diff --git a/CHANGELOG.md b/CHANGELOG.md index 892dbc5..afc0a96 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,10 +4,123 @@ ## 2.0.0 -### Changed +This major release brings a host of additions and breaking changes across +multiple modules. For detailed information, please refer to the +[API documentation][apidocs]. + +### Added โœจ + +#### 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 โ™ป๏ธ * 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.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.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.omerotools` + +* `imcflibs.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 ๐Ÿ—‘๏ธ + +#### `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 ๐Ÿ“ + +* Update `README.md` installation instructions to install imcflibs into a + "vanilla" Fiji, including required dependencies. + +### Interactive Tests ๐Ÿงช + +* All interactive test files in `tests/interactive-imagej` are now `.py`, so + that they can be dragged directly into a Fiji and run. + ## 1.5.0 This release brings a lot of additions, not all changes and functions are