Mantid Imaging 2.5

This release brings some significant new features:

Stochastic PDHG Reconstruction

New reconstruction option from CIL. This gives faster convergence and lower memory usage by splitting the input data into subsets.

Golden Ratio datasets

Datasets recorded using the golden ration method can now be opened correctly, using angle information in the log file.

Performance improvements

  • Startup time

  • Arithmetic filter

  • CIL reconstruction

  • TIFF loading

Spectrum Viewer

Complete the base feature set of the Spectrum viewer.

  • Multiple ROIs and spectrum plots

  • Output ROI coordinates

User interface improvements

  • Better stack selection in main window

  • Modifying image stack in a dataset

  • Operations ROI defaults to a sensible size

Improved Nexus Support

  • Loading reconstructions

  • Better nexus spec conformance

  • Saving data as float32 (for NXtomoproc this is not yet in the official spec)

Windows Installer

See Installing with Windows installer

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

New Features and improvements

  • #1601 : arithmetic filter optimisation

  • #1620 : Add multiple ROI to spectrum viewer

  • #1616 : Change selected stack with single click on tree widget

  • #1625 : Allow adding extra stacks to a dataset

  • #1625 : Load recons to an existing dataset

  • #1625 : Change selection in tree view when switching tabs

  • #1626 : Move stacks between datasets

  • #1622 : Add, Remove and Rename ROIs in spectrum viewer

  • #1464 : NeXus Recon: Add entry/reconstruction/date information

  • #1463 : NeXus Recon: Add entry/SAMPLE/name information

  • #1468 : NeXus Recon: Load recons

  • #1467 : NeXus Recon: Add other entry/data information

  • #1661 : Use tifffile for writing and reading tiff files

  • #1512, #1725 : Speedups for CIL setup

  • #1465 : NeXus Recon: Add entry/reconstruction/parameters information

  • #1666 : PyInstaller single file

  • #1665 : PyInstaller exe icon

  • #1680 : Multiple Spectrum Line Plots in Spectrum Viewer

  • #1691 : Remove “Beta” from spectrum viewer

  • #1697 : For NXtomoproc store data in float32

  • #1711 : Update CIL to 22.2.0

  • #1714 : Improve ROI hover behavior within Spectrum Viewer to be more intuitive.

  • #1664 : PyInstaller version at build time

  • #1632 : Add Stochastic PDHG

  • #1696 : Export ROI positional data following Pascal VOC format in separate .csv when exporting spectrum data in spectrum view.

  • #1225 : Loading of Golden Ratio datasets

  • #1739 : Load processed NeXus data

  • #1762 : NSIS installer for Windows

  • #1765 : NeXus float/int save option

  • #1588 : Improve application startup time

Fixes

  • #1589 : Recommend new update command

  • #1330 : Initial ROI box is sometimes much larger than image for relevant filters

  • #1602 : Prevent multiple ROI selector windows opening from Operations window

  • #1610 : Apply bug fix to disable Spectrum Viewer export button when no data is loaded

  • #1669 : Fix table or ROIs falling out of synchronisation with ROIs visible in the image when changing between samples

  • #1659 : PyInstaller missing cupy files

  • #1657 : PyInstaller: order of operations in menu is not sorted

  • #1712 : Fix redrawing of all ROIs and spectrum line plots of toggle and change of normalized stacks within spectrum viewer

  • #1219 : Fix image_180deg.tiff being included in sample stack

  • #1730 : Allow any characters in filenames

  • #1698 : Store processed (but not reconstructed) data in a different place in the nexus file

  • #1748 : Stop BHC promoting data arrays to float64

  • #1747 : Fix API links in docs

  • #1721 : For SPDHG show projections per subset

  • #1720 : Update memory requirements for SPDHG

  • #1742 : Restore native dialogs on Linux

  • #1761 : Hide float64 loading

  • #1774 : Force numexpr from conda-forge channel

  • #1779 : Saving images with log file loaded

Developer Changes

  • #1472 : Investigate issues reported by flake8-bugbear

  • #1607 : Add flake8-bugbear to environment, github actions and precommit

  • #1613 : Refactor Operations window ROI selector to be in its own class

  • #1652 : PEP440 compliant versions for alpha builds

  • #1595 : Store version number in package

  • #1663 : Postponed Evaluation of Annotations

  • #1670 : tostring() Deprecation Warning

  • #1673 : Update license year across the repository from 2022 to 2023

  • #1678 : Allow multiple datasets to be opened at once in the GUI when using the CLI –path flag

  • #1695 : Use FilenameGroup for Load Images

  • #1693 : Increase test coverage for spectrum widget

  • #1703 : Optimize Re-Drawing of ROIs within the Spectrum Viewer

  • #1630 : Update numexpr to 2.8 to resolve dependency deprecation warning

  • #1641 : More robust logging and error handling in automated testing

  • #1643 : Deprecations in GitHub actions

  • #1726, #1728 : Use FilenameGroup for Load Dataset

  • #1754 : Migrate Centos7 and Ubuntu18 Docker images from DockerHub to GitHub Container Registry

  • #1757 : CLI log level only on to mantidimaging