WIP: Add group modules

applications/pctfdk/pctfdk.py

@@ -16,16 +16,6 @@ def build_parser():
     parser.add_argument(
         "--geometry", "-g", help="XML geometry file name", type=str, required=True
     )
-    parser.add_argument(
-        "--path", "-p", help="Path containing projections", type=str, required=True
-    )
-    parser.add_argument(
-        "--regexp",
-        "-r",
-        help="Regular expression to select projection files in path",
-        type=str,
-        required=True,
-    )
     parser.add_argument(
         "--output", "-o", help="Output file name", type=str, required=True
     )
@@ -35,12 +25,6 @@ def build_parser():
         help="Load only one projection per thread in memory",
         action="store_true",
     )
-    parser.add_argument(
-        "--wpc",
-        help="Water precorrection coefficients (default is no correction)",
-        type=float,
-        nargs="+",
-    )
 
     # Ramp filter
     parser.add_argument(
@@ -81,29 +65,21 @@ def build_parser():
         help="Copy info from image (origin, size, spacing, direction)",
         type=str,
     )
+
+    pct.add_pctinputprojections_group(parser)
+
     return parser
 
 
 def process(args_info: argparse.Namespace):
     from itk import RTK as rtk
 
-    # Generate file names
-    names = itk.RegularExpressionSeriesFileNames.New()
-    names.SetDirectory(args_info.path)
-    names.SetNumericSort(False)
-    names.SetRegularExpression(args_info.regexp)
-    names.SetSubMatch(0)
-    if args_info.verbose:
-        print(f"Regular expression matches {len(names.GetFileNames())} file(s)...")
-
     # Projections reader
     OutputPixelType = itk.F
     ProjectionImageType = itk.Image[OutputPixelType, 4]
     ReaderType = rtk.ProjectionsReader[ProjectionImageType]
     reader = ReaderType.New()
-    reader.SetFileNames(names.GetFileNames())
-    if args_info.wpc:
-        reader.SetWaterPrecorrectionCoefficients([float(c) for c in args_info.wpc])
+    pct.SetProjectionsReaderFromArgParse(reader, args_info)
 
     # Geometry
     if args_info.verbose:

applications/pctinputprojection_group.py

@@ -0,0 +1,77 @@
+import itk
+from itk import PCT as pct
+
+__all__ = [
+    "add_pctinputprojections_group",
+    "GetProjectionsFileNamesFromArgParse",
+]
+
+
+# Mimicks pctinputprojections_section.ggo
+def add_pctinputprojections_group(parser):
+    pctinputprojections_group = parser.add_argument_group(
+        "Input projections and their pre-processing"
+    )
+    pctinputprojections_group.add_argument(
+        "--path", "-p", help="Path containing projections", required=True
+    )
+    pctinputprojections_group.add_argument(
+        "--regexp",
+        "-r",
+        help="Regular expression to select projection files in path",
+        required=True,
+    )
+    pctinputprojections_group.add_argument(
+        "--nsort",
+        help="Numeric sort for regular expression matches",
+        action="store_true",
+    )
+    pctinputprojections_group.add_argument(
+        "--submatch",
+        help="Index of the submatch that will be used to sort matches",
+        type=int,
+        default=0,
+    )
+    pctinputprojections_group.add_argument(
+        "--wpc",
+        help="Water precorrection coefficients (default is no correction)",
+        type=float,
+        nargs="+",
+    )
+
+
+# Mimicks GetProjectionsFileNamesFromGgo
+def GetProjectionsFileNamesFromArgParse(args_info):
+    # Generate file names
+    names = itk.RegularExpressionSeriesFileNames.New()
+    names.SetDirectory(args_info.path)
+    names.SetNumericSort(args_info.nsort)
+    names.SetRegularExpression(args_info.regexp)
+    names.SetSubMatch(args_info.submatch)
+
+    if args_info.verbose:
+        print(f"Regular expression matches {len(names.GetFileNames())} file(s)...")
+
+    fileNames = []
+    for fn in names.GetFileNames():
+        imageio = itk.ImageIOFactory.CreateImageIO(
+            fn, itk.CommonEnums.IOFileMode_ReadMode
+        )
+        if imageio is None:
+            print(f"Ignoring file: {fn}")
+            continue
+        fileNames.append(fn)
+
+    return fileNames
+
+
+def SetProjectionsReaderFromArgParse(reader, args_info):
+    fileNames = GetProjectionsFileNamesFromArgParse(args_info)
+
+    # Water precorrection
+    if args_info.wpc is not None:
+        reader.SetWaterPrecorrectionCoefficients([float(c) for c in args_info.wpc])
+
+    # Pass list to projections reader and update information
+    reader.SetFileNames(fileNames)
+    reader.UpdateOutputInformation()

wrapping/CMakeLists.txt

@@ -9,24 +9,21 @@ configure_file(
 )
 
 file(
-  GLOB PCT_PYTHON_APP
+  GLOB PCT_GROUP_SCRIPTS
+  CONFIGURE_DEPENDS
+  "${PCT_SOURCE_DIR}/applications/pct*_group.py"
+)
+file(
+  GLOB PCT_APP_SCRIPTS
   CONFIGURE_DEPENDS
   "${PCT_SOURCE_DIR}/applications/pct*/pct*.py"
 )
 
 wrap_itk_python_bindings_install(/itk "PCT"
   __init_pct__.py
-  ${PCT_PYTHON_APP}
+  ${PCT_GROUP_SCRIPTS}
+  ${PCT_APP_SCRIPTS}
   ${PCT_VERSION_SCRIPT}
   ${PCT_SOURCE_DIR}/wrapping/pctExtras.py
   ${PCT_SOURCE_DIR}/applications/pctargumentparser.py
 )
-
-# Copy python applications to the ITK wrapping directory to ensure they can be imported in tests.
-# This directory is added to the PYTHONPATH by itk_python_add_test.
-if(ITK_DIR)
-  set(itk_wrap_python_binary_dir "${ITK_DIR}/Wrapping/Generators/Python")
-else()
-  set(itk_wrap_python_binary_dir "${ITK_BINARY_DIR}/Wrapping/Generators/Python")
-endif()
-file(COPY ${PCT_PYTHON_APP} DESTINATION "${itk_wrap_python_binary_dir}")

wrapping/__init_pct__.py

@@ -9,6 +9,7 @@
     "itk.pctversion",
     "itk.pctargumentparser",
     "itk.pctExtras",
+    "itk.pctinputprojection_group",
 ]
 for mod_name in pct_submodules:
     mod = importlib.import_module(mod_name)