Merge pull request #174 from jhlegarreta/RefactorArgParsingToOwnMethods

STYLE: Refactor argparsing to own methods in scripts

bin/harden_transform_with_slicer.py

@@ -42,11 +42,12 @@ def harden_transform(polydata, transform, inverse, outdir):
 
     slicer.util.saveNode(polydata_node, output_name)
 
-def main():
+
+def _build_arg_parser():
+
     parser = argparse.ArgumentParser(
         description="Harden transform with Slicer.",
         epilog="Written by Fan Zhang, [email protected]")
-
     parser.add_argument("-v", "--version",
         action="version", default=argparse.SUPPRESS,
         version='1.0',
@@ -63,9 +64,20 @@ def main():
     parser.add_argument(
         'outdir',
         help='')
-
-    args = parser.parse_args()
-
+
+    return parser
+
+
+def _parse_args(parser):
+
+    return parser.parse_args()
+
+
+def main():
+
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
+
     if os.path.isfile(args.polydata):
         harden_transform(args.polydata, args.transform, args.inverse, args.outdir)
     elif os.path.isdir(args.polydata):

bin/wm_append_clusters.py

@@ -7,10 +7,9 @@
 
 import whitematteranalysis as wma
 
-def main():
-    #-----------------
-    # Parse arguments
-    #-----------------
+
+def _build_arg_parser():
+
     parser = argparse.ArgumentParser(
         description="Append multiple fiber clusters into one fiber tract.",
         epilog="Written by Fan Zhang, [email protected]")
@@ -30,9 +29,20 @@ def main():
     parser.add_argument(
         '-tractMRML', action="store", type=str,
         help='A MRML file that contains the fiber clusters to be appended. If neither -clusterList nor -tractMRML are provided, all vtk/vtp files in the input folder will be appended.')
-
-    args = parser.parse_args()
-
+
+    return parser
+
+
+def _parse_args(parser):
+
+    return parser.parse_args()
+
+
+def main():
+
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
+
     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.")

bin/wm_append_clusters_to_anatomical_tracts.py

@@ -9,14 +9,11 @@
 import whitematteranalysis as wma
 
 
-def main():
-    #-----------------
-    # Parse arguments
-    #-----------------
+def _build_arg_parser():
+
     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).')
@@ -27,7 +24,18 @@ def main():
         'outputDirectory',
         help='The output directory should be a new empty directory. It will be created if needed.')
 
-    args = parser.parse_args()
+    return parser
+
+
+def _parse_args(parser):
+
+    return parser.parse_args()
+
+
+def main():
+
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
 
     inputdir = os.path.abspath(args.inputDirectory)
     if not os.path.isdir(args.inputDirectory):

bin/wm_append_diffusion_measures_across_subjects.py

@@ -8,10 +8,8 @@
 import glob
 
 
-def main():
-    #-----------------
-    # Parse arguments
-    #-----------------
+def _build_arg_parser():
+
     parser = argparse.ArgumentParser(
         description="Append diffusion measure files from multiple subjects",
         epilog="Written by Fan Zhang, [email protected].")
@@ -22,7 +20,18 @@ def main():
         'appenedmeasurefile',
         help='Output csv file.')
 
-    args = parser.parse_args()
+    return parser
+
+
+def _parse_args(parser):
+
+    return parser.parse_args()
+
+
+def main():
+
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
 
     subject_folders = sorted(glob.glob(os.path.join(args.inputfolder, '*')))
 

bin/wm_assess_cluster_location_by_hemisphere.py

@@ -21,10 +21,9 @@
 import whitematteranalysis as wma
 
 
-def main():
-    #-----------------
-    # Parse arguments
-    #-----------------
+
+def _build_arg_parser():
+
     parser = argparse.ArgumentParser(
         description="Assess if a fiber within the clusters belongs to left hemispheric, right hemispheric, or commissural tracts. "
                     "This code needs to be run in the ATLAS space, where the brain is clustered at the RAS origin. ",
@@ -51,7 +50,17 @@ def main():
     parser.add_argument(
         '-outputDirectory',
         help='If this is given, separated clusters will be output under this folder. The output directory will be created if it does not exist.')
-
+
+    return parser
+
+
+def _parse_args(parser):
+
+    return parser.parse_args()
+
+
+def main():
+
     def list_cluster_files(input_dir):
         # Find input files
         input_mask = f"{input_dir}/cluster_*.vtk"
@@ -109,9 +118,10 @@ def read_mask_location_from_vtk(inpd):
                     break
 
         return flag_location, mask_location
-
-    args = parser.parse_args()
-
+
+    parser = _build_arg_parser()
+    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.")
         exit()

bin/wm_average_tract_measures.py

@@ -8,10 +8,8 @@
 import re
 
 
-def main():
-    #-----------------
-    # Parse arguments
-    #-----------------
+def _build_arg_parser():
+
     parser = argparse.ArgumentParser(
         description="Compute averaged statistics of the anatomical tracts. For diffusion measure with multiple statistics, only the Mean will be outputted.",
         epilog="Written by Fan Zhang, [email protected].")
@@ -28,7 +26,18 @@ def main():
         '-tractList', action="store", type=str, nargs='+',
         help='A list of tracts to be appended, e.g., AF_left AF_right.')
 
-    args = parser.parse_args()
+    return parser
+
+
+def _parse_args(parser):
+
+    return parser.parse_args()
+
+
+def main():
+
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
 
     stats = pandas.read_table(args.inputmeasure, delimiter=',')
 

bin/wm_change_nrrd_dir.py

@@ -13,14 +13,11 @@
 from joblib import Parallel, delayed
 
 
-def main():
-    #-----------------
-    # Parse arguments
-    #-----------------
+def _build_arg_parser():
+
     parser = argparse.ArgumentParser(
         description="Make sign change of the gradient direction",
         epilog="Written by Fan Zhang, [email protected]")
-
     parser.add_argument(
         'inputnrrd',
         help='Nrrd header in .nhdr format')
@@ -31,8 +28,18 @@ def main():
         '-d', action="store", dest="dim", type=str,
         help='The dimension to change: x, y, or z.')
 
-    args = parser.parse_args()
+    return parser
+
+
+def _parse_args(parser):
+
+    return parser.parse_args()
+
+
+def main():
 
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
 
     inputnrrd = args.inputnrrd
     outputnrrd = args.outputnrrd

bin/wm_cluster_atlas.py

@@ -261,10 +261,6 @@ def main():
     # contain almost as much information and reduce noise for single subject clustering
     #number_of_eigenvectors = 20
 
-    # =======================================================================
-    # Above this line is argument parsing. Below this line is the pipeline.
-    # =======================================================================
-
     input_polydatas = wma.io.list_vtk_files(args.inputDirectory)
     number_of_subjects = len(input_polydatas)
 

bin/wm_cluster_from_atlas.py

@@ -10,10 +10,9 @@
 
 import whitematteranalysis as wma
 
-def main():
-    #-----------------
-    # Parse arguments
-    #-----------------
+
+def _build_arg_parser():
+
     parser = argparse.ArgumentParser(
         description="Clusters tractography (propagates clusters) from a cluster atlas (a multi-subject/multi-atlas cluster representation).",
         epilog="Written by Lauren O\'Donnell, [email protected].  Please reference \"O'Donnell, Lauren J., and C-F. Westin. Automatic tractography segmentation using a high-dimensional white matter atlas. Medical Imaging, IEEE Transactions on 26.11 (2007): 1562-1575.\"")
@@ -51,10 +50,20 @@ def main():
     parser.add_argument(
         '-norender', action='store_true', dest="flag_norender",
         help='No Render. Prevents rendering of images that would require an X connection.')
-
-    args = parser.parse_args()
-
-
+
+    return parser
+
+
+def _parse_args(parser):
+
+    return parser.parse_args()
+
+
+def main():
+
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
+
     if not os.path.exists(args.inputFile):
         print(f"<{os.path.basename(__file__)}> Error: Input file", args.inputFile, "does not exist.")
         exit()
@@ -118,10 +127,6 @@ def main():
     render = not args.flag_norender
 
     print("==========================\n")
-
-    # =======================================================================
-    # Above this line is argument parsing. Below this line is the pipeline.
-    # =======================================================================
 
     # read atlas
     print(f"<{os.path.basename(__file__)}> Loading input atlas:", args.atlasDirectory)

bin/wm_cluster_remove_outliers.py

@@ -19,10 +19,9 @@
     print(f"<{os.path.basename(__file__)}> Failed to import joblib, cannot multiprocess.")
     print(f"<{os.path.basename(__file__)}> Please install joblib for this functionality.")
 
-def main():
-    #-----------------
-    # Parse arguments
-    #-----------------
+
+def _build_arg_parser():
+
     parser = argparse.ArgumentParser(
         description="Removes outliers in a subject dataset that was clustered from a cluster atlas. This script uses the atlas to identifies and remove outliers in each cluster of the subject. The atlas must be the same one used to cluster the subject dataset",
         epilog="Written by Lauren O\'Donnell, [email protected].  Please reference \"O'Donnell, Lauren J., and C-F. Westin. Automatic tractography segmentation using a high-dimensional white matter atlas. Medical Imaging, IEEE Transactions on 26.11 (2007): 1562-1575.\"")
@@ -52,7 +51,18 @@ def main():
         '-j', action="store", dest="numberOfJobs", type=str,
         help='Number of processors to use.')
 
-    args = parser.parse_args()
+    return parser
+
+
+def _parse_args(parser):
+
+    return parser.parse_args()
+
+
+def main():
+
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
 
     if not os.path.isdir(args.inputDirectory):
         print(f"<{os.path.basename(__file__)}> Error: Input subject directory", args.inputDirectory, "does not exist.")
@@ -100,10 +110,6 @@ def main():
     verbose = args.flag_verbose
 
     print("==========================\n")
-
-    # =======================================================================
-    # Above this line is argument parsing. Below this line is the pipeline.
-    # =======================================================================
 
     # Copy all MRML files to the new subject directory
     input_mask = f"{args.inputDirectory}/clustered_tracts*.mrml"