NODE_MT_context_menu.remove(NODE_CONTEXT) - node_menu.unregister() + bpy.types.VIEW3D_MT_object_context_menu.remove(OBJECT_CONTEXT) + # bpy.types.NODE_MT_context_menu.remove(NODE_CONTEXT) diff --git a/src/bioxelnodes/node.py b/src/bioxelnodes/node.py new file mode 100644 index 0000000..566bee6 --- /dev/null +++ b/src/bioxelnodes/node.py @@ -0,0 +1,149 @@ +from pathlib import Path +import bpy + +# LookupError replaced with built-in LookupError +from .constants import LATEST_NODE_LIB_PATH + + +def move_node_to_node(node, target_node, offset=(0, 0)): + node.location.x = target_node.location.x + offset[0] + node.location.y = target_node.location.y + offset[1] + + +def move_node_between_nodes(node, target_nodes, offset=(0, 0)): + xs = [] + ys = [] + for target_node in target_nodes: + xs.append(target_node.location.x) + ys.append(target_node.location.y) + + node.location.x = sum(xs) / len(xs) + offset[0] + node.location.y = sum(ys) / len(ys) + offset[1] + + +def get_node_type(node): + node_type = type(node).__name__ + if node_type == "GeometryNodeGroup": + node_type = node.node_tree.name + + return node_type + + +def get_nodes_by_type(node_group, type_name: str): + return [node for node in node_group.nodes if get_node_type(node) == type_name] + + +def get_node_tree(node_type: str, use_link=True): + try: + return bpy.data.node_groups[node_type] + except KeyError: + lib_path_str = str(LATEST_NODE_LIB_PATH) + with bpy.data.libraries.load(lib_path_str, link=use_link, relative=True) as ( + data_from, + data_to, + ): + data_to.node_groups = [ + n for n in data_from.node_groups if n == node_type] + node_tree = data_to.node_groups[0] + + if node_tree is None: + raise LookupError("No custom node found") + + return node_tree + + +def assign_node_tree(node, node_tree): + node.node_tree = node_tree + node.width = 200.0 + node.name = node_tree.name + return node + + +def add_node_to_graph(node_name: str, node_group, node_label=None, use_link=True): + node_type = f"O {node_name}" + node_label = node_label or node_name + + # Deselect all nodes first + for node in node_group.nodes: + if node.select: + node.select = False + + node_tree = get_node_tree(node_type, use_link) + node = node_group.nodes.new("GeometryNodeGroup") + assign_node_tree(node, node_tree) + + node.label = node_label + node.show_options = False + bpy.ops.node.view_selected() + return node + + +def get_output_node(node_group): + try: + output_node = get_nodes_by_type(node_group, "NodeGroupOutput")[0] + except: + output_node = node_group.nodes.new("NodeGroupOutput") + + return output_node + + +def add_bioxel_node(name: str): + # bpy.ops.node.add_group_asset( + # asset_library_type="CUSTOM", + # asset_library_identifier = "O Bioxel", + # relative_asset_identifier = "NodeTreO Crop Layer" + # ) + # bpy.ops.node.add_group_asset( + # asset_library_type="CUSTOM", + # asset_library_identifier="O Bioxel", + # relative_asset_identifier="Nodes.blend\\NodeTree\\O Render Structure" + # ) + + try: + node_tree = bpy.data.node_groups[name] + except KeyError: + bpy.ops.object.modifier_add_node_group( + asset_library_type="CUSTOM", + asset_library_identifier="O Bioxel", + relative_asset_identifier=f"Nodes.blend\\NodeTree\\{name}", + ) + bpy.ops.object.modifier_remove(modifier=name) + try: + node_tree = bpy.data.node_groups[name] + except Exception as e: + raise e + + bpy.ops.node.add_node( + "INVOKE_DEFAULT", type="GeometryNodeGroup", use_transform=True + ) + + node = bpy.context.active_node + node.node_tree = node_tree + node.show_options = False + + return bpy.context.active_node + + +def get_layer_nodes(node_group): + """Return all O Layer nodes in the given node_tree.""" + return [ + n + for n in node_group.nodes + if n.bl_idname == "GeometryNodeGroup" + and getattr(n, "node_tree", None) + and n.node_tree.name.startswith("O Layer") + ] + + +def get_main_node_group(context): + space = getattr(context, "space_data", None) or getattr( + context, "space", None) + if not space: + return None + node_tree = getattr(space, "node_tree", None) + if not node_tree: + return None + # accept GeometryNodeTree by bl_idname or class name for compatibility + if getattr(node_tree, "bl_idname", "") == "GeometryNodeTree" or node_tree.__class__.__name__ == "GeometryNodeTree": + return node_tree + return None diff --git a/src/bioxelnodes/node_menu.py b/src/bioxelnodes/node_menu.py deleted file mode 100644 index f64cd5b..0000000 --- a/src/bioxelnodes/node_menu.py +++ /dev/null @@ -1,87 +0,0 @@ -import bpy -from .operators.node import AddNode - - -class NodeMenu(): - def __init__( - self, - menu_items, - ) -> None: - - self.menu_items = menu_items - self.class_prefix = f"BIOXELNODES_MT" - root_label = "Bioxel Nodes" - menu_classes = [] - self._create_menu_class( - items=menu_items, - label=root_label, - menu_classes=menu_classes - ) - self.menu_classes = menu_classes - - idname = f"{self.class_prefix}_{root_label.replace(' ', '').upper()}" - icon = "FILE_VOLUME" - - def drew_menu(self, context): - if (bpy.context.area.spaces[0].tree_type == 'GeometryNodeTree'): - layout = self.layout - layout.separator() - layout.menu(idname, - icon=icon) - self.drew_menu = drew_menu - - def _create_menu_class(self, menu_classes, items, label='CustomNodes', icon=0, idname_namespace=None): - idname_namespace = idname_namespace or self.class_prefix - idname = f"{idname_namespace}_{label.replace(' ', '').upper()}" - - # create submenu class if item is menu. - for item in items: - item_items = item.get('items') if item != 'separator' else None - if item_items: - menu_class = self._create_menu_class( - menu_classes=menu_classes, - items=item_items, - label=item.get('label') or 'CustomNodes', - icon=item.get('icon') or 0, - idname_namespace=idname - ) - item['menu_class'] = menu_class - - # create menu class - class Menu(bpy.types.Menu): - bl_idname = idname - bl_label = label - - def draw(self, context): - layout = self.layout - for item in items: - if item == "separator": - layout.separator() - elif item.get('menu_class'): - layout.menu( - item.get('menu_class').bl_idname, - icon=item.get('icon') or 'NONE' - ) - else: - op = layout.operator( - AddNode.bl_idname, - text=item.get('label'), - icon=item.get('icon') or 'NONE' - ) - op.node_name = item['name'] - op.node_label = item.get('label') or "" - op.node_description = item.get( - 'node_description') or "" - - menu_classes.append(Menu) - return Menu - - def register(self): - for cls in self.menu_classes: - bpy.utils.register_class(cls) - bpy.types.NODE_MT_add.append(self.drew_menu) - - def unregister(self): - bpy.types.NODE_MT_add.remove(self.drew_menu) - for cls in reversed(self.menu_classes): - bpy.utils.unregister_class(cls) diff --git a/src/bioxelnodes/operators/container.py b/src/bioxelnodes/operators/container.py deleted file mode 100644 index d4dad97..0000000 --- a/src/bioxelnodes/operators/container.py +++ /dev/null @@ -1,649 +0,0 @@ -import bpy - - -import bmesh - -from ..constants import COMPONENT_OUTPUT_NODES -from ..utils import get_cache_dir, get_use_link, select_object -from ..bioxel.io import load_container, save_container -from ..bioxelutils.container import container_to_obj, obj_to_container -from ..bioxelutils.node import add_node_to_graph -from ..bioxelutils.common import (get_container_layer_objs, get_container_obj, get_node_type, - get_nodes_by_type, get_output_node, is_missing_layer, - move_node_between_nodes, - move_node_to_node, - get_all_layer_objs) -from .layer import RemoveLayers, SaveLayersCache - - -class SaveContainer(bpy.types.Operator): - bl_idname = "bioxelnodes.save_container" - bl_label = "Save Container (.bioxel) (BETA)" - bl_description = "Clean all caches saved in temp" - - filepath: bpy.props.StringProperty( - subtype="FILE_PATH" - ) # type: ignore - - filename_ext = ".bioxel" - - def execute(self, context): - container_obj = get_container_obj(context.object) - - if container_obj is None: - self.report({"WARNING"}, "Cannot find any bioxel container.") - return {'FINISHED'} - - container = obj_to_container(container_obj) - save_path = f"{self.filepath.split('.')[0]}.bioxel" - save_container(container, save_path, overwrite=True) - - self.report({"INFO"}, f"Successfully save to {save_path}") - return {'FINISHED'} - - def invoke(self, context, event): - context.window_manager.fileselect_add(self) - return {'RUNNING_MODAL'} - - -class LoadContainer(bpy.types.Operator): - bl_idname = "bioxelnodes.load_container" - bl_label = "Load Container (.bioxel) (BETA)" - bl_description = "Clean all caches saved in temp" - - filepath: bpy.props.StringProperty( - subtype="FILE_PATH" - ) # type: ignore - - filename_ext = ".bioxel" - - def execute(self, context): - load_path = self.filepath - container = load_container(self.filepath) - is_first_import = len(get_all_layer_objs()) == 0 - - container_obj = container_to_obj(container, - scene_scale=0.01, - cache_dir=get_cache_dir()) - select_object(container_obj) - - if is_first_import: - bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT', - preset="preview_c") - - self.report({"INFO"}, f"Successfully load {load_path}") - return {'FINISHED'} - - def invoke(self, context, event): - context.window_manager.fileselect_add(self) - return {'RUNNING_MODAL'} - - -class ExtractNodeObject(): - bl_options = {'UNDO'} - - def execute(self, context): - container_obj = get_container_obj(context.object) - - if container_obj is None: - self.report({"WARNING"}, "Cannot find any bioxel container.") - return {'FINISHED'} - - # nodes = [node for node in context.selected_nodes - # if get_node_type(node).removeprefix("BioxelNodes_") in COMPONENT_OUTPUT_NODES] - - if len(context.selected_nodes) == 0: - self.report({"WARNING"}, "No node selected.") - return {'FINISHED'} - - selected_node = context.selected_nodes[0] - container_node_group = container_obj.modifiers[0].node_group - - container_output_node = get_output_node(container_node_group) - - if len(container_output_node.inputs[0].links) == 0: - pre_socket = None - else: - pre_socket = container_output_node.inputs[0].links[0].from_socket - - container_node_group.links.new(selected_node.outputs[0], - container_output_node.inputs[0]) - - bpy.ops.mesh.primitive_cube_add( - size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) - obj = bpy.context.active_object - - obj.name = f"{container_obj.name}_{self.object_type}" - - bpy.ops.node.new_geometry_nodes_modifier() - modifier = obj.modifiers[0] - node_group = modifier.node_group - - output_node = get_nodes_by_type(node_group, 'NodeGroupOutput')[0] - fetch_mesh_node = add_node_to_graph(f"Fetch{self.object_type}", - node_group, - node_label=f"Fetch {self.object_type}", - use_link=get_use_link()) - - fetch_mesh_node.inputs[0].default_value = container_obj - node_group.links.new(fetch_mesh_node.outputs[0], output_node.inputs[0]) - - for modifier in obj.modifiers: - bpy.ops.object.modifier_apply(modifier=modifier.name) - - obj.data.materials.clear() - - if pre_socket: - container_node_group.links.new(pre_socket, - container_output_node.inputs[0]) - - select_object(obj) - - self.report({"INFO"}, f"Successfully picked") - - return {'FINISHED'} - - -class ExtractNodeMesh(bpy.types.Operator, ExtractNodeObject): - bl_idname = "bioxelnodes.extract_node_mesh" - bl_label = "Extract Mesh" - bl_description = "Extract Mesh" - bl_icon = "OUTLINER_OB_MESH" - object_type = "Mesh" - - -class ExtractNodeShapeWire(bpy.types.Operator, ExtractNodeObject): - bl_idname = "bioxelnodes.extract_node_shape_wire" - bl_label = "Extract Shape Wire" - bl_description = "Extract Shape Wire" - bl_icon = "FILE_VOLUME" - object_type = "ShapeWire" - - -class ExtractNodeBboxWire(bpy.types.Operator, ExtractNodeObject): - bl_idname = "bioxelnodes.extract_node_bbox_wire" - bl_label = "Extract Bbox Wire" - bl_description = "Extract Bbox Wire" - bl_icon = "MESH_CUBE" - object_type = "BboxWire" - - -class ExtractObject(): - bl_options = {'UNDO'} - - def execute(self, context): - container_obj = get_container_obj(context.object) - - if container_obj is None: - self.report({"WARNING"}, "Cannot find any bioxel container.") - return {'FINISHED'} - - bpy.ops.mesh.primitive_cube_add( - size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) - obj = bpy.context.active_object - - obj.name = f"{container_obj.name}_{self.object_type}" - - bpy.ops.node.new_geometry_nodes_modifier() - modifier = obj.modifiers[0] - node_group = modifier.node_group - - output_node = get_output_node(node_group) - - fetch_mesh_node = add_node_to_graph(f"Fetch{self.object_type}", - node_group, - node_label=f"Fetch {self.object_type}", - use_link=get_use_link()) - - fetch_mesh_node.inputs[0].default_value = container_obj - - if self.object_type == "Mesh": - node_group.links.new( - fetch_mesh_node.outputs[0], output_node.inputs[0]) - else: - curve_to_mesh_node = node_group.nodes.new( - "GeometryNodeCurveToMesh") - node_group.links.new( - fetch_mesh_node.outputs[0], curve_to_mesh_node.inputs[0]) - node_group.links.new( - curve_to_mesh_node.outputs[0], output_node.inputs[0]) - - for modifier in obj.modifiers: - bpy.ops.object.modifier_apply(modifier=modifier.name) - - obj.data.materials.clear() - - select_object(obj) - - self.report({"INFO"}, f"Successfully picked") - - return {'FINISHED'} - - -class ExtractMesh(bpy.types.Operator, ExtractObject): - bl_idname = "bioxelnodes.extract_mesh" - bl_label = "Extract Mesh" - bl_description = "Extract Mesh" - bl_icon = "OUTLINER_OB_MESH" - object_type = "Mesh" - - -class ExtractShapeWire(bpy.types.Operator, ExtractObject): - bl_idname = "bioxelnodes.extract_shape_wire" - bl_label = "Extract Shape Wire" - bl_description = "Extract Shape Wire" - bl_icon = "FILE_VOLUME" - object_type = "ShapeWire" - - -class ExtractBboxWire(bpy.types.Operator, ExtractObject): - bl_idname = "bioxelnodes.extract_bbox_wire" - bl_label = "Extract Bbox Wire" - bl_description = "Extract Bbox Wire" - bl_icon = "MESH_CUBE" - object_type = "BboxWire" - - -class AddCutter(): - bl_options = {'UNDO'} - - def execute(self, context): - container_obj = get_container_obj(context.object) - - if container_obj is None: - self.report({"WARNING"}, "Cannot find any bioxel container.") - return {'FINISHED'} - # TODO: do not use operator to create obj - if self.cutter_type == "plane": - bpy.ops.mesh.primitive_plane_add( - size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) - elif self.cutter_type == "cylinder": - bpy.ops.mesh.primitive_cylinder_add( - radius=1, depth=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) - bpy.context.object.rotation_euler[0] = container_obj.rotation_euler[0] - elif self.cutter_type == "cube": - bpy.ops.mesh.primitive_cube_add( - size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) - elif self.cutter_type == "sphere": - bpy.ops.mesh.primitive_ico_sphere_add( - radius=1, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) - elif self.cutter_type == "pie": - bpy.ops.mesh.primitive_plane_add( - size=2, enter_editmode=False, align='WORLD', location=(0, 0, 0), scale=(1, 1, 1)) - pie_obj = bpy.context.active_object - orig_data = pie_obj.data - - # Create mesh - pie_mesh = bpy.data.meshes.new('Pie') - pie_obj.data = pie_mesh - bpy.data.meshes.remove(orig_data) - - # # Create object - # pie = bpy.data.objects.new('Pie', pie_mesh) - - # # Link object to scene - # bpy.context.scene.collection.objects.link(pie) - - # Get a BMesh representation - bm = bmesh.new() # create an empty BMesh - bm.from_mesh(pie_mesh) # fill it in from a Mesh - - # Hot to create vertices - v_0 = bm.verts.new((0.0, -1.0, 0.0)) - v_1 = bm.verts.new((-1.0, -1.0, 1.0)) - v_2 = bm.verts.new((0.0, 1.0, 0.0)) - v_3 = bm.verts.new((-1.0, 1.0, 1.0)) - v_4 = bm.verts.new((1.0, -1.0, 1.0)) - v_5 = bm.verts.new((1.0, 1.0, 1.0)) - - # Initialize the index values of this sequence. - bm.verts.index_update() - - # How to create a face - # it's not necessary to create the edges before, I made it only to show how create - # edges too - bm.faces.new((v_0, v_1, v_3, v_2)) - bm.faces.new((v_0, v_2, v_5, v_4)) - - # Finish up, write the bmesh back to the mesh - bm.to_mesh(pie_mesh) - # bpy.context.view_layer.objects.active = pie - - cutter_obj = bpy.context.active_object - - # vcos = [container_obj.matrix_world @ - # v.co for v in container_obj.data.vertices] - - # def find_center(l): return (max(l) + min(l)) / 2 - - # x, y, z = [[v[i] for v in vcos] for i in range(3)] - # center = [find_center(axis) for axis in [x, y, z]] - - # cutter_obj.location = center - name = f"{self.cutter_type.capitalize()}_Cutter" - cutter_obj.name = name - cutter_obj.data.name = name - cutter_obj.visible_camera = False - cutter_obj.visible_diffuse = False - cutter_obj.visible_glossy = False - cutter_obj.visible_transmission = False - cutter_obj.visible_volume_scatter = False - cutter_obj.visible_shadow = False - cutter_obj.hide_render = True - cutter_obj.display_type = 'WIRE' - cutter_obj.lineart.usage = 'EXCLUDE' - - select_object(container_obj) - - modifier = container_obj.modifiers[0] - node_group = modifier.node_group - - cut_nodes = get_nodes_by_type(node_group, - 'BioxelNodes_Cut') - if len(cut_nodes) == 0: - cutter_node = add_node_to_graph("ObjectCutter", - node_group, - node_label=f"{self.cutter_type.capitalize()} Cutter", - use_link=get_use_link()) - cutter_node.inputs[0].default_value = self.cutter_type.capitalize() - cutter_node.inputs[1].default_value = cutter_obj - - cut_node = add_node_to_graph("Cut", - node_group, - use_link=get_use_link()) - - output_node = get_output_node(node_group) - - if len(output_node.inputs[0].links) == 0: - node_group.links.new(cut_node.outputs[0], - output_node.inputs[0]) - move_node_to_node(cut_node, output_node, (-300, 0)) - else: - pre_output_node = output_node.inputs[0].links[0].from_node - node_group.links.new(pre_output_node.outputs[0], - cut_node.inputs[0]) - node_group.links.new(cut_node.outputs[0], - output_node.inputs[0]) - move_node_between_nodes(cut_node, - [pre_output_node, output_node]) - - node_group.links.new(cutter_node.outputs[0], - cut_node.inputs[1]) - - move_node_to_node(cutter_node, cut_node, (-300, -300)) - else: - bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT', - node_name="ObjectCutter", - node_label=name) - node = bpy.context.active_node - node.inputs[0].default_value = self.cutter_type.capitalize() - node.inputs[1].default_value = cutter_obj - - return {'FINISHED'} - - -class AddPlaneCutter(bpy.types.Operator, AddCutter): - bl_idname = "bioxelnodes.add_plane_cutter" - bl_label = "Add a Plane Cutter" - bl_description = "Add a plane cutter to current container" - bl_icon = "MESH_PLANE" - cutter_type = "plane" - - -class AddCylinderCutter(bpy.types.Operator, AddCutter): - bl_idname = "bioxelnodes.add_cylinder_cutter" - bl_label = "Add a Cylinder Cutter" - bl_description = "Add a cylinder cutter to current container" - bl_icon = "MESH_CYLINDER" - cutter_type = "cylinder" - - -class AddCubeCutter(bpy.types.Operator, AddCutter): - bl_idname = "bioxelnodes.add_cube_cutter" - bl_label = "Add a Cube Cutter" - bl_description = "Add a cube cutter to current container" - bl_icon = "MESH_CUBE" - cutter_type = "cube" - - -class AddSphereCutter(bpy.types.Operator, AddCutter): - bl_idname = "bioxelnodes.add_sphere_cutter" - bl_label = "Add a Sphere Cutter" - bl_description = "Add a sphere cutter to current container" - bl_icon = "MESH_UVSPHERE" - cutter_type = "sphere" - - -class AddPieCutter(bpy.types.Operator, AddCutter): - bl_idname = "bioxelnodes.add_pie_cutter" - bl_label = "Add a Pie Cutter" - bl_description = "Add a pie cutter to current container" - bl_icon = "MESH_CONE" - cutter_type = "pie" - - -class AddSlicer(bpy.types.Operator): - bl_idname = "bioxelnodes.add_slicer" - bl_label = "Add a Slicer" - bl_description = "Add a slicer to current container" - bl_icon = "TEXTURE" - bl_options = {'UNDO'} - - def execute(self, context): - container_obj = get_container_obj(context.object) - - if container_obj is None: - self.report({"WARNING"}, "Cannot find any bioxel container.") - return {'FINISHED'} - - bpy.ops.mesh.primitive_plane_add(size=2, - enter_editmode=False, - align='WORLD', - location=(0, 0, 0), - scale=(1, 1, 1)) - - slicer_obj = bpy.context.active_object - slicer_obj.name = "Slicer" - slicer_obj.data.name = "Slicer" - - slicer_obj.visible_camera = False - slicer_obj.visible_diffuse = False - slicer_obj.visible_glossy = False - slicer_obj.visible_transmission = False - slicer_obj.visible_volume_scatter = False - slicer_obj.visible_shadow = False - slicer_obj.hide_render = True - slicer_obj.display_type = 'WIRE' - slicer_obj.lineart.usage = 'EXCLUDE' - - select_object(container_obj) - - modifier = container_obj.modifiers[0] - node_group = modifier.node_group - - slice_node = add_node_to_graph("Slice", - node_group, - use_link=get_use_link()) - - slice_node.inputs[1].default_value = slicer_obj - - output_node = get_output_node(node_group) - - if len(output_node.inputs[0].links) == 0: - node_group.links.new(slice_node.outputs[0], - output_node.inputs[0]) - move_node_to_node(slice_node, output_node, (-300, 0)) - else: - pre_output_node = output_node.inputs[0].links[0].from_node - node_group.links.new(pre_output_node.outputs[0], - slice_node.inputs[0]) - node_group.links.new(slice_node.outputs[0], - output_node.inputs[0]) - move_node_between_nodes(slice_node, - [pre_output_node, output_node]) - - return {'FINISHED'} - - -class AddLocator(bpy.types.Operator): - bl_idname = "bioxelnodes.add_locator" - bl_label = "Add a Locator" - bl_description = "Add a locator to current container" - bl_icon = "EMPTY_AXIS" - bl_options = {'UNDO'} - - def execute(self, context): - container_obj = get_container_obj(context.object) - - if container_obj is None: - self.report({"WARNING"}, "Cannot find any bioxel container.") - return {'FINISHED'} - - bpy.ops.object.empty_add(type='ARROWS', - align='WORLD', - location=(0, 0, 0), - scale=(1, 1, 1)) - - locator_obj = bpy.context.active_object - locator_obj.name = "Locator" - select_object(container_obj) - - modifier = container_obj.modifiers[0] - node_group = modifier.node_group - try: - selected_node = context.selected_nodes[0] - except: - selected_node = None - - parent_node = add_node_to_graph("TransformParent", - node_group, - node_label="Transform Parent", - use_link=get_use_link()) - - parent_node.inputs[1].default_value = locator_obj - - if selected_node is None or len(selected_node.outputs) == 0: - output_node = get_output_node(node_group) - if len(output_node.inputs[0].links) == 0: - node_group.links.new(parent_node.outputs[0], - output_node.inputs[0]) - move_node_to_node(parent_node, output_node, (-300, 0)) - else: - pre_output_node = output_node.inputs[0].links[0].from_node - node_group.links.new(pre_output_node.outputs[0], - parent_node.inputs[0]) - node_group.links.new(parent_node.outputs[0], - output_node.inputs[0]) - move_node_between_nodes(parent_node, - [pre_output_node, output_node]) - else: - try: - to_node = selected_node.outputs[0].links[0].to_node - except: - to_node = None - - if to_node is None: - node_group.links.new(selected_node.outputs[0], - parent_node.inputs[0]) - move_node_to_node(parent_node, selected_node, (300, 0)) - else: - node_group.links.new(selected_node.outputs[0], - parent_node.inputs[0]) - node_group.links.new(parent_node.outputs[0], - to_node.inputs[0]) - move_node_between_nodes(parent_node, - [selected_node, to_node]) - - return {'FINISHED'} - - -class ContainerProps(bpy.types.Operator): - bl_idname = "bioxelnodes.container_props" - bl_label = "Change Container Properties" - bl_description = "Change current ontainer properties" - bl_icon = "FILE_TICK" - bl_options = {'UNDO'} - - scene_scale: bpy.props.FloatProperty(name="Scene Scale", - soft_min=0.0001, soft_max=10.0, - min=1e-6, max=1e6, - default=0.01) # type: ignore - - step_size: bpy.props.FloatProperty(name="Step Size", - soft_min=0.1, soft_max=100.0, - min=0.1, max=1e2, - default=1) # type: ignore - - def execute(self, context): - container_obj = get_container_obj(context.object) - - if container_obj is None: - self.report({"WARNING"}, "Cannot find any bioxel container.") - return {'FINISHED'} - - container_obj.scale[0] = self.scene_scale - container_obj.scale[1] = self.scene_scale - container_obj.scale[2] = self.scene_scale - container_obj["scene_scale"] = self.scene_scale - container_obj["step_size"] = self.step_size - - for layer_obj in get_container_layer_objs(container_obj): - layer_obj.data.render.space = 'WORLD' - layer_obj.data.render.step_size = self.scene_scale * self.step_size - - return {'FINISHED'} - - def invoke(self, context, event): - container_obj = get_container_obj(context.object) - - if container_obj is None: - return self.execute(context) - else: - self.scene_scale = container_obj.get("scene_scale") or 0.01 - self.step_size = container_obj.get("step_size") or 1 - context.window_manager.invoke_props_dialog(self) - return {'RUNNING_MODAL'} - - -def get_container_layers(context, layer_filter=None): - def _layer_filter(layer_obj, context): - return True - - layer_filter = layer_filter or _layer_filter - container_obj = context.object - layer_objs = get_container_layer_objs(container_obj) - return [obj for obj in layer_objs if layer_filter(obj, context)] - - -class SaveContainerLayersCache(bpy.types.Operator, SaveLayersCache): - bl_idname = "bioxelnodes.save_container_layers_cache" - bl_label = "Save Container Layers' Cache" - bl_description = "Save all current container layers' cache to directory." - bl_icon = "FILE_TICK" - - success_msg = "Successfully saved all container layers." - - def get_layers(self, context): - def is_not_missing(layer_obj, context): - return not is_missing_layer(layer_obj) - return get_container_layers(context, is_not_missing) - - -class RemoveContainerMissingLayers(bpy.types.Operator, RemoveLayers): - bl_idname = "bioxelnodes.remove_container_missing_layers" - bl_label = "Remove Container Missing Layers" - bl_description = "Remove all current container missing layers" - bl_icon = "BRUSH_DATA" - - success_msg = "Successfully removed all container missing layers." - - def get_layers(self, context): - def is_missing(layer_obj, context): - return is_missing_layer(layer_obj) - return get_container_layers(context, is_missing) - - def invoke(self, context, event): - context.window_manager.invoke_confirm(self, - event, - message=f"Are you sure to remove all **Missing** layers?") - return {'RUNNING_MODAL'} diff --git a/src/bioxelnodes/operators/io.py b/src/bioxelnodes/operators/io.py index 0fce9cf..96e1b5f 100644 --- a/src/bioxelnodes/operators/io.py +++ b/src/bioxelnodes/operators/io.py @@ -1,145 +1,168 @@ import math -import bpy import shutil import threading -import numpy as np from pathlib import Path +import bpy +import numpy as np +import SimpleITK as sitk +import transforms3d -from ..exceptions import CancelledByUser -from ..props import BIOXELNODES_Series -from ..bioxelutils.common import (get_all_layer_objs, get_container_obj, - get_layer_obj, is_incompatible) -from ..bioxelutils.container import (Container, - add_layers, - container_to_obj) -from ..bioxel.layer import Layer -from ..bioxel.parse import (DICOM_EXTS, SUPPORT_EXTS, - get_ext, parse_volumetric_data) +# KeyboardInterrupt replaced with built-in KeyboardInterrupt +from ..props import BIOXEL_Series +from ..utils import get_layer_obj, wrapped_label -from ..utils import (get_cache_dir, progress_update, progress_bar, - select_object) +from ..bioxel.layer import Layer +from ..bioxel.parse import DICOM_EXTS, SUPPORT_EXTS, get_ext, parse_volumetric_data -# 3rd-party -import SimpleITK as sitk -import transforms3d +from ..utils import get_cache_dir, progress_update, progress_bar +from ..layer import get_layer_caches, save_layers_to_json def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple): - shape = (int(orig_shape[0] / bioxel_size * orig_spacing[0]), - int(orig_shape[1] / bioxel_size * orig_spacing[1]), - int(orig_shape[2] / bioxel_size * orig_spacing[2])) + shape = ( + int(orig_shape[0] / bioxel_size * orig_spacing[0]), + int(orig_shape[1] / bioxel_size * orig_spacing[1]), + int(orig_shape[2] / bioxel_size * orig_spacing[2]), + ) - return (shape[0] if shape[0] > 0 else 1, - shape[1] if shape[1] > 0 else 1, - shape[2] if shape[2] > 0 else 1) + return ( + shape[0] if shape[0] > 0 else 1, + shape[1] if shape[1] > 0 else 1, + shape[2] if shape[2] > 0 else 1, + ) def get_layer_size(shape: tuple, bioxel_size: float, scale: float = 1.0): - size = (float(shape[0] * bioxel_size * scale), - float(shape[1] * bioxel_size * scale), - float(shape[2] * bioxel_size * scale)) + size = ( + float(shape[0] * bioxel_size * scale), + float(shape[1] * bioxel_size * scale), + float(shape[2] * bioxel_size * scale), + ) return size """ -ImportVolumetricData - -> ParseVolumetricData -> ImportVolumetricDataDialog -FH_ImportVolumetricData - - start import parse data execute import +ImportData -> ParseVolumetricData -> ImportDataDialog + start import parse data execute import """ -class ImportVolumetricData(): - bl_options = {'UNDO'} - +class ImportDataBase: + bl_options = {"UNDO"} filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore + read_as = None - read_as = "SCALAR" + def draw(self, context): + """ + Display helpful information in the file browser's properties region + when the file selector is open for this operator. + """ + layout = self.layout + exts_list = sorted(SUPPORT_EXTS) + layout.label(text="Supported formats:") + chunk_size = 6 # adjust per-line count to taste + for i in range(0, len(exts_list), chunk_size): + layout.label(text=" ".join(exts_list[i : i + chunk_size])) + + layout.separator() + layout.label(text="Tips:") + wrapped_label( + layout, "- Use 'Import Data' button in Bioxel panel to import data" + ) + wrapped_label( + layout, "- Use 'Import as ...' to choose data type (Scalar/Label/Color)" + ) + wrapped_label( + layout, "- If the file contains multiple series, select series after open" + ) def execute(self, context): data_path = Path(self.filepath).resolve() ext = get_ext(data_path) if ext not in SUPPORT_EXTS: self.report({"WARNING"}, "Not supported format.") - return {'CANCELLED'} + return {"CANCELLED"} + + if self.read_as is None: + bpy.ops.bioxel.parse_volumetric_data( + "INVOKE_DEFAULT", filepath=self.filepath, skip_read_as=False + ) + else: - bpy.ops.bioxelnodes.parse_volumetric_data('INVOKE_DEFAULT', - filepath=self.filepath, - skip_read_as=True, - read_as=self.read_as) + bpy.ops.bioxel.parse_volumetric_data( + "INVOKE_DEFAULT", + filepath=self.filepath, + skip_read_as=True, + read_as=self.read_as, + ) - return {'FINISHED'} + return {"FINISHED"} def invoke(self, context, event): context.window_manager.fileselect_add(self) - return {'RUNNING_MODAL'} + return {"RUNNING_MODAL"} -class ImportAsScalar(bpy.types.Operator, ImportVolumetricData): - bl_idname = "bioxelnodes.import_as_scalar" +class ImportData(bpy.types.Operator, ImportDataBase): + bl_idname = "bioxel.import_data" + bl_label = "Import Data" + bl_description = "Import Volumetric Data to Layer" + bl_icon = "EVENT_S" + + +class ImportAsScalar(bpy.types.Operator, ImportDataBase): + bl_idname = "bioxel.import_as_scalar" bl_label = "Import as Scalar" bl_description = "Import Volumetric Data to Container as Scalar" bl_icon = "EVENT_S" read_as = "SCALAR" -class ImportAsLabel(bpy.types.Operator, ImportVolumetricData): - bl_idname = "bioxelnodes.import_as_label" +class ImportAsLabel(bpy.types.Operator, ImportDataBase): + bl_idname = "bioxel.import_as_label" bl_label = "Import as Label" bl_description = "Import Volumetric Data to Container as Label" bl_icon = "EVENT_L" read_as = "LABEL" -class ImportAsColor(bpy.types.Operator, ImportVolumetricData): - bl_idname = "bioxelnodes.import_as_color" +class ImportAsColor(bpy.types.Operator, ImportDataBase): + bl_idname = "bioxel.import_as_color" bl_label = "Import as Color" bl_description = "Import Volumetric Data to Container as Color" bl_icon = "EVENT_C" read_as = "COLOR" -class BIOXELNODES_FH_ImportVolumetricData(bpy.types.FileHandler): - bl_idname = "BIOXELNODES_FH_ImportVolumetricData" +class BIOXELNODES_FH_ImportData(bpy.types.FileHandler): + bl_idname = "BIOXELNODES_FH_ImportData" bl_label = "File handler for dicom import" - bl_import_operator = "bioxelnodes.parse_volumetric_data" + bl_import_operator = "bioxel.parse_volumetric_data" bl_file_extensions = ";".join(SUPPORT_EXTS) @classmethod def poll_drop(cls, context): - if not context.area: - return False - - if context.area.type == 'VIEW_3D': - return True - elif context.area.type == 'NODE_EDITOR': - container_obj = get_container_obj(context.object) - return container_obj is not None - else: - return False + return ( + bpy.context.area.type == "NODE_EDITOR" + and bpy.context.space_data.node_tree.bl_idname == "GeometryNodeTree" + ) def get_series_ids(self, context): items = [] for index, series_id in enumerate(self.series_ids): - items.append(( - series_id.id, - series_id.label, - "", - index - )) + items.append((series_id.id, series_id.label, "", index)) return items class ParseVolumetricData(bpy.types.Operator): - bl_idname = "bioxelnodes.parse_volumetric_data" + bl_idname = "bioxel.parse_volumetric_data" bl_label = "Import Volumetric Data (BioxelNodes)" bl_description = "Import Volumetric Data as Layer" - bl_options = {'UNDO'} + bl_options = {"UNDO"} meta = None label_count = 0 @@ -147,62 +170,53 @@ class ParseVolumetricData(bpy.types.Operator): thread = None _timer = None - progress: bpy.props.FloatProperty(name="Progress", - options={"SKIP_SAVE"}, - default=1) # type: ignore + progress: bpy.props.FloatProperty( + name="Progress", options={"SKIP_SAVE"}, default=1 + ) # type: ignore filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore - skip_read_as: bpy.props.BoolProperty(name="Skip Read As", - default=False, - options={"SKIP_SAVE"}) # type: ignore + skip_read_as: bpy.props.BoolProperty( + name="Skip Read As", default=False, options={"SKIP_SAVE"} + ) # type: ignore - skip_series_select: bpy.props.BoolProperty(name="Skip Sries Select", - default=True, - options={"SKIP_SAVE"}) # type: ignore + skip_series_select: bpy.props.BoolProperty( + name="Skip Sries Select", default=True, options={"SKIP_SAVE"} + ) # type: ignore - read_as: bpy.props.EnumProperty(name="Read as", - default="SCALAR", - items=[("SCALAR", "Scalar", ""), - ("LABEL", "Label", ""), - ("COLOR", "Color", "")]) # type: ignore + read_as: bpy.props.EnumProperty( + name="Read as", + default="SCALAR", + items=[ + ("SCALAR", "Scalar", ""), + ("LABEL", "Label", ""), + ("COLOR", "Color", ""), + ], + ) # type: ignore - series_id: bpy.props.EnumProperty(name="Select Series", - items=get_series_ids) # type: ignore + series_id: bpy.props.EnumProperty( + name="Select Series", items=get_series_ids + ) # type: ignore - series_ids: bpy.props.CollectionProperty( - type=BIOXELNODES_Series) # type: ignore + series_ids: bpy.props.CollectionProperty(type=BIOXEL_Series) # type: ignore def execute(self, context): - if is_incompatible(): - self.report({"ERROR"}, - "Current addon verison is not compatible to this file. If you insist on editing this file please keep the same addon version") - return {'CANCELLED'} - - if not self.filepath: - self.report({"WARNING"}, "No file selected.") - return {'CANCELLED'} - - data_path = Path(self.filepath).resolve() - ext = get_ext(data_path) - if ext not in SUPPORT_EXTS: - self.report({"WARNING"}, "Not supported format.") - return {'CANCELLED'} - print("Collecting Meta Data...") def parse_volumetric_data_func(self, context, cancel): def progress_callback(factor, text): if cancel(): - raise CancelledByUser + raise KeyboardInterrupt("Cancelled by user") progress_update(context, factor, text) try: series_id = self.series_id if self.series_id != "empty" else "" - data, meta = parse_volumetric_data(data_file=self.filepath, - series_id=series_id, - progress_callback=progress_callback) - except CancelledByUser: + data, meta = parse_volumetric_data( + data_file=self.filepath, + series_id=series_id, + progress_callback=progress_callback, + ) + except KeyboardInterrupt: return except Exception as e: self.has_error = e @@ -220,38 +234,41 @@ def progress_callback(factor, text): self.has_error = None # Create the thread - self.thread = threading.Thread(target=parse_volumetric_data_func, - args=(self, context, lambda: self.is_cancelled)) + self.thread = threading.Thread( + target=parse_volumetric_data_func, + args=(self, context, lambda: self.is_cancelled), + ) # Start the thread self.thread.start() # Add a timmer for modal - self._timer = context.window_manager.event_timer_add(time_step=0.1, - window=context.window) + self._timer = context.window_manager.event_timer_add( + time_step=0.1, window=context.window + ) # Append progress bar to status bar bpy.types.STATUSBAR_HT_header.append(progress_bar) # Start modal handler context.window_manager.modal_handler_add(self) - return {'RUNNING_MODAL'} + return {"RUNNING_MODAL"} def modal(self, context, event): # Check if user press 'ESC' - if event.type == 'ESC': + if event.type == "ESC": self.is_cancelled = True progress_update(context, 0.0, "Canceling...") - return {'PASS_THROUGH'} + return {"PASS_THROUGH"} # Check if is the timer time - if event.type != 'TIMER': - return {'PASS_THROUGH'} + if event.type != "TIMER": + return {"PASS_THROUGH"} # Force update status bar bpy.context.workspace.status_text_set_internal(None) # Check if thread is still running if self.thread.is_alive(): - return {'PASS_THROUGH'} + return {"PASS_THROUGH"} # Release the thread self.thread.join() @@ -264,7 +281,7 @@ def modal(self, context, event): # Check if thread is cancelled by user if self.is_cancelled: self.report({"WARNING"}, "Canncelled by user.") - return {'CANCELLED'} + return {"CANCELLED"} # Check if thread is cancelled by user if self.has_error: @@ -273,7 +290,7 @@ def modal(self, context, event): # Check if has return if self.meta is None: self.report({"ERROR"}, "Some thing went wrong.") - return {'CANCELLED'} + return {"CANCELLED"} # If not canncelled... for key, value in self.meta.items(): @@ -282,14 +299,14 @@ def modal(self, context, event): if self.read_as == "LABEL": if self.label_count > 100 or self.dtype.kind not in ["i", "u"]: self.report({"ERROR"}, "Invaild label data.") - return {'CANCELLED'} + return {"CANCELLED"} if self.label_count == 0: self.report({"ERROR"}, "Get no label.") - return {'CANCELLED'} + return {"CANCELLED"} - orig_shape = self.meta['xyz_shape'] - orig_spacing = self.meta['spacing'] + orig_shape = self.meta["xyz_shape"] + orig_spacing = self.meta["spacing"] min_log10 = math.floor(math.log10(min(*orig_spacing))) max_log10 = math.floor(math.log10(max(*orig_spacing))) @@ -297,82 +314,75 @@ def modal(self, context, event): # max_space = max(*orig_spacing) if orig_spacing[2] == 1 and min_log10 < -1: - orig_spacing = (orig_spacing[0] * math.pow(10, -min_log10-2), - orig_spacing[1] * math.pow(10, -min_log10-2), - 1) + orig_spacing = ( + orig_spacing[0] * math.pow(10, -min_log10 - 2), + orig_spacing[1] * math.pow(10, -min_log10 - 2), + 1, + ) elif min_log10 > 0: - orig_spacing = (orig_spacing[0] * math.pow(10, -min_log10-1), - orig_spacing[1] * math.pow(10, -min_log10-1), - orig_spacing[2] * math.pow(10, -min_log10-1)) + orig_spacing = ( + orig_spacing[0] * math.pow(10, -min_log10 - 1), + orig_spacing[1] * math.pow(10, -min_log10 - 1), + orig_spacing[2] * math.pow(10, -min_log10 - 1), + ) elif max_log10 < 0: - orig_spacing = (orig_spacing[0] * math.pow(10, -max_log10-1), - orig_spacing[1] * math.pow(10, -max_log10-1), - orig_spacing[2] * math.pow(10, -max_log10-1)) + orig_spacing = ( + orig_spacing[0] * math.pow(10, -max_log10 - 1), + orig_spacing[1] * math.pow(10, -max_log10 - 1), + orig_spacing[2] * math.pow(10, -max_log10 - 1), + ) bioxel_size = max(min(*orig_spacing), 1.0) - layer_shape = get_layer_shape(bioxel_size, - orig_shape, - orig_spacing) - layer_size = get_layer_size(layer_shape, - bioxel_size, - 0.01) + layer_shape = get_layer_shape(bioxel_size, orig_shape, orig_spacing) + layer_size = get_layer_size(layer_shape, bioxel_size, 0.01) min_log10 = math.floor(math.log10(min(*layer_size))) max_log10 = math.floor(math.log10(max(*layer_size))) if min_log10 > 0: - scene_scale = math.pow(10, -min_log10-2) + scene_scale = math.pow(10, -min_log10 - 2) elif max_log10 < 0: - scene_scale = math.pow(10, -max_log10-2) + scene_scale = math.pow(10, -max_log10 - 2) else: scene_scale = 0.01 - if context.area.type == "NODE_EDITOR": - container_obj = context.object - container_name = container_obj.name - container_obj_name = container_name - else: - container_name = self.meta['name'] - container_obj_name = "" - series_id = self.series_id if self.series_id != "empty" else "" - bpy.ops.bioxelnodes.import_volumetric_data_dialog( - 'INVOKE_DEFAULT', + bpy.ops.bioxel.import_volumetric_data_dialog( + "INVOKE_DEFAULT", filepath=self.filepath, - container_name=container_name, - layer_name=self.meta['description'], + layer_name=self.meta["description"], orig_shape=orig_shape, orig_spacing=orig_spacing, bioxel_size=bioxel_size, series_id=series_id, - frame_count=self.meta['frame_count'], - channel_count=self.meta['channel_count'], - container_obj_name=container_obj_name, + frame_count=self.meta["frame_count"], + channel_count=self.meta["channel_count"], read_as=self.read_as, label_count=self.label_count, - scene_scale=scene_scale + scene_scale=scene_scale, ) self.report({"INFO"}, "Successfully Readed.") - return {'FINISHED'} + return {"FINISHED"} def invoke(self, context, event): # why not report in execute? # If this operator is executing, a new execute will when pre-one done. - if context.window_manager.bioxelnodes_progress_factor < 1: + if context.window_manager.bioxel_progress_factor < 1: print("A process is executing, please wait for it to finish.") - return {'CANCELLED'} + return {"CANCELLED"} if not self.filepath: - return self.execute(context) + self.report({"WARNING"}, "No file selected.") + return {"CANCELLED"} data_path = Path(self.filepath).resolve() ext = get_ext(data_path) + if ext not in SUPPORT_EXTS: + self.report({"WARNING"}, "Not supported format.") + return {"CANCELLED"} - if context.area.type == "NODE_EDITOR": - title = f"Add to **{context.object.name}**" - else: - title = "Init a Container" + title = f"Add to **{context.object.name}**" # Series Selection if ext in DICOM_EXTS: @@ -386,7 +396,8 @@ def invoke(self, context, event): for series_id in series_ids: series_files = reader.GetGDCMSeriesFileNames( - str(data_dirpath), series_id) + str(data_dirpath), series_id + ) single = sitk.ImageFileReader() single.SetFileName(series_files[0]) single.LoadPrivateTagsOn() @@ -395,10 +406,12 @@ def invoke(self, context, event): def get_meta(key): try: stirng = single.GetMetaData(key).removesuffix(" ") - stirng.encode('utf-8') - if stirng in ["No study description", - "No series description", - ""]: + stirng.encode("utf-8") + if stirng in [ + "No study description", + "No series description", + "", + ]: return "Unknown" else: return stirng @@ -421,8 +434,10 @@ def get_meta(key): if series_id == "": series_id = "empty" - label = "{:<20} {:>1}".format(f"{study_description}>{series_description}({series_modality})", - f"({size_x}x{size_y})x{count}") + label = "{:<20} {:>1}".format( + f"{study_description}>{series_description}({series_modality})", + f"({size_x}x{size_y})x{count}", + ) series_items[series_id] = label @@ -433,32 +448,27 @@ def get_meta(key): if len(series_items.keys()) > 1: self.skip_series_select = False - context.window_manager.invoke_props_dialog(self, - width=400, - title=title) - return {'RUNNING_MODAL'} + context.window_manager.invoke_props_dialog(self, width=400, title=title) + return {"RUNNING_MODAL"} elif len(series_items.keys()) == 1: self.series_id = list(series_items.keys())[0] else: self.report({"ERROR"}, "Get no vaild series.") - return {'CANCELLED'} + return {"CANCELLED"} if self.skip_read_as: return self.execute(context) else: - context.window_manager.invoke_props_dialog(self, - width=400, - title=title) - return {'RUNNING_MODAL'} + context.window_manager.invoke_props_dialog(self, width=400, title=title) + return {"RUNNING_MODAL"} def draw(self, context): layout = self.layout if not self.skip_read_as: - layout.label( - text='What kind is the data read as?') + layout.label(text="What kind is the data read as?") layout.prop(self, "read_as") if not self.skip_series_select: - layout.label(text='Which series to import?') + layout.label(text="Which series to import?") layout.prop(self, "series_id") @@ -477,66 +487,63 @@ def get_frame_sources(self, context): return items -class ImportVolumetricDataDialog(bpy.types.Operator): - bl_idname = "bioxelnodes.import_volumetric_data_dialog" +class ImportDataDialog(bpy.types.Operator): + bl_idname = "bioxel.import_volumetric_data_dialog" bl_label = "Import Volumetric Data" bl_description = "Import Volumetric Data as Layer" - bl_options = {'UNDO'} + bl_options = {"UNDO"} layers = None thread = None _timer = None filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore - - container_name: bpy.props.StringProperty( - name="Container Name") # type: ignore - - layer_name: bpy.props.StringProperty(name="Layer Name") # type: ignore - - series_id: bpy.props.StringProperty() # type: ignore - - container_obj_name: bpy.props.StringProperty() # type: ignore - + layer_name: bpy.props.StringProperty(name="Layer Name") # type: ignore + series_id: bpy.props.StringProperty() # type: ignore frame_count: bpy.props.IntProperty() # type: ignore - channel_count: bpy.props.IntProperty() # type: ignore - label_count: bpy.props.IntProperty() # type: ignore - - smooth: bpy.props.IntProperty(name="Smooth Size (Larger takes longer time)", - default=0) # type: ignore - - read_as: bpy.props.EnumProperty(name="Read as", - default="SCALAR", - items=[("SCALAR", "Scalar", ""), - ("LABEL", "Label", ""), - ("COLOR", "Color", "")]) # type: ignore - - bioxel_size: bpy.props.FloatProperty(name="Bioxel Size (Larger size means small resolution)", - soft_min=0.1, soft_max=10.0, - min=0.1, max=1e2, - default=1) # type: ignore - - orig_spacing: bpy.props.FloatVectorProperty(name="Original Spacing", - default=(1, 1, 1)) # type: ignore - - orig_shape: bpy.props.IntVectorProperty(name="Original Shape", - default=(100, 100, 100)) # type: ignore - - scene_scale: bpy.props.FloatProperty(name="Scene Scale (Bioxel Unit pre Blender Unit)", - soft_min=0.0001, soft_max=10.0, - min=1e-6, max=1e6, - default=0.01) # type: ignore - - remap: bpy.props.BoolProperty(name="Remap to 0~1", - default=False) # type: ignore - - split_channel: bpy.props.BoolProperty(name="Split Channels", - default=False) # type: ignore - - frame_source: bpy.props.EnumProperty(name="Frame From", - items=get_frame_sources) # type: ignore + smooth: bpy.props.IntProperty( + name="Smooth Size (Larger takes longer time)", default=0 + ) # type: ignore + read_as: bpy.props.EnumProperty( + name="Read as", + default="SCALAR", + items=[ + ("SCALAR", "Scalar", ""), + ("LABEL", "Label", ""), + ("COLOR", "Color", ""), + ], + ) # type: ignore + bioxel_size: bpy.props.FloatProperty( + name="Bioxel Size (Larger size means small resolution)", + soft_min=0.1, + soft_max=10.0, + min=0.1, + max=1e2, + default=1, + ) # type: ignore + orig_spacing: bpy.props.FloatVectorProperty( + name="Original Spacing", default=(1, 1, 1) + ) # type: ignore + orig_shape: bpy.props.IntVectorProperty( + name="Original Shape", default=(100, 100, 100) + ) # type: ignore + scene_scale: bpy.props.FloatProperty( + name="Scene Scale (Bioxel Unit pre Blender Unit)", + soft_min=0.0001, + soft_max=10.0, + min=1e-6, + max=1e6, + default=0.01, + ) # type: ignore + remap: bpy.props.BoolProperty(name="Remap to 0~1", default=False) # type: ignore + split_channel: bpy.props.BoolProperty( + name="Split Channels", default=False + ) # type: ignore + frame_source: bpy.props.EnumProperty( + name="Frame From", items=get_frame_sources + ) # type: ignore def execute(self, context): def import_volumetric_data_func(self, context, cancel): @@ -544,14 +551,32 @@ def import_volumetric_data_func(self, context, cancel): def progress_callback(factor, text): if cancel(): - raise CancelledByUser - progress_update(context, factor*0.2, text) + raise KeyboardInterrupt("Cancelled by user") + progress_update(context, factor * 0.2, text) + + def progress_callback_factory(layer_name, progress, progress_step): + def progress_callback(frame, total): + if cancel(): + raise KeyboardInterrupt("Cancelled by user") + sub_progress_step = progress_step / total + sub_progress = progress + frame * sub_progress_step + progress_update( + context, + sub_progress, + f"Processing {layer_name} Frame {frame+1}...", + ) + print(f"Processing {layer_name} Frame {frame+1}...") + + return progress_callback try: - data, meta = parse_volumetric_data(data_file=self.filepath, - series_id=self.series_id, - progress_callback=progress_callback) - except CancelledByUser: + data, meta = parse_volumetric_data( + data_file=self.filepath, + series_id=self.series_id, + progress_callback=progress_callback, + ) + + except KeyboardInterrupt: return except Exception as e: self.has_error = e @@ -560,12 +585,12 @@ def progress_callback(factor, text): if cancel(): return - shape = get_layer_shape(self.bioxel_size, - self.orig_shape, - self.orig_spacing) + shape = get_layer_shape( + self.bioxel_size, self.orig_shape, self.orig_spacing + ) mat_scale = transforms3d.zooms.zfdir2aff(self.bioxel_size) - affine = np.dot(meta['affine'], mat_scale) + affine = np.dot(meta["affine"], mat_scale) kind = self.read_as.lower() if cancel(): @@ -593,51 +618,39 @@ def progress_callback(factor, text): # channel as frame data = data.transpose(4, 1, 2, 3, 0) - def progress_callback_factory(layer_name, progress, progress_step): - def progress_callback(frame, total): - if cancel(): - raise CancelledByUser - sub_progress_step = progress_step/total - sub_progress = progress + frame * sub_progress_step - progress_update(context, sub_progress, - f"Processing {layer_name} Frame {frame+1}...") - print(f"Processing {layer_name} Frame {frame+1}...") - return progress_callback - layers = [] if kind == "label": name = self.layer_name or "Label" data = data.astype(int) label_count = int(np.max(data)) - progress_step = 0.7/label_count + progress_step = 0.7 / label_count for i in range(label_count): if cancel(): return name_i = f"{name}_{i+1}" - progress = 0.2+i*progress_step - progress_update(context, progress, - f"Processing {name_i}...") - - progress_callback = progress_callback_factory(name_i, - progress, - progress_step) - label_data = data == np.full_like(data, i+1) + progress = 0.2 + i * progress_step + progress_update(context, progress, f"Processing {name_i}...") + + progress_callback = progress_callback_factory( + name_i, progress, progress_step + ) + label_data = data == np.full_like(data, i + 1) # label_data = label_data.astype(np.float32) try: - layer = Layer(data=label_data, - name=name_i, - kind=kind) + layer = Layer(data=label_data, name=name_i, kind=kind) - layer.resize(shape=shape, - smooth=self.smooth, - progress_callback=progress_callback) + layer.resize( + shape=shape, + smooth=self.smooth, + progress_callback=progress_callback, + ) layer.affine = affine layers.append(layer) - except CancelledByUser: + except KeyboardInterrupt: return except Exception as e: self.has_error = e @@ -645,9 +658,8 @@ def progress_callback(frame, total): if kind == "color": if np.issubdtype(np.uint8, data.dtype): - data = np.multiply(data, 1.0 / 256, - dtype=np.float32) - elif data.dtype.kind in ['u', 'i']: + data = np.multiply(data, 1.0 / 256, dtype=np.float32) + elif data.dtype.kind in ["u", "i"]: # Convert the normalized array to float dtype data = data.astype(np.float32) @@ -681,24 +693,18 @@ def progress_callback(frame, total): if cancel(): return - progress_update(context, 0.2, - f"Processing {name}...") - progress_callback = progress_callback_factory(name, - 0.2, - 0.7) + progress_update(context, 0.2, f"Processing {name}...") + progress_callback = progress_callback_factory(name, 0.2, 0.7) try: - layer = Layer(data=data, - name=name, - kind=kind) + layer = Layer(data=data, name=name, kind=kind) - layer.resize(shape=shape, - progress_callback=progress_callback) + layer.resize(shape=shape, progress_callback=progress_callback) layer.affine = affine layers.append(layer) - except CancelledByUser: + except KeyboardInterrupt: return except Exception as e: self.has_error = e @@ -722,31 +728,31 @@ def progress_callback(frame, total): data = np.zeros_like(data, dtype=np.float32) if self.split_channel: - progress_step = 0.7/self.channel_count + progress_step = 0.7 / self.channel_count for i in range(self.channel_count): if cancel(): return name_i = f"{name}_{i+1}" - progress = 0.2 + i*progress_step - progress_update(context, progress, - f"Processing {name_i}...") - progress_callback = progress_callback_factory(name_i, - progress, - progress_step) + progress = 0.2 + i * progress_step + progress_update(context, progress, f"Processing {name_i}...") + progress_callback = progress_callback_factory( + name_i, progress, progress_step + ) try: - layer = Layer(data=data[:, :, :, :, i:i+1], - name=name_i, - kind=kind) + layer = Layer( + data=data[:, :, :, :, i : i + 1], name=name_i, kind=kind + ) - layer.resize(shape=shape, - progress_callback=progress_callback) + layer.resize( + shape=shape, progress_callback=progress_callback + ) layer.affine = affine layers.append(layer) - except CancelledByUser: + except KeyboardInterrupt: return except Exception as e: self.has_error = e @@ -755,24 +761,18 @@ def progress_callback(frame, total): if cancel(): return - progress_update(context, 0.2, - f"Processing {name}...") - progress_callback = progress_callback_factory(name, - 0.2, - 0.7) + progress_update(context, 0.2, f"Processing {name}...") + progress_callback = progress_callback_factory(name, 0.2, 0.7) try: - layer = Layer(data=data, - name=name, - kind=kind) + layer = Layer(data=data, name=name, kind=kind) - layer.resize(shape=shape, - progress_callback=progress_callback) + layer.resize(shape=shape, progress_callback=progress_callback) layer.affine = affine layers.append(layer) - except CancelledByUser: + except KeyboardInterrupt: return except Exception as e: self.has_error = e @@ -787,29 +787,32 @@ def progress_callback(frame, total): self.is_cancelled = False self.has_error = None - self.thread = threading.Thread(target=import_volumetric_data_func, - args=(self, context, lambda: self.is_cancelled)) + self.thread = threading.Thread( + target=import_volumetric_data_func, + args=(self, context, lambda: self.is_cancelled), + ) self.thread.start() - self._timer = context.window_manager.event_timer_add(time_step=0.1, - window=context.window) + self._timer = context.window_manager.event_timer_add( + time_step=0.1, window=context.window + ) bpy.types.STATUSBAR_HT_header.append(progress_bar) context.window_manager.modal_handler_add(self) - return {'RUNNING_MODAL'} + return {"RUNNING_MODAL"} def modal(self, context, event): - if event.type == 'ESC': + if event.type == "ESC": self.is_cancelled = True progress_update(context, 0.0, "Canceling...") - return {'PASS_THROUGH'} + return {"PASS_THROUGH"} - if event.type != 'TIMER': - return {'PASS_THROUGH'} + if event.type != "TIMER": + return {"PASS_THROUGH"} bpy.context.workspace.status_text_set_internal(None) if self.thread.is_alive(): - return {'PASS_THROUGH'} + return {"PASS_THROUGH"} self.thread.join() context.window_manager.event_timer_remove(self._timer) @@ -818,7 +821,7 @@ def modal(self, context, event): if self.is_cancelled: self.report({"WARNING"}, "Canncelled by user.") - return {'CANCELLED'} + return {"CANCELLED"} # Check if thread is cancelled by user if self.has_error: @@ -827,69 +830,30 @@ def modal(self, context, event): # Check if has return if self.layers is None: self.report({"ERROR"}, "Some thing went wrong.") - return {'CANCELLED'} - - is_first_import = len(get_all_layer_objs()) == 0 - - if self.container_obj_name: - container_obj = bpy.data.objects.get(self.container_obj_name) - if container_obj is None: - raise Exception("Could not find target container") + return {"CANCELLED"} - container_obj = add_layers(self.layers, - container_obj=container_obj, - cache_dir=get_cache_dir()) - else: - name = self.container_name or "Container" - container = Container(name=name, - layers=self.layers) - - step_size = container.layers[0].bioxel_size[0]*10 - container_obj = container_to_obj(container, - scene_scale=self.scene_scale, - step_size=step_size, - cache_dir=get_cache_dir()) + is_first_import = len(get_layer_caches()) == 0 + ids = save_layers_to_json(self.layers, cache_dir=get_cache_dir() / "layers") - select_object(container_obj) + setattr(context.window_manager, "bioxel_layer_library", ids[-1]) # Change render setting for better result if is_first_import: - try: - bpy.ops.bioxelnodes.render_setting_preset('EXEC_DEFAULT', - preset="balance") - bpy.ops.bioxelnodes.add_eevee_env('EXEC_DEFAULT') - bpy.context.scene.eevee.use_taa_reprojection = False - bpy.context.scene.render.engine = 'BLENDER_EEVEE_NEXT' - - view_3d = None - if context.area.type == 'VIEW_3D': - view_3d = context.area - else: - for area in context.screen.areas: - if area.type == 'VIEW_3D': - view_3d = area - break - if view_3d: - view_3d.spaces[0].shading.type = 'RENDERED' - except: - self.report({"WARNING"}, "Fail to change render setting.") + bpy.ops.bioxel.render_setting_preset("EXEC_DEFAULT", preset="balance") self.report({"INFO"}, "Successfully Imported") - return {'FINISHED'} + return {"FINISHED"} def invoke(self, context, event): layer_kind = self.read_as.capitalize() - title = f"Add to **{self.container_obj_name}**, As {layer_kind}" \ - if self.container_obj_name != "" else f"Init a Container, As {layer_kind}" - context.window_manager.invoke_props_dialog(self, - width=500, - title=title) - return {'RUNNING_MODAL'} + title = f"Add to **{context.object.name}**, As {layer_kind}" + context.window_manager.invoke_props_dialog(self, width=500, title=title) + return {"RUNNING_MODAL"} def draw(self, context): - layer_shape = get_layer_shape(self.bioxel_size, - self.orig_shape, - self.orig_spacing) + layer_shape = get_layer_shape( + self.bioxel_size, self.orig_shape, self.orig_spacing + ) orig_shape = tuple(self.orig_shape) @@ -925,24 +889,13 @@ def draw(self, context): channel_count = 3 bioxel_count = layer_shape[0] * layer_shape[1] * layer_shape[2] - orig_shape_text = f"[{self.frame_count}, ({orig_shape[0]},{orig_shape[1]},{orig_shape[2]}), {self.channel_count}]" - layer_shape_text = f"{layer_count} x [{frame_count}, ({layer_shape[0]},{layer_shape[1]},{layer_shape[2]}), {channel_count}]" + orig_shape_text = f"[{self.frame_count}, {orig_shape[0]},{orig_shape[1]},{orig_shape[2]}, {self.channel_count}]" + layer_shape_text = f"{layer_count} x [{frame_count}, {layer_shape[0]},{layer_shape[1]},{layer_shape[2]}, {channel_count}]" if bioxel_count > 100000000: layer_shape_text += "**TOO LARGE!**" - layer_size = get_layer_size(layer_shape, - self.bioxel_size, - self.scene_scale) - layer_size_text = f"Size will be: ({layer_size[0]:.2f}, {layer_size[1]:.2f}, {layer_size[2]:.2f}) m" - layout = self.layout - if self.container_obj_name == "": - panel = layout.box() - panel.prop(self, "container_name") - panel.prop(self, "scene_scale") - panel.label(text=layer_size_text) - panel = layout.box() panel.prop(self, "layer_name") panel.prop(self, "bioxel_size") @@ -951,26 +904,21 @@ def draw(self, context): panel.prop(self, "frame_source") if self.read_as == "SCALAR": - panel.prop(self, "split_channel", - text=f"Split Channel as Multi Layer") + panel.prop(self, "split_channel", text=f"Split Channel as Multi Layer") elif self.read_as == "LABEL": panel.prop(self, "smooth") - panel.label( - text="Dimension Order: [Frame, (X-axis,Y-axis,Z-axis), Channel]") - panel.label( - text=f"Shape from {orig_shape_text} to {layer_shape_text}") + panel.label(text=f"Shape from {orig_shape_text} to {layer_shape_text}") + panel.label(text="Dimension Order: [Frame, X-axis, Y-axis, Z-axis, Channel]") class ExportVolumetricData(bpy.types.Operator): - bl_idname = "bioxelnodes.export_volumetric_data" + bl_idname = "bioxel.export_volumetric_data" bl_label = "Export Layer as VDB" bl_description = "Export Layer as VDB" - bl_options = {'UNDO'} + bl_options = {"UNDO"} - filepath: bpy.props.StringProperty( - subtype="FILE_PATH" - ) # type: ignore + filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore filename_ext = ".vdb" @@ -981,7 +929,7 @@ def poll(cls, context): def invoke(self, context, event): context.window_manager.fileselect_add(self) - return {'RUNNING_MODAL'} + return {"RUNNING_MODAL"} def execute(self, context): layer_obj = get_layer_obj(bpy.context.active_object) @@ -998,4 +946,4 @@ def execute(self, context): self.report({"INFO"}, f"Successfully exported to {output_path}") - return {'FINISHED'} + return {"FINISHED"} diff --git a/src/bioxelnodes/operators/layer.py b/src/bioxelnodes/operators/layer.py index 5cbf71b..6825012 100644 --- a/src/bioxelnodes/operators/layer.py +++ b/src/bioxelnodes/operators/layer.py @@ -1,619 +1,320 @@ from pathlib import Path -import bpy - -import numpy as np - - -from ..exceptions import NoContent -from ..bioxel.layer import Layer -from ..bioxelutils.node import add_node_to_graph -from ..bioxelutils.common import (get_container_obj, get_layer_kind, get_layer_label, get_layer_name, - get_layer_prop_value, - get_container_layer_objs, - get_node_type, is_missing_layer, move_node_to_node, set_layer_prop_value) -from ..bioxelutils.layer import layer_to_obj, obj_to_layer -from ..utils import get_cache_dir, copy_to_dir, get_use_link - - -def get_label_layer_selection(self, context): - items = [("None", "None", "")] - container_obj = get_container_obj(bpy.context.active_object) - - for layer_obj in get_container_layer_objs(container_obj): - kind = get_layer_prop_value(layer_obj, "kind") - name = get_layer_prop_value(layer_obj, "name") - if kind == "label": - items.append((layer_obj.name, - name, - "")) - - return items - - -class FetchLayer(bpy.types.Operator): - bl_idname = "bioxelnodes.fetch_layer" - bl_label = "Fetch Layer" - bl_description = "Fetch layer from current container" - bl_icon = "NODE" - bl_options = {'UNDO'} - - layer_obj_name: bpy.props.StringProperty( - options={"HIDDEN"}) # type: ignore - - @classmethod - def description(cls, context, properties): - layer_obj_name = properties.layer_obj_name - layer_obj = bpy.data.objects.get(layer_obj_name) - return "\n".join([f"{prop}: {get_layer_prop_value(layer_obj, prop)}" - for prop in ["kind", - "bioxel_size", - "shape", - "frame_count", - "channel_count", - "min", "max"]]) - - @property - def layer_obj(self): - return bpy.data.objects.get(self.layer_obj_name) - - def execute(self, context): - if self.layer_obj == None: - self.report({"WARNING"}, "Get no layer.") - return {'FINISHED'} - - if is_missing_layer(self.layer_obj): - self.report({"WARNING"}, "Selected layer is lost.") - return {'FINISHED'} - - bpy.ops.bioxelnodes.add_node('EXEC_DEFAULT', - node_name="FetchLayer", - node_label="Fetch Layer") - node = bpy.context.active_node - - node.inputs[0].default_value = self.layer_obj - node.label = get_layer_label(self.layer_obj) +import shutil - return {"FINISHED"} - - -def get_selected_layers(context, layer_filter=None): - def _layer_filter(layer_obj, context): - return True - - layer_filter = layer_filter or _layer_filter - select_objs = [] - # node_group = context.space_data.edit_tree - for node in context.selected_nodes: - if get_node_type(node) == "BioxelNodes_FetchLayer": - layer_obj = node.inputs[0].default_value - if layer_obj is not None: - if layer_filter(layer_obj, context): - select_objs.append(layer_obj) - - return list(set(select_objs)) +import bpy +from ..node import add_bioxel_node, get_layer_nodes, get_main_node_group +from ..utils import refresh_bioxel_panels +from ..layer import get_layer_caches, set_layer_caches -def get_selected_layer(context, layer_filter=None): - layer_objs = get_selected_layers(context, layer_filter) - return layer_objs[0] if len(layer_objs) > 0 else None +class RenameLayer(bpy.types.Operator): + """Rename a cached Bioxel layer""" -class OutputLayerOperator(): - new_layer_name: bpy.props.StringProperty(name="New Name", - options={"SKIP_SAVE"}) # type: ignore + bl_idname = "bioxel.rename_layer" + bl_label = "Rename Layer" + bl_options = {"REGISTER", "UNDO"} - def operate(self, orig_layer: Layer, context): - """do the operation""" - return orig_layer + cache_id: bpy.props.StringProperty(options={"HIDDEN"}) # type: ignore + new_name: bpy.props.StringProperty( + name="New name", default="") # type: ignore - def add_layer_node(self, context, layer): - orig_node = context.selected_nodes[0] - layer_obj = layer_to_obj(layer, - container_obj=context.object, - cache_dir=get_cache_dir()) - node_group = context.space_data.edit_tree - fetch_node = add_node_to_graph("FetchLayer", - node_group, - use_link=get_use_link()) - fetch_node.label = get_layer_prop_value(layer_obj, "name") - fetch_node.inputs[0].default_value = layer_obj - move_node_to_node(fetch_node, orig_node, (0, -100)) + def invoke(self, context, event): + caches = get_layer_caches() + entry = next((c for c in caches if str( + c.get("id", "")) == self.cache_id), None) + if entry: + self.new_name = str(entry.get("name", "")) + return context.window_manager.invoke_props_dialog(self) def execute(self, context): - layer_obj = get_selected_layer(context) - if layer_obj == None: - self.report({"WARNING"}, "Get no layer.") - return {'FINISHED'} + if not self.new_name: + self.report({"ERROR"}, "Name cannot be empty") + return {"CANCELLED"} - if is_missing_layer(layer_obj): - self.report({"WARNING"}, "Selected layer is lost.") - return {'FINISHED'} + caches = get_layer_caches() + for c in caches: + if str(c.get("id", "")) == self.cache_id: + c["name"] = self.new_name + break - orig_layer = obj_to_layer(layer_obj) try: - new_layer = self.operate(orig_layer, context) - except NoContent as e: - self.report({"WARNING"}, e.message) - return {'FINISHED'} - - self.add_layer_node(context, new_layer) - return {'FINISHED'} + set_layer_caches(caches) + refresh_bioxel_panels(context) + self.report({"INFO"}, "Layer renamed") + return {"FINISHED"} + except Exception as e: + self.report({"ERROR"}, f"Failed to save changes: {e}") + return {"CANCELLED"} -class LayerOperator(): +class DeleteLayer(bpy.types.Operator): + """Delete a saved Bioxel layer""" - def operate(self, layer_obj: bpy.types.Object, context): - """do the operation""" - ... + bl_idname = "bioxel.delete_layer" + bl_label = "Delete Layer" + bl_options = {"REGISTER", "UNDO"} - def execute(self, context): - layer_obj = get_selected_layer(context) - if layer_obj == None: - self.report({"WARNING"}, "Get no layer.") - return {'FINISHED'} - - if is_missing_layer(layer_obj): - self.report({"WARNING"}, "Selected layer is lost.") - return {'FINISHED'} - - self.operate(layer_obj, context) - - return {'FINISHED'} - - -class RetimeLayer(bpy.types.Operator, LayerOperator): - bl_idname = "bioxelnodes.retime_layer" - bl_label = "Retime Sequence" - bl_description = "Retime layer time sequence" - bl_icon = "TIME" - - frame_duration: bpy.props.IntProperty(name="Frames") # type: ignore - frame_start: bpy.props.IntProperty(name="Start") # type: ignore - frame_offset: bpy.props.IntProperty(name="Offset") # type: ignore - sequence_mode: bpy.props.EnumProperty(name="Mode", - default="REPEAT", - items=[("CLIP", "Clip", ""), - ("EXTEND", "Extend", ""), - ("REPEAT", "Repeat", ""), - ("PING_PONG", "Ping-Pong", "")]) # type: ignore - - def operate(self, layer_obj, context): - layer_obj.data.frame_duration = self.frame_duration - layer_obj.data.frame_start = self.frame_start - layer_obj.data.frame_offset = self.frame_offset - layer_obj.data.sequence_mode = self.sequence_mode + cache_id: bpy.props.StringProperty() # type: ignore def invoke(self, context, event): - layer_obj = get_selected_layer(context) - if layer_obj: - self.frame_duration = layer_obj.data.frame_duration - self.frame_start = layer_obj.data.frame_start - self.frame_offset = layer_obj.data.frame_offset - self.sequence_mode = layer_obj.data.sequence_mode - name = get_layer_label(layer_obj) - context.window_manager.invoke_props_dialog(self, - title=f"Retime {name}") - return {'RUNNING_MODAL'} - else: - return self.execute(context) - - -class RelocateLayer(bpy.types.Operator): - bl_idname = "bioxelnodes.relocate_layer" - bl_label = "Relocate Layer Cache" - bl_description = "Relocate layer cache" - bl_icon = "FILE" - - filepath: bpy.props.StringProperty(subtype="FILE_PATH") # type: ignore + return context.window_manager.invoke_confirm(self, event) def execute(self, context): - layer_obj = get_selected_layer(context) - if layer_obj == None: - self.report({"WARNING"}, "Get no layer.") - return {'FINISHED'} - - self.operate(layer_obj, context) + if not self.cache_id: + self.report({"ERROR"}, "Missing cache id") + return {"CANCELLED"} - return {'FINISHED'} + caches = get_layer_caches() + new_list = [c for c in caches if str(c.get("id", "")) != self.cache_id] + removed = next( + (c for c in caches if str(c.get("id", "")) == self.cache_id), None + ) - def operate(self, layer_obj, context): - layer_obj.data.filepath = self.filepath - - def invoke(self, context, event): - layer_obj = get_selected_layer(context) - if layer_obj: - context.window_manager.fileselect_add(self) - return {'RUNNING_MODAL'} - else: - return self.execute(context) - - -class RenameLayer(bpy.types.Operator, LayerOperator): - bl_idname = "bioxelnodes.rename_layer" - bl_label = "Rename Layer" - bl_description = "Rename layer" - bl_icon = "FILE_FONT" - - new_name: bpy.props.StringProperty(name="New Name", - options={"SKIP_SAVE"}) # type: ignore - - def operate(self, layer_obj, context): - name = f"{layer_obj.parent.name}_{self.new_name}" - layer_obj.name = name - layer_obj.data.name = name + try: + set_layer_caches(new_list) + refresh_bioxel_panels(context) + except Exception as e: + self.report({"ERROR"}, f"Failed to update layer list: {e}") + return {"CANCELLED"} - set_layer_prop_value(layer_obj, "name", self.new_name) + self.report({"INFO"}, "Layer removed") + return {"FINISHED"} - node_group = context.space_data.edit_tree - for node in node_group.nodes: - if get_node_type(node) == "BioxelNodes_FetchLayer": - if node.inputs[0].default_value == layer_obj: - node.label = self.new_name - def invoke(self, context, event): - layer_obj = get_selected_layer(context) - if layer_obj: - self.new_name = get_layer_name(layer_obj) - name = get_layer_label(layer_obj) - context.window_manager.invoke_props_dialog(self, - title=f"Rename {name}") - return {'RUNNING_MODAL'} - else: - return self.execute(context) +# 添加图层到节点图的操作器 +class AddLayerNode(bpy.types.Operator): + """将选中的图层添加到几何节点图""" + bl_idname = "bioxel.add_layer_node" + bl_label = "添加图层节点" + bl_options = {"REGISTER", "UNDO"} -class ResampleLayer(bpy.types.Operator, OutputLayerOperator): - bl_idname = "bioxelnodes.resample_layer" - bl_label = "Resample Value" - bl_description = "Resample value" - bl_icon = "ALIASED" + cache_id: bpy.props.StringProperty() # type: ignore # 图层ID - smooth: bpy.props.IntProperty(name="Smooth Size", - default=0, - soft_min=0, soft_max=5, - options={"SKIP_SAVE"}) # type: ignore + def execute(self, context): + # 获取图层数据 + caches = get_layer_caches() - bioxel_size: bpy.props.FloatProperty( - name="Bioxel Size", - soft_min=0.1, soft_max=10.0, - default=1, - ) # type: ignore + # 查找目标图层 + entry = next( + (c for c in caches if str(c.get("id", "")) == str(self.cache_id)), None + ) - @staticmethod - def get_new_shape(orig_shape, orig_size, new_size): - return (int(orig_shape[0]*orig_size/new_size), - int(orig_shape[1]*orig_size/new_size), - int(orig_shape[2]*orig_size/new_size)) - - def operate(self, orig_layer: Layer, context): - new_layer = orig_layer.copy() - new_shape = self.get_new_shape(new_layer.shape, - new_layer.bioxel_size[0], - self.bioxel_size) - - new_layer.resize(new_shape, self.smooth) - new_layer.name = self.new_layer_name \ - or f"{orig_layer.name}_R-{self.bioxel_size:.2f}" - return new_layer - - def draw(self, context): - layer_obj = get_selected_layer(context) - orig_shape = get_layer_prop_value(layer_obj, "shape") - orig_size = get_layer_prop_value(layer_obj, "bioxel_size") - new_shape = self.get_new_shape(orig_shape, - orig_size, - self.bioxel_size) - - orig_shape = tuple(orig_shape) - bioxel_count = new_shape[0] * new_shape[1] * new_shape[2] - - layer_shape_text = f"Shape from {str(orig_shape)} to {str(new_shape)}" - if bioxel_count > 100000000: - layer_shape_text += "**TOO LARGE!**" - - layout = self.layout - layout.prop(self, "new_layer_name") - layout.prop(self, "bioxel_size") - layout.prop(self, "smooth") - layout.label(text=layer_shape_text) + if not entry: + self.report({"ERROR"}, "Layer not found") + return {"CANCELLED"} - def invoke(self, context, event): - layer_obj = get_selected_layer(context) - if layer_obj: - name = get_layer_label(layer_obj) - self.bioxel_size = get_layer_prop_value(layer_obj, - "bioxel_size") - context.window_manager.invoke_props_dialog(self, - title=f"Resample {name}") - return {'RUNNING_MODAL'} + # 创建并设置节点属性 + try: + layer_node = add_bioxel_node("O Layer") + except: + self.report({"ERROR"}, "Fail to add layer node") + return {"CANCELLED"} + + layer_node.node_tree.make_local() + layer_node.inputs["Path"].default_value = entry["path"] + layer_node.inputs["Name"].default_value = entry["name"] + layer_node.inputs["Shape"].default_value = entry["shape"] + layer_node.inputs["Min"].default_value = entry["min"] + layer_node.inputs["Max"].default_value = entry["max"] + layer_node.inputs["ID"].default_value = entry["id"] + + # 将特定属性隐藏到hidden面板 + hidden_sockets = ["Path", "Shape", "Min", "Max", "ID", "Animation"] + + if entry["frame_count"] > 1: + layer_node.inputs["Frame Count"].default_value = entry["frame_count"] + layer_node.inputs["Animation"].default_value = True else: - return self.execute(context) + hidden_sockets = hidden_sockets + \ + ["Frame Count", "Frame Offset", "Cycle"] + # 将特定属性隐藏到hidden面板 + for socket_name in hidden_sockets: + if socket_name in layer_node.inputs: + layer_node.inputs[socket_name].hide = True -class SignScalar(bpy.types.Operator, OutputLayerOperator): - bl_idname = "bioxelnodes.sign_scalar" - bl_label = "Sign Value" - bl_description = "Sign value" - bl_icon = "REMOVE" + for socket_name in layer_node.outputs.keys(): + if socket_name != entry["kind"].capitalize(): + layer_node.outputs[socket_name].hide = True - def operate(self, orig_layer: Layer, context): - new_layer = orig_layer.copy() - new_layer.data = -orig_layer.data - new_layer.name = self.new_layer_name \ - or f"{orig_layer.name}_Sign" - return new_layer + self.report({"INFO"}, f"Successfully created node: {entry['name']}") + return {"FINISHED"} - def invoke(self, context, event): - layer_obj = get_selected_layer(context) - if layer_obj: - name = get_layer_label(layer_obj) - context.window_manager.invoke_props_dialog(self, - title=f"Sign {name}") - return {'RUNNING_MODAL'} - else: - return self.execute(context) +class RelocatePath(bpy.types.Operator): + """Locate and update the missing layer folder, and update all related nodes""" -class FillOperator(OutputLayerOperator): + bl_idname = "bioxel.find_layer_folder" + bl_label = "Relocate" + bl_options = {"REGISTER", "UNDO"} - fill_value: bpy.props.FloatProperty( - name="Fill Value", - soft_min=0, soft_max=1024.0, - default=0, - ) # type: ignore + cache_id: bpy.props.StringProperty(options={"HIDDEN"}) # type: ignore - invert: bpy.props.BoolProperty( - name="Invert Aera", + use_relative: bpy.props.BoolProperty( + name="Relative Path", + description="Store the path relative to the current Blender file", default=True, ) # type: ignore - def invoke(self, context, event): - layer_obj = get_selected_layer(context) - if layer_obj: - name = get_layer_label(layer_obj) - context.window_manager.invoke_props_dialog(self, - title=f"Fill {name}") - return {'RUNNING_MODAL'} - else: - return self.execute(context) - - -class FillByThreshold(bpy.types.Operator, FillOperator): - bl_idname = "bioxelnodes.fill_by_threshold" - bl_label = "Fill Value by Threshold" - bl_description = "Fill value by threshold" - bl_icon = "EMPTY_SINGLE_ARROW" - - threshold: bpy.props.FloatProperty( - name="Threshold", - soft_min=0, soft_max=1024, - default=128, - ) # type: ignore - - def operate(self, orig_layer: Layer, context): - data = np.amax(orig_layer.data, -1) - mask = data <= self.threshold \ - if self.invert else data > self.threshold - - new_layer = orig_layer.copy() - new_layer.fill(self.fill_value, mask, 0) - new_layer.name = self.new_layer_name \ - or f"{orig_layer.name}_F-{self.threshold:.2f}" - return new_layer - - -class FillByRange(bpy.types.Operator, FillOperator): - bl_idname = "bioxelnodes.fill_by_range" - bl_label = "Fill Value by Range" - bl_description = "Fill value by range" - bl_icon = "IPO_CONSTANT" - - from_min: bpy.props.FloatProperty( - name="From Min", - soft_min=0, soft_max=1024, - default=128, + directory: bpy.props.StringProperty( + name="Layer Folder", + description="Select the correct folder for this layer", + subtype="DIR_PATH", ) # type: ignore - from_max: bpy.props.FloatProperty( - name="From Max", - soft_min=0, soft_max=1024, - default=256, - ) # type: ignore - - def operate(self, orig_layer: Layer, context): - data = np.amax(orig_layer.data, -1) - mask = (data <= self.from_min) | (data >= self.from_max) if self.invert else \ - (data > self.from_min) & (data < self.from_max) - - new_layer = orig_layer.copy() - new_layer.fill(self.fill_value, mask, 0) - new_layer.name = self.new_layer_name \ - or f"{orig_layer.name}_F-{self.from_min:.2f}-{self.from_max:.2f}" - return new_layer - - -class FillByLabel(bpy.types.Operator, FillOperator): - bl_idname = "bioxelnodes.fill_by_label" - bl_label = "Fill Value by Label" - bl_description = "Fill value by label" - bl_icon = "MESH_CAPSULE" - - smooth: bpy.props.IntProperty(name="Smooth Size", - default=0, - soft_min=0, soft_max=5, - options={"SKIP_SAVE"}) # type: ignore - - label_obj_name: bpy.props.EnumProperty(name="Label Layer", - items=get_label_layer_selection) # type: ignore - - def operate(self, orig_layer: Layer, context): - label_obj = bpy.data.objects.get(self.label_obj_name) - if label_obj is None: - raise NoContent("Cannot find any label layer.") - - label_layer = obj_to_layer(label_obj) - label_layer.resize(orig_layer.shape, self.smooth) - mask = np.amax(label_layer.data, -1) - if self.invert: - mask = 1 - mask - - new_layer = orig_layer.copy() - new_layer.fill(self.fill_value, mask, 0) - new_layer.name = self.new_layer_name \ - or f"{orig_layer.name}_F-{label_layer.name}" - return new_layer - - -class CombineLabels(bpy.types.Operator, OutputLayerOperator): - bl_idname = "bioxelnodes.combine_labels" - bl_label = "Combine Labels" - bl_description = "Combine all selected labels" - bl_icon = "MOD_BUILD" - - def execute(self, context): - def layer_filter(layer_obj, context): - return get_layer_kind(layer_obj) == "label" - - label_objs = get_selected_layers(context, layer_filter) - - if len(label_objs) < 2: - self.report({"WARNING"}, "Not enough layers.") - return {'FINISHED'} - - base_obj = label_objs[0] - label_objs = label_objs[1:] - - base_layer = obj_to_layer(base_obj) - new_layer = base_layer.copy() - label_names = [base_layer.name] - - for label_obj in label_objs: - label_layer = obj_to_layer(label_obj) - label_layer.resize(base_layer.shape) - new_layer.data = np.maximum( - new_layer.data, label_layer.data) - label_names.append(label_layer.name) - - new_layer.name = self.new_layer_name \ - or f"C-{'-'.join(label_names)}" - - self.add_layer_node(context, new_layer) - return {'FINISHED'} - - -class BatchLayerOperator(): - success_msg = "Successfully done selected layers." - fail_msg = "fails." + def invoke(self, context, event): + context.window_manager.fileselect_add(self) + return {"RUNNING_MODAL"} def execute(self, context): - layer_objs = self.get_layers(context) + if not self.cache_id: + self.report({"ERROR"}, "Missing cache id") + return {"CANCELLED"} + if not self.directory: + self.report({"ERROR"}, "Please select a folder") + return {"CANCELLED"} + + caches = get_layer_caches() + entry = next((c for c in caches if str( + c.get("id", "")) == self.cache_id), None) + if not entry: + self.report({"ERROR"}, "Layer not found") + return {"CANCELLED"} + + old_path = entry["path"] + new_path = ( + bpy.path.relpath(self.directory) + if self.use_relative and bpy.data.filepath + else bpy.path.abspath(self.directory) + ) + entry["path"] = new_path + + set_layer_caches(caches) + refresh_bioxel_panels(context) + + # 更新所有 node group 中 O Layer 节点的 Path + for node_group in bpy.data.node_groups: + for node in get_layer_nodes(node_group): + node_path = getattr(node.inputs.get("Path"), "default_value") + if node_path and node_path == old_path: + node.inputs["Path"].default_value = new_path - fails = [] - for layer_obj in layer_objs: - try: - self.operate(layer_obj, context) - except: - fails.append(layer_obj) + self.report({"INFO"}, f"Cache path updated: {new_path}") + return {"FINISHED"} - if len(fails) == 0: - self.report({"INFO"}, self.success_msg) - else: - self.report( - {"WARNING"}, f"{','.join([layer_obj.name for layer_obj in fails])} {self.fail_msg}") - return {'FINISHED'} +class SaveLayer(bpy.types.Operator): + """Copy the entire layer folder (named by id) to a target folder and update its path in the cache""" + bl_idname = "bioxel.cache_layer_to_folder" + bl_label = "Save Layer" + bl_options = {"REGISTER", "UNDO"} -class SaveLayersCache(BatchLayerOperator): - fail_msg = "fail to save." + cache_id: bpy.props.StringProperty(options={"HIDDEN"}) # type: ignore - cache_dir: bpy.props.StringProperty( - name="Cache Directory", - subtype='DIR_PATH', - default="//" + use_relative: bpy.props.BoolProperty( + name="Relative Path", + description="Store the path relative to the current Blender file", + default=True, ) # type: ignore - def operate(self, layer_obj, context): - output_dir = bpy.path.abspath(self.cache_dir) - source_dir = bpy.path.abspath(layer_obj.data.filepath) - - source_path: Path = Path(source_dir).resolve() - is_sequence = layer_obj.data.is_sequence - - name = layer_obj.name if is_sequence else f"{layer_obj.name}.vdb" - output_path: Path = Path(output_dir, name, source_path.name).resolve() \ - if is_sequence else Path(output_dir, name).resolve() - - if output_path != source_path: - copy_to_dir(source_path.parent if is_sequence else source_path, - output_path.parent.parent if is_sequence else output_path.parent, - new_name=name) - - blend_path = Path(bpy.path.abspath("//")).resolve() - - layer_obj.data.filepath = bpy.path.relpath(str(output_path), - start=str(blend_path)) - - return {'FINISHED'} + directory: bpy.props.StringProperty( + name="Target Folder", + description="Select a folder to cache the layer files", + subtype="DIR_PATH", + ) # type: ignore def invoke(self, context, event): - context.window_manager.invoke_props_dialog(self) - return {'RUNNING_MODAL'} - - -class RemoveLayers(BatchLayerOperator): - fail_msg = "fail to remove." - - def operate(self, layer_obj, context): - for node_group in bpy.data.node_groups: - for node in node_group.nodes: - if get_node_type(node) == "BioxelNodes_FetchLayer": - if node.inputs[0].default_value == layer_obj: - node_group.nodes.remove(node) + # Default to Blender file directory if possible + blend_dir = Path( + bpy.data.filepath).parent if bpy.data.filepath else Path.cwd() + context.window_manager.fileselect_add(self) + if not self.directory: + self.directory = str(blend_dir) + return {"RUNNING_MODAL"} - cache_filepath = Path(bpy.path.abspath( - layer_obj.data.filepath)).resolve() - - if cache_filepath.is_file(): - if layer_obj.data.is_sequence: - for f in cache_filepath.parent.iterdir(): - f.unlink(missing_ok=True) - else: - cache_filepath.unlink(missing_ok=True) + def execute(self, context): + if not self.cache_id: + self.report({"ERROR"}, "Missing cache id") + return {"CANCELLED"} + if not self.directory: + self.report({"ERROR"}, "Please select a target folder") + return {"CANCELLED"} + + caches = get_layer_caches() + entry = next((c for c in caches if str( + c.get("id")) == self.cache_id), None) + cache_id = entry.get("id") + + if not entry: + self.report({"ERROR"}, "Layer not found") + return {"CANCELLED"} + + old_path = entry["path"] + src_path = bpy.path.abspath(old_path) + if not src_path or not Path(src_path).is_dir(): + self.report({"ERROR"}, "Source folder not found") + return {"CANCELLED"} + + src_dir = Path(src_path).resolve() + dst_root = Path(self.directory) + # copy as a subfolder named by id + dst_dir = (dst_root / src_dir.name).resolve() - # also remove layer object - bpy.data.volumes.remove(layer_obj.data) + try: + if src_dir != dst_dir: + if dst_dir.exists(): + shutil.rmtree(dst_dir) + shutil.copytree(src_dir, dst_dir) - return {'FINISHED'} + # Save as relative path if requested and possible - def invoke(self, context, event): - context.window_manager.invoke_confirm(self, - event, - message=f"Are you sure to remove them?") - return {'RUNNING_MODAL'} + new_path = ( + bpy.path.relpath(str(dst_dir)) + if self.use_relative and bpy.data.filepath + else bpy.path.abspath(str(dst_dir)) + ) + entry["path"] = new_path -class SaveSelectedLayersCache(bpy.types.Operator, SaveLayersCache): - bl_idname = "bioxelnodes.save_selected_layers_cache" - bl_label = "Save Selected Layers Cache" - bl_description = "Save selected layers' Cache" - bl_icon = "FILE_TICK" + set_layer_caches(caches) + refresh_bioxel_panels(context) - success_msg = "Successfully saved all selected layers." + # 遍历所有 node group + for node_group in bpy.data.node_groups: + for node in get_layer_nodes(node_group): + if cache_id == getattr(node.inputs.get("ID"), "default_value"): + node.inputs["Path"].default_value = new_path - def get_layers(self, context): - def is_not_missing(layer_obj, context): - return not is_missing_layer(layer_obj) - return get_selected_layers(context, is_not_missing) + self.report({"INFO"}, f"Layer cached to {dst_dir}") + return {"FINISHED"} + except Exception as e: + self.report({"ERROR"}, f"Failed to cache layer: {e}") + return {"CANCELLED"} -class RemoveSelectedLayers(bpy.types.Operator, RemoveLayers): - bl_idname = "bioxelnodes.remove_selected_layers" - bl_label = "Remove Selected Layers" - bl_description = "Remove selected layers" - bl_icon = "TRASH" +class SelectAndFocusNode(bpy.types.Operator): + """Select and focus the specified node in the current node tree""" - success_msg = "Successfully removed all selected layers." + bl_idname = "bioxel.select_and_focus_node" + bl_label = "Select and Focus Node" + node_name: bpy.props.StringProperty() # type: ignore - def get_layers(self, context): - return get_selected_layers(context) + def execute(self, context): + node_group = get_main_node_group(context) + if not node_group: + self.report({"ERROR"}, "No node group found.") + return {"CANCELLED"} + node = node_group.nodes.get(self.node_name) + if not node: + self.report({"ERROR"}, f"Node '{self.node_name}' not found.") + return {"CANCELLED"} + # Deselect all, select and focus this node + for n in node_group.nodes: + n.select = False + node.select = True + node_group.nodes.active = node + bpy.ops.node.view_selected() + return {"FINISHED"} diff --git a/src/bioxelnodes/operators/misc.py b/src/bioxelnodes/operators/misc.py index c0275e8..7693ece 100644 --- a/src/bioxelnodes/operators/misc.py +++ b/src/bioxelnodes/operators/misc.py @@ -1,110 +1,21 @@ +import json +import uuid import webbrowser import bpy from pathlib import Path import shutil -from ..bioxelutils.common import get_all_layer_objs, get_node_lib_path, get_node_version, is_missing_layer, set_file_prop -from .layer import RemoveLayers, SaveLayersCache - -from ..constants import LATEST_NODE_LIB_PATH, VERSIONS -from ..utils import get_cache_dir - - -class ReLinkNodeLib(bpy.types.Operator): - bl_idname = "bioxelnodes.relink_node_lib" - bl_label = "Relink Node Library" - bl_description = "Relink all nodes to addon library source" - bl_options = {'UNDO'} - - index: bpy.props.IntProperty() # type: ignore - - def execute(self, context): - node_version = VERSIONS[self.index]['node_version'] - lib_path = get_node_lib_path(node_version) \ - if self.index != 0 else LATEST_NODE_LIB_PATH - - node_libs = [] - for node_group in bpy.data.node_groups: - if node_group.name.startswith("BioxelNodes"): - node_lib = node_group.library - if node_lib: - node_libs.append(node_lib) - - node_libs = list(set(node_libs)) - - for node_lib in node_libs: - node_lib.filepath = str(lib_path) - # FIXME: may cause crash - node_lib.reload() - - set_file_prop("node_version", node_version) - - self.report({"INFO"}, f"Successfully relinked.") - - return {'FINISHED'} - - -class SaveNodeLib(bpy.types.Operator): - bl_idname = "bioxelnodes.save_node_lib" - bl_label = "Save Node Library" - bl_description = "Save node library file to local" - bl_options = {'UNDO'} - - lib_dir: bpy.props.StringProperty( - name="Library Directory", - subtype='DIR_PATH', - default="//" - ) # type: ignore - - def execute(self, context): - node_version = get_node_version() - - if node_version is None: - node_version = VERSIONS[0]["node_version"] - else: - if node_version not in [v["node_version"] for v in VERSIONS]: - node_version = VERSIONS[0]["node_version"] - - if node_version == VERSIONS[0]["node_version"]: - lib_path = LATEST_NODE_LIB_PATH - else: - lib_path = get_node_lib_path(node_version) - - version_str = "v"+".".join([str(i) for i in list(node_version)]) - - lib_dir = bpy.path.abspath(self.lib_dir) - local_lib_path: Path = Path(lib_dir, - f"BioxelNodes_{version_str}.blend").resolve() - node_lib_path: Path = lib_path - blend_path = Path(bpy.path.abspath("//")).resolve() - - if local_lib_path != node_lib_path: - shutil.copy(node_lib_path, local_lib_path) - - libs = [] - for node_group in bpy.data.node_groups: - if node_group.name.startswith("BioxelNodes"): - if node_group.library: - libs.append(node_group.library) - - libs = list(set(libs)) - for lib in libs: - lib.filepath = bpy.path.relpath(str(local_lib_path), - start=str(blend_path)) - - return {'FINISHED'} - - def invoke(self, context, event): - context.window_manager.invoke_props_dialog(self) - return {'RUNNING_MODAL'} - - @classmethod - def poll(cls, context): - return bpy.data.is_saved +from ..constants import LATEST_NODE_LIB_PATH +from ..utils import ( + get_all_layer_objs, + get_cache_dir, + get_node_version, + is_missing_layer, +) class CleanTemp(bpy.types.Operator): - bl_idname = "bioxelnodes.clear_temp" + bl_idname = "bioxel.clear_temp" bl_label = "Clean Temp" bl_description = "Clean all cache in temp (include other project cache)" @@ -113,24 +24,26 @@ def execute(self, context): try: shutil.rmtree(cache_dir) self.report({"INFO"}, f"Successfully cleaned temp.") - return {'FINISHED'} + return {"FINISHED"} except: - self.report({"WARNING"}, - "Fail to clean temp, you may do it manually.") - return {'CANCELLED'} + self.report( + {"WARNING"}, "Fail to clean temp, you may do it manually.") + return {"CANCELLED"} def invoke(self, context, event): - context.window_manager.invoke_confirm(self, - event, - message="All temp files will be removed, include other project cache, do you still want to clean?") - return {'RUNNING_MODAL'} + context.window_manager.invoke_confirm( + self, + event, + message="All temp files will be removed, include other project cache, do you still want to clean?", + ) + return {"RUNNING_MODAL"} class RenderSettingPreset(bpy.types.Operator): - bl_idname = "bioxelnodes.render_setting_preset" + bl_idname = "bioxel.render_setting_preset" bl_label = "Render Setting Presets" bl_description = "Render setting presets for bioxel" - bl_options = {'UNDO'} + bl_options = {"UNDO"} PRESETS = { "performance": "Performance", @@ -138,166 +51,201 @@ class RenderSettingPreset(bpy.types.Operator): "quality": "Quality", } - preset: bpy.props.EnumProperty(name="Preset", - default="balance", - items=[(k, v, "") - for k, v in PRESETS.items()]) # type: ignore + preset: bpy.props.EnumProperty( + name="Preset", default="balance", items=[(k, v, "") for k, v in PRESETS.items()] + ) # type: ignore def execute(self, context): if self.preset == "performance": # EEVEE - # bpy.context.scene.eevee.use_taa_reprojection = False - bpy.context.scene.eevee.use_shadow_jitter_viewport = True - bpy.context.scene.eevee.volumetric_tile_size = '2' + bpy.context.scene.eevee.use_taa_reprojection = False + # bpy.context.scene.eevee.use_shadow_jitter_viewport = True + bpy.context.scene.eevee.volumetric_tile_size = "4" bpy.context.scene.eevee.volumetric_shadow_samples = 32 bpy.context.scene.eevee.volumetric_samples = 64 bpy.context.scene.eevee.volumetric_ray_depth = 1 bpy.context.scene.eevee.use_volumetric_shadows = True # Cycles - bpy.context.scene.cycles.volume_bounces = 0 + bpy.context.scene.cycles.volume_bounces = 4 bpy.context.scene.cycles.transparent_max_bounces = 4 - bpy.context.scene.cycles.volume_preview_step_rate = 4 - bpy.context.scene.cycles.volume_step_rate = 4 + bpy.context.scene.cycles.volume_biased = True + bpy.context.scene.cycles.volume_preview_step_rate = 100 + bpy.context.scene.cycles.volume_step_rate = 100 elif self.preset == "balance": # EEVEE - # bpy.context.scene.eevee.use_taa_reprojection = False - bpy.context.scene.eevee.use_shadow_jitter_viewport = True - bpy.context.scene.eevee.volumetric_tile_size = '2' + bpy.context.scene.eevee.use_taa_reprojection = False + # bpy.context.scene.eevee.use_shadow_jitter_viewport = True + bpy.context.scene.eevee.volumetric_tile_size = "2" bpy.context.scene.eevee.volumetric_shadow_samples = 64 bpy.context.scene.eevee.volumetric_samples = 128 bpy.context.scene.eevee.volumetric_ray_depth = 8 bpy.context.scene.eevee.use_volumetric_shadows = True # Cycles - bpy.context.scene.cycles.volume_bounces = 4 - bpy.context.scene.cycles.transparent_max_bounces = 8 - bpy.context.scene.cycles.volume_preview_step_rate = 1 - bpy.context.scene.cycles.volume_step_rate = 1 + bpy.context.scene.cycles.volume_bounces = 8 + bpy.context.scene.cycles.transparent_max_bounces = 16 + bpy.context.scene.cycles.volume_biased = True + bpy.context.scene.cycles.volume_preview_step_rate = 10 + bpy.context.scene.cycles.volume_step_rate = 10 elif self.preset == "quality": # EEVEE - # bpy.context.scene.eevee.use_taa_reprojection = False - bpy.context.scene.eevee.use_shadow_jitter_viewport = True - bpy.context.scene.eevee.volumetric_tile_size = '2' + bpy.context.scene.eevee.use_taa_reprojection = False + # bpy.context.scene.eevee.use_shadow_jitter_viewport = True + bpy.context.scene.eevee.volumetric_tile_size = "1" bpy.context.scene.eevee.volumetric_shadow_samples = 128 bpy.context.scene.eevee.volumetric_samples = 256 bpy.context.scene.eevee.volumetric_ray_depth = 16 bpy.context.scene.eevee.use_volumetric_shadows = True # Cycles - bpy.context.scene.cycles.volume_bounces = 8 - bpy.context.scene.cycles.transparent_max_bounces = 16 - bpy.context.scene.cycles.volume_preview_step_rate = 0.5 - bpy.context.scene.cycles.volume_step_rate = 0.5 - - return {'FINISHED'} - - -class SliceViewer(bpy.types.Operator): - bl_idname = "bioxelnodes.slice_viewer" - bl_label = "Slice Viewer" - bl_description = "A preview scene setting for viewing slicers" - bl_icon = "FILE_VOLUME" - - def execute(self, context): - # bpy.context.scene.eevee.use_taa_reprojection = False - bpy.context.scene.eevee.volumetric_tile_size = '2' - bpy.context.scene.eevee.volumetric_shadow_samples = 128 - bpy.context.scene.eevee.volumetric_samples = 128 - bpy.context.scene.eevee.volumetric_ray_depth = 1 - - bpy.context.scene.eevee.use_shadows = False - bpy.context.scene.eevee.use_volumetric_shadows = False - - view_3d = None - if context.area.type == 'VIEW_3D': - view_3d = context.area - else: - for area in context.screen.areas: - if area.type == 'VIEW_3D': - view_3d = area - break - if view_3d: - view_3d.spaces[0].shading.type = 'MATERIAL' - view_3d.spaces[0].shading.studio_light = 'studio.exr' - view_3d.spaces[0].shading.studiolight_intensity = 1.5 - view_3d.spaces[0].shading.use_scene_lights = False - view_3d.spaces[0].shading.use_scene_world = False - - return {'FINISHED'} - - -def get_all_layers(layer_filter=None): - def _layer_filter(layer_obj): - return True - - layer_filter = layer_filter or _layer_filter - layer_objs = get_all_layer_objs() - return [obj for obj in layer_objs if layer_filter(obj)] - + bpy.context.scene.cycles.volume_bounces = 16 + bpy.context.scene.cycles.transparent_max_bounces = 32 + bpy.context.scene.cycles.volume_biased = False -class SaveAllLayersCache(bpy.types.Operator, SaveLayersCache): - bl_idname = "bioxelnodes.save_all_layers_cache" - bl_label = "Save All Layers Cache" - bl_description = "Save all cache of this file" - bl_icon = "FILE_TICK" - - success_msg = "Successfully saved all layers." - - def get_layers(self, context): - def is_not_missing(layer_obj): - return not is_missing_layer(layer_obj) - return get_all_layers(is_not_missing) - - -class RemoveAllMissingLayers(bpy.types.Operator, RemoveLayers): - bl_idname = "bioxelnodes.remove_all_missing_layers" - bl_label = "Remove All Missing Layers" - bl_description = "Remove all current container missing layers" - bl_icon = "BRUSH_DATA" - - success_msg = "Successfully removed all missing layers." - - def get_layers(self, context): - def is_missing(layer_obj): - return is_missing_layer(layer_obj) - return get_all_layers(is_missing) - - def invoke(self, context, event): - context.window_manager.invoke_confirm(self, - event, - message=f"Are you sure to remove all **Missing** layers?") - return {'RUNNING_MODAL'} + return {"FINISHED"} class Help(bpy.types.Operator): - bl_idname = "bioxelnodes.help" + bl_idname = "bioxel.help" bl_label = "Need Help?" bl_description = "Online Manual for Beginner" bl_icon = "HELP" def execute(self, context): - webbrowser.open( - 'https://omoolab.github.io/BioxelNodes/latest/', new=2) + webbrowser.open("https://omoolab.github.io/BioxelNodes/latest/", new=2) - return {'FINISHED'} + return {"FINISHED"} -class AddEeveeEnv(bpy.types.Operator): - bl_idname = "bioxelnodes.add_eevee_env" - bl_label = "Add EEVEE Env Light" - bl_description = "To make volume shadow less dark" +# 定义虚无化切换操作 +class TogglePhantom(bpy.types.Operator): + """Toggle object phantom state (ray invisible, no shadows, semi-transparent wireframe)""" + + bl_idname = "bioxel.toggle_phantom" + bl_label = "Toggle Phantom" + bl_options = {"REGISTER", "UNDO"} def execute(self, context): - bpy.ops.wm.append( - directory=f"{str(LATEST_NODE_LIB_PATH)}/Object", - filename="EeveeEnv" - ) + obj = context.active_object + if not obj: + self.report({"WARNING"}, "No object selected") + return {"CANCELLED"} + + # 获取3D视图空间 + view_space = None + for area in bpy.context.screen.areas: + if area.type == "VIEW_3D": + for space in area.spaces: + if space.type == "VIEW_3D": + view_space = space + break + if view_space: + break + + # 确保存储状态的文本数据块存在 + text_name = "phantom_orig_states" + if text_name not in bpy.data.texts: + bpy.data.texts.new(text_name) - bpy.context.scene.eevee.use_shadows = True - bpy.context.scene.eevee.use_volumetric_shadows = True + # 从文本数据块加载状态 + states_text = bpy.data.texts[text_name] + try: + states = json.loads(states_text.as_string()) + except: + states = {} + + def get_obj_uuid(obj): + if "bioxel_uuid" not in obj: + obj["bioxel_uuid"] = uuid.uuid4().hex + return obj["bioxel_uuid"] + + # 使用物体的唯一标识符来追踪 + obj_uuid = get_obj_uuid(obj) + + # 检查物体是否已经处于虚无化状态 + is_phantom = ( + obj.display_type == "SOLID" + and obj.show_wire + and obj.show_in_front + and round(obj.color[3], 2) == 0.10 + and not obj.visible_camera + and not obj.visible_diffuse + and not obj.visible_glossy + and not obj.visible_transmission + and not obj.visible_volume_scatter + and not obj.visible_shadow + ) - return {'FINISHED'} + if is_phantom: + # 恢复原始状态 + if obj_uuid in states: + state = states[obj_uuid] + obj.display_type = state["display_type"] + obj.show_wire = state["show_wire"] + obj.show_in_front = state["show_in_front"] + obj.color = state["color"] + obj.visible_camera = state["visible_camera"] + obj.visible_diffuse = state["visible_diffuse"] + obj.visible_glossy = state["visible_glossy"] + obj.visible_transmission = state["visible_transmission"] + obj.visible_volume_scatter = state["visible_volume_scatter"] + obj.visible_shadow = state["visible_shadow"] + + # 恢复视图着色设置（如果之前有保存） + if view_space and "viewport_color_type" in state: + view_space.shading.color_type = state["viewport_color_type"] + + del states[obj_uuid] + self.report({"INFO"}, f"Object restored") + else: + # 保存原始状态 + state_data = { + "display_type": obj.display_type, + "show_wire": obj.show_wire, + "show_in_front": obj.show_in_front, + "color": list(obj.color), # 保存RGBA颜色值 + "visible_camera": obj.visible_camera, + "visible_diffuse": obj.visible_diffuse, + "visible_glossy": obj.visible_glossy, + "visible_transmission": obj.visible_transmission, + "visible_volume_scatter": obj.visible_volume_scatter, + "visible_shadow": obj.visible_shadow, + } + + # 检查并处理视图着色设置 + if view_space: + # 保存当前视图着色设置 + state_data["viewport_color_type"] = view_space.shading.color_type + + # 检查当前是否为object, random或attribute + valid_types = {"OBJECT", "RANDOM", "ATTRIBUTE"} + if view_space.shading.color_type not in valid_types: + # 改为object模式 + view_space.shading.color_type = "OBJECT" + + states[obj_uuid] = state_data + + # 设置虚无化状态 + obj.display_type = "SOLID" # 以实体方式显示 + obj.show_wire = True # 显示线框 + obj.show_in_front = True # 显示在其他物体前面 + # 保持RGB不变，仅修改alpha透明度为0.1 + obj.color[3] = 0.1 + # 关闭所有射线可见性和投影 + obj.visible_camera = False + obj.visible_diffuse = False + obj.visible_glossy = False + obj.visible_transmission = False + obj.visible_volume_scatter = False + obj.visible_shadow = False + self.report({"INFO"}, f"Object phantomed") + + # 保存状态到文本数据块 + states_text.clear() + states_text.write(json.dumps(states, indent=2)) + + return {"FINISHED"} diff --git a/src/bioxelnodes/operators/node.py b/src/bioxelnodes/operators/node.py index e0d1229..09ba8ef 100644 --- a/src/bioxelnodes/operators/node.py +++ b/src/bioxelnodes/operators/node.py @@ -1,12 +1,12 @@ import bpy -from ..bioxelutils.common import is_incompatible, local_lib_not_updated -from ..bioxelutils.node import assign_node_tree, get_node_tree +from ..utils import is_incompatible, local_lib_not_updated +from ..node import assign_node_tree, get_node_tree from ..utils import get_use_link class AddNode(bpy.types.Operator): - bl_idname = "bioxelnodes.add_node" + bl_idname = "bioxel.add_node" bl_label = "Add Node" bl_options = {"REGISTER", "UNDO"} @@ -24,7 +24,7 @@ class AddNode(bpy.types.Operator): @property def node_type(self): - return f"BioxelNodes_{self.node_name}" + return f"O {self.node_name}" def execute(self, context): space = context.space_data diff --git a/src/bioxelnodes/operators/structure.py b/src/bioxelnodes/operators/structure.py new file mode 100644 index 0000000..c4acf87 --- /dev/null +++ b/src/bioxelnodes/operators/structure.py @@ -0,0 +1,107 @@ +import bpy +from ..utils import get_use_link +from ..node import add_node_to_graph, get_output_node, get_main_node_group + + +class ExtractMesh(bpy.types.Operator): + bl_idname = "bioxel.extract_mesh" + bl_label = "Extract Mesh" + bl_description = "Extract Mesh" + bl_icon = "OUTLINER_OB_MESH" + bl_options = {"UNDO"} + + @classmethod + def poll(cls, context): + # Check if there is a selected node in the node group + node_group = get_main_node_group(context) + selected_nodes = [n for n in node_group.nodes if n.select] + + if len(selected_nodes) == 0: + return False + else: + source_node = selected_nodes[0] + return "Structure" in source_node.outputs + + def execute(self, context): + container_obj = context.object + + if container_obj is None: + self.report({"WARNING"}, "Cannot find any bioxel container.") + return {"FINISHED"} + + node_group = container_obj.modifiers[0].node_group + selected_nodes = [n for n in node_group.nodes if n.select] + + source_node = selected_nodes[0] + + # Check if the selected node has a "Structure" output + if "Structure" not in source_node.outputs: + self.report({"ERROR"}, "Selected node has no 'Structure' output.") + return {"CANCELLED"} + + # 记录原始输出连接（用于后续复原） + output_node = get_output_node(node_group) + original_links = list(output_node.inputs[0].links) + + # 添加Component to Mesh节点 + to_mesh_node = add_node_to_graph( + "Structure to Mesh", node_group, use_link=get_use_link() + ) + + # 连接节点：源节点 -> Component to Mesh -> 输出节点 + node_group.links.new( + source_node.outputs["Structure"], to_mesh_node.inputs[0]) + node_group.links.new(to_mesh_node.outputs[0], output_node.inputs[0]) + + new_obj = None + + try: + deps = context.evaluated_depsgraph_get() + eval_obj = container_obj.evaluated_get(deps) + # obtain evaluated mesh (from modifiers including Geometry Nodes) + mesh_eval = eval_obj.to_mesh() + if mesh_eval is None: + raise RuntimeError("Failed to produce evaluated mesh") + + mesh_name = f"{container_obj.name}_Mesh" + mesh_copy = mesh_eval.copy() + mesh_copy.name = mesh_name + # clear the temporary evaluated mesh + try: + eval_obj.to_mesh_clear() + except Exception: + pass + + # create the new object with same transform as source + new_obj = bpy.data.objects.new(mesh_name, mesh_copy) + # link to same collection as the container (fallback to current collection) + col = ( + container_obj.users_collection[0] + if getattr(container_obj, "users_collection", None) + else context.collection + ) + if col is None: + col = context.collection + col.objects.link(new_obj) + + # copy world transform exactly + new_obj.matrix_world = container_obj.matrix_world.copy() + except Exception as e: + self.report({"ERROR"}, f"Failed to extract mesh: {e}") + + # 恢复原始连接 + for link in original_links: + node_group.links.new(link.from_socket, output_node.inputs[0]) + + # 删除临时添加的Component to Mesh节点 + node_group.nodes.remove(to_mesh_node) + if new_obj: + # deselect everything, select and activate new_obj + for o in list(context.selected_objects): + o.select_set(False) + new_obj.select_set(True) + context.view_layer.objects.active = new_obj + self.report({"INFO"}, f"Mesh extracted: {new_obj.name}") + return {"FINISHED"} + else: + return {"CANCELLED"} diff --git a/src/bioxelnodes/panels.py b/src/bioxelnodes/panels.py new file mode 100644 index 0000000..5c87684 --- /dev/null +++ b/src/bioxelnodes/panels.py @@ -0,0 +1,180 @@ +from pathlib import Path +import bpy + +from .node import get_layer_nodes, get_main_node_group +from .utils import load_icon +from .layer import get_layer_caches +from .operators.io import ImportAsColor, ImportAsLabel, ImportAsScalar, ImportData +from .operators.misc import Help, RenderSettingPreset +from .operators.layer import ( + AddLayerNode, + DeleteLayer, + RelocatePath, + RenameLayer, + SaveLayer, +) + + +class ImportMenu(bpy.types.Menu): + bl_label = "Bioxel Import" + bl_idname = "BIOXEL_MT_import" + + def draw(self, context): + layout = self.layout + layout.operator(ImportAsScalar.bl_idname, + text="Import As Scalar").filepath = "" + layout.operator(ImportAsLabel.bl_idname, + text="Import As Label").filepath = "" + layout.operator(ImportAsColor.bl_idname, + text="Import As Color").filepath = "" + + +class RenderSettingMenu(bpy.types.Menu): + bl_label = "Render Setting Presets" + bl_idname = "BIOXEL_MT_render_setting" + + def draw(self, context): + layout = self.layout + for k, v in RenderSettingPreset.PRESETS.items(): + op = layout.operator(RenderSettingPreset.bl_idname, text=v) + op.preset = k + + +class BioxelPanelBase: + """ + Abstract base panel for all Bioxel UI panels. + + - Ensures the panel appears only when the active area is the Node Editor + and the Node Editor is editing a Geometry Nodes tree. + - Places the panel under the "Bioxel" sidebar tab. + - Provides an optional bl_order for panel ordering inside the category. + """ + + bl_space_type = "NODE_EDITOR" + bl_region_type = "UI" + bl_context = "geometry_node" + bl_category = "胞素（Bioxel）" + # try to make Bioxel panels order early (may be respected by Blender) + + @classmethod + def poll(cls, context): + node_group = get_main_node_group(context) + return node_group is not None + + +class HeaderPanel(bpy.types.Panel, BioxelPanelBase): + bl_label = "胞素（Bioxel）" + bl_idname = "BIOXEL_PT_header_panel" + bl_order = 0 + + def draw(self, context): + layout = self.layout + + layout.operator( + Help.bl_idname, text="Help", icon=Help.bl_icon # 复用原操作的图标定义 + ) + + layout.menu( + RenderSettingMenu.bl_idname, text="Render Preset", icon="RENDER_STILL" + ) + + +class LayerNodePanel(BioxelPanelBase, bpy.types.Panel): + bl_label = "Layer Nodes" + bl_idname = "BIOXEL_PT_o_layer_nodes" + bl_order = 1 + + def draw(self, context): + layout = self.layout + node_group = get_main_node_group(context) + + layout.template_list( + "BIOXEL_UL_layer_nodes", + "", + node_group, + "nodes", + context.window_manager, + "bioxel_layer_list_index", + rows=3, + ) + + +class LibraryPanel(BioxelPanelBase, bpy.types.Panel): + bl_label = "Layer Library" + bl_idname = "BIOXEL_PT_library_panel" + bl_order = 2 + + def draw(self, context): + layout = self.layout + wm = context.window_manager + caches = get_layer_caches() + + row = layout.row() + row.scale_y = 2.0 + row.operator(ImportData.bl_idname, icon="IMPORT") + # row.menu(ImportMenu.bl_idname, icon="IMPORT", text="Import") + layout.separator() + layout.template_icon_view( + bpy.context.window_manager, + "bioxel_layer_library", + show_labels=False, + scale=10.0, + scale_popup=6.0, + ) + + selected_id = getattr(wm, "bioxel_layer_library", None) + selected_id = None if selected_id == "nothing_found" else selected_id + entry = next((c for c in caches if c.get("id") == selected_id), None) + if entry: + cache_id = entry["id"] + path = entry["path"] + name = entry.get("name", "?") + kind = entry.get("kind", "?") + path_exists = Path(bpy.path.abspath(path)).exists() + + layout.prop(wm, "bioxel_snapshot_z", text="Z Slice", slider=True) + layout.separator() + # operations and meta_box as before + ops_row = layout.row(align=True) + if path_exists: + ops_row.operator( + AddLayerNode.bl_idname, text="Add", icon="PLUS" + ).cache_id = selected_id + ops_row.operator( + SaveLayer.bl_idname, text="Save", icon="FILE_TICK" + ).cache_id = selected_id + ops_row.operator( + RenameLayer.bl_idname, text="Name", icon="FONT_DATA" + ).cache_id = selected_id + ops_row.operator( + DeleteLayer.bl_idname, text="", icon="TRASH" + ).cache_id = selected_id + else: + ops_row.operator( + RelocatePath.bl_idname, text="Relocate", icon="FILE_FOLDER" + ).cache_id = selected_id + ops_row.operator( + DeleteLayer.bl_idname, text="", icon="TRASH" + ).cache_id = selected_id + + meta_box = layout.box() + if hasattr(meta_box, "alert"): + meta_box.alert = True + meta_box.label(text=f"Cache is missing...") + meta_box.label(text=f"Please relocate the cache path!") + return + + meta_box = layout.box() + meta_box.label(text=f"Name: {name}") + meta_box.label(text=f"Path: {path}") + meta_box.label(text=f"Kind: {kind}") + meta_box.label( + text=f"Dims: [{entry.get('frame_count',1)},{tuple(entry.get('shape',''))},{entry.get('channel_count',1)}]" + ) + if kind in ["scalar", "color", "vector"]: + path = Path(bpy.path.abspath(entry["path"])) + histogram = load_icon( + path / "histogram.png", f"{cache_id}_histogram") + meta_box.template_icon(histogram, scale=10.0) + else: + layout.label(text="No layer selected", icon="QUESTION") diff --git a/src/bioxelnodes/preferences.py b/src/bioxelnodes/preferences.py index ff9f9ea..650e990 100644 --- a/src/bioxelnodes/preferences.py +++ b/src/bioxelnodes/preferences.py @@ -8,22 +8,10 @@ class BioxelNodesPreferences(bpy.types.AddonPreferences): cache_dir: bpy.props.StringProperty( name="Set Cache Directory", subtype='DIR_PATH', - default=str(Path(Path.home(), '.bioxelnodes')) + default=str(Path(Path.home(), '.bioxel')) ) # type: ignore - change_render_setting: bpy.props.BoolProperty( - name="Change Render Setting on First Import", - default=True, - ) # type: ignore - - node_import_method: bpy.props.EnumProperty(name="Node Import Method", - default="LINK", - items=[("LINK", "Link", ""), - ("APPEND", "Append (Reuse Data)", "")]) # type: ignore - def draw(self, context): layout = self.layout layout.label(text="Configuration") layout.prop(self, 'cache_dir') - layout.prop(self, "change_render_setting") - layout.prop(self, "node_import_method") diff --git a/src/bioxelnodes/props.py b/src/bioxelnodes/props.py index e931831..e79b38b 100644 --- a/src/bioxelnodes/props.py +++ b/src/bioxelnodes/props.py @@ -1,44 +1,134 @@ +from pathlib import Path import bpy -from .bioxelutils.common import get_node_type +from .operators.layer import SelectAndFocusNode +from .utils import load_icon +from .layer import get_layer_caches, set_layer_caches -class BIOXELNODES_UL_layer_list(bpy.types.UIList): - def draw_item(self, context, layout, data, item, icon, active_data, active_propname): - layout.label(text=item.label, translate=False, icon_value=icon) +def get_snapshot_icon(cache, z: float): + cache_id = str(cache["id"]) + shape = (64, 64, 32) + zidx = int(z * (shape[2] - 1)) + path = Path(bpy.path.abspath(cache["path"])) + return load_icon(path / f"snapshot_{zidx}.png", f"{cache_id}_{zidx}") -class BIOXELNODES_Series(bpy.types.PropertyGroup): - id: bpy.props.StringProperty() # type: ignore - label: bpy.props.StringProperty() # type: ignore +def _bioxel_layer_items(self, context): + """ + EnumProperty items callback: 从 get_layer_caches 构造枚举项。 + 使用 PREVIEWS 加载每个 layer 的 thumbnail_png（如果存在）并返回 icon_id。 + """ + items = [] + caches = get_layer_caches() -def select_layer(self, context): - layer_list_UL = bpy.context.window_manager.bioxelnodes_layer_list_UL - layer_list = layer_list_UL.layer_list - layer_list_active = layer_list_UL.layer_list_active + for idx, cache in enumerate(caches): + cache_id = str(cache["id"]) + name = cache.get("name", f"Layer ?") + description = cache.get("kind", "?") + z = cache.get("snapshot_z", 0.5) + icon = get_snapshot_icon(cache, z) + # 在这个context下，只能加载无法生成。 + items.append((cache_id, name, description, icon, idx)) - if len(layer_list) > 0 and layer_list_active != -1 and layer_list_active < len(layer_list): - layer_obj = bpy.data.objects[layer_list[layer_list_active].obj_name] - node_group = context.space_data.edit_tree - for node in node_group.nodes: - node.select = False - if get_node_type(node) == "BioxelNodes_FetchLayer": - if node.inputs[0].default_value == layer_obj: - node.select = True + if not items: + items = [("nothing_found", "No Layers", + "No layers found", "QUESTION", 0)] - layer_list_UL.layer_list_active = -1 + return items -class BIOXELNODES_Layer(bpy.types.PropertyGroup): - obj_name: bpy.props.StringProperty() # type: ignore - label: bpy.props.StringProperty() # type: ignore - info_text: bpy.props.StringProperty() # type: ignore +def _update_layer_gallery(self, context): + wm = context.window_manager + selected_id = getattr(wm, "bioxel_layer_library", None) + cache = next( + (c for c in get_layer_caches() if str(c.get("id", "")) == str(selected_id)), + None, + ) + z = cache.get("snapshot_z", 0.5) if cache else 0.5 + setattr(wm, "bioxel_snapshot_z", z) -class BIOXELNODES_LayerListUL(bpy.types.PropertyGroup): - layer_list: bpy.props.CollectionProperty( - type=BIOXELNODES_Layer) # type: ignore - layer_list_active: bpy.props.IntProperty(default=-1, - update=select_layer, - options=set()) # type: ignore +def _update_snapshot_z(self, context): + """ + update callback for WindowManager.bioxel_thumb_z + - write a slice PNG from the saved .npy + - update PREVIEWS entry for the selected layer + - force template_icon_view to refresh by briefly cycling the EnumProperty value + - force UI redraw + """ + wm = context.window_manager + selected_id = getattr(wm, "bioxel_layer_library", None) + + if not selected_id or selected_id == "nothing_found": + return + + try: + selected_id = int(selected_id) + except Exception: + return + + caches = get_layer_caches() + z = getattr(wm, "bioxel_snapshot_z", 0.5) + + for cache in caches: + if int(cache.get("id", -1)) == selected_id: + cache["snapshot_z"] = z + break + + set_layer_caches(caches) + + +class BIOXEL_Series(bpy.types.PropertyGroup): + id: bpy.props.StringProperty() # type: ignore + label: bpy.props.StringProperty() # type: ignore + + +class BIOXEL_UL_layer_nodes(bpy.types.UIList): + """UIList for O Layer nodes only""" + + bl_idname = "BIOXEL_UL_layer_nodes" + + def filter_items(self, context, data, propname): + nodes = getattr(data, propname) + flt_flags = [] + flt_neworder = [] + + for node in nodes: + # 只保留 O Layer 节点 + if ( + hasattr(node, "bl_idname") + and node.bl_idname.startswith("GeometryNodeGroup") + and getattr(getattr(node, "node_tree", None), "name", "").startswith( + "O Layer" + ) + ): + flt_flags.append(self.bitflag_filter_item) + else: + flt_flags.append(0) + return flt_flags, flt_neworder + + def draw_item( + self, context, layout, data, item, icon, active_data, active_propname, index + ): + node = item + # 这里只画 O Layer 节点，其他已被 filter_items 过滤 + split = layout.split(factor=0.3, align=True) + col1 = split.row(align=True) + col2 = split.row(align=True) + name_socket = node.inputs["Name"] + resample_socket = node.inputs["Resample"] + scale_socket = node.inputs["Bioxel Scale"] + name = str(node.inputs["Name"].default_value) + + # row.prop(name_socket, "default_value", text="") + col1.prop(resample_socket, "default_value", + icon="UV_DATA", text="", toggle=1) + col1.prop(scale_socket, "default_value", text="") + col2.label(text=name) + + op = col2.operator( + SelectAndFocusNode.bl_idname, text="", icon="RESTRICT_SELECT_OFF", emboss=True + ) + op.node_name = node.name diff --git a/src/bioxelnodes/utils.py b/src/bioxelnodes/utils.py index 2bce786..953e792 100644 --- a/src/bioxelnodes/utils.py +++ b/src/bioxelnodes/utils.py @@ -1,6 +1,12 @@ from pathlib import Path +from ast import literal_eval + import shutil import bpy +import numpy as np + +from .node import get_nodes_by_type +from .constants import LATEST_NODE_LIB_PATH, NODE_LIB_DIRPATH, PREVIEW_COLLECTIONS def copy_to_dir(source_path, dir_path, new_name=None, exist_ok=True): @@ -44,16 +50,16 @@ def select_object(target_obj): def progress_bar(self, context): row = self.layout.row() row.progress( - factor=context.window_manager.bioxelnodes_progress_factor, + factor=context.window_manager.bioxel_progress_factor, type="BAR", - text=context.window_manager.bioxelnodes_progress_text + text=context.window_manager.bioxel_progress_text ) row.scale_x = 2 def progress_update(context, factor, text=""): - context.window_manager.bioxelnodes_progress_factor = factor - context.window_manager.bioxelnodes_progress_text = text + bpy.context.window_manager.bioxel_progress_factor = factor + bpy.context.window_manager.bioxel_progress_text = text def get_preferences(): @@ -62,11 +68,335 @@ def get_preferences(): def get_cache_dir(): preferences = get_preferences() - cache_path = Path(preferences.cache_dir, 'VDBs') + cache_path = Path(preferences.cache_dir) cache_path.mkdir(parents=True, exist_ok=True) - return str(cache_path) + return cache_path def get_use_link(): preferences = get_preferences() return preferences.node_import_method == "LINK" + + +def get_container_objs_from_selection(): + container_objs = [] + for obj in bpy.context.selected_objects: + if get_container_obj(obj): + container_objs.append(obj) + + return list(set(container_objs)) + + +def get_container_obj(current_obj): + if current_obj: + if current_obj.get('bioxel_container'): + return current_obj + elif current_obj.get('bioxel_layer'): + parent = current_obj.parent + return parent if parent.get('bioxel_container') else None + return None + + +def get_layer_prop_value(layer_obj: bpy.types.Object, prop_name: str): + node_group = layer_obj.modifiers[0].node_group + layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0] + prop = layer_node.inputs.get(prop_name) + if prop is None: + return None + + value = prop.default_value + + if type(value).__name__ == "bpy_prop_array": + value = tuple(value) + return tuple([int(v) for v in value]) \ + if prop in ["shape"] else value + elif type(value).__name__ == "str": + return str(value) + elif type(value).__name__ == "float": + value = float(value) + return round(value, 2) \ + if prop in ["bioxel_size"] else value + elif type(value).__name__ == "int": + value = int(value) + return value + else: + return value + + +def get_layer_name(layer_obj): + return get_layer_prop_value(layer_obj, "name") + + +def get_layer_kind(layer_obj): + return get_layer_prop_value(layer_obj, "kind") + + +def get_layer_label(layer_obj): + name = get_layer_name(layer_obj) + # kind = get_layer_kind(layer_obj) + + label = f"{name}" + + if is_missing_layer(layer_obj): + return "**MISSING**" + label + elif is_temp_layer(layer_obj): + return "* " + label + else: + return label + + +def is_missing_layer(layer_obj): + cache_filepath = Path(bpy.path.abspath( + layer_obj.data.filepath)).resolve() + return not cache_filepath.is_file() + + +def is_temp_layer(layer_obj): + cache_filepath = Path(bpy.path.abspath( + layer_obj.data.filepath)).resolve() + cache_dirpath = Path(get_cache_dir()) + return cache_dirpath in cache_filepath.parents + + +def set_layer_prop_value(layer_obj: bpy.types.Object, prop: str, value): + node_group = layer_obj.modifiers[0].node_group + layer_node = get_nodes_by_type(node_group, "BioxelNodes__Layer")[0] + layer_node.inputs[prop].default_value = value + + +def get_layer_obj(current_obj: bpy.types.Object): + if current_obj: + if current_obj.get('bioxel_layer') and current_obj.parent: + if current_obj.parent.get('bioxel_container'): + return current_obj + return None + + +def get_container_layer_objs(container_obj: bpy.types.Object): + layer_objs = [] + for obj in bpy.data.objects: + if obj.parent == container_obj and get_layer_obj(obj): + layer_objs.append(obj) + + return layer_objs + + +def get_all_layer_objs(): + layer_objs = [] + for obj in bpy.data.objects: + if get_layer_obj(obj): + layer_objs.append(obj) + + return layer_objs + + +def add_driver(target, target_prop, var_sources, expression): + driver = target.driver_add(target_prop) + is_vector = isinstance(driver, list) + drivers = driver if is_vector else [driver] + + for i, driver in enumerate(drivers): + for j, var_source in enumerate(var_sources): + + source = var_source['source'] + prop = var_source['prop'] + + var = driver.driver.variables.new() + var.name = f"var{j}" + + var.targets[0].id_type = source.id_type + var.targets[0].id = source + var.targets[0].data_path = f'["{prop}"][{i}]'\ + if is_vector else f'["{prop}"]' + + driver.driver.expression = expression + + +def add_direct_driver(target, target_prop, source, source_prop): + drivers = [ + { + "source": source, + "prop": source_prop + } + ] + expression = "var0" + add_driver(target, target_prop, drivers, expression) + + +def read_file_prop(content: str): + props = {} + for line in content.split("\n"): + line = line.replace(" ", "") + p = line.split("=")[0] + if p != "": + v = line.split("=")[-1] + props[p] = v + return props + + +def write_file_prop(props: dict): + lines = [] + for p, v in props.items(): + lines.append(f"{p} = {v}") + return "\n".join(lines) + + +def set_file_prop(prop, value): + if bpy.data.texts.get("BioxelNodes") is None: + bpy.data.texts.new("BioxelNodes") + + props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string()) + props[prop] = value + bpy.data.texts["BioxelNodes"].clear() + bpy.data.texts["BioxelNodes"].write(write_file_prop(props)) + + +def get_file_prop(prop): + if bpy.data.texts.get("BioxelNodes") is None: + bpy.data.texts.new("BioxelNodes") + + props = read_file_prop(bpy.data.texts["BioxelNodes"].as_string()) + return props.get(prop) + + +def get_node_version(): + node_version = get_file_prop("node_version") + return literal_eval(node_version) if node_version else None + + +def is_incompatible(): + return False + + +def get_node_lib_path(node_version): + version_str = "v"+".".join([str(i) for i in list(node_version)]) + lib_filename = f"BioxelNodes_{version_str}.blend" + return Path(NODE_LIB_DIRPATH, + lib_filename).resolve() + + +def local_lib_not_updated(): + return False + + +def ndarray_to_png(array: np.ndarray, save_path: str): + """ + Create a PNG from a 2D or 3-channel slice array using Blender API. + slice_arr expected shape: (W, H) or (W, H, 1) or (W,H,3). Values assumed numeric. + + The function: + - Converts single-channel arrays to RGB by repeating channel. + - Flips the image vertically to match Blender's origin. + - Writes the image file to save_path using a temporary Blender image datablock. + + Parameters: + - array: numpy ndarray representing the slice (W,H,C) or (W,H,1) or (W,H) + - save_path: destination PNG filepath + """ + save_path = Path(save_path) + h, w = array.shape[0], array.shape[1] + if array.shape[2] == 1: + img = np.concatenate([array, array, array], axis=2) + else: + img = array[..., :3] + + # Blender expects pixels as sequence of floats in RGBA, length w*h*4 + # NOTE: Blender's image origin is bottom-left; we'll flip vertically for visual consistency. + img = np.flipud(img) + pixels = np.empty((h * w * 4,), dtype=np.float32) + # fill + pixels[0::4] = img[..., 0].ravel() + pixels[1::4] = img[..., 1].ravel() + pixels[2::4] = img[..., 2].ravel() + pixels[3::4] = 1.0 + + # create a temporary image datablock, save then remove + name = "tmp" + image = bpy.data.images.new( + name, width=w, height=h, alpha=True, float_buffer=False) + image.pixels = pixels.tolist() + # ensure format and filepath then save + image.filepath_raw = str(save_path) + image.file_format = "PNG" + image.save() + # remove from data to avoid clutter + try: + bpy.data.images.remove(image) + except Exception: + pass + + +def split_text_to_lines(text: str, max_chars: int = 60) -> list: + """ + Split `text` into multiple lines not exceeding `max_chars` where possible. + Breaks on whitespace; long words are chunked. + Returns list of line strings. + """ + if not text: + return [] + words = text.split() + lines = [] + cur = "" + for w in words: + if cur: + candidate = cur + " " + w + else: + candidate = w + if len(candidate) <= max_chars: + cur = candidate + else: + if cur: + lines.append(cur) + # if single word longer than max_chars, chunk it + if len(w) > max_chars: + for i in range(0, len(w), max_chars): + lines.append(w[i: i + max_chars]) + cur = "" + else: + cur = w + if cur: + lines.append(cur) + return lines + + +def wrapped_label(layout, text: str, max_chars: int = 42): + """ + Helper to add multiple layout.label calls for a long text. + """ + for line in split_text_to_lines(text, max_chars=max_chars): + layout.label(text=line) + + +def refresh_bioxel_panels(context): + """ + Force Bioxel UI to refresh. + + - Tags relevant areas for redraw. + - Nudges the bioxel_layer_gallery EnumProperty to force items() re-evaluation + when possible (helps template_icon_view pick up updated icons/paths). + Use this from operators after they change b i o x e l _ l a y e r s or previews. + """ + + # tag redraw for all windows/areas + for window in context.window_manager.windows: + for area in window.screen.areas: + # target node editor and other UI areas that may show previews + if area.type in {"NODE_EDITOR", "VIEW_3D", "IMAGE_EDITOR", "OUTLINER"}: + area.tag_redraw() + + +def load_icon(filepath: Path, key: str): + pcoll = PREVIEW_COLLECTIONS["layers"] + + try: + icon = pcoll[key].icon_id + except KeyError: + if filepath.exists(): + pcoll.load(key, str(filepath), "IMAGE") + + try: + icon = pcoll[key].icon_id + except KeyError: + icon = "TEXTURE" + + return icon diff --git a/tests/__init__.py b/tests/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/uv.lock b/uv.lock index 8eab207..58a3050 100644 --- a/uv.lock +++ b/uv.lock @@ -1,5 +1,5 @@ version = 1 -revision = 1 +revision = 2 requires-python = ">=3.11.0, <3.12" [[package]] @@ -9,26 +9,27 @@ source = { registry = "https://pypi.org/simple" } dependencies = [ { name = "pycodestyle" }, ] -sdist = { url = "https://files.pythonhosted.org/packages/6c/52/65556a5f917a4b273fd1b705f98687a6bd721dbc45966f0f6687e90a18b0/autopep8-2.3.1.tar.gz", hash = "sha256:8d6c87eba648fdcfc83e29b788910b8643171c395d9c4bcf115ece035b9c9dda", size = 92064 } +sdist = { url = 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formats, data properties, and edge cases. - Included tests for real data files to ensure functionality with actual datasets. --- .gitignore | 4 +- AGENTS.md | 5 + src/bioxelnodes/bioxel/__init__.py | 34 ++ src/bioxelnodes/bioxel/data.py | 831 +++++++++++++++++++++++++++++ src/bioxelnodes/bioxel/layer.py | 6 + src/bioxelnodes/layer.py | 15 +- src/bioxelnodes/node.py | 2 +- src/bioxelnodes/operators/io.py | 280 +--------- src/bioxelnodes/operators/layer.py | 18 +- tests/README.md | 43 ++ tests/test_bioxel.py | 539 +++++++++++++++++++ 11 files changed, 1502 insertions(+), 275 deletions(-) create mode 100644 src/bioxelnodes/bioxel/data.py create mode 100644 tests/README.md create mode 100644 tests/test_bioxel.py diff --git a/.gitignore b/.gitignore index 30b51f1..960f98e 100644 --- a/.gitignore +++ b/.gitignore @@ -135,4 +135,6 @@ pythonlib* # Blender *.blend1 blendcache_* -*.cats.txt~ \ No newline at end of file +*.cats.txt~ + +tests/data \ No newline at end of file diff --git a/AGENTS.md b/AGENTS.md index d409372..661944b 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -24,6 +24,11 @@ uv sync uv run build.py # platforms: windows-x64, linux-x64, macos-arm64, macos-x64 ``` +### Unit Test +```bash +uv run pytest tests/ +``` + ### Code Quality ```bash # Format code (autopep8) diff --git a/src/bioxelnodes/bioxel/__init__.py b/src/bioxelnodes/bioxel/__init__.py index e69de29..039ca35 100644 --- a/src/bioxelnodes/bioxel/__init__.py +++ b/src/bioxelnodes/bioxel/__init__.py @@ -0,0 +1,34 @@ +from .layer import Layer +from .container import Container +from .io import load_container, save_container +from .data import ( + Data, + read, + read_meta, + calc_layer_shape, + calc_layer_size, + get_ext, + SUPPORT_EXTS, + DICOM_EXTS, + OME_EXTS, + MRC_EXTS, + SEQUENCE_EXTS +) + +__all__ = [ + 'Layer', + 'Container', + 'load_container', + 'save_container', + 'Data', + 'read', + 'read_meta', + 'calc_layer_shape', + 'calc_layer_size', + 'get_ext', + 'SUPPORT_EXTS', + 'DICOM_EXTS', + 'OME_EXTS', + 'MRC_EXTS', + 'SEQUENCE_EXTS' +] diff --git a/src/bioxelnodes/bioxel/data.py b/src/bioxelnodes/bioxel/data.py new file mode 100644 index 0000000..a9c199d --- /dev/null +++ b/src/bioxelnodes/bioxel/data.py @@ -0,0 +1,831 @@ +from dataclasses import dataclass, field +from pathlib import Path +from typing import Optional, Callable, List +import numpy as np +import SimpleITK as sitk +from pyometiff import OMETIFFReader +import mrcfile +import transforms3d + +from .layer import Layer + +# 类型定义 +ProgressCallback = Optional[Callable[[float, str], None]] + + +SUPPORT_EXTS = [ + "", + ".dcm", + ".DCM", + ".DICOM", + ".ima", + ".IMA", + ".ome.tiff", + ".ome.tif", + ".tif", + ".TIF", + ".tiff", + ".TIFF", + ".mrc", + ".mrc.gz", + ".map", + ".map.gz", + ".bmp", + ".BMP", + ".png", + ".PNG", + ".jpg", + ".JPG", + ".jpeg", + ".JPEG", + ".PIC", + ".pic", + ".gipl", + ".gipl.gz", + ".lsm", + ".LSM", + ".mnc", + ".MNC", + ".mrc", + ".rec", + ".mha", + ".mhd", + ".hdf", + ".h4", + ".hdf4", + ".he2", + ".h5", + ".hdf5", + ".he5", + ".nia", + ".nii", + ".nii.gz", + ".hdr", + ".img", + ".img.gz", + ".nrrd", + ".nhdr", + ".vtk", + ".gz", +] + +OME_EXTS = [".ome.tiff", ".ome.tif", ".tif", ".TIF", ".tiff", ".TIFF"] + +MRC_EXTS = [".mrc", ".mrc.gz", ".map", ".map.gz"] + +DICOM_EXTS = ["", ".dcm", ".DCM", ".DICOM", ".ima", ".IMA"] + +SEQUENCE_EXTS = [ + ".bmp", + ".BMP", + ".jpg", + ".JPG", + ".jpeg", + ".JPEG", + ".tif", + ".TIF", + ".tiff", + ".TIFF", + ".png", + ".PNG", + ".mrc", +] + + +@dataclass +class Data: + filepath: str + series_id: str + _data: Optional[np.ndarray] = field(default=None, repr=False) + _meta: Optional[dict] = field(default=None, repr=False) + + @property + def data(self) -> np.ndarray: + if self._data is None: + self.load_data() + return self._data + + @property + def meta(self) -> dict: + if self._meta is None: + self.load_meta() + return self._meta + + @property + def name(self) -> str: + return self.meta["name"] + + @property + def description(self) -> str: + return self.meta["description"] + + @property + def shape(self) -> tuple: + return ( + self.meta["frame_count"], + *self.meta["xyz_shape"], + self.meta["channel_count"], + ) + + @property + def xyz_shape(self) -> tuple: + return self.meta["xyz_shape"] + + @property + def spacing(self) -> tuple: + return self.meta["spacing"] + + @property + def affine(self) -> np.ndarray: + return self.meta["affine"] + + @property + def frame_count(self) -> int: + return self.meta["frame_count"] + + @property + def channel_count(self) -> int: + return self.meta["channel_count"] + + @property + def dtype(self) -> np.dtype: + return self.meta.get("dtype", np.float32) + + def load_meta(self, progress_callback: ProgressCallback = None): + data, meta = self._parse_file(progress_callback) + self._meta = meta + del data + + def load_data(self, progress_callback: ProgressCallback = None): + if not self.is_loaded(): + data, meta = self._parse_file(progress_callback) + self._data = data + self._meta = meta + + def is_loaded(self) -> bool: + return self._data is not None + + def to_layers( + self, + kind: str = "scalar", + layer_name: str = "", + bioxel_size: float = 1.0, + smooth: int = 0, + remap: bool = False, + split_channel: bool = False, + frame_source: str = "-1", + progress_callback: ProgressCallback = None, + ) -> List[Layer]: + from .layer import Layer + + data = self.data.copy() + + data, layer_shape = self._transform_shape(data, frame_source) + + data = self._preprocess(data, kind, remap) + + mat_scale = transforms3d.zooms.zfdir2aff(bioxel_size) + affine = np.dot(self.meta["affine"], mat_scale) + + base_name = layer_name or kind.capitalize() + + if kind == "label": + return self._create_label_layers( + data, base_name, layer_shape, affine, smooth, progress_callback + ) + elif kind == "color": + return self._create_color_layers( + data, base_name, layer_shape, affine, progress_callback + ) + elif kind == "scalar": + return self._create_scalar_layers( + data, + base_name, + layer_shape, + affine, + smooth, + split_channel, + progress_callback, + ) + + return [] + + def _parse_file(self, progress_callback: ProgressCallback = None): + data_path = Path(self.filepath).resolve() + ext = self._get_ext(data_path) + + if progress_callback: + progress_callback(0.0, "Reading Data...") + + is_sequence = False + sequence = None + if ext in SEQUENCE_EXTS: + sequence = self._collect_sequence(data_path) + if sequence and len(sequence) > 1: + is_sequence = True + + data = None + name = "" + description = "" + affine = np.identity(4) + spacing = (1, 1, 1) + origin = (0, 0, 0) + direction = (1, 0, 0, 0, 1, 0, 0, 0, 1) + + if data is None and ext in MRC_EXTS and not is_sequence: + data, name, spacing = self._parse_mrc(data_path) + + if data is None and ext in OME_EXTS and not is_sequence: + data, name, spacing = self._parse_ome_tiff(data_path, progress_callback) + + if data is None: + data, name, description, spacing, origin, direction = self._parse_sitk( + data_path, ext, is_sequence, sequence, progress_callback + ) + + t = origin + r = np.array(direction).reshape((3, 3)) + affine = np.dot(affine, transforms3d.affines.compose(t, r, [1, 1, 1])) + + meta = { + "name": name, + "description": description, + "spacing": spacing, + "affine": affine, + "xyz_shape": data.shape[1:4], + "frame_count": data.shape[0], + "channel_count": data.shape[-1], + "dtype": data.dtype, + } + + return data, meta + + def _parse_mrc(self, data_path: Path): + print("Parsing with mrcfile...") + with mrcfile.open(data_path, "r") as mrc: + mrc_data = mrc.data + + if mrc.is_single_image(): + data = np.expand_dims(np.asarray(mrc_data), axis=0) + data = np.expand_dims(data, axis=-1) + data = np.expand_dims(data, axis=-1) + elif mrc.is_image_stack(): + data = np.expand_dims(np.asarray(mrc_data), axis=-1) + data = np.expand_dims(data, axis=-1) + elif mrc.is_volume(): + data = np.expand_dims(np.asarray(mrc_data), axis=0) + data = np.expand_dims(data, axis=-1) + elif mrc.is_volume_stack(): + data = np.expand_dims(np.asarray(mrc_data), axis=-1) + + name = self._get_file_no_digits_name(data_path) + spacing = (mrc.voxel_size.x, mrc.voxel_size.y, mrc.voxel_size.z) + + return data, name, spacing + + def _parse_ome_tiff(self, data_path: Path, progress_callback=None): + print("Parsing with OMETIFFReader...") + reader = OMETIFFReader(fpath=data_path) + ome_image, metadata, xml_metadata = reader.read() + + if progress_callback: + progress_callback(0.5, "Transpose to 'TXYZC'...") + + try: + ome_order = metadata["DimOrder BF Array"] + data = self._transpose_ome_image(ome_image, ome_order) + + try: + spacing = ( + metadata["PhysicalSizeX"], + metadata["PhysicalSizeY"], + metadata["PhysicalSizeZ"], + ) + except: + spacing = (1, 1, 1) + + name = self._get_file_no_digits_name(data_path) + except Exception as e: + print(f"Error parsing OME-TIFF: {e}") + data = np.zeros((1, 1, 1, 1, 1), dtype=np.float32) + name = "" + spacing = (1, 1, 1) + + return data, name, spacing + + def _parse_sitk( + self, + data_path: Path, + ext: str, + is_sequence: bool, + sequence: Optional[list], + progress_callback=None, + ): + print("Parsing with SimpleITK...") + + if ext in DICOM_EXTS: + data_dirpath = data_path.parent + reader = sitk.ImageSeriesReader() + reader.MetaDataDictionaryArrayUpdateOn() + reader.LoadPrivateTagsOn() + series_files = reader.GetGDCMSeriesFileNames( + str(data_dirpath), self.series_id + ) + reader.SetFileNames(series_files) + + itk_image = reader.Execute() + name, description = self._extract_dicom_meta(reader, data_dirpath) + + elif ext in SEQUENCE_EXTS and is_sequence and sequence: + sequence_list = sequence if sequence else [] + itk_image = sitk.ReadImage(sequence_list) + name = self._get_file_no_digits_name(data_path) + description = "" + + else: + itk_image = sitk.ReadImage(data_path) + name = self._get_filename(data_path) + description = "" + + if progress_callback: + progress_callback(0.5, "Transpose to 'TXYZC'...") + + data = self._convert_sitk_to_numpy(itk_image, ext, is_sequence) + + if itk_image.GetDimension() >= 3 and ext not in SEQUENCE_EXTS: + spacing = tuple(itk_image.GetSpacing()) + origin = tuple(itk_image.GetOrigin()) + direction = tuple(itk_image.GetDirection()) + else: + spacing = (1, 1, 1) + origin = (0, 0, 0) + direction = (1, 0, 0, 0, 1, 0, 0, 0, 1) + + return data, name, description, spacing, origin, direction + + def _transpose_ome_image(self, ome_image, ome_order: str): + if ome_image.ndim == 2: + ome_order = ome_order.replace("T", "").replace("C", "").replace("Z", "") + bioxel_order = (ome_order.index("X"), ome_order.index("Y")) + data = np.transpose(ome_image, bioxel_order) + data = np.expand_dims(data, axis=0) + data = np.expand_dims(data, axis=-1) + data = np.expand_dims(data, axis=-1) + + elif ome_image.ndim == 3: + ome_order = ome_order.replace("T", "").replace("C", "") + bioxel_order = ( + ome_order.index("X"), + ome_order.index("Y"), + ome_order.index("Z"), + ) + data = np.transpose(ome_image, bioxel_order) + data = np.expand_dims(data, axis=0) + data = np.expand_dims(data, axis=-1) + + elif ome_image.ndim == 4: + ome_order = ome_order.replace("T", "") + bioxel_order = ( + ome_order.index("X"), + ome_order.index("Y"), + ome_order.index("Z"), + ome_order.index("C"), + ) + data = np.transpose(ome_image, bioxel_order) + data = np.expand_dims(data, axis=0) + + elif ome_image.ndim == 5: + bioxel_order = ( + ome_order.index("T"), + ome_order.index("X"), + ome_order.index("Y"), + ome_order.index("Z"), + ome_order.index("C"), + ) + data = np.transpose(ome_image, bioxel_order) + + return data + + def _convert_sitk_to_numpy(self, itk_image, ext: str, is_sequence: bool): + if itk_image.GetDimension() == 2: + data = sitk.GetArrayFromImage(itk_image) + + if data.ndim == 3: + data = np.transpose(data, (1, 0, 2)) + data = np.expand_dims(data, axis=-2) + else: + data = np.transpose(data) + data = np.expand_dims(data, axis=-1) + data = np.expand_dims(data, axis=-1) + + data = np.expand_dims(data, axis=0) + + elif itk_image.GetDimension() == 3: + if ext not in SEQUENCE_EXTS: + itk_image = sitk.DICOMOrient(itk_image, "RAS") + + data = sitk.GetArrayFromImage(itk_image) + + if data.ndim == 4: + data = np.transpose(data, (2, 1, 0, 3)) + else: + data = np.transpose(data) + data = np.expand_dims(data, axis=-1) + + data = np.expand_dims(data, axis=0) + + elif itk_image.GetDimension() == 4: + data = sitk.GetArrayFromImage(itk_image) + + if data.ndim == 5: + data = np.transpose(data, (0, 3, 2, 1, 4)) + else: + data = np.transpose(data, (0, 3, 2, 1)) + data = np.expand_dims(data, axis=-1) + + return data + + def _extract_dicom_meta(self, reader, data_dirpath: Path): + def get_meta(key): + try: + string = reader.GetMetaData(0, key).removesuffix(" ") + string.encode("utf-8") + if string in ["No study description", "No series description", ""]: + return None + else: + return string + except: + return None + + study_description = get_meta("0008|1030") or data_dirpath.name + series_description = get_meta("0008|103e") + series_modality = get_meta("0008|0060") + + if series_description and series_modality: + description = f"{series_description}-{series_modality}" + elif series_description: + description = series_description + elif series_modality: + description = series_modality + else: + description = "" + + name = study_description.replace(" ", "-") + description = description.replace(" ", "-") + + return name, description + + @staticmethod + def _get_ext(filepath: Path) -> str: + if filepath.name.endswith(".nii.gz"): + return ".nii.gz" + elif filepath.name.endswith(".img.gz"): + return ".img.gz" + elif filepath.name.endswith(".gipl.gz"): + return ".gipl.gz" + elif filepath.name.endswith(".ome.tiff"): + return ".ome.tiff" + elif filepath.name.endswith(".ome.tif"): + return ".ome.tif" + elif filepath.name.endswith(".mrc.gz"): + return ".mrc.gz" + elif filepath.name.endswith(".map.gz"): + return ".map.gz" + else: + suffix = filepath.suffix + return "" if len(suffix) > 5 else suffix + + @staticmethod + def _get_filename(filepath: Path) -> str: + ext = Data._get_ext(filepath) + return filepath.name.removesuffix(ext) + + @staticmethod + def _get_file_no_digits_name(filepath: Path) -> str: + prefix, digits, suffix = Data._get_filename_parts(filepath) + prefix = Data._remove_end_str(prefix, "_") + prefix = Data._remove_end_str(prefix, ".") + prefix = Data._remove_end_str(prefix, "-") + prefix = Data._remove_end_str(prefix, " ") + return prefix + suffix + + @staticmethod + def _get_filename_parts(filepath: Path) -> tuple: + def has_digits(s): + return any(char.isdigit() for char in s) + + name = Data._get_filename(filepath) + parts = name.replace(".", " ").replace("_", " ").split(" ") + skip_prefixs = ["CH", "ch", "channel"] + number_part = None + number_part_i = None + + for i, part in enumerate(parts[::-1]): + if has_digits(part): + if not any([part.startswith(prefix) for prefix in skip_prefixs]): + number_part = part + number_part_i = len(parts) - i + break + + if number_part is None: + return name, "", "" + + prefix_parts = parts[: number_part_i - 1] + prefix_parts_count = sum([len(part) + 1 for part in prefix_parts]) + + digits = "" + suffix = "" + + started = False + for char in number_part[::-1]: + if char.isdigit(): + started = True + digits += char + else: + if started: + break + else: + suffix += char + + digits = digits[::-1] + + prefix_parts_count += len(number_part) - len(digits) - len(suffix) + + prefix = name[:prefix_parts_count] + suffix = name[prefix_parts_count + len(digits) :] + + return prefix, digits, suffix + + @staticmethod + def _get_file_index(filepath: Path) -> int: + prefix, digits, suffix = Data._get_filename_parts(filepath) + return int(digits) if digits != "" else 0 + + @staticmethod + def _collect_sequence(filepath: Path): + file_dict = {} + for f in filepath.parent.iterdir(): + if ( + f.is_file() + and Data._get_ext(filepath) == Data._get_ext(f) + and Data._get_file_no_digits_name(filepath) + == Data._get_file_no_digits_name(f) + ): + index = Data._get_file_index(f) + file_dict[index] = f + + for key in list(file_dict.keys()): + if not file_dict.get(key + 1) and not file_dict.get(key - 1): + del file_dict[key] + + file_dict = dict(sorted(file_dict.items())) + sequence = [str(f) for f in file_dict.values()] + + if len(sequence) == 0: + sequence = [str(filepath)] + + return sequence + + @staticmethod + def _remove_end_str(string: str, end: str) -> str: + while string.endswith(end) and len(string) > 0: + string = string.removesuffix(end) + return string + + def _transform_shape(self, data, frame_source: str) -> tuple: + orig_shape = self.xyz_shape + + if frame_source == "-1": + data = data[0:1, :, :, :, :] + new_shape = orig_shape + elif frame_source == "0": + new_shape = orig_shape + elif frame_source == "1": + data = data.transpose(1, 0, 2, 3, 4) + new_shape = (1, orig_shape[1], orig_shape[2]) + elif frame_source == "2": + data = data.transpose(2, 1, 0, 3, 4) + new_shape = (orig_shape[0], 1, orig_shape[2]) + elif frame_source == "3": + data = data.transpose(3, 1, 2, 0, 4) + new_shape = (orig_shape[0], orig_shape[1], 1) + else: + data = data.transpose(4, 1, 2, 3, 0) + new_shape = orig_shape + + return data, new_shape + + def _preprocess(self, data, kind: str, remap: bool) -> np.ndarray: + if kind == "color": + if np.issubdtype(data.dtype, np.uint8): + data = np.multiply(data, 1.0 / 256, dtype=np.float32) + elif data.dtype.kind in ["u", "i"]: + data = data.astype(np.float32) + min_val, max_val = data.min(), data.max() + if max_val != min_val: + data = (data - min_val) / (max_val - min_val) + else: + data = np.zeros_like(data, dtype=np.float32) + else: + data = data.astype(np.float32) + + if data.shape[4] == 1: + data = np.repeat(data, repeats=3, axis=4) + elif data.shape[4] == 2: + zeros_shape = list(data.shape[:4]) + [1] + zeros = np.zeros(zeros_shape, dtype=np.float32) + data = np.concatenate((data, zeros), axis=-1) + elif data.shape[4] > 3: + data = data[:, :, :, :, :3] + + elif kind == "scalar": + if remap: + data = data.astype(np.float32) + min_val, max_val = data.min(), data.max() + if max_val != min_val: + data = (data - min_val) / (max_val - min_val) + else: + data = np.zeros_like(data, dtype=np.float32) + + elif kind == "label": + data = data.astype(int) + + return data + + def _create_progress_cb_factory(self, progress_callback): + def factory(name, progress, progress_step): + def callback(frame, total): + if progress_callback: + sub_progress = progress + frame * (progress_step / total) + progress_callback( + sub_progress, f"Processing {name} Frame {frame+1}..." + ) + + return callback + + return factory + + def _create_label_layers( + self, + data, + base_name, + layer_shape, + affine, + smooth, + progress_callback: ProgressCallback, + ): + from .layer import Layer + + layers = [] + label_count = int(np.max(data)) + if label_count == 0: + return layers + + progress_step = 0.7 / label_count + cb_factory = self._create_progress_cb_factory(progress_callback) + + for i in range(label_count): + name_i = f"{base_name}_{i+1}" + progress = 0.2 + i * progress_step + if progress_callback: + progress_callback(progress, f"Processing {name_i}...") + + label_data = data == np.full_like(data, i + 1) + progress_cb = cb_factory(name_i, progress, progress_step) + + layer = Layer(data=label_data, name=name_i, kind="label") + layer.resize( + shape=layer_shape, smooth=smooth, progress_callback=progress_cb + ) + layer.affine = affine + layers.append(layer) + + return layers + + def _create_color_layers( + self, data, base_name, layer_shape, affine, progress_callback: ProgressCallback + ): + from .layer import Layer + + if progress_callback: + progress_callback(0.2, f"Processing {base_name}...") + + cb_factory = self._create_progress_cb_factory(progress_callback) + progress_cb = cb_factory(base_name, 0.2, 0.7) + + layer = Layer(data=data, name=base_name, kind="color") + layer.resize(shape=layer_shape, progress_callback=progress_cb) + layer.affine = affine + + return [layer] + + def _create_scalar_layers( + self, + data, + base_name, + layer_shape, + affine, + smooth, + split_channel, + progress_callback: ProgressCallback, + ): + from .layer import Layer + + layers = [] + cb_factory = self._create_progress_cb_factory(progress_callback) + + if split_channel: + channel_count = data.shape[-1] + progress_step = 0.7 / channel_count + + for i in range(channel_count): + name_i = f"{base_name}_{i+1}" + progress = 0.2 + i * progress_step + if progress_callback: + progress_callback(progress, f"Processing {name_i}...") + + progress_cb = cb_factory(name_i, progress, progress_step) + layer = Layer( + data=data[:, :, :, :, i : i + 1], name=name_i, kind="scalar" + ) + layer.resize( + shape=layer_shape, smooth=smooth, progress_callback=progress_cb + ) + layer.affine = affine + layers.append(layer) + else: + if progress_callback: + progress_callback(0.2, f"Processing {base_name}...") + + progress_cb = cb_factory(base_name, 0.2, 0.7) + layer = Layer(data=data, name=base_name, kind="scalar") + layer.resize( + shape=layer_shape, smooth=smooth, progress_callback=progress_cb + ) + layer.affine = affine + layers.append(layer) + + return layers + + +# 模块级函数签名 +def read( + filepath: str, series_id: str = "", progress_callback: ProgressCallback = None +) -> Data: + filepath = Path(filepath).resolve() + if not filepath.exists(): + raise FileNotFoundError(f"File not found: {filepath}") + + data_obj = Data(filepath=filepath, series_id=series_id) + data_obj.load_data(progress_callback) + return data_obj + + +def read_meta(filepath: str, series_id: str = "") -> Data: + data_obj = Data(filepath=filepath, series_id=series_id) + data_obj.load_meta() + return data_obj + + +def calc_layer_shape( + bioxel_size: float, orig_shape: tuple, orig_spacing: tuple +) -> tuple: + shape = ( + int(orig_shape[0] / bioxel_size * orig_spacing[0]), + int(orig_shape[1] / bioxel_size * orig_spacing[1]), + int(orig_shape[2] / bioxel_size * orig_spacing[2]), + ) + return ( + shape[0] if shape[0] > 0 else 1, + shape[1] if shape[1] > 0 else 1, + shape[2] if shape[2] > 0 else 1, + ) + + +def calc_layer_size(shape: tuple, bioxel_size: float, scale: float = 1.0) -> tuple: + size = ( + float(shape[0] * bioxel_size * scale), + float(shape[1] * bioxel_size * scale), + float(shape[2] * bioxel_size * scale), + ) + return size + + +def get_ext(filepath: Path) -> str: + if filepath.name.endswith(".nii.gz"): + return ".nii.gz" + elif filepath.name.endswith(".img.gz"): + return ".img.gz" + elif filepath.name.endswith(".gipl.gz"): + return ".gipl.gz" + elif filepath.name.endswith(".ome.tiff"): + return ".ome.tiff" + elif filepath.name.endswith(".ome.tif"): + return ".ome.tif" + elif filepath.name.endswith(".mrc.gz"): + return ".mrc.gz" + elif filepath.name.endswith(".map.gz"): + return ".map.gz" + else: + suffix = filepath.suffix + return "" if len(suffix) > 5 else suffix diff --git a/src/bioxelnodes/bioxel/layer.py b/src/bioxelnodes/bioxel/layer.py index d9449df..5dd9a32 100644 --- a/src/bioxelnodes/bioxel/layer.py +++ b/src/bioxelnodes/bioxel/layer.py @@ -1,6 +1,12 @@ import copy import numpy as np +# 条件导入 openvdb（只在 Blender 环境中存在） +try: + import openvdb as vdb +except ImportError: + vdb = None + from . import scipy from . import scipy as ndi diff --git a/src/bioxelnodes/layer.py b/src/bioxelnodes/layer.py index c6fb53d..a3926a0 100644 --- a/src/bioxelnodes/layer.py +++ b/src/bioxelnodes/layer.py @@ -6,7 +6,11 @@ import bpy import numpy as np -import openvdb as vdb + +try: + import openvdb as vdb +except ImportError: + vdb = None from .bioxel.layer import Layer from .utils import ndarray_to_png @@ -57,12 +61,10 @@ def cache_layer_data(layer: Layer, cache_path: str): grid.copyFromArray(data[f, :, :, :].copy().astype(np.float32)) else: # 颜色类型 grid = vdb.Vec3SGrid() - grid.copyFromArray( - data[f, :, :, :, :].copy().astype(np.float32)) + grid.copyFromArray(data[f, :, :, :, :].copy().astype(np.float32)) # 仅设置transform，不存储metadata - grid.transform = vdb.createLinearTransform( - layer.affine.transpose()) + grid.transform = vdb.createLinearTransform(layer.affine.transpose()) grid.name = layer.kind # 保存序列帧VDB @@ -272,6 +274,5 @@ def save_layers_to_json(layers: List[Layer], cache_dir: str) -> List[int]: added_ids.append(cache_id) set_layer_caches(existing_data) - print( - f"Successfully added {len(added_ids)} layers to the internal text datablock") + print(f"Successfully added {len(added_ids)} layers to the internal text datablock") return added_ids diff --git a/src/bioxelnodes/node.py b/src/bioxelnodes/node.py index 566bee6..b09b66b 100644 --- a/src/bioxelnodes/node.py +++ b/src/bioxelnodes/node.py @@ -105,7 +105,7 @@ def add_bioxel_node(name: str): bpy.ops.object.modifier_add_node_group( asset_library_type="CUSTOM", asset_library_identifier="O Bioxel", - relative_asset_identifier=f"Nodes.blend\\NodeTree\\{name}", + relative_asset_identifier=f"BioxelNodes.blend\\NodeTree\\{name}", ) bpy.ops.object.modifier_remove(modifier=name) try: diff --git a/src/bioxelnodes/operators/io.py b/src/bioxelnodes/operators/io.py index 96e1b5f..a94fdd2 100644 --- a/src/bioxelnodes/operators/io.py +++ b/src/bioxelnodes/operators/io.py @@ -12,37 +12,20 @@ from ..props import BIOXEL_Series from ..utils import get_layer_obj, wrapped_label -from ..bioxel.layer import Layer -from ..bioxel.parse import DICOM_EXTS, SUPPORT_EXTS, get_ext, parse_volumetric_data +from ..bioxel import ( + DICOM_EXTS, + SUPPORT_EXTS, + read, + read_meta, + calc_layer_shape, + calc_layer_size, + get_ext, +) from ..utils import get_cache_dir, progress_update, progress_bar from ..layer import get_layer_caches, save_layers_to_json -def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple): - shape = ( - int(orig_shape[0] / bioxel_size * orig_spacing[0]), - int(orig_shape[1] / bioxel_size * orig_spacing[1]), - int(orig_shape[2] / bioxel_size * orig_spacing[2]), - ) - - return ( - shape[0] if shape[0] > 0 else 1, - shape[1] if shape[1] > 0 else 1, - shape[2] if shape[2] > 0 else 1, - ) - - -def get_layer_size(shape: tuple, bioxel_size: float, scale: float = 1.0): - size = ( - float(shape[0] * bioxel_size * scale), - float(shape[1] * bioxel_size * scale), - float(shape[2] * bioxel_size * scale), - ) - - return size - - """ ImportData -> ParseVolumetricData -> ImportDataDialog start import parse data execute import @@ -211,11 +194,7 @@ def progress_callback(factor, text): try: series_id = self.series_id if self.series_id != "empty" else "" - data, meta = parse_volumetric_data( - data_file=self.filepath, - series_id=series_id, - progress_callback=progress_callback, - ) + data = read_meta(self.filepath, series_id=series_id) except KeyboardInterrupt: return except Exception as e: @@ -225,8 +204,8 @@ def progress_callback(factor, text): if cancel(): return - self.meta = meta - self.label_count = int(np.max(data)) + self.meta = data.meta + self.label_count = int(np.max(data.data)) self.dtype = data.dtype # Init cancel flag @@ -334,8 +313,8 @@ def modal(self, context, event): bioxel_size = max(min(*orig_spacing), 1.0) - layer_shape = get_layer_shape(bioxel_size, orig_shape, orig_spacing) - layer_size = get_layer_size(layer_shape, bioxel_size, 0.01) + layer_shape = calc_layer_shape(bioxel_size, orig_shape, orig_spacing) + layer_size = calc_layer_size(layer_shape, bioxel_size, 0.01) min_log10 = math.floor(math.log10(min(*layer_size))) max_log10 = math.floor(math.log10(max(*layer_size))) @@ -547,33 +526,23 @@ class ImportDataDialog(bpy.types.Operator): def execute(self, context): def import_volumetric_data_func(self, context, cancel): - progress_update(context, 0.0, "Parsing Volumetirc Data...") - def progress_callback(factor, text): if cancel(): raise KeyboardInterrupt("Cancelled by user") progress_update(context, factor * 0.2, text) - def progress_callback_factory(layer_name, progress, progress_step): - def progress_callback(frame, total): - if cancel(): - raise KeyboardInterrupt("Cancelled by user") - sub_progress_step = progress_step / total - sub_progress = progress + frame * sub_progress_step - progress_update( - context, - sub_progress, - f"Processing {layer_name} Frame {frame+1}...", - ) - print(f"Processing {layer_name} Frame {frame+1}...") - - return progress_callback - try: - data, meta = parse_volumetric_data( - data_file=self.filepath, - series_id=self.series_id, - progress_callback=progress_callback, + data = read(self.filepath, self.series_id, progress_callback) + + self.layers = data.to_layers( + kind=self.read_as.lower(), + layer_name=self.layer_name, + bioxel_size=self.bioxel_size, + smooth=self.smooth, + remap=self.remap, + split_channel=self.split_channel, + frame_source=self.frame_source, + progress_callback=lambda f, t: progress_callback(0.2 + f * 0.7, t), ) except KeyboardInterrupt: @@ -585,203 +554,6 @@ def progress_callback(frame, total): if cancel(): return - shape = get_layer_shape( - self.bioxel_size, self.orig_shape, self.orig_spacing - ) - - mat_scale = transforms3d.zooms.zfdir2aff(self.bioxel_size) - affine = np.dot(meta["affine"], mat_scale) - kind = self.read_as.lower() - - if cancel(): - return - - # change shape as sequence or not - if self.frame_source == "-1": - data = data[0:1, :, :, :, :] - elif self.frame_source == "0": - # frame as frame - pass - elif self.frame_source == "1": - # X as frame - data = data.transpose(1, 0, 2, 3, 4) - shape = (1, shape[1], shape[2]) - elif self.frame_source == "2": - # Y as frame - data = data.transpose(2, 1, 0, 3, 4) - shape = (shape[0], 1, shape[2]) - elif self.frame_source == "3": - # Z as frame - data = data.transpose(3, 1, 2, 0, 4) - shape = (shape[0], shape[1], 1) - else: - # channel as frame - data = data.transpose(4, 1, 2, 3, 0) - - layers = [] - if kind == "label": - name = self.layer_name or "Label" - data = data.astype(int) - label_count = int(np.max(data)) - progress_step = 0.7 / label_count - - for i in range(label_count): - if cancel(): - return - - name_i = f"{name}_{i+1}" - progress = 0.2 + i * progress_step - progress_update(context, progress, f"Processing {name_i}...") - - progress_callback = progress_callback_factory( - name_i, progress, progress_step - ) - label_data = data == np.full_like(data, i + 1) - # label_data = label_data.astype(np.float32) - try: - layer = Layer(data=label_data, name=name_i, kind=kind) - - layer.resize( - shape=shape, - smooth=self.smooth, - progress_callback=progress_callback, - ) - - layer.affine = affine - - layers.append(layer) - except KeyboardInterrupt: - return - except Exception as e: - self.has_error = e - return - - if kind == "color": - if np.issubdtype(np.uint8, data.dtype): - data = np.multiply(data, 1.0 / 256, dtype=np.float32) - elif data.dtype.kind in ["u", "i"]: - # Convert the normalized array to float dtype - data = data.astype(np.float32) - - min_val = data.min() - max_val = data.max() - # Avoid division by zero if all values are the same - if max_val != min_val: - # Normalize the array to the range (0,1) - data = (data - min_val) / (max_val - min_val) - else: - # If all values are the same, the normalized array will be all zeros - data = np.zeros_like(data, dtype=np.float32) - - else: - data = data.astype(np.float32) - - # Gamma Correct - # data = data ** 2.2 - - name = self.layer_name or "Color" - if data.shape[4] == 1: - data = np.repeat(data, repeats=3, axis=4) - elif data.shape[4] == 2: - d_shape = list(data.shape) - d_shape = d_shape[:4] + [1] - zore = np.zeros(tuple(d_shape), dtype=np.float32) - data = np.concatenate((data, zore), axis=-1) - elif data.shape[4] > 3: - data = data[:, :, :, :, :3] - - if cancel(): - return - - progress_update(context, 0.2, f"Processing {name}...") - progress_callback = progress_callback_factory(name, 0.2, 0.7) - - try: - layer = Layer(data=data, name=name, kind=kind) - - layer.resize(shape=shape, progress_callback=progress_callback) - - layer.affine = affine - - layers.append(layer) - except KeyboardInterrupt: - return - except Exception as e: - self.has_error = e - return - - elif kind == "scalar": - name = self.layer_name or "Scalar" - - if self.remap: - # Convert the normalized array to float dtype - data = data.astype(np.float32) - - min_val = data.min() - max_val = data.max() - # Avoid division by zero if all values are the same - if max_val != min_val: - # Normalize the array to the range (0,1) - data = (data - min_val) / (max_val - min_val) - else: - # If all values are the same, the normalized array will be all zeros - data = np.zeros_like(data, dtype=np.float32) - - if self.split_channel: - progress_step = 0.7 / self.channel_count - - for i in range(self.channel_count): - if cancel(): - return - - name_i = f"{name}_{i+1}" - progress = 0.2 + i * progress_step - progress_update(context, progress, f"Processing {name_i}...") - progress_callback = progress_callback_factory( - name_i, progress, progress_step - ) - try: - layer = Layer( - data=data[:, :, :, :, i : i + 1], name=name_i, kind=kind - ) - - layer.resize( - shape=shape, progress_callback=progress_callback - ) - - layer.affine = affine - - layers.append(layer) - except KeyboardInterrupt: - return - except Exception as e: - self.has_error = e - return - else: - if cancel(): - return - - progress_update(context, 0.2, f"Processing {name}...") - progress_callback = progress_callback_factory(name, 0.2, 0.7) - - try: - layer = Layer(data=data, name=name, kind=kind) - - layer.resize(shape=shape, progress_callback=progress_callback) - - layer.affine = affine - - layers.append(layer) - except KeyboardInterrupt: - return - except Exception as e: - self.has_error = e - return - - if cancel(): - return - - self.layers = layers progress_update(context, 0.9, "Creating Layers...") self.is_cancelled = False @@ -851,7 +623,7 @@ def invoke(self, context, event): return {"RUNNING_MODAL"} def draw(self, context): - layer_shape = get_layer_shape( + layer_shape = calc_layer_shape( self.bioxel_size, self.orig_shape, self.orig_spacing ) diff --git a/src/bioxelnodes/operators/layer.py b/src/bioxelnodes/operators/layer.py index 6825012..cc95bdc 100644 --- a/src/bioxelnodes/operators/layer.py +++ b/src/bioxelnodes/operators/layer.py @@ -16,13 +16,11 @@ class RenameLayer(bpy.types.Operator): bl_options = {"REGISTER", "UNDO"} cache_id: bpy.props.StringProperty(options={"HIDDEN"}) # type: ignore - new_name: bpy.props.StringProperty( - name="New name", default="") # type: ignore + new_name: bpy.props.StringProperty(name="New name", default="") # type: ignore def invoke(self, context, event): caches = get_layer_caches() - entry = next((c for c in caches if str( - c.get("id", "")) == self.cache_id), None) + entry = next((c for c in caches if str(c.get("id", "")) == self.cache_id), None) if entry: self.new_name = str(entry.get("name", "")) return context.window_manager.invoke_props_dialog(self) @@ -127,8 +125,7 @@ def execute(self, context): layer_node.inputs["Frame Count"].default_value = entry["frame_count"] layer_node.inputs["Animation"].default_value = True else: - hidden_sockets = hidden_sockets + \ - ["Frame Count", "Frame Offset", "Cycle"] + hidden_sockets = hidden_sockets + ["Frame Count", "Frame Offset", "Cycle"] # 将特定属性隐藏到hidden面板 for socket_name in hidden_sockets: @@ -177,8 +174,7 @@ def execute(self, context): return {"CANCELLED"} caches = get_layer_caches() - entry = next((c for c in caches if str( - c.get("id", "")) == self.cache_id), None) + entry = next((c for c in caches if str(c.get("id", "")) == self.cache_id), None) if not entry: self.report({"ERROR"}, "Layer not found") return {"CANCELLED"} @@ -228,8 +224,7 @@ class SaveLayer(bpy.types.Operator): def invoke(self, context, event): # Default to Blender file directory if possible - blend_dir = Path( - bpy.data.filepath).parent if bpy.data.filepath else Path.cwd() + blend_dir = Path(bpy.data.filepath).parent if bpy.data.filepath else Path.cwd() context.window_manager.fileselect_add(self) if not self.directory: self.directory = str(blend_dir) @@ -244,8 +239,7 @@ def execute(self, context): return {"CANCELLED"} caches = get_layer_caches() - entry = next((c for c in caches if str( - c.get("id")) == self.cache_id), None) + entry = next((c for c in caches if str(c.get("id")) == self.cache_id), None) cache_id = entry.get("id") if not entry: diff --git a/tests/README.md b/tests/README.md new file mode 100644 index 0000000..db4d862 --- /dev/null +++ b/tests/README.md @@ -0,0 +1,43 @@ +# BioxelNodes Unit Tests + +This directory contains unit tests for the bioxel module. + +## Test Data + +Test files should be placed in `tests/data/`: + +## Running Tests + +Run all tests: +```bash +uv run pytest +``` + +Run specific test file: +```bash +uv run pytest tests/test_bioxel.py +``` + +Run specific test class: +```bash +uv run pytest tests/test_bioxel.py::TestDataClass +``` + +Run with verbose output: +```bash +uv run pytest -v +``` + +Run with coverage: +```bash +uv run pytest --cov=bioxelnodes.bioxel --cov-report=html +``` + +## Test Categories + +- **TestDataClass**: Data class initialization and properties +- **TestDataToLayers**: Data.to_layers() method +- **TestUtilityFunctions**: Utility functions +- **TestLayerClass**: Layer class functionality +- **TestConstants**: Module constants +- **TestEdgeCases**: Edge cases and error handling diff --git a/tests/test_bioxel.py b/tests/test_bioxel.py new file mode 100644 index 0000000..43cbe6c --- /dev/null +++ b/tests/test_bioxel.py @@ -0,0 +1,539 @@ +""" +Unit tests for bioxel module. + +Tests cover: +- Data class functionality +- Parsing NRRD and DICOM formats +- Layer creation and transformation +- Utility functions +""" + +from bioxelnodes.bioxel import ( + Data, + read, + read_meta, + calc_layer_shape, + calc_layer_size, + Layer, +) +import pytest +import numpy as np +from pathlib import Path + +import sys + +sys.path.insert(0, str(Path(__file__).parent.parent / "src")) + + +# Test data files +NRRD_FILE = Path(__file__).parent / "data/VHP_M.nrrd" +DICOM_FILE = Path(__file__).parent / "data/VHP_M_CT_Head/IM000001.dcm" +DICOM_DIR = Path(__file__).parent / "data/VHP_M_CT_Head/" + + +class TestDataClass: + """Test Data class initialization and properties""" + + def test_data_initialization(self): + """Test basic Data initialization with NRRD""" + data = Data(filepath=str(NRRD_FILE), series_id="") + + assert data.filepath is not None + assert data.series_id == "" + assert data._data is None + assert data._meta is None + + def test_read_meta_nrrd(self): + """Test reading only meta from NRRD file""" + data_obj = read_meta(str(NRRD_FILE)) + + assert data_obj._data is None + assert data_obj._meta is not None + assert "name" in data_obj.meta + assert "spacing" in data_obj.meta + assert "affine" in data_obj.meta + assert "xyz_shape" in data_obj.meta + assert "frame_count" in data_obj.meta + assert "channel_count" in data_obj.meta + assert "dtype" in data_obj.meta + + def test_read_meta_dicom(self): + """Test reading only meta from DICOM file""" + data_obj = read_meta(str(DICOM_FILE), series_id="") + + assert data_obj._data is None + assert data_obj._meta is not None + assert "name" in data_obj.meta + + def test_read_full_data_nrrd(self): + """Test reading full NRRD data""" + data_obj = read(str(NRRD_FILE)) + + assert data_obj._data is not None + assert data_obj._meta is not None + assert isinstance(data_obj.data, np.ndarray) + assert data_obj.data.ndim == 5 + + def test_read_full_data_dicom(self): + """Test reading full DICOM data""" + data_obj = read(str(DICOM_FILE), series_id="") + + assert data_obj._data is not None + assert data_obj._meta is not None + assert isinstance(data_obj.data, np.ndarray) + + def test_data_properties_nrrd(self): + """Test Data property accessors""" + data_obj = read(str(NRRD_FILE)) + + assert hasattr(data_obj, "name") + assert hasattr(data_obj, "description") + assert hasattr(data_obj, "shape") + assert hasattr(data_obj, "xyz_shape") + assert hasattr(data_obj, "spacing") + assert hasattr(data_obj, "affine") + assert hasattr(data_obj, "frame_count") + assert hasattr(data_obj, "channel_count") + assert hasattr(data_obj, "dtype") + + assert isinstance(data_obj.shape, tuple) + assert isinstance(data_obj.xyz_shape, tuple) + assert isinstance(data_obj.spacing, tuple) + assert isinstance(data_obj.affine, np.ndarray) + assert isinstance(data_obj.dtype, np.dtype) + + def test_data_lazy_loading(self): + """Test lazy loading behavior""" + data_obj = Data(filepath=str(NRRD_FILE), series_id="") + + assert data_obj.is_loaded() is False + + data_obj.load_meta() + assert data_obj._data is None + assert data_obj._meta is not None + + data_obj.load_data() + assert data_obj._data is not None + assert data_obj.is_loaded() is True + + def test_shape_property(self): + """Test shape property returns TXYZC format""" + data_obj = read(str(NRRD_FILE)) + + shape = data_obj.shape + assert len(shape) == 5 + assert shape[0] == data_obj.meta["frame_count"] + assert shape[1:4] == data_obj.meta["xyz_shape"] + assert shape[4] == data_obj.meta["channel_count"] + + def test_load_meta_method(self): + """Test load_meta() method exists and works""" + data_obj = Data(filepath=str(NRRD_FILE), series_id="") + + assert hasattr(data_obj, "load_meta") + + data_obj.load_meta() + assert data_obj._meta is not None + assert data_obj._data is None + + +class TestDataToLayers: + """Test Data.to_layers() method""" + + def test_to_layers_dicom_scalar(self): + """Test converting DICOM data to scalar layers""" + data_obj = read(str(DICOM_FILE), series_id="") + + layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0) + + assert len(layers) == 1 + assert layers[0].kind == "scalar" + assert isinstance(layers[0], Layer) + + def test_to_layers_nrrd_scalar(self): + """Test converting NRRD data to scalar layers""" + data_obj = read(str(NRRD_FILE)) + + layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0) + + assert len(layers) == 1 + assert layers[0].kind == "scalar" + assert isinstance(layers[0], Layer) + + def test_to_layers_with_remap(self): + """Test data remapping""" + data_obj = read(str(NRRD_FILE)) + + layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0, remap=True) + + assert len(layers) == 1 + assert layers[0].data.dtype == np.float32 + assert np.all(layers[0].data >= 0) + assert np.all(layers[0].data <= 1) + + def test_to_layers_with_bioxel_size(self): + """Test with different bioxel sizes""" + data_obj = read(str(NRRD_FILE)) + + layers_1x = data_obj.to_layers(kind="scalar", bioxel_size=1.0) + layers_2x = data_obj.to_layers(kind="scalar", bioxel_size=2.0) + + assert len(layers_1x) == 1 + assert len(layers_2x) == 1 + + # Larger bioxel size means smaller layer + shape_1x = layers_1x[0].shape + shape_2x = layers_2x[0].shape + assert shape_2x[0] <= shape_1x[0] + assert shape_2x[1] <= shape_1x[1] + assert shape_2x[2] <= shape_1x[2] + + def test_to_layers_with_smooth(self): + """Test with smoothing parameter""" + data_obj = read(str(NRRD_FILE)) + + layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0, smooth=1) + + assert len(layers) == 1 + assert isinstance(layers[0], Layer) + + def test_to_layers_frame_source_first_frame(self): + """Test frame_source = '-1' (first frame only)""" + data_obj = read(str(NRRD_FILE)) + + layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0, frame_source="-1") + + assert len(layers) == 1 + assert layers[0].frame_count == 1 + + +class TestUtilityFunctions: + """Test utility functions""" + + def test_calc_layer_shape(self): + """Test layer shape calculation""" + shape = calc_layer_shape( + bioxel_size=1.0, orig_shape=(100, 100, 100), orig_spacing=(1.0, 1.0, 1.0) + ) + + assert len(shape) == 3 + assert shape[0] == 100 + assert shape[1] == 100 + assert shape[2] == 100 + + def test_calc_layer_shape_small_bioxel(self): + """Test layer shape with small bioxel size""" + shape = calc_layer_shape( + bioxel_size=2.0, orig_shape=(100, 100, 100), orig_spacing=(1.0, 1.0, 1.0) + ) + + assert len(shape) == 3 + assert shape[0] == 50 + assert shape[1] == 50 + assert shape[2] == 50 + + def test_calc_layer_shape_minimum(self): + """Test layer shape doesn't go below 1""" + shape = calc_layer_shape( + bioxel_size=100.0, orig_shape=(100, 100, 100), orig_spacing=(1.0, 1.0, 1.0) + ) + + assert shape == (1, 1, 1) + + def test_calc_layer_size(self): + """Test layer size calculation""" + size = calc_layer_size(shape=(100, 100, 100), bioxel_size=1.0, scale=1.0) + + assert len(size) == 3 + assert size[0] == 100.0 + assert size[1] == 100.0 + assert size[2] == 100.0 + + def test_calc_layer_size_with_scale(self): + """Test layer size with scale factor""" + size = calc_layer_size(shape=(100, 100, 100), bioxel_size=1.0, scale=0.01) + + assert len(size) == 3 + assert size[0] == 1.0 + assert size[1] == 1.0 + assert size[2] == 1.0 + + +class TestLayerClass: + """Test Layer class functionality""" + + def test_layer_initialization(self): + """Test Layer initialization""" + data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) + layer = Layer(data=data, name="test_layer", kind="scalar") + + assert layer.name == "test_layer" + assert layer.kind == "scalar" + assert np.array_equal(layer.data, data) + + def test_layer_properties(self): + """Test Layer property accessors""" + data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) + layer = Layer( + data=data, name="test_layer", kind="scalar", affine=np.identity(4) + ) + + assert hasattr(layer, "bioxel_size") + assert hasattr(layer, "shape") + assert hasattr(layer, "dtype") + assert hasattr(layer, "origin") + assert hasattr(layer, "euler") + assert hasattr(layer, "frame_count") + assert hasattr(layer, "channel_count") + assert hasattr(layer, "min") + assert hasattr(layer, "max") + + def test_layer_shape_property(self): + """Test layer shape returns XYZ (not TXYZC)""" + data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) + layer = Layer(data=data, name="test", kind="scalar") + + shape = layer.shape + assert len(shape) == 3 + assert shape[0] == 8 + assert shape[1] == 8 + assert shape[2] == 8 + + def test_layer_affine_property(self): + """Test affine transformation matrix""" + data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) + affine = np.array( + [ + [1.0, 0.0, 0.0, 0.0], + [0.0, 1.0, 0.0, 0.0], + [0.0, 0.0, 1.0, 0.0], + [0.0, 0.0, 0.0, 1.0], + ] + ) + layer = Layer(data=data, name="test", kind="scalar", affine=affine) + + result_affine = layer.affine + assert result_affine.shape == (4, 4) + assert np.allclose(result_affine, affine) + + def test_layer_min_max(self): + """Test layer min/max properties""" + data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) + layer = Layer(data=data, name="test", kind="scalar") + + assert isinstance(layer.min, float) + assert isinstance(layer.max, float) + assert layer.min <= layer.max + + def test_layer_copy(self): + """Test layer deep copy""" + data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) + layer = Layer(data=data, name="test", kind="scalar") + layer_copy = layer.copy() + + assert layer_copy.name == layer.name + assert layer_copy.kind == layer.kind + assert np.array_equal(layer_copy.data, layer.data) + + assert layer_copy is not layer + layer_copy.data[0, 0, 0, 0, 0] = 999.0 + assert layer.data[0, 0, 0, 0, 0] != 999.0 + + def test_layer_invalid_data_shape(self): + """Test Layer raises error for invalid data shape""" + data = np.random.rand(8, 8, 8).astype(np.float32) + + with pytest.raises(Exception): + Layer(data=data, name="test", kind="scalar") + + def test_layer_invalid_affine_shape(self): + """Test Layer raises error for invalid affine shape""" + data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) + affine = np.identity(3) + + with pytest.raises(Exception): + Layer(data=data, name="test", kind="scalar", affine=affine) + + +class TestConstants: + """Test module constants""" + + def test_support_exts_exists(self): + """Test SUPPORT_EXTS constant""" + from bioxelnodes.bioxel import SUPPORT_EXTS + + assert isinstance(SUPPORT_EXTS, list) + assert len(SUPPORT_EXTS) > 0 + assert ".h5" in SUPPORT_EXTS + assert ".nrrd" in SUPPORT_EXTS + assert ".nii.gz" in SUPPORT_EXTS + assert ".dcm" in SUPPORT_EXTS + + def test_dicom_exts_exists(self): + """Test DICOM_EXTS constant""" + from bioxelnodes.bioxel import DICOM_EXTS + + assert isinstance(DICOM_EXTS, list) + assert "" in DICOM_EXTS + assert ".dcm" in DICOM_EXTS + assert ".DCM" in DICOM_EXTS + + def test_ome_exts_exists(self): + """Test OME_EXTS constant""" + from bioxelnodes.bioxel import OME_EXTS + + assert isinstance(OME_EXTS, list) + assert ".tiff" in OME_EXTS + assert ".ome.tiff" in OME_EXTS + + def test_mrc_exts_exists(self): + """Test MRC_EXTS constant""" + from bioxelnodes.bioxel import MRC_EXTS + + assert isinstance(MRC_EXTS, list) + assert ".mrc" in MRC_EXTS + + +class TestEdgeCases: + """Test edge cases and error handling""" + + def test_nonexistent_file(self): + """Test handling of nonexistent file""" + with pytest.raises(FileNotFoundError): + data_obj = read("/nonexistent/file.nii.gz", "") + + def test_frame_count_property_multiframe(self): + """Test frame_count property for multi-frame data""" + data_obj = read(str(NRRD_FILE)) + + assert data_obj.frame_count >= 1 + assert data_obj.frame_count == data_obj.meta["frame_count"] + + def test_channel_count_property(self): + """Test channel_count property""" + data_obj = read(str(NRRD_FILE)) + + assert data_obj.channel_count >= 1 + assert data_obj.channel_count == data_obj.meta["channel_count"] + + def test_nrrd_format_support(self): + """Test NRRD format is in supported extensions""" + from bioxelnodes.bioxel import SUPPORT_EXTS + + assert ".nrrd" in SUPPORT_EXTS + + def test_dicom_format_support(self): + """Test DICOM format is in supported extensions""" + from bioxelnodes.bioxel import SUPPORT_EXTS + + assert ".dcm" in SUPPORT_EXTS + assert "" in SUPPORT_EXTS + + +class TestRealDataFiles: + """Test with real data files""" + + def test_nrrd_file_exists(self): + """Test NRRD test file exists""" + assert NRRD_FILE.exists() + assert NRRD_FILE.is_file() + + def test_dicom_file_exists(self): + """Test DICOM test file exists""" + assert DICOM_FILE.exists() + assert DICOM_FILE.is_file() + + def test_dicom_directory_exists(self): + """Test DICOM directory exists""" + assert DICOM_DIR.exists() + assert DICOM_DIR.is_dir() + + def test_read_nrrd_data(self): + """Test reading real NRRD data""" + data_obj = read(str(NRRD_FILE)) + + assert data_obj._data is not None + assert data_obj._meta is not None + assert isinstance(data_obj.data, np.ndarray) + assert data_obj.data.size > 0 + + def test_read_dicom_data(self): + """Test reading real DICOM data""" + data_obj = read(str(DICOM_FILE), series_id="") + + assert data_obj._data is not None + assert data_obj._meta is not None + assert isinstance(data_obj.data, np.ndarray) + assert data_obj.data.size > 0 + + def test_nrrd_meta_contains_required_fields(self): + """Test NRRD meta contains all required fields""" + data_obj = read(str(NRRD_FILE)) + meta = data_obj.meta + + required_fields = [ + "name", + "description", + "spacing", + "affine", + "xyz_shape", + "frame_count", + "channel_count", + "dtype", + ] + + for field in required_fields: + assert field in meta, f"Meta missing field: {field}" + + def test_dicom_meta_contains_required_fields(self): + """Test DICOM meta contains all required fields""" + data_obj = read(str(DICOM_FILE), series_id="") + meta = data_obj.meta + + required_fields = [ + "name", + "description", + "spacing", + "affine", + "xyz_shape", + "frame_count", + "channel_count", + "dtype", + ] + + for field in required_fields: + assert field in meta, f"Meta missing field: {field}" + + def test_data_to_layers_with_real_nrrd(self): + """Test to_layers with real NRRD data""" + data_obj = read(str(NRRD_FILE)) + + layers = data_obj.to_layers(kind="scalar", bioxel_size=3.0) + + assert len(layers) > 0 + assert all(isinstance(layer, Layer) for layer in layers) + + def test_data_to_layers_with_real_dicom(self): + """Test to_layers with real DICOM data""" + data_obj = read(str(DICOM_FILE), series_id="") + + layers = data_obj.to_layers(kind="scalar", bioxel_size=3.0) + + assert len(layers) > 0 + assert all(isinstance(layer, Layer) for layer in layers) + + def test_nrrd_spacing_values(self): + """Test NRRD spacing values are reasonable""" + data_obj = read(str(NRRD_FILE)) + spacing = data_obj.spacing + + assert len(spacing) == 3 + assert all(s > 0 for s in spacing) + + def test_dicom_spacing_values(self): + """Test DICOM spacing values are reasonable""" + data_obj = read(str(DICOM_FILE), series_id="") + spacing = data_obj.spacing + + assert len(spacing) == 3 + assert all(s > 0 for s in spacing) From b83dd0acd90754cf8b216d03c5a871c928a92924 Mon Sep 17 00:00:00 2001 From: nan Date: Mon, 25 May 2026 09:15:47 +0800 Subject: [PATCH 03/14] feat: Update .gitattributes and .gitignore for improved asset management and ignore patterns chore: Add app.json and omoolab.css for Obsidian integration refactor: Clean up AGENTS.md and remove outdated test files --- .gitattributes | 132 +++++++- .gitignore | 304 +++++++++++++++++-- .obsidian/app.json | 22 ++ .obsidian/snippets/omoolab.css | 30 ++ .python-version | 1 + AGENTS.md | 236 +-------------- CLAUDE.md | 1 + tests/README.md | 43 --- tests/test_bioxel.py | 539 --------------------------------- 9 files changed, 477 insertions(+), 831 deletions(-) create mode 100644 .obsidian/app.json create mode 100644 .obsidian/snippets/omoolab.css create mode 100644 .python-version create mode 100644 CLAUDE.md delete mode 100644 tests/README.md delete mode 100644 tests/test_bioxel.py diff --git a/.gitattributes b/.gitattributes index 80a1944..f471a1f 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,131 @@ -*.blend filter=lfs diff=lfs merge=lfs -text +# Define macros (only works in top-level gitattributes files) +[attr]lfs filter=lfs diff=lfs merge=lfs -text + +# 3D models +*.collada lfs +*.dae lfs +*.dxf lfs +*.FBX lfs +*.fbx lfs +*.jas lfs +*.lws lfs +*.lxo lfs +*.obj lfs +*.ply lfs +*.skp lfs +*.stl lfs +*.stp lfs +*.usd lfs +*.usda lfs +*.usdc lfs +*.usdz lfs +*.glb lfs +*.gltf lfs + +# Audio +*.aif lfs +*.aiff lfs +*.it lfs +*.mod lfs +*.mp3 lfs +*.ogg lfs +*.s3m lfs +*.wav lfs +*.xm lfs + +# Video +*.asf lfs +*.avi lfs +*.flv lfs +*.mov lfs +*.mp4 lfs +*.mpeg lfs +*.mpg lfs +*.ogv lfs +*.wmv lfs +*.mkv lfs + +# Images +*.bmp lfs +*.exr lfs +*.gif lfs +*.hdr lfs +*.iff lfs +*.jpeg lfs +*.jpg lfs +*.pict lfs +*.png lfs +*.psd lfs +*.tga lfs +*.tif lfs +*.tiff lfs +*.webp lfs + +# Compressed Archive +*.7z lfs +*.bz2 lfs +*.gz lfs +*.rar lfs +*.tar lfs +*.zip lfs + +# Compiled Dynamic Library +*.dll lfs +*.pdb lfs +*.so lfs + +# Fonts +*.otf lfs +*.ttf lfs +*.woff lfs +*.woff2 lfs + +# Executable/Installer +*.apk lfs +*.exe lfs + +# Documents +*.pdf lfs +*.doc lfs +*.xls lfs +*.ppt lfs +*.docx lfs +*.xlsx lfs +*.pptx lfs + +# Adobe +*.psd lfs +*.ai lfs +*.aep lfs +*.prproj lfs +*.spp lfs + +# Zbrush +*.zbr lfs +*.zpr lfs +*.ztl lfs +*.c4d lfs + +# Autodesk +*.max lfs +*.ma lfs +*.mb lfs +*.3dm lfs +*.3ds lfs + +# Blender +*.blend lfs +*.blend1 lfs +*.c4d lfs + +# Imaging +*.dicom lfs +*.dcm lfs +*.nii lfs +*.ome lfs +*.map lfs +*.mrc lfs + +# Others +*.abr lfs +*.tpl lfs \ No newline at end of file diff --git a/.gitignore b/.gitignore index 960f98e..9063c92 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,51 @@ +# Tempary files +temp +sandbox.* +notes/ + +# Environments +.env +.envrc +.venv +.env.* +!.env.example +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +.secrets +.secrets.* +!.secrets.example +secrets/ +SECRETS/ +secrets.bak/ + +# Claude +.claudian + +# Obsidian + +.obsidian/* +!.obsidian/snippets +!.obsidian/app.json + +*.canvas + +# Keep odox for extract to openwiki +!.obsidian/plugins +.obsidian/plugins/* +!.obsidian/plugins/odox + +# Blender +*.blend1 +blender_assets.cats.txt~ +blendcache_* + # Byte-compiled / optimized / DLL files __pycache__/ -*.py[cod] +*.py[codz] *$py.class # C extensions @@ -20,7 +65,6 @@ parts/ sdist/ var/ wheels/ -pip-wheel-metadata/ share/python-wheels/ *.egg-info/ .installed.cfg @@ -28,8 +72,8 @@ share/python-wheels/ MANIFEST # PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. *.manifest *.spec @@ -47,8 +91,10 @@ htmlcov/ nosetests.xml coverage.xml *.cover +*.py.cover .hypothesis/ .pytest_cache/ +cover/ # Translations *.mo @@ -71,6 +117,7 @@ instance/ docs/_build/ # PyBuilder +.pybuilder/ target/ # Jupyter Notebook @@ -81,30 +128,70 @@ profile_default/ ipython_config.py # pyenv -.python-version +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version # pipenv # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. # However, in case of collaboration, if having platform-specific dependencies or dependencies # having no cross-platform support, pipenv may install dependencies that don't work, or not # install all needed dependencies. -#Pipfile.lock +# Pipfile.lock + +# UV +# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# uv.lock -# celery beat schedule file +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +# poetry.lock +# poetry.toml + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +# pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python. +# https://pdm-project.org/en/latest/usage/project/#working-with-version-control +# pdm.lock +# pdm.toml +.pdm-python +.pdm-build/ + +# pixi +# Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control. +# pixi.lock +# Pixi creates a virtual environment in the .pixi directory, just like venv module creates one +# in the .venv directory. It is recommended not to include this directory in version control. +.pixi + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff celerybeat-schedule +celerybeat.pid + +# Redis +*.rdb +*.aof +*.pid + +# RabbitMQ +mnesia/ +rabbitmq/ +rabbitmq-data/ + +# ActiveMQ +activemq-data/ # SageMath parsed files *.sage.py -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - # Spyder project settings .spyderproject .spyproject @@ -123,18 +210,183 @@ dmypy.json # Pyre type checker .pyre/ -pythonlib* +# pytype static type analyzer +.pytype/ -*.ipynb +# Cython debug symbols +cython_debug/ -.secrets -.vdb +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +# .idea/ -!scipy_ndimage/*/** +# Abstra +# Abstra is an AI-powered process automation framework. +# Ignore directories containing user credentials, local state, and settings. +# Learn more at https://abstra.io/docs +.abstra/ -# Blender -*.blend1 -blendcache_* -*.cats.txt~ +# Visual Studio Code +# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore +# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore +# and can be added to the global gitignore or merged into this file. However, if you prefer, +# you could uncomment the following to ignore the entire vscode folder +# .vscode/ + +# Ruff stuff: +.ruff_cache/ + +# PyPI configuration file +.pypirc + +# Marimo +marimo/_static/ +marimo/_lsp/ +__marimo__/ + +# Streamlit +.streamlit/secrets.toml + +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +lerna-debug.log* + +# Diagnostic reports (https://nodejs.org/api/report.html) +report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json + +# Runtime data +pids +*.pid +*.seed +*.pid.lock + +# Directory for instrumented libs generated by jscoverage/JSCover +lib-cov + +# Coverage directory used by tools like istanbul +coverage +*.lcov + +# nyc test coverage +.nyc_output + +# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files) +.grunt + +# Bower dependency directory (https://bower.io/) +bower_components + +# node-waf configuration +.lock-wscript + +# Compiled binary addons (https://nodejs.org/api/addons.html) +build/Release + +# Dependency directories +node_modules/ +jspm_packages/ + +# Snowpack dependency directory (https://snowpack.dev/) +web_modules/ + +# TypeScript cache +*.tsbuildinfo + +# Optional npm cache directory +.npm + +# Optional eslint cache +.eslintcache + +# Optional stylelint cache +.stylelintcache + +# Optional REPL history +.node_repl_history + +# Output of 'npm pack' +*.tgz + +# Yarn Integrity file +.yarn-integrity + + +# parcel-bundler cache (https://parceljs.org/) +.cache +.parcel-cache + +# Next.js build output +.next +out + +# Nuxt.js build / generate output +.nuxt +dist +.output + +# Gatsby files +.cache/ +# Comment in the public line in if your project uses Gatsby and not Next.js +# https://nextjs.org/blog/next-9-1#public-directory-support +# public + +# vuepress build output +.vuepress/dist + +# vuepress v2.x temp and cache directory +.temp +.cache + +# Sveltekit cache directory +.svelte-kit/ + +# vitepress build output +**/.vitepress/dist + +# vitepress cache directory +**/.vitepress/cache + +# Docusaurus cache and generated files +.docusaurus + +# Serverless directories +.serverless/ + +# FuseBox cache +.fusebox/ + +# DynamoDB Local files +.dynamodb/ + +# Firebase cache directory +.firebase/ + +# TernJS port file +.tern-port + +# Stores VSCode versions used for testing VSCode extensions +.vscode-test + +# pnpm +.pnpm-store + +# yarn v3 +.pnp.* +.yarn/* +!.yarn/patches +!.yarn/plugins +!.yarn/releases +!.yarn/sdks +!.yarn/versions -tests/data \ No newline at end of file +# Vite files +vite.config.js.timestamp-* +vite.config.ts.timestamp-* +.vite/ \ No newline at end of file diff --git a/.obsidian/app.json b/.obsidian/app.json new file mode 100644 index 0000000..ac3bb1b --- /dev/null +++ b/.obsidian/app.json @@ -0,0 +1,22 @@ +{ + "showInlineTitle": false, + "useMarkdownLinks": true, + "pdfExportSettings": { + "pageSize": "Letter", + "landscape": false, + "margin": "0", + "downscalePercent": 100 + }, + "userIgnoreFilters": [ + "notes/assets/" + ], + "showUnsupportedFiles": false, + "attachmentFolderPath": "notes/assets", + "livePreview": true, + "showIndentGuide": false, + "alwaysUpdateLinks": true, + "openBehavior": "file:README", + "newFileLocation": "folder", + "newFileFolderPath": "notes", + "newLinkFormat": "relative" +} \ No newline at end of file diff --git a/.obsidian/snippets/omoolab.css b/.obsidian/snippets/omoolab.css new file mode 100644 index 0000000..92c8a0d --- /dev/null +++ b/.obsidian/snippets/omoolab.css @@ -0,0 +1,30 @@ +/* not show label in canvas */ +.canvas-node-label { + display: none; +} + +.canvas-node-container:hover + .canvas-node-label { + display: inherit; +} + +/* image caption */ +.image-embed { + flex-wrap: wrap; +} + +.image-embed[alt]:after { + content: attr(alt); + display: block; + padding-bottom: 12px; + line-height: 2.0; + font-style: italic; + color: var(--text-faint); + text-align: center; + width: 100%; +} + + +/* fix image in canvas */ +.image-embed { + padding: 0; +} \ No newline at end of file diff --git a/.python-version b/.python-version new file mode 100644 index 0000000..2c07333 --- /dev/null +++ b/.python-version @@ -0,0 +1 @@ +3.11 diff --git a/AGENTS.md b/AGENTS.md index 661944b..870aad8 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -1,227 +1,19 @@ -# BioxelNodes - Agent Development Guide +## 总规范 -This file contains essential information for agentic coding agents working on the BioxelNodes codebase. +- 说明性内容（例如提交说明、文档、注释、mermaid），以中文为主，专有名词、约定俗称可用英文 -## Project Overview +## Markdown 规范 -BioxelNodes is a Blender addon for scientific volumetric data visualization. It integrates with Blender's Geometry Nodes and Cycles rendering engine to process and visualize medical/scientific data. +- 不使用`---`分割器 +- `# Heading` 一级标题仅用于开头 +- mermaid 节点名用英文字符 -**Language:** Python 3.11 -**Framework:** Blender Python API (bpy) -**Package Manager:** uv +## 代码规范 -## Development Commands - -### Environment Setup -```bash -# Install dependencies -uv sync -``` - -### Build Commands -```bash -# Build for specific platform -uv run build.py # platforms: windows-x64, linux-x64, macos-arm64, macos-x64 -``` - -### Unit Test -```bash -uv run pytest tests/ -``` - -### Code Quality -```bash -# Format code (autopep8) -autopep8 --in-place --recursive src/ -``` - -### Documentation -```bash -# Serve documentation locally -uv run mkdocs serve - -# Build documentation -uv run mike deploy --push --update-aliases 0.2.x latest -``` - -## Code Style Guidelines - -### Formatting -- **4-space indentation** -- **PEP 8** compliance enforced via autopep8 - -### Naming Conventions -- **snake_case** for functions, variables, and files -- **PascalCase** for classes (Blender convention) -- **UPPER_CASE** for constants -- **bioxel_** prefix for addon-specific properties - -### Import Organization -```python -# Standard library imports first -import pathlib -import uuid - -# Third-party imports -import bpy -import numpy as np -import SimpleITK as sitk - -# Relative imports for internal modules -from ..exceptions import CancelledByUser -from ..utils import get_layer_obj -``` - -### Type Hints -- Use sparingly, mainly for Blender property annotations -- Focus on function signatures and complex data structures -- Example: `def process_data(data: np.ndarray) -> np.ndarray:` - -## Architecture Patterns - -### Auto-Registration System -- Uses `auto_load.py` for automatic class registration -- Classes are discovered automatically via reflection -- Registration order resolved via topological sorting -- All Blender classes must inherit from appropriate base types - -### Module Structure -``` -src/bioxelnodes/ -├── __init__.py # Addon entry point, asset library setup -├── auto_load.py # Auto-registration system -├── constants.py # Constants and paths -├── utils.py # Utility functions -├── preferences.py # Addon preferences -├── props.py # Blender properties -├── panels.py # UI panels -├── menus.py # UI menus -├── node.py # Node utilities -├── layer.py # Layer management -├── operators/ # Blender operators -├── bioxel/ # Core bioxel functionality -└── assets/ # Blender assets and node libraries -``` - -### Blender Integration Patterns - -#### Property Groups -```python -class BioxelProperties(bpy.types.PropertyGroup): - bl_label = "Bioxel Properties" - - bioxel_custom_prop: bpy.props.StringProperty( - name="Custom Property", - default="", - description="Description for UI" - ) -``` - -#### Operators -```python -class BIOXEL_OT_custom_operator(bpy.types.Operator): - bl_idname = "bioxel.custom_operator" - bl_label = "Custom Operator" - bl_options = {'REGISTER', 'UNDO'} - - def execute(self, context): - # Operator logic here - return {'FINISHED'} -``` - -#### Panels -```python -class BIOXEL_PT_custom_panel(bpy.types.Panel): - bl_label = "Custom Panel" - bl_idname = "BIOXEL_PT_custom_panel" - bl_space_type = 'VIEW_3D' - bl_region_type = 'UI' - bl_category = "Bioxel" - - def draw(self, context): - layout = self.layout - # UI drawing code here -``` - -## Error Handling - -### Error Handling Patterns -- Use try-catch blocks for file operations -- Handle user cancellation gracefully -- Report progress for long operations using `bioxel_progress_factor` and `bioxel_progress_text` -- Log warnings with print statements for debugging - - -## Key Dependencies - -### Core Libraries -- **bpy** (Blender Python API) - Core integration -- **numpy** - Array processing -- **SimpleITK** - Medical image processing -- **h5py** - HDF5 file handling - -### Scientific Libraries -- **matplotlib** - Plotting and visualization -- **transforms3d** - 3D transformations -- **pyometiff** - OME-TIFF support -- **mrcfile** - MRC file format support - -## Development Workflow - -### Making Changes -1. Identify the appropriate module (operators, panels, bioxel, etc.) -2. Follow existing naming conventions and patterns -3. Use auto-registration - no manual registration needed -4. Test with Blender's Python console -5. Format code with autopep8 before committing - -### Adding New Features -1. Create appropriate classes in relevant modules -2. Use proper prefixes (BIOXEL_OT_, BIOXEL_PT_, etc.) -3. Add to auto_load system automatically discovers new classes -4. Update documentation if needed - -### File Operations -- Use `pathlib.Path` for path operations -- Check file existence before operations -- Handle permissions and missing files gracefully -- Use appropriate file formats (HDF5 for data, PNG for images) - -## Blender Integration Notes - -### Asset Library -- Automatically managed via `add_asset_library_if_missing()` -- Located at `NODE_LIB_DIRPATH` -- Uses "PACK" import method -- Name: "O Bioxel" - -### Progress Reporting -- Use `bioxel_progress_factor` (0.0 to 1.0) for progress -- Use `bioxel_progress_text` for status messages -- Update via WindowManager properties - -### Layer Management -- Layers stored as HDF5 files -- Container objects manage multiple layers -- Use `layer.py` for layer operations -- Support for various medical image formats - -## Common Pitfalls - -### Blender API -- Always check context validity -- Handle different Blender versions (check `bpy.app.version`) -- Use proper property types for UI -- Register classes in correct order (auto_load handles this) - -### Performance -- Use NumPy for array operations -- Avoid expensive operations in UI draw calls -- Cache computed values where appropriate -- Use background threads for long operations - -### File I/O -- Always close file handles -- Use context managers for file operations -- Handle large files in chunks -- Validate file formats before processing \ No newline at end of file +- 避免嵌套结构 +- 特殊的、非常规的需要写注释 +- 变量、函数名、Docstring 用全英文 +- 同一事物用统一表达 +- 使用的依赖越少越好 +- 选用简单直接的方式实现 +- 代码、执行方式改变，调整已有的文档、计划，而非新建 diff --git a/CLAUDE.md b/CLAUDE.md new file mode 100644 index 0000000..eef4bd2 --- /dev/null +++ b/CLAUDE.md @@ -0,0 +1 @@ +@AGENTS.md \ No newline at end of file diff --git a/tests/README.md b/tests/README.md deleted file mode 100644 index db4d862..0000000 --- a/tests/README.md +++ /dev/null @@ -1,43 +0,0 @@ -# BioxelNodes Unit Tests - -This directory contains unit tests for the bioxel module. - -## Test Data - -Test files should be placed in `tests/data/`: - -## Running Tests - -Run all tests: -```bash -uv run pytest -``` - -Run specific test file: -```bash -uv run pytest tests/test_bioxel.py -``` - -Run specific test class: -```bash -uv run pytest tests/test_bioxel.py::TestDataClass -``` - -Run with verbose output: -```bash -uv run pytest -v -``` - -Run with coverage: -```bash -uv run pytest --cov=bioxelnodes.bioxel --cov-report=html -``` - -## Test Categories - -- **TestDataClass**: Data class initialization and properties -- **TestDataToLayers**: Data.to_layers() method -- **TestUtilityFunctions**: Utility functions -- **TestLayerClass**: Layer class functionality -- **TestConstants**: Module constants -- **TestEdgeCases**: Edge cases and error handling diff --git a/tests/test_bioxel.py b/tests/test_bioxel.py deleted file mode 100644 index 43cbe6c..0000000 --- a/tests/test_bioxel.py +++ /dev/null @@ -1,539 +0,0 @@ -""" -Unit tests for bioxel module. - -Tests cover: -- Data class functionality -- Parsing NRRD and DICOM formats -- Layer creation and transformation -- Utility functions -""" - -from bioxelnodes.bioxel import ( - Data, - read, - read_meta, - calc_layer_shape, - calc_layer_size, - Layer, -) -import pytest -import numpy as np -from pathlib import Path - -import sys - -sys.path.insert(0, str(Path(__file__).parent.parent / "src")) - - -# Test data files -NRRD_FILE = Path(__file__).parent / "data/VHP_M.nrrd" -DICOM_FILE = Path(__file__).parent / "data/VHP_M_CT_Head/IM000001.dcm" -DICOM_DIR = Path(__file__).parent / "data/VHP_M_CT_Head/" - - -class TestDataClass: - """Test Data class initialization and properties""" - - def test_data_initialization(self): - """Test basic Data initialization with NRRD""" - data = Data(filepath=str(NRRD_FILE), series_id="") - - assert data.filepath is not None - assert data.series_id == "" - assert data._data is None - assert data._meta is None - - def test_read_meta_nrrd(self): - """Test reading only meta from NRRD file""" - data_obj = read_meta(str(NRRD_FILE)) - - assert data_obj._data is None - assert data_obj._meta is not None - assert "name" in data_obj.meta - assert "spacing" in data_obj.meta - assert "affine" in data_obj.meta - assert "xyz_shape" in data_obj.meta - assert "frame_count" in data_obj.meta - assert "channel_count" in data_obj.meta - assert "dtype" in data_obj.meta - - def test_read_meta_dicom(self): - """Test reading only meta from DICOM file""" - data_obj = read_meta(str(DICOM_FILE), series_id="") - - assert data_obj._data is None - assert data_obj._meta is not None - assert "name" in data_obj.meta - - def test_read_full_data_nrrd(self): - """Test reading full NRRD data""" - data_obj = read(str(NRRD_FILE)) - - assert data_obj._data is not None - assert data_obj._meta is not None - assert isinstance(data_obj.data, np.ndarray) - assert data_obj.data.ndim == 5 - - def test_read_full_data_dicom(self): - """Test reading full DICOM data""" - data_obj = read(str(DICOM_FILE), series_id="") - - assert data_obj._data is not None - assert data_obj._meta is not None - assert isinstance(data_obj.data, np.ndarray) - - def test_data_properties_nrrd(self): - """Test Data property accessors""" - data_obj = read(str(NRRD_FILE)) - - assert hasattr(data_obj, "name") - assert hasattr(data_obj, "description") - assert hasattr(data_obj, "shape") - assert hasattr(data_obj, "xyz_shape") - assert hasattr(data_obj, "spacing") - assert hasattr(data_obj, "affine") - assert hasattr(data_obj, "frame_count") - assert hasattr(data_obj, "channel_count") - assert hasattr(data_obj, "dtype") - - assert isinstance(data_obj.shape, tuple) - assert isinstance(data_obj.xyz_shape, tuple) - assert isinstance(data_obj.spacing, tuple) - assert isinstance(data_obj.affine, np.ndarray) - assert isinstance(data_obj.dtype, np.dtype) - - def test_data_lazy_loading(self): - """Test lazy loading behavior""" - data_obj = Data(filepath=str(NRRD_FILE), series_id="") - - assert data_obj.is_loaded() is False - - data_obj.load_meta() - assert data_obj._data is None - assert data_obj._meta is not None - - data_obj.load_data() - assert data_obj._data is not None - assert data_obj.is_loaded() is True - - def test_shape_property(self): - """Test shape property returns TXYZC format""" - data_obj = read(str(NRRD_FILE)) - - shape = data_obj.shape - assert len(shape) == 5 - assert shape[0] == data_obj.meta["frame_count"] - assert shape[1:4] == data_obj.meta["xyz_shape"] - assert shape[4] == data_obj.meta["channel_count"] - - def test_load_meta_method(self): - """Test load_meta() method exists and works""" - data_obj = Data(filepath=str(NRRD_FILE), series_id="") - - assert hasattr(data_obj, "load_meta") - - data_obj.load_meta() - assert data_obj._meta is not None - assert data_obj._data is None - - -class TestDataToLayers: - """Test Data.to_layers() method""" - - def test_to_layers_dicom_scalar(self): - """Test converting DICOM data to scalar layers""" - data_obj = read(str(DICOM_FILE), series_id="") - - layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0) - - assert len(layers) == 1 - assert layers[0].kind == "scalar" - assert isinstance(layers[0], Layer) - - def test_to_layers_nrrd_scalar(self): - """Test converting NRRD data to scalar layers""" - data_obj = read(str(NRRD_FILE)) - - layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0) - - assert len(layers) == 1 - assert layers[0].kind == "scalar" - assert isinstance(layers[0], Layer) - - def test_to_layers_with_remap(self): - """Test data remapping""" - data_obj = read(str(NRRD_FILE)) - - layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0, remap=True) - - assert len(layers) == 1 - assert layers[0].data.dtype == np.float32 - assert np.all(layers[0].data >= 0) - assert np.all(layers[0].data <= 1) - - def test_to_layers_with_bioxel_size(self): - """Test with different bioxel sizes""" - data_obj = read(str(NRRD_FILE)) - - layers_1x = data_obj.to_layers(kind="scalar", bioxel_size=1.0) - layers_2x = data_obj.to_layers(kind="scalar", bioxel_size=2.0) - - assert len(layers_1x) == 1 - assert len(layers_2x) == 1 - - # Larger bioxel size means smaller layer - shape_1x = layers_1x[0].shape - shape_2x = layers_2x[0].shape - assert shape_2x[0] <= shape_1x[0] - assert shape_2x[1] <= shape_1x[1] - assert shape_2x[2] <= shape_1x[2] - - def test_to_layers_with_smooth(self): - """Test with smoothing parameter""" - data_obj = read(str(NRRD_FILE)) - - layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0, smooth=1) - - assert len(layers) == 1 - assert isinstance(layers[0], Layer) - - def test_to_layers_frame_source_first_frame(self): - """Test frame_source = '-1' (first frame only)""" - data_obj = read(str(NRRD_FILE)) - - layers = data_obj.to_layers(kind="scalar", bioxel_size=2.0, frame_source="-1") - - assert len(layers) == 1 - assert layers[0].frame_count == 1 - - -class TestUtilityFunctions: - """Test utility functions""" - - def test_calc_layer_shape(self): - """Test layer shape calculation""" - shape = calc_layer_shape( - bioxel_size=1.0, orig_shape=(100, 100, 100), orig_spacing=(1.0, 1.0, 1.0) - ) - - assert len(shape) == 3 - assert shape[0] == 100 - assert shape[1] == 100 - assert shape[2] == 100 - - def test_calc_layer_shape_small_bioxel(self): - """Test layer shape with small bioxel size""" - shape = calc_layer_shape( - bioxel_size=2.0, orig_shape=(100, 100, 100), orig_spacing=(1.0, 1.0, 1.0) - ) - - assert len(shape) == 3 - assert shape[0] == 50 - assert shape[1] == 50 - assert shape[2] == 50 - - def test_calc_layer_shape_minimum(self): - """Test layer shape doesn't go below 1""" - shape = calc_layer_shape( - bioxel_size=100.0, orig_shape=(100, 100, 100), orig_spacing=(1.0, 1.0, 1.0) - ) - - assert shape == (1, 1, 1) - - def test_calc_layer_size(self): - """Test layer size calculation""" - size = calc_layer_size(shape=(100, 100, 100), bioxel_size=1.0, scale=1.0) - - assert len(size) == 3 - assert size[0] == 100.0 - assert size[1] == 100.0 - assert size[2] == 100.0 - - def test_calc_layer_size_with_scale(self): - """Test layer size with scale factor""" - size = calc_layer_size(shape=(100, 100, 100), bioxel_size=1.0, scale=0.01) - - assert len(size) == 3 - assert size[0] == 1.0 - assert size[1] == 1.0 - assert size[2] == 1.0 - - -class TestLayerClass: - """Test Layer class functionality""" - - def test_layer_initialization(self): - """Test Layer initialization""" - data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) - layer = Layer(data=data, name="test_layer", kind="scalar") - - assert layer.name == "test_layer" - assert layer.kind == "scalar" - assert np.array_equal(layer.data, data) - - def test_layer_properties(self): - """Test Layer property accessors""" - data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) - layer = Layer( - data=data, name="test_layer", kind="scalar", affine=np.identity(4) - ) - - assert hasattr(layer, "bioxel_size") - assert hasattr(layer, "shape") - assert hasattr(layer, "dtype") - assert hasattr(layer, "origin") - assert hasattr(layer, "euler") - assert hasattr(layer, "frame_count") - assert hasattr(layer, "channel_count") - assert hasattr(layer, "min") - assert hasattr(layer, "max") - - def test_layer_shape_property(self): - """Test layer shape returns XYZ (not TXYZC)""" - data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) - layer = Layer(data=data, name="test", kind="scalar") - - shape = layer.shape - assert len(shape) == 3 - assert shape[0] == 8 - assert shape[1] == 8 - assert shape[2] == 8 - - def test_layer_affine_property(self): - """Test affine transformation matrix""" - data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) - affine = np.array( - [ - [1.0, 0.0, 0.0, 0.0], - [0.0, 1.0, 0.0, 0.0], - [0.0, 0.0, 1.0, 0.0], - [0.0, 0.0, 0.0, 1.0], - ] - ) - layer = Layer(data=data, name="test", kind="scalar", affine=affine) - - result_affine = layer.affine - assert result_affine.shape == (4, 4) - assert np.allclose(result_affine, affine) - - def test_layer_min_max(self): - """Test layer min/max properties""" - data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) - layer = Layer(data=data, name="test", kind="scalar") - - assert isinstance(layer.min, float) - assert isinstance(layer.max, float) - assert layer.min <= layer.max - - def test_layer_copy(self): - """Test layer deep copy""" - data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) - layer = Layer(data=data, name="test", kind="scalar") - layer_copy = layer.copy() - - assert layer_copy.name == layer.name - assert layer_copy.kind == layer.kind - assert np.array_equal(layer_copy.data, layer.data) - - assert layer_copy is not layer - layer_copy.data[0, 0, 0, 0, 0] = 999.0 - assert layer.data[0, 0, 0, 0, 0] != 999.0 - - def test_layer_invalid_data_shape(self): - """Test Layer raises error for invalid data shape""" - data = np.random.rand(8, 8, 8).astype(np.float32) - - with pytest.raises(Exception): - Layer(data=data, name="test", kind="scalar") - - def test_layer_invalid_affine_shape(self): - """Test Layer raises error for invalid affine shape""" - data = np.random.rand(1, 8, 8, 8, 1).astype(np.float32) - affine = np.identity(3) - - with pytest.raises(Exception): - Layer(data=data, name="test", kind="scalar", affine=affine) - - -class TestConstants: - """Test module constants""" - - def test_support_exts_exists(self): - """Test SUPPORT_EXTS constant""" - from bioxelnodes.bioxel import SUPPORT_EXTS - - assert isinstance(SUPPORT_EXTS, list) - assert len(SUPPORT_EXTS) > 0 - assert ".h5" in SUPPORT_EXTS - assert ".nrrd" in SUPPORT_EXTS - assert ".nii.gz" in SUPPORT_EXTS - assert ".dcm" in SUPPORT_EXTS - - def test_dicom_exts_exists(self): - """Test DICOM_EXTS constant""" - from bioxelnodes.bioxel import DICOM_EXTS - - assert isinstance(DICOM_EXTS, list) - assert "" in DICOM_EXTS - assert ".dcm" in DICOM_EXTS - assert ".DCM" in DICOM_EXTS - - def test_ome_exts_exists(self): - """Test OME_EXTS constant""" - from bioxelnodes.bioxel import OME_EXTS - - assert isinstance(OME_EXTS, list) - assert ".tiff" in OME_EXTS - assert ".ome.tiff" in OME_EXTS - - def test_mrc_exts_exists(self): - """Test MRC_EXTS constant""" - from bioxelnodes.bioxel import MRC_EXTS - - assert isinstance(MRC_EXTS, list) - assert ".mrc" in MRC_EXTS - - -class TestEdgeCases: - """Test edge cases and error handling""" - - def test_nonexistent_file(self): - """Test handling of nonexistent file""" - with pytest.raises(FileNotFoundError): - data_obj = read("/nonexistent/file.nii.gz", "") - - def test_frame_count_property_multiframe(self): - """Test frame_count property for multi-frame data""" - data_obj = read(str(NRRD_FILE)) - - assert data_obj.frame_count >= 1 - assert data_obj.frame_count == data_obj.meta["frame_count"] - - def test_channel_count_property(self): - """Test channel_count property""" - data_obj = read(str(NRRD_FILE)) - - assert data_obj.channel_count >= 1 - assert data_obj.channel_count == data_obj.meta["channel_count"] - - def test_nrrd_format_support(self): - """Test NRRD format is in supported extensions""" - from bioxelnodes.bioxel import SUPPORT_EXTS - - assert ".nrrd" in SUPPORT_EXTS - - def test_dicom_format_support(self): - """Test DICOM format is in supported extensions""" - from bioxelnodes.bioxel import SUPPORT_EXTS - - assert ".dcm" in SUPPORT_EXTS - assert "" in SUPPORT_EXTS - - -class TestRealDataFiles: - """Test with real data files""" - - def test_nrrd_file_exists(self): - """Test NRRD test file exists""" - assert NRRD_FILE.exists() - assert NRRD_FILE.is_file() - - def test_dicom_file_exists(self): - """Test DICOM test file exists""" - assert DICOM_FILE.exists() - assert DICOM_FILE.is_file() - - def test_dicom_directory_exists(self): - """Test DICOM directory exists""" - assert DICOM_DIR.exists() - assert DICOM_DIR.is_dir() - - def test_read_nrrd_data(self): - """Test reading real NRRD data""" - data_obj = read(str(NRRD_FILE)) - - assert data_obj._data is not None - assert data_obj._meta is not None - assert isinstance(data_obj.data, np.ndarray) - assert data_obj.data.size > 0 - - def test_read_dicom_data(self): - """Test reading real DICOM data""" - data_obj = read(str(DICOM_FILE), series_id="") - - assert data_obj._data is not None - assert data_obj._meta is not None - assert isinstance(data_obj.data, np.ndarray) - assert data_obj.data.size > 0 - - def test_nrrd_meta_contains_required_fields(self): - """Test NRRD meta contains all required fields""" - data_obj = read(str(NRRD_FILE)) - meta = data_obj.meta - - required_fields = [ - "name", - "description", - "spacing", - "affine", - "xyz_shape", - "frame_count", - "channel_count", - "dtype", - ] - - for field in required_fields: - assert field in meta, f"Meta missing field: {field}" - - def test_dicom_meta_contains_required_fields(self): - """Test DICOM meta contains all required fields""" - data_obj = read(str(DICOM_FILE), series_id="") - meta = data_obj.meta - - required_fields = [ - "name", - "description", - "spacing", - "affine", - "xyz_shape", - "frame_count", - "channel_count", - "dtype", - ] - - for field in required_fields: - assert field in meta, f"Meta missing field: {field}" - - def test_data_to_layers_with_real_nrrd(self): - """Test to_layers with real NRRD data""" - data_obj = read(str(NRRD_FILE)) - - layers = data_obj.to_layers(kind="scalar", bioxel_size=3.0) - - assert len(layers) > 0 - assert all(isinstance(layer, Layer) for layer in layers) - - def test_data_to_layers_with_real_dicom(self): - """Test to_layers with real DICOM data""" - data_obj = read(str(DICOM_FILE), series_id="") - - layers = data_obj.to_layers(kind="scalar", bioxel_size=3.0) - - assert len(layers) > 0 - assert all(isinstance(layer, Layer) for layer in layers) - - def test_nrrd_spacing_values(self): - """Test NRRD spacing values are reasonable""" - data_obj = read(str(NRRD_FILE)) - spacing = data_obj.spacing - - assert len(spacing) == 3 - assert all(s > 0 for s in spacing) - - def test_dicom_spacing_values(self): - """Test DICOM spacing values are reasonable""" - data_obj = read(str(DICOM_FILE), series_id="") - spacing = data_obj.spacing - - assert len(spacing) == 3 - assert all(s > 0 for s in spacing) From e06cadc67e565dea64d81192d14e3fa40f4c5f17 Mon Sep 17 00:00:00 2001 From: nan Date: Mon, 25 May 2026 14:08:38 +0800 Subject: [PATCH 04/14] feat: Update .gitignore to include scipy_ndimage directory --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.gitignore b/.gitignore index 9063c92..b7b41bc 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ +# Scipy +!scipy_ndimage/*/** + # Tempary files temp sandbox.* From cd00c2bfef24f6b1d512f4fc6fde3df36df2530d Mon Sep 17 00:00:00 2001 From: nan Date: Mon, 25 May 2026 14:09:44 +0800 Subject: [PATCH 05/14] feat: Update release workflow and manifest for improved dependency management and layer handling --- .github/workflows/release.yml | 18 +- build.py | 27 +-- src/bioxelnodes/blender_manifest.toml | 20 +- src/bioxelnodes/constants.py | 2 +- src/bioxelnodes/operators/io.py | 280 +++++++++++++++++++++++--- 5 files changed, 282 insertions(+), 65 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 8553984..13adde0 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -3,6 +3,7 @@ name: Release Version on: push: tags: + # Publish on any tag starting with a `v`, e.g., v0.1.0 - 'v*' jobs: @@ -42,14 +43,17 @@ jobs: uses: actions/checkout@v4 with: lfs: "true" - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: 3.11 + - name: Install uv + uses: astral-sh/setup-uv@v7 + - name: Install Dependencies + run: | + uv python install 3.11 + uv python pin 3.11 + uv sync - name: Build Extension run: | # build.py need tomlkit to edit blender_manifest.toml - pip install tomlkit - python build.py ${{ matrix.platform }} + uv run build.py ${{ matrix.platform }} 3.11 + uv run build.py ${{ matrix.platform }} 3.13 cd src/bioxelnodes zip -r ../../package.zip . - name: Upload Extension @@ -60,5 +64,5 @@ jobs: with: upload_url: ${{ needs.draft_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps asset_path: ./package.zip - asset_name: BioxelNodes_${{ needs.draft_release.outputs.version }}_${{ matrix.platform }}.zip + asset_name: BioxelNodes.${{ needs.draft_release.outputs.version }}.${{ matrix.platform }}.zip asset_content_type: application/zip diff --git a/build.py b/build.py index f0d83c4..6d44946 100644 --- a/build.py +++ b/build.py @@ -12,10 +12,10 @@ class Platform: blender_tag: str -required_packages = ["SimpleITK==2.3.1", +required_packages = ["SimpleITK==2.5.5", "pyometiff==1.0.0", "mrcfile==1.5.1", - "h5py==3.11.0", + "h5py==3.16.0", "transforms3d==0.4.2", "tifffile==2024.7.24", "matplotlib==3.10.7", @@ -42,7 +42,7 @@ def run_python(args: str): subprocess.run([python] + args.split(" ")) -def build_extension(platform: Platform, python_version="3.11") -> None: +def build_extension(platform: Platform, python_version: str) -> None: wheel_dirpath = Path("./src/bioxelnodes/wheels") toml_filepath = Path("./src/bioxelnodes/blender_manifest.toml") scipy_ndimage_dirpath = Path("./scipy_ndimage", platform.blender_tag) @@ -52,26 +52,28 @@ def build_extension(platform: Platform, python_version="3.11") -> None: f"-m pip download {' '.join(required_packages)} --dest {wheel_dirpath.as_posix()} --only-binary=:all: --python-version={python_version} --platform={platform.pypi_suffix}" ) - for f in wheel_dirpath.glob('*.whl'): + for f in wheel_dirpath.glob("*.whl"): if any([package in f.name for package in packages_to_remove]): f.unlink(missing_ok=True) - elif platform.blender_tag == "macos-arm64" and \ - "lxml" in f.name and "universal2" in f.name: - f.rename(Path(f.parent, - f.name.replace("universal2", "arm64"))) + elif ( + platform.blender_tag == "macos-arm64" + and "lxml" in f.name + and "universal2" in f.name + ): + f.rename(Path(f.parent, f.name.replace("universal2", "arm64"))) for ndimage_filepath in scipy_ndimage_dirpath.iterdir(): to_filepath = Path("./src/bioxelnodes/bioxel/scipy", ndimage_filepath.name) shutil.copy(ndimage_filepath, to_filepath) - + # Load the TOML file with toml_filepath.open("r") as file: manifest = tomlkit.parse(file.read()) manifest["platforms"] = [platform.blender_tag] - manifest["wheels"] = [f"./wheels/{f.name}" - for f in wheel_dirpath.glob('*.whl')] + manifest["wheels"] = [ + f"./wheels/{f.name}" for f in wheel_dirpath.glob("*.whl")] # build.append('generated', generated) # manifest.append('build', build) @@ -84,8 +86,9 @@ def build_extension(platform: Platform, python_version="3.11") -> None: def main(): platform_name = sys.argv[1] + python_version = sys.argv[2] or "3.11" platform = platforms[platform_name] - build_extension(platform) + build_extension(platform, python_version) if __name__ == "__main__": diff --git a/src/bioxelnodes/blender_manifest.toml b/src/bioxelnodes/blender_manifest.toml index d982f0d..9fb8990 100644 --- a/src/bioxelnodes/blender_manifest.toml +++ b/src/bioxelnodes/blender_manifest.toml @@ -14,25 +14,7 @@ license = ['SPDX:GPL-3.0-or-later'] copyright = ["2024 OmooLab"] platforms = ["windows-x64"] -wheels = [ - "./wheels/contourpy-1.3.3-cp311-cp311-win_amd64.whl", - "./wheels/cycler-0.12.1-py3-none-any.whl", - "./wheels/fonttools-4.60.1-cp311-cp311-win_amd64.whl", - "./wheels/h5py-3.11.0-cp311-cp311-win_amd64.whl", - "./wheels/kiwisolver-1.4.9-cp311-cp311-win_amd64.whl", - "./wheels/lxml-6.0.2-cp311-cp311-win_amd64.whl", - "./wheels/matplotlib-3.10.7-cp311-cp311-win_amd64.whl", - "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl", - "./wheels/packaging-25.0-py3-none-any.whl", - "./wheels/pillow-11.2.1-cp311-cp311-win_amd64.whl", - "./wheels/pyometiff-1.0.0-py3-none-any.whl", - "./wheels/pyparsing-3.2.5-py3-none-any.whl", - "./wheels/python_dateutil-2.9.0.post0-py2.py3-none-any.whl", - "./wheels/SimpleITK-2.3.1-cp311-cp311-win_amd64.whl", - "./wheels/six-1.17.0-py2.py3-none-any.whl", - "./wheels/tifffile-2024.7.24-py3-none-any.whl", - "./wheels/transforms3d-0.4.2-py3-none-any.whl", -] +wheels = ["./wheels/contourpy-1.3.3-cp311-cp311-win_amd64.whl", "./wheels/contourpy-1.3.3-cp313-cp313-win_amd64.whl", "./wheels/cycler-0.12.1-py3-none-any.whl", "./wheels/fonttools-4.63.0-cp311-cp311-win_amd64.whl", "./wheels/fonttools-4.63.0-cp313-cp313-win_amd64.whl", "./wheels/h5py-3.16.0-cp311-cp311-win_amd64.whl", "./wheels/h5py-3.16.0-cp313-cp313-win_amd64.whl", "./wheels/kiwisolver-1.5.0-cp311-cp311-win_amd64.whl", "./wheels/kiwisolver-1.5.0-cp313-cp313-win_amd64.whl", "./wheels/lxml-6.1.1-cp311-cp311-win_amd64.whl", "./wheels/lxml-6.1.1-cp313-cp313-win_amd64.whl", "./wheels/matplotlib-3.10.7-cp311-cp311-win_amd64.whl", "./wheels/matplotlib-3.10.7-cp313-cp313-win_amd64.whl", "./wheels/mrcfile-1.5.1-py2.py3-none-any.whl", "./wheels/packaging-26.2-py3-none-any.whl", "./wheels/pillow-11.2.1-cp311-cp311-win_amd64.whl", "./wheels/pillow-11.2.1-cp313-cp313-win_amd64.whl", "./wheels/pyometiff-1.0.0-py3-none-any.whl", "./wheels/pyparsing-3.3.2-py3-none-any.whl", "./wheels/python_dateutil-2.9.0.post0-py2.py3-none-any.whl", "./wheels/simpleitk-2.5.5-cp311-abi3-win_amd64.whl", "./wheels/six-1.17.0-py2.py3-none-any.whl", "./wheels/tifffile-2024.7.24-py3-none-any.whl", "./wheels/transforms3d-0.4.2-py3-none-any.whl"] [permissions] files = "Import/export volume data from/to disk" diff --git a/src/bioxelnodes/constants.py b/src/bioxelnodes/constants.py index 322b703..1fa5afc 100644 --- a/src/bioxelnodes/constants.py +++ b/src/bioxelnodes/constants.py @@ -1,7 +1,7 @@ from pathlib import Path NODE_LIB_DIRPATH = Path(Path(__file__).parent, - "assets/O Bioxel").resolve() + "assets/O_Bioxel").resolve() LATEST_NODE_LIB_PATH = Path(NODE_LIB_DIRPATH, "BioxelNodes.blend").resolve() diff --git a/src/bioxelnodes/operators/io.py b/src/bioxelnodes/operators/io.py index a94fdd2..96e1b5f 100644 --- a/src/bioxelnodes/operators/io.py +++ b/src/bioxelnodes/operators/io.py @@ -12,20 +12,37 @@ from ..props import BIOXEL_Series from ..utils import get_layer_obj, wrapped_label -from ..bioxel import ( - DICOM_EXTS, - SUPPORT_EXTS, - read, - read_meta, - calc_layer_shape, - calc_layer_size, - get_ext, -) +from ..bioxel.layer import Layer +from ..bioxel.parse import DICOM_EXTS, SUPPORT_EXTS, get_ext, parse_volumetric_data from ..utils import get_cache_dir, progress_update, progress_bar from ..layer import get_layer_caches, save_layers_to_json +def get_layer_shape(bioxel_size: float, orig_shape: tuple, orig_spacing: tuple): + shape = ( + int(orig_shape[0] / bioxel_size * orig_spacing[0]), + int(orig_shape[1] / bioxel_size * orig_spacing[1]), + int(orig_shape[2] / bioxel_size * orig_spacing[2]), + ) + + return ( + shape[0] if shape[0] > 0 else 1, + shape[1] if shape[1] > 0 else 1, + shape[2] if shape[2] > 0 else 1, + ) + + +def get_layer_size(shape: tuple, bioxel_size: float, scale: float = 1.0): + size = ( + float(shape[0] * bioxel_size * scale), + float(shape[1] * bioxel_size * scale), + float(shape[2] * bioxel_size * scale), + ) + + return size + + """ ImportData -> ParseVolumetricData -> ImportDataDialog start import parse data execute import @@ -194,7 +211,11 @@ def progress_callback(factor, text): try: series_id = self.series_id if self.series_id != "empty" else "" - data = read_meta(self.filepath, series_id=series_id) + data, meta = parse_volumetric_data( + data_file=self.filepath, + series_id=series_id, + progress_callback=progress_callback, + ) except KeyboardInterrupt: return except Exception as e: @@ -204,8 +225,8 @@ def progress_callback(factor, text): if cancel(): return - self.meta = data.meta - self.label_count = int(np.max(data.data)) + self.meta = meta + self.label_count = int(np.max(data)) self.dtype = data.dtype # Init cancel flag @@ -313,8 +334,8 @@ def modal(self, context, event): bioxel_size = max(min(*orig_spacing), 1.0) - layer_shape = calc_layer_shape(bioxel_size, orig_shape, orig_spacing) - layer_size = calc_layer_size(layer_shape, bioxel_size, 0.01) + layer_shape = get_layer_shape(bioxel_size, orig_shape, orig_spacing) + layer_size = get_layer_size(layer_shape, bioxel_size, 0.01) min_log10 = math.floor(math.log10(min(*layer_size))) max_log10 = math.floor(math.log10(max(*layer_size))) @@ -526,23 +547,33 @@ class ImportDataDialog(bpy.types.Operator): def execute(self, context): def import_volumetric_data_func(self, context, cancel): + progress_update(context, 0.0, "Parsing Volumetirc Data...") + def progress_callback(factor, text): if cancel(): raise KeyboardInterrupt("Cancelled by user") progress_update(context, factor * 0.2, text) + def progress_callback_factory(layer_name, progress, progress_step): + def progress_callback(frame, total): + if cancel(): + raise KeyboardInterrupt("Cancelled by user") + sub_progress_step = progress_step / total + sub_progress = progress + frame * sub_progress_step + progress_update( + context, + sub_progress, + f"Processing {layer_name} Frame {frame+1}...", + ) + print(f"Processing {layer_name} Frame {frame+1}...") + + return progress_callback + try: - data = read(self.filepath, self.series_id, progress_callback) - - self.layers = data.to_layers( - kind=self.read_as.lower(), - layer_name=self.layer_name, - bioxel_size=self.bioxel_size, - smooth=self.smooth, - remap=self.remap, - split_channel=self.split_channel, - frame_source=self.frame_source, - progress_callback=lambda f, t: progress_callback(0.2 + f * 0.7, t), + data, meta = parse_volumetric_data( + data_file=self.filepath, + series_id=self.series_id, + progress_callback=progress_callback, ) except KeyboardInterrupt: @@ -554,6 +585,203 @@ def progress_callback(factor, text): if cancel(): return + shape = get_layer_shape( + self.bioxel_size, self.orig_shape, self.orig_spacing + ) + + mat_scale = transforms3d.zooms.zfdir2aff(self.bioxel_size) + affine = np.dot(meta["affine"], mat_scale) + kind = self.read_as.lower() + + if cancel(): + return + + # change shape as sequence or not + if self.frame_source == "-1": + data = data[0:1, :, :, :, :] + elif self.frame_source == "0": + # frame as frame + pass + elif self.frame_source == "1": + # X as frame + data = data.transpose(1, 0, 2, 3, 4) + shape = (1, shape[1], shape[2]) + elif self.frame_source == "2": + # Y as frame + data = data.transpose(2, 1, 0, 3, 4) + shape = (shape[0], 1, shape[2]) + elif self.frame_source == "3": + # Z as frame + data = data.transpose(3, 1, 2, 0, 4) + shape = (shape[0], shape[1], 1) + else: + # channel as frame + data = data.transpose(4, 1, 2, 3, 0) + + layers = [] + if kind == "label": + name = self.layer_name or "Label" + data = data.astype(int) + label_count = int(np.max(data)) + progress_step = 0.7 / label_count + + for i in range(label_count): + if cancel(): + return + + name_i = f"{name}_{i+1}" + progress = 0.2 + i * progress_step + progress_update(context, progress, f"Processing {name_i}...") + + progress_callback = progress_callback_factory( + name_i, progress, progress_step + ) + label_data = data == np.full_like(data, i + 1) + # label_data = label_data.astype(np.float32) + try: + layer = Layer(data=label_data, name=name_i, kind=kind) + + layer.resize( + shape=shape, + smooth=self.smooth, + progress_callback=progress_callback, + ) + + layer.affine = affine + + layers.append(layer) + except KeyboardInterrupt: + return + except Exception as e: + self.has_error = e + return + + if kind == "color": + if np.issubdtype(np.uint8, data.dtype): + data = np.multiply(data, 1.0 / 256, dtype=np.float32) + elif data.dtype.kind in ["u", "i"]: + # Convert the normalized array to float dtype + data = data.astype(np.float32) + + min_val = data.min() + max_val = data.max() + # Avoid division by zero if all values are the same + if max_val != min_val: + # Normalize the array to the range (0,1) + data = (data - min_val) / (max_val - min_val) + else: + # If all values are the same, the normalized array will be all zeros + data = np.zeros_like(data, dtype=np.float32) + + else: + data = data.astype(np.float32) + + # Gamma Correct + # data = data ** 2.2 + + name = self.layer_name or "Color" + if data.shape[4] == 1: + data = np.repeat(data, repeats=3, axis=4) + elif data.shape[4] == 2: + d_shape = list(data.shape) + d_shape = d_shape[:4] + [1] + zore = np.zeros(tuple(d_shape), dtype=np.float32) + data = np.concatenate((data, zore), axis=-1) + elif data.shape[4] > 3: + data = data[:, :, :, :, :3] + + if cancel(): + return + + progress_update(context, 0.2, f"Processing {name}...") + progress_callback = progress_callback_factory(name, 0.2, 0.7) + + try: + layer = Layer(data=data, name=name, kind=kind) + + layer.resize(shape=shape, progress_callback=progress_callback) + + layer.affine = affine + + layers.append(layer) + except KeyboardInterrupt: + return + except Exception as e: + self.has_error = e + return + + elif kind == "scalar": + name = self.layer_name or "Scalar" + + if self.remap: + # Convert the normalized array to float dtype + data = data.astype(np.float32) + + min_val = data.min() + max_val = data.max() + # Avoid division by zero if all values are the same + if max_val != min_val: + # Normalize the array to the range (0,1) + data = (data - min_val) / (max_val - min_val) + else: + # If all values are the same, the normalized array will be all zeros + data = np.zeros_like(data, dtype=np.float32) + + if self.split_channel: + progress_step = 0.7 / self.channel_count + + for i in range(self.channel_count): + if cancel(): + return + + name_i = f"{name}_{i+1}" + progress = 0.2 + i * progress_step + progress_update(context, progress, f"Processing {name_i}...") + progress_callback = progress_callback_factory( + name_i, progress, progress_step + ) + try: + layer = Layer( + data=data[:, :, :, :, i : i + 1], name=name_i, kind=kind + ) + + layer.resize( + shape=shape, progress_callback=progress_callback + ) + + layer.affine = affine + + layers.append(layer) + except KeyboardInterrupt: + return + except Exception as e: + self.has_error = e + return + else: + if cancel(): + return + + progress_update(context, 0.2, f"Processing {name}...") + progress_callback = progress_callback_factory(name, 0.2, 0.7) + + try: + layer = Layer(data=data, name=name, kind=kind) + + layer.resize(shape=shape, progress_callback=progress_callback) + + layer.affine = affine + + layers.append(layer) + except KeyboardInterrupt: + return + except Exception as e: + self.has_error = e + return + + if cancel(): + return + + self.layers = layers progress_update(context, 0.9, "Creating Layers...") self.is_cancelled = False @@ -623,7 +851,7 @@ def invoke(self, context, event): return {"RUNNING_MODAL"} def draw(self, context): - layer_shape = calc_layer_shape( + layer_shape = get_layer_shape( self.bioxel_size, self.orig_shape, self.orig_spacing ) From 9ba0c6abeb2ba7f808afd25d2eebb0dd1597a126 Mon Sep 17 00:00:00 2001 From: nan Date: Mon, 25 May 2026 14:16:56 +0800 Subject: [PATCH 06/14] feat: Update .gitignore and add binary files for scipy_ndimage across multiple platforms --- .gitignore | 9 +++++---- .../_nd_image.cpython-313-x86_64-linux-gnu.so | 3 +++ .../_nd_image.cpython-313-darwin.so | 3 +++ .../macos-x64/_nd_image.cpython-313-darwin.so | 3 +++ .../windows-x64/_nd_image.cp313-win_amd64.pyd | Bin 0 -> 177664 bytes 5 files changed, 14 insertions(+), 4 deletions(-) create mode 100644 scipy_ndimage/linux-x64/_nd_image.cpython-313-x86_64-linux-gnu.so create mode 100644 scipy_ndimage/macos-arm64/_nd_image.cpython-313-darwin.so create mode 100644 scipy_ndimage/macos-x64/_nd_image.cpython-313-darwin.so create mode 100644 scipy_ndimage/windows-x64/_nd_image.cp313-win_amd64.pyd diff --git a/.gitignore b/.gitignore index b7b41bc..4075260 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,3 @@ -# Scipy -!scipy_ndimage/*/** - # Tempary files temp sandbox.* @@ -392,4 +389,8 @@ dist # Vite files vite.config.js.timestamp-* vite.config.ts.timestamp-* -.vite/ \ No newline at end of file +.vite/ + + +# Scipy +!scipy_ndimage/*/** \ No newline at end of file diff --git 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zR?|p1u2yzq=2X@Iwk0(I#(zM6B(5c)K;P^@q#`D6>6Y=M7(7I5+|3&m`1 zfdGF@#&4)LO*6dcTHLumt zy0q2ZTHV^z+T0p#?P!g)?rrUEJ=`kVvfH$_yf#PM(l&Qnbz4(gb6d2nqb=69x2?PF zaGPk)Zr9rL+THEd?ZNhj_NMmc_LlZd?a}tm_Fe6J+q>Eiws*Jpw2Mcbk47IAO}y7c z*&H42j_QtJM?*(!Ti3SkZ9Ut>_MGk7cKde6cIS5Y_TcuW?Je7*+dH?%whO^;Cy6sI QYLCu~I- Date: Mon, 25 May 2026 14:18:01 +0800 Subject: [PATCH 07/14] feat: Add OPSX commands for archiving, exploring, and proposing changes --- .claude/commands/opsx/apply.md | 152 +++++++++ .claude/commands/opsx/archive.md | 157 ++++++++++ .claude/commands/opsx/explore.md | 173 +++++++++++ .claude/commands/opsx/propose.md | 106 +++++++ .claude/skills/openspec-apply-change/SKILL.md | 156 ++++++++++ .../skills/openspec-archive-change/SKILL.md | 114 +++++++ .claude/skills/openspec-explore/SKILL.md | 288 ++++++++++++++++++ .claude/skills/openspec-propose/SKILL.md | 110 +++++++ openspec/config.yaml | 20 ++ 9 files changed, 1276 insertions(+) create mode 100644 .claude/commands/opsx/apply.md create mode 100644 .claude/commands/opsx/archive.md create mode 100644 .claude/commands/opsx/explore.md create mode 100644 .claude/commands/opsx/propose.md create mode 100644 .claude/skills/openspec-apply-change/SKILL.md create mode 100644 .claude/skills/openspec-archive-change/SKILL.md create mode 100644 .claude/skills/openspec-explore/SKILL.md create mode 100644 .claude/skills/openspec-propose/SKILL.md create mode 100644 openspec/config.yaml diff --git a/.claude/commands/opsx/apply.md b/.claude/commands/opsx/apply.md new file mode 100644 index 0000000..ae14f0f --- /dev/null +++ b/.claude/commands/opsx/apply.md @@ -0,0 +1,152 @@ +--- +name: "OPSX: Apply" +description: Implement tasks from an OpenSpec change (Experimental) +category: Workflow +tags: [workflow, artifacts, experimental] +--- + +Implement tasks from an OpenSpec change. + +**Input**: Optionally specify a change name (e.g., `/opsx:apply add-auth`). If omitted, check if it can be inferred from conversation context. If vague or ambiguous you MUST prompt for available changes. + +**Steps** + +1. **Select the change** + + If a name is provided, use it. Otherwise: + - Infer from conversation context if the user mentioned a change + - Auto-select if only one active change exists + - If ambiguous, run `openspec list --json` to get available changes and use the **AskUserQuestion tool** to let the user select + + Always announce: "Using change: " and how to override (e.g., `/opsx:apply `). + +2. **Check status to understand the schema** + ```bash + openspec status --change "" --json + ``` + Parse the JSON to understand: + - `schemaName`: The workflow being used (e.g., "spec-driven") + - Which artifact contains the tasks (typically "tasks" for spec-driven, check status for others) + +3. **Get apply instructions** + + ```bash + openspec instructions apply --change "" --json + ``` + + This returns: + - `contextFiles`: artifact ID -> array of concrete file paths (varies by schema) + - Progress (total, complete, remaining) + - Task list with status + - Dynamic instruction based on current state + + **Handle states:** + - If `state: "blocked"` (missing artifacts): show message, suggest using `/opsx:continue` + - If `state: "all_done"`: congratulate, suggest archive + - Otherwise: proceed to implementation + +4. **Read context files** + + Read every file path listed under `contextFiles` from the apply instructions output. + The files depend on the schema being used: + - **spec-driven**: proposal, specs, design, tasks + - Other schemas: follow the contextFiles from CLI output + +5. **Show current progress** + + Display: + - Schema being used + - Progress: "N/M tasks complete" + - Remaining tasks overview + - Dynamic instruction from CLI + +6. **Implement tasks (loop until done or blocked)** + + For each pending task: + - Show which task is being worked on + - Make the code changes required + - Keep changes minimal and focused + - Mark task complete in the tasks file: `- [ ]` → `- [x]` + - Continue to next task + + **Pause if:** + - Task is unclear → ask for clarification + - Implementation reveals a design issue → suggest updating artifacts + - Error or blocker encountered → report and wait for guidance + - User interrupts + +7. **On completion or pause, show status** + + Display: + - Tasks completed this session + - Overall progress: "N/M tasks complete" + - If all done: suggest archive + - If paused: explain why and wait for guidance + +**Output During Implementation** + +``` +## Implementing: (schema: ) + +Working on task 3/7: +[...implementation happening...] +✓ Task complete + +Working on task 4/7: +[...implementation happening...] +✓ Task complete +``` + +**Output On Completion** + +``` +## Implementation Complete + +**Change:** +**Schema:** +**Progress:** 7/7 tasks complete ✓ + +### Completed This Session +- [x] Task 1 +- [x] Task 2 +... + +All tasks complete! You can archive this change with `/opsx:archive`. +``` + +**Output On Pause (Issue Encountered)** + +``` +## Implementation Paused + +**Change:** +**Schema:** +**Progress:** 4/7 tasks complete + +### Issue Encountered + + +**Options:** +1.