Merge pull request #72 from lguerard/issues/34

Add info about changes for BDV

Author: ehrenfeu

CHANGELOG.md

@@ -4,34 +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.
+  * `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 +48,20 @@ 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.
@@ -64,15 +75,13 @@ 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"
-    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.
   * `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.