import slicer import vtk import os from slicer.ScriptedLoadableModule import * class resample(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): ScriptedLoadableModule.__init__(self, parent) parent.title = "Resample" parent.categories = ["Examples"] parent.dependencies = [] parent.contributors = ["Andrej Studen (FMF/JSI)"] # replace with "Firstname Lastname (Org)" parent.helpText = """ Resample to different shapes """ parent.acknowledgementText = """ This module was developed within the frame of the ARRS sponsored medical physics research programe to investigate quantitative measurements of cardiac function using sestamibi-like tracers """ # replace with organization, grant and thanks. self.parent.helpText += self.getDefaultModuleDocumentationLink() self.parent = parent # # resampleWidget # class resampleWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): ScriptedLoadableModuleWidget.setup(self) self.logic=resampleLogic(self) class resampleLogic(ScriptedLoadableModuleLogic): """This class should implement all the actual computation done by your module. The interface should be such that other python code can import this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self,parent): ScriptedLoadableModuleLogic.__init__(self, parent) def printMe(self): print("resampleLogic ready") def rebinNode(self,node,refNode): #refNodeName="2SBMIRVolume19" #nodeName="2SMobrVolume19" #node=slicer.util.getFirstNodeByName(nodeName) #refNode=slicer.util.getFirstNodeByName(refNodeName) #transformNodeName="2SMobr_DF" #transformNode=slicer.util.getFirstNodeByName(transformNodeName) #node.SetAndObserveTransformNodeID(transformNode.GetID()) print("rebinNode: {} {}").format(node,refNode) refImage=refNode.GetImageData() n=refImage.GetNumberOfPoints() refIJKtoRAS=vtk.vtkMatrix4x4() refNode.GetIJKToRASMatrix(refIJKtoRAS) nodeRAStoIJK=vtk.vtkMatrix4x4() node.GetRASToIJKMatrix(nodeRAStoIJK) nodeName=node.GetName() coeff=vtk.vtkImageBSplineCoefficients() coeff.SetInputData(node.GetImageData()) coeff.SetBorderMode(vtk.VTK_IMAGE_BORDER_CLAMP) #between 3 and 5 coeff.SetSplineDegree(5) coeff.Update() #interpolation ready to use #this is tought. COpy only links (ie. shallow copy) newImage=vtk.vtkImageData() newImage.DeepCopy(refNode.GetImageData()) newScalars=newImage.GetPointData().GetScalars() #doesn't set the scalars for i in range(0,n): refIJK=refImage.GetPoint(i) refIJK=list(refIJK) refIJK.append(1) #shift to world coordinates to match global points refPos=refIJKtoRAS.MultiplyPoint(refIJK) refPos=refPos[0:3] fWorld=[0,0,0] #apply potential transformations refNode.TransformPointToWorld(refPos,fWorld) #now do the opposite on the target node; reuse fPos nodePos=[0,0,0] node.TransformPointFromWorld(fWorld,nodePos) nodePos.append(1) nodeIJK=nodeRAStoIJK.MultiplyPoint(nodePos) #here we should apply some sort of interpolation nodeIJK=nodeIJK[0:3] v=coeff.Evaluate(nodeIJK) v0=newScalars.GetTuple1(i) newScalars.SetTuple1(i,v) #print("[{}]: {}->{}").format(i,v0,v) node.SetName(nodeName+"_BU") newNode=slicer.vtkMRMLScalarVolumeNode() newNode.SetName(nodeName) newNode.SetOrigin(refNode.GetOrigin()) newNode.SetSpacing(refNode.GetSpacing()) newNode.SetIJKToRASMatrix(refIJKtoRAS) newNode.SetAndObserveImageData(newImage) slicer.mrmlScene.AddNode(newNode) class resampleTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): """ Do whatever is needed to reset the state - typically a scene clear will be enough. """ slicer.mrmlScene.Clear(0) refNodeName="2SBMIRVolume19" nodeName="2SMobrVolume19" transformNodeName="2SMobr_DF" path="c:\\Users\\studen\\labkeyCache\\dinamic_spect\\Patients\\@files" refPath=os.path.join(path,"2SBMIR") refPath=os.path.join(refPath,refNodeName+".nrrd") slicer.util.loadNodeFromFile(refPath,'VolumeFile') transformPath=os.path.join(path,"2SMobr") transformPath=os.path.join(transformPath,transformNodeName+".h5") slicer.util.loadNodeFromFile(transformPath,'TransformFile') nodePath=os.path.join(path,"2SMobr") nodePath=os.path.join(nodePath,nodeName+".nrrd") slicer.util.loadNodeFromFile(nodePath,'VolumeFile') self.node=slicer.util.getFirstNodeByName(nodeName) self.refNode=slicer.util.getFirstNodeByName(refNodeName) self.transformNode=slicer.util.getFirstNodeByName(transformNodeName) self.node.SetAndObserveTransformNodeID(self.transformNode.GetID()) self.resampler=resampleLogic(None) def runTest(self): """Run as few or as many tests as needed here. """ self.setUp() self.test_resample() def test_resample(self): """ Ideally you should have several levels of tests. At the lowest level tests should exercise the functionality of the logic with different inputs (both valid and invalid). At higher levels your tests should emulate the way the user would interact with your code and confirm that it still works the way you intended. One of the most important features of the tests is that it should alert other developers when their changes will have an impact on the behavior of your module. For example, if a developer removes a feature that you depend on, your test should break so they know that the feature is needed. """ self.delayDisplay("Starting the test") # # first, get some data # self.resampler.rebinNode(self.node,self.refNode) self.delayDisplay('Test passed!')