ParaView-5.0.1: Added the source-tree to ThirdParty-dev and patched as described in the README file

Resolves bug-report http://bugs.openfoam.org/view.php?id=2098

ParaView-5.0.1/VTK/IO/Image/Testing/Python/TestNIFTIReaderWriter.py

@@ -0,0 +1,154 @@
+#! /usr/bin/env python
+
+"""
+Test NIFTI support in VTK by reading a file, writing it, and
+then re-reading it to ensure that the contents are identical.
+"""
+
+import vtk
+from vtk.test import Testing
+from vtk.util.misc import vtkGetDataRoot
+from vtk.util.misc import vtkGetTempDir
+
+VTK_DATA_ROOT = vtkGetDataRoot()
+VTK_TEMP_DIR = vtkGetTempDir()
+
+import sys
+import os
+
+testfiles = [
+    ["minimal.nii.gz", "out_minimal.nii.gz"],
+    ["minimal.img.gz", "out_minimal.hdr"]
+]
+
+dispfile = "avg152T1_RL_nifti.nii.gz"
+
+def TestDisplay(file1):
+    """Display the output"""
+
+    inpath = os.path.join(str(VTK_DATA_ROOT), "Data", file1)
+
+    reader = vtk.vtkNIFTIImageReader()
+    reader.SetFileName(inpath)
+    reader.Update()
+
+    size = reader.GetOutput().GetDimensions()
+    center = reader.GetOutput().GetCenter()
+    spacing = reader.GetOutput().GetSpacing()
+    center1 = (center[0], center[1], center[2])
+    center2 = (center[0], center[1], center[2])
+    if size[2] % 2 == 1:
+        center1 = (center[0], center[1], center[2] + 0.5*spacing[2])
+    if size[0] % 2 == 1:
+        center2 = (center[0] + 0.5*spacing[0], center[1], center[2])
+    vrange = reader.GetOutput().GetScalarRange()
+
+    map1 = vtk.vtkImageSliceMapper()
+    map1.BorderOn()
+    map1.SliceAtFocalPointOn()
+    map1.SliceFacesCameraOn()
+    map1.SetInputConnection(reader.GetOutputPort())
+    map2 = vtk.vtkImageSliceMapper()
+    map2.BorderOn()
+    map2.SliceAtFocalPointOn()
+    map2.SliceFacesCameraOn()
+    map2.SetInputConnection(reader.GetOutputPort())
+
+    slice1 = vtk.vtkImageSlice()
+    slice1.SetMapper(map1)
+    slice1.GetProperty().SetColorWindow(vrange[1]-vrange[0])
+    slice1.GetProperty().SetColorLevel(0.5*(vrange[0]+vrange[1]))
+    slice2 = vtk.vtkImageSlice()
+    slice2.SetMapper(map2)
+    slice2.GetProperty().SetColorWindow(vrange[1]-vrange[0])
+    slice2.GetProperty().SetColorLevel(0.5*(vrange[0]+vrange[1]))
+
+    ratio = size[0]*1.0/(size[0]+size[2])
+
+    ren1 = vtk.vtkRenderer()
+    ren1.SetViewport(0,0,ratio,1.0)
+    ren2 = vtk.vtkRenderer()
+    ren2.SetViewport(ratio,0.0,1.0,1.0)
+    ren1.AddViewProp(slice1)
+    ren2.AddViewProp(slice2)
+
+    cam1 = ren1.GetActiveCamera()
+    cam1.ParallelProjectionOn()
+    cam1.SetParallelScale(0.5*spacing[1]*size[1])
+    cam1.SetFocalPoint(center1[0], center1[1], center1[2])
+    cam1.SetPosition(center1[0], center1[1], center1[2] - 100.0)
+
+    cam2 = ren2.GetActiveCamera()
+    cam2.ParallelProjectionOn()
+    cam2.SetParallelScale(0.5*spacing[1]*size[1])
+    cam2.SetFocalPoint(center2[0], center2[1], center2[2])
+    cam2.SetPosition(center2[0] + 100.0, center2[1], center2[2])
+
+    if "-I" in sys.argv:
+        style = vtk.vtkInteractorStyleImage()
+        style.SetInteractionModeToImageSlicing()
+
+        iren = vtk.vtkRenderWindowInteractor()
+        iren.SetInteractorStyle(style)
+
+    renwin = vtk.vtkRenderWindow()
+    renwin.SetSize(size[0] + size[2], size[1])
+    renwin.AddRenderer(ren1)
+    renwin.AddRenderer(ren2)
+
+    renwin.Render()
+
+    if "-I" in sys.argv:
+        renwin.SetInteractor(iren)
+        iren.Initialize()
+        iren.Start()
+
+    return renwin
+
+def TestReadWriteRead(infile, outfile):
+    """Read, write, and re-read a file, return difference."""
+
+    inpath = os.path.join(str(VTK_DATA_ROOT), "Data", infile)
+    outpath = os.path.join(str(VTK_TEMP_DIR), outfile)
+
+    # read a NIFTI file
+    reader = vtk.vtkNIFTIImageReader()
+    reader.SetFileName(inpath)
+    reader.TimeAsVectorOn()
+    reader.Update()
+
+    writer = vtk.vtkNIFTIImageWriter()
+    writer.SetInputConnection(reader.GetOutputPort())
+    writer.SetFileName(outpath)
+    # copy most information directoy from the header
+    writer.SetNIFTIHeader(reader.GetNIFTIHeader())
+    # this information will override the reader's header
+    writer.SetQFac(reader.GetQFac())
+    writer.SetTimeDimension(reader.GetTimeDimension())
+    writer.SetQFormMatrix(reader.GetQFormMatrix())
+    writer.SetSFormMatrix(reader.GetSFormMatrix())
+    writer.Write()
+
+    reader2 = vtk.vtkNIFTIImageReader()
+    reader2.SetFileName(outpath)
+    reader2.TimeAsVectorOn()
+    reader2.Update()
+
+    diff = vtk.vtkImageMathematics()
+    diff.SetOperationToSubtract()
+    diff.SetInputConnection(0,reader.GetOutputPort())
+    diff.SetInputConnection(1,reader2.GetOutputPort())
+    diff.Update()
+    diffrange = diff.GetOutput().GetScalarRange()
+    differr = diffrange[0]**2 + diffrange[1]**2
+
+    return differr
+
+for infile, outfile in testfiles:
+    err = TestReadWriteRead(infile, outfile)
+    if err:
+        sys.stderr.write(
+            "Input " + infile + " differs from outfile " + outfile)
+        sys.exit(1)
+
+renWin = TestDisplay(dispfile)