python-imcflibs-2.0.0

This major release brings a host of additions and breaking changes across
multiple modules. For detailed information, please refer to the
API documentation.

Added ✨

New functions in imcflibs.imagej.bioformats

• imcflibs.imagej.bioformats.get_reader gets the reader used for opening a
  file, allowing support for multi series files, and gets the highest pyramid
  level for infos.

New functions in imcflibs.imagej.bdv

• imcflibs.imagej.bdv.read_metadata_from_xml allows reading metadata back
  from the xml of a H5/XML couple.

New functions in imcflibs.imagej.misc

• imcflibs.imagej.misc.bytes_to_human_readable converts size from bytes to a
  more readable format.

New functions in imcflibs.imagej.trackmate

• imcflibs.imagej.trackmate.set_spotfilter to set a TrackMate spot filter
  with specified filter key and values.

New functions in imcflibs.imagej.pathtools

• imcflibs.imagej.pathtools.join_files_with_channel_suffix to generate lists
  of filenames with channel suffixes, facilitating workflows where each
  channel is stored in a separate file.

Changed ♻️

• Minimum required version for [python-micrometa] increased to 15.2.3.

imcflibs.imagej.bdv

• imcflibs.imagej.bdv.define_dataset_auto does not split time points by
  default any more.
• imcflibs.imagej.bdv.define_dataset_manual now supports passing a list of
  files (list_files) directly, enabling the use of explicit file lists in
  "show_list" mode rather than relying solely on file patterns.
• imcflibs.imagej.bdv.fuse_dataset_bdvp:
  • Fix a bug and expose additional parameters.
  • Allow specifying the number of resolution levels, LZW compression, and the
    fusion method; update parameter names and documentation for clarity and
    flexibility.
• imcflibs.imagej.bdv.interest_points_registration: Fix typo and add missing
  options.
• imcflibs.imagej.bdv.resave_as_h5: use the correct processing options
  object and change the ImageJ command to "Resave as HDF5 (local)" for better
  accuracy.

imcflibs.imagej.bioformats

• imcflibs.imagej.bioformats.import_image now accepts importing a
  specified image region (crop). Also fix a spelling mistake.
• imcflibs.imagej.bioformats.get_stage_coords returns the filename
  instead of full path.

imcflibs.imagej.misc

• imcflibs.imagej.misc.run_imarisconvert:
  • Now allows to select an output folder.
  • Adds pixel calibration to the converted file.
• imcflibs.imagej.misc.subtract_images now validates the slice count is equal
  for both images.
• imcflibs.imagej.misc.save_image_with_extension: fix issue with java path
  object.
• imcflibs.imagej.misc.save_image_in_format: This method also accepts a new
  optional parameter suffixto append custom text to output filenames.

imcflibs.imagej.objects3d

• imcflibs.imagej.objects3d.segment_3d_image: add option to filter out 3D
  objects touching the image borders when creating a label image.

imcflibs.imagej.resultstable

• imcflibs.imagej.resultstable.add_results_to_resultstable:
  • Add support for writing values to specific rows in a results table.
  • Raise an error when provided values don't match target rows.
  • Update docstring description and examples.

imcflibs.imagej.trackmate

• Improve support for 3D data and fix an issue for diameter of objects to be
  found using TrackMate.

imcflibs.imagej.omerotools

• imcflibs.imagej.omerotools.parse_url: safely handle empty input strings, and
  strip the link to ignore trailing white spaces.

imcflibs.pathtools

• imcflibs.pathtools.listdir_matching:
  • Add support for recursive directory traversal.
  • Add recursive parameter to include files from subdirectories.

Removed 🗑️

imcflibs.imagej.objects3d

• imcflibs.imagej.objects3d.get_objects_within_intensity has been removed as
  it is now present in the Image3D suite. The method
  mcib3d.geom.Objects3DPopulation.getObjectsWithinIntensityRange performs
  the same function as the removed method from this package.

Documentation 📝

• Update README.md installation instructions to install imcflibs into a
  "vanilla" Fiji, including required dependencies.

Interactive Tests 🧪

• All interactive test files in tests/interactive-imagej are now .py, so
  that they can be dragged directly into a Fiji and run.

python-imcflibs-2.0.0.a6

What's Changed

• Add calibration to the converted file by @lguerard in #92
• Fix issue with java path object by @lguerard in #104
• feat(pathtools): add recursive option to listdir_matching by @lguerard in #116
• Add dependencies to installation instructions by @CellKai in #110
• Add tmspotfilter function by @CellKai in #112
• Fix issue with CZI autostitch options by @lguerard in #105
• Fix bioformats.get_stage_coords and add option to resultstable.add_results by @rohangirishrao in #97
• Fix Ruff errors by @CellKai in #124
• Add the option to add a suffix to the newly created file name by @lguerard in #103
• Add method to save Fiji script parameters, and add example to opening an image by @rohangirishrao in #111
• Fix typo in apply_threshold by @rohangirishrao in #121
• fix(bdv): correct lambda spelling and improve formatting by @lguerard in #130
• Validate slice count before subtraction by @lguerard in #117
• Fix/129 bdv variable type mixup by @lguerard in #131
• Validate processing settings by @lguerard in #132
• Add method to read metadata back from the xml by @lguerard in #102
• Bdv update library by @lguerard in #118
• Remove method objects3d.get_objects_within_intensity by @rohangirishrao in #123
• Add option to save IMS file in a specified location by @lguerard in #100
• Add option to crop region by @CellKai in #108
• Add installation instructions by @rohangirishrao in #133
• Add markdownlint action by @ehrenfeu in #135
• Sanitize input string in omerotools.parse_url by @rohangirishrao in #134
• Fix function to not split time points by default by @CellKai in #107
• Update installation instructions for Omero packages by @rohangirishrao in #141
• Add function to convert size from bytes to a more readable format by @lguerard in #101
• Add options to segment_3d_image for removing objects touching borders by @lguerard in #139
• Add tests for pathtools.listdir_matching by @lguerard in #122

Full Changelog: python-imcflibs-1.5.0...python-imcflibs-2.0.0.a6

python-imcflibs-2.0.0.a5

What's Changed

• Add calibration to the converted file by @lguerard in #92
• Fix issue with java path object by @lguerard in #104
• feat(pathtools): add recursive option to listdir_matching by @lguerard in #116
• Add dependencies to installation instructions by @CellKai in #110
• Add tmspotfilter function by @CellKai in #112
• Fix issue with CZI autostitch options by @lguerard in #105
• Fix bioformats.get_stage_coords and add option to resultstable.add_results by @rohangirishrao in #97
• Fix Ruff errors by @CellKai in #124
• Add the option to add a suffix to the newly created file name by @lguerard in #103
• Add method to save Fiji script parameters, and add example to opening an image by @rohangirishrao in #111
• Fix typo in apply_threshold by @rohangirishrao in #121
• fix(bdv): correct lambda spelling and improve formatting by @lguerard in #130
• Validate slice count before subtraction by @lguerard in #117
• Fix/129 bdv variable type mixup by @lguerard in #131
• Validate processing settings by @lguerard in #132
• Add method to read metadata back from the xml by @lguerard in #102
• Bdv update library by @lguerard in #118
• Remove method objects3d.get_objects_within_intensity by @rohangirishrao in #123
• Add option to save IMS file in a specified location by @lguerard in #100
• Add option to crop region by @CellKai in #108
• Add installation instructions by @rohangirishrao in #133
• Add markdownlint action by @ehrenfeu in #135
• Sanitize input string in omerotools.parse_url by @rohangirishrao in #134

Full Changelog: python-imcflibs-1.5.0...python-imcflibs-2.0.0.a5

python-imcflibs-1.5.0

What's Changed

• 3d suite by @lguerard in #11
• Changes to tracker creation by @rohangirishrao in #13
• Add testing file and formatting changes by @rohangirishrao in #15
• Add simple_flatfield_correction() to shading module by @ehrenfeu in #16
• Add missing import by @lguerard in #18
• Improve and add docstring by @lguerard in #14
• Remove wrong and duplicate import by @ehrenfeu in #28
• Fix the Works on convention by @lguerard in #27
• Merge changes in labelimage branch by @ehrenfeu in #29
• Small fix for BDV and improve documentation for global vars by @lguerard in #30
• Add imagej.projections.project_stack() by @CellKai in #40
• Pathtools docs and tests for tab, newline and other special chars by @ehrenfeu in #42
• Enable automatic ruff linting by @ehrenfeu in #44
• Add some pathtools tests by @ehrenfeu in #48
• Re-remove create_directory() by @CellKai in #50
• Use pre-releases of imcf-fiji-mocks in Python2 setups by @ehrenfeu in #51
• Update for latest version BigStitcher, add fusion (BDV-playground) by @lguerard in #39
• Remove docstrings for internal globals by @ehrenfeu in #54
• BDV docstrings by @ehrenfeu in #55
• Follow-ups from the coding session on 2025-03-11 by @lguerard in #49
• Changes to send_mail function by @rohangirishrao in #52
• Change log updates for 1.5.0 release by @rohangirishrao in #63
• Move pad_number() to strtools by @lguerard in #64
• Rename function to apply_rollingball_bg_subtraction() by @lguerard in #65
• Update documentation for OMERO tools requirements by @lguerard in #66
• Add notes to calculate_mean_and_stdv for empty input handling by @lguerard in #67
• Fix indentation of function by @lguerard in #68
• Fix fix_ij_options docstring and set tested options by @rohangirishrao in #69
• Attempt to fix docstring rendering in pdoc by @ehrenfeu in #70
• Add info about changes for BDV by @lguerard in #72
• Fix path with BDV test by @lguerard in #73
• Fix issues with TrackMate by @lguerard in #75
• Usage instructions for send_notification_email by @CellKai in #76
• Add methods to changelog by @lguerard in #78
• Rename methods and fix docstrings by @lguerard in #79
• Changes to bioformats module's metadata retrieval by @rohangirishrao in #74
• Update Changelog.md for project_stack function by @CellKai in #77
• Add methods for imcflibs.imagej.processing by @lguerard in #80
• Update changelog by @lguerard in #81
• Fix changelog broken link by @lguerard in #85
• Start finalizing the imcflibs-1.5.0 release by @ehrenfeu in #86
• Explain IJ options iterations and count by @CellKai in #87
• Final changes for the imcflibs-1.5.0 release by @ehrenfeu in #88

Contributors

• @rohangirishrao
• @ehrenfeu
• @CellKai
• @lguerard

Full Changelog: python-imcflibs-1.4.0...python-imcflibs-1.5.0

python-imcflibs-1.4.1

Nothing changed except packaging metadata for the Python wheel (despite the README still claiming no such thing exists).

python-imcflibs-1.4.0

✨ 🎁 See the Change Log in the public API Documentation for a nice overview with clickable links! 🎁 ✨

Added

• imcflibs.strtools.sort_alphanumerically to sort a list of strings taking
  into account numerical values correctly.

Changed

• imcflibs.pathtools.listdir_matching is now using the new
  sort_alphanumerically() function from above.

Artifacts

• python-imcflibs-1.4.0.jar (on maven.scijava.org)

python-imcflibs-1.3.0

✨ 🎁 See the Change Log in the public API Documentation for a nice overview with clickable links! 🎁 ✨

Added

• New functions in imcflibs.pathtools:
  • imcflibs.pathtools.join2 can be used to join paths, much like
    os.path.join except that it will work with java.io.File objects as well
    (but doesn't support more than two path components / parameters).
  • imcflibs.pathtools.find_dirs_containing_filetype
  • imcflibs.pathtools.folder_size
• New functions in imcflibs.imagej.misc:
  • imcflibs.imagej.misc.calculate_mean_and_stdv
  • imcflibs.imagej.misc.elapsed_time_since
  • imcflibs.imagej.misc.find_focus
  • imcflibs.imagej.misc.get_free_memory
  • imcflibs.imagej.misc.percentage
  • imcflibs.imagej.misc.progressbar
  • imcflibs.imagej.misc.setup_clean_ij_environment
  • imcflibs.imagej.misc.timed_log
• New imcflibs.imagej.labelimage submodule, providing:
  • imcflibs.imagej.labelimage.filter_objects
  • imcflibs.imagej.labelimage.label_image_to_roi_list
  • imcflibs.imagej.labelimage.measure_objects_size_shape_2d
  • imcflibs.imagej.labelimage.relate_label_images
• New imcflibs.imagej.gpu submodule, providing:
  • imcflibs.imagej.gpu.erode_labels
  • imcflibs.imagej.gpu.dilate_labels
  • imcflibs.imagej.gpu.merge_labels
• New imcflibs.imagej.resultstable submodule, providing:
  • imcflibs.imagej.resultstable.add_results_to_resultstable
  • imcflibs.imagej.resultstable.get_resultstable
  • imcflibs.imagej.resultstable.preset_results_column
• New imcflibs.imagej.roimanager submodule, providing:
  • imcflibs.imagej.roimanager.add_rois_to_roimanager
  • imcflibs.imagej.roimanager.change_roi_color
  • imcflibs.imagej.roimanager.clear_ij_roi_manager
  • imcflibs.imagej.roimanager.count_all_rois
  • imcflibs.imagej.roimanager.enlarge_all_rois
  • imcflibs.imagej.roimanager.extract_color_of_all_rois
  • imcflibs.imagej.roimanager.get_roimanager
  • imcflibs.imagej.roimanager.load_rois_from_zip
  • imcflibs.imagej.roimanager.measure_in_all_rois
  • imcflibs.imagej.roimanager.rename_rois_by_number
  • imcflibs.imagej.roimanager.rename_rois
  • imcflibs.imagej.roimanager.save_rois_to_zip
  • imcflibs.imagej.roimanager.scale_all_rois
  • imcflibs.imagej.roimanager.select_rois_above_min_intensity
  • imcflibs.imagej.roimanager.shift_roi_by_bounding_box
  • imcflibs.imagej.roimanager.show_all_rois_on_image

Changed

• The functions below now also accept parameters of type java.io.File (instead
  of str), making them safe for being used directly with variables retrieved
  via ImageJ2's Script Parameter @# File:
  • imcflibs.pathtools.parse_path
  • imcflibs.strtools.filename
• Several changes in imcflibs.pathtools.parse_path:
  • The returned dict now contains an additional key basename that provides
    the filename without extension.
  • OME-TIFF filenames are now treated as special cases in the sense that the
    .ome part is stripped from the basename key and added to the ext key
    instead (as it is part of the suffix).
• imcflibs.pathtools.listdir_matching now has an additional optional argument
  sort (defaulting to False) to request the resulting list to be sorted.
• Many improvements / clarifications in function docstrings.

Artifacts

• python-imcflibs-1.3.0.jar (on maven.scijava.org)

python-imcflibs-1.2.0

Changes

• 64cfb3a: import submodules automatically, so any part of the package can be accessed with a simple import imcflibs and then using the fully qualified name of a function

Artifacts

• python-imcflibs-1.2.0.jar (on maven.scijava.org)

python-imcflibs-1.1.0

Changes

• 5d3b5f3: add imagej.shading.process_files()
• cf1e290: add an optional parameter fullpath to pathtools.listdir_matching()
• a61a260: make imagej.projections.create_and_save() return a bool
• 1aed64f: make imagej.shading.correct_and_project() return a tuple of bool
• 5d3b5f3: update dependency for jython-scijava-logging to 0.5.2

Fixes

• a0fd333: fix an issue in imagej.bioformats.export()
• fed8217: fix an issue in imagej.shading.correct_and_project() when model is None

Artifacts

• python-imcflibs-1.1.0.jar (on maven.scijava.org)

python-imcflibs-1.0.0

Changes

• 92b9b2f: calls to show_status() and show_progress() don't require a logger object any more
• 58ab521: add imagej.stitching module
• b65c563: add pathtools.derive_out_dir()
• 710070f: add imagej.misc.error_exit()
• 25b8746: allow shading model to be None in imagej.shading.correct_and_project()
• ab1d6ed: allow model file name to be - or NONE in imagej.shading.process_folder()

Fixes

• f6f545e: add a workaround for uncalibrated ICS / IDS exports in Bio-Formats 6.0 series

Artifacts

• python-imcflibs-1.0.0.jar (on maven.scijava.org)