Slicer merge requestshttps://gitlab.kitware.com/sjh26/Slicer/-/merge_requests2014-08-24T20:40:36-04:00https://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/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/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/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/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/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/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/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/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/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/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/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/160ENH: update multivolume modules tag2014-08-03T06:54:28-04:00Sam HorvathENH: update multivolume modules tag*Created by: fedorov*
- fix an issue due to missing cast to int
- initialize DICOM.instanceUIDs attribute
*Created by: fedorov*
- fix an issue due to missing cast to int
- initialize DICOM.instanceUIDs attribute
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/159ENH: Update OpenIGTLink from 1.10.4 to 1.10.10 to include bug fixes.2016-01-25T22:03:58-05:00Sam HorvathENH: Update OpenIGTLink from 1.10.4 to 1.10.10 to include bug fixes.*Created by: jcfr*
```
$ git shortlog 3ac5311..849b434 --no-merges
Andras Lasso (1):
Add the MSG_NOSIGNAL flag to socket send calls to prevent application crash on disconnect on linux systems
Gergely Zombori (1):
Bug #1912 ...*Created by: jcfr*
```
$ git shortlog 3ac5311..849b434 --no-merges
Andras Lasso (1):
Add the MSG_NOSIGNAL flag to socket send calls to prevent application crash on disconnect on linux systems
Gergely Zombori (1):
Bug #1912 - Merged the changes and enhancements from upstream into 'master'
Isaiah Norton (1):
BUG: use shutdown() instead of close() for sockets
Junichi Tokuda (7):
BUG: Address issue #29: copy igtl_win32hearder.h to the install directory.
ENH: Update patch number.
STYLE: Update patch number.
COMP: Fix compilation error due to lack of MSG_NOSIGNAL option in send() in Mac OS X. For Mac OS X, call setsockopt() with SO_NOSIGPIPE instead.
STYLE: Update revision number.
BUG: Set timestamp zero, when no timestamp object is registered to image meta message.
STYLE: Update patch number
Laurent Chauvin (1):
BUG: Initialize ImageMessage matrix to identity (issue #39)
Matt Clarkson (3):
#44: Put nanosleep in loop to ensure sleep is for the correct time.
#49: Avoid crash on division by zero, which should never happen
#50: Convenience methods to set/get igtl_image matrix from 4x4 array of floats
z0022myy (1):
BUG: Intializing pointer should not be in a loop
```
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/158BUG: update MultiVolumeExplorer tag2014-07-30T17:04:51-04:00Sam HorvathBUG: update MultiVolumeExplorer tag*Created by: fedorov*
This fixes an issue due to missing cast from float to int that disabled frame
scrolling.
*Created by: fedorov*
This fixes an issue due to missing cast from float to int that disabled frame
scrolling.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/157Slice view annotations2014-07-30T11:32:28-04:00Sam HorvathSlice view annotations*Created by: mehrtash*
Adding Slice View annotations and ruler to Dataprobe module
*Created by: mehrtash*
Adding Slice View annotations and ruler to Dataprobe module
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/156BUG: update multivolume modules2014-07-23T12:59:42-04:00Sam HorvathBUG: update multivolume modules*Created by: fedorov*
Fixed to work with both VTK5 and VTK6 API
https://github.com/fedorov/MultiVolumeExplorer/commit/1053c40846e80c277f20c7af474eaee64ef4a16d
https://github.com/fedorov/MultiVolumeImporter/commit/351226a1dfeb2e9113424f...*Created by: fedorov*
Fixed to work with both VTK5 and VTK6 API
https://github.com/fedorov/MultiVolumeExplorer/commit/1053c40846e80c277f20c7af474eaee64ef4a16d
https://github.com/fedorov/MultiVolumeImporter/commit/351226a1dfeb2e9113424f4a42e57390bb17ceb9
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/155ENH: Added developer mode and base classes for scripted modules2014-07-29T20:01:08-04:00Andras LassoENH: Added developer mode and base classes for scripted modules- Added "Enable developer mode" option in the application settings (Developer section, next to Enable QtTesting)
- Added base classes for scripted module, widget, logic, and test: they make scripted modules simpler and shorter and also m...- Added "Enable developer mode" option in the application settings (Developer section, next to Enable QtTesting)
- Added base classes for scripted module, widget, logic, and test: they make scripted modules simpler and shorter and also more functions and helper methods can be added in the future without changing each scripted module
*\* Module handles selftest registration
*\* Widget handles reload&test (shown on GUI only in developer mode)
*\* Logic and Test contains delayDisplay utility function
- As an example, updated ScriptedLoadableModuleTemplate and SurfaceToolbox to use the new base classes
- A minor fix for crash caused by invalid recently loaded files (fixed by changing assert to properly handling the situation) is also included. Actually, this change was not intended to be part of this commit, but if it looks good to others, then it can be merged, too.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/15420140719 brains tools integration2014-07-20T16:13:14-04:00Hans Johnson20140719 brains tools integrationThis patch set passed compilation. It required updates to ITK in order to get the external linkage correct for some ITKIODCMTK classes.
This patch set passed compilation. It required updates to ITK in order to get the external linkage correct for some ITKIODCMTK classes.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/153ENH: update MultiVolumeImporter2014-07-23T12:11:55-04:00Sam HorvathENH: update MultiVolumeImporter*Created by: fedorov*
SetNumberOfScalarComponents() used by this external module has been deprecated
in VTK6, now it is using AllocateScalars() instead
*Created by: fedorov*
SetNumberOfScalarComponents() used by this external module has been deprecated
in VTK6, now it is using AllocateScalars() instead