Tomviz 2.0.0-rc1

What's Changed

• Update the copyright year on the license by @bnmajor in #2173
• Add "Conform Volume" to pipeline view context menu by @psavery in #2182
• Allow custom parameters in FXI workflow operator by @psavery in #2181
• More useful fields in the databroker run dialog by @alesgenova in #2184
• Fix crashing with odd number of elements while running Direct Reconstruction by @sukhsung in #2127
• Try downgrading TBB on Mac by @psavery in #2188
• 'Done' Button Implementation by @jepietryga in #2177
• Real-Time-Tomography integration into tomviz by @jtschwar in #2192
• Bump pillow from 8.1.1 to 8.3.2 in /acquisition by @dependabot in #2194
• Fix typos discovered by codespell by @cclauss in #2191
• Install python files located in _realtime/ folder by @jtschwar in #2199
• Fix installation issue by @jtschwar in #2200
• Add ability to set custom axes titles to outline by @psavery in #2195
• Allow extra test rotation parameters to be added to FXI Workflow Widget by @psavery in #2198
• Recreate links in correct location by @cjh1 in #2202
• Save the description.json alongside the script by @psavery in #2201
• Fix issues for real time on windows environment by @jtschwar in #2204
• Fix link for install location by @jtschwar in #2205
• Move the install location one folder up by @jtschwar in #2207
• Add a button to create solid colormaps by @psavery in #2206
• Fix up realtime tomography packaging by @cjh1 in #2208
• Allow real_time computation to exit when user completes the experiment by @jtschwar in #2209
• Override qSetMessagePattern in tomviz by @psavery in #2210
• Clean up language for json files by @jtschwar in #2213
• Add "dataset" parameter option to description.json by @psavery in #2215
• Add manual manipulation operator by @psavery in #2216
• Add ITK Elastix registration operator by @psavery in #2218
• Add help for the new operators by @psavery in #2219
• Upgrade Mac on azure-pipelines to 10.15 by @psavery in #2221
• Add time series steps to DataSource and loading by @psavery in #2212
• Use variable paths for installing targets by @psavery in #2222
• Use cmake_path to compute path to python libraries by @psavery in #2223
• Add support for operator data source arguments to state files by @psavery in #2226
• Use file(RELATIVE_PATH ...) so we don't need 3.20 by @cjh1 in #2227
• FXI Workflow Improvements by @psavery in #2230
• Add animation helper dialog with camera orbit by @psavery in #2224
• First pass at migrating the code to use tiled by @cryos in #2228
• Fxi workflow improvements by @psavery in #2232
• First pass at PyXRF workflow by @psavery in #2229
• Bump windows CI to windows-2019 by @psavery in #2234
• PyXRF Workflow Fixes by @psavery in #2235
• Fix python paths during pyxrf process dialog setup by @psavery in #2236
• Add cross-correlation to real-time tomography by @jtschwar in #2239
• Ctf correction by @jtschwar in #2240
• Show PyXRF import error in tooltip by @psavery in #2247
• Tiled tweaks by @cryos in #2250
• Databroker/Tiled optimization: use a small in-memory cache. by @danielballan in #2237
• Get the angles for the FXI data in degrees by @cryos in #2251
• Add filter by scan id by @cjh1 in #2252
• All raw FXI data is now nested by @cryos in #2253
• Guard again 'stop' being None by @cjh1 in #2254
• Force gradient opacity for multi-volumes only by @psavery in #2255
• Add support for exporting dataset to Tiled by @cjh1 in #2256

New Contributors

• @sukhsung made their first contribution in #2127
• @jepietryga made their first contribution in #2177
• @cclauss made their first contribution in #2191

Full Changelog: 1.10.0...2.0.0-rc1

Tomviz 1.10.0

This release introduces a number of new features, including RGB visualization of 3-component volumes, support for multiple overlapping volumes, the ability to move and resize volumes interactively, an ImageJ-like brightness and contrast editor, an image viewer mode, and holographic rendering on Looking Glass devices.

This release upgrades ParaView to version 5.9 as well.

Tomviz 1.9.0

Tag the 1.9.0 release

Tomviz 1.8.0

This release features a number of improvements for the X-ray tomography community with support for white and dark fields, initial support for using TomoPy in a Docker pipeline, and some additional color presets that were requested after we reworked our presets in the last release. We have made improvements under the hood too, with a more Pythonic interface for the operators to use (the old API was retained to support existing operators), and new API to support X-ray data.

A new crop operator was added which currently crops volume rendered data, it will be extended to support more visualization types in the future. The slice operator was improved to support “thick” slices, i.e. aggregation over multiple slices. We have improved the integration of the documentation within the application, offering more links from dialogs to the relevant help page/section. The documentation has been updated and improved to cover a wider array of use cases. We dropped support for Python 2 many years ago, and continue to support Python 3.7 at this point, with plans to move to Python 3.8 soon. The ParaView and VTK libraries were updated for this release, bringing in a number of fixes and improvements.

Tomviz 1.7.0

This release features a number of improvements including a new color map preset dialog with an improved small form factor, the ability to save custom color maps, and preview all available color maps. The HDF5 support was improved, with a new generic HDF5 file reader, and a DataExchange format reader. The HDF5 formats also support striding before loading for large volumes. A number of major dependencies were updated including Python, NumPy, SciPy, ParaView, VTK and ITK. The data properties panel was improved to show the number of voxels, memory usage, and other important parameters.

This release was made in preparation for the Kitware Summer Courses held in July, and the Microscopy and Microanalysis (M&M) Conference held in Portland, OR. This announcement was delayed a little – it was a busy summer! Chris Harris and Marcus Hanwell ran the short half-day course, with slides available here, and I presented the latest innovations in the Tomviz project at M&M. We are also very pleased to announce a new documentation site, which features content expanded from previous tutorials.

Tomviz 1.6.0

This release features a number of improvements to application startup time, and a splash screen to show that the application is starting up on the occasions where it doesn't start as quickly as we would like. The reconstruction operators were also improved to use less memory, default to 32 bit floating point output, and to execute more efficiently. New operators support improved data wrangling from picking a single component when input data has multiple channels (e.g. RGB) to casting/rescaling data to reduce memory requirements (8 and 16 bit unsigned integers for example).

We have made a number of improvements to the "live" pipeline, where updated reconstructions can be viewed as an iterative reconstruction proceeds, or data can be viewed as projections are acquired. The EMD format saw a number of improvements for saving/loading metadata including lengths/angles. An issue with array ordering was discovered, meaning old EMD files will look corrupt, but all future files will be saved with the appropriate array ordering. We added a transpose data operator that will reorder these old files to enable recovery of data (or you can use an older version of Tomviz to read the file). NumPy files were also improved, and round tripping to/from Python visualizations were tested with both EMD and NumPy. Files, directories and state files can all be opened from the command line now too.

The release also features many other bug fixes and improvements.

Tomviz 1.5.1

This is a bug fix release that fixes a few issues that could cause Tomviz to crash, such as when manually aligning images in a tilt series, or when loading a state file if the data file is not located in the specified location.

Tomviz 1.5.0

Fixed a critical crash affecting macOS Mojave on application start up. Fixed an issue where image stacks would not load correctly from the recent file menu, made a number of speed improvements when loading/previewing image stacks. Reduced application start up times, and added support for loading atomic structure data into the application. Added the ability to lock the aspect ratio when exporting a screenshot.

Tomviz 1.4.0

This release features a number of improvements to the new pipeline that debuted with our 1.3.0 release, including support for live updates of volumes from operators, atomic coordinates emitted from operators, improved support for loading image stacks, and a number of improvements to our data acquisition. Many improvements have been made to the user interface, with some serious speed improvements for histogram calculation and contour determination.

Tomviz 1.3.1

This is a bug fix release that fixes an issue where state files wouldn't restore the file name of the data source, a crash when showing the color legend with no loaded data, ensure visualizations are correctly removed from the pipeline when deleted, and removing a warning when loading state files.