Recent Releases of https://github.com/openchemistry/tomviz
https://github.com/openchemistry/tomviz - Tomviz 2.0.0-rc1
What's Changed
- Update the copyright year on the license by @bnmajor in https://github.com/OpenChemistry/tomviz/pull/2173
- Add "Conform Volume" to pipeline view context menu by @psavery in https://github.com/OpenChemistry/tomviz/pull/2182
- Allow custom parameters in FXI workflow operator by @psavery in https://github.com/OpenChemistry/tomviz/pull/2181
- More useful fields in the databroker run dialog by @alesgenova in https://github.com/OpenChemistry/tomviz/pull/2184
- Fix crashing with odd number of elements while running Direct Reconstruction by @sukhsung in https://github.com/OpenChemistry/tomviz/pull/2127
- Try downgrading TBB on Mac by @psavery in https://github.com/OpenChemistry/tomviz/pull/2188
- 'Done' Button Implementation by @jepietryga in https://github.com/OpenChemistry/tomviz/pull/2177
- Real-Time-Tomography integration into tomviz by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2192
- Bump pillow from 8.1.1 to 8.3.2 in /acquisition by @dependabot in https://github.com/OpenChemistry/tomviz/pull/2194
- Fix typos discovered by codespell by @cclauss in https://github.com/OpenChemistry/tomviz/pull/2191
- Install python files located in _realtime/ folder by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2199
- Fix installation issue by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2200
- Add ability to set custom axes titles to outline by @psavery in https://github.com/OpenChemistry/tomviz/pull/2195
- Allow extra test rotation parameters to be added to FXI Workflow Widget by @psavery in https://github.com/OpenChemistry/tomviz/pull/2198
- Recreate links in correct location by @cjh1 in https://github.com/OpenChemistry/tomviz/pull/2202
- Save the description.json alongside the script by @psavery in https://github.com/OpenChemistry/tomviz/pull/2201
- Fix issues for real time on windows environment by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2204
- Fix link for install location by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2205
- Move the install location one folder up by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2207
- Add a button to create solid colormaps by @psavery in https://github.com/OpenChemistry/tomviz/pull/2206
- Fix up realtime tomography packaging by @cjh1 in https://github.com/OpenChemistry/tomviz/pull/2208
- Allow real_time computation to exit when user completes the experiment by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2209
- Override qSetMessagePattern in tomviz by @psavery in https://github.com/OpenChemistry/tomviz/pull/2210
- Clean up language for json files by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2213
- Add "dataset" parameter option to description.json by @psavery in https://github.com/OpenChemistry/tomviz/pull/2215
- Add manual manipulation operator by @psavery in https://github.com/OpenChemistry/tomviz/pull/2216
- Add ITK Elastix registration operator by @psavery in https://github.com/OpenChemistry/tomviz/pull/2218
- Add help for the new operators by @psavery in https://github.com/OpenChemistry/tomviz/pull/2219
- Upgrade Mac on azure-pipelines to 10.15 by @psavery in https://github.com/OpenChemistry/tomviz/pull/2221
- Add time series steps to DataSource and loading by @psavery in https://github.com/OpenChemistry/tomviz/pull/2212
- Use variable paths for installing targets by @psavery in https://github.com/OpenChemistry/tomviz/pull/2222
- Use cmake_path to compute path to python libraries by @psavery in https://github.com/OpenChemistry/tomviz/pull/2223
- Add support for operator data source arguments to state files by @psavery in https://github.com/OpenChemistry/tomviz/pull/2226
- Use file(RELATIVE_PATH ...) so we don't need 3.20 by @cjh1 in https://github.com/OpenChemistry/tomviz/pull/2227
- FXI Workflow Improvements by @psavery in https://github.com/OpenChemistry/tomviz/pull/2230
- Add animation helper dialog with camera orbit by @psavery in https://github.com/OpenChemistry/tomviz/pull/2224
- First pass at migrating the code to use tiled by @cryos in https://github.com/OpenChemistry/tomviz/pull/2228
- Fxi workflow improvements by @psavery in https://github.com/OpenChemistry/tomviz/pull/2232
- First pass at PyXRF workflow by @psavery in https://github.com/OpenChemistry/tomviz/pull/2229
- Bump windows CI to windows-2019 by @psavery in https://github.com/OpenChemistry/tomviz/pull/2234
- PyXRF Workflow Fixes by @psavery in https://github.com/OpenChemistry/tomviz/pull/2235
- Fix python paths during pyxrf process dialog setup by @psavery in https://github.com/OpenChemistry/tomviz/pull/2236
- Add cross-correlation to real-time tomography by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2239
- Ctf correction by @jtschwar in https://github.com/OpenChemistry/tomviz/pull/2240
- Show PyXRF import error in tooltip by @psavery in https://github.com/OpenChemistry/tomviz/pull/2247
- Tiled tweaks by @cryos in https://github.com/OpenChemistry/tomviz/pull/2250
- Databroker/Tiled optimization: use a small in-memory cache. by @danielballan in https://github.com/OpenChemistry/tomviz/pull/2237
- Get the angles for the FXI data in degrees by @cryos in https://github.com/OpenChemistry/tomviz/pull/2251
- Add filter by scan id by @cjh1 in https://github.com/OpenChemistry/tomviz/pull/2252
- All raw FXI data is now nested by @cryos in https://github.com/OpenChemistry/tomviz/pull/2253
- Guard again 'stop' being None by @cjh1 in https://github.com/OpenChemistry/tomviz/pull/2254
- Force gradient opacity for multi-volumes only by @psavery in https://github.com/OpenChemistry/tomviz/pull/2255
- Add support for exporting dataset to Tiled by @cjh1 in https://github.com/OpenChemistry/tomviz/pull/2256
New Contributors
- @sukhsung made their first contribution in https://github.com/OpenChemistry/tomviz/pull/2127
- @jepietryga made their first contribution in https://github.com/OpenChemistry/tomviz/pull/2177
- @cclauss made their first contribution in https://github.com/OpenChemistry/tomviz/pull/2191
Full Changelog: https://github.com/OpenChemistry/tomviz/compare/1.10.0...2.0.0-rc1
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Published by cjh1 over 3 years ago
https://github.com/openchemistry/tomviz - 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.
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Published by bnmajor over 4 years ago
https://github.com/openchemistry/tomviz - 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.
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Published by cryos about 6 years ago
https://github.com/openchemistry/tomviz - 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.
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Published by cryos over 6 years ago
https://github.com/openchemistry/tomviz - 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.
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Published by cryos almost 7 years ago
https://github.com/openchemistry/tomviz - 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.
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Published by cryos about 7 years ago
https://github.com/openchemistry/tomviz - 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.
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Published by cryos over 7 years ago
https://github.com/openchemistry/tomviz - 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.
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Published by cryos over 7 years ago
https://github.com/openchemistry/tomviz - 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.
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Published by cryos almost 8 years ago
https://github.com/openchemistry/tomviz - Tomviz 1.3.0
This release features some big changes to the Tomviz pipeline, state file, and related functionality. The pipeline now explicitly shows the input and output data, with the visualization modules attached to the data that is being visualized. These changes have been carried through to the state file, which is now represented using JSON. The pipeline supports live updates (experimentally) for both reconstructions and data acquisition.
The user interface saw a number of updates to improve the default layouts, and make the best use of space. A number of enhancements have focused on improving load times of the application at startup, and when executing the Python environment. Tilt angles can be loaded from a file now, and custom Python operators can be easily added from a menu item. Support for images with multiple components has been added, and separate images can be merged.
Usability has been improved, with manual alignment operations supporting reopening of the dialog to further edit, and a view code button added to Python operators. Image stack loading has seen improvements, basic consistency of image sizes is verified and errors displayed. There are a huge number of bug fixes and improvements that were developed by our team.
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Published by cryos almost 8 years ago
https://github.com/openchemistry/tomviz - Tomviz 1.3.0 Release Candidate 2
This release candidate features a number of major updates to our data processing pipeline, state file, and associated interfaces. Old state files are not supported, and the pipelines in this new version feature a number of differences in how they are presented in the interface. We would appreciate your testing and feedback as we stabilize new features, and work towards the final release.
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Published by cryos almost 8 years ago
https://github.com/openchemistry/tomviz - Tomviz 1.2.1
This is a bug fix release that adds ~/tomviz to the search list for local Python operators, updated SciPy and NumPy versions to match across all operating systems, restored some menu entries to the view menu, and added some missing support libraries for the Linux binary package.
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Published by cryos over 8 years ago
https://github.com/openchemistry/tomviz - Tomviz 1.2.0
Featuring a number of bug fixes, updated software libraries, fixes for units in MRC and EMD file formats, improved binary file reading dialog, support for external Python operators in the home directory, support for saving the output of visualization modules, optionally directly visualize scalars without using a lookup table, and various interface improvements.
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Published by cryos over 8 years ago
https://github.com/openchemistry/tomviz - Tomviz 1.1.0
Featuring a number of bug fixes, updated ITK, pore segmentation, and a technology preview of a new 2D transfer function for volume rendering.
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Published by cryos over 8 years ago
https://github.com/openchemistry/tomviz - Tomviz 1.0.1
This is the first bug fix release since 1.0.0. It addresses a few issues discovered since release that include: * Updated dependencies with numerous bug fixes * Fixed errors in web export functionality with Python 3 (non-functional in 1.0.0 binaries) * Tweaks and minor improvements for macOS retinal displays
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Published by cryos over 8 years ago
https://github.com/openchemistry/tomviz - Tomviz 1.0.0
Our first stable release of Tomviz offering image pre-processing, image alignment, reconstruction, segmentation, visualization and analysis. Download Tomviz for Windows, macOS, and Linux or access the full source code. This release is the result of years of development, collaboratively developed by software experts and domain experts. It offers a reproducible data pipeline with editable Python data operators, highly optimized routines, and state-of-the-art volume rendering/geometry rendering. Import and export data using industry standard formats such as TIFF, MRC, and EMD.
The entire processing pipeline can be saved, restored and/or shared for further analysis by peers. The final results can also be saved as screenshots, movies, or interactive HTML5 pages using the latest advances in WebGL. Developed collaboratively, with full access to the source code for the project and its dependencies. Our Python environment is integrated, offering NumPy, SciPy along with Python-wrapped VTK and ITK. Data samples are provided with the application, as well as a bundled guide to getting started with Tomviz.
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Published by cryos almost 9 years ago
https://github.com/openchemistry/tomviz - Tomviz 0.9.4
This release features improvements to volume and contour rendering, updated icons, further refinement of the Qt 5 interface, and antialiasing improvements for the main histogram view. The reconstruction algorithms have seen a number of improvements, and a initial support for exporting the current visualization to a web viewer were added. The pipeline interaction was improved to make changes to multiple items at a time. The manual alignment dialog was also improved to explicitly display the current reference slice, and respect settings whether using the graphical elements or keyboards shortcuts. There are also new visual elements to display length both in the scene and/or in the visual overlay.
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Published by cryos almost 9 years ago
https://github.com/openchemistry/tomviz - Tomviz 0.9.3
This release features improved 3D rendering, with a number of updates to support modern operating systems. The use of full retinal resolution on macOS has been enabled for the first time in this release, and a number of warning messages issues on that operating system are now resolved. The pipeline has seen a number of improvements, and the Python operator interface has been improved to offer better feedback on what is happening.
New features include: - Support for different color palettes, and setting the default palette - Support for loading a stack of TIFF images - Ruler tool added to make measurements in 3D scene - Improvements to Python operators including more feedback as they execute - Improvements made to the reconstruction capabilities - Pipeline state fully expressed, and execution of paused pipeline can be requested - Python 3 now supported, but not used by default (or in the binaries) - Support for retinal resolution enabled in macOS binaries - Using Qt 5.8.0 with improved 3D rendering widget developed in VTK - Switched to MSI installer on Windows - better integration with Windows - Various improvements to the user interface, and bug fixes
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Published by cryos about 9 years ago
https://github.com/openchemistry/tomviz - Tomviz 0.9.2
This release has refined the use of Qt 5, with additional tools for tomographic reconstruction for electron tomography. The data pipeline has been tweaked and improved further, offering a unified view of the data sources, data operators, and visualization modules in a multi-threaded application where responsiveness is preserved. The volume rendering, reconstruction, and several other key pieces of the application have been improved, and benefit from the threaded execution of operators. The user interface has seen a number of improvements too.
New features in this release include: - Extend the data operators to run in a background thread, support progress updates, and cancellation - Use PyBind11 to wrap some of the C++ interface to make the operator Python API richer and more expressive - Improved pipeline view to unify all pipeline objects, show state of operators, and display child data when present - Many new segmentation routines exposed, numerical output can be viewed in a sppreadsheet view - Enabled full scene antialiasing to improve rendered scenes with minimal overhead - Exposed additional volume rendering options, with more to follow - Added the Tomviz version to the state file to improve future reproducibility - Custom interfaces in most module settings to improve presentation of options, display the name of operators when they are selected - Updated dependencies including Qt 5.7.0, and ParaView 5.2, now build with latest Visual Studio 2015 on Windows - Various updates to reconstruction routines including the addition of progress updates, executing in a background thread, and refinements - Save screen captures with a transparent background - Improved drag and drop installer on Mac OS X - First version of a Tomviz user guide was developed
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Published by cryos over 9 years ago
https://github.com/openchemistry/tomviz - tomviz 0.9.1
This release addresses a few bugs found since the release of 0.9.0, and one or two minor enhancements.
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Published by cryos over 9 years ago
https://github.com/openchemistry/tomviz - tomviz 0.9.0
This release has refined the use of Qt 5, with additional tools for tomographic reconstruction for electron tomography. The data pipeline has been refactored, and now offers a unified view of the data sources, data operators, and visualization modules. The central histogram has also seen a number of improvements that enable editing of the opacity and color transfer functions in one central location.
New features in this release include: - Improved design - Interactive histogram with opacity editor and color bar - Redesigned data viz pipeline - Clear subvolume tool - Move volumes relative to one another - Fast, interactive surface contours - New colormaps from matplotlib (1.5.1) - Orthographic or perspective projection - Improved stability and performance - Pad data, Invert data - Normalize image intensity in tilt series - Generate 3D electron probe shape - Colormaps added to manual image align - Difference mode added to manual image align - Constraint based reconstruction - Qt 5.7 for improved graphical user interface - Improved state file save/load - Improved integration with ITK
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Published by cryos over 9 years ago
https://github.com/openchemistry/tomviz - tomviz 0.8.0
This release is the first to use Qt 5, with additional tools for tomographic reconstruction for electron tomography. The move to Qt 5 has a number of advantages, but this release has a few known issues on Mac OS X (toolbar rendering and color map dock rendering issues) that will be addressed in future releases. - Moved to Qt 5 for improved graphical user interface - Linux binary package in addition to Windows and Mac OS X - Integrated opacity editor, color bar, and histogram widget - Added support for moving volumes relative to one another - Improvements to state file save/load - Improved integration with ITK, some initial segmentation operations - Simplified the user interface for visualization properties - Added simple examples of ITK usage in operator pipelines
This release features some big changes moving to Qt 5 and exposing ITK segmentation. We consider this an early preview release of these new features which will be improved upon before the next release.
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Published by cryos over 9 years ago
https://github.com/openchemistry/tomviz - tomviz 0.7.2
This release addresses some bugs discovered after the 0.7.1 release, builds against the ParaView 5.0.0 release, and several new features were added including accelerated contours using a multithreaded algorithm, color maps were added from matplotlib, orthographic or perspective projection, editing of slice offsets, C++ operators were integrated better into the data operation pipeline, and other minor updates.
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Published by cryos about 10 years ago
https://github.com/openchemistry/tomviz - tomviz 0.7.1
This release addresses a few bugs discovered since the 0.7.0 release, including slow downs when performing many transform operations, and a possible crash when using the simulated data functionality.
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Published by cryos about 10 years ago
https://github.com/openchemistry/tomviz - tomviz 0.7.0
This release introduces tools for tomographic reconstruction for electron tomography. Now you can load tilt series of micrograph, align the datasets, and complete a tomographic reconstruction.
Highlights of new features in this release include: - Tools for tomographic reconstruction - Tilt series alignment tool: zoom to region for alignment - Determine tilt axis tool - Weighted back projection reconstruction - Direct Fourier recontruction - Algebraic reconstruction technique - Set tilt Angles in a tilt series - Predict tilt angles - Background subtraction tool - Default animation (just press the play button) - Random particles sample data set - Constant sample dataset - Delete subvolume tool - Generate projections from volume - Resample transform - Gaussian, Laplace, and Sobel Filters - UX improvements for transforms - Autosave for backup - Improved state file - Better Python performance - ITK integration for advanced data processing in Python - Example ITK script for segmentation
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Published by cryos about 10 years ago
https://github.com/openchemistry/tomviz - tomviz 0.6.1
This release focused on fixing some bugs discovered after the previous release, some improvements to the user interface and how properties are displayed, and the default file type for saving data. The binaries for this release are available from our downloads page at http://tomviz.org/downloads.
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Published by cryos over 10 years ago
https://github.com/openchemistry/tomviz - tomviz 0.6.0
This release focused on adding features for reproducible visualization and data processing. SciPy was added to this release to augment NumPy for data processing. The binaries for this release are available from our downloads page at http://tomviz.org/downloads.
Highlights of new features in this release include: - SciPy added to augment NumPy! - MRC file reader - Save animations as videos - Improved state files - Volumetric rendering speedup for Mac OS X - Uses relative paths for better data sharing - Downsample of data - New icons for slice and orthograthic slice tools - The slice tool's orientation arrow can be turned off - Right-click to delete visualizations and clone data - Right-click to change background colors - Prominent display of version information
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Published by cryos over 10 years ago
https://github.com/openchemistry/tomviz - tomviz 0.5.1
New tomviz release for tomographic data processing and visualization. Binaries of this release are available from our downloads page at http://tomviz.org/downloads.
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Published by cryos over 10 years ago
https://github.com/openchemistry/tomviz - tomviz 0.5.0
The second tomviz tomographic for data processing and visualization. Binaries of this release are available from our downloads page at http://tomviz.org/downloads.
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Published by cryos over 10 years ago
https://github.com/openchemistry/tomviz - tomviz 0.4.0
The first tomviz release to demonstrate basic alignment, reconstruction, and visualization. Binaries of this release are available from our downloads page at http://tomviz.org/downloads.
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Published by cryos over 11 years ago