clitkDicomRTPlan2Gate tool added

diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 8ab0488a06274e61fd5f7ccf5d0511b91b0c1517..f7d426d216310f8845efc889d69cf92e3eaab93d 100644 (file)
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -252,6 +252,13 @@ IF (CLITK_BUILD_TOOLS)
     SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkMeshViewer)
   ENDIF(CLITK_EXPERIMENTAL)
 
+  IF(ITK_VERSION_MAJOR VERSION_LESS 4)
+    MESSAGE(WARNING "clitkDicomRTPlan2Gate is not compatible with GDCM<2 (ITK<4). It will not be build.")
+  ELSE(ITK_VERSION_MAJOR VERSION_LESS 4)
+    ADD_EXECUTABLE(clitkDicomRTPlan2Gate clitkDicomRTPlan2Gate.cxx clitkDicomRTPlan2Gate_ggo.c)
+    TARGET_LINK_LIBRARIES(clitkDicomRTPlan2Gate clitkCommon ${ITK_LIBRARIES})
+  ENDIF(ITK_VERSION_MAJOR VERSION_LESS 4)
+
   SET_TARGET_PROPERTIES(${TOOLS_INSTALL} PROPERTIES INSTALL_RPATH "${VTK_DIR}:${ITK_DIR}" )  
   INSTALL (TARGETS ${TOOLS_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
 

diff --git a/tools/clitkDicomRTPlan2Gate.cxx b/tools/clitkDicomRTPlan2Gate.cxx
new file mode 100644 (file)
index 0000000..2026861
--- /dev/null
+++ b/tools/clitkDicomRTPlan2Gate.cxx
@@ -0,0 +1,283 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to:
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef CLITKDICOMRTPLAN2GATE_CXX
+#define CLITKDICOMRTPLAN2GATE_CXX
+
+#include "clitkDicomRTPlan2Gate_ggo.h"
+
+#include "clitkIO.h"
+#include "clitkCommon.h"
+
+#include "gdcmFile.h"
+#include "gdcmReader.h"
+#include "gdcmAttribute.h"
+
+int main(int argc, char * argv[])
+{
+
+  // init command line
+  GGO(clitkDicomRTPlan2Gate, args_info);
+  CLITK_INIT;
+  char* input_file = args_info.input_arg;
+  char* output_file = args_info.output_arg;
+
+  gdcm::Reader reader;
+  reader.SetFileName(input_file);
+  if( !reader.Read() )
+  {
+    std::cerr << "Failed to read: " << input_file << std::endl;
+    return 1;
+  }
+
+  const gdcm::DataSet & ds = reader.GetFile().GetDataSet();
+
+  //Check file type
+  gdcm::MediaStorage ms;
+  ms.SetFromFile(reader.GetFile());
+  if( ms != gdcm::MediaStorage::RTIonPlanStorage )
+  {
+    std::cerr << "The file <" << input_file << "> is not a RT Ion Plan." << std::endl;
+    exit(0);
+  }
+  
+  std::ofstream output;
+  output.open(output_file);
+  output << "#TREATMENT-PLAN-DESCRIPTION" << "\n";
+  
+  gdcm::Attribute<0x300a,0x2> label;
+  label.SetFromDataSet(ds);
+  gdcm::Attribute<0x300a,0x3> planName;
+  planName.SetFromDataSet(ds);
+  
+  output << "#PlanName\n"<< planName.GetValue() << "\n";
+  
+  gdcm::Tag tFractionGroupSQ(0x300a,0x70);
+  gdcm::Attribute<0x300a,0x71> fractionID;
+  gdcm::Attribute<0x300a,0x78> numberOfFractions;
+  gdcm::Attribute<0x300a,0x80> numberOfBeams;
+  
+  gdcm::Tag tReferencedBeamSQ(0x300c,0x4);
+  gdcm::Attribute<0x300a,0x86> meterSet;
+  gdcm::Attribute<0x300c,0x6> beamID;
+  
+  const gdcm::DataElement &FractionGroupSQ = ds.GetDataElement( tFractionGroupSQ );
+  gdcm::SmartPointer<gdcm::SequenceOfItems> sqf = FractionGroupSQ.GetValueAsSQ();
+  gdcm::Item &ReferencedBeamItem = sqf->GetItem(1);
+  gdcm::DataSet &ReferencedBeamData = ReferencedBeamItem.GetNestedDataSet();
+  numberOfFractions.SetFromDataSet(ReferencedBeamData);
+  
+  output << "#NumberOfFractions\n"<< numberOfFractions.GetValue() << "\n";
+  
+  for( unsigned int fidx = 1; fidx <= sqf->GetNumberOfItems(); ++fidx )
+  {
+    gdcm::Item &ReferencedBeamItem = sqf->GetItem(fidx);
+    gdcm::DataSet &ReferencedBeamData = ReferencedBeamItem.GetNestedDataSet();
+    
+    fractionID.SetFromDataSet(ReferencedBeamData);
+    numberOfFractions.SetFromDataSet(ReferencedBeamData);
+    numberOfBeams.SetFromDataSet(ReferencedBeamData);
+    output << "##FractionID\n"<<  fractionID.GetValue() << "\n";
+    output << "##NumberOfFields\n"<<  numberOfBeams.GetValue() << "\n";
+        
+    const gdcm::DataElement &ReferencedBeamSQ = ReferencedBeamData.GetDataElement(tReferencedBeamSQ);
+    gdcm::SmartPointer<gdcm::SequenceOfItems> sqb = ReferencedBeamSQ.GetValueAsSQ();   
+    for( unsigned int bidx = 1; bidx <= sqb->GetNumberOfItems(); ++bidx )
+    {
+      gdcm::Item &ReferencedBeamGroupItem = sqb->GetItem(bidx);
+      gdcm::DataSet &ReferencedBeamGroupData = ReferencedBeamGroupItem.GetNestedDataSet();
+      
+      meterSet.SetFromDataSet(ReferencedBeamGroupData);
+      beamID.SetFromDataSet(ReferencedBeamGroupData);
+      output << "###FieldsID\n"<<  beamID.GetValue() << "\n";
+    }
+  }
+  
+  gdcm::Tag tPatientSetupSQ(0x300a,0x180);
+  gdcm::Attribute<0x0018,0x5100> position;
+  gdcm::Attribute<0x300a,0x1b0> setupTechnique;
+  gdcm::Attribute<0x300a,0x182> setupID;
+  
+  const gdcm::DataElement &PatientSetupSQ = ds.GetDataElement( tPatientSetupSQ );
+  gdcm::SmartPointer<gdcm::SequenceOfItems> sqs = PatientSetupSQ.GetValueAsSQ();
+  for( unsigned int sidx = 1; sidx <= sqs->GetNumberOfItems(); ++sidx )
+  {
+    gdcm::Item &PatientSetupItem = sqs->GetItem(sidx);
+    gdcm::DataSet &PatientSetupData = PatientSetupItem.GetNestedDataSet();
+    
+    position.SetFromDataSet(PatientSetupData);
+    setupTechnique.SetFromDataSet(PatientSetupData);
+    setupID.SetFromDataSet(PatientSetupData);
+  }
+  
+  gdcm::Tag tIonBeamSQ(0x300a,0x3a2);
+  gdcm::Attribute<0x300a,0xb2> machine;
+  gdcm::Attribute<0x300a,0xc6> radiationType;
+  gdcm::Attribute<0x300a,0xce> treatmentType;
+  gdcm::Attribute<0x300a,0xc0> ionBeamID;
+  gdcm::Attribute<0x300a,0x10e> finalCumulativeMeterSetWeight;
+  gdcm::Attribute<0x300a,0x110> numberOfControlPoints;
+  gdcm::Attribute<0x300c,0x6a> patientSetupID;
+  gdcm::Attribute<0x300a,0xd0> numberOfWedges;
+  gdcm::Attribute<0x300a,0xe0> numberOfCompensators;
+  gdcm::Attribute<0x300a,0xed> numberOfBoli;
+  gdcm::Attribute<0x300a,0xf0> numberOfBlocks;
+  gdcm::Attribute<0x300a,0x312> numberOfRangeShifters;
+  gdcm::Attribute<0x300a,0x330> numberOfLateralSpreadingDevices;
+  gdcm::Attribute<0x300a,0x340> numberOfRangeModulators;
+  
+  gdcm::Tag tSnoutSQ(0x300a,0x30c);
+  gdcm::Attribute<0x300a,0x30f> snoutID;
+  
+  gdcm::Tag tControlPointSQ(0x300a,0x3a8);
+  gdcm::Attribute<0x300a,0x15> energyUnit;
+  gdcm::Attribute<0x300a,0x114> energyValue;
+  gdcm::Attribute<0x300a,0x112> controlPointIndex;
+  gdcm::Attribute<0x300a,0x134> cumulativeMetersetWeight;
+  gdcm::Attribute<0x300a,0x392> numberOfScannedSpots;
+  gdcm::Attribute<0x300a,0x390> spotTunnedID;
+  
+  gdcm::Tag tSpotPositionsData(0x300a,0x394);
+  gdcm::Attribute<0x300a,0x394> spotPositions;
+  gdcm::Tag tSpotWeightsData(0x300a,0x396);
+  gdcm::Attribute<0x300a,0x396> spotWeights;
+  
+  gdcm::Attribute<0x300a,0x11e> gantryAngle;
+  gdcm::Attribute<0x300a,0x122> patientSupportAngle;
+  gdcm::Attribute<0x300a,0x12c> isocenterPosition;
+  
+  int totalCumMeterSet = 0;
+  
+  const gdcm::DataElement &IonBeamSQ = ds.GetDataElement( tIonBeamSQ );
+  gdcm::SmartPointer<gdcm::SequenceOfItems> sqi = IonBeamSQ.GetValueAsSQ();
+  
+  for( unsigned int iidx = 1; iidx <= sqi->GetNumberOfItems(); ++iidx )
+  {
+    gdcm::Item &IonBeamItem = sqi->GetItem(iidx);
+    gdcm::DataSet &IonBeamData = IonBeamItem.GetNestedDataSet();
+    finalCumulativeMeterSetWeight.SetFromDataSet(IonBeamData);
+    totalCumMeterSet += finalCumulativeMeterSetWeight.GetValue();
+  }
+  
+  output << "#TotalMetersetWeightOfAllFields\n" <<  totalCumMeterSet << "\n";
+  
+  for( unsigned int iidx = 1; iidx <= sqi->GetNumberOfItems(); ++iidx )
+  {
+    gdcm::Item &IonBeamItem = sqi->GetItem(iidx);
+    gdcm::DataSet &IonBeamData = IonBeamItem.GetNestedDataSet();
+    
+    machine.SetFromDataSet(IonBeamData);
+    radiationType.SetFromDataSet(IonBeamData);
+    treatmentType.SetFromDataSet(IonBeamData);
+    ionBeamID.SetFromDataSet(IonBeamData);
+    finalCumulativeMeterSetWeight.SetFromDataSet(IonBeamData);
+    numberOfControlPoints.SetFromDataSet(IonBeamData);
+    patientSetupID.SetFromDataSet(IonBeamData);
+    numberOfWedges.SetFromDataSet(IonBeamData);
+    numberOfCompensators.SetFromDataSet(IonBeamData);
+    numberOfBoli.SetFromDataSet(IonBeamData);
+    numberOfBlocks.SetFromDataSet(IonBeamData);
+    numberOfRangeShifters.SetFromDataSet(IonBeamData);
+    numberOfLateralSpreadingDevices.SetFromDataSet(IonBeamData);
+    numberOfRangeModulators.SetFromDataSet(IonBeamData);
+    
+    const gdcm::DataElement &SnoutSQ = IonBeamData.GetDataElement(tSnoutSQ);
+    gdcm::SmartPointer<gdcm::SequenceOfItems> sqsn = SnoutSQ.GetValueAsSQ();
+    for( unsigned int snidx = 1; snidx <= sqsn->GetNumberOfItems(); ++snidx )
+    {
+      gdcm::Item &SnoutItem = sqsn->GetItem(snidx);
+      gdcm::DataSet &SnoutData = SnoutItem.GetNestedDataSet();
+      
+      snoutID.SetFromDataSet(SnoutData);
+    }
+    
+    const gdcm::DataElement &ControlPointSQ = IonBeamData.GetDataElement(tControlPointSQ);
+    gdcm::SmartPointer<gdcm::SequenceOfItems> sqcp = ControlPointSQ.GetValueAsSQ();
+    gdcm::Item &ControlPointItem = sqcp->GetItem(1);
+    gdcm::DataSet &ControlPointData = ControlPointItem.GetNestedDataSet();
+    
+    gantryAngle.SetFromDataSet(ControlPointData);
+    patientSupportAngle.SetFromDataSet(ControlPointData);
+    isocenterPosition.SetFromDataSet(ControlPointData);
+    
+    output << "\n#FIELD-DESCRIPTION" << "\n";
+    output << "###FieldID\n"<< ionBeamID.GetValue() << "\n";
+    output << "###FinalCumulativeMeterSetWeight\n"<<  finalCumulativeMeterSetWeight.GetValue() << "\n";
+    output << "###GantryAngle\n" << gantryAngle.GetValue() << "\n";
+    output << "###PatientSupportAngle\n" << patientSupportAngle.GetValue() << "\n";
+    output << "###IsocenterPosition\n" << isocenterPosition.GetValue(0);
+    output << " " << isocenterPosition.GetValue(1);
+    output << " " << isocenterPosition.GetValue(2) << "\n";
+    output << "###NumberOfControlPoints\n" << numberOfControlPoints.GetValue() << "\n\n";
+    output << "#SPOTS-DESCRIPTION" << "\n";
+    
+    for( unsigned int cpidx = 1; cpidx <= sqcp->GetNumberOfItems(); ++cpidx )
+    {
+      gdcm::Item &ControlPointItem = sqcp->GetItem(cpidx);
+      gdcm::DataSet &ControlPointData = ControlPointItem.GetNestedDataSet();
+      
+      if ( cpidx == 1 )
+      {
+       gantryAngle.SetFromDataSet(ControlPointData);
+       patientSupportAngle.SetFromDataSet(ControlPointData);
+       isocenterPosition.SetFromDataSet(ControlPointData);
+      }
+      
+      if ( cpidx < sqcp->GetNumberOfItems() )
+      {
+       energyUnit.SetFromDataSet(ControlPointData);
+       energyValue.SetFromDataSet(ControlPointData);
+       controlPointIndex.SetFromDataSet(ControlPointData);
+       cumulativeMetersetWeight.SetFromDataSet(ControlPointData);
+       numberOfScannedSpots.SetFromDataSet(ControlPointData);
+       spotTunnedID.SetFromDataSet(ControlPointData);
+       
+       const gdcm::DataElement &spotPositionsData = ControlPointData.GetDataElement(tSpotPositionsData);
+       spotPositions.SetFromDataElement(spotPositionsData);
+       const gdcm::DataElement &spotWeightsData = ControlPointData.GetDataElement(tSpotWeightsData);
+       spotWeights.SetFromDataElement(spotWeightsData);
+      }
+      
+      if ( cpidx == sqcp->GetNumberOfItems() )
+      {
+       energyUnit.SetValue( "0" );
+       energyValue.SetValue( 0 );
+       controlPointIndex.SetFromDataSet(ControlPointData);
+       cumulativeMetersetWeight.SetFromDataSet(ControlPointData);
+       numberOfScannedSpots.SetValue( 0 );
+       spotTunnedID.SetValue( "0" );
+      }
+      
+      output << "####ControlPointIndex\n" << controlPointIndex.GetValue() << "\n";
+      output << "####SpotTunnedID\n" << spotTunnedID.GetValue() << "\n";
+      output << "####CumulativeMetersetWeight\n" << cumulativeMetersetWeight.GetValue() << "\n";
+      output << "####Energy (MeV)\n"<< energyValue.GetValue() << "\n";
+      output << "####NbOfScannedSpots\n" << numberOfScannedSpots.GetValue() << "\n";
+      output << "####X Y Weight\n";
+      for ( unsigned int sp=0; sp < numberOfScannedSpots.GetValue(); ++sp)
+      {
+       output << spotPositions.GetValue(2*sp) << " " << spotPositions.GetValue(2*sp+1) << " " << spotWeights.GetValue(sp) << "\n";
+      }
+      
+    }
+    
+  }
+    
+  return 0;
+}
+
+#endif

diff --git a/tools/clitkDicomRTPlan2Gate.ggo b/tools/clitkDicomRTPlan2Gate.ggo
new file mode 100644 (file)
index 0000000..21b23eb
--- /dev/null
+++ b/tools/clitkDicomRTPlan2Gate.ggo
@@ -0,0 +1,8 @@
+# file DicomRTPlan2Gate
+package "clitk"
+version "1.0"
+purpose "Convert DicomRTPlan to Gate compatible file"
+option "config"         -    "config file"                     string  no
+option "input"          i    "Input dicom file name"           string  yes
+option "output"         o    "Output text file name"           string  yes
+option "verbose"        v    "verbose"                         flag    off