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)