From 5250a33b00c99484e264e2a78823b0625be64f80 Mon Sep 17 00:00:00 2001 From: Rohan Girish Date: Thu, 27 Mar 2025 14:02:43 +0100 Subject: [PATCH] Update change log describing additions to misc --- CHANGELOG.md | 28 +++++++++++++++++++++++----- 1 file changed, 23 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a51201ec..0051efda 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,21 +4,28 @@ ## 1.5.0 -FIXME: complete description for `send_mail` configuration below! +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_mail` to send notification emails to users, e.g. - upon completion of long running scripts (configurable via user preferences). + * `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. * `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.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 `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 an Objects3DPopulation into an ImagePlus (2D/3D). @@ -53,6 +60,17 @@ FIXME: complete description for `send_mail` configuration below! * `imcflibs.imagej.bdv.fuse_dataset` to call BigStitcher's "Fuse 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