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#! /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.
"""
from vtkmodules.vtkIOImage import (
vtkNIFTIImageReader,
vtkNIFTIImageWriter,
)
from vtkmodules.vtkImagingMath import vtkImageMathematics
from vtkmodules.vtkInteractionStyle import vtkInteractorStyleImage
from vtkmodules.vtkRenderingCore import (
vtkImageSlice,
vtkImageSliceMapper,
vtkRenderWindow,
vtkRenderWindowInteractor,
vtkRenderer,
)
import vtkmodules.vtkInteractionStyle
import vtkmodules.vtkRenderingFreeType
import vtkmodules.vtkRenderingOpenGL2
from vtkmodules.util.misc import vtkGetDataRoot
from vtkmodules.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(VTK_DATA_ROOT, "Data", file1)
reader = 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 = vtkImageSliceMapper()
map1.BorderOn()
map1.SliceAtFocalPointOn()
map1.SliceFacesCameraOn()
map1.SetInputConnection(reader.GetOutputPort())
map2 = vtkImageSliceMapper()
map2.BorderOn()
map2.SliceAtFocalPointOn()
map2.SliceFacesCameraOn()
map2.SetInputConnection(reader.GetOutputPort())
slice1 = vtkImageSlice()
slice1.SetMapper(map1)
slice1.GetProperty().SetColorWindow(vrange[1]-vrange[0])
slice1.GetProperty().SetColorLevel(0.5*(vrange[0]+vrange[1]))
slice2 = 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 = vtkRenderer()
ren1.SetViewport(0,0,ratio,1.0)
ren2 = 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 = vtkInteractorStyleImage()
style.SetInteractionModeToImageSlicing()
iren = vtkRenderWindowInteractor()
iren.SetInteractorStyle(style)
renwin = vtkRenderWindow()
renwin.SetSize((size[0] + size[2]) // 2 * 2, size[1] // 2 * 2) # keep size even
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(VTK_DATA_ROOT, "Data", infile)
outpath = os.path.join(str(VTK_TEMP_DIR), outfile)
# read a NIFTI file
reader = vtkNIFTIImageReader()
reader.SetFileName(inpath)
reader.TimeAsVectorOn()
reader.Update()
writer = vtkNIFTIImageWriter()
writer.SetInputConnection(reader.GetOutputPort())
writer.SetFileName(outpath)
# copy most information directory 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 = vtkNIFTIImageReader()
reader2.SetFileName(outpath)
reader2.TimeAsVectorOn()
reader2.Update()
diff = 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)
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