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ehrenfeu merged 4 commits into from
Apr 8, 2025
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Add methods to changelog #78

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10c5517
Add missing methods to changelog and reformatting
lguerard Apr 8, 2025
fcb2bc6
Attempt to configure codecov reports
ehrenfeu Apr 8, 2025
dde74d9
Validate and fix codecov.yml
ehrenfeu Apr 8, 2025
6eabd3e
Rewraps (line length)
ehrenfeu Apr 8, 2025
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13 changes: 13 additions & 0 deletions .github/codecov.yml
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coverage:
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# notification blocks
# https://docs.codecov.io/docs/codecovyml-reference#section-coverage-notify
# notify:
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# changes: off
112 changes: 84 additions & 28 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,9 @@ detailed information, please refer to the updated API documentation.

### Added

* `imcflibs.strtools.pad_number` to pad a number with leading zeros.
* `imcflibs.pathtools.create_directory` to create a new directory at the
specified path if it does not exist (needed with python 2.7)
* Various additions to `imcflibs.imagej.misc`:
* `imcflibs.imagej.misc.send_notification_email` to send email notifications
upon completion of long-running scripts.
Expand All @@ -23,45 +26,56 @@ detailed information, please refer to the updated API documentation.
* `imcflibs.imagej.misc.sanitize_image_title` to remove special chars and
various suffixes from an ImagePlus.
* `imcflibs.imagej.misc.subtract_images` to subtract an image from another.
* `imcflibs.imagej.misc.close_images` for closing selected image windows.
* `imcflibs.imagej.misc.close_images` for closing all ImagePluses from a list.
* `imcflibs.imagej.misc.get_threshold_value_from_method` to get the value that
a selected AutoThreshold method would be using.
* `imcflibs.imagej.misc.write_orderddict_to_csv` to write data from an ordered
dictionary to a CSV file.
* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image to
get a label image (2D/3D).
* `imcflibs.imagej.misc.save_image_in_format` to save an ImagePlus image in a
specified format, such as ImageJ-TIF or OME-TIFF etc., to a given directory.
* `imcflibs.imagej.misc.run_imarisconvert` to convert a given file to Imaris
format using the utility ImarisConvert. Method uses
`imcflibs.imagej.misc.locate_latest_imaris` to find the path to the Imaris
installation.

* `imcflibs.imagej.misc.write_ordereddict_to_csv` to write data from an
ordered dictionary (or list of ordered dictionaries) to a CSV file.
* `imcflibs.imagej.misc.save_image_in_format` to save an ImagePlus in a
specified format, such as ImageJ-TIF or OME-TIFF etc., to a given directory.
* `imcflibs.imagej.misc.run_imarisconvert` to convert a given file to Imaris
format using the utility ImarisConvert. Method uses
`imcflibs.imagej.misc.locate_latest_imaris` to find the path to the Imaris
installation.
* New functions in `imcflibs.imagej.labelimage`:
* `imcflibs.imagej.labelimage.cookie_cut_labels` to use a label image as a
mask for another label image. Objects might get split or merged depending on
the mask.
* `imcflibs.imagej.labelimage.binary_to_label` for segmenting a binary image
to get a label image (2D/3D).
* `imcflibs.imagej.labelimage.relate_label_images` to relate two label images
(2D/3D) using the 3D Association plugin from the 3DImageJSuite.
* `imcflibs.imagej.labelimage.dilate_labels_2d` to dilate a label image slice
by slice. Works for 2D or 3D images.
* New `imcflibs.imagej.objects3d` submodule, providing:
* `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn
an Objects3DPopulation into an ImagePlus (2D/3D).
* `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn an
Objects3DPopulation into an ImagePlus (2D/3D).
* `imcflibs.imagej.objects3d.imgplus_to_population3d` to get the
Objects3DPopulation from an ImagePlus (2D/3D).
* `imcflibs.imagej.objects3d.segment_3d_image` to threshold an image into a
labeled stack.
* `imcflibs.imagej.objects3d.get_objects_within_intensity` to filter a
population of 3D objects by intensity.
* `imcflibs.imagej.objects3d.maxima_finder_3d` to find local maxima in a
3D image.
* `imcflibs.imagej.objects3d.seeded_watershed` to perform a seeded watershed
segmentation on a binary image using seeds points.
* New `imcflibs.imagej.bdv` submodule, providing BigDataViewer related
functions:
* New classes:
* `ProcessingOptions` to store all options on how to process the dataset.
* `DefinitionOptions` to store all options on how to define the dataset.
* `imcflibs.imagej.bdv.check_processing_input` to sanitize and clarify
the acitt input selection.
* `imcflibs.imagej.bdv.get_processing_settings` to generate the strings
needed for the processing.
* `imcflibs.imagej.bdv.check_processing_input` to sanitize and clarify the
acitt input selection.
* `imcflibs.imagej.bdv.get_processing_settings` to generate the strings needed
for the processing.
* `imcflibs.imagej.bdv.backup_xml_files` to create a backup of BDV-XML files.
* `imcflibs.imagej.bdv.define_dataset_auto` to run "Define Multi-View Dataset"
using the "Auto-Loader" option.
* `imcflibs.imagej.bdv.define_dataset_manual` to run "Define Multi-View
Dataset" using the "Manual Loader" option.
* `imcflibs.imagej.bdv.resave_as_h5` to resave the dataset in H5 to
make it compatible with BigDataViewer/BigStitcher.
* `imcflibs.imagej.bdv.resave_as_h5` to resave the dataset in H5 to make it
compatible with BigDataViewer/BigStitcher.
* `imcflibs.imagej.bdv.flip_axes` tocall BigStitcher's "Flip Axes" command.
* `imcflibs.imagej.bdv.phase_correlation_pairwise_shifts_calculation` to
calculate pairwise shifts using Phase Correlation.
Expand All @@ -77,14 +91,56 @@ detailed information, please refer to the updated API documentation.
propagating transformation parameters to other channels.
* `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "Fuse Multi-View
Dataset" command.
* New `imcflibs.imagej.trackmate` submodule to provide helper functions to interface with Trackmate:
* Multiple functions to set up Trackmate settings with different detectors, such as `cellpose`, `StarDist` or a `sparseLAP tracker`.
* `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter detected spots based on optional thresholds for quality, area, circularity & intensity.
* `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.
* `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.
* 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.

* `imcflibs.pathtools.create_directory` to create a new directory at the specified path.
* New `imcflibs.imagej.trackmate` submodule to provide helper functions to
interface with Trackmate:
* Multiple functions to set up Trackmate settings with different detectors,
such as `cellpose`, `StarDist` or a `log detector`.
* `imcflibs.imagej.trackmate.spot_filtering` to create settings to filter
detected spots based on optional thresholds for quality, area, circularity &
intensity.
* `imcflibs.imagej.trackmate.sparse_lap_tracker` to create default settings
for the sparse LAP tracker.
* `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.
* `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.
* 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.
* `imcflibs.imagej.omerotools.parse_url` to parse the OMERO URL and get a list
of `ImageWrappers` from multiple image or datasets IDs.
* `imcflibs.imagej.omerotools.connect` to connect to OMERO using user
credentials.
* `imcflibs.imagej.omerotools.fetch_image` to fetch an image from OMERO using
the image ID.
* `imcflibs.imagej.omerotools.upload_image_to_omero` to upload a local image
to OMERO and returning the new image ID.
* `imcflibs.imagej.omerotools.add_keyvalue_annotation` to add an annotation to
an OMERO object.
* `imcflibs.imagej.omerotools.delete_keyvalue_annotations` to delete
annotations from an OMERO object.
* `imcflibs.imagej.omerotools.find_dataset` to find a dataset in OMERO using
the dataset ID.
* `imcflibs.imagej.get_acquisition_metadata` to get the acquisition metadata
from an image in OMERO.
* `imcflibs.imagej.omerotools.get_info_from_original_metadata` to get the
original metadata from an image in OMERO.
* `imcflibs.imagej.omerotools.create_table_columns` to create OMERO table
headings from a list of column names.
* `imcflibs.imagej.omerotools.upload_array_as_omero_table` to upload a table
to OMERO.
* `imcflibs.imagej.omerotools.save_rois_to_omero` to save ROIs to OMERO.
* New `imcflibs.imagej.shading` module for everything background correction.
* `imcflibs.imagej.shading.simple_flatfield_correction` to perform a
simple flatfield correction to an ImagePlus.
* `imcflibs.imagej.projection.project_stack` to project a stack using
different projection methods, such as `max`, `min`, `mean`, `sum` or
`standard_deviation` using a defined axis.
* `imcflibs.imagej.prefs.set_default_ij_options` to configure ImageJ default
options for consistency.

## 1.4.0

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