def test_nrrd_dwi_roundtrip(test_nrrd_path):
"""DWI NRRD round-trip test
- loads and saves a NRRD file via Slicer's I/O, twice
- checks the node values against the original file each time
"""
import tempfile
# load and re-save NRRD once
storagenode1 = slicer.vtkMRMLNRRDStorageNode()
storagenode1.SetFileName(test_nrrd_path)
dw_node1 = slicer.vtkMRMLDiffusionWeightedVolumeNode()
storagenode1.ReadData(dw_node1)
__f_tmp_nrrd1 = tempfile.NamedTemporaryFile(suffix=".nhdr",
dir=tmp_dir,
delete=False)
tmp_nrrd1 = __f_tmp_nrrd1.name
storagenode1.SetFileName(tmp_nrrd1)
storagenode1.WriteData(dw_node1)
parsed_nrrd2, dw_node2 = test_nrrd_dwi_load(test_nrrd_path, tmp_nrrd1)
# re-save NRRD again
storagenode2 = slicer.vtkMRMLNRRDStorageNode()
__f_tmp_nrrd2 = tempfile.NamedTemporaryFile(suffix=".nhdr",
dir=tmp_dir,
delete=False)
tmp_nrrd2 = __f_tmp_nrrd2.name
storagenode2.SetFileName(tmp_nrrd2)
storagenode2.WriteData(dw_node2)
# test twice-saved file against original NRRD
parsed_nrrd3, dw_node3 = test_nrrd_dwi_load(test_nrrd_path, tmp_nrrd2)
def test_nrrd_dwi_roundtrip(test_nrrd_path):
"""DWI NRRD round-trip test
- loads and saves a NRRD file via Slicer's I/O, twice
- checks the node values against the original file each time
"""
import tempfile
# load and re-save NRRD once
storagenode1 = slicer.vtkMRMLNRRDStorageNode()
storagenode1.SetFileName(test_nrrd_path)
dw_node1 = slicer.vtkMRMLDiffusionWeightedVolumeNode()
storagenode1.ReadData(dw_node1)
__f_tmp_nrrd1 = tempfile.NamedTemporaryFile(suffix=".nhdr", dir=tmp_dir, delete=False)
tmp_nrrd1 = __f_tmp_nrrd1.name
storagenode1.SetFileName(tmp_nrrd1)
storagenode1.WriteData(dw_node1)
parsed_nrrd2, dw_node2 = test_nrrd_dwi_load(test_nrrd_path, tmp_nrrd1)
# re-save NRRD again
storagenode2 = slicer.vtkMRMLNRRDStorageNode()
__f_tmp_nrrd2 = tempfile.NamedTemporaryFile(suffix=".nhdr", dir=tmp_dir, delete=False)
tmp_nrrd2 = __f_tmp_nrrd2.name
storagenode2.SetFileName(tmp_nrrd2)
storagenode2.WriteData(dw_node2)
# test twice-saved file against original NRRD
parsed_nrrd3, dw_node3 = test_nrrd_dwi_load(test_nrrd_path, tmp_nrrd2)
def computeSingleColormap(self, inputScan, inputSegmentation, CLIname,
valueDict, outputName):
parameters = dict(valueDict)
parameters["inputVolume"] = inputScan
parameters["inputMask"] = inputSegmentation
volumeNode = slicer.vtkMRMLDiffusionWeightedVolumeNode()
slicer.mrmlScene.AddNode(volumeNode)
displayNode = slicer.vtkMRMLDiffusionWeightedVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
colorNode = slicer.util.getNode('Rainbow')
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
volumeNode.SetName(outputName)
parameters["outputVolume"] = volumeNode
slicer.cli.run(CLIname, None, parameters, wait_for_completion=False)
def run_extract_to_bvals(tempdata, args):
"""
returns array of bvalues
"""
print("ExtractDWIShell runtests, running: " + repr(args))
proc = subprocess.Popen(args)
proc.wait()
if proc.returncode != 0:
print("ExtractDWIShells failed!")
sys.exit(-1)
# load NRRD into Slicer
sn = slicer.vtkMRMLNRRDStorageNode()
sn.SetFileName(tempdata)
dw_node = slicer.vtkMRMLDiffusionWeightedVolumeNode()
sn.ReadData(dw_node)
bvals = vtk.util.numpy_support.vtk_to_numpy(dw_node.GetBValues())
return bvals
def test_nrrd_dwi_load(first_file, second_file=None):
"""
- load a DWI NRRD file into Slicer
- validate b values and gradient vectors against original header
- check the values in the vtkMRMLDiffusionWeightedVolumeNode
- check the values in the vtkMRMLDWVNode attribute dictionary
"""
if second_file is None:
second_file = first_file
# load NRRD into Slicer
storagenode = slicer.vtkMRMLNRRDStorageNode()
storagenode.SetFileName(first_file)
dw_node = slicer.vtkMRMLDiffusionWeightedVolumeNode()
storagenode.ReadData(dw_node)
slicer_grads = numpy_support.vtk_to_numpy(dw_node.GetDiffusionGradients())
slicer_numgrads = slicer_grads.shape[0]
# load NRRD with pure-python parser
parsed_nrrd = parse_nhdr(second_file)
##################################
# 1) check the number of gradients
assert (len(parsed_nrrd.gradients) == slicer_numgrads)
##################################
# 2) check the node b values and gradients are correct
# Note: vtkDataArray.GetMaxNorm gives max for scalar array.
# max b value from the node
nose.tools.assert_equal(parsed_nrrd.bvalue,
dw_node.GetBValues().GetMaxNorm())
max_parsed_grad_norm = np.max(
np.apply_along_axis(np.linalg.norm, 1, parsed_nrrd.gradients))
for i in range(0, slicer_numgrads):
g_parsed_raw = parsed_nrrd.gradients[i]
g_parsed_normed = normalize(g_parsed_raw)
bval_parsed = parsed_nrrd.bvalue * pow(
np.linalg.norm(g_parsed_raw) / max_parsed_grad_norm, 2)
np.testing.assert_almost_equal(
bval_parsed,
dw_node.GetBValue(i),
decimal=7,
err_msg="MRMLNode b value does not match NRRD header")
g_from_node = slicer_grads[i, :]
# gradients stored in the vtkMRMLDiffusionWeightedVolumeNode must be *normalized*.
np.testing.assert_allclose(np.linalg.norm(g_parsed_normed -
g_from_node),
0.0,
atol=1e-15)
# b value from the node attribute dictionary
np.testing.assert_equal(parsed_nrrd.bvalue,
float(dw_node.GetAttribute("DWMRI_b-value")))
# 3) check gradients in the node attribute dictionary
# gradients must match the value on-disk.
for i in range(0, slicer_numgrads):
grad_key = f"DWMRI_gradient_{i:04d}"
parsed_gradient = np.fromstring(parsed_nrrd.header[grad_key],
count=3,
sep=' ',
dtype=np.float64)
attr_gradient = np.fromstring(dw_node.GetAttribute(grad_key),
count=3,
sep=' ',
dtype=np.float64)
np.testing.assert_array_almost_equal(
parsed_gradient,
attr_gradient,
decimal=12,
err_msg=
"NHDR gradient does not match gradient in node attribute dictionary"
)
return (parsed_nrrd, dw_node)
def test_nrrd_dwi_load(first_file, second_file=None):
"""
- load a DWI NRRD file into Slicer
- validate b values and gradient vectors against original header
- check the values in the vtkMRMLDiffusionWeightedVolumeNode
- check the values in the vtkMRMLDWVNode attribute dictionary
"""
if second_file is None:
second_file = first_file
# load NRRD into Slicer
storagenode = slicer.vtkMRMLNRRDStorageNode()
storagenode.SetFileName(first_file)
dw_node = slicer.vtkMRMLDiffusionWeightedVolumeNode()
storagenode.ReadData(dw_node)
slicer_grads = numpy_support.vtk_to_numpy(dw_node.GetDiffusionGradients())
slicer_numgrads = slicer_grads.shape[0]
# load NRRD with pure-python parser
parsed_nrrd = parse_nhdr(second_file)
##################################
# 1) check the number of gradients
assert( len(parsed_nrrd.gradients) == slicer_numgrads )
##################################
# 2) check the node b values and gradients are correct
# Note: vtkDataArray.GetMaxNorm gives max for scalar array.
# max b value from the node
nose.tools.assert_equal(parsed_nrrd.bvalue, dw_node.GetBValues().GetMaxNorm())
max_parsed_grad_norm = np.max(np.apply_along_axis(np.linalg.norm, 1, parsed_nrrd.gradients))
for i in range(0, slicer_numgrads):
g_parsed_raw = parsed_nrrd.gradients[i]
g_parsed_normed = normalize(g_parsed_raw)
bval_parsed = parsed_nrrd.bvalue * pow(np.linalg.norm(g_parsed_raw) / max_parsed_grad_norm, 2)
np.testing.assert_almost_equal(bval_parsed, dw_node.GetBValue(i), decimal=7,
err_msg="MRMLNode b value does not match NRRD header")
g_from_node = slicer_grads[i, :]
# gradients stored in the vtkMRMLDiffusionWeightedVolumeNode must be *normalized*.
np.testing.assert_allclose(np.linalg.norm(g_parsed_normed - g_from_node), 0.0, atol=1e-15)
# b value from the node attribute dictionary
np.testing.assert_equal(parsed_nrrd.bvalue, float(dw_node.GetAttribute("DWMRI_b-value")))
# 3) check gradients in the node attribute dictionary
# gradients must match the value on-disk.
for i in range(0, slicer_numgrads):
grad_key = "DWMRI_gradient_{:04d}".format(i)
parsed_gradient = np.fromstring(parsed_nrrd.header[grad_key], count=3, sep=' ', dtype=np.float64)
attr_gradient = np.fromstring(dw_node.GetAttribute(grad_key), count=3, sep=' ', dtype=np.float64)
np.testing.assert_array_almost_equal(parsed_gradient, attr_gradient, decimal=12,
err_msg="NHDR gradient does not match gradient in node attribute dictionary")
return (parsed_nrrd, dw_node)