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CHANGELOG.md

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Changelog 🧾

1.4.0

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.

1.3.0

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.