CLI Interface, argparse moved to utils

imgtools/autopipeline.py

@@ -1,4 +1,4 @@
-import os, pathlib
+import os, pathlib, sys
 import shutil
 import glob
 import pickle
@@ -8,6 +8,7 @@
 
 from imgtools.ops import StructureSetToSegmentation, ImageAutoInput, ImageAutoOutput, Resample
 from imgtools.pipeline import Pipeline
+from imgtools.utils import parser
 from joblib import Parallel, delayed
 
 ###############################################################
@@ -203,34 +204,9 @@ def run(self):
             Parallel(n_jobs=self.n_jobs, verbose=verbose)(
                     delayed(self._process_wrapper)(subject_id) for subject_id in subject_ids)
             self.save_data()
-
-
-if __name__ == "__main__":
-    parser = ArgumentParser("imgtools Automatic Processing Pipeline.")
-
-    #arguments
-    parser.add_argument("input_directory", type=str,
-                        help="Path to top-level directory of dataset.")
 
-    parser.add_argument("output_directory", type=str,
-                        help="Path to output directory to save processed images.")
-
-    parser.add_argument("--modalities", type=str, default="CT",
-                        help="List of desired modalities. Type as string for ex: RTSTRUCT,CT,RTDOSE")
-
-    parser.add_argument("--visualize", type=bool, default=False,
-                        help="Whether to visualize the data graph")
-
-    parser.add_argument("--spacing", nargs=3, type=float, default=(1., 1., 0.),
-                        help="The resampled voxel spacing in  (x, y, z) directions.")
-
-    parser.add_argument("--n_jobs", type=int, default=-1,
-                        help="The number of parallel processes to use.")
-
-    parser.add_argument("--show_progress", action="store_true",
-                        help="Whether to print progress to standard output.")
-
-    args = parser.parse_args()
+def main():
+    args = parser()
     pipeline = AutoPipeline(args.input_directory,
                             args.output_directory,
                             modalities=args.modalities,
@@ -243,4 +219,9 @@ def run(self):
     pipeline.run()
 
 
-    print(f'finished Pipeline!')
+    print(f'finished Pipeline!')
+
+if __name__ == "__main__":
+    main()
+
+

imgtools/utils/__init__.py

@@ -2,3 +2,4 @@
 from .arrayutils import *
 from .crawl import *
 from .dicomutils import *
+from .args import *

imgtools/utils/args.py

@@ -0,0 +1,28 @@
+from argparse import ArgumentParser
+
+def parser():
+    parser = ArgumentParser("imgtools Automatic Processing Pipeline.")
+
+    #arguments
+    parser.add_argument("input_directory", type=str,
+                        help="Path to top-level directory of dataset.")
+
+    parser.add_argument("output_directory", type=str,
+                        help="Path to output directory to save processed images.")
+
+    parser.add_argument("--modalities", type=str, default="CT",
+                        help="List of desired modalities. Type as string for ex: RTSTRUCT,CT,RTDOSE")
+
+    parser.add_argument("--visualize", type=bool, default=False,
+                        help="Whether to visualize the data graph")
+
+    parser.add_argument("--spacing", nargs=3, type=float, default=(1., 1., 0.),
+                        help="The resampled voxel spacing in  (x, y, z) directions.")
+
+    parser.add_argument("--n_jobs", type=int, default=-1,
+                        help="The number of parallel processes to use.")
+
+    parser.add_argument("--show_progress", action="store_true",
+                        help="Whether to print progress to standard output.")
+
+    return parser.parse_known_args()[0]

setup.py

@@ -20,6 +20,7 @@
     extras_require={
         'debug': ['pyvis'],
     },
+    entry_points={'console_scripts': ['autopipe = imgtools.autopipeline:main']},
     classifiers=[
         "Programming Language :: Python :: 3",
         "Operating System :: OS Independent",