From 4b73fcb3bbccdd3d24f2b9a428f7ecde1b9675e6 Mon Sep 17 00:00:00 2001 From: Laurent Guerard Date: Mon, 31 Mar 2025 17:19:56 +0200 Subject: [PATCH 1/4] Add info about changes for BDV --- CHANGELOG.md | 49 ++++++++++++++++++++++++------------------------- 1 file changed, 24 insertions(+), 25 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 816a70ff..5e7758ac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,29 +9,22 @@ As this is a major release, not all changes and functions are listed below. For ### Added * Various additions to `imcflibs.imagej.misc`: - * `imcflibs.imagej.misc.send_notification_email` to send email notifications upon - completion of long-running scripts. - * Sends a mail with job details, such as recipient, file name, execution time & an - optional message. - * To enable email notifications, the following preferences must be set in - `~/.imagej/IJ_Prefs.txt`: + * `imcflibs.imagej.misc.send_notification_email` to send email notifications upon completion of long-running scripts. + * Sends a mail with job details, such as recipient, file name, execution time & an optional message. + * To enable email notifications, the following preferences must be set in `~/.imagej/IJ_Prefs.txt`: * .imcf.sender_email: sender's email address. * .imcf.smtpserver: the SMTP server used for sending emails. - * If the sender email or SMTP server is not configured, method logs a message and - exits. - * `imcflibs.imagej.misc.sanitize_image_title` to remove special chars and various - suffixes from an ImagePlus. + * If the sender email or SMTP server is not configured, method logs a message and exits. + * `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.get_threshold_value_from_method` to get the value that a - selected AutoThreshold method would be using. - * `imcflibs.imagej.misc.write_ordereddict_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.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. * New `imcflibs.imagej.objects3d` submodule, providing: * `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn @@ -44,13 +37,20 @@ As this is a major release, not all changes and functions are listed below. For population of 3D objects by intensity. * New `imcflibs.imagej.bdv` submodule, providing BigDataViewer related functions: - * `imcflibs.imagej.bdv.backup_xml_files` to create a backup of BDV-XML files + * 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.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 xml dataset in a new format - (either all or single timepoints). + * `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. @@ -64,19 +64,18 @@ As this is a major release, not all changes and functions are listed below. For Dataset based on Interest Points" command. * `imcflibs.imagej.bdv.duplicate_transformations` for duplicating / propagating transformation parameters to other channels. - * `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "Fuse Dataset" + * `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. + ## 1.4.0 ### Added From f9b29875079d0b7efaf935670f8c3a0439c73400 Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Tue, 8 Apr 2025 11:06:38 +0200 Subject: [PATCH 2/4] Fix markdown syntax for pdoc --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e7758ac..8724addb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,11 +20,11 @@ As this is a major release, not all changes and functions are listed below. For * `imcflibs.imagej.misc.subtract_images` to subtract an image from another. * `imcflibs.imagej.misc.close_images` for closing selected image windows. * `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.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.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 `imcflibs.imagej.objects3d` submodule, providing: * `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn From d932efba41539e22abb6441dc0028c63bae5d09a Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Tue, 8 Apr 2025 11:09:10 +0200 Subject: [PATCH 3/4] Fix line length --- CHANGELOG.md | 37 ++++++++++++++++++++++++------------- 1 file changed, 24 insertions(+), 13 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8724addb..c7f8fdd8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,27 +4,38 @@ ## 1.5.0 -As this is a major release, not all changes and functions are listed below. For detailed information, please refer to the updated API documentation. +As this is a major release, not all changes and functions are listed below. For +detailed information, please refer to the updated API documentation. ### Added * Various additions to `imcflibs.imagej.misc`: - * `imcflibs.imagej.misc.send_notification_email` to send email notifications upon completion of long-running scripts. - * Sends a mail with job details, such as recipient, file name, execution time & an optional message. - * To enable email notifications, the following preferences must be set in `~/.imagej/IJ_Prefs.txt`: + * `imcflibs.imagej.misc.send_notification_email` to send email notifications + upon completion of long-running scripts. + * Sends a mail with job details, such as recipient, file name, execution + time & an optional message. + * To enable email notifications, the following preferences must be set in + `~/.imagej/IJ_Prefs.txt`: * .imcf.sender_email: sender's email address. * .imcf.smtpserver: the SMTP server used for sending emails. - * If the sender email or SMTP server is not configured, method logs a message and exits. + * If the sender email or SMTP server is not configured, method logs a + message and exits. * `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.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.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. * New `imcflibs.imagej.objects3d` submodule, providing: * `imcflibs.imagej.objects3d.population3d_to_imgplus` to turn @@ -64,8 +75,8 @@ As this is a major release, not all changes and functions are listed below. For Dataset based on Interest Points" command. * `imcflibs.imagej.bdv.duplicate_transformations` for duplicating / propagating transformation parameters to other channels. - * `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "Fuse Multi-View Dataset" - command. + * `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. From 37f3cd27a7ed15c5ca4bc6def49b4583f8e6e1fd Mon Sep 17 00:00:00 2001 From: Niko Ehrenfeuchter Date: Tue, 8 Apr 2025 11:09:20 +0200 Subject: [PATCH 4/4] Markdownlint --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c7f8fdd8..802e9c22 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -86,7 +86,6 @@ detailed information, please refer to the updated API documentation. * `imcflibs.pathtools.create_directory` to create a new directory at the specified path. - ## 1.4.0 ### Added