Black re-format

dicom2stl/Dicom2STL.py

@@ -51,7 +51,7 @@ def elapsedTime(start_time):
 
 def loadVolume(fname, tempDir=None, verbose=0):
     """Load the volume image from a zip file, a directory of Dicom files,
-       or a single volume image.  Return the SimpleITK image and the modality."""
+    or a single volume image.  Return the SimpleITK image and the modality."""
     modality = None
     zipFlag = False
     dirFlag = False
@@ -92,8 +92,7 @@ def loadVolume(fname, tempDir=None, verbose=0):
             print("zip")
         if not tempDir:
             with tempfile.TemporaryDirectory() as defaultTempDir:
-                img, modality = dicomutils.loadZipDicom(fname[0],
-                                                        defaultTempDir)
+                img, modality = dicomutils.loadZipDicom(fname[0], defaultTempDir)
         else:
             img, modality = dicomutils.loadZipDicom(fname[0], tempDir)
 
@@ -159,8 +158,7 @@ def writeMetadataFile(img, metaName):
 
 
 def volumeProcessingPipeline(
-    img, shrinkFlag=True, anisotropicSmoothing=False, thresholds=[],
-    medianFilter=False
+    img, shrinkFlag=True, anisotropicSmoothing=False, thresholds=[], medianFilter=False
 ):
     """Apply a series of filters to the volume image"""
     #
@@ -204,8 +202,7 @@ def volumeProcessingPipeline(
         print("Double Threshold: ", thresholds)
         t = time.perf_counter()
         img = sitk.DoubleThreshold(
-            img, thresholds[0], thresholds[1], thresholds[2], thresholds[3],
-            255, 0
+            img, thresholds[0], thresholds[1], thresholds[2], thresholds[3], 255, 0
         )
         elapsedTime(t)
         gc.collect()
@@ -308,7 +305,7 @@ def getTissueThresholds(tissueType):
 
 
 def Dicom2STL(args):
-    """ The primary dicom2stl function """
+    """The primary dicom2stl function"""
     # Global variables
     #
     thresholds = []
@@ -436,7 +433,7 @@ def Dicom2STL(args):
 
 
 def main():
-    """ Main function """
+    """Main function"""
     args = dicom2stl.utils.parseargs.parseargs()
     Dicom2STL(args)
 

dicom2stl/utils/dicomutils.py

@@ -35,7 +35,7 @@ def testDicomFile(file_path):
 
 
 def scanDirForDicom(dicomdir):
-    """ Scan directory for dicom series."""
+    """Scan directory for dicom series."""
     matches = []
     found_dirs = []
     try:

dicom2stl/utils/parseargs.py

@@ -16,6 +16,7 @@
 
 class disableFilter(argparse.Action):
     """Disable a filter"""
+
     def __call__(self, parser, args, values, option_string=None):
         # print("action, baby!", self.dest, values)
         # print(args, type(args))
@@ -27,7 +28,8 @@ def __call__(self, parser, args, values, option_string=None):
 
 
 class enableAnisotropic(argparse.Action):
-    """ Enable anisotropic filtering """
+    """Enable anisotropic filtering"""
+
     def __init__(self, nargs=0, **kw):
         super().__init__(nargs=nargs, **kw)
 
@@ -39,7 +41,8 @@ def __call__(self, parser, args, values, option_string=None):
 
 
 class enableLargest(argparse.Action):
-    """ Enable filtering for large objects """
+    """Enable filtering for large objects"""
+
     def __init__(self, nargs=0, **kw):
         super().__init__(nargs=nargs, **kw)
 
@@ -49,7 +52,7 @@ def __call__(self, parser, args, values, option_string=None):
 
 
 def createParser():
-    """ Create the command line argument parser """
+    """Create the command line argument parser"""
     parser = argparse.ArgumentParser()
 
     parser.add_argument("filenames", nargs="*")
@@ -121,7 +124,6 @@ def createParser():
 
     parser.add_argument("--version", action="version", version=f"{__version__}")
 
-
     # Options that apply to the volumetric portion of the pipeline
     vol_group = parser.add_argument_group("Volume options")
 
@@ -236,7 +238,7 @@ def createParser():
 
 
 def parseargs():
-    """ Parse the command line arguments """
+    """Parse the command line arguments"""
     parser = createParser()
     args = parser.parse_args()
     return args

dicom2stl/utils/regularize.py

@@ -10,8 +10,8 @@
 
 
 def regularize(img, maxdim=-1, verbose=False):
-    """ Regularize a volume.  I.e. resample it so that the voxels are cubic and the
-    orientation matrix is identity. """
+    """Regularize a volume.  I.e. resample it so that the voxels are cubic and the
+    orientation matrix is identity."""
     dims = img.GetSize()
 
     if verbose:
@@ -89,7 +89,7 @@ def regularize(img, maxdim=-1, verbose=False):
 
 
 def usage():
-    """ Usage info for the command line script """
+    """Usage info for the command line script"""
     print("")
     print("regularize.py [options] input_volume output_volume")
     print("")

dicom2stl/utils/vtkutils.py

@@ -21,7 +21,7 @@
 
 
 def elapsedTime(start_time):
-    """ time elapsed """
+    """time elapsed"""
     dt = time.perf_counter() - start_time
     print(f"    {dt:4.3f} hseconds")
 
@@ -466,23 +466,23 @@ def writeVTIVolume(vtkimg, name):
 
 
 def memquery1():
-    """ memory query 1 """
+    """memory query 1"""
     print("Hiya 1")
 
 
 # @profile
 
 
 def memquery2():
-    """ memory query 2 """
+    """memory query 2"""
     print("Hiya 2")
 
 
 # @profile
 
 
 def memquery3():
-    """ memory query 3 """
+    """memory query 3"""
     print("Hiya 3")