WIP: Add group modules

applications/pctfdk/CMakeLists.txt

@@ -1,4 +1,4 @@
-wrap_ggo(pctfdk_GGO_C pctfdk.ggo)
+wrap_ggo(pctfdk_GGO_C pctfdk.ggo ../pctinputprojections_section.ggo)
 add_executable(
   pctfdk
   pctfdk.cxx

applications/pctfdk/pctfdk.cxx

@@ -1,4 +1,5 @@
 #include "pctfdk_ggo.h"
+#include "pctGgoFunctions.h"
 #include "rtkGgoFunctions.h"
 
 #include "rtkThreeDCircularProjectionGeometryXMLFile.h"
@@ -7,7 +8,6 @@
 #include "pctFDKDDConeBeamReconstructionFilter.h"
 #include "pctFDKDDConeBeamVarianceReconstructionFilter.h"
 
-#include <itkRegularExpressionSeriesFileNames.h>
 #include <itkImageFileWriter.h>
 
 int
@@ -23,26 +23,10 @@ main(int argc, char * argv[])
   itk::MultiThreaderBase::SetGlobalMaximumNumberOfThreads(
     std::min<double>(8, itk::MultiThreaderBase::GetGlobalMaximumNumberOfThreads()));
 
-  // Generate file names
-  itk::RegularExpressionSeriesFileNames::Pointer names = itk::RegularExpressionSeriesFileNames::New();
-  names->SetDirectory(args_info.path_arg);
-  names->SetNumericSort(false);
-  names->SetRegularExpression(args_info.regexp_arg);
-  names->SetSubMatch(0);
-
-  if (args_info.verbose_flag)
-    std::cout << "Regular expression matches " << names->GetFileNames().size() << " file(s)..." << std::endl;
-
   // Projections reader
   using ProjectionImageType = itk::Image<OutputPixelType, Dimension + 1>;
   auto reader = rtk::ProjectionsReader<ProjectionImageType>::New();
-  reader->SetFileNames(names->GetFileNames());
-  if (args_info.wpc_given)
-  {
-    std::vector<double> coeffs;
-    coeffs.assign(args_info.wpc_arg, args_info.wpc_arg + args_info.wpc_given);
-    reader->SetWaterPrecorrectionCoefficients(coeffs);
-  }
+  pct::SetProjectionsReaderFromGgo<rtk::ProjectionsReader<ProjectionImageType>, args_info_pctfdk>(reader, args_info);
 
   // Geometry
   if (args_info.verbose_flag)

applications/pctfdk/pctfdk.ggo

@@ -3,11 +3,8 @@ version "Reconstruct a 3D volume from a sequence of projections [Feldkamp, David
 
 option "verbose"   v "Verbose execution"                                         flag                         off
 option "geometry"  g  "XML geometry file name"                                   string                       yes
-option "path"      p  "Path containing projections"                              string                       yes
-option "regexp"    r  "Regular expression to select projection files in path"    string                       yes
 option "output"    o "Output file name"                                          string                       yes
 option "lowmem"    l "Load only one projection per thread in memory"             flag                         off
-option "wpc"       - "Water precorrection coefficients (default is no correction)" double  multiple no
 
 section "Ramp filter"
 option "pad"       - "Data padding parameter to correct for truncation"           double                       no   default="0.0"

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/pctinputprojections_group.py

@@ -0,0 +1,183 @@
+import itk
+from itk import PCT as pct
+import numpy as np
+
+__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(
+        "--newdirection",
+        help="New value of input projections (before pre-processing)",
+        type=float,
+        nargs="+",
+    )
+    pctinputprojections_group.add_argument(
+        "--neworigin",
+        help="New origin of input projections (before pre-processing)",
+        type=float,
+        nargs="+",
+    )
+    pctinputprojections_group.add_argument(
+        "--newspacing",
+        help="New spacing of input projections (before pre-processing)",
+        type=float,
+        nargs="+",
+    )
+    pctinputprojections_group.add_argument(
+        "--lowercrop",
+        help="Lower boundary crop size",
+        type=int,
+        nargs="+",
+        default=[0],
+    )
+    pctinputprojections_group.add_argument(
+        "--uppercrop",
+        help="Upper boundary crop size",
+        type=int,
+        nargs="+",
+        default=[0],
+    )
+    pctinputprojections_group.add_argument(
+        "--binning",
+        help="Shrink / Binning factos in each direction",
+        type=int,
+        nargs="+",
+        default=[1],
+    )
+    pctinputprojections_group.add_argument(
+        "--wpc",
+        help="Water precorrection coefficients (default is no correction)",
+        type=float,
+        nargs="+",
+    )
+    pctinputprojections_group.add_argument(
+        "--radius",
+        help="Radius of neighborhood for conditional median filtering",
+        type=int,
+        nargs="+",
+        default=[0],
+    )
+    pctinputprojections_group.add_argument(
+        "--multiplier",
+        help="Threshold multiplier for conditional median filtering",
+        type=float,
+        default=0,
+    )
+
+
+# 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)
+
+    # Vector component extraction (not in PCT ggo)
+
+    # Change image information
+    Dimension = reader.GetOutput().GetImageDimension()
+    if args_info.newdirection is not None:
+        direction = [args_info.newdirection[0]] * 9
+        for i in range(min(9, len(args_info.newdirection))):
+            direction[i] = args_info.newdirection[i]
+        direction = np.array(direction).reshape((3, 3))
+        reader.SetDirection(itk.matrix_from_array(direction))
+
+    if args_info.newspacing is not None:
+        spacing = itk.Vector[itk.D, Dimension]()
+        spacing.Fill(args_info.newspacing[0])
+        for i in range(len(args_info.newspacing)):
+            spacing[i] = args_info.newspacing[i]
+        reader.SetSpacing(spacing)
+
+    if args_info.neworigin is not None:
+        origin = itk.Point[itk.D, Dimension]()
+        origin.Fill(args_info.neworigin[0])
+        for i in range(len(args_info.neworigin)):
+            origin[i] = args_info.neworigin[i]
+        reader.SetOrigin(origin)
+
+    # Crop boundaries
+    upperCrop = [0] * Dimension
+    lowerCrop = [0] * Dimension
+    if args_info.lowercrop is not None:
+        for i in range(len(args_info.lowercrop)):
+            lowerCrop[i] = args_info.lowercrop[i]
+    reader.SetLowerBoundaryCropSize(lowerCrop)
+    if args_info.uppercrop is not None:
+        for i in range(len(args_info.uppercrop)):
+            upperCrop[i] = args_info.uppercrop[i]
+    reader.SetUpperBoundaryCropSize(upperCrop)
+
+    # Conditional median
+    medianRadius = reader.GetMedianRadius()
+    if args_info.radius is not None:
+        for i in range(len(args_info.radius)):
+            medianRadius[i] = args_info.radius[i]
+    reader.SetMedianRadius(medianRadius)
+    if args_info.multiplier is not None:
+        reader.SetConditionalMedianThresholdMultiplier(args_info.multiplier)
+
+    # Shrink / Binning
+    binFactors = reader.GetShrinkFactors()
+    if args_info.binning is not None:
+        for i in range(len(args_info.binning)):
+            binFactors[i] = args_info.binning[i]
+    reader.SetShrinkFactors(binFactors)
+
+    # Water precorrection
+    if args_info.wpc is not None:
+        reader.SetWaterPrecorrectionCoefficients(args_info.wpc)
+
+    # Pass list to projections reader and update information
+    reader.SetFileNames(fileNames)
+    reader.UpdateOutputInformation()

applications/pctinputprojections_section.ggo

@@ -0,0 +1,14 @@
+section "Input projections and their pre-processing"
+option "path"         p "Path containing projections"                                   string           yes
+option "regexp"       r "Regular expression to select projection files in path"         string           yes
+option "nsort"        - "Numeric sort for regular expression matches"                   flag             off
+option "submatch"     - "Index of the submatch that will be used to sort matches"       int              no   default="0"
+option "newdirection" - "New value of input projections (before pre-processing)"        double  multiple no
+option "neworigin"    - "New origin of input projections (before pre-processing)"       double  multiple no
+option "newspacing"   - "New spacing of input projections (before pre-processing)"      double  multiple no
+option "lowercrop"    - "Lower boundary crop size"                                      int     multiple no   default="0"
+option "uppercrop"    - "Upper boundary crop size"                                      int     multiple no   default="0"
+option "binning"      - "Shrink / Binning factos in each direction"                     int     multiple no   default="1"
+option "wpc"          - "Water precorrection coefficients (default is no correction)"   double  multiple no
+option "radius"       - "Radius of neighborhood for conditional median filtering"       int     multiple no   default="0"
+option "multiplier"   - "Threshold multiplier for conditional median filtering"         double           no   default="0"