Fix for Windows dvp.

README.md

@@ -13,7 +13,12 @@ The module can either be used as a Python library, as CLI, or as Docker containe
 pip install git+https://github.com/dbouget/raidionics-seg-lib.git
 ```
 
-No GPU support for TensorFlow on macOS.
+No GPU support for TensorFlow by default. A manual installation of CUDA and of
+the following Python package is necessary.
+
+```
+pip install tensorflow-gpu==1.14.0
+```
 
 # Usage
 ## CLI

main.py

@@ -24,13 +24,13 @@ def main(argv):
         elif opt in ("-c", "--Config"):
             config_filename = arg
         elif opt in ("-v", "--Verbose"):
-            if opt.lower() == 'debug':
+            if arg.lower() == 'debug':
                 logging.getLogger().setLevel(logging.DEBUG)
-            elif opt.lower() == 'info':
+            elif arg.lower() == 'info':
                 logging.getLogger().setLevel(logging.INFO)
-            elif opt.lower() == 'warning':
+            elif arg.lower() == 'warning':
                 logging.getLogger().setLevel(logging.WARNING)
-            elif opt.lower() == 'error':
+            elif arg.lower() == 'error':
                 logging.getLogger().setLevel(logging.ERROR)
 
     if not config_filename or not os.path.exists(config_filename):

raidionicsseg/PreProcessing/brain_clipping.py

@@ -1,4 +1,5 @@
 import configparser
+import sys
 from typing import Tuple, List
 import numpy as np
 from copy import deepcopy
@@ -10,6 +11,7 @@
 import shutil
 import os
 import logging
+from pathlib import PurePath
 from raidionicsseg.Utils.io import load_nifti_volume, convert_and_export_to_nifti
 from raidionicsseg.Utils.configuration_parser import generate_runtime_config
 from raidionicsseg.Utils.configuration_parser import ConfigResources
@@ -116,9 +118,17 @@ def skull_stripping_tf(filepath, volume: np.ndarray, new_spacing: Tuple[float],
         new_parameters.set('Runtime', 'reconstruction_order', 'resample_first')
         with open(brain_config_filename, 'w') as cf:
             new_parameters.write(cf)
-        script_path = '/'.join(os.path.dirname(os.path.realpath(__file__)).split('/')[:-1]) + '/__main__.py'
-        subprocess.call(['python3', '{script}'.format(script=script_path),
-                         '{config}'.format(config=brain_config_filename)])
+        if os.name == 'nt':
+            script_path_parts = list(PurePath(os.path.realpath(__file__)).parts[:-2] + ('__main__.py',))
+            script_path = PurePath()
+            for x in script_path_parts:
+                script_path = script_path.joinpath(x)
+            subprocess.call([sys.executable, '{script}'.format(script=script_path),
+                             '{config}'.format(config=brain_config_filename)])
+        else:
+            script_path = '/'.join(os.path.dirname(os.path.realpath(__file__)).split('/')[:-1]) + '/__main__.py'
+            subprocess.call(['python3', '{script}'.format(script=script_path),
+                             '{config}'.format(config=brain_config_filename)])
         brain_mask_filename = os.path.join(storage_path, 'labels_Brain.nii.gz')
         os.remove(brain_config_filename)
     else:

raidionicsseg/Utils/configuration_parser.py

@@ -75,6 +75,7 @@ def __setup(self):
         self.runtime_lungs_mask_filepath = ''
         self.runtime_brain_mask_filepath = ''
 
+
     def init_environment(self, config_filename):
         self.config_filename = config_filename
         self.config = configparser.ConfigParser()