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This is release is mainly for fixing some problems reported by users. The main feature set is described in the release v4.2. Many changes concern the build server.
The following issues were addressed in this release.
- Issue 428 - Minor release test issues.
- Issue 427 - Build problems on Ubuntu
- Issue 425 - Image viewer sensitive to nan and inf
- Issue 424 - Muhrec crashes at end of recon
- Issue 418 - Problem with boundary check on projection filter
- Issue 378 - Fix build server
- Issue 369 - Implement wall clock time the timer class
- Issue 368 - BB wrong number of ext images does not throw the right exception
- Issue 14 - ImageviewerWidget: ROIs with Zoom and Pan
In this release, we continued working on the performance of some algorithms and modules. The reconstruction filter has now moved to become a part of the back projector module, it is still available as preprocessing for those who still want it as a separate module. A new feature is that a publication list for the used modules is now saved in the same location as the reconstructed slices. Each used publication is cited with its corresponding DOI. We have also increased the portability of the configuration files, which now can be moved between different computers. Once again we have added some new GUI features like a preview of reference images. A handy feature if you suspect something is wrong with your reference data. Also, the preprocessing chain has now been equipped with a progress dialog that allows the user to cancel the loading procedure in case there is a wish to abort the configuration. The algorithm modules that have been updated are the Morphspot clean which is now more robust and also got a speed-up mainly thanks to the introduction of multithreading. The black body correction also obtained the option to load a single file for the tomography use case. Of course, we also fixed many issues reported by users and ourselves. A complete list of implemented features and fixed problems is provided below.
Please note: To use this new version it is as always recommended to delete the CurrentRecon.xml file.
- Issue 407 - Change label in center dialog
- Issue 406 - Recon from list file separator
- Issue 404 - CBCT doesn't add any publication
- Issue 402 - Muhrec debug messages in the log
- Issue 401 - MuhRec Memory limit dialog
- Issue 400 - Imageviewer widget histograms
- Issue 392 - MuhRec - config modules receives unprocessed images
- Issue 381 - kipl::base::morphology LabelImage crashes on Win
- Issue 374 - BB - exception is not thrown when automatic segmentation fails
- Issue 371 - MuhRec: module dialogs don't open after merging issue123_configfiles
- Issue 370 - BB module, add automatic counting of external background images
- Issue 365 - MorphSpotClean crashes on windows
- Issue 355 - Wavelet ring cleaning crashing
- Issue 346 - Add roi labels
- Issue 343 - Plot widget updates
- Issue 340 - Image viewer levels sensitive to nan and inf
- Issue 334 - Reconstruction by dilation hangs
- Issue 328 - Move the recon filter to backprojector
- Issue 322 - Slices to multi frame tiff
- Issue 315 - Revise skiplist dialog
- Issue 310 - MuhRec - add Exceptions when reference images and projection data have different sizes
- Issue 308 - MuhRec - Crashing after "Get piercing point"
- Issue 306 - Add new defaults to polynomial correction
- Issue 303 - golden ratio order
- Issue 299 - MuhRec doesn't delete CurrentRecon
- Issue 298 - PyBind Imaging algorithms
- Issue 297 - Modules to produce citations in reporting
- Issue 296 - CBCT doesn't return correct attune coefs
- Issue 295 - MuhRec: CBCT feedback
- Issue 294 - MuhRec - BB plugin option for single external BB images
- Issue 282 - Muhrec: implement inspection of references
- Issue 281 - MuhRec: Revise center of rotation
- Issue 273 - Review how we get more conform to the FAIR principle
- Issue 250 - PixelIterator returns pixels outside image
- Issue 162 - MuhRec Open saved config doesn't update correctly
- Issue 130 - CBCT writes detector pixel size in slices
- Issue 120 - Recon crash with file list
- Issue 95 - ImageViewerWidget data interval with NaNs and Infs
- Issue 48 - MuhRec - Extend projection preview
- Issue 39 - Morph spot clean performance tuning
- Issue 23 - Config files compatible cross platform
We have been improving the set of processing algorithms and fixed a long list of bugs. The user interface has been further revised and new features like the pixel size estimator have been added.
These efforts have resulted in more precise reconstructions both for parallel and cone beam CT. We have in particular worked on BBlognorm where the segmentation has improved and also robustness when the transmission is very low. MorphspotClean now has separate thresholds for peaks and holes, also the blockwise errors have been fixed. ProjectionFilterSingle also got a refresh with cleaner images as a result. We also discovered that the switch between CW and CCW was useless for parallel beam recon, this has now been fixed. In the user interface the most visible changes are the new plotting areas that also allow saving the plot. The pixel size estimator is a convenient tool to estimate the pixel size from an object with known dimensions. Finally, we improved the center of rotation estimate by allowing the user to exclude the fraction of centers that deviate most from the line. A small but useful change is that the boundary between the image viewers to the right can be adjusted to give more space to the more relevant viewer. The sliders have also be equipped with spinboxes to enter a specific slice or projection number.
Note: Please delete or rename the /home folder/.imagningtools/CurrentRecon.xml. We have added parameters to some of the revised modules.
In addition to these visible changes, we have also cleaned up the code on several places making it more readable. The build scripts have been revised to allow automated builds for windows too. The automated build now produces packages ready to run as alternative for those who need features in the very latest development.
We hope these updates will help you to get the most out of your data.
- Issue 280 - MuhRec - golden ratio starting at different angle than 0
- Issue 278 - MuhRec - load config files does not update the ROIs
- Issue 277 - Revise the MorphSpotCleanModule
- Issue 276 - MuhRec - add the pixel size estimator
- Issue 260 - FrameSplitter crashes on windows
- Issue 255 - Update MuhRec plots to Charts
- Issue 254 - MuhRec produce NaN slices
- Issue 230 - MuhRec - FDK attenuation coefficients (There is a remaining issue to be solved here)
- Issue 228 - File conversion tool
- Issue 220 - ROI is lost in communication with UXROIwidget
- Issue 219 - Reduce starvation artefacts in BB
- Issue 209 - Increasing amount of noise when setting slice block large
- Issue 205 - Boundary handling MorphSpotClean
- Issue 201 - Color scheme PlotWidget is not good with dark
- Issue 200 - MuhRec ROI calculation in engine
- Issue 191 - PlotWidget add tool tips
- Issue 186 - PlotWidget save data
- Issue 184 - Check kiptool CLI operation
- Issue 182 - Basic threshold progress bar
- Issue 179 - Levels in viewer
- Issue 171 - ModuleConfigWidget crash
- Issue 170 - Verify conversion tools
- Issue 164 - BB plugin - enhance speed in for loops
- Issue 161 - BB plugin - error when interpolating missing angles do not start from 0
- Issue 157 - MuhRec - improvements on the BB plugin
- Issue 151 - Banded noisy reconstructions
- Issue 150 - Add support for multi-frame tiff
- Issue 144 - CBCT crashes when running from CLI
- Issue 142 - MuhRec: CW/CCW does not work for parallel beam
- Issue 128 - Revise MorphSpotClean dialog
- Issue 125 - Problems with ROI handling in MuhRec
- Issue 123 - Add BB instruction in the manual wiki
- Issue 100 - MuhRec - configure geometry dialog first and last slices
- Issue 87 - MorphSpotClean crash sometimes
- Issue 51 - MuhRec - artifacts in reconstruction when not using dose correction
Please look at the issues page of this repository
Release note MuhRec 4.0.1 - September 2018
- Issue 100: MuhRec - configure geometry dialog first and last slices
- Issue 123: Add BB instruction in the manual wiki
- Issue 125: Problems with ROI handling in MuhRec bug
- Issue 144: CBCT crashes when running from CLI bug
- Issue 150: Add support for multi-frame tiff in the core library
- Issue 157: MuhRec - improvements on the BB plugin enhancement
Release note MuhRec 4.0.0 - July 2018
- Revised GUI,
- Rearranged the views for a more logic workflow.
- Changed color scheme and started to use colors actively to guide the user.
- Introduced an new widget to select ROIs.
- Logging now appears as a modeless dialog on the side of the main window.
- Tool tips have been added to all GUI items
- The application now suggests reference images when a new projection is chosen.
- We have tried to reduce the height of the main window to allow smaller screens.
- Added a normalization module (BBLogNorm) that provides more accurate attenuation coefficients and reduces cupping radically.
- It is now possible to save results in NeXus format.
- Improved CBCT quality and speed.
- Transferred the user documentation to the github wiki.
- The piercing point estimation dialog has been added for the CBCT parametrisation.
- Added several automated code tests for code quality assessment.
- The application is now compiled on windows 10. There may still be some widget scaling issues.
- A lot of stability fixes.
This list reports both fixes and new features.
- Issue 8: MuhRec - Piercing point dialog crashes bug
- Issue 9: MuhRec - Slow CBCT recon on windows enhancement
- Issue 18: Size of GUI window enhancement
- Issue 19: GUI size enhancement
- Issue 21: MuhRec - error in opening new config file bug
- Issue 28: MuhRec - CBCTimprove repeated slices bug
- Issue 42: Check correctness of the statistics class bug
- Issue 43: Check default parameter handling on Mac
- Issue 44: MuhRec - CBCT allow ROI in reconstruction
- Issue 50: Check size of FOV before module configuration enhancement
- Issue 53: UI redesign - low-hanging fruit enhancement
- Issue 54: Create ROI widget enhancement
- Issue 59: Add missing tool tips bug
- Issue 66: MuhRec - crash on wrong angles when using Golden Ratio
- Issue 67: MuhRec - info on GR or sequence scanning on geom dialog
- Issue 68: Suggest reference image paths enhancement
- Issue 70: Implement a logging dialog enhancement
- Issue 71: MuhRec: Transfer User doc to wiki enhancement
- Issue 76: Add a dialog to estimate the pixel size
- Issue 77: CBCT does not rotate
- Issue 78: Muhrec: Config add CLI parameters for CBCT enhancement
- Issue 79: MuhRec - deployment with QT in Linux
- Issue 81: MuhRec running from CLI in windows
- Issue 82: MuhRec - saving NeXus
- Issue 83: Make a MuhRec-CLI application enhancement
- Issue 85: MuhRec CBCT - errors in ROI bug
- Issue 86: MuhRec Matrix ROI gets confused after reconstruction
- Issue 89: MuhRec - projection roi in the new UI
- Issue 92: Muhrec - Geometry dialog crash when no OB
- Issue 98: Transfer RobustLogNorm to imaging suite
- Issue 99: GUI adjustments
- Issue 102: MuhRec - BB plugin - add tool tips
- Issue 116: MuhRec - windows bug moving modules bug
- Issue 118: MuhRec - BB plugin crash with radius >=4 on Mac bug
Unsolved issues are listed on https://github.com/neutronimaging/imagingsuite/issues
- Updated some build scripts.
Release note MuhRec3 3.14 - December 2017
In the current release we focussed on stability and the open source release including making automated build scripts.
- Improved the performance of the CBCT reconstruction. Including tidying the user interface.
- Added menu items for bug reporting and to sign up for the news letter.
- Now using Qt 5.9.3 as base API for the development.
- Added bound checking to avoid out of bound related crashes.
- NeXuS reading (BOA style nexus) is supported on all platforms.
- GUI clean-up
- All platforms now have a progress dialog while processing.
- Many issues with crashes as consequence have been fixed. E.g fixed an issue that made the logging display to crash.
- MuhRec and its dependencies are now uploaded on GitHub under GPL 3.0 License. Location https://github.com/neutronimaging/imagingsuite
- Build scripts for automated builds on all platforms are implemented.
Unsolved issues are listed on https://github.com/neutronimaging/imagingsuite/issues