Version 25.1.0

New Functionality:

• Added toolbar to control the slice and volume render in QCILViewerWidget (#458)
• added methods to access the state of the viewer3D (#479)

Enhancements:

• Update recipe to require eqt Version 2.0.0 #458
• Add a toolbar and settings menus to the 3D viewer #458
• Add script to generate numpy array test data #458
• Removed init.py in ccpi namespace, PEP-420 #483
• Dependencies:
  • removed python pinning (#482)
  • removed importlib_metadata, required for python <3.8 (#482)
• CI:
  • Created new action for conda build and publish - no longer uses conda-package-publish-action (#486)

Version 25.0.0

Enhancements:

• Have hdf5_attrs as attribute to HDF5InputDialog #452
• Add SaveableRawInputDialog #444
• Standalone viewer uses SaveableRawInputDialog - this allows user to save and reload settings for loading raw data #444

Bugfix:

• Fix cilHDF5CroppedReader #462
• Correctly handle the Alt modifier and non 1 display pixel ratio, for Qt application with the viewer #464

Requirements:

• Reduced the requirements to the basic packages, add extra requirements in ui_env.yml file #451
• Use the qtpy abstraction layer #464

Documentation:

• Update readme, contributing, documentation #451

Build and CI:

• Renamed mambaforge to miniforge to fix docker action #446
• Use ubuntu v22.04 in the actions #446
• Add setuptools as a build requirement #446

Version 24.1.0

Enhancements:

• Add option to edit help text #441
• Update corner annotation with axis label #433
• Add title to ViewerCoordsDockWidget #422
• Adds methods to CILviewer and CILviewer2D #425

Bugfix:

• Fix error when visualising 2D images #439
• Hides the slider when one image dimension is 1 #432
• Differentiate 3D and 2D images in the converter numpy2vtkImage #437
• Edit slider min value #420
• Fix extent error when user clicks in the viewer to create a box by clicking outside of the image #425
• Fix extent error when user enlarges the box outside the image #425
• Deprecates GetImageWorldExtent #425

Version 24.0.1

Build and CI:

• removed python pinning from conda recipe #418

Bugfix:

• removed deprecated code by numpy v2.0 #418

Version 24.0.0

New functionality:

• Added preview to 'RawImportDialog' #410
• Add method to edit axes label text and tests, hide one label on 2D viewer #389 #408
• Add slider widget #365 and option to not install it #386. Link slider events #413

Bugfixes:

• Fix failing unit test #394
• Bugfix on resample reader. Standalone viewer app defaults to downsample in all dimensions. #362
• Fix bug with 'setInputAsNumpy' using deprecated 'numpy2vtkImporter' in 'CILViewer2D' - now uses 'numpy2vtkImage' #346

CI:

• Update eqt requirements to >=1.0.0 and update yml recipe #385
• Remove VTK 8 variants from conda recipe #375
• Change Python variants: removed 3.6 and 3.7, added 3.11 #375 (not Python 3.12 for incompatibility with EQT #399)
• Removed the 'paskino' channel from the install command as eqt is on 'conda-forge' #368
• Edit conda build and publish #371
• Fix dependencies in recipe #369

Documentation

• Add CONTRIBUTING.md #403
• Edit web-viewer readme #401
• Transfer repository to 'TomographicImaging' #402
• Add PR template #244 #373
• Edit README.md #344

Version 23.1.0

• Adds a cilviewer entrypoint:
  • This launches a standalone viewer application with a 2D and 3D viewer and allows users to load any image file types we support using the File menu.
  • This launches a StandaloneViewer instance (standalone_viewer.py)
• Updates README with how to run standalone viewer app and web viewer, and more image examples
• Raise error if try to add multiple widgets with the same name to CILViewer or CILViewer2D.
• Adds the following base classes to ui.main_windows.py:
  • Add ViewerMainWindow and ViewerMainWindowWithSessionManagement - base classes for windows which would house viewers, with methods needed for creating settings dialogs, creating a coordinate settings dockwidget, and loading images.
  • Add TwoViewersMainWindow and TwoViewersMainWindowWithSessionManagement - baseclasses which create a main window with 2 linked viewers in dockwidgets.
  • TwoViewersMainWindowMixin - a mixin which provides methods to both TwoViewersMainWindowWithSessionManagement and TwoViewersMainWindow. These methods are for adding viewers to the window, setting them up, linking them and adding a dockwidget for coordinate settings.
• Adds the following dialogs to ui.dialogs.py:
  • ViewerSettingsDialog - allows user to set downsample size settings and whether to use GPU for volume render.
  • RawInputDialog - for setting info for loading a raw file including, size of dimensions, data type etc.
  • HDF5InputDialog - for setting info for loading a HDF5 file, including the dataset name
  • Unit tests for creating each dialog.
    Adds the following widgets to ui.qt_widgets.py:
  • ViewerCoordsDockWidget - for showing original and downsampled image size and allowing user to select which coord system to show on viewer.
• Adds methods to CILViewerBase:
• setVisualisationDownsampling (moved out of CILViewer2D)
• getVisualisationDownsampling (moved out of CILViewer2D)
• Adds methods to CILViewer:
  • setVolumeMapper
  • getVolumeMapper
• Modifies ImageReader:
  • Previously could read only from a file, now can read from memory instead by setting vtk_image parameter instead of file_name parameter.
  • Add SetVTKImage method
  • Added unit tests to cover providing a VTK image instead of file name
• Add methods to cilviewerHDF5Reader:
  • GetOriginalImageAttrs
  • GetLoadedImageAttrs
  • These methods are the same as those in ImageReader to be consistent.

Version 23.0.0

• add deleteWidget method to CILViewerBase
• Add environment file for development of the viewer
• ImageWriter writes out with file extension set in FileFormat variable - previously didn't necessarily
  do this for some hdf5 formats.
• Fix bug with returning HDF5 attributes from HDF5Reader
• Move code for resetting camera out of TrameViewer3D and into CILViewer
• Adds the following methods to CILViewer (and corresponding unit tests):
  • getGradientOpacityPercentiles
  • getScalarOpacityPercentiles
  • getVolumeColorPercentiles
• Adds to CILViewerBase (and corresponding unit tests):
  • getSliceColorPercentiles
• setup.py:
  • Always normalise the version from git describe to pep440

Version 22.4.0

• Add command line tool for resampling a dataset, with entrypoint: resample (and unit tests)
• Add ImageReader:
  • Generic reader for reading to vtkImageData
  • Reads: HDF5, MetaImage, Numpy, Raw, TIFF stacks
  • Supports resampling OR cropping the dataset whilst reading.
• Add ImageWriter:
  • Writer for writing out a modified i.e. resampled or cropped dataset.
  • Supports writing to HDF5 and metaimage.
• Add ImageWriterInterface:
  • Interface for writers, with methods for setting and getting information about modified
    (i.e. resampled or cropped) image data to write to a file.
• Add cilviewerHDF5Writer:
  • This is a writer which expects to be writing an original dataset or attributes of the original dataset,
    plus one or more 'child' versions of the dataset which have been resampled and/or cropped.
  • Stores the information needed to reload a resampled or cropped dataset on the viewer.
• Add cilviewerHDF5Reader:
  • for reading datasets generated by the cilviewerHDF5Writer.
• Add new requirements:
  • schema
  • pyyaml
• Examples:
  • examples/image_reader_and_writer.py is an example of using the ImageReader and ImageWriter
  • examples/opacity_in_viewer.py updated to use head dataset from utils/example_data.py
• Unit tests for all of the new readers and writers.
• Removed obsolete TIFF code from conversion.py. The following have been removed:
  • vtkTiffStack2numpy
  • tiffStack2numpy
  • tiffStack2numpyEnforceBounds
  • _tiffStack2numpy
  • normalize
  • highest_tuple_element
• Fixed cilTIFFResampler so that if original TIFF file has a set spacing and origin, this is taken into account when resampling.
• Fixed bug in iviewer with display of volume render.
• iviewer now shows gradient opacity volume render of head dataset from utils/example_data.py by default.
• Fix bug in CILViewer if volume render method is adjusted before volume render turned on.

Version 22.3.0

• Add a dictionary of widgets to the CILViewerBaseClass, and ability to add and retrieve widgets to/from the dict with methods .addWidgetReference and .getWidget
• Add a new file widgets/box_widgets.py which contains classes cilviewerBoxWidget and cilviewerLineWidget for creating Box and Line widgets on the viewer.
• Add example: BoxWidgetAroundSlice.py - which demonstrates using the above classes.
• Use the cilviewerBoxWidget class for creating and positioning the ROIWidget on the CILViewer2D, which involved removing the CILViewer2D._truncateBox method.

Version 22.2.0

• Qt examples use example_data
• Updates in all classes to take into account the backward incompatible methods name changes (see below)
• cilPlaneClipper:
  • change signature of creator, and defaults to empty list of items to be clipped on init
  • renamed Get/SetInteractor->Get/SetInteractorStyle
• Renamed all classes bearing name baseReader to ReaderInterface as they provide the interface not a abstract reader class.
• Added TIFF resample and cropped readers with unit tests.
• Add Set/GetOrientationType methods to TIFF resample and cropped readers, with default value 1: ORIENTATION_TOPLEFT (row 0 top, col 0 lhs)
• web_viewer:
  • added web viewer using trame for viewer3D and viewer2D
  • add entry point for running the web viewers
  • added docker container to be deployed
• GitHub Action: autoyapf added
• Added example_data module to load the head data from the CIL-Data repository
• CILViewer2D:
  • add ChangeOrientation, AutoWindowLevel, getSliceWindowLevelFromRange
  • Backward incompatible rename of a few methods:
    • Get/SetActiveSlice -> get/setActiveSlice,
    • GetSliceOrientation -> getSliceOrientation,
    • setColourWindowLevel -> setSliceColorWindowLevel,
    • getColourLevel -> getSliceColourLevel,
    • getColourWindow -> getSliceColorWindow,
    • setColourWindowLevel -> setSliceColorWindowLevel
  • fix definition of window range to be = max - min
  • use CILViewerBase as base class
• CILViewer3D:
  • added methods in interactor style to enable interaction with web app, rather than just key event binding
  • add volume render opacity scalar and gradient
  • add slice histogram
  • fix method to change window and level for slice actor, by range or percentiles
  • fix definition of window range to be = max - min
  • use CILViewerBase as base class
• colormaps: added get_color_transfer_function
• added examples of running the 2D and 3D viewers without Qt
• Added CILViewer base class
• Conda recipe:
  • Fix windows build recipe
  • Add build variants for VTK to prevent need for multiple viewer release numbers for different VTK versions