v3.1.1

What's Changed

Changes

• Update dependencies in Dockerfile by @yousefmoazzam in #702

Full Changelog: v3.1...v3.1.1

v3.1

What's Changed

Notable Changes for Users

• Add CLI flag to set continuous scan subset start and stop indices by @yousefmoazzam in #690

Changes

• Preview extender if a method with padding present by @dkazanc in #670
• Fix potential skipping of non-auto params in YAML checker by @yousefmoazzam in #671
• Allow omitting image key path loader param in YAML checker by @yousefmoazzam in #673
• reslice clock time added into the log by @dkazanc in #674
• a fix for the preview expansion to work in parallel by @dkazanc in #676
• Block to cpu move to _execute_section_block by @dkazanc in #675
• YAML checker catches pipelines omitting required params by @yousefmoazzam in #677
• Snapshot saver feature to help with debugging by @dkazanc in #679
• Include padding in max slices and number of blocks calculations by @yousefmoazzam in #680
• Fix failure to ignore darks/flats when getting the other from separate file by @yousefmoazzam in #683
• fixing a bug around block to cpu logic by @dkazanc in #686
• Apply black formatting to fix CI by @yousefmoazzam in #688
• fix Paganin slices estimation in sweep runner by @mfep in #687
• Autogenerate release notes and upload user release notes asset by @yousefmoazzam in #685
• Refactor darks/flats config class to more clearly represent the various use-cases by @yousefmoazzam in #684
• Fix f-string incompatibility with python 3.11 by @yousefmoazzam in #691
• Radway 69 iterative lprec estimator by @ferenc-gh in #681
• Add gcc transitive dependency to Dockerfile by @yousefmoazzam in #692
• Cupy 14.0 + numpy 2.4 environment related changes by @dkazanc in #682
• Add PIL mock import to sphinx autodoc config by @yousefmoazzam in #696
• adding artifacts upload to docs build by @dkazanc in #701
• enabling errors for gpu-disabled devices by @dkazanc in #698
• Apply black code formatter by @yousefmoazzam in #704
• Set reslice dir default value to output dir by @yousefmoazzam in #703
• Fix incorrect link target in loader docs by @yousefmoazzam in #694
• Explicitly finalise source to cleanup hdf5 file backing dataset store by @yousefmoazzam in #706

Full Changelog: v3.0...v3.1

v3.0

What's Changed

• Adding archived templates into Documentation by @dkazanc in #639
• Changes to accomodate 32bit image saving in sweeps by @dkazanc in #648
• Add option for turning off click's standalone_mode by @ferenc-gh in #647
• Paganin filter related changes by @dkazanc in #650
• Add loader functionality to select subset of data along angular dimension by @yousefmoazzam in #649
• Data checker auto insertion by @dkazanc in #653
• Transform section pattern for some cases of non-auto axis image saver by @yousefmoazzam in #654
• fixing rotation phase crosscorrelation issue by @dkazanc in #657
• Fix broken reference in full YAML pipeline docs by @yousefmoazzam in #664
• Add CLI flag for enabling MPI abort hook by @yousefmoazzam in #662
• Remove explicitly setting frames per chunk to 1 by @yousefmoazzam in #661
• removing normalisation step from centering algorithms by @dkazanc in #660
• Fix memory pool leakage in dezinging by changing the order of execution by @mfep in #666
• Iterative search method for memory estimator by @mfep in #652
• adding function to remove redundant methods in sweep pipeline by @dkazanc in #668

Full Changelog: v2.6...v3.0

v2.6

What's Changed

• Running full pipelines in parallel in tests by @dkazanc in #600
• Darks or/and flats images ignore by @dkazanc in #599
• Sweep intensity fix by @dkazanc in #612
• Changes around the logic of the rotation wrapper by @dkazanc in #604
• Don't insert intermediate file saving method in sweep run by @yousefmoazzam in #615
• Making a keyword (null) to work for image_key_path in the loader by @dkazanc in #616
• Add MPI abort handler for unhandled exceptions by @yousefmoazzam in #614
• Some corrections to documentation by @dkazanc in #621
• Fix code formatting by @yousefmoazzam in #624
• Add httomo version comment to pipeline file copied to output dir by @yousefmoazzam in #623
• modification of the parallel test to allow detector padding by @dkazanc in #618
• making sweep runs to save 16 bit images instead of 8bit by @dkazanc in #625
• Run framework and pipeline tests on IRIS sequentially rather than in parallel by @yousefmoazzam in #627
• Communicate min block len only on first block in section by @dkazanc in #622
• reducing the preview size for a quicker test run by @dkazanc in #629
• Sweep run changes to avoid multiple rescaling by @dkazanc in #628
• Block to cpu function changes of base_block by @dkazanc in #620
• Adding a new test that executes a new directive by @dkazanc in #630
• OutputRef cannot be accessed in a method when padding is also enabled by @dkazanc in #631
• Reslice reduced memory v3 clean by @neon60 in #636
• Fix code formatting by @yousefmoazzam in #638
• Create output directory if it doesn't exist by @yousefmoazzam in #633
• Fix rank 2 case by @neon60 in #640
• Use numpy.split in reslice by @neon60 in #641
• Add new reslice algorithm with lower memory usage by @dkazanc in #637
• Enable padding in sections after 0th section by @yousefmoazzam in #644

New Contributors

• @neon60 made their first contribution in #636

Full Changelog: v2.5...v2.6

v2.5

What's Changed

• Remove default conda channels from CI by @yousefmoazzam in #551
• Distortion correction pipeline and a test with big data by @dkazanc in #552
• Fix CI lint errors from black update by @yousefmoazzam in #555
• Remove unused compressed tomo standard test data by @yousefmoazzam in #554
• Update test data to be NXtomo compliant by @yousefmoazzam in #556
• Enable automatic discovery of NXtomo entry in input data by @yousefmoazzam in #553
• Full real data pipeline test for sweep by @dkazanc in #557
• Simplify temp dir setup/teardown in tests by @yousefmoazzam in #559
• Speed up CLI tests by @yousefmoazzam in #560
• Add CLI flag for choosing recon filename stem by @yousefmoazzam in #562
• Add container image and release build to ghcr by @yousefmoazzam in #567
• Minimise conda usage in installation process by @yousefmoazzam in #564
• Remove unused logger object by @yousefmoazzam in #571
• Simplify BlockSplitter's iterator implementation by @yousefmoazzam in #572
• Separate BlockSplitter docstring into sections by @yousefmoazzam in #573
• reusing flats/darks from a different scan by @dkazanc in #569
• Add loader auto parameter value support to YAML checker by @yousefmoazzam in #575
• Execute intermediate data wrapper in output recon file naming tests by @yousefmoazzam in #578
• Use minimum block length as frames-per-chunk value if frames-per-chunk calculation exceeds minimum block length by @yousefmoazzam in #581
• Add missing type hints to UI layer tests by @yousefmoazzam in #586
• Expect error status in CLI test with no args passed by @yousefmoazzam in #588
• Fix sweep runner not passing minimum block length to intermediate data wrapper by @yousefmoazzam in #592
• full pipelines tests fix and agnostic loader changes to tests by @dkazanc in #580
• Add simple JSON pipeline loader that handles range and manual parameter sweeps by @yousefmoazzam in #583
• Add JSON pipeline support to UI layer by @yousefmoazzam in #590
• Cli pipeline compatibility by @itsdiy0 in #594
• Update container image for compatibility with workflows system by @yousefmoazzam in #596
• Center360 and stitching method corrections by @dkazanc in #598
• Logpolar full pipeline test by @dkazanc in #595

New Contributors

• @itsdiy0 made their first contribution in #594

Full Changelog: v2.4...v2.5

v2.4

What's Changed

• Pipeline auto generator by @dkazanc in #541
• Decide the value of frames_per_chunk from saturation bandwidth by @ptim0626 in #537
• Remove some unnecessary copies during iteration over splitter that's given a file-based dataset source by @yousefmoazzam in #544
• New testing structure with auto-pipelines generation by @dkazanc in #542

Full Changelog: v2.3...v2.4

v2.3

What's Changed

• Enabling begin, mid, end preview keywords by @dkazanc in #531
• Remove cudatoolkit explicit dependency by @yousefmoazzam in #536
• Remove backends information and get it from httomo-backends instead by @yousefmoazzam in #532
• adding average_radius parameter into the rotation wrapper by @dkazanc in #534
• adding inline comments for some pipelines by @dkazanc in #540

Full Changelog: v2.2...v2.3

v2.2

What's Changed

• Account for input data size in memory hook test without inline cupy array copy by @yousefmoazzam in #513
• Add docstrings for members of preview.py module by @yousefmoazzam in #509
• Update transform loader params API docs by @yousefmoazzam in #514
• Add and update docstrings in section.py module by @yousefmoazzam in #517
• Add docstrings for darks_flats.py module and members by @yousefmoazzam in #519
• Remove python pipeline file support by @yousefmoazzam in #527
• Remove pipeline file extension check by @yousefmoazzam in #529
• Paganinsweep by @dkazanc in #521
• removing autoinsertion of rescale_to_int for sweep runs by @dkazanc in #523
• adding raven filter memory estimator by @dkazanc in #530

Full Changelog: v2.1.1...v2.2

v2.1.1

What's Changed

• updating docs and some yaml pipelines by @dkazanc in #464
• fixing the pypi path by @dkazanc in #467
• Remove template generation as a part of the CI by @namannimmo10 in #471
• Add python version <3.13 constraint in docs env by @yousefmoazzam in #473
• Add CLI flag to pass an existing output directory to httomo (instead of httomo creating one) by @yousefmoazzam in #460
• Remove refs to unused loader params name, in_file, pad, dimension by @yousefmoazzam in #482
• Remove --output-folder-path CLI flag by @yousefmoazzam in #484
• Migrate from sphinx-panels to sphinx-design by @yousefmoazzam in #488
• Fix docs build warnings and generate API docs with autosummary extension by @yousefmoazzam in #494
• Various small docs fixes by @yousefmoazzam in #497
• Remove data/hdf/loaders.py by @namannimmo10 in #502
• Update loader module docs by @yousefmoazzam in #505
• adding extraction of angles related to data indices only by @dkazanc in #508
• Add distortion correction wrapper by @yousefmoazzam in #507
• Update parameters in distortion correction memory hook test by @yousefmoazzam in #511

Full Changelog: v2.1.0...v2.1.1

v2.1.0

• Memory estimators improved for several packages in httomolibgpu.
• Memory leak fixed in the FBP method and in the corresponding wrapper in HTTomo
• Sweeping feature with parameters watermarking on top of the images
• Padding feature to enable true 3D processing (e.g. median filter or outliers removal)
• Various fixes and some refactoring