def transform_polydata_from_disk(in_filename, transform_filename, out_filename):
# Read it in.
print "<io.py> Transforming ", in_filename, "->", out_filename, "..."
# Read the transform from disk because we cannot pickle it
(root, ext) = os.path.splitext(transform_filename)
print root, ext
if ext == '.xfm':
reader = vtk.vtkMNITransformReader()
reader.SetFileName(transform_filename)
reader.Update()
transform = reader.GetTransform()
elif ext == '.img':
reader = vtk.vtkImageReader()
reader.SetFileName(transform_filename)
reader.Update()
coeffs = reader.GetOutput()
transform = vtk.vtkBSplineTransform()
transform.SetCoefficients(coeffs)
print coeffs
print transform
else:
f = open(transform_filename, 'r')
transform = vtk.vtkTransform()
matrix = vtk.vtkMatrix4x4()
for i in range(0,4):
for j in range(0,4):
matrix_val = float(f.readline())
matrix.SetElement(i,j, matrix_val)
transform.SetMatrix(matrix)
del matrix
start_time = time.time()
pd = read_polydata(in_filename)
elapsed_time = time.time() - start_time
print "READ:", elapsed_time
# Transform it.
start_time = time.time()
transformer = vtk.vtkTransformPolyDataFilter()
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
transformer.SetInputData(pd)
else:
transformer.SetInput(pd)
transformer.SetTransform(transform)
transformer.Update()
elapsed_time = time.time() - start_time
print "TXFORM:", elapsed_time
# Write it out.
start_time = time.time()
pd2 = transformer.GetOutput()
write_polydata(pd2, out_filename)
elapsed_time = time.time() - start_time
print "WRITE:", elapsed_time
# Clean up.
del transformer
del pd2
del pd
del transform
def transform_polydata_from_disk(in_filename, transform_filename, out_filename):
# Read it in.
print "<io.py> Transforming ", in_filename, "->", out_filename, "..."
# Read the transform from disk because we cannot pickle it
(root, ext) = os.path.splitext(transform_filename)
print root, ext
if ext == '.xfm':
reader = vtk.vtkMNITransformReader()
reader.SetFileName(transform_filename)
reader.Update()
transform = reader.GetTransform()
elif ext == '.img':
reader = vtk.vtkImageReader()
reader.SetFileName(transform_filename)
reader.Update()
coeffs = reader.GetOutput()
transform = vtk.vtkBSplineTransform()
transform.SetCoefficients(coeffs)
print coeffs
print transform
else:
f = open(transform_filename, 'r')
transform = vtk.vtkTransform()
matrix = vtk.vtkMatrix4x4()
for i in range(0,4):
for j in range(0,4):
matrix_val = float(f.readline())
matrix.SetElement(i,j, matrix_val)
transform.SetMatrix(matrix)
del matrix
start_time = time.time()
pd = read_polydata(in_filename)
elapsed_time = time.time() - start_time
print "READ:", elapsed_time
# Transform it.
start_time = time.time()
transformer = vtk.vtkTransformPolyDataFilter()
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
transformer.SetInputData(pd)
else:
transformer.SetInput(pd)
transformer.SetTransform(transform)
transformer.Update()
elapsed_time = time.time() - start_time
print "TXFORM:", elapsed_time
# Write it out.
start_time = time.time()
pd2 = transformer.GetOutput()
write_polydata(pd2, out_filename)
elapsed_time = time.time() - start_time
print "WRITE:", elapsed_time
# Clean up.
del transformer
del pd2
del pd
del transform
def pipeline(inputPolyDatas, sidx, args):
# get subject identifier from unique input filename
# -------------------
#subjectID = os.path.splitext(os.path.basename(inputPolyDatas[sidx]))[0]
fname = os.path.basename(inputPolyDatas[sidx])
print("<wm_preprocess.py> ", sidx + 1, "/", len(inputPolyDatas))
# read input vtk data
# -------------------
inpd = wma.io.read_polydata(inputPolyDatas[sidx])
# Read in the transform
reader = vtk.vtkMNITransformReader()
reader.SetFileName(args.transformFile)
reader.Update()
transform = reader.GetTransform()
if args.invert_flag == True:
transform.Inverse()
# Apply the transform
transformer = vtk.vtkTransformPolyDataFilter()
transformer.SetInput(inpd)
transformer.SetTransform(transform)
transformer.Update()
outpd = transformer.GetOutput()
# outputs
# -------------------
fname = os.path.join(args.outputDirectory, fname)
try:
print("Writing output polydata", fname, "...")
wma.io.write_polydata(outpd, fname)
except:
print("Unknown exception in IO")
raise
del outpd
del inpd
def pipeline(inputPolyDatas, sidx, args):
# get subject identifier from unique input filename
# -------------------
#subjectID = os.path.splitext(os.path.basename(inputPolyDatas[sidx]))[0]
fname = os.path.basename(inputPolyDatas[sidx])
print "<wm_preprocess.py> ", sidx + 1, "/", len(inputPolyDatas)
# read input vtk data
# -------------------
inpd = wma.io.read_polydata(inputPolyDatas[sidx])
# Read in the transform
reader = vtk.vtkMNITransformReader()
reader.SetFileName(args.transformFile)
reader.Update()
transform = reader.GetTransform()
if args.invert_flag == True:
transform.Inverse()
# Apply the transform
transformer = vtk.vtkTransformPolyDataFilter()
transformer.SetInput(inpd)
transformer.SetTransform(transform)
transformer.Update()
outpd = transformer.GetOutput()
# outputs
# -------------------
fname = os.path.join(args.outputDirectory, fname)
try:
print "Writing output polydata", fname, "..."
wma.io.write_polydata(outpd, fname)
except:
print "Unknown exception in IO"
raise
del outpd
del inpd
p2.SetPoint(5, 159, 159, 0)
p2.SetPoint(6, 159, 96, 0)
p2.SetPoint(7, 96, 96, 0)
thinPlate0 = vtk.vtkThinPlateSplineTransform()
thinPlate0.SetSourceLandmarks(p1)
thinPlate0.SetTargetLandmarks(p2)
thinPlate0.SetBasisToR2LogR()
# write the tps to a file
tpsWriter = vtk.vtkMNITransformWriter()
tpsWriter.SetFileName(filename)
tpsWriter.SetTransform(thinPlate0)
tpsWriter.Write()
# read it back
tpsReader = vtk.vtkMNITransformReader()
if (tpsReader.CanReadFile(filename) != 0):
tpsReader.SetFileName(filename)
thinPlate = tpsReader.GetTransform()
# make a linear transform
linearTransform = vtk.vtkTransform()
linearTransform.PostMultiply()
linearTransform.Translate(-127.5, -127.5, 0)
linearTransform.RotateZ(30)
linearTransform.Translate(+127.5, +127.5, 0)
# remove the linear part of the thin plate
tpsGeneral = vtk.vtkGeneralTransform()
tpsGeneral.SetInput(thinPlate)
p2.SetPoint(5, 159, 159, 0)
p2.SetPoint(6, 159, 96, 0)
p2.SetPoint(7, 96, 96, 0)
thinPlate0 = vtk.vtkThinPlateSplineTransform()
thinPlate0.SetSourceLandmarks(p1)
thinPlate0.SetTargetLandmarks(p2)
thinPlate0.SetBasisToR2LogR()
# write the tps to a file
tpsWriter = vtk.vtkMNITransformWriter()
tpsWriter.SetFileName(filename)
tpsWriter.SetTransform(thinPlate0)
tpsWriter.Write()
# read it back
tpsReader = vtk.vtkMNITransformReader()
if (tpsReader.CanReadFile(filename) != 0):
tpsReader.SetFileName(filename)
thinPlate = tpsReader.GetTransform()
# make a linear transform
linearTransform = vtk.vtkTransform()
linearTransform.PostMultiply()
linearTransform.Translate(-127.5, -127.5, 0)
linearTransform.RotateZ(30)
linearTransform.Translate(+127.5, +127.5, 0)
# remove the linear part of the thin plate
tpsGeneral = vtk.vtkGeneralTransform()
tpsGeneral.SetInput(thinPlate)
print("==========================")
# =======================================================================
# Above this line is argument parsing. Below this line is the pipeline.
# =======================================================================
# Loop over input DWIs
inputPolyDatas = wma.io.list_vtk_files(args.inputDirectory)
print("<wm_preprocess.py> Input number of files: ", len(inputPolyDatas))
# Read in the transform to print its contents for the user
reader = vtk.vtkMNITransformReader()
reader.SetFileName(args.transformFile)
reader.Update()
transform = reader.GetTransform()
print(transform)
def pipeline(inputPolyDatas, sidx, args):
# get subject identifier from unique input filename
# -------------------
#subjectID = os.path.splitext(os.path.basename(inputPolyDatas[sidx]))[0]
fname = os.path.basename(inputPolyDatas[sidx])
print("<wm_preprocess.py> ", sidx + 1, "/", len(inputPolyDatas))
# read input vtk data
# -------------------
inpd = wma.io.read_polydata(inputPolyDatas[sidx])
print "=========================="
# =======================================================================
# Above this line is argument parsing. Below this line is the pipeline.
# =======================================================================
# Loop over input DWIs
inputPolyDatas = wma.io.list_vtk_files(args.inputDirectory)
print "<wm_preprocess.py> Input number of files: ", len(inputPolyDatas)
# Read in the transform to print its contents for the user
reader = vtk.vtkMNITransformReader()
reader.SetFileName(args.transformFile)
reader.Update()
transform = reader.GetTransform()
print transform
def pipeline(inputPolyDatas, sidx, args):
# get subject identifier from unique input filename
# -------------------
#subjectID = os.path.splitext(os.path.basename(inputPolyDatas[sidx]))[0]
fname = os.path.basename(inputPolyDatas[sidx])
print "<wm_preprocess.py> ", sidx + 1, "/", len(inputPolyDatas)
# read input vtk data
# -------------------
inpd = wma.io.read_polydata(inputPolyDatas[sidx])