Adding vtkInterface

vtkInterface/vtkInterface.py

@@ -0,0 +1,111 @@
+import vtk, qt, ctk, slicer
+import numpy as np
+import SimpleITK as sitk
+
+#set of routines to transform images from one form to another, most notably
+#numpy to vtk to itk and all possible combinations inbetween. Keep track of
+#orientation, origin and spacing between transforms
+
+class vtkInterface:
+  def __init__(self, parent):
+    #parent.title = "vtk Interface"
+    #parent.categories = ["LabKey"]
+    parent.dependencies = []
+    parent.title ="vtkInterface"
+    parent.contributors = ["Andrej Studen (FMF/JSI)"] # replace with "Firstname Lastname (Org)"
+    parent.helpText = """
+    Convert native numpy data structures to vtk
+    """
+    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 = parent
+
+
+def numpyToVTK(numpy_array, shape, data_type=vtk.VTK_FLOAT):
+    v=vtk.vtkImageData()
+    v.GetPointData().SetScalars(
+        vtk.util.numpy_support.numpy_to_vtk(
+            np.ravel(numpy_array,order='F'),deep=True, array_type=data_type))
+    v.SetOrigin(0,0,0)
+    v.SetSpacing(1,1,1)
+    v.SetDimensions(shape)
+    return v
+
+
+def completeOrientation(orientation):
+    o=orientation
+    o.append(o[1]*o[5]-o[2]*o[4])#0,3
+    o.append(o[2]*o[3]-o[0]*o[5])#1,4
+    o.append(o[0]*o[4]-o[1]*o[3])#2,5
+    return o
+
+
+def ITK2VTK(img):
+    #convert itk to vtk format.
+    #get the array
+    data=sitk.GetArrayFromImage(img)
+    #reverse the shape (don't ask, look at vtk manual if really curios)
+    shape=list(reversed(data.shape))
+    return numpyToVTK(data.ravel(),shape)
+
+def VTK2ITK(v):
+    #convert vtk image to sitk image
+    #convert to numpy first and then go to sitk
+    scalars=v.GetPointData().GetScalars()
+    shape=v.GetDimensions()
+    data=vtk.util.numpy_support.vtk_to_numpy(scalars)
+    #now convert to sitk (notice the little reversal of the shape)
+    return sitk.GetImageFromArray(np.reshape(data,list(reversed(shape))))
+
+def ITKfromNode(nodeName):
+    #use node as data source and generate an itk image
+    node=slicer.mrmlScene.GetFirstNodeByName(nodeName)
+    if node==None:
+        print("Node {0} not available".format(nodeName))
+        return
+
+    img=VTK2ITK(node.GetImageData())
+
+    img.SetOrigin(node.GetOrigin())
+    img.SetSpacing(node.GetSpacing())
+    m=vtk.vtkMatrix4x4()
+    node.GetIJKToRASDirectionMatrix(m)
+    orientation=[0]*9
+    for i in range(0,3):
+        for j in range (0,3):
+            orientation[3*j+i]=m.GetElement(i,j)
+    img.SetDirection(orientation)
+    return img
+
+
+
+def ITKtoNode(img,nodeName):
+    #display itk image and assign it a volume node
+    #useful for displaying outcomes of itk calculations
+    node=slicer.mrmlScene.GetFirstNodeByName(nodeName)
+    if node==None:
+        node=slicer.vtkMRMLScalarVolumeNode()
+        node.SetName(nodeName)
+        slicer.mrmlScene.AddNode(node)
+
+    node.SetAndObserveImageData(ITK2VTK(img))
+
+    #hairy - keep orientation, spacing and origin from node and pass it to itk
+    #for future reference
+    spacing=img.GetSpacing()
+    orientation=img.GetDirection()
+    origin=img.GetOrigin()
+
+    #we should get orientation, spacing and origin from somewhere
+    ijkToRAS = vtk.vtkMatrix4x4()
+    
+    for i in range(0,3):
+       for j in range(0,3):
+           ijkToRAS.SetElement(i,j,spacing[i]*orientation[3*j+i])
+
+       ijkToRAS.SetElement(i,3,origin[i])
+
+    node.SetIJKToRASMatrix(ijkToRAS)