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‎.github/workflows/lint.yml‎

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name: Code Linting 🔎⚡
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name: Linting 📑🔎⚡
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on:
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push:
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pull_request:
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workflow_dispatch:
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jobs:
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lint:
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ruff:
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name: Ruff ⚡🕵
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runs-on: ubuntu-latest
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steps:
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- name: 📥 Checkout repo
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uses: actions/checkout@v4
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- name: Run Ruff checks ⚡
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uses: astral-sh/ruff-action@v3
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with:
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args: check
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markdownlint:
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name: Markdownlint 📑🕵
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runs-on: ubuntu-latest
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steps:
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- name: 📥 Checkout repo
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uses: actions/checkout@v4
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- name: Run markdownlint-cli2-action 📑
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uses: DavidAnson/markdownlint-cli2-action@v22
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with:
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globs: |
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*.md
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!test/*.md

‎.github/workflows/pytest-poetry.yml‎

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- devel
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‎.github/workflows/pytest-python2.yml‎

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‎.gitignore‎

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docs/_build/*
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MANIFEST
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AGENTS.md

‎.vscode/settings.json‎

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"tables": false
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}
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},
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"cSpell.words": [
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"acitt",
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"bdvp",
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"bigstitcher",
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"biop",
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"caplog",
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"clij",
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"Dscijava",
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"flatfield",
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"Fluo",
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"Haase",
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"IJPB",
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"imageplus",
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"imarisconvert",
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"imglib",
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"imgplus",
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"interestpoint",
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"intermodes",
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"javax",
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"keyvalue",
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"Kheops",
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"labelimage",
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"listdir",
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"micrometa",
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"Morpholib",
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"multiresolution",
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"olefile",
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"omerotools",
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"ordereddict",
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"otsu",
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"pathtools",
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"phmax",
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"Prefs",
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"processingoptions",
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"PTBIOP",
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"PYENV",
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"pylint",
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"ransac",
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"relnotes",
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"renyi",
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"repartitions",
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"resultstable",
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"RETVAL",
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"roimanager",
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"rois",
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"rollingball",
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"scijava",
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"shanbhag",
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"SJLOG",
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"sjlogging",
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"smtpserver",
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"spimdata",
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"stardist",
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"stdv",
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"strtools",
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"subfolders",
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"subsampling",
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"sumpix",
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"TESTDATA",
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"thresholding",
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"trackmate",
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"virtualenv",
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"virtualfish",
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"voxelsizex",
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"voxelsizey",
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"voxelsizez"
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],
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}

‎CHANGELOG.md‎

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# Changelog 🧾
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## 2.0.0
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This major release brings a host of additions and breaking changes across
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multiple modules. For detailed information, please refer to the
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[API documentation][apidocs].
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### Added ✨
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#### New functions in `imcflibs.imagej.bioformats`
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* `imcflibs.imagej.bioformats.get_reader` gets the reader used for opening a
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file, allowing support for multi series files, and gets the highest pyramid
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level for infos.
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#### New functions in `imcflibs.imagej.bdv`
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* `imcflibs.imagej.bdv.read_metadata_from_xml` allows reading metadata back
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from the xml of a H5/XML couple.
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#### New functions in `imcflibs.imagej.misc`
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* `imcflibs.imagej.misc.bytes_to_human_readable` converts size from bytes to a
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more readable format.
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#### New functions in `imcflibs.imagej.trackmate`
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* `imcflibs.imagej.trackmate.set_spotfilter` to set a TrackMate spot filter
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with specified filter key and values.
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#### New functions in `imcflibs.imagej.pathtools`
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* `imcflibs.imagej.pathtools.join_files_with_channel_suffix` to generate lists
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of filenames with channel suffixes, facilitating workflows where each
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channel is stored in a separate file.
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### Changed ♻️
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* Minimum required version for [python-micrometa] increased to `15.2.3`.
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#### `imcflibs.imagej.bdv`
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* `imcflibs.imagej.bdv.define_dataset_auto` does not split time points by
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default any more.
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* `imcflibs.imagej.bdv.define_dataset_manual` now supports passing a list of
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files (`list_files`) directly, enabling the use of explicit file lists in
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"show_list" mode rather than relying solely on file patterns.
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* `imcflibs.imagej.bdv.fuse_dataset_bdvp`:
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* Fix a bug and expose additional parameters.
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* Allow specifying the number of resolution levels, LZW compression, and the
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fusion method; update parameter names and documentation for clarity and
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flexibility.
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* `imcflibs.imagej.bdv.interest_points_registration`: Fix typo and add missing
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options.
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* `imcflibs.imagej.bdv.resave_as_h5`: use the correct processing options
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object and change the ImageJ command to "Resave as HDF5 (local)" for better
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accuracy.
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#### `imcflibs.imagej.bioformats`
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* `imcflibs.imagej.bioformats.import_image` now accepts importing a
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specified image region (crop). Also fix a spelling mistake.
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* `imcflibs.imagej.bioformats.get_stage_coords` returns the filename
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instead of full path.
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#### `imcflibs.imagej.misc`
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* `imcflibs.imagej.misc.run_imarisconvert`:
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* Now allows to select an output folder.
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* Adds pixel calibration to the converted file.
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* `imcflibs.imagej.misc.subtract_images` now validates the slice count is equal
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for both images.
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* `imcflibs.imagej.misc.save_image_with_extension`: fix issue with java path
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object.
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* `imcflibs.imagej.misc.save_image_in_format`: This method also accepts a new
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optional parameter `suffix`to append custom text to output filenames.
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#### `imcflibs.imagej.objects3d`
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* `imcflibs.imagej.objects3d.segment_3d_image`: add option to filter out 3D
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objects touching the image borders when creating a label image.
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#### `imcflibs.imagej.resultstable`
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* `imcflibs.imagej.resultstable.add_results_to_resultstable`:
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* Add support for writing values to specific rows in a results table.
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* Raise an error when provided values don't match target rows.
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* Update docstring description and examples.
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#### `imcflibs.imagej.trackmate`
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* Improve support for 3D data and fix an issue for diameter of objects to be
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found using TrackMate.
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#### `imcflibs.omerotools`
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* `imcflibs.omerotools.parse_url`: safely handle empty input strings, and strip
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the link to ignore trailing white spaces.
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#### `imcflibs.pathtools`
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* `imcflibs.pathtools.listdir_matching`:
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* Add support for recursive directory traversal.
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* Add `recursive` parameter to include files from subdirectories.
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### Removed 🗑️
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#### `imcflibs.imagej.objects3d`
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* `imcflibs.imagej.objects3d.get_objects_within_intensity` has been removed as
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it is now present in the Image3D suite. The method
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`mcib3d.geom.Objects3DPopulation.getObjectsWithinIntensityRange` performs
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the same function as the removed method from this package.
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### Documentation 📝
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* Update `README.md` installation instructions to install imcflibs into a
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"vanilla" Fiji, including required dependencies.
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### Interactive Tests 🧪
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* All interactive test files in `tests/interactive-imagej` are now `.py`, so
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that they can be dragged directly into a Fiji and run.
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## 1.5.0
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* `imcflibs.pathtools.listdir_matching` now has an additional optional argument
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`sort` (defaulting to `False`) to request the resulting list to be sorted.
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* Many improvements / clarifications in function docstrings.
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[python-micrometa]: https://pypi.org/project/python-micrometa/

‎DESC.md‎

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<!-- markdownlint-disable MD041 (first-line-heading) -->
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:snake::coffee::nut_and_bolt::wrench:
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A collection of commonly used Python helper functions.

‎DEVELOPMENT.md‎

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```
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**IMPORTANT 2**: in case a **pre-releaes** was created, the last commit needs to
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**IMPORTANT 2**: in case a **pre-release** was created, the last commit needs to
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be discarded as the *release-script* places a wrong version / snapshot
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combination in the `pom.xml`:
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