Slicer merge requestshttps://gitlab.kitware.com/sjh26/Slicer/-/merge_requests2018-12-16T15:37:15-05:00https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1064STYLE: Typo in vtkMRMLStorageNode documentation2018-12-16T15:37:15-05:00SunderlandkylSTYLE: Typo in vtkMRMLStorageNode documentationhttps://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1044ENH: Add vtkMRMLStorageNode::GetStorableNode() method2018-12-16T15:37:10-05:00SunderlandkylENH: Add vtkMRMLStorageNode::GetStorableNode() methodSee discussion here: https://discourse.slicer.org/t/no-getstorablenode-method-in-vtkmrmlstoragenode/4764/2See discussion here: https://discourse.slicer.org/t/no-getstorablenode-method-in-vtkmrmlstoragenode/4764/2https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1063STYLE: Add SampleData.downloadSample2018-12-15T08:07:59-05:00Sam HorvathSTYLE: Add SampleData.downloadSample*Created by: jcfr*
This is a follow of https://github.com/Slicer/Slicer/pull/1062
Other possible improvement:
* decouple downloading and loading by having `loadFromURL` and `downloadFromURL`
* rename `downloadSample` into `loadSamp...*Created by: jcfr*
This is a follow of https://github.com/Slicer/Slicer/pull/1062
Other possible improvement:
* decouple downloading and loading by having `loadFromURL` and `downloadFromURL`
* rename `downloadSample` into `loadSample`. Since this may break existing code .. may be we should keep this for Slicer 5.0 ? https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1062Improve SampleData module: add downloadFromURL API2018-12-14T20:23:47-05:00Sam HorvathImprove SampleData module: add downloadFromURL API*Created by: jcfr*
This changes are first step toward improving testing infrastructure discussed in https://discourse.slicer.org/t/improving-testing-data-management-for-self-test/5014/6*Created by: jcfr*
This changes are first step toward improving testing infrastructure discussed in https://discourse.slicer.org/t/improving-testing-data-management-for-self-test/5014/6https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1058ENH: If building VTK 8 with C++11 enable CXX11_FEATURES.2018-12-11T21:24:26-05:00Hans JohnsonENH: If building VTK 8 with C++11 enable CXX11_FEATURES.Hans JohnsonHans Johnsonhttps://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1056ENH: Future proof null pointer behavior for ITKv52018-12-11T17:18:03-05:00Hans JohnsonENH: Future proof null pointer behavior for ITKv5Enhancements in nullptr behavior in ITKv5 provide more clear
type checking and respect the nullptr identifier. The 'long 0' value
known as NULL causes an abiguity for overload compilations of the ITKv5 smartpointers.
Using ITK_NULL...Enhancements in nullptr behavior in ITKv5 provide more clear
type checking and respect the nullptr identifier. The 'long 0' value
known as NULL causes an abiguity for overload compilations of the ITKv5 smartpointers.
Using ITK_NULLPTR is both backwards and forwards compatible.Hans JohnsonHans Johnsonhttps://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1053ENH: Speedup (from 2x to 10x faster) and simplify python tests2018-12-08T02:06:41-05:00Sam HorvathENH: Speedup (from 2x to 10x faster) and simplify python tests*Created by: jcfr*
* Run python self tests with a messageDelay of 100ms. Message delay is used
in function "delayDisplay" to (1) let the event loop catch up to the state
of the test and (2) to display a meaningful message when runni...*Created by: jcfr*
* Run python self tests with a messageDelay of 100ms. Message delay is used
in function "delayDisplay" to (1) let the event loop catch up to the state
of the test and (2) to display a meaningful message when running test
interactively from Slicer.
When running tests on the dashboard, there is no need to wait too long
before each test steps. This commit sets a default of 50ms when tests
are executed from the module panel. It also provides a Slicer to change
the value.
* Refactor tests to use ScriptedLoadableModule base classes
* Remove redundant test case AbdominalAtlasTest already coverted by
AtlasTests
* Remove duplicated implementation of functions like takeScreenshot.https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1051ENH: Add MRMLSliceNode property to allow show/hide of reformat widget outline2018-12-06T12:01:35-05:00Sam HorvathENH: Add MRMLSliceNode property to allow show/hide of reformat widget outline*Created by: jcfr*
*Created by: jcfr*
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/498Upgrade to scipy 0.14.12018-12-06T02:46:27-05:00Francois BudinUpgrade to scipy 0.14.1https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1050STYLE: Arbitrary change to trigger preview.apidocs.slicer.org build2018-12-06T00:18:45-05:00Sam HorvathSTYLE: Arbitrary change to trigger preview.apidocs.slicer.org build*Created by: jcfr*
**DO NOT MERGE***Created by: jcfr*
**DO NOT MERGE**https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1048Support per view interaction mode2018-12-05T19:38:13-05:00Sam HorvathSupport per view interaction mode*Created by: jcfr*
*Created by: jcfr*
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1049BUG: Fix cutoff in DICOM browser toolbar2018-12-05T14:47:33-05:00Csaba PinterBUG: Fix cutoff in DICOM browser toolbarThe DICOM browser's toolbar looks like this on Windows in 4.10:
![image](https://user-images.githubusercontent.com/1325980/49537703-a104da00-f897-11e8-87a9-91eb548ba49d.png)
It is not a good idea to set fixed number of pixels for any...The DICOM browser's toolbar looks like this on Windows in 4.10:
![image](https://user-images.githubusercontent.com/1325980/49537703-a104da00-f897-11e8-87a9-91eb548ba49d.png)
It is not a good idea to set fixed number of pixels for anything in Qt5, and this negative margin does not seem to be safe any more.https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1008ENH: Configure extension build-tree launcher for starting Slicer2018-12-03T16:10:44-05:00Sam HorvathENH: Configure extension build-tree launcher for starting Slicer*Created by: jcfr*
This convenience launcher allows to start Slicer ensuring the extensions
being developed (and its dependencies) are properly loaded.
Co-authored-by: Csaba Pinter <csaba.pinter@queensu.ca>*Created by: jcfr*
This convenience launcher allows to start Slicer ensuring the extensions
being developed (and its dependencies) are properly loaded.
Co-authored-by: Csaba Pinter <csaba.pinter@queensu.ca>https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1046Sh terminology and transform improvements2018-11-30T10:55:28-05:00Csaba PinterSh terminology and transform improvementsTwo sets of changes in subject hierarchy:
Colors and terminologies:
- Add new column for color between visibility and transform columns. It shows the color for segments, models, and markup fiducials (selected color)
- Double-clickin...Two sets of changes in subject hierarchy:
Colors and terminologies:
- Add new column for color between visibility and transform columns. It shows the color for segments, models, and markup fiducials (selected color)
- Double-clicking the color brings up terminology selector where terminology and color can be selected. Terminology information is stored in segments as before (segment attributes), and for models and markups it is stored in MRML node attributes. When selecting a terminology type, color is overwritten but name is not by default
- Terminology selector has been improved to accommodate setting terminologies to model and markup fiducial nodes, for which it's not mandatory to set terminology (unlike segments)
- None type always appears in type list unless type search term is specified
- Multi-select is enabled for categories, and by default all the categories are selected so that all the types show up in the types list and a search finds any type in the context
- Expand button added to hide categories list
- Both categories and anatomy lists are hidden by default
- Type search box has the focus when opened and selection can be accepted by Enter press (so terminology can be selected very quickly by just typing search term then pressing Enter)
Fixes https://issues.slicer.org/view.php?id=4658
Re https://github.com/PerkLab/SlicerOpenAnatomy/issues/4
Transforms:
- Transform column now shows icon instead of the first few letters of the transform name. There is a separate icon for linear and deformable transforms
- Double-clicking the icon brings up a menu instead of a node selector that had to be clicked again
- Subject hierarchy reference highlights are now updated immediately after selecting a transforms, so the highlighted transform node is always correct
Re https://issues.slicer.org/view.php?id=4401
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1047BUG: Fixed virtual reality picking error2018-11-26T00:46:47-05:00Andras LassoBUG: Fixed virtual reality picking errorWhen the pick position was close or inside non-selectable object, picking often failed because VTK's cell picker found that actor.
Now if a model, segmentation, or volume rendering node is not selectable then it is completely excluded...When the pick position was close or inside non-selectable object, picking often failed because VTK's cell picker found that actor.
Now if a model, segmentation, or volume rendering node is not selectable then it is completely excluded from picking.
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/888ENH: Support passing markups to CLI specifying IJK coordinate2018-11-15T11:34:26-05:00Sam HorvathENH: Support passing markups to CLI specifying IJK coordinate*Created by: jcfr*
### NOTE: Commit will be squashed before integration
-------
This commit allows associating any markupsNode with a reference image. The
association is then used to automatically convert to/from IJK coordinate
...*Created by: jcfr*
### NOTE: Commit will be squashed before integration
-------
This commit allows associating any markupsNode with a reference image. The
association is then used to automatically convert to/from IJK coordinate
using SetMarkupPointIJK()/GetMarkupPointIJK() used in vtkMarkupsNode::WriteCLI().
Co-authored-by: Deepak Chittajallu <deepak.chittajallu@kitware.com>https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1038ENH: Add vtkMRMLStorageNode CompressionParameter and presets2018-11-14T15:51:03-05:00SunderlandkylENH: Add vtkMRMLStorageNode CompressionParameter and presets-Adds a framework for specifying different preset levels of compression in vtkMRMLStorageNode
-Changes in vtkStreamingVolumeCodec also allow codecs to specify their own presets
-Replaces previous CompressionLevel int
![image](https:...-Adds a framework for specifying different preset levels of compression in vtkMRMLStorageNode
-Changes in vtkStreamingVolumeCodec also allow codecs to specify their own presets
-Replaces previous CompressionLevel int
![image](https://user-images.githubusercontent.com/9222709/47896281-203f6200-de43-11e8-86ba-3fefd21fc138.png)
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/989Change default colormap for model scalars and displacement volumes2018-11-13T22:01:33-05:00FernandoChange default colormap for model scalars and displacement volumesSee https://github.com/Slicer/Slicer/pull/741
Also, in my vessels network with `Radius` set as Active scalar:
Using Viridis, I can easily figure out that dark lines represent thin vessels and yellow ones are thicker:
![viridis](ht...See https://github.com/Slicer/Slicer/pull/741
Also, in my vessels network with `Radius` set as Active scalar:
Using Viridis, I can easily figure out that dark lines represent thin vessels and yellow ones are thicker:
![viridis](https://user-images.githubusercontent.com/12688084/42581203-1ff80d10-8524-11e8-8295-ad69e734cc97.png)
Using Rainbow, the current default, the result is more fun but more confusing:
![rainbow](https://user-images.githubusercontent.com/12688084/42581304-599d1a1a-8524-11e8-9bd7-18644d5d0912.png)
https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/1042BUG: Update SimpleFilters remote to fix errors on close2018-11-13T21:31:01-05:00Sam HorvathBUG: Update SimpleFilters remote to fix errors on close*Created by: jamesobutler*
Update SimpleFilters remote module
Fix calling disconnect on destroyed object when Slicer is closing.*Created by: jamesobutler*
Update SimpleFilters remote module
Fix calling disconnect on destroyed object when Slicer is closing.https://gitlab.kitware.com/sjh26/Slicer/-/merge_requests/696Support per view visibility of slicer intersection2018-11-13T21:29:25-05:00Sam HorvathSupport per view visibility of slicer intersection*Created by: jcfr*
This commit updates the SliceModel displayable manager to allow hiding part of slice intersection on selected views.
For example, let's consider this scene with:
* 1 model
* slice intersection enabled
* slice vi...*Created by: jcfr*
This commit updates the SliceModel displayable manager to allow hiding part of slice intersection on selected views.
For example, let's consider this scene with:
* 1 model
* slice intersection enabled
* slice views visible in two 3D views
![setting_viewids_start](https://cloud.githubusercontent.com/assets/219043/24574752/5cee146e-1665-11e7-9161-fd100501a3f7.png)
Now, with this change, we can (for example) show the red slice intersection only on the green slice viewer.
The following tweaks have been done:
* model is removed from View1
* "red slice node" is hidden in ThreeD view 2
* only intersection of red slice with green slice is shown
![setting_viewids_done](https://cloud.githubusercontent.com/assets/219043/24574756/5f713bf8-1665-11e7-8523-771113736362.png)