Slicer Wiki - User contributions [en]

Documentation/Labs/FlyThroughNavigation

2015-12-01T21:04:21Z

Alexis.girault: add references to camera path module

This page describes possible approaches to implement general object to do fly through navigation.

There is already a scripted module named [[Documentation/Nightly/Modules/Endoscopy|Endoscopy]], as well as an external module for a custom application made by [mailto:alexis.girault@kitware.com Alexis Girault]. The idea would be to learn the lesson from those modules and other projects to create more general structure to store, represent and manage fly through navigation.

== Representation ==

* fly through path as a line

== References ==
* Virtual endoscopy in Slicer2: http://groups.csail.mit.edu/vision/medical-vision/virtual-endoscopy/
* vtkMRMLCameraPathNode & vtkMRMLPointSplineNode : [mailto:alexis.girault@kitware.com contact]
* CameraPath Loadable Module : [mailto:alexis.girault@kitware.com contact]
* vtkFlightInteractorStyle : [mailto:alexis.girault@kitware.com contact]

== Examples ==

* 3D Virtual Colonoscopy - Colon Fly Through : https://www.youtube.com/watch?v=uQP8J_lrJ7c
* Backward and forward playing is important: https://www.youtube.com/watch?v=pi79dw36jrI
* CameraPath Loadable Module interface :
{|
|[[Image: Camerapath_module.png|thumb|200px]]
|}

File:Camerapath module.png

2015-12-01T20:59:35Z

Alexis.girault:

Documentation/Labs

2015-12-01T20:47:01Z

Alexis.girault: /* Internals */

This is the place where we will keep track of our experiments and projects.

__NOTOC__

= On-going =

== Internals ==
* [[{{FULLPAGENAME}}/Segmentations|Segmentations]]
* [[{{FULLPAGENAME}}/DeprecatedModules|DeprecatedModules extension]]
* [[{{FULLPAGENAME}}/StartupTimeImprovement|Slicer startup time improvement]]
* [[{{FULLPAGENAME}}/FHSCompliantDirectoryStructure|FHS compliant directory structure]]
* [[{{FULLPAGENAME}}/FiberTractMeasurementAndVisualization|Fiber Tract measurement and visualization]]
* [[{{FULLPAGENAME}}/VTKWidgets|VTK Widgets improvements]]
* [[{{FULLPAGENAME}}/CLIInfrastructureCleanupAndRefactoring|CLI infrastructure cleanup and refactoring]]
* [[{{FULLPAGENAME}}/SlicerConfigAndUseSlicerTweaks|SlicerConfig and UseSlicer Tweaks]]
* [[{{FULLPAGENAME}}/UpgradingCompilerInfrastructure|Upgrading Compiler Infrastructure]]
* [[{{FULLPAGENAME}}/ViewInfrastructureImprovements| View Infrastructure Improvements]]
* [[{{FULLPAGENAME}}/CDash Improvements|CDash Improvements]]

== Libraries ==
* [[{{FULLPAGENAME}}/Qt5|Migration to Qt5]]
* [[{{FULLPAGENAME}}/OpenCV|Integration with OpenCV]]

== Python ==
* [[{{FULLPAGENAME}}/CallingPythonMethodsFromCpp|Calling Python methods from Cpp]]
* [[{{FULLPAGENAME}}/IPython|IPython]]
* [[{{FULLPAGENAME}}/Pip|Pip]]
* [[{{FULLPAGENAME}}/PythonCondaBuild|Python conda build]]

== Compilers & IDE ==
* [[{{FULLPAGENAME}}/Ninja|Ninja]]

== Virtual Machines ==
* [[{{FULLPAGENAME}}/GPU Virtualization|GPU Virtualization]]

== Documentation ==
* [[{{FULLPAGENAME}}/DocumentationImprovments|Documentation Improvements (Wiki, website, ...)]]

== Tutorials ==
* [[{{FULLPAGENAME}}/IPythonSlicerTutorials|IPython Slicer Tutorials]]

== Source code management ==
* [[{{FULLPAGENAME}}/TransitionToGit|Transition to Git]]

== Extension ==

* [[{{FULLPAGENAME}}/ExtensionsFrameworkRoadmap|Extensions Framework Roadmap]]
* [[{{FULLPAGENAME}}/CustomSlicerGenerator|Custom Slicer Generator]]

== Functionalities ==
* [[{{FULLPAGENAME}}/Video Support|Video support]]
* [[{{FULLPAGENAME}}/FlyThroughNavigation|Fly-through Navigation]]

= Completed =

* [[Slicer4:Developers|Developer Projects]]

== Extension ==
* [[{{FULLPAGENAME}}/EasyExtensionContribution|Easy Extension Contribution]] - See [[Documentation/Nightly/Developers/ExtensionWizard|ExtensionWizard]]

== Internals ==
* [[{{FULLPAGENAME}}/CMake-ified Python|CMake-ified Python]] - See [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21911 r21911], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21912 r21912], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21913 r21913]
* [[{{FULLPAGENAME}}/NonlinearTransforms|Full support for non-linear transforms]]

== Libraries ==
* [[{{FULLPAGENAME}}/ITKv4|ITKv4]]
* [[{{FULLPAGENAME}}/Qt484|Qt484]]
* [[{{FULLPAGENAME}}/VTK6|VTK6]]

== Python ==
* [[{{FULLPAGENAME}}/DevelopmentWithGit|Development with Git]] - See [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21863 r21863], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21867 r21867], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21869 r21869], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21879 r21879], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=21891 r21891]
* [[{{FULLPAGENAME}}/PythonObserverCallbacks|Python observer callbacks]]

== Compilers & IDE ==
* [[{{FULLPAGENAME}}/VS2012|VS2012]]
* [[{{FULLPAGENAME}}/NUMPY171|Support for Numpy 1.7.1]]

== Modules ==
* [[{{FULLPAGENAME}}/SimpleFilters|Simple Filters]]
* [[{{FULLPAGENAME}}/Editor|Editor]]

== Tutorials testing ==
* [[{{FULLPAGENAME}}/TutorialTesting/4.3-Release|4.3 Release]]

== Debug ==
* [[{{FULLPAGENAME}}/BRAINS_and_ITKv4_issue|BRAINS and ITKv4 issue]]

== Internals ==
* [[{{FULLPAGENAME}}/MultiDimensional Data Management|MultiDimensional Data Management]]
* [[{{FULLPAGENAME}}/DICOMExport|DICOM Export]]
* [[{{FULLPAGENAME}}/SliceViewAnnotations|Slice View Annotations]]
* [[{{FULLPAGENAME}}/SubjectHierarchy|Subject hierarchy module and plugins]]
* [[{{FULLPAGENAME}}/I18N|Internationalization]]
* [[{{FULLPAGENAME}}/Units|Units]]
* [https://github.com/TubeTK/SlicerExecutionModel/wiki/SlicerExecutionModel-Parameter-Serialization SlicerExecutionModel Parameter Serialization]

Documentation/Labs/ViewInfrastructureImprovements

2015-12-01T20:44:41Z

Alexis.girault:

= Goals =
* Update Slicer code base to listen to interactor instead of interactor style
* Add support for interactor style switch per view
* Allow access to vtkRenderWindow from vtkMRMLViewNode

= Motivation =

* We would like to conveniently be able to change the interactor style without having to reset all observer for the displayable managers.
* Accessing the vtkRenderWindow would allow us to do (for example) screenshots given a specific viewNode.

= InteractorStyle management =
== Workaround ==
=== Access 3D View ===
* Created a new Action menu in qSlicerMouseModeToolBar following [https://github.com/Slicer/Slicer/blob/a331fb0/Base/QTGUI/qSlicerMouseModeToolBar.cxx#L59-L103 this method.]
* Accessed all qMRMLThreeDView through the layoutManager :
<pre>
void qSlicerMouseModeToolBar::switchToTrackBallInteractorStyle()
{
qMRMLLayoutManager *layoutManager = qSlicerApplication::application()->layoutManager();

// loop through all existing threeDViews
vtkNew<vtkThreeDViewInteractorStyle> interactorStyle;
for (int i=0; i < layoutManager->threeDViewCount(); ++i)
{
qMRMLThreeDView* view = layoutManager->threeDWidget(i)->threeDView();
// Update Interactor style
this->SetInteractorStyle(view, interactorStyle.GetPointer());
// Reset focal point
view->resetFocalPoint();
}

// Update icon
Q_D(qSlicerMouseModeToolBar);
d->InteractorStyleToolButton->setIcon(QIcon(":/Icons/TrackBall.png"));
}
</pre>

* Issue : not setting the interactor per view but for all views
* Possible solution : adding the switch in each 3D View Qt controller

=== Update InteractorStyle ===
* Set the interactorStyle to the qMRMLThreeDView interactor :
<pre>
void qSlicerMouseModeToolBar::SetInteractorStyle(qMRMLThreeDView* view,
vtkInteractorStyle* interactorStyle)
{
// Set InteractorStyle on renderview
view->interactor()->SetInteractorStyle(interactorStyle);

// Get DMs
vtkNew<vtkCollection> collection;
view->getDisplayableManagers(collection.GetPointer());
int numManagers = collection->GetNumberOfItems();

// Set and Observe InteractorStyle for cameraDM
for (int i = 0; i < numManagers; ++i)
{
vtkMRMLCameraDisplayableManager *cameraDM =
vtkMRMLCameraDisplayableManager::SafeDownCast(collection->GetItemAsObject(i));
if (cameraDM)
{
cameraDM->SetCameraToInteractor();
}
}

collection->RemoveAllItems();
}
</pre>

* Issues :
** Should need to update the observations for all the DM using [https://github.com/Slicer/Slicer/blob/8617758/Libs/MRML/DisplayableManager/vtkMRMLAbstractDisplayableManager.cxx#L309-L338 SetAndObserveInteractorStyle()], but this crashes Slicer.
** The camera was not set anymore after a change of interactor styles in the vtkMRMLCameraDisplayableManager, so we had to use [https://github.com/Slicer/Slicer/blob/5ca7d0f/Libs/MRML/DisplayableManager/vtkMRMLCameraDisplayableManager.cxx#L518 SetCameraToInteractor()] and define it as a public method.

* Possible solution : updating Slicer core so that it listen only to the interactor instead of the interactorStyle.

== Design & implementation ==
TODO

= vtkRenderWindow mapping =
== Workaround ==
* Created a method that accessed the renderWindow through the layout manager MRMLViewFactory :
<pre>
vtkRenderWindow* getMRMLViewRenderWindow(vtkMRMLViewNode* viewNode)
{
qSlicerLayoutManager *layoutManager = qSlicerApplication::application()->layoutManager();
qMRMLThreeDWidget* threeDWidget = qobject_cast<qMRMLThreeDWidget*>(layoutManager->mrmlViewFactory("vtkMRMLViewNode")->viewWidget(viewNode));
vtkRenderWindow *renderWindow = threeDWidget->threeDView()->renderWindow();

return renderWindow;
}
</pre>

* Issue : calls to qMRML while we would prefer to stay with vtkMRML only
* Possible solution : map the vtkRenderWindow to the vtkMRMLViewNode in the view factory when creating the widget

== Design & implementation ==
TODO

Documentation/Labs/ViewInfrastructureImprovements

2015-12-01T19:36:39Z

Alexis.girault: Update InteractorStyle

= Goals =
* Update Slicer code base to listen to interactor instead of interactor style
* Add support for interactor style switch per view
* Allow access to vtkRenderWindow from vtkMRMLViewNode

= Motivation =

* We would like to conveniently be able to change the interactor style without having to reset all observer for the displayable managers.
* Accessing the vtkRenderWindow would allow us to do (for example) screenshots given a specific viewNode.

= InteractorStyle management =
== Workaround ==
=== Access 3D View ===
* Created a new Action menu in qSlicerMouseModeToolBar following [https://github.com/Slicer/Slicer/blob/a331fb0/Base/QTGUI/qSlicerMouseModeToolBar.cxx#L59-L103 this method.]
* Accessed all qMRMLThreeDView through the layoutManager :
<pre>
void qSlicerMouseModeToolBar::switchToTrackBallInteractorStyle()
{
qMRMLLayoutManager *layoutManager = qSlicerApplication::application()->layoutManager();

// loop through all existing threeDViews
vtkNew<vtkThreeDViewInteractorStyle> interactorStyle;
for (int i=0; i < layoutManager->threeDViewCount(); ++i)
{
qMRMLThreeDView* view = layoutManager->threeDWidget(i)->threeDView();
// Update Interactor style
this->SetInteractorStyle(view, interactorStyle.GetPointer());
// Reset focal point
view->resetFocalPoint();
}

// Update icon
Q_D(qSlicerMouseModeToolBar);
d->InteractorStyleToolButton->setIcon(QIcon(":/Icons/TrackBall.png"));
}
</pre>

* Issue : not setting the interactor per view but for all views
* Solution : adding the switch in each 3D View Qt controller

=== Update InteractorStyle ===
* Set the interactorStyle to the qMRMLThreeDView interactor :
<pre>
void qSlicerMouseModeToolBar::SetInteractorStyle(qMRMLThreeDView* view,
vtkInteractorStyle* interactorStyle)
{
// Set InteractorStyle on renderview
view->interactor()->SetInteractorStyle(interactorStyle);

// Get DMs
vtkNew<vtkCollection> collection;
view->getDisplayableManagers(collection.GetPointer());
int numManagers = collection->GetNumberOfItems();

// Set and Observe InteractorStyle for cameraDM
for (int i = 0; i < numManagers; ++i)
{
vtkMRMLCameraDisplayableManager *cameraDM =
vtkMRMLCameraDisplayableManager::SafeDownCast(collection->GetItemAsObject(i));
if (cameraDM)
{
cameraDM->SetCameraToInteractor();
}
}

collection->RemoveAllItems();
}
</pre>

* Issues :
** Should need to update the observations for all the DM using [https://github.com/Slicer/Slicer/blob/8617758/Libs/MRML/DisplayableManager/vtkMRMLAbstractDisplayableManager.cxx#L309-L338 SetAndObserveInteractorStyle()], but this crashes Slicer.
** The camera was not set anymore after a change of interactor styles in the vtkMRMLCameraDisplayableManager, so we had to use [https://github.com/Slicer/Slicer/blob/5ca7d0f/Libs/MRML/DisplayableManager/vtkMRMLCameraDisplayableManager.cxx#L518 SetCameraToInteractor()] and define it as a public method.

* Solution : updating Slicer core so that it listen only to the interactor instead of the interactorStyle.

== Design & implementation ==
TODO

= vtkRenderWindow mapping =
== Current workaround ==
TODO
== Issues ==
TODO
== Design & implementation ==
TODO

Documentation/Labs/ViewInfrastructureImprovements

2015-12-01T19:20:33Z

Alexis.girault: Access 3D View

Documentation/Labs/ViewInfrastructureImprovements

2015-12-01T18:52:37Z

Alexis.girault:

Documentation/Labs/ViewInfrastructureImprovements

2015-12-01T18:36:50Z

Alexis.girault: moved Documentation/Labs/InteractorStyle to Documentation/Labs/ViewInfrastructureImprovements: including improvements for interactorstyle & mapping between vtkRenderWindow & vtkMRMLViewNode

= Goal =

* Update Slicer code base to listen to interactor instead of interator style

= Motivation =

* It is convenient to be able to easily change the interactor style without having to reset all observer.

Documentation/Labs/InteractorStyle

2015-12-01T18:36:50Z

#REDIRECT [[Documentation/Labs/ViewInfrastructureImprovements]]

Documentation/Nightly/Developers/FAQ/IO

2015-11-05T22:32:40Z

Alexis.girault: /* Why is my node writer not showing up in the Save dialog ? */

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>__TOC__
={{#titleparts: {{PAGENAME}} | | -1 }}=</noinclude><includeonly>
='''Developer FAQ: {{{1}}}'''=
</includeonly>

== Why is my node writer not showing up in the Save dialog ? ==
You have implemented a loadable module with a new MRML node, its storage node, and the [{{documentation/{{documentation/version}}/doxygen-class-url|qSlicerNodeWriter}} qSlicerNodeWriter] needed to save your node on your system file. If the writer is not showing up for your node in the [{{documentation/{{documentation/version}}/doxygen-class-url|qSlicerSaveDataDialog}} qSlicerSaveDataDialog], it could be one of those following reasons :

* You need to register your writer in the [{{documentation/{{documentation/version}}/doxygen-class-url|qSlicerIOManager}} qSlicerIOManager] in ''qSlicerYourModule::setup()''.
Example: [https://github.com/Slicer/Slicer/blob/3dd75da/Modules/Loadable/Markups/qSlicerMarkupsModule.cxx#L136-L138 qSlicerMarkupsModule writer registration]
* Your node needs to be a sub-class of [{{documentation/{{documentation/version}}/doxygen-class-url|vtkMRMLStorableNode}} vtkMRMLStorableNode].

Documentation/Nightly/Developers/FAQ/IO

2015-11-05T22:21:32Z

Alexis.girault: /* Why is my node writer not showing up in the Save dialog ? */

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>__TOC__
={{#titleparts: {{PAGENAME}} | | -1 }}=</noinclude><includeonly>
='''Developer FAQ: {{{1}}}'''=
</includeonly>

== Why is my node writer not showing up in the Save dialog ? ==
You have implemented a loadable module with a new MRML node, its storage node, and the [http://slicer.org/doc/html/classqSlicerNodeWriter.html qSlicerNodeWriter] needed to save your node on your system file. If the writer is not showing up for your node in the [http://slicer.org/doc/html/classqSlicerSaveDataDialog.html qSlicerSaveDataDialog], it could be one of those following reasons :

* You need to register your writer in the [http://slicer.org/doc/html/classqSlicerIOManager.html qSlicerIOManager] in ''qSlicerYourModule::setup()''.
Example: [https://github.com/Slicer/Slicer/blob/3dd75da/Modules/Loadable/Markups/qSlicerMarkupsModule.cxx#L136-L138 qSlicerMarkupsModule writer registration]
* Your node needs to be a sub-class of [http://slicer.org/doc/html/classvtkMRMLStorableNode.html vtkMRMLStorableNode].

Documentation/Nightly/Developers/FAQ/IO

2015-11-05T22:20:12Z

Alexis.girault: Node writer not showing up in the Save dialog

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>__TOC__
={{#titleparts: {{PAGENAME}} | | -1 }}=</noinclude><includeonly>
='''Developer FAQ: {{{1}}}'''=
</includeonly>

== Why is my node writer not showing up in the Save dialog ? ==
You have implemented a loadable module with a new MRML node, its storage node, and the [http://slicer.org/doc/html/classqSlicerNodeWriter.html qSlicerNodeWriter] needed to save your node on your system. If the writer is not showing up for your node in the [http://slicer.org/doc/html/classqSlicerSaveDataDialog.html qSlicerSaveDataDialog], it could be one of those following reasons :

* You need to register your writer in the [http://slicer.org/doc/html/classqSlicerIOManager.html qSlicerIOManager] in ''qSlicerYourModule::setup()''.
Example: [https://github.com/Slicer/Slicer/blob/3dd75da/Modules/Loadable/Markups/qSlicerMarkupsModule.cxx#L136-L138 qSlicerMarkupsModule writer registration]
* Your node needs to be a sub-class of [http://slicer.org/doc/html/classvtkMRMLStorableNode.html vtkMRMLStorableNode].