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ENH: Define main methods to contain computation logic across scripts #167

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Oct 12, 2023
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ENH: Define main methods to contain computation logic across scripts #167

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331 changes: 168 additions & 163 deletions bin/wm_append_clusters_to_anatomical_tracts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,177 +10,182 @@
print(f"<{os.path.basename(__file__)}> Error importing white matter analysis package\n")
raise

#-----------------
# Parse arguments
#-----------------
parser = argparse.ArgumentParser(
description="Append multiple fiber clusters into anatomical tracts based on the ORG atlas.",
epilog="Written by Fan Zhang, [email protected]")

parser.add_argument(
'inputDirectory',
help='Contains fiber clusters as vtkPolyData file(s).')
parser.add_argument(
'atlasDirectory',
help='The ORG atlas folder that contains the anatomical tract MRML files.')
parser.add_argument(
'outputDirectory',
help='The output directory should be a new empty directory. It will be created if needed.')

args = parser.parse_args()

inputdir = os.path.abspath(args.inputDirectory)
if not os.path.isdir(args.inputDirectory):
print(f"<{os.path.basename(__file__)}> Error: Input directory", args.inputDirectory, "does not exist.")
exit()

inputdir_left = os.path.join(inputdir, 'tracts_left_hemisphere')
inputdir_right = os.path.join(inputdir, 'tracts_right_hemisphere')
inputdir_comm = os.path.join(inputdir, 'tracts_commissural')

if not os.path.isdir(inputdir_left):
print(f"<{os.path.basename(__file__)}> Error: Input directory", inputdir_left, "does not exist.")
exit()
if not os.path.isdir(inputdir_right):
print(f"<{os.path.basename(__file__)}> Error: Input directory", inputdir_right, "does not exist.")
exit()
if not os.path.isdir(inputdir_comm):
print(f"<{os.path.basename(__file__)}> Error: Input directory", inputdir_comm, "does not exist.")
exit()

atlasdir = os.path.abspath(args.atlasDirectory)
if not os.path.isdir(args.atlasDirectory):
print(f"<{os.path.basename(__file__)}> Error: Atlas directory", args.atlasDirectory, "does not exist.")
exit()

def list_mrml_files(input_dir):
# Find input files
input_mask = f"{input_dir}/T*.mrml"
input_mrml_fnames = glob.glob(input_mask)
return (input_mrml_fnames)

mrml_files = list_mrml_files(atlasdir)

if len(mrml_files) == 0:
print(f"<{os.path.basename(__file__)}> Error: There is no mrml files in the input atlas folder.")
else:
print(f"<{os.path.basename(__file__)}>", len(mrml_files)-1, "mrml files are detected.")

outdir = os.path.abspath(args.outputDirectory)
if not os.path.exists(args.outputDirectory):
print(f"<{os.path.basename(__file__)}> Output directory", args.outputDirectory, "does not exist, creating it.")
os.makedirs(outdir)

def output_appended_tract(cluster_vtp_list, outputfile):
appender = vtk.vtkAppendPolyData()
for c_idx in range(len(cluster_vtp_list)):
cluster_vtp = cluster_vtp_list[c_idx]
pd_cluster = wma.io.read_polydata(cluster_vtp)

vtk_array = vtk.vtkIntArray()
vtk_array.SetName('cluster_idx')
for p_idx in range(0, pd_cluster.GetNumberOfPoints()):
vtk_array.InsertNextTuple1(int(c_idx))

pd_cluster.GetPointData().AddArray(vtk_array)

#print '<wm_append_clusters_to_anatomical_tracts>', cluster_vtp, ', number of fibers', pd_cluster.GetNumberOfLines()

if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
appender.AddInputData(pd_cluster)
else:
appender.AddInput(pd_cluster)

appender.Update()
pd_appended_cluster = appender.GetOutput()

wma.io.write_polydata(pd_appended_cluster, outputfile)

hemispheric_tracts = ["T_AF", "T_CB", "T_CPC", "T_MdLF", "T_PLIC", "T_SLF-I", "T_SLF-II", "T_SLF-III", "T_EC", "T_EmC", "T_ICP", "T_ILF", "T_IOFF", "T_UF",
"T_Intra-CBLM-I&P", "T_Intra-CBLM-PaT", "T_CR-F", "T_CR-P", "T_CST", "T_SF", "T_SO", "T_SP", "T_TF", "T_TO", "T_TP",
"T_Sup-F", "T_Sup-FP", "T_Sup-O", "T_Sup-OT", "T_Sup-P", "T_Sup-PO", "T_Sup-PT", "T_Sup-T"]

commissural_tracts = ["T_CC1", "T_CC2", "T_CC3", "T_CC4", "T_CC5", "T_CC6", "T_CC7", "T_MCP"]


print(f"<{os.path.basename(__file__)}> hemispheric tracts (left and right): ")
tract_idx = 1
for tract in hemispheric_tracts:

print(" *", tract_idx, "-", tract)
tract_idx = tract_idx + 1
mrml = os.path.join(atlasdir, tract+".mrml")

if not os.path.exists(mrml):
print(f"<{os.path.basename(__file__)}> Error: Cannot locate", mrml)

def main():
#-----------------
# Parse arguments
#-----------------
parser = argparse.ArgumentParser(
description="Append multiple fiber clusters into anatomical tracts based on the ORG atlas.",
epilog="Written by Fan Zhang, [email protected]")

parser.add_argument(
'inputDirectory',
help='Contains fiber clusters as vtkPolyData file(s).')
parser.add_argument(
'atlasDirectory',
help='The ORG atlas folder that contains the anatomical tract MRML files.')
parser.add_argument(
'outputDirectory',
help='The output directory should be a new empty directory. It will be created if needed.')

args = parser.parse_args()

inputdir = os.path.abspath(args.inputDirectory)
if not os.path.isdir(args.inputDirectory):
print(f"<{os.path.basename(__file__)}> Error: Input directory", args.inputDirectory, "does not exist.")
exit()

cluster_vtp_list_left = list()
cluster_vtp_list_right = list()
f = open(mrml)
for line in f:
idx = line.find('.vtp')
if idx > 0:
cluster_vtp_filename = line[idx-13:idx+4]

cluster_vtp_filename_left = os.path.join(inputdir_left, cluster_vtp_filename);
if not os.path.exists(cluster_vtp_filename_left):
print(f"<{os.path.basename(__file__)}> Error:", cluster_vtp_filename_left, "does not exist.")
exit()
cluster_vtp_list_left.append(cluster_vtp_filename_left)

cluster_vtp_filename_right = os.path.join(inputdir_right, cluster_vtp_filename);
if not os.path.exists(cluster_vtp_filename_right):
print(f"<{os.path.basename(__file__)}> Error:", cluster_vtp_filename_right, "does not exist.")
exit()
cluster_vtp_list_right.append(cluster_vtp_filename_right)

output_tract_left = os.path.join(outdir, tract + '_left.vtp')
output_tract_right = os.path.join(outdir, tract + '_right.vtp')

output_appended_tract(cluster_vtp_list_left, output_tract_left)
output_appended_tract(cluster_vtp_list_right, output_tract_right)

print(f"<{os.path.basename(__file__)}> commissural tracts: ")
for tract in commissural_tracts:

print(" *", tract_idx, "-", tract)
tract_idx = tract_idx + 1

mrml = os.path.join(atlasdir, tract+".mrml")

if not os.path.exists(mrml):
print(f"<{os.path.basename(__file__)}> Error: Cannot locate", mrml)
inputdir_left = os.path.join(inputdir, 'tracts_left_hemisphere')
inputdir_right = os.path.join(inputdir, 'tracts_right_hemisphere')
inputdir_comm = os.path.join(inputdir, 'tracts_commissural')

if not os.path.isdir(inputdir_left):
print(f"<{os.path.basename(__file__)}> Error: Input directory", inputdir_left, "does not exist.")
exit()
if not os.path.isdir(inputdir_right):
print(f"<{os.path.basename(__file__)}> Error: Input directory", inputdir_right, "does not exist.")
exit()
if not os.path.isdir(inputdir_comm):
print(f"<{os.path.basename(__file__)}> Error: Input directory", inputdir_comm, "does not exist.")
exit()

atlasdir = os.path.abspath(args.atlasDirectory)
if not os.path.isdir(args.atlasDirectory):
print(f"<{os.path.basename(__file__)}> Error: Atlas directory", args.atlasDirectory, "does not exist.")
exit()

def list_mrml_files(input_dir):
# Find input files
input_mask = f"{input_dir}/T*.mrml"
input_mrml_fnames = glob.glob(input_mask)
return (input_mrml_fnames)

mrml_files = list_mrml_files(atlasdir)

if len(mrml_files) == 0:
print(f"<{os.path.basename(__file__)}> Error: There is no mrml files in the input atlas folder.")
else:
print(f"<{os.path.basename(__file__)}>", len(mrml_files)-1, "mrml files are detected.")

outdir = os.path.abspath(args.outputDirectory)
if not os.path.exists(args.outputDirectory):
print(f"<{os.path.basename(__file__)}> Output directory", args.outputDirectory, "does not exist, creating it.")
os.makedirs(outdir)

def output_appended_tract(cluster_vtp_list, outputfile):
appender = vtk.vtkAppendPolyData()
for c_idx in range(len(cluster_vtp_list)):
cluster_vtp = cluster_vtp_list[c_idx]
pd_cluster = wma.io.read_polydata(cluster_vtp)

vtk_array = vtk.vtkIntArray()
vtk_array.SetName('cluster_idx')
for p_idx in range(0, pd_cluster.GetNumberOfPoints()):
vtk_array.InsertNextTuple1(int(c_idx))

pd_cluster.GetPointData().AddArray(vtk_array)

#print '<wm_append_clusters_to_anatomical_tracts>', cluster_vtp, ', number of fibers', pd_cluster.GetNumberOfLines()

if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
appender.AddInputData(pd_cluster)
else:
appender.AddInput(pd_cluster)

appender.Update()
pd_appended_cluster = appender.GetOutput()

wma.io.write_polydata(pd_appended_cluster, outputfile)

hemispheric_tracts = ["T_AF", "T_CB", "T_CPC", "T_MdLF", "T_PLIC", "T_SLF-I", "T_SLF-II", "T_SLF-III", "T_EC", "T_EmC", "T_ICP", "T_ILF", "T_IOFF", "T_UF",
"T_Intra-CBLM-I&P", "T_Intra-CBLM-PaT", "T_CR-F", "T_CR-P", "T_CST", "T_SF", "T_SO", "T_SP", "T_TF", "T_TO", "T_TP",
"T_Sup-F", "T_Sup-FP", "T_Sup-O", "T_Sup-OT", "T_Sup-P", "T_Sup-PO", "T_Sup-PT", "T_Sup-T"]

commissural_tracts = ["T_CC1", "T_CC2", "T_CC3", "T_CC4", "T_CC5", "T_CC6", "T_CC7", "T_MCP"]


print(f"<{os.path.basename(__file__)}> hemispheric tracts (left and right): ")
tract_idx = 1
for tract in hemispheric_tracts:

print(" *", tract_idx, "-", tract)
tract_idx = tract_idx + 1
mrml = os.path.join(atlasdir, tract+".mrml")

if not os.path.exists(mrml):
print(f"<{os.path.basename(__file__)}> Error: Cannot locate", mrml)
exit()

cluster_vtp_list_left = list()
cluster_vtp_list_right = list()
f = open(mrml)
for line in f:
idx = line.find('.vtp')
if idx > 0:
cluster_vtp_filename = line[idx-13:idx+4]

cluster_vtp_filename_left = os.path.join(inputdir_left, cluster_vtp_filename);
if not os.path.exists(cluster_vtp_filename_left):
print(f"<{os.path.basename(__file__)}> Error:", cluster_vtp_filename_left, "does not exist.")
exit()
cluster_vtp_list_left.append(cluster_vtp_filename_left)

cluster_vtp_filename_right = os.path.join(inputdir_right, cluster_vtp_filename);
if not os.path.exists(cluster_vtp_filename_right):
print(f"<{os.path.basename(__file__)}> Error:", cluster_vtp_filename_right, "does not exist.")
exit()
cluster_vtp_list_right.append(cluster_vtp_filename_right)

output_tract_left = os.path.join(outdir, tract + '_left.vtp')
output_tract_right = os.path.join(outdir, tract + '_right.vtp')

output_appended_tract(cluster_vtp_list_left, output_tract_left)
output_appended_tract(cluster_vtp_list_right, output_tract_right)

print(f"<{os.path.basename(__file__)}> commissural tracts: ")
for tract in commissural_tracts:

print(" *", tract_idx, "-", tract)
tract_idx = tract_idx + 1

mrml = os.path.join(atlasdir, tract+".mrml")

if not os.path.exists(mrml):
print(f"<{os.path.basename(__file__)}> Error: Cannot locate", mrml)
exit()

cluster_vtp_list_comm = list()
f = open(mrml)
for line in f:
idx = line.find('.vtp')
if idx > 0:
cluster_vtp_filename = line[idx-13:idx+4]

cluster_vtp_list_comm = list()
f = open(mrml)
for line in f:
idx = line.find('.vtp')
if idx > 0:
cluster_vtp_filename = line[idx-13:idx+4]
cluster_vtp_filename_comm = os.path.join(inputdir_comm, cluster_vtp_filename);
if not os.path.exists(cluster_vtp_filename_comm):
print(f"<{os.path.basename(__file__)}> Error:", cluster_vtp_filename_comm, "does not exist.")
exit()
cluster_vtp_list_comm.append(cluster_vtp_filename_comm)

cluster_vtp_filename_comm = os.path.join(inputdir_comm, cluster_vtp_filename);
if not os.path.exists(cluster_vtp_filename_comm):
print(f"<{os.path.basename(__file__)}> Error:", cluster_vtp_filename_comm, "does not exist.")
exit()
cluster_vtp_list_comm.append(cluster_vtp_filename_comm)
output_tract_comm = os.path.join(outdir, tract + '.vtp')

output_tract_comm = os.path.join(outdir, tract + '.vtp')
output_appended_tract(cluster_vtp_list_comm, output_tract_comm)

output_appended_tract(cluster_vtp_list_comm, output_tract_comm)
def list_cluster_files(input_dir):
# Find input files
input_mask = f"{input_dir}/T_*.vtk"
input_mask2 = f"{input_dir}/T_*.vtp"
input_pd_fnames = glob.glob(input_mask) + glob.glob(input_mask2)
input_pd_fnames = sorted(input_pd_fnames)
return(input_pd_fnames)

def list_cluster_files(input_dir):
# Find input files
input_mask = f"{input_dir}/T_*.vtk"
input_mask2 = f"{input_dir}/T_*.vtp"
input_pd_fnames = glob.glob(input_mask) + glob.glob(input_mask2)
input_pd_fnames = sorted(input_pd_fnames)
return(input_pd_fnames)
list_tracts= list_cluster_files(outdir)

list_tracts= list_cluster_files(outdir)
print('')
print(f'<{os.path.basename(__file__)}> Appended tracts can be found at', outdir, '\n')
print(f'<{os.path.basename(__file__)}> A total of', len(list_tracts), 'tracts\n')

print('')
print(f'<{os.path.basename(__file__)}> Appended tracts can be found at', outdir, '\n')
print(f'<{os.path.basename(__file__)}> A total of', len(list_tracts), 'tracts\n')

if __name__ == "__main__":
main()
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