Mantid Imaging 2.3#

This release brings some significant new features:

Bad data indicators: Show pixel values that can cause issues during reconstruction, NaNs (not a number) caused by missing data or invalid math operations and non-positive values caused by noise or issues with dark frame subtraction.
Beam hardening correction: Mantid Imaging now implements a linearization correction to compensate for the beam hardening effect.
Dataset side-bar: The main window now shows a tree-view of loaded datasets and their stacks. Internally Mantid Imaging now has a more structured view of the loaded data, which will allow further user interface improvements.
User interface improvements: The parameter controls in operations and reconstruction windows now have finer step sizes and better defaults. Auto preview in the reconstruction window can be disabled.

There have also been many smaller changes and fixes which are listed below.

New Features#

#1044 : Command line argument to load a dataset
#1023 : Switch from Sarepy to Algotom
#1049 : NeXus Loader: 180deg images
#1167 : Bad data indicator icons
#1185 : Bad data overlays
#1168 : Dataset tree view
#1202 : NaN Removal filter - replace with median
#1205 : Linearisation correction for beam hardening
#1197 : Dataset Tree View: Delete image stack
#1197 : Dataset Tree View : Show tab from treeview
#1200 : Default save option set to float32
#1235 : Improvements to input value defaults and spin box step sizes
#1230 : Update CIL to 21.3 reducing memory requirements
#1191 : Loading 180 should only show datasets
#1279 : Add auto update checkbox option to turn off live reconstruction
#1273 : Move sinograms into the Dataset
#1220 : Make reconstruction window side bar scrollable for smaller screens
#1280 : Don’t display full file path for loaded images in the tree view

Fixes#

#1138 : Improve version number handling
#1134 : NeXus Loader: OSError
#1178 : –operation argument sometimes opens wrong operation
#1117 : Median operation preserves NaNs
#1151 : IndexError with sinograms and stripe tools
#1174 : TypeError in link_before_after_histogram_scales
#1161 : Remove run_ring_removal argument from Ring Removal operation and always run filter
#1226 : AttributeError when trying to open reconstruction auto colour dialog
#1236 : Aspect ratio not preserved in COR inspector or operations window
#1162 : Raise exceptions when invalid parameter values are passed to filter functions
#1248 : Rebin operations not working for small image dimensions
#1190 : Add recon item to right part of tree view
#1239 : 180 warning when applying ring removal to recon
#1297 : Auto colour dialog not working in compare images
#1292 : Attribute error if apply filter after closing and re-opening Operations window
#1294 : Dataset Tree View: Allow for deleting recons
#1289 : Trigger recon redraws when stack is modified
#1299 : CIL: when reconstructing from sinograms use right dimensions and ordering
#1305 : Delete recon group from tree view
#1285 : Error when load two 180 stacks
#1278 : It should not be possible to attempt loading 180 projections to a MixedDataset
#1311 : Operation applied to 180 twice
#1310 : Disable Auto color menu item when no image shown
#1295 : Failed recon still increments recon counter
#1313 : Restore metadata when choosing original
#1324 : Bad data overlay not showing with large files

Developer Changes#

#1022 : Switch to use Mambaforge
#1085 : Fix rotation of images in GUI tests
#1045 : Command line argument to open Operation or Reconstruction windows
#1154 : collections.abc is deprecated
#1155 : DeprecationWarning an integer is required self.progressBar.setValue
#1153 : Remove package_name argument from load_filter_packages
#1172 : Add MIMiniImageView widget
#1070 : Remove pytest repeat
#1182 : Handle exception in _post_filter
#1173 : Sometimes tests open many operations windows
#860 : Clean up super calls to use python 3 syntax
#1181 : Version check update command uses mamba if available
#1212 : Model Change: Put everything in datasets
#1245 : Remove empty init methods from test classes
#1251 : System tests: test_correlate ValueError
#1259 : Update license year in code files and add pre-commit check
#1243 #1276 : Stack selector based on datasets
#1184 : Make more use of QTest in gui testing

2.3.1#

#1332 : Load dataset dialog wont accept non standard names