ENH: Use comma separator for lists in python command arguments

applications/rtk3Doutputimage_group.py

@@ -1,4 +1,5 @@
 import itk
+from itk import RTK as rtk
 
 __all__ = [
     'add_rtk3Doutputimage_group',
@@ -8,10 +9,10 @@
 # Mimicks rtk3Doutputimage_section.ggo
 def add_rtk3Doutputimage_group(parser):
   rtk3Doutputimage_group = parser.add_argument_group('Output 3D image properties')
-  rtk3Doutputimage_group.add_argument('--origin', help='Origin (default=centered)', type=float, nargs='+')
-  rtk3Doutputimage_group.add_argument('--dimension', help='Dimension', type=int, nargs='+', default=[256])
-  rtk3Doutputimage_group.add_argument('--spacing', help='Spacing', type=float, nargs='+', default=[1])
-  rtk3Doutputimage_group.add_argument('--direction', help='Direction', type=float, nargs='+')
+  rtk3Doutputimage_group.add_argument('--origin', help='Origin (default=centered)', type=rtk.comma_separated_args(float))
+  rtk3Doutputimage_group.add_argument('--dimension', help='Dimension', type=rtk.comma_separated_args(int), default=[256])
+  rtk3Doutputimage_group.add_argument('--spacing', help='Spacing', type=rtk.comma_separated_args(float), default=[1])
+  rtk3Doutputimage_group.add_argument('--direction', help='Direction', type=rtk.comma_separated_args(float))
   rtk3Doutputimage_group.add_argument('--like', help='Copy information from this image (origin, dimension, spacing, direction)')
 
 # Mimicks SetConstantImageSourceFromGgo

applications/rtkinputprojections_group.py

@@ -1,4 +1,5 @@
 import itk
+from itk import RTK as rtk
 
 __all__ = [
     'add_rtkinputprojections_group',
@@ -13,20 +14,20 @@ def add_rtkinputprojections_group(parser):
   rtkinputprojections_group.add_argument('--nsort', help='Numeric sort for regular expression matches', action='store_true')
   rtkinputprojections_group.add_argument('--submatch', help='Index of the submatch that will be used to sort matches', type=int, default=0)
   rtkinputprojections_group.add_argument('--nolineint', help='Disable raw to line integral conversion, just casts to float', type=bool, default=False)
-  rtkinputprojections_group.add_argument('--newdirection', help='New value of input projections (before pre-processing)', type=float, nargs='+')
-  rtkinputprojections_group.add_argument('--neworigin', help='New origin of input projections (before pre-processing)', type=float, nargs='+')
-  rtkinputprojections_group.add_argument('--newspacing', help='New spacing of input projections (before pre-processing)', type=float, nargs='+')
-  rtkinputprojections_group.add_argument('--lowercrop', help='Lower boundary crop size', type=int, nargs='+', default=[0])
-  rtkinputprojections_group.add_argument('--uppercrop', help='Upper boundary crop size', type=int, nargs='+', default=[0])
-  rtkinputprojections_group.add_argument('--binning', help='Shrink / Binning factos in each direction', type=int, nargs='+', default=[1])
-  rtkinputprojections_group.add_argument('--wpc', help='Water precorrection coefficients (default is no correction)', type=float, nargs='+')
+  rtkinputprojections_group.add_argument('--newdirection', help='New value of input projections (before pre-processing)', type=rtk.comma_separated_args(float))
+  rtkinputprojections_group.add_argument('--neworigin', help='New origin of input projections (before pre-processing)', type=rtk.comma_separated_args(float))
+  rtkinputprojections_group.add_argument('--newspacing', help='New spacing of input projections (before pre-processing)', type=rtk.comma_separated_args(float))
+  rtkinputprojections_group.add_argument('--lowercrop', help='Lower boundary crop size', type=rtk.comma_separated_args(int))
+  rtkinputprojections_group.add_argument('--uppercrop', help='Upper boundary crop size', type=rtk.comma_separated_args(int))
+  rtkinputprojections_group.add_argument('--binning', help='Shrink / Binning factos in each direction', type=rtk.comma_separated_args(int), default=[1])
+  rtkinputprojections_group.add_argument('--wpc', help='Water precorrection coefficients (default is no correction)', type=rtk.comma_separated_args(float))
   rtkinputprojections_group.add_argument('--spr', help='Boellaard scatter correction: scatter-to-primary ratio', type=float, default=0)
   rtkinputprojections_group.add_argument('--nonneg', help='Boellaard scatter correction: non-negativity threshold', type=float)
   rtkinputprojections_group.add_argument('--airthres', help='Boellaard scatter correction: air threshold', type=float)
   rtkinputprojections_group.add_argument('--i0', help='I0 value (when assumed constant per projection), 0 means auto', type=float)
   rtkinputprojections_group.add_argument('--idark', help='IDark value, i.e., value when beam is off', type=float, default=0)
   rtkinputprojections_group.add_argument('--component', help='Vector component to extract, for multi-material projections', type=int, default=0)
-  rtkinputprojections_group.add_argument('--radius', help='Radius of neighborhood for conditional median filtering', type=int, nargs='+', default=[0])
+  rtkinputprojections_group.add_argument('--radius', help='Radius of neighborhood for conditional median filtering', type=rtk.comma_separated_args(int), default=[0])
   rtkinputprojections_group.add_argument('--multiplier', help='Threshold multiplier for conditional median filtering', type=float, default=0)
 
 # Mimicks GetProjectionsFileNamesFromGgo

applications/rtkorageometry/rtkorageometry.py

@@ -13,7 +13,7 @@ def main():
   parser.add_argument('--output', '-o', help='Output file name', required=True)
   parser.add_argument('--path', '-p', help='Path containing projections', required=True)
   parser.add_argument('--regexp', '-r', help='Regular expression to select projection files in path')
-  parser.add_argument('--margin', '-m', help='Collimation margin (uinf, usup, vinf, vsup)', type=float, nargs='+', default=0.)
+  parser.add_argument('--margin', '-m', help='Collimation margin (uinf, usup, vinf, vsup)', type=rtk.comma_separated_args(float), default=0.)
 
   args = parser.parse_args()
 
@@ -25,8 +25,8 @@ def main():
   print(margin)
 
   names = itk.RegularExpressionSeriesFileNames.New()
-  names.SetDirectory(args.path);
-  names.SetRegularExpression(args.regexp);
+  names.SetDirectory(args.path)
+  names.SetRegularExpression(args.regexp)
 
   reader = rtk.OraGeometryReader.New()
   reader.SetProjectionsFileNames(names.GetFileNames())

wrapping/rtkExtra.py

@@ -33,6 +33,11 @@ def CudaImageFromImage(img):
         return cuda_img
     return img  # Return the original image if CUDA is not available
 
+# Returns a lambda function that parses a comma-separated string and converts each element to the specified type.
+def comma_separated_args(value_type):
+    return lambda value: [value_type(s.strip()) for s in value.split(',')]
+
+# Returns the progress percentage
 class PercentageProgressCommand:
     def __init__(self,caller):
         self.percentage = -1
@@ -45,4 +50,4 @@ def callback(self):
             self.percentage = new_percentage
 
     def End(self):
-        print()  # Print newline when execution ends
+        print()  # Print newline when execution ends