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)

python-imcflibs-0.5.1

Changes

• Add missing build-dependency jython-scijava-logging to POM