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