STYLE: Prefer using f-strings

Prefer using f-strings.
SlicerDMRI · Nov 30, 2023 · a29c1f3 · a29c1f3
1 parent afcb30b
commit a29c1f3
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Showing 54 changed files with 742 additions and 773 deletions.
diff --git a/bin/harden_transform_with_slicer.py b/bin/harden_transform_with_slicer.py
@@ -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
 

diff --git a/bin/wm_append_clusters.py b/bin/wm_append_clusters.py
@@ -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):
@@ -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)
 
@@ -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:
@@ -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()
@@ -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()
diff --git a/bin/wm_append_clusters_to_anatomical_tracts.py b/bin/wm_append_clusters_to_anatomical_tracts.py
@@ -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):
@@ -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):
@@ -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()
@@ -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)
 
@@ -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()
@@ -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)
 
@@ -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__":

diff --git a/bin/wm_append_diffusion_measures_across_subjects.py b/bin/wm_append_diffusion_measures_across_subjects.py
@@ -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
@@ -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 = []
@@ -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]
@@ -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):

diff --git a/bin/wm_assess_cluster_location_by_hemisphere.py b/bin/wm_assess_cluster_location_by_hemisphere.py
@@ -136,7 +136,7 @@ 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
@@ -171,7 +171,7 @@ 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')

diff --git a/bin/wm_average_tract_measures.py b/bin/wm_average_tract_measures.py
@@ -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.")
@@ -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):
@@ -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()
 

diff --git a/bin/wm_change_nrrd_dir.py b/bin/wm_change_nrrd_dir.py
@@ -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__":