Removing resample.py/available from labkeySlicerPythonAPI/utils

cardiacSPECT/resample.py

@@ -1,442 +0,0 @@
-import slicer
-import vtk
-import os
-from slicer.ScriptedLoadableModule import *
-import ctk
-import qt
-
-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)
-
-    datasetCollapsibleButton = ctk.ctkCollapsibleButton()
-    datasetCollapsibleButton.text = "Dataset"
-    self.layout.addWidget(datasetCollapsibleButton)
-    # Layout within the dummy collapsible button
-    datasetFormLayout = qt.QFormLayout(datasetCollapsibleButton)
-
-    self.transformNode=qt.QLineEdit("NodeToTransform")
-    datasetFormLayout.addRow("TransformedNode:",self.transformNode)
-    self.referenceNode=qt.QLineEdit("ReferenceNode")
-    datasetFormLayout.addRow("ReferenceNode:",self.referenceNode)
-
-    self.transformButton=qt.QPushButton("Transform")
-    self.transformButton.clicked.connect(self.onTransformButtonClicked)
-    datasetFormLayout.addRow("Volume:",self.transformButton)
-
-    self.transformSegmentationButton=qt.QPushButton("Transform")
-    self.transformSegmentationButton.clicked.connect(self.onTransformSegmentationButtonClicked)
-    datasetFormLayout.addRow("Segmentation:",self.transformSegmentationButton)
-
-
-  def onTransformButtonClicked(self):
-    node=slicer.util.getFirstNodeByName(self.transformNode.text)
-    if node==None:
-        print("Transform node [{}] not found").format(self.transformNode.text)
-        return
-    refNode=slicer.util.getFirstNodeByName(self.referenceNode.text)
-    if refNode==None:
-        print("Reference node [{}] not found").format(self.referenceNode.text)
-        return
-
-    self.logic.rebinNode(node,refNode)
-
-  def onTransformSegmentationButtonClicked(self):
-
-      segNodes=slicer.util.getNodesByClass("vtkMRMLSegmentationNode")
-      segNode=None
-      for s in segNodes:
-          print ("SegmentationNode: {}").format(s.GetName())
-          if s.GetName()==self.transformNode.text:
-              segNode=s
-              break
-
-      if segNode==None:
-          print("Segmentation node [{}] not found").format(self.transformNode.text)
-          return
-
-      refNode=slicer.util.getFirstNodeByName(self.referenceNode.text)
-      if refNode==None:
-          print("Reference node [{}] not found").format(self.referenceNode.text)
-          return
-
-      self.logic.rebinSegmentation(segNode,refNode)
-
-
-
-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)
-      try:
-          fhome=os.environ["HOME"]
-      except:
-             #in windows, the variable is called HOMEPATH
-          fhome=os.environ['HOMEDRIVE']+os.environ['HOMEPATH']
-      self.baseLog=os.path.join(fhome,".resample")
-      if not os.path.isdir(self.baseLog):
-          os.mkdir(self.baseLog)
-
-  def printMe(self):
-      print("resampleLogic ready")
-      print("Log: {}").format(self.baseLog)
-
-
-  def cast(self,newImage,originalImage):
-      if newImage.GetPointData().GetScalars().GetDataType()==originalImage.GetPointData().GetScalars().GetDataType():
-          return newImage
-      outputType=originalImage.GetPointData().GetScalars().__class__.__name__
-      shifter=vtk.vtkImageShiftScale()
-      shifter.SetInputData(newImage)
-      if outputType=="vtkUnsignedShortArray":
-          shifter.SetOutputScalarTypeToUnsignedShort()
-      if outputType=="vtkShortArray":
-          shifter.SetOutputScalarTypeToShort()
-      shifter.SetScale(1)
-      shifter.SetShift(0)
-      shifter.Update()
-      return shifter.GetOutput()
-
-
-
-  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())
-
-      log=open(os.path.join(self.baseLog,"rebinNode.log"),"w")
-
-
-      log.write(("rebinNode: volume: {} ref: {}\n").format(node.GetName(),refNode.GetName()))
-      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())
-      newImage=self.cast(newImage,node.GetImageData())
-      newScalars=newImage.GetPointData().GetScalars()
-      #doesn't set the scalars
-      log.write(("Iterating: {} points\n").format(n))
-
-
-      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)
-            if i%10000==0:
-                log.write(("[{}]: {}->{}\n").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)
-      log.write(("Adding node {}\n").format(newNode.GetName()))
-      log.close()
-      return newNode
-
-
-  def inMask(self,binaryRep,fpos):
-
-       local=[0,0,0]
-
-       segNode=binaryRep['node']
-       segNode.TransformPointFromWorld(fpos,local)
-
-       mask=binaryRep['mask']
-       maskWorldToImageMatrix=vtk.vtkMatrix4x4()
-       mask.GetWorldToImageMatrix(maskWorldToImageMatrix)
-       local.append(1)
-       maskIJK=maskWorldToImageMatrix.MultiplyPoint(local)
-       #mask IJK is in image coordinates. However, binaryLabelMap is a truncated
-       #version of vtkImageData, so more work is required
-       maskIJK=maskIJK[0:3]#skip last (dummy) coordinate
-       maskIJK=[r*s for r,s in zip(maskIJK,mask.GetSpacing())]
-       maskIJK=[r+c for r,c in zip(maskIJK,mask.GetOrigin())]
-
-       maskI=mask.FindPoint(maskIJK)
-       try:
-           return mask.GetPointData().GetScalars().GetTuple1(maskI)
-       except:
-           return 0
-
-  def rebinSegment(self,refNode,binaryRep):
-
-       refIJKtoRAS=vtk.vtkMatrix4x4()
-       refNode.GetIJKToRASMatrix(refIJKtoRAS)
-       refImage=refNode.GetImageData()
-
-       #create new node for each segment
-       newImage=vtk.vtkImageData()
-       newImage.DeepCopy(refNode.GetImageData())
-       n=newImage.GetNumberOfPoints()
-       newScalars=newImage.GetPointData().GetScalars()
-
-       segNode=binaryRep['node']
-       mask=binaryRep['mask']
-
-       for j in range(0,n):
-           refIJK=refImage.GetPoint(j)
-           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)
-
-           v=self.inMask(binaryRep,fWorld)
-           #print("[{}]  Setting ({}) to: {}\n").format(j,fWorld,v)
-           newScalars.SetTuple1(j,v)
-
-       newNode=slicer.vtkMRMLScalarVolumeNode()
-       newNode.SetName(segNode.GetName()+'_'+binaryRep['segId'])
-       newNode.SetOrigin(refNode.GetOrigin())
-       newNode.SetSpacing(refNode.GetSpacing())
-       newNode.SetIJKToRASMatrix(refIJKtoRAS)
-
-       newNode.SetAndObserveImageData(newImage)
-       slicer.mrmlScene.AddNode(newNode)
-       return newNode
-
-
-  def rebinSegmentation(self,segNode,refNode):
-
-       log=open(os.path.join(self.baseLog,"rebinSegmentation.log"),"w")
-
-       log.write(("rebinNode: {} {}\n").format(segNode.GetName(),refNode.GetName()))
-
-       nSeg=segNode.GetSegmentation().GetNumberOfSegments()
-       ## DEBUG:
-       #nSeg=1
-       #n=1000
-
-       for i in range(0,nSeg):
-           #segID
-           segID=segNode.GetSegmentation().GetNthSegmentID(i)
-           log.write(("Parsing segment {}").format(segNode.GetSegmentation.GetNthSegment(i).GetName()))
-           binaryRep={'node':segNode,
-                      'mask':segNode.GetBinaryLabelmapRepresentation(segID)}
-           newNode=self.rebinSegment(refNode,binaryRep)
-           log.write(("Adding node: {}").format(newNode.GetName()))
-
-       log.close()
-
-  def rebinSegmentation1(self,segNode,refNode):
-
-
-     logfile="C:\\Users\\studen\\labkeyCache\\log\\resample.log"
-     print("rebinNode: {} {}\n").format(segNode.GetName(),refNode.GetName())
-     refImage=refNode.GetImageData()
-     refIJKtoRAS=vtk.vtkMatrix4x4()
-     refNode.GetIJKToRASMatrix(refIJKtoRAS)
-     refRAStoIJK=vtk.vtkMatrix4x4()
-     refNode.GetRASToIJKMatrix(refRAStoIJK)
-
-     nSeg=segNode.GetSegmentation().GetNumberOfSegments()
-     ## DEBUG:
-     nSeg=1
-
-     for i in range(0,nSeg):
-         #segID
-         segID=segNode.GetSegmentation().GetNthSegmentID(i)
-         binaryRep={'node':segNode,
-                    'mask': segNode.GetBinaryLabelmapRepresentation(segID)}
-
-         mask=binaryRep['mask']
-         #create new node for each segment
-         newImage=vtk.vtkImageData()
-         newImage.DeepCopy(refNode.GetImageData())
-         newScalars=newImage.GetPointData().GetScalars()
-         refN=newImage.GetNumberOfPoints()
-         for k in range(0,refN):
-             newScalars.SetTuple1(k,0)
-
-         maskN=binaryRep['mask'].GetNumberOfPoints()
-         maskScalars=mask.GetPointData().GetScalars()
-         maskImageToWorldMatrix=vtk.vtkMatrix4x4()
-         binaryRep['mask'].GetImageToWorldMatrix(maskImageToWorldMatrix)
-
-         for j in range(0,maskN):
-
-             if maskScalars.GetTuple1(j)==0:
-                 continue
-
-             maskIJK=mask.GetPoint(j)
-             maskIJK=[r-c for r,c in zip(maskIJK,mask.GetOrigin())]
-             maskIJK=[r/s for r,s in zip(maskIJK,mask.GetSpacing())]
-             maskIJK.append(1)
-             maskPos=maskImageToWorldMatrix.MultiplyPoint(maskIJK)
-             maskPos=maskPos[0:3]
-             fWorld=[0,0,0]
-             #apply segmentation transformation
-             segNode.TransformPointToWorld(maskPos,fWorld)
-
-             refPos=[0,0,0]
-
-             #apply potential reference transformations
-             refNode.TransformPointFromWorld(fWorld,refPos)
-             refPos.append(1)
-             refIJK=refRAStoIJK.MultiplyPoint(refPos)
-             refIJK=refIJK[0:3]
-             i1=newImage.FindPoint(refIJK)
-             if i1<0:
-                 continue
-             if i1<refN:
-                 newScalars.SetTuple1(i1,1)
-
-         newNode=slicer.vtkMRMLScalarVolumeNode()
-         newNode.SetName(segNode.GetName()+'_'+segNode.GetSegmentation().GetNthSegmentID(i))
-         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!')