Merge branch 'RTKConsortium:master' into doc

RTKConsortium · Feb 20, 2025 · cae7d0b · cae7d0b
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diff --git a/applications/rtkadmmtotalvariation/rtkadmmtotalvariation.ggo b/applications/rtkadmmtotalvariation/rtkadmmtotalvariation.ggo
@@ -1,4 +1,3 @@
-package "rtkadmmtotalvariation"
 purpose "Performs an iterative 3D reconstruction with 3D TV regularization"
 
 option "verbose"   v "Verbose execution"                                         flag                         off

diff --git a/applications/rtkadmmwavelets/rtkadmmwavelets.ggo b/applications/rtkadmmwavelets/rtkadmmwavelets.ggo
@@ -1,4 +1,3 @@
-package "rtkadmmwavelets"
 purpose "Performs an iterative 3D reconstruction with Daubechies wavelets regularization"
 
 option "verbose"   v "Verbose execution"                                         flag                         off

diff --git a/applications/rtkamsterdamshroud/rtkamsterdamshroud.ggo b/applications/rtkamsterdamshroud/rtkamsterdamshroud.ggo
@@ -1,4 +1,3 @@
-package "rtkamsterdamshroud"
 purpose "Creates an Amsterdam Shroud image from a sequence of projections [Zijp et al, ICCR, 2004]."
 
 option "verbose"  v "Verbose execution"                                          flag            off

diff --git a/applications/rtkbackprojections/rtkbackprojections.ggo b/applications/rtkbackprojections/rtkbackprojections.ggo
@@ -1,4 +1,3 @@
-package "rtkbackprojections"
 purpose "Backprojects a volume according to a geometry file."
 
 option "verbose"   v "Verbose execution"                                         flag     off

diff --git a/applications/rtkbioscangeometry/rtkbioscangeometry.ggo b/applications/rtkbioscangeometry/rtkbioscangeometry.ggo
@@ -1,4 +1,3 @@
-package "rtkbioscangeometry"
 purpose "Creates an RTK geometry file from a sequence of x-ray projections of a Bioscan NanoSPECT/CT scanner."
 
 option "verbose"     v "Verbose execution"                           flag   off

diff --git a/applications/rtkcheckimagequality/rtkcheckimagequality.ggo b/applications/rtkcheckimagequality/rtkcheckimagequality.ggo
@@ -1,4 +1,3 @@
-package "rtkcheckimagequality"
 purpose "Checks the MSE of a reconstructed image against a reference."
 
 option "verbose" v "Verbose execution" flag   off

diff --git a/applications/rtkconjugategradient/rtkconjugategradient.ggo b/applications/rtkconjugategradient/rtkconjugategradient.ggo
@@ -1,4 +1,3 @@
-package "rtkconjugategradient"
 purpose "Reconstructs a 3D volume from a sequence of projections with a conjugate gradient technique"
 
 option "verbose"        v "Verbose execution"                                                                         flag   off

diff --git a/applications/rtkdigisensgeometry/rtkdigisensgeometry.ggo b/applications/rtkdigisensgeometry/rtkdigisensgeometry.ggo
@@ -1,4 +1,3 @@
-package "rtkdigisensgeometry"
 purpose "Creates an RTK geometry file from a Digisens geometry calibration."
 
 option "verbose"   v "Verbose execution"                                     flag            off

diff --git a/applications/rtkdrawgeometricphantom/rtkdrawgeometricphantom.ggo b/applications/rtkdrawgeometricphantom/rtkdrawgeometricphantom.ggo
@@ -1,4 +1,3 @@
-package "rtkdrawgeometricphantom"
 purpose "Computes a 3D voxelized phantom from a phantom description file"
 
 option "verbose"      v "Verbose execution"                         flag            off

diff --git a/applications/rtkdrawshepploganphantom/rtkdrawshepploganphantom.ggo b/applications/rtkdrawshepploganphantom/rtkdrawshepploganphantom.ggo
@@ -1,4 +1,3 @@
-package "rtkdrawshepploganphantom"
 purpose "Computes a 3D voxelized Shepp & Logan phantom with noise [https://www.slaney.org/pct/pct-errata.html]"
 
 option "verbose"      v "Verbose execution"                         flag            off

diff --git a/applications/rtkdualenergyforwardmodel/rtkdualenergyforwardmodel.cxx b/applications/rtkdualenergyforwardmodel/rtkdualenergyforwardmodel.cxx
@@ -40,7 +40,7 @@ main(int argc, char * argv[])
   using DualEnergyProjectionsType = itk::VectorImage<PixelValueType, Dimension>;
   using DualEnergyProjectionWriterType = itk::ImageFileWriter<DualEnergyProjectionsType>;
 
-  using IncidentSpectrumImageType = itk::VectorImage<PixelValueType, Dimension - 1>;
+  using IncidentSpectrumImageType = itk::Image<PixelValueType, Dimension>;
   using IncidentSpectrumReaderType = itk::ImageFileReader<IncidentSpectrumImageType>;
 
   using DetectorResponseImageType = itk::Image<PixelValueType, Dimension - 1>;
@@ -66,6 +66,10 @@ main(int argc, char * argv[])
   materialAttenuationsReader->SetFileName(args_info.attenuations_arg);
   materialAttenuationsReader->Update();
 
+  // Get parameters from the images
+  const unsigned int MaximumEnergy =
+    incidentSpectrumReaderHighEnergy->GetOutput()->GetLargestPossibleRegion().GetSize(0);
+
   // If the detector response is given by the user, use it. Otherwise, assume it is included in the
   // incident spectrum, and fill the response with ones
   DetectorResponseReaderType::Pointer detectorResponseReader = DetectorResponseReaderType::New();
@@ -82,16 +86,13 @@ main(int argc, char * argv[])
       rtk::ConstantImageSource<DetectorResponseImageType>::New();
     DetectorResponseImageType::SizeType sourceSize;
     sourceSize[0] = 1;
-    sourceSize[1] = incidentSpectrumReaderHighEnergy->GetOutput()->GetVectorLength();
+    sourceSize[1] = MaximumEnergy;
     detectorSource->SetSize(sourceSize);
     detectorSource->SetConstant(1.0);
     detectorSource->Update();
     detectorImage = detectorSource->GetOutput();
   }
 
-  // Get parameters from the images
-  const unsigned int MaximumEnergy = incidentSpectrumReaderHighEnergy->GetOutput()->GetVectorLength();
-
   // Generate a set of zero-filled intensity projections
   DualEnergyProjectionsType::Pointer dualEnergyProjections = DualEnergyProjectionsType::New();
   dualEnergyProjections->CopyInformation(decomposedProjectionReader->GetOutput());

diff --git a/applications/rtkdualenergyforwardmodel/rtkdualenergyforwardmodel.ggo b/applications/rtkdualenergyforwardmodel/rtkdualenergyforwardmodel.ggo
@@ -1,4 +1,3 @@
-package "rtkspectralforwardmodel"
 purpose "Computes expected photon counts from incident spectrum, material attenuations, detector response and material-decomposed projections"
 
 option "verbose"    v "Verbose execution"                                                 flag                         off

diff --git a/applications/rtkdualenergysimplexdecomposition/rtkdualenergysimplexdecomposition.cxx b/applications/rtkdualenergysimplexdecomposition/rtkdualenergysimplexdecomposition.cxx
@@ -41,7 +41,7 @@ main(int argc, char * argv[])
   using DualEnergyProjectionsType = itk::VectorImage<PixelValueType, Dimension>;
   using DualEnergyProjectionReaderType = itk::ImageFileReader<DualEnergyProjectionsType>;
 
-  using IncidentSpectrumImageType = itk::VectorImage<PixelValueType, Dimension - 1>;
+  using IncidentSpectrumImageType = itk::Image<PixelValueType, Dimension>;
   using IncidentSpectrumReaderType = itk::ImageFileReader<IncidentSpectrumImageType>;
 
   using DetectorResponseImageType = itk::Image<PixelValueType, Dimension - 1>;
@@ -71,6 +71,10 @@ main(int argc, char * argv[])
   materialAttenuationsReader->SetFileName(args_info.attenuations_arg);
   materialAttenuationsReader->Update();
 
+  // Get parameters from the images
+  const unsigned int MaximumEnergy =
+    incidentSpectrumReaderHighEnergy->GetOutput()->GetLargestPossibleRegion().GetSize(0);
+
   // If the detector response is given by the user, use it. Otherwise, assume it is included in the
   // incident spectrum, and fill the response with ones
   DetectorResponseReaderType::Pointer detectorResponseReader = DetectorResponseReaderType::New();
@@ -87,23 +91,13 @@ main(int argc, char * argv[])
       rtk::ConstantImageSource<DetectorResponseImageType>::New();
     DetectorResponseImageType::SizeType sourceSize;
     sourceSize[0] = 1;
-    sourceSize[1] = incidentSpectrumReaderHighEnergy->GetOutput()->GetVectorLength();
+    sourceSize[1] = MaximumEnergy;
     detectorSource->SetSize(sourceSize);
     detectorSource->SetConstant(1.0);
     detectorSource->Update();
     detectorImage = detectorSource->GetOutput();
   }
 
-  // Get parameters from the images
-  const unsigned int MaximumEnergy = incidentSpectrumReaderHighEnergy->GetOutput()->GetVectorLength();
-
-  IncidentSpectrumImageType::IndexType indexIncident;
-  indexIncident.Fill(0);
-  if (incidentSpectrumReaderLowEnergy->GetOutput()->GetPixel(indexIncident).Size() != MaximumEnergy)
-    itkGenericExceptionMacro(<< "Low energy incident spectrum image has vector size "
-                             << incidentSpectrumReaderLowEnergy->GetOutput()->GetPixel(indexIncident).Size()
-                             << ", should be " << MaximumEnergy);
-
   if (detectorImage->GetLargestPossibleRegion().GetSize()[1] != MaximumEnergy)
     itkGenericExceptionMacro(<< "Detector response image has " << detectorImage->GetLargestPossibleRegion().GetSize()[1]
                              << "energies, should have " << MaximumEnergy);

diff --git a/applications/rtkdualenergysimplexdecomposition/rtkdualenergysimplexdecomposition.ggo b/applications/rtkdualenergysimplexdecomposition/rtkdualenergysimplexdecomposition.ggo
@@ -1,4 +1,3 @@
-package "rtkdualenergysimplexdecomposition"
 purpose "Decomposes dual energy projections into materials"
 
 option "verbose"          v "Verbose execution"                                                 flag                         off

diff --git a/applications/rtkelektasynergygeometry/rtkelektasynergygeometry.ggo b/applications/rtkelektasynergygeometry/rtkelektasynergygeometry.ggo
@@ -1,4 +1,3 @@
-package "rtkelektasynergygeometry"
 purpose "Creates an RTK geometry file from an Elekta Synergy acquisition."
 
 option "verbose"   v "Verbose execution"                    flag   off

diff --git a/applications/rtkextractphasesignal/rtkextractphasesignal.ggo b/applications/rtkextractphasesignal/rtkextractphasesignal.ggo
@@ -1,4 +1,3 @@
-package "rtkextractshroudsignal"
 purpose "Extracts the phase from a signal."
 
 option "verbose"    v   "Verbose execution"                                   flag                    off

diff --git a/applications/rtkextractshroudsignal/rtkextractshroudsignal.ggo b/applications/rtkextractshroudsignal/rtkextractshroudsignal.ggo
@@ -1,4 +1,3 @@
-package "rtkextractshroudsignal"
 purpose "Extracts the breathing signal from a shroud image."
 
 option "verbose"    v   "Verbose execution"                           flag                    off

diff --git a/applications/rtkfdk/rtkfdk.ggo b/applications/rtkfdk/rtkfdk.ggo
@@ -1,4 +1,3 @@
-package "rtkfdk"
 purpose "Reconstructs a 3D volume from a sequence of projections [Feldkamp, David, Kress, 1984]."
 
 option "verbose"    v "Verbose execution"                                           flag                         off

diff --git a/applications/rtkfdktwodweights/rtkfdktwodweights.ggo b/applications/rtkfdktwodweights/rtkfdktwodweights.ggo
@@ -1,4 +1,3 @@
-package "rtkfdktwodweights"
 purpose "Weights projection stack with 2D weights of Feldkamp cone-beam reconstruction algorithm."
 
 option "verbose"   v "Verbose execution"                                         flag                off

diff --git a/applications/rtkfieldofview/rtkfieldofview.ggo b/applications/rtkfieldofview/rtkfieldofview.ggo
@@ -1,4 +1,3 @@
-package "rtkfieldofview"
 purpose "Computes the field of view of a reconstruction."
 
 option "verbose"        v "Verbose execution"                                         flag     off

diff --git a/applications/rtkforwardprojections/rtkforwardprojections.ggo b/applications/rtkforwardprojections/rtkforwardprojections.ggo
@@ -1,4 +1,3 @@
-package "rtkforwardprojections"
 purpose "Projects a volume according to a geometry file."
 
 option "verbose"   v "Verbose execution"                                         flag     off

diff --git a/applications/rtkfourdconjugategradient/rtkfourdconjugategradient.ggo b/applications/rtkfourdconjugategradient/rtkfourdconjugategradient.ggo
@@ -1,4 +1,3 @@
-package "rtkfourdconjugategradient"
 purpose "Reconstructs a 3D + time sequence of volumes from a projection stack and a respiratory/cardiac signal, with a conjugate gradient technique"
 
 option "verbose"     v "Verbose execution"                                     flag   off

diff --git a/applications/rtkfourdfdk/rtkfourdfdk.ggo b/applications/rtkfourdfdk/rtkfourdfdk.ggo
@@ -1,4 +1,3 @@
-package "rtkfourdfdk"
 purpose "Reconstructs a 4D volume from a sequence of projections using FDK with one projection per respiratory cycle in each frame."
 
 option "verbose"    v "Verbose execution"                                           flag                off

diff --git a/applications/rtkfourdrooster/rtkfourdrooster.ggo b/applications/rtkfourdrooster/rtkfourdrooster.ggo
@@ -1,4 +1,3 @@
-package "rtkfourdrooster"
 purpose "Reconstructs a 3D + time sequence of volumes from a projection stack and a respiratory/cardiac signal, applying TV regularization in space and time, and restricting motion to a region of interest"
 
 option "verbose"     v "Verbose execution"                                     flag   off

diff --git a/applications/rtkfourdsart/rtkfourdsart.ggo b/applications/rtkfourdsart/rtkfourdsart.ggo
@@ -1,4 +1,3 @@
-package "rtkfourdsart"
 purpose "Reconstructs a 4D sequence of volumes from a sequence of projections with a 4D version of the Simulatenous Algebraic Reconstruction Technique [Andersen, 1984]."
 
 option "verbose"     v "Verbose execution"                                     flag   off

diff --git a/applications/rtkgaincorrection/rtkgaincorrection.ggo b/applications/rtkgaincorrection/rtkgaincorrection.ggo
@@ -1,4 +1,3 @@
-package "rtk"
 purpose "Polynomial gain correction projections"
 
 option  "config"     - "Config file"                                              string        no

diff --git a/applications/rtki0estimation/rtki0estimation.ggo b/applications/rtki0estimation/rtki0estimation.ggo
@@ -1,4 +1,3 @@
-package "rtki0estimation"
 purpose "Reads projection images and estimates the I0 value for each of them"
 
 option "verbose"  v "Verbose execution"                                         flag      off

diff --git a/applications/rtkimagxgeometry/rtkimagxgeometry.ggo b/applications/rtkimagxgeometry/rtkimagxgeometry.ggo
@@ -1,4 +1,3 @@
-package "rtkimagxgeometry"
 purpose "Creates an RTK geometry file from an iMagX  acquisition."
 
 option "config"      - "Config file"                       string no

diff --git a/applications/rtkiterativefdk/rtkiterativefdk.ggo b/applications/rtkiterativefdk/rtkiterativefdk.ggo
@@ -1,4 +1,3 @@
-package "rtkiterativefdk"
 purpose "Reconstructs a 3D volume from a sequence of projections [Feldkamp, David, Kress, 1984]."
 
 option "verbose"    v "Verbose execution"                                           flag                         off

diff --git a/applications/rtklagcorrection/rtklagcorrection.ggo b/applications/rtklagcorrection/rtklagcorrection.ggo
@@ -1,4 +1,3 @@
-package "rtklagcorrection"
 purpose "4th order LTI Lag correction"
 
 option  "config"       - "Config file"                                       string         no

diff --git a/applications/rtklastdimensionl0gradientdenoising/rtklastdimensionl0gradientdenoising.ggo b/applications/rtklastdimensionl0gradientdenoising/rtklastdimensionl0gradientdenoising.ggo
@@ -1,4 +1,3 @@
-package "rtklastdimensionl0gradientdenoising"
 purpose "Performs denoising by minimizing the l0 norm of the gradient"
 
 option "verbose"   v "Verbose execution"                                            flag         off

diff --git a/applications/rtklut/rtklut.ggo b/applications/rtklut/rtklut.ggo
@@ -1,4 +1,3 @@
-package "rtklut"
 purpose "Converts pixel intensities of projection images according to lookup table"
 
 option "verbose"   v "Verbose execution"                                         flag     off

diff --git a/applications/rtkmaskcollimation/rtkmaskcollimation.ggo b/applications/rtkmaskcollimation/rtkmaskcollimation.ggo
@@ -1,4 +1,3 @@
-package "rtkmaskcollimation"
 purpose "Masks out the collimator from the projections"
 
 option "verbose"    v "Verbose execution"                                         flag     off

diff --git a/applications/rtkmcrooster/rtkmcrooster.ggo b/applications/rtkmcrooster/rtkmcrooster.ggo
@@ -1,4 +1,3 @@
-package "rtkmcrooster"
 purpose "Reconstructs a 3D + time sequence of volumes from a projection stack and a respiratory/cardiac signal, applying TV regularization in space and time, and restricting motion to a region of interest"
 
 option "verbose"     v "Verbose execution"                                     flag   off

diff --git a/...rtkmotioncompensatedfourdconjugategradient/rtkmotioncompensatedfourdconjugategradient.ggo b/...rtkmotioncompensatedfourdconjugategradient/rtkmotioncompensatedfourdconjugategradient.ggo
@@ -1,4 +1,3 @@
-package "rtkmotioncompensatedfourdconjugategradient"
 purpose "Performs a motion-compensated 4D reconstruction by the conjugate gradient method"
 
 option "verbose"     v "Verbose execution"                                     flag   off

diff --git a/applications/rtkorageometry/rtkorageometry.ggo b/applications/rtkorageometry/rtkorageometry.ggo
@@ -1,4 +1,3 @@
-package "rtkorageometry"
 purpose "Creates an RTK geometry file from a sequence of ora.xml files (radART / medPhoton file format)."
 
 option "verbose"     v "Verbose execution"                           flag   off

diff --git a/applications/rtkosem/rtkosem.ggo b/applications/rtkosem/rtkosem.ggo
@@ -1,4 +1,3 @@
-package "rtkosem"
 purpose "Reconstructs a 3D volume from a sequence of projections with Ordered subset expectation maximization."
 
 option "verbose"     v "Verbose execution"                                     flag   off

diff --git a/applications/rtkoverlayphaseandshroud/rtkoverlayphaseandshroud.ggo b/applications/rtkoverlayphaseandshroud/rtkoverlayphaseandshroud.ggo
@@ -1,4 +1,3 @@
-package "rtkoverlayphaseandshroud"
 purpose "Generates an RGB image showing the phase peaks on top of the shroud"
 
 option "verbose"    v   "Verbose execution"                           flag                    off

diff --git a/applications/rtkparkershortscanweighting/rtkparkershortscanweighting.ggo b/applications/rtkparkershortscanweighting/rtkparkershortscanweighting.ggo
@@ -1,4 +1,3 @@
-package "rtkparkershortscanweighting"
 purpose "Weights projection stack with parker weights for short scan with a divergent geometry."
 
 option "verbose"    v "Verbose execution"                                           flag                off

diff --git a/applications/rtkprojectgeometricphantom/rtkprojectgeometricphantom.ggo b/applications/rtkprojectgeometricphantom/rtkprojectgeometricphantom.ggo
@@ -1,4 +1,3 @@
-package "rtkprojectgeometricphantom"
 purpose "Computes projections through a 3D phantom described by a file, according to a geometry"
 
 option "verbose"      v "Verbose execution"                         flag            off

diff --git a/applications/rtkprojectionmatrix/rtkprojectionmatrix.ggo b/applications/rtkprojectionmatrix/rtkprojectionmatrix.ggo
@@ -1,4 +1,3 @@
-package "rtkprojectionmatrix"
 purpose "Saves the sparse system matrix of rtk::JosephForwardProjectionImageFilter in a file. Only works in 2D."
 
 option "verbose"   v "Verbose execution"                                     flag   off

diff --git a/applications/rtkprojections/rtkprojections.ggo b/applications/rtkprojections/rtkprojections.ggo
@@ -1,4 +1,3 @@
-package "rtkprojections"
 purpose "Reads raw projection images, converts them to attenuation and stacks them into a single output image file"
 
 option "verbose"  v "Verbose execution"                                         flag      off

diff --git a/applications/rtkprojectshepploganphantom/rtkprojectshepploganphantom.ggo b/applications/rtkprojectshepploganphantom/rtkprojectshepploganphantom.ggo
@@ -1,4 +1,3 @@
-package "rtkprojectshepploganphantom"
 purpose "Computes projections through a 3D Shepp & Logan phantom, according to a geometry"
 
 option "verbose"      v "Verbose execution"                         flag     off

diff --git a/applications/rtkramp/rtkramp.ggo b/applications/rtkramp/rtkramp.ggo
@@ -1,4 +1,3 @@
-package "rtkramp"
 purpose "Reads raw projection images, converts to attenuation, ramp filters and stacks them into a single output image file"
 
 option "verbose"    v "Verbose execution"                                           flag                off

diff --git a/applications/rtkrayboxintersection/rtkrayboxintersection.ggo b/applications/rtkrayboxintersection/rtkrayboxintersection.ggo
@@ -1,4 +1,3 @@
-package "rtkrayboxintersection"
 purpose "Computes the intersection length between rays of 2D projections and a 3D volume."
 
 option "verbose"   v "Verbose execution"                                         flag     off

diff --git a/applications/rtkrayellipsoidintersection/rtkrayellipsoidintersection.ggo b/applications/rtkrayellipsoidintersection/rtkrayellipsoidintersection.ggo
@@ -1,4 +1,3 @@
-package "rtkrayellipsoidintersection"
 purpose "Computes the intersection length between rays of 2D projections and a 3D ellipsoid"
 
 option "verbose"    v "Verbose execution"                                         flag     off

diff --git a/applications/rtkrayquadricintersection/rtkrayquadricintersection.ggo b/applications/rtkrayquadricintersection/rtkrayquadricintersection.ggo
@@ -1,4 +1,3 @@
-package "rtkrayquadricintersection"
 purpose "Computes the intersection length between rays of 2D projections and a 3D quadric"
 
 option "verbose"    v "Verbose execution"                                         flag     off

diff --git a/applications/rtkregularizedconjugategradient/rtkregularizedconjugategradient.ggo b/applications/rtkregularizedconjugategradient/rtkregularizedconjugategradient.ggo
@@ -1,4 +1,3 @@
-package "rtkregularizedconjugategradient"
 purpose "Alternates between conjugate gradient reconstruction and regularization"
 
 option "verbose"        v "Verbose execution"                                                                         flag   off

diff --git a/applications/rtksart/rtksart.ggo b/applications/rtksart/rtksart.ggo
@@ -1,4 +1,3 @@
-package "rtksart"
 purpose "Reconstructs a 3D volume from a sequence of projections with Simulatenous Algebraic Reconstruction Technique [Andersen, 1984]."
 
 option "verbose"     v "Verbose execution"                                     flag   off

diff --git a/applications/rtkscatterglarecorrection/rtkscatterglarecorrection.ggo b/applications/rtkscatterglarecorrection/rtkscatterglarecorrection.ggo
@@ -1,4 +1,3 @@
-package "rtkscatterglarecorrection"
 purpose "Reads projection images and correct them for scatter glare"
 
 option "verbose"      v "Verbose execution"                                         flag      off

diff --git a/applications/rtksimulatedgeometry/rtksimulatedgeometry.ggo b/applications/rtksimulatedgeometry/rtksimulatedgeometry.ggo
@@ -1,4 +1,3 @@
-package "rtksimulatedgeometry"
 purpose "Creates an RTK geometry file from simulated/regular trajectory. See https://docs.openrtk.org/en/latest/documentation/docs/Geometry.html for more information."
 
 option "verbose"     v "Verbose execution"                                                    flag   off

diff --git a/applications/rtkspectraldenoiseprojections/rtkspectraldenoiseprojections.ggo b/applications/rtkspectraldenoiseprojections/rtkspectraldenoiseprojections.ggo
@@ -1,4 +1,3 @@
-package "rtkspectraldenoiseprojections"
 purpose "Replaces aberrant pixels by the median in a small neighborhood around them. Pixels are aberrant if the difference between their value and the median is larger that threshold multiplier * the standard deviation in the neighborhood"
 
 option "verbose"  v "Verbose execution"                                                                                   flag      off

diff --git a/applications/rtkspectralforwardmodel/rtkspectralforwardmodel.cxx b/applications/rtkspectralforwardmodel/rtkspectralforwardmodel.cxx
@@ -34,7 +34,7 @@ main(int argc, char * argv[])
   constexpr unsigned int Dimension = 3;
   using DecomposedProjectionType = itk::VectorImage<PixelValueType, Dimension>;
   using MeasuredProjectionsType = itk::VectorImage<PixelValueType, Dimension>;
-  using IncidentSpectrumImageType = itk::VectorImage<PixelValueType, Dimension - 1>;
+  using IncidentSpectrumImageType = itk::Image<PixelValueType, Dimension>;
   using DetectorResponseImageType = itk::Image<PixelValueType, Dimension - 1>;
   using MaterialAttenuationsImageType = itk::Image<PixelValueType, Dimension - 1>;
 
@@ -55,7 +55,7 @@ main(int argc, char * argv[])
   // Get parameters from the images
   const unsigned int NumberOfMaterials = materialAttenuations->GetLargestPossibleRegion().GetSize()[0];
   const unsigned int NumberOfSpectralBins = args_info.thresholds_given;
-  const unsigned int MaximumEnergy = incidentSpectrum->GetVectorLength();
+  const unsigned int MaximumEnergy = incidentSpectrum->GetLargestPossibleRegion().GetSize()[0];
 
   // Generate a set of zero-filled photon count projections
   MeasuredProjectionsType::Pointer measuredProjections = MeasuredProjectionsType::New();
@@ -88,12 +88,6 @@ main(int argc, char * argv[])
                              << measuredProjections->GetPixel(indexSpect).Size() << ", should be "
                              << NumberOfSpectralBins);
 
-  IncidentSpectrumImageType::IndexType indexIncident;
-  indexIncident.Fill(0);
-  if (incidentSpectrum->GetPixel(indexIncident).Size() != MaximumEnergy)
-    itkGenericExceptionMacro(<< "Incident spectrum image has vector size "
-                             << incidentSpectrum->GetPixel(indexIncident).Size() << ", should be " << MaximumEnergy);
-
   if (detectorResponse->GetLargestPossibleRegion().GetSize()[0] != MaximumEnergy)
     itkGenericExceptionMacro(<< "Detector response image has "
                              << detectorResponse->GetLargestPossibleRegion().GetSize()[0] << "energies, should have "

diff --git a/applications/rtkspectralforwardmodel/rtkspectralforwardmodel.ggo b/applications/rtkspectralforwardmodel/rtkspectralforwardmodel.ggo
@@ -1,4 +1,3 @@
-package "rtkspectralforwardmodel"
 purpose "Computes expected photon counts from incident spectrum, material attenuations, detector response and material-decomposed projections"
 
 option "verbose"    v "Verbose execution"                                                 flag                         off

diff --git a/applications/rtkspectralonestep/rtkspectralonestep.ggo b/applications/rtkspectralonestep/rtkspectralonestep.ggo
@@ -1,4 +1,3 @@
-package "rtkconjugategradient"
 purpose "Reconstructs a set of 3D volumes from a set of photon counts projections, using the method described by Mechlem et al. in IEEE TMI in 2017"
 
 option "verbose"               v "Verbose execution"                                                 flag   off

diff --git a/applications/rtkspectralrooster/rtkspectralrooster.ggo b/applications/rtkspectralrooster/rtkspectralrooster.ggo
@@ -1,4 +1,3 @@
-package "rtkspectralrooster"
 purpose "Reconstructs a 3D + material vector volume from a vector projection stack, alternating between conjugate gradient optimization and regularization, including between materials"
 
 option "verbose"     v "Verbose execution"                                     flag   off