Slicer merge requestshttps://gitlab.kitware.com/sjh26/Slicer/-/merge_requests2014-08-03T21:51:07-04:00https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/161Add the capability to pass derived items from the plugin2014-08-03T21:51:07-04:00Sam HorvathAdd the capability to pass derived items from the plugin*Created by: fedorov*
Files corresponding to derived DICOM objects are saved as a list in the attribute of loadable, and are added to the Slicer DICOM database upon load completion. This topic has been coordinated with @pieper.
*Created by: fedorov*
Files corresponding to derived DICOM objects are saved as a list in the attribute of loadable, and are added to the Slicer DICOM database upon load completion. This topic has been coordinated with @pieper.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/162ENH: Slice view annotations2015-03-23T11:22:30-04:00Sam HorvathENH: Slice view annotations*Created by: mehrtash*
@pieper, @fedorov
This is an implementation of slice view annotations in DataProbe as a part of QIICR Project [1]. It includes the following features:
- Corner text annotations including DICOM annotations.
- Color...*Created by: mehrtash*
@pieper, @fedorov
This is an implementation of slice view annotations in DataProbe as a part of QIICR Project [1]. It includes the following features:
- Corner text annotations including DICOM annotations.
- Color scalar bar for background volume
- Scaling ruler
This is a working script, however we would also try to add the following extra features on Wednesday:
- Smarter logic for
- Height of scalar bar
- Maximum length of corner annotation lines
- Hiding of the top right corner annotation
Some Known Issues:
- We could not add the color scalar bar for foreground as there is no method in vtkMRMLSliceLogic
to get Foreground window level and range ( for background we use GetBackgroundWindowLevelAndRange)
- There is a random behavior which makes color scalar bars to disappear or placed at random positions. It has something to do with multi-sampleing option as deleting the MSAA flag in Slicer settings file (*.ini) fixes this.
- There is also a bug in Windows that makes the annotations texts not readable on the white background (it looks like that the shadowing does not work correctly). It is introduced recently so I am suspicious to either MSAA or vtk6.
- In color scalar bar there is no control on the font size of the label. One solution can be to use vtkPVScalarBarActor [2] from paraview.
[1] [QIICR Slicer infrastructure projects](https://github.com/QIICR/ProjectIssuesAndWiki/wiki/Slicer-Infrastructure-Projects)
[2] http://www.paraview.org/ParaView3/Doc/Nightly/html/classvtkPVScalarBarActor.html
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/163BUG: Fixed issue of DICOM browser not closed after loading a volume2014-08-05T13:59:12-04:00Andras LassoBUG: Fixed issue of DICOM browser not closed after loading a volumeBrowser was not closed after loading a volume even if "Persistent" checkbox was unchecked.
Also added a settings (DICOM/BrowserPersistent) to remember the checkbox setting.
Browser was not closed after loading a volume even if "Persistent" checkbox was unchecked.
Also added a settings (DICOM/BrowserPersistent) to remember the checkbox setting.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/164ENH: Added the enhanced scalarbar actor class based on VTK6.2014-08-14T11:41:11-04:00Nicole AucoinENH: Added the enhanced scalarbar actor class based on VTK6.The VTK6 vtkScalarBarActor class allows displaying annotations in conjunction with labels.
However, in Slicer we want to sample the annotations for display just like color values since some color
tables have more than 10000 values and an...The VTK6 vtkScalarBarActor class allows displaying annotations in conjunction with labels.
However, in Slicer we want to sample the annotations for display just like color values since some color
tables have more than 10000 values and annotations.
The vtkSlicerScalarBarActor is based on vtkScalarBarActor class and only overrides its LayoutTicks method
to slightly modify the method to enable sampling the annotations and display it as labels.
Also change colors module logic using the new class.
Keep backward compatibility to VTK5.
Also added a python selftest.
Added a check box to toggle using the color names as labels, and set default label formats when it's toggled
to support strings or numbers. Added simple label format testing to avoid crashes that were seen when using
a string format with a number value.
Joint work between Kevin Wang and Nicole Aucoin
Issue #2919
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/165BUG: Fixed crash when cloned volume does not have display node2014-08-07T14:47:03-04:00Csaba PinterBUG: Fixed crash when cloned volume does not have display nodeWe had a crash when cloning a volume node with no display node. Is this a good fix? Or should we create a default display node? Or refuse cloning without a display node?
We had a crash when cloning a volume node with no display node. Is this a good fix? Or should we create a default display node? Or refuse cloning without a display node?
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/166ENH: fixed issue #2771 kill preivious storescp executables2015-03-23T11:22:22-04:00Sam HorvathENH: fixed issue #2771 kill preivious storescp executables*Created by: mehrtash*
@pieper
This fixes slicer bug 2771 [1] by killing all the instances of storescp before starting a new one. I tested it on Windows and Linux and works fine.
Based on this change the text of toggleListener button i...*Created by: mehrtash*
@pieper
This fixes slicer bug 2771 [1] by killing all the instances of storescp before starting a new one. I tested it on Windows and Linux and works fine.
Based on this change the text of toggleListener button is updated based on the process status not only user's click.
[1] http://na-mic.org/Mantis/view.php?id=2771
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/167ENH: Added the enhanced scalarbar actor class based on VTK6.2014-08-14T14:18:28-04:00Nicole AucoinENH: Added the enhanced scalarbar actor class based on VTK6.The VTK6 vtkScalarBarActor class allows displaying annotations in conjunction with labels.
However, in Slicer we want to sample the annotations for display just like color values since some color
tables have more than 10000 values and an...The VTK6 vtkScalarBarActor class allows displaying annotations in conjunction with labels.
However, in Slicer we want to sample the annotations for display just like color values since some color
tables have more than 10000 values and annotations.
The vtkSlicerScalarBarActor is based on vtkScalarBarActor class and only overrides its LayoutTicks method
to slightly modify the method to enable sampling the annotations and display it as labels.
Also change colors module logic using the new class.
Keep backward compatibility to VTK5.
Also added a python selftest based on scripted module superclass.
Added a check box to toggle using the color names as labels, and set default label formats when it's toggled
to support strings or numbers. Added simple label format testing to avoid crashes that were seen when using
a string format with a number value. Refer to bug report in TODO.
Joint work between Kevin Wang and Nicole Aucoin
Issue #2919
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/168BUG: Ensure slice intersection position are updated using VTK6. Fixes #3...2014-08-15T14:42:05-04:00Sam HorvathBUG: Ensure slice intersection position are updated using VTK6. Fixes #3...*Created by: jcfr*
...803
This commit fixes a regression introduced when transitioning to VTK6.
Note that ideally a pipeline should be created, that would avoid to
manually call Update or Modified.
*Created by: jcfr*
...803
This commit fixes a regression introduced when transitioning to VTK6.
Note that ideally a pipeline should be created, that would avoid to
manually call Update or Modified.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1693401 remove legacy module2014-08-21T23:37:14-04:00Sam Horvath3401 remove legacy module*Created by: jcfr*
The PR removed the following CLIs from the Slicer code base (see slicer issue [#3401](http://na-mic.org/Mantis/view.php?id=3401) and [this wiki page](http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/Depr...*Created by: jcfr*
The PR removed the following CLIs from the Slicer code base (see slicer issue [#3401](http://na-mic.org/Mantis/view.php?id=3401) and [this wiki page](http://wiki.slicer.org/slicerWiki/index.php/Documentation/Labs/DeprecatedModules)):
- AffineRegistration
- BSplineDeformableRegistration
- LinearRegistration
- RigidRegistration
- MRIBiasFieldCorrection
- MultiResolutionAffineRegistration
- OtsuThresholdImageFilter
- OtsuThresholdSegmentation
The code (and testing data) associated with each CLI modules has been added to a dedicated GitHub repository:
- https://github.com/Slicer/Slicer-AffineRegistration
- https://github.com/Slicer/Slicer-BSplineDeformableRegistration
- https://github.com/Slicer/Slicer-LinearRegistration
- https://github.com/Slicer/Slicer-RigidRegistration
- https://github.com/Slicer/Slicer-MRIBiasFieldCorrection
- https://github.com/Slicer/Slicer-MultiResolutionAffineRegistration
- https://github.com/Slicer/Slicer-OtsuThresholdImageFilter
- https://github.com/Slicer/Slicer-OtsuThresholdSegmentation
Note that the Slicer license and a README.md file has been automatically added to each repo to explain that the module has been deprecated and is not maintained.
For example: https://github.com/Slicer/Slicer-OtsuThresholdSegmentation#otsu-threshold-segmentation
For reference, the script that allows to automatically add the README file is https://gist.github.com/jcfr/367bd37e8d5b5c78b0d0
@pieper, @fedorov, @lassoan Please let me know if one of this module should NOT be removed.
What is the status regarding the `FiducialRegistration` module ? Since we now have `LandmarkRegistration`, can we confirm it should also be removed ?
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/170ENH: Slice view annotations2015-03-23T11:22:28-04:00Sam HorvathENH: Slice view annotations*Created by: mehrtash*
@pieper, @fedorov, @jcfr
This is an implementation of slice view annotations in DataProbe as a part of QIICR Project [1]. It includes the following features:
- Corner text annotations including DICOM annotations....*Created by: mehrtash*
@pieper, @fedorov, @jcfr
This is an implementation of slice view annotations in DataProbe as a part of QIICR Project [1]. It includes the following features:
- Corner text annotations including DICOM annotations.
- Color scalar bar for background volume
- Scaling ruler
The previous pull request can be found at [2].
[1] [QIICR Slicer infrastructure projects](https://github.com/QIICR/ProjectIssuesAndWiki/wiki/Slicer-Infrastructure-Projects)
[2] [Closed pull request](https://github.com/Slicer/Slicer/pull/162)
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/171Merge bug-fix for peformance issue with PlusRemote.2014-08-21T18:57:50-04:00Junichi TokudaMerge bug-fix for peformance issue with PlusRemote.This will fix the issue posted in:
http://na-mic.org/Mantis/view.php?id=3813
This will fix the issue posted in:
http://na-mic.org/Mantis/view.php?id=3813
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/172BUG: Made color scalar bar RepositionableOff2014-08-24T20:40:36-04:00Sam HorvathBUG: Made color scalar bar RepositionableOff*Created by: mehrtash*
@fedorov
This is a quick temporary fix for color scalar bar re-positioning behavior which not works in horizontal mode.
*Created by: mehrtash*
@fedorov
This is a quick temporary fix for color scalar bar re-positioning behavior which not works in horizontal mode.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/173Fix color scalarbar2015-03-23T11:22:19-04:00Sam HorvathFix color scalarbar*Created by: mehrtash*
@jcfr @fedorov @lassoan
ENH: Fixed color scalar bar by replacing vtkScalarBaractor with vtkPVScalarBarActor
Improvements:
- Color scalar bar was enhanced and the bugs were fixed by adding Paraview vtkPVScalarBar...*Created by: mehrtash*
@jcfr @fedorov @lassoan
ENH: Fixed color scalar bar by replacing vtkScalarBaractor with vtkPVScalarBarActor
Improvements:
- Color scalar bar was enhanced and the bugs were fixed by adding Paraview vtkPVScalarBarActor to module's logic
- Replaced vtkScalarBarActor with vtkPVScalarBarActor
- Made the logic sensitive to dicom volume. (for none dicom volumes the
color scalar bar would occupy 100% of the view's width)
- Change the format of foreground volume and label opacities to percentage
(e.g. from 0.4 to 40%)
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/174ENH: Fixed issues 3579, 3798 and other dicom browser improvements2015-03-23T11:22:25-04:00Sam HorvathENH: Fixed issues 3579, 3798 and other dicom browser improvements*Created by: mehrtash*
@jcfr @pieper
Improvements:
- Added the table density control to the slicer dicom browser for controlling table densities in three levels: comact, cozy and comfortable. The default value would be compact. Chang...*Created by: mehrtash*
@jcfr @pieper
Improvements:
- Added the table density control to the slicer dicom browser for controlling table densities in three levels: comact, cozy and comfortable. The default value would be compact. Changing the settings
would be saved in slicer user settings. (This will fix [1])
- Re-arranged the patient, study and series search boxex so that the search box will be on the top of tables for both horizontal and vertical cases (This will add more space to dicom tables)
- The bug with browser size change on advanced view is fixed (issue #3798 [2])
- The feature to resize tables based on contents was added to the tables.
[1] http://na-mic.org/Mantis/view.php?id=3579
[2] http://na-mic.org/Mantis/view.php?id=3798
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/175Editor with checkable effects2014-08-29T15:03:03-04:00Sam HorvathEditor with checkable effects*Created by: jcfr*
This PR change the editor effect button to be checkable. This provide an other visual feedback to the user.
Additionally, the UI will be updated with parameter are directly set in the associated Editor parameter node.
*Created by: jcfr*
This PR change the editor effect button to be checkable. This provide an other visual feedback to the user.
Additionally, the UI will be updated with parameter are directly set in the associated Editor parameter node.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/176ENH: Added option to copy log file contents to clipboard2014-09-01T18:47:13-04:00Andras LassoENH: Added option to copy log file contents to clipboardAvailable in application settings / Developer panel
Available in application settings / Developer panel
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/177BUG: Fix missing DLL for extensions that use OpenMP (requires CMake 3.1)2015-03-27T14:26:26-04:00Sam HorvathBUG: Fix missing DLL for extensions that use OpenMP (requires CMake 3.1)*Created by: gregsharp*
*Created by: gregsharp*
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/178ENH: Moved error log copying to separate error reporting dialog2014-09-03T11:09:26-04:00Andras LassoENH: Moved error log copying to separate error reporting dialogError reporting dialog accessible from menu: Help / Report a bug
Error reporting dialog accessible from menu: Help / Report a bug
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1793808 fiducial picking2014-09-06T16:39:23-04:00Steve Pieper3808 fiducial pickingNote this branch is for testing and should not be merged as-is, but it can be built for testing if needed.
This version depends on changes in Slicer/VTK [1].
[1] https://github.com/pieper/VTK/compare/Slicer:slicer-v6.2.0-7167ad1_2014-0...Note this branch is for testing and should not be merged as-is, but it can be built for testing if needed.
This version depends on changes in Slicer/VTK [1].
[1] https://github.com/pieper/VTK/compare/Slicer:slicer-v6.2.0-7167ad1_2014-08-21_v2...3808-fiducial-picking
If all looks good, merge the VTK changes and then update SuperBuild/External_VTKv6.cmake to point to the right place before committing to slicer svn.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/180ENH: Added a test for the ExtractSkeleton CLI2014-09-06T16:29:09-04:00Sam HorvathENH: Added a test for the ExtractSkeleton CLI*Created by: dirkpadfield*
This is a pull request I have been discussing with Steve Pieper.
*Created by: dirkpadfield*
This is a pull request I have been discussing with Steve Pieper.