Mantid Imaging 2.2
==================

This release brings some new features and bug fixes.

The key new features of 2.2 are NeXuS import and a new reconstruction algorithm, Primal-Dual Hybrid Gradient from the `Core Imaging Library (CIL) <https://www.ccpi.ac.uk/cil>`_.

New features
------------

- #927 : ROI norm: use averaged view in ROI selector
- #925 : Jenks / Otsu everywhere
- #926 : Manual arithmetic filter
- #988 : Use averaged view in ROI selector for crop
- #964 : Open NeXus files
- #1010 : Write slope and offset into int tiffs
- #987 : Allow Flat-fielding without dark subtraction
- #1011 : Pixel size should allow setting decimal places
- #1013 : NeXus Loading Window
- #904 : Default to using image center for ring removal COR
- #1025 : Add the Total Variation (TV) with Primal-Dual Hybrid Gradient (PDHG) from CIL
- #1027 : Flat field warning if output has negative values
- #1027 : NeXus Loader: Message when loading large files
- #1026 : Recon warn if input has NaNs
- #816 : NaN Removal Filter
- #1035 : NeXus Loader: Select every Nth image
- #1035 : List of bad slices in error message could be compressed

Fixes
-----

- #939 : median: NameError: name 'cp' is not defined
- #957 : Crop Coordinates ROI not changing
- #961 : Test failure: ImportError: libcuda.so.1
- #959 : Median GPU does not work with even values
- #990 : Remove combine histogram checkbox
- #989 : Remove legend checkbox
- #1001 : Exception when selecting Log in Load Dataset dialog
- #991 : Handle longer running previews better
- #1021 : Prevent simultaneous Astra calls
- #1036 : Exception in ReconstructWindowView.show_recon_volume prevents recon closing
- #1046 : Can't rotate NeXus images
- #1048 : NeXus Loader: ValueError: Illegal slicing argument for scalar dataspace
- #1055: Arithmetic operation breaks flat-fielding
- #898: Improve user documentation for operations
- #1059: Crash in recon Minimise Error with CIL
- #1032: Crash in RingRemovalFilter
- #1057: Fix crash when refining COR
- #1056: Cannot set range [nan, nan] in ROI normalisation
- #1019: ERROR: Presenter error: Error applying filter for preview - when closing stacks
- #1068: Don't show misleading success message when operation cancelled
- #1082: CIL show memory warning
- #1014: KeyError when closing stacks
- #1029: Segmentation fault in image_in_vb
- #1081: Error if pressing preview button before selecting a dataset
- #940: Ops window, pixel value not updating for part of image
- #1093: TIFF output blank if NaN in stack
- #1095: AttributeError loading 180 deg projection
- #1110: Segmentation fault COR table refine
- #1115: Copy everything from metadata dialog
- #1112: Minimise Error, number of slices input should have minimum of 2
- #1067: Failed to load stack "log file is not recognised"
- #1121: FF when negative values in output, no completed message

Developer Changes
-----------------

- #917 : Intermittent failure of StripeRemovalTest.test_memory_executed_wf
- #980 : Use pre-commit
- #978 : Update Qt API usage
- #998 : setup.py command to install current developer requirements
- #969 : Improve mypy coverage in core.io
- #1007 : Change applitools check level to content
- #1086 : GUI system tests

Dependency updates
------------------

- pyqtgraph 0.12, scikit-image 0.18, tomopy 1.9, numpy 1.18