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ENH: WIP: Issue Slicer#7179 Curved Planar Reformation
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Invoke vtkMRMLAbstractVolumeResampler interface
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@Leengit
Leengit committed Dec 17, 2024
1 parent 9681b95 commit aae2a6a
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Showing 2 changed files with 50 additions and 38 deletions.
86 changes: 49 additions & 37 deletions Libs/MRML/Logic/vtkMRMLSliceLogic.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -12,22 +12,25 @@
=========================================================================auto=*/

#if 0
// Includes that are not available
#include <vtkMRMLCommandLineModuleNode.h>
#include <vtkMRMLMarkupsCurveNode.h>
#include <vtkSlicerCLIModuleLogic.h>
#include <vtkSlicerMarkupsLogic.h>
#endif

// MRMLLogic includes
#include <vtkMRMLApplicationLogic.h>
#include <vtkMRMLSliceLayerLogic.h>
#include <vtkMRMLSliceLogic.h>

// SlicerLogic includes
#include <vtkSlicerCLIModuleLogic.h>
#include <vtkSlicerMarkupsLogic.h>

// MRML includes
#include <vtkMRMLCommandLineModuleNode.h>
#include <vtkMRMLAbstractVolumeResampler.h>
#include <vtkMRMLCrosshairNode.h>
#include <vtkMRMLGlyphableVolumeDisplayNode.h>
#include <vtkMRMLGlyphableVolumeSliceDisplayNode.h>
#include <vtkMRMLLinearTransformNode.h>
#include <vtkMRMLMarkupsCurveNode.h>
#include <vtkMRMLModelNode.h>
#include <vtkMRMLScalarVolumeDisplayNode.h>
#include <vtkMRMLScene.h>
Expand All @@ -39,6 +42,7 @@
#include <vtkAppendPolyData.h>
#include <vtkCollection.h>
#include <vtkCollectionIterator.h>
#include <vtkDoubleArray.h>
#include <vtkEventBroker.h>
#include <vtkGeneralTransform.h>
#include <vtkImageAppendComponents.h>
Expand All @@ -50,6 +54,7 @@
#include <vtkMath.h>
#include <vtkNew.h>
#include <vtkOrientedGridTransform.h>
#include <vtkParallelTransportFrame.h>
#include <vtkPlane.h>
#include <vtkPlaneSource.h>
#include <vtkPointData.h>
Expand Down Expand Up @@ -1054,14 +1059,13 @@ vtkMRMLSliceLogic::CurvedPlanarReformationGetPointsProjectedToPlane(vtkPoints *
// Returns points projected to the plane coordinate system (plane normal = plane Z axis).

// Compute the inverse transformation
vtkNew<vtkMatrix4x4> transformPlaneToWorld;
// TODO: Remove me vtkSmartPointer<vtkMatrix4x4> transformPlaneToWorld = vtkSmartPointer<vtkMatrix4x4>::New();
vtkSmartPointer<vtkMatrix4x4> transformPlaneToWorld = vtkSmartPointer<vtkMatrix4x4>::New();
vtkMatrix4x4::Invert(transformWorldToPlane, transformPlaneToWorld);

const vtkIdType numPoints = pointsArrayIn->GetNumberOfPoints();
double pIn[4] = { 0.0, 0.0, 0.0, 1.0 }; // TODO: Or should this be double[3]?
double pIn[4] = { 0.0, 0.0, 0.0, 1.0 }; // TODO: Or should this be double[3]?
double pMiddle[4] = { 0.0, 0.0, 0.0, 1.0 }; // TODO: Or should this be double[3]?
double pOut[4] = { 0.0, 0.0, 0.0, 1.0 }; // TODO: Or should this be double[3]?
double pOut[4] = { 0.0, 0.0, 0.0, 1.0 }; // TODO: Or should this be double[3]?

for (vtkIdType i = 0; i < numPoints; ++i)
{
Expand Down Expand Up @@ -1239,7 +1243,7 @@ vtkMRMLSliceLogic::CurvedPlanarReformationComputeStraighteningTransform(
sampledPoints->Reset();
if (!vtkMRMLMarkupsCurveNode::ResamplePoints(originalCurvePoints, sampledPoints, resamplingCurveSpacing, false))
{
throw std::runtime_error("Resampling curve failed"); // TODO: Or another response?
throw std::runtime_error("Resampling curve failed"); // TODO: Or some other response?
}
for (int i = resampledCurveNode->GetNumberOfControlPoints() - 1; i >= 0; --i)
{
Expand Down Expand Up @@ -1412,15 +1416,15 @@ vtkMRMLSliceLogic::CurvedPlanarReformationStraightenVolume(vtkMRMLScalarVolumeNo
if (!outputStraightenedVolume || !volumeNode || !straighteningTransformNode)
{
std::cerr << "Invalid input parameters." << std::endl;
return false; // TODO: Instead throw or similar?
return false; // TODO: Or some other response?
}

vtkOrientedGridTransform * gridTransform = vtkOrientedGridTransform::SafeDownCast(
straighteningTransformNode->GetTransformFromParentAs("vtkOrientedGridTransform"));
if (!gridTransform)
{
std::cerr << "Straightening transform must contain a vtkOrientedGridTransform from parent" << std::endl;
return false; // TODO: Instead throw or similar?
return false; // TODO: Or some other response?
}

// Get transformation grid geometry
Expand Down Expand Up @@ -1468,35 +1472,43 @@ vtkMRMLSliceLogic::CurvedPlanarReformationStraightenVolume(vtkMRMLScalarVolumeNo
outputStraightenedVolume->SetIJKToRASMatrix(straightenedVolumeIJKToRASMatrix);

// Resample input volume to straightened volume
vtkSmartPointer<vtkMRMLCommandLineModuleNode> parameterNode = vtkSmartPointer<vtkMRMLCommandLineModuleNode>::New();
this->GetMRMLScene()->AddNode(parameterNode); // TODO: Is some like this appropriate?
parameterNode->SetParameterAsString("inputVolume", volumeNode->GetID());
parameterNode->SetParameterAsString("outputVolume", outputStraightenedVolume->GetID());
parameterNode->SetParameterAsString("referenceVolume", outputStraightenedVolume->GetID());
parameterNode->SetParameterAsString("transformationFile", straighteningTransformNode->GetID());
// Use nearest neighbor interpolation for label volumes (to avoid incorrect labels at boundaries) and higher-order
// (bspline) interpolation for scalar volumes.
parameterNode->SetParameterAsString("interpolationType", volumeNode->IsA("vtkMRMLLabelMapVolumeNode") ? "nn" : "bs");
// resamplerModule = slicer.modules.resamplescalarvectordwivolume
// module = app.moduleManager().module(moduleName)
// logic = getModuleGui(module).logic
// logic = module.logic()
vtkSlicerCLIModuleLogic * resamplerModule = vtkSlicerCLIModuleLogic::SafeDownCast(
this->GetMRMLApplicationLogic()->GetModuleLogic("ResampleScalarVectorDWIVolume"));
if (!resamplerModule)
{
std::cerr << "Failed to get CLI logic for module: ResampleScalarVectorDWIVolume" << std::endl;
return false; // TODO: Instead throw or similar?
}
resamplerModule->ApplyAndWait(parameterNode); // TODO: Is this right?
vtkMRMLApplicationLogic * appLogic = this->GetMRMLApplicationLogic();
std::string resampleScalarVectorDWIVolume = "ResampleScalarVectorDWIVolume";
vtkSmartPointer<vtkMRMLAbstractVolumeResampler> abstractResampler;
if (!appLogic->IsVolumeResamplerRegistered(resampleScalarVectorDWIVolume))
{
abstractResampler = vtkSmartPointer<vtkMRMLAbstractVolumeResampler>::New(); // TODO: This fails. Bug or should we do this another way?
appLogic->RegisterVolumeResampler(resampleScalarVectorDWIVolume, abstractResampler);
if (!appLogic->IsVolumeResamplerRegistered(resampleScalarVectorDWIVolume))
{
std::cerr << "Failed to get CLI logic for module: " << resampleScalarVectorDWIVolume << std::endl;
return false; // TODO: Or some other response?
}
}
vtkMRMLScalarVolumeNode * inputVolume = volumeNode;
vtkMRMLScalarVolumeNode * outputVolume = outputStraightenedVolume;
vtkMRMLTransformNode * resamplingTransform = straighteningTransformNode;
std::string interpolationType = (volumeNode->IsA("vtkMRMLLabelMapVolumeNode") ? "nn" : "bs");
vtkMRMLScalarVolumeNode * referenceVolume = outputStraightenedVolume;
vtkMRMLAbstractVolumeResampler::ResamplingParameters resamplingParameters;
resamplingParameters["inputVolume"] = inputVolume->GetID();
resamplingParameters["outputVolume"] = outputVolume->GetID();
resamplingParameters["referenceVolume"] = referenceVolume->GetID();
resamplingParameters["transformationFile"] = resamplingTransform->GetID();
resamplingParameters["interpolationType"] = interpolationType;
bool success = appLogic->ResampleVolume(resampleScalarVectorDWIVolume,
inputVolume,
outputVolume,
resamplingTransform,
resamplingParameters,
referenceVolume);

outputStraightenedVolume->CreateDefaultDisplayNodes();
vtkMRMLDisplayNode * volumeDisplayNode = volumeNode->GetDisplayNode();
if (volumeDisplayNode)
{
outputStraightenedVolume->GetDisplayNode()->CopyContent(volumeDisplayNode);
}
this->GetMRMLScene()->RemoveNode(parameterNode);
return true;
}

Expand All @@ -1510,7 +1522,7 @@ vtkMRMLSliceLogic::CurvedPlanarReformationProjectVolume(vtkMRMLScalarVolumeNode

if ((projectionAxisIndex < 0) || (projectionAxisIndex >= 3))
{
return false; // TODO: Instead throw or similar?
return false; // TODO: Or some other response?
}

// Create a new vtkImageData for the projected volume
Expand All @@ -1521,7 +1533,7 @@ vtkMRMLSliceLogic::CurvedPlanarReformationProjectVolume(vtkMRMLScalarVolumeNode
vtkImageData * straightenedImageData = inputStraightenedVolume->GetImageData();
if (!straightenedImageData)
{
return false; // TODO: Instead throw or similar?
return false; // TODO: Or some other response?
}

// Get the dimensions of the straightened volume
Expand Down
2 changes: 1 addition & 1 deletion Libs/MRML/Logic/vtkMRMLSliceLogic.h
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@

class vtkMRMLDisplayNode;
class vtkMRMLLinearTransformNode;
class vtkMRMLMarkupsCurveNode;
class vtkMRMLMarkupsCurveNode; //TODO: Not available
class vtkMRMLModelDisplayNode;
class vtkMRMLModelNode;
class vtkMRMLScalarVolumeNode;
Expand Down

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