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STYLE: Prefer using f-strings #196

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Dec 7, 2023
Merged

STYLE: Prefer using f-strings #196

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6 changes: 3 additions & 3 deletions bin/harden_transform_with_slicer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,16 +19,16 @@ def harden_transform(polydata, transform, inverse, outdir):

check_load, polydata_node = slicer.util.loadFiberBundle(str(polydata), 1)
if not check_load:
print('Could not load polydata file:', polydata)
print(f'Could not load polydata file: {polydata}')
return

check_load, transform_node = slicer.util.loadTransform(str(transform), 1)
if not check_load:
print('Could not load transform file:', transform)
print(f'Could not load transform file: {transform}')
return

if polydata_node.GetPolyData().GetNumberOfCells() == 0:
print('Empty cluster:', polydata)
print(f'Empty cluster: {polydata}')
shutil.copyfile(polydata, output_name)
return

Expand Down
18 changes: 9 additions & 9 deletions bin/wm_append_clusters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,12 +46,12 @@ def main():

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

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

if (args.clusterList is not None) and (args.tractMRML is not None):
Expand All @@ -71,7 +71,7 @@ def main():
for c_idx in args.clusterList:
cluster_vtp_filename = 'cluster_' + str(c_idx).zfill(5) + '.vtp'
if not os.path.exists(os.path.join(inputdir, cluster_vtp_filename)):
print(f"<{os.path.basename(__file__)}> Error:", cluster_vtp_filename, "does not exist.")
print(f"<{os.path.basename(__file__)}> Error: {cluster_vtp_filename} does not exist.")
exit()
cluster_vtp_list.append(cluster_vtp_filename)

Expand All @@ -83,7 +83,7 @@ def main():
if idx > 0:
cluster_vtp_filename = line[idx-13:idx+4]
if not os.path.exists(os.path.join(inputdir, cluster_vtp_filename)):
print(f"<{os.path.basename(__file__)}> Error:", cluster_vtp_filename, "does not exist.")
print(f"<{os.path.basename(__file__)}> Error: {cluster_vtp_filename} does not exist.")
exit()
cluster_vtp_list.append(cluster_vtp_filename)
else:
Expand All @@ -92,9 +92,9 @@ def main():
print("")
print(f"<{os.path.basename(__file__)}> Start to append clusters.")
print("")
print("=====input directory======\n", inputdir)
print("=====output directory=====\n", outdir)
print("=====clusters to be appended====\n", cluster_vtp_list)
print(f"=====input directory======\n {inputdir}")
print(f"=====output directory=====\n {outdir}")
print(f"=====clusters to be appended====\n {cluster_vtp_list}")
print("")

appender = vtk.vtkAppendPolyData()
Expand Down Expand Up @@ -122,9 +122,9 @@ def main():
wma.io.write_polydata(pd_appended_cluster, outputfile)

print('')
print(f'<{os.path.basename(__file__)}> Appended fiber tract: number of fibers', pd_appended_cluster.GetNumberOfLines())
print(f'<{os.path.basename(__file__)}> Appended fiber tract: number of fibers {pd_appended_cluster.GetNumberOfLines()}')
print('')
print(f'<{os.path.basename(__file__)}> Save result to', outputfile, '\n')
print(f'<{os.path.basename(__file__)}> Save result to {outputfile}\n')

if __name__ == '__main__':
main()
32 changes: 16 additions & 16 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 @@ -67,26 +67,26 @@ def main():

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

def list_mrml_files(input_dir):
Expand All @@ -100,11 +100,11 @@ def list_mrml_files(input_dir):
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.")
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.")
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):
Expand Down Expand Up @@ -142,12 +142,12 @@ def output_appended_tract(cluster_vtp_list, outputfile):
tract_idx = 1
for tract in hemispheric_tracts:

print(" *", tract_idx, "-", tract)
print(f" * {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)
print(f"<{os.path.basename(__file__)}> Error: Cannot locate {mrml}")
exit()

cluster_vtp_list_left = list()
Expand All @@ -160,13 +160,13 @@ def output_appended_tract(cluster_vtp_list, outputfile):

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.")
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.")
print(f"<{os.path.basename(__file__)}> Error: {cluster_vtp_filename_right} does not exist.")
exit()
cluster_vtp_list_right.append(cluster_vtp_filename_right)

Expand All @@ -179,13 +179,13 @@ def output_appended_tract(cluster_vtp_list, outputfile):
print(f"<{os.path.basename(__file__)}> commissural tracts: ")
for tract in commissural_tracts:

print(" *", tract_idx, "-", tract)
print(f" * {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)
print(f"<{os.path.basename(__file__)}> Error: Cannot locate {mrml}")
exit()

cluster_vtp_list_comm = list()
Expand All @@ -197,7 +197,7 @@ def output_appended_tract(cluster_vtp_list, outputfile):

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.")
print(f"<{os.path.basename(__file__)}> Error {cluster_vtp_filename_comm} does not exist.")
exit()
cluster_vtp_list_comm.append(cluster_vtp_filename_comm)

Expand All @@ -216,8 +216,8 @@ def list_cluster_files(input_dir):
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(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__":
Expand Down
18 changes: 9 additions & 9 deletions bin/wm_append_diffusion_measures_across_subjects.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def main():

subject_IDs = [os.path.basename(folder) for folder in subject_folders]
print()
print('Subject IDs: (n=%d): ' % len(subject_IDs))
print(f'Subject IDs: (n={len(subject_IDs)}): ')
print(subject_IDs)

# anatomical tracts
Expand All @@ -49,22 +49,22 @@ def main():
fields = [col.strip() for col in stats.columns]
fields = fields[1:]
print()
print('Tract diffusion measures per subject: (n=%d): ' % len(fields))
print(f'Tract diffusion measures per subject: (n={len(fields)}): ')
print(fields)

tracts = stats.to_numpy()[:, 0]
tracts = [os.path.basename(filepath).replace('.vtp', '').replace('.vtk', '').strip() for filepath in tracts]
print()
print('White matter tracts per subject: (n=%d): ' % len(tracts))
print(f'White matter tracts per subject: (n={len(tracts)}): ')
print(tracts)

appended_fields = ['subjectkey']
for tract in tracts:
for field in fields:
appended_fields.append("%s.%s" % (tract, field))
appended_fields.append(f"{tract}.{field}")

print()
print('Appended tract diffusion measure fields per subject: (n=%d): ' % len(appended_fields))
print(f'Appended tract diffusion measure fields per subject: (n={len(appended_fields)}): ')
print(appended_fields[:10], ' ... ')

data = []
Expand Down Expand Up @@ -101,13 +101,13 @@ def main():
fields = [col.strip() for col in stats.columns]
fields = fields[1:]
print()
print('Fiber cluster diffusion measures per subject: (n=%d): ' % len(fields))
print(f'Fiber cluster diffusion measures per subject: (n={len(fields)}): ')
print(fields)

clusters = stats.to_numpy()[:, 0]
clusters = [os.path.basename(filepath).replace('.vtp', '').replace('.vtk', '').strip() for filepath in clusters]
print()
print('Fiber clusters per subject: (n=%d): ' % len(clusters))
print(f'Fiber clusters per subject: (n={len(clusters)}): ')

if len(clusters) == 800 and len(tracts) == 73:
comm_clusters = [3, 8, 33, 40, 46, 52, 56, 57, 62, 68, 69, 73, 86, 91, 109, 110, 114, 142, 144, 145, 146, 159, 163, 250, 251, 252, 257, 262, 263, 268, 271, 305, 311, 314, 322, 330, 334, 338, 342, 350, 363, 371, 375, 403, 410, 437, 440, 448, 456, 465, 468, 475, 484, 485, 488, 519, 522, 525, 543, 545, 549, 557, 576, 577, 582, 587, 591, 597, 601, 614, 620, 623, 627, 633, 645, 653, 658, 663, 670, 677, 683, 702, 770, 781]
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Contributor Author

@jhlegarreta jhlegarreta Nov 30, 2023 •
edited
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These should not be hard-coded here; they should be in a separate file so that

  • they can be located easily.
  • they can be reused by other scripts, if necessary.
  • if they need to be changed, this can be done easily in a place that contains only data-/atlas-related labels, and does not pollute the code.

To be done in a separate PR.

Expand All @@ -132,10 +132,10 @@ def main():

for cluster in clusters_loc:
for field in fields:
appended_fields.append("%s.%s.%s" % (loc, cluster, field))
appended_fields.append(f"{loc}.{cluster}.{field}")

print()
print('Appended cluster diffusion measure fields per subject: (n=%d): ' % len(appended_fields))
print(f'Appended cluster diffusion measure fields per subject: (n={len(appended_fields)}): ')

data = []
for s_idx, subject_folder in enumerate(subject_folders):
Expand Down
4 changes: 2 additions & 2 deletions bin/wm_assess_cluster_location_by_hemisphere.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,7 @@ def _read_location(_inpd):
args = _parse_args(parser)

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

clusterLocationFile = args.clusterLocationFile
Expand Down Expand Up @@ -172,7 +172,7 @@ def _read_location(_inpd):
if outdir is not None:
print(f"<{os.path.basename(__file__)}> Separated clusters will be ouput.")
if not os.path.exists(outdir):
print(f"<{os.path.basename(__file__)}> Output directory", outdir, "does not exist, creating it.")
print(f"<{os.path.basename(__file__)}> Output directory {outdir} does not exist, creating it.")
os.makedirs(outdir)

outdir_right = os.path.join(outdir, 'tracts_right_hemisphere')
Expand Down
8 changes: 4 additions & 4 deletions bin/wm_average_tract_measures.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,13 +51,13 @@ def main():

print('All available tracts:')
all_tracts = [f_name.replace('.Num_Points', '') for f_name in fields if f_name.endswith('.Num_Points')]
print('N = ', str(len(all_tracts)), ':')
print(f'N = {len(all_tracts)} :')
print(all_tracts)

append_list = []
print('Tracts and related measures to be appended.')
for t_idx, tract in enumerate(args.tractList):
print('*', t_idx, '-', tract)
print(f'* {t_idx} - {tract}')
indices = [index for index in range(len(fields)) if fields[index].startswith(tract+'.Num_') or re.search(tract+".*.Mean", fields[index])]
if len(indices) == 0:
print("Error: tract not founded in the input file.")
Expand All @@ -68,7 +68,7 @@ def main():
append_list = np.array(append_list)
append_measures = [field.replace(args.tractList[-1], '') for field in fields[indices]]

print("Output measures:", append_measures)
print(f"Output measures: {append_measures}")

avg_stats = [stats.to_numpy()[:, 0]]
for m_idx, m_name in enumerate(append_measures):
Expand Down Expand Up @@ -125,7 +125,7 @@ def main():

df.to_csv(args.outoutmeasure, index=False)
print()
print('Output file at:', os.path.abspath(args.outoutmeasure))
print(f'Output file at: {os.path.abspath(args.outoutmeasure)}')

exit()

Expand Down
2 changes: 1 addition & 1 deletion bin/wm_change_nrrd_dir.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ def main():
with open(outputnrrd, 'w') as o:
o.write(outstr)

print('Done! New nrrd header: ' + outputnrrd)
print(f'Done! New nrrd header {outputnrrd}')


if __name__ == "__main__":
Expand Down
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