Merge pull request #55 from neuronflow/54-feature-request-we-want-for…

…matted-code

blacked and formatted

brats_toolkit/__init__.py

@@ -1 +0,0 @@
-

brats_toolkit/cli.py

@@ -6,13 +6,12 @@
 # Please refer to README.md and LICENSE.md for further documentation
 # This software is not certified for clinical use.
 
-import sys
-import subprocess
-import pprint
 import argparse
+import pprint
+import subprocess
+import sys
 
-
-from . import segmentor, fusionator, preprocessor
+from . import fusionator, preprocessor, segmentor
 
 
 def list_dockers():
@@ -42,7 +41,7 @@ def list_docker_cpu():
         if seg.config[id]["runtime"] == "runc":
             print(id)
 
-    
+
 def fusion():
     parser = argparse.ArgumentParser(
         description="Runs the Docker orchestra to fuse segmentations. All inputs have to have equal shape and label values"
@@ -84,6 +83,7 @@ def fusion():
     except Exception as e:
         print("ERROR DETAIL: ", e)
 
+
 def segmentation():
     parser = argparse.ArgumentParser(
         description="Runs the Docker orchestra to segment and fuse segmentations based on the"
@@ -179,6 +179,7 @@ def segmentation():
     except Exception as e:
         print("ERROR DETAIL: ", e)
 
+
 def batchpreprocess():
     parser = argparse.ArgumentParser(
         description="Runs the preprocessing for MRI scans on a folder of images."
@@ -242,6 +243,7 @@ def batchpreprocess():
     except Exception as e:
         print("ERROR DETAIL: ", e)
 
+
 def singlepreprocess():
     parser = argparse.ArgumentParser(
         description="Runs the preprocessing for MRI scans on a single set of images."

brats_toolkit/fusionator.py

@@ -4,20 +4,20 @@
 #
 # Please refer to README.md and LICENSE.md for further documentation
 # This software is not certified for clinical use.
-import os
-import logging
 import itertools
+import logging
 import math
+import os
+import os.path as op
 
 import numpy as np
-import os.path as op
-from .util import own_itk as oitk
+
 from .util import filemanager as fm
+from .util import own_itk as oitk
 from .util.citation_reminder import citation_reminder
 
 
 class Fusionator(object):
-
     @citation_reminder
     def __init__(self, verbose=True):
         self.verbose = verbose

brats_toolkit/util/docker_functions.py

@@ -1,12 +1,18 @@
-import shlex
-import platform
+import os
 import pathlib
+import platform
+import shlex
 import subprocess
-import os
 
 
-def start_docker(exam_import_folder=None,
-                 exam_export_folder=None, dicom_import_folder=None, nifti_export_folder=None, mode="cpu", gpuid='0'):
+def start_docker(
+    exam_import_folder=None,
+    exam_export_folder=None,
+    dicom_import_folder=None,
+    nifti_export_folder=None,
+    mode="cpu",
+    gpuid="0",
+):
     # deal with missing arguments
     if dicom_import_folder is None:
         dicom_import_folder = exam_import_folder
@@ -38,28 +44,31 @@ def start_docker(exam_import_folder=None,
 
     operatingSystem = platform.system()
     if operatingSystem == "Windows":
-        bashscript = os.path.join(cwd, os.path.normpath(
-            './backend_scripts/win_docker.cmd'))
+        bashscript = os.path.join(
+            cwd, os.path.normpath("./backend_scripts/win_docker.cmd")
+        )
     else:
         if mode == "cpu":
-            bashscript = os.path.normpath(
-                './backend_scripts/unix_docker.sh')
+            bashscript = os.path.normpath("./backend_scripts/unix_docker.sh")
         elif mode == "robex":
-            bashscript = os.path.normpath(
-                './backend_scripts/unix_docker.sh')
+            bashscript = os.path.normpath("./backend_scripts/unix_docker.sh")
         elif mode == "gpu":
-            bashscript = os.path.normpath(
-                './backend_scripts/unix_docker_gpu.sh')
+            bashscript = os.path.normpath("./backend_scripts/unix_docker_gpu.sh")
         elif mode == "gpu_hdbet":
-            bashscript = os.path.normpath(
-                './backend_scripts/unix_docker_gpu.sh')
+            bashscript = os.path.normpath("./backend_scripts/unix_docker_gpu.sh")
 
     # generate subprocess call
-    command = [bashscript, "3", dicom_import_folder,
-               nifti_export_folder, exam_import_folder, exam_export_folder, gpuid]
+    command = [
+        bashscript,
+        "3",
+        dicom_import_folder,
+        nifti_export_folder,
+        exam_import_folder,
+        exam_export_folder,
+        gpuid,
+    ]
     print(*command)
 
-
     print("starting docker!")
     subprocess.run(command, cwd=cwd)
     print("docker started!")