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Merge pull request #78 from lguerard/issues/34
Add methods to changelog
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‎CHANGELOG.md‎

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@@ -9,6 +9,9 @@ detailed information, please refer to the updated API documentation.
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### Added
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* `imcflibs.strtools.pad_number` to pad a number with leading zeros.
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* `imcflibs.pathtools.create_directory` to create a new directory at the
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specified path if it does not exist (needed with python 2.7)
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* Various additions to `imcflibs.imagej.misc`:
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* `imcflibs.imagej.misc.send_notification_email` to send email notifications
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upon completion of long-running scripts.
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* `imcflibs.imagej.misc.sanitize_image_title` to remove special chars and
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various suffixes from an ImagePlus.
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* `imcflibs.imagej.misc.subtract_images` to subtract an image from another.
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* `imcflibs.imagej.misc.close_images` for closing selected image windows.
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* `imcflibs.imagej.misc.close_images` for closing all ImagePluses from a list.
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* `imcflibs.imagej.misc.get_threshold_value_from_method` to get the value that
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a selected AutoThreshold method would be using.
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* `imcflibs.imagej.misc.write_orderddict_to_csv` to write data from an ordered
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dictionary to a CSV file.
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* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image to
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get a label image (2D/3D).
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* `imcflibs.imagej.misc.save_image_in_format` to save an ImagePlus image in a
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specified format, such as ImageJ-TIF or OME-TIFF etc., to a given directory.
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* `imcflibs.imagej.misc.run_imarisconvert` to convert a given file to Imaris
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format using the utility ImarisConvert. Method uses
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`imcflibs.imagej.misc.locate_latest_imaris` to find the path to the Imaris
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installation.
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* `imcflibs.imagej.misc.write_ordereddict_to_csv` to write data from an
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ordered dictionary (or list of ordered dictionaries) to a CSV file.
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* `imcflibs.imagej.misc.save_image_in_format` to save an ImagePlus in a
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specified format, such as ImageJ-TIF or OME-TIFF etc., to a given directory.
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* `imcflibs.imagej.misc.run_imarisconvert` to convert a given file to Imaris
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format using the utility ImarisConvert. Method uses
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`imcflibs.imagej.misc.locate_latest_imaris` to find the path to the Imaris
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installation.
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* New functions in `imcflibs.imagej.labelimage`:
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* `imcflibs.imagej.labelimage.cookie_cut_labels` to use a label image as a
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mask for another label image. Objects might get split or merged depending on
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the mask.
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* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image
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to get a label image (2D/3D).
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* `imcflibs.imagej.labelimage.relate_label_images` to relate two label images
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(2D/3D) using the 3D Association plugin from the 3DImageJSuite.
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* `imcflibs.imagej.labelimage.dilate_labels_2d` to dilate a label image slice
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by slice. Works for 2D or 3D images.
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* New `imcflibs.imagej.objects3d` submodule, providing:
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* `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn
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an Objects3DPopulation into an ImagePlus (2D/3D).
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* `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn an
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Objects3DPopulation into an ImagePlus (2D/3D).
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* `imcflibs.imagej.objects3d.imgplus_to_population3d` to get the
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Objects3DPopulation from an ImagePlus (2D/3D).
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* `imcflibs.imagej.objects3d.segment_3d_image` to threshold an image into a
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labeled stack.
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* `imcflibs.imagej.objects3d.get_objects_within_intensity` to filter a
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population of 3D objects by intensity.
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* `imcflibs.imagej.objects3d.maxima_finder_3d` to find local maxima in a
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3D image.
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* `imcflibs.imagej.objects3d.seeded_watershed` to perform a seeded watershed
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segmentation on a binary image using seeds points.
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* New `imcflibs.imagej.bdv` submodule, providing BigDataViewer related
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functions:
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* New classes:
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* `ProcessingOptions` to store all options on how to process the dataset.
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* `DefinitionOptions` to store all options on how to define the dataset.
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* `imcflibs.imagej.bdv.check_processing_input` to sanitize and clarify
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the acitt input selection.
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* `imcflibs.imagej.bdv.get_processing_settings` to generate the strings
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needed for the processing.
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* `imcflibs.imagej.bdv.check_processing_input` to sanitize and clarify the
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acitt input selection.
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* `imcflibs.imagej.bdv.get_processing_settings` to generate the strings needed
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for the processing.
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* `imcflibs.imagej.bdv.backup_xml_files` to create a backup of BDV-XML files.
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* `imcflibs.imagej.bdv.define_dataset_auto` to run "Define Multi-View Dataset"
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using the "Auto-Loader" option.
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* `imcflibs.imagej.bdv.define_dataset_manual` to run "Define Multi-View
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Dataset" using the "Manual Loader" option.
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* `imcflibs.imagej.bdv.resave_as_h5` to resave the dataset in H5 to
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make it compatible with BigDataViewer/BigStitcher.
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* `imcflibs.imagej.bdv.resave_as_h5` to resave the dataset in H5 to make it
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compatible with BigDataViewer/BigStitcher.
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* `imcflibs.imagej.bdv.flip_axes` tocall BigStitcher's "Flip Axes" command.
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* `imcflibs.imagej.bdv.phase_correlation_pairwise_shifts_calculation` to
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calculate pairwise shifts using Phase Correlation.
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propagating transformation parameters to other channels.
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* `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "Fuse Multi-View
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Dataset" command.
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* New `imcflibs.imagej.trackmate` submodule to provide helper functions to interface with Trackmate:
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* Multiple functions to set up Trackmate settings with different detectors, such as `cellpose`, `StarDist` or a `sparseLAP tracker`.
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* `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter detected spots based on optional thresholds for quality, area, circularity & intensity.
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* `imcflibs.imagej.trackmate.track_filtering` to create settings to filter detected tracks based upon optional distances, such as maximum linking, gap closing, track splitting & merging and maximum frame gap.
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* `imcflibs.imagej.trackmate.run_trackmate` to run Fiji's Trackmate plugin on an open ImagePlus with given settings, which can be set up with available methods in the `imcflibs.imagej.trackmate` submodule. The method then returns a label image.
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* New `imcflibs.imagej.omerotools` submodule, providing helper functions to connect to OMERO using user credentials, fetch and upload an image, retrieve a dataset, or save ROIs to OMERO.
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* `imcflibs.pathtools.create_directory` to create a new directory at the specified path.
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* New `imcflibs.imagej.trackmate` submodule to provide helper functions to
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interface with Trackmate:
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* Multiple functions to set up Trackmate settings with different detectors,
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such as `cellpose`, `StarDist` or a `log detector`.
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* `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter
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detected spots based on optional thresholds for quality, area, circularity &
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intensity.
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* `imcflibs.imagej.trackmate.sparse_lap_tracker` to create default settings
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for the sparse LAP tracker.
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* `imcflibs.imagej.trackmate.track_filtering` to create settings to filter
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detected tracks based upon optional distances, such as maximum linking, gap
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closing, track splitting & merging and maximum frame gap.
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* `imcflibs.imagej.trackmate.run_trackmate` to run Fiji's Trackmate plugin on
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an open ImagePlus with given settings, which can be set up with available
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methods in the `imcflibs.imagej.trackmate` submodule. The method then
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returns a label image.
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* New `imcflibs.imagej.omerotools` submodule, providing helper functions to
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connect to OMERO using user credentials, fetch and upload an image, retrieve a
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dataset, or save ROIs to OMERO.
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* `imcflibs.imagej.omerotools.parse_url` to parse the OMERO URL and get a list
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of `ImageWrappers` from multiple image or datasets IDs.
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* `imcflibs.imagej.omerotools.connect` to connect to OMERO using user
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credentials.
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* `imcflibs.imagej.omerotools.fetch_image` to fetch an image from OMERO using
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the image ID.
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* `imcflibs.imagej.omerotools.upload_image_to_omero` to upload a local image
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to OMERO and returning the new image ID.
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* `imcflibs.imagej.omerotools.add_keyvalue_annotation` to add an annotation to
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an OMERO object.
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* `imcflibs.imagej.omerotools.delete_keyvalue_annotations` to delete
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annotations from an OMERO object.
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* `imcflibs.imagej.omerotools.find_dataset` to find a dataset in OMERO using
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the dataset ID.
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* `imcflibs.imagej.get_acquisition_metadata` to get the acquisition metadata
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from an image in OMERO.
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* `imcflibs.imagej.omerotools.get_info_from_original_metadata` to get the
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original metadata from an image in OMERO.
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* `imcflibs.imagej.omerotools.create_table_columns` to create OMERO table
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headings from a list of column names.
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* `imcflibs.imagej.omerotools.upload_array_as_omero_table` to upload a table
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to OMERO.
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* `imcflibs.imagej.omerotools.save_rois_to_omero` to save ROIs to OMERO.
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* New `imcflibs.imagej.shading` module for everything background correction.
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* `imcflibs.imagej.shading.simple_flatfield_correction` to perform a
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simple flatfield correction to an ImagePlus.
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* `imcflibs.imagej.projection.project_stack` to project a stack using
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different projection methods, such as `max`, `min`, `mean`, `sum` or
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`standard_deviation` using a defined axis.
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* `imcflibs.imagej.prefs.set_default_ij_options` to configure ImageJ default
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options for consistency.
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## 1.4.0
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