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IDProjectCategoryView StatusDate SubmittedLast Update
0003610Slicer4Module Transformspublic2014-03-03 12:412017-06-10 08:51
Reporterlassoan Assigned Tolassoan  
PrioritynormalSeveritycrashReproducibilityalways
Status closedResolutionfixed 
Product Version 
Target VersionSlicer 4.4.0Fixed in VersionSlicer 4.4.0 
Summary0003610: Crash when transforms are received through OpenIGTLink
Description

Slicer crashes when a transform is received through OpenIGTLink.

How to reproduce:

  • Set up an OpenIGTLink server, e.g., using Slicer:
    Start 3D Slicer
     Go to the Transforms module and create a new LinearTransform
    Go to the OpenIGTLinkIF module, create a new connection, set it as Server, set status to Active
     In the I/O configuration tab select Scene/IGTLConnector/OUT
    ** Click on '+' next to the Add/remove Node selector to add the linear transform to the list of transforms that are broadcasted through OpenIGTLink

  • Start a new instance Slicer (keep the other running)

  • Create an OpenIGTLink client connection in OpenIGTLinkIF

  • Choose it to be a client, set active

  • Send transforms through OpenIGTLink (by changing the linear transform in the other Slicer instance)

  • Go to the Transforms module, the received transform should be listed

  • Send an updated transform through OpenIGTLink => Slicer crashes

TagsNo tags attached.

Activities

lassoan

lassoan

2014-03-03 13:27

developer   ~0010666

The issue is caused by this call in qMRMLLinearTransformSlider::applyTransformation(double _sliderPosition):

(A)
d->MRMLTransformNode->SetAndObserveMatrixTransformToParent(transform->GetMatrix());

This version worked before the big transforms rework, but it's not fully functional anymore (doesn't trigger proper updates anymore):

(B)
d->MRMLTransformNode->GetMatrixTransformToParent()->DeepCopy(transform->GetMatrix());

So, there are at least two things to fix:

  1. Version (A) should not crash

  2. Version (B) should trigger the proper updates: currently if we replace (A) by (B) then translation sliders break (moving the translation sliders do not update the position of the transformed volume in the slice viewers)
lassoan

lassoan

2014-03-03 13:27

developer   ~0010667

The issue is caused by this call in qMRMLLinearTransformSlider::applyTransformation(double _sliderPosition):

(A)
d->MRMLTransformNode->SetAndObserveMatrixTransformToParent(transform->GetMatrix());

This version worked before the big transforms rework, but it's not fully functional anymore (doesn't trigger proper updates anymore):

(B)
d->MRMLTransformNode->GetMatrixTransformToParent()->DeepCopy(transform->GetMatrix());

So, there are at least two things to fix:

  1. Version (A) should not crash

  2. Version (B) should trigger the proper updates: currently if we replace (A) by (B) then translation sliders break (moving the translation sliders do not update the position of the transformed volume in the slice viewers)
lassoan

lassoan

2014-03-05 02:44

developer   ~0010680

I'm working on this, probably a patch will be ready today or tomorrow.
lassoan

lassoan

2014-03-05 14:45

developer   ~0010686

Pull request with the fix submitted:
https://github.com/Slicer/Slicer/pull/111
lassoan

lassoan

2014-03-19 09:56

developer   ~0011451

Fix merged into the trunk:
http://viewvc.na-mic.org/viewvc.cgi/Slicer4?view=revision&revision=23008
jcfr

jcfr

2014-09-17 23:01

administrator   ~0012571

Closing resolved issues that have not been updated in more than 3 months.

Related Changesets

Import 2017-06-07 23:51:09: master 29dc6a68

2014-03-19 13:41:09

lassoan

Details Diff 		ENH: Several fixes and improvements in transform handling

Major fixes:
* Added mechanism to prevent immediate invocation of TransformModified events (similarly to Modified events) to allow atomic changes of transforms and prevent multiple event invocations (fixes 0003610, 0003611).
* Fixed vtkITKBSplineTransform inverse computation (the bulk component was ignored in the inverse computation due to a shadow variable)
* Fixed DeepCopy of vtkITKBSplineTransform.cxx (InternalDeepCopy method had to be implemented)
* Use vtkTransform's ability to compute inverse transforms instead of keeping separate transforms for forward and inverse transforms (still kept the two member variables in the transform node base class to allow storing of forward and inverse transform if they are both computed, e.g., some Demons registration provides both the forward and inverse transforms as outputs).
* Fixed ReadWriteAsTransformToParent logic in the storage node class (as inverse warp transforms usually cannot be written, the flag should point to the forward transform class). For convenience, the flag is updated automatically when a To/FromParentTransform is set in the transform node.
* Fixed transform node copy: now a true deep copy is performed (earlier only the pointer of the transforms were copied, therefore changing a transform in a node changed the copied node, too)
* Removed vtkMRMLNonlinearTransformNode, as non-linear transforms are not special cases anymore: the base transform class can manage them the same way as linear transforms.
* Changed Get/SetMatrixTransformToParent and Get/SetMatrixTransformFromParent method to make it clear that it makes a copy of the input and output, so changing a matrix is only possible by using the Set... method (and not Get...()->DeepCopy(...)). Kept the old functions to prevent build errors, but they are deprecated and a warning is logged if they are used (as the behavior of the Get... function is changed from a shallow copy to a deep copy). This API change required changing of a lot of file in the Slicer core and extensions.

Minor fixes:
* Made vtkMRMLTransformNode non-abstract: this is the class that can handle arbitrarily complex composite transforms (e.g., grid transform hardened on a bspline transform).
* Fixed invalid NonLinearTransformScene.mrml scene: wrong storage node ref ID caused warnings in the tests
* Changed the Bspline-f-m.tfm test data to include larger bulk component to make errors more detectable
* Added tests for composite transforms (e.g., hardened combination of grid and bspline transform)
* Split the transform node's huge read/write methods to separate smaller methods (one for each transform type)
* Added the option of loading a .mha file as a grid transform

Extensions updated according to the API change: OpenIGTLinkIF, SlicerIGT, SlicerRT, and TransformVisualizer. See details at:
https://github.com/openigtlink/OpenIGTLinkIF/pull/25
https://github.com/SlicerIGT/FiducialRegistrationWizard/pull/14
https://github.com/SlicerIGT/BreachWarning/pull/1
https://github.com/SlicerIGT/PivotCalibration/pull/13
https://github.com/SlicerIGT/TransformFusion/pull/2
https://www.assembla.com/spaces/slicerrt/tickets/563

Tests performed:

* All automatic tests passed (except those that are known to fail in the nightly builds)

* Load MRBrainTumor1 & MRBrainTumor2 sample
* Create model of MRBrainTumor2, threshold=50
* Linear registration with BRAINS (fixed: MRBrainTumor1 & moving: MRBrainTumor2)
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume, checked on several slices
* Save the transform as tfm from file, load the transform from file, apply the transform to the moving image
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume
* Apply transform to the model
* VERIFY: model is deformed in the 3D view, aligned with the volume slices
* Harden transform to the model
* VERIFY: model in the 3D view doesn’t change, model slice intersections are aligned with the volume
* Harden the transform on the volume
* VERIFY: the image doesn’t change too much

* BSpline registration with BRAINS (fixed: MRBrainTumor1 & moving: MRBrainTumor2)
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume
* Save the transform as tfm from file, load the transform from file, apply the transform to the moving image
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume
* Apply transform to the model
* VERIFY: model is deformed in the 3D view, aligned with the volume slices
* Harden transform to the model
* VERIFY: model in the 3D view doesn’t change, model slice intersections are aligned with the volume
* Insert linear transform between bspline and volume, move sliders
* VERIFY: volume deforms as it travels through the BSpline region
* Harden the transform on the volume
* VERIFY: the image doesn’t change too much

* Create a two markup list (each having 15 points), all but 3 in the same position
* Landwarp registration with Plastimatch with the markup lists, save the displacement field to file
* Load the displacement field
* VERIFY: the resampled output image should look the same as the dynamically transformed moving volume
* Apply the displacement field to the moving fiducials
* VERIFY: all the fiducials are now in the same position
* Harden the transform on the fiducials
* VERIFY: the fiducials don’t move
* Apply transform to the model
* VERIFY: model is deformed in the 3D view, aligned with the volume slices
* Harden transform to the model
* VERIFY: model in the 3D view doesn’t change, model slice intersections are aligned with the volume
* Harden the transform on the volume
* VERIFY: the image doesn’t change too much

* Load MRI head, create new linear transform, apply to the volume, move the sliders
* VERIFY: the volume moves in the slice viewer, the numbers change in the matrix
* Click Invert, Identity
* VERIFY: volume jumps to other side, to the center
* Connect to an OpenIGTLink server, apply a transform to a volume
* VERIFY: transform matrix values updated in transforms module, volume moves


git-svn-id: http://svn.slicer.org/Slicer4/trunk@23008 3bd1e089-480b-0410-8dfb-8563597acbee
mod - Base/Logic/vtkSlicerApplicationLogic.cxx Diff File
mod - Base/QTCore/qSlicerSlicer2SceneReader.cxx Diff File
mod - Base/QTCore/qSlicerXcedeCatalogReader.cxx Diff File
mod - Libs/MRML/Core/CMakeLists.txt Diff File
mod - Libs/MRML/Core/Testing/NonLinearTransformScene.mrml Diff File
mod - Libs/MRML/Core/Testing/TestData/Bspline-f-m.tfm Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLLinearTransformNodeEventsTest.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLNonlinearTransformNodeTest1.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLTransformNodeTest1.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLTransformableNodeOnNodeReferenceAddTest.cxx Diff File
mod - Libs/MRML/Core/Testing/vtkMRMLTransformableNodeTest1.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLBSplineTransformNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLBSplineTransformNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLCoreTestingMacros.h Diff File
mod - Libs/MRML/Core/vtkMRMLGridTransformNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLGridTransformNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLLinearTransformNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLLinearTransformNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLScene.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLTransformNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLTransformNode.h Diff File
mod - Libs/MRML/Core/vtkMRMLTransformStorageNode.cxx Diff File
mod - Libs/MRML/Core/vtkMRMLTransformStorageNode.h Diff File
mod - Libs/MRML/Logic/vtkMRMLSliceLogic.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLNodeComboBoxTest1.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLNodeComboBoxTest2.cxx Diff File
mod - Libs/MRML/Widgets/Testing/qMRMLNodeSelectorTest1.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLLinearTransformSlider.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLMatrixWidget.cxx Diff File
mod - Libs/MRML/Widgets/qMRMLUtils.cxx Diff File
mod - Libs/vtkITK/vtkITKBSplineTransform.cxx Diff File
mod - Libs/vtkITK/vtkITKBSplineTransform.h Diff File
mod - Modules/CLI/ACPCTransform/ACPCTransform.cxx Diff File
mod - Modules/Loadable/ModelMirror/Logic/vtkModelMirrorLogic.cxx Diff File
mod - Modules/Loadable/Models/Logic/vtkSlicerModelsLogic.cxx Diff File
mod - Modules/Loadable/Transforms/Testing/Cxx/qSlicerTransformsModuleWidgetTest.cxx Diff File
mod - Modules/Loadable/Transforms/qSlicerTransformsModuleWidget.cxx Diff File
mod - Modules/Loadable/Transforms/qSlicerTransformsReader.cxx Diff File
mod - Modules/Scripted/Endoscopy/Endoscopy.py Diff File
mod - SuperBuild.cmake Diff File
mod - Testing/TextureModel.py Diff File

Issue History

Date Modified Username Field Change
2014-03-03 12:41 lassoan New Issue
2014-03-03 13:27 lassoan Note Added: 0010666
2014-03-03 13:27 lassoan Note Added: 0010667
2014-03-05 02:43 lassoan Status new => assigned
2014-03-05 02:43 lassoan Assigned To => lassoan
2014-03-05 02:44 lassoan Note Added: 0010680
2014-03-05 14:45 lassoan Note Added: 0010686
2014-03-19 09:56 lassoan Note Added: 0011451
2014-03-19 09:57 lassoan Status assigned => resolved
2014-03-19 09:57 lassoan Resolution open => fixed
2014-03-26 08:50 jcfr Fixed in Version => Slicer 4.4.0
2014-03-26 08:50 jcfr Target Version => Slicer 4.4.0
2014-09-17 22:59 jcfr Status resolved => closed
2014-09-17 23:01 jcfr Note Added: 0012571
2017-06-10 08:51 lassoan Changeset attached => Slicer master 29dc6a68