+++ /dev/null
-/*=========================================================================
- 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
-===========================================================================*/
-/*=========================================================================
-
- Program: GDCM (Grassroots DICOM). A DICOM library
-
- Copyright (c) 2006-2011 Mathieu Malaterre
- All rights reserved.
- See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
-
- This software is distributed WITHOUT ANY WARRANTY; without even
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the above copyright notice for more information.
-
-=========================================================================*/
-#include "vtkGDCMPolyDataReader.h"
-
-#include "vtkObjectFactory.h"
-#include "vtkInformation.h"
-#include "vtkInformationVector.h"
-#include "vtkPolyData.h"
-#include "vtkStreamingDemandDrivenPipeline.h"
-#include "vtkDoubleArray.h"
-#include "vtkCellArray.h"
-#include "vtkCellData.h"
-#include "vtkMedicalImageProperties.h"
-#include "vtkRTStructSetProperties.h"
-
-#include "gdcmReader.h"
-#include "gdcmSmartPointer.h"
-#include "gdcmAttribute.h"
-#include "gdcmSequenceOfItems.h"
-
-vtkCxxRevisionMacro(vtkGDCMPolyDataReader, "$Revision: 1.1 $")
-vtkStandardNewMacro(vtkGDCMPolyDataReader)
-
-//----------------------------------------------------------------------------
-vtkGDCMPolyDataReader::vtkGDCMPolyDataReader()
-{
- this->FileName = NULL;
- this->SetNumberOfInputPorts(0);
- this->MedicalImageProperties = vtkMedicalImageProperties::New();
- this->RTStructSetProperties = vtkRTStructSetProperties::New();
-}
-
-//----------------------------------------------------------------------------
-vtkGDCMPolyDataReader::~vtkGDCMPolyDataReader()
-{
- this->SetFileName(0);
- this->MedicalImageProperties->Delete();
- this->RTStructSetProperties->Delete();
-}
-
-//----------------------------------------------------------------------------
-// inline keyword is needed since GetStringValueFromTag was copy/paste from vtkGDCMImageReader
-// FIXME: need to restructure code to avoid copy/paste
-inline const char *GetStringValueFromTag(const gdcm::Tag& t, const gdcm::DataSet& ds)
-{
- static std::string buffer;
- buffer = ""; // cleanup previous call
-
- if( ds.FindDataElement( t ) )
- {
- const gdcm::DataElement& de = ds.GetDataElement( t );
- const gdcm::ByteValue *bv = de.GetByteValue();
- if( bv ) // Can be Type 2
- {
- buffer = std::string( bv->GetPointer(), bv->GetLength() );
- // Will be padded with at least one \0
- }
- }
-
- // Since return is a const char* the very first \0 will be considered
- return buffer.c_str();
-}
-
-//----------------------------------------------------------------------------
-void vtkGDCMPolyDataReader::FillMedicalImageInformation(const gdcm::Reader &reader)
-{
- const gdcm::File &file = reader.GetFile();
- const gdcm::DataSet &ds = file.GetDataSet();
-
- this->RTStructSetProperties->SetStructureSetLabel( GetStringValueFromTag( gdcm::Tag(0x3006,0x0002), ds) );
- this->RTStructSetProperties->SetStructureSetName( GetStringValueFromTag( gdcm::Tag(0x3006,0x0004), ds) );
- this->RTStructSetProperties->SetStructureSetDate( GetStringValueFromTag( gdcm::Tag(0x3006,0x0008), ds) );
- this->RTStructSetProperties->SetStructureSetTime( GetStringValueFromTag( gdcm::Tag(0x3006,0x0009), ds) );
- this->RTStructSetProperties->SetSOPInstanceUID( GetStringValueFromTag( gdcm::Tag(0x0008,0x0018), ds) );
- this->RTStructSetProperties->SetStudyInstanceUID( GetStringValueFromTag( gdcm::Tag(0x0020,0x000d), ds) );
- this->RTStructSetProperties->SetSeriesInstanceUID( GetStringValueFromTag( gdcm::Tag(0x0020,0x000e), ds) );
-
- // $ grep "vtkSetString\|DICOM" vtkMedicalImageProperties.h
- // For ex: DICOM (0010,0010) = DOE,JOHN
- this->MedicalImageProperties->SetPatientName( GetStringValueFromTag( gdcm::Tag(0x0010,0x0010), ds) );
- // For ex: DICOM (0010,0020) = 1933197
- this->MedicalImageProperties->SetPatientID( GetStringValueFromTag( gdcm::Tag(0x0010,0x0020), ds) );
- // For ex: DICOM (0010,1010) = 031Y
- this->MedicalImageProperties->SetPatientAge( GetStringValueFromTag( gdcm::Tag(0x0010,0x1010), ds) );
- // For ex: DICOM (0010,0040) = M
- this->MedicalImageProperties->SetPatientSex( GetStringValueFromTag( gdcm::Tag(0x0010,0x0040), ds) );
- // For ex: DICOM (0010,0030) = 19680427
- this->MedicalImageProperties->SetPatientBirthDate( GetStringValueFromTag( gdcm::Tag(0x0010,0x0030), ds) );
-#if ( VTK_MAJOR_VERSION == 5 && VTK_MINOR_VERSION > 0 )
- // For ex: DICOM (0008,0020) = 20030617
- this->MedicalImageProperties->SetStudyDate( GetStringValueFromTag( gdcm::Tag(0x0008,0x0020), ds) );
-#endif
- // For ex: DICOM (0008,0022) = 20030617
- this->MedicalImageProperties->SetAcquisitionDate( GetStringValueFromTag( gdcm::Tag(0x0008,0x0022), ds) );
-#if ( VTK_MAJOR_VERSION == 5 && VTK_MINOR_VERSION > 0 )
- // For ex: DICOM (0008,0030) = 162552.0705 or 230012, or 0012
- this->MedicalImageProperties->SetStudyTime( GetStringValueFromTag( gdcm::Tag(0x0008,0x0030), ds) );
-#endif
- // For ex: DICOM (0008,0032) = 162552.0705 or 230012, or 0012
- this->MedicalImageProperties->SetAcquisitionTime( GetStringValueFromTag( gdcm::Tag(0x0008,0x0032), ds) );
- // For ex: DICOM (0008,0023) = 20030617
- this->MedicalImageProperties->SetImageDate( GetStringValueFromTag( gdcm::Tag(0x0008,0x0023), ds) );
- // For ex: DICOM (0008,0033) = 162552.0705 or 230012, or 0012
- this->MedicalImageProperties->SetImageTime( GetStringValueFromTag( gdcm::Tag(0x0008,0x0033), ds) );
- // For ex: DICOM (0020,0013) = 1
- this->MedicalImageProperties->SetImageNumber( GetStringValueFromTag( gdcm::Tag(0x0020,0x0013), ds) );
- // For ex: DICOM (0020,0011) = 902
- this->MedicalImageProperties->SetSeriesNumber( GetStringValueFromTag( gdcm::Tag(0x0020,0x0011), ds) );
- // For ex: DICOM (0008,103e) = SCOUT
- this->MedicalImageProperties->SetSeriesDescription( GetStringValueFromTag( gdcm::Tag(0x0008,0x103e), ds) );
- // For ex: DICOM (0020,0010) = 37481
- this->MedicalImageProperties->SetStudyID( GetStringValueFromTag( gdcm::Tag(0x0020,0x0010), ds) );
- // For ex: DICOM (0008,1030) = BRAIN/C-SP/FACIAL
- this->MedicalImageProperties->SetStudyDescription( GetStringValueFromTag( gdcm::Tag(0x0008,0x1030), ds) );
- // For ex: DICOM (0008,0060)= CT
- this->MedicalImageProperties->SetModality( GetStringValueFromTag( gdcm::Tag(0x0008,0x0060), ds) );
- // For ex: DICOM (0008,0070) = Siemens
- this->MedicalImageProperties->SetManufacturer( GetStringValueFromTag( gdcm::Tag(0x0008,0x0070), ds) );
- // For ex: DICOM (0008,1090) = LightSpeed QX/i
- this->MedicalImageProperties->SetManufacturerModelName( GetStringValueFromTag( gdcm::Tag(0x0008,0x1090), ds) );
- // For ex: DICOM (0008,1010) = LSPD_OC8
- this->MedicalImageProperties->SetStationName( GetStringValueFromTag( gdcm::Tag(0x0008,0x1010), ds) );
- // For ex: DICOM (0008,0080) = FooCity Medical Center
- this->MedicalImageProperties->SetInstitutionName( GetStringValueFromTag( gdcm::Tag(0x0008,0x0080), ds) );
- // For ex: DICOM (0018,1210) = Bone
- this->MedicalImageProperties->SetConvolutionKernel( GetStringValueFromTag( gdcm::Tag(0x0018,0x1210), ds) );
- // For ex: DICOM (0018,0050) = 0.273438
- this->MedicalImageProperties->SetSliceThickness( GetStringValueFromTag( gdcm::Tag(0x0018,0x0050), ds) );
- // For ex: DICOM (0018,0060) = 120
- this->MedicalImageProperties->SetKVP( GetStringValueFromTag( gdcm::Tag(0x0018,0x0060), ds) );
- // For ex: DICOM (0018,1120) = 15
- this->MedicalImageProperties->SetGantryTilt( GetStringValueFromTag( gdcm::Tag(0x0018,0x1120), ds) );
- // For ex: DICOM (0018,0081) = 105
- this->MedicalImageProperties->SetEchoTime( GetStringValueFromTag( gdcm::Tag(0x0018,0x0081), ds) );
- // For ex: DICOM (0018,0091) = 35
- this->MedicalImageProperties->SetEchoTrainLength( GetStringValueFromTag( gdcm::Tag(0x0018,0x0091), ds) );
- // For ex: DICOM (0018,0080) = 2040
- this->MedicalImageProperties->SetRepetitionTime( GetStringValueFromTag( gdcm::Tag(0x0018,0x0080), ds) );
- // For ex: DICOM (0018,1150) = 5
- this->MedicalImageProperties->SetExposureTime( GetStringValueFromTag( gdcm::Tag(0x0018,0x1150), ds) );
- // For ex: DICOM (0018,1151) = 400
- this->MedicalImageProperties->SetXRayTubeCurrent( GetStringValueFromTag( gdcm::Tag(0x0018,0x1151), ds) );
- // For ex: DICOM (0018,1152) = 114
- this->MedicalImageProperties->SetExposure( GetStringValueFromTag( gdcm::Tag(0x0018,0x1152), ds) );
-
- // virtual void AddWindowLevelPreset(double w, double l);
- // (0028,1050) DS [ 498\ 498] # 12, 2 WindowCenter
- // (0028,1051) DS [ 1063\ 1063] # 12, 2 WindowWidth
- gdcm::Tag twindowcenter(0x0028,0x1050);
- gdcm::Tag twindowwidth(0x0028,0x1051);
- if( ds.FindDataElement( twindowcenter ) && ds.FindDataElement( twindowwidth) )
- {
- const gdcm::DataElement& windowcenter = ds.GetDataElement( twindowcenter );
- const gdcm::DataElement& windowwidth = ds.GetDataElement( twindowwidth );
- const gdcm::ByteValue *bvwc = windowcenter.GetByteValue();
- const gdcm::ByteValue *bvww = windowwidth.GetByteValue();
- if( bvwc && bvww ) // Can be Type 2
- {
- //gdcm::Attributes<0x0028,0x1050> at;
- gdcm::Element<gdcm::VR::DS,gdcm::VM::VM1_n> elwc;
- std::stringstream ss1;
- std::string swc = std::string( bvwc->GetPointer(), bvwc->GetLength() );
- ss1.str( swc );
- gdcm::VR vr = gdcm::VR::DS;
- unsigned int vrsize = vr.GetSizeof();
- unsigned int count = gdcm::VM::GetNumberOfElementsFromArray(swc.c_str(), swc.size());
- elwc.SetLength( count * vrsize );
- elwc.Read( ss1 );
- std::stringstream ss2;
- std::string sww = std::string( bvww->GetPointer(), bvww->GetLength() );
- ss2.str( sww );
- gdcm::Element<gdcm::VR::DS,gdcm::VM::VM1_n> elww;
- elww.SetLength( count * vrsize );
- elww.Read( ss2 );
- //assert( elww.GetLength() == elwc.GetLength() );
- for(unsigned int i = 0; i < elwc.GetLength(); ++i)
- {
- this->MedicalImageProperties->AddWindowLevelPreset( elww.GetValue(i), elwc.GetValue(i) );
- }
- }
- }
- gdcm::Tag twindowexplanation(0x0028,0x1055);
- if( ds.FindDataElement( twindowexplanation ) )
- {
- const gdcm::DataElement& windowexplanation = ds.GetDataElement( twindowexplanation );
- const gdcm::ByteValue *bvwe = windowexplanation.GetByteValue();
- if( bvwe ) // Can be Type 2
- {
- int n = this->MedicalImageProperties->GetNumberOfWindowLevelPresets();
- gdcm::Element<gdcm::VR::LO,gdcm::VM::VM1_n> elwe; // window explanation
- gdcm::VR vr = gdcm::VR::LO;
- std::stringstream ss;
- ss.str( "" );
- std::string swe = std::string( bvwe->GetPointer(), bvwe->GetLength() );
- unsigned int count = gdcm::VM::GetNumberOfElementsFromArray(swe.c_str(), swe.size()); (void)count;
- // I found a case with only one W/L but two comments: WINDOW1\WINDOW2
- // SIEMENS-IncompletePixelData.dcm
- //assert( count >= (unsigned int)n );
- elwe.SetLength( /*count*/ n * vr.GetSizeof() );
- ss.str( swe );
- elwe.Read( ss );
- for(int i = 0; i < n; ++i)
- {
- this->MedicalImageProperties->SetNthWindowLevelPresetComment(i, elwe.GetValue(i).c_str() );
- }
- }
- }
-
-#if 0
- // gdcmData/JDDICOM_Sample4.dcm
- // -> (0008,0060) CS [DM Digital microscopy] # 24, 1 Modality
- gdcm::MediaStorage ms1 = gdcm::MediaStorage::SecondaryCaptureImageStorage;
- ms1.GuessFromModality( this->MedicalImageProperties->GetModality(), this->FileDimensionality );
- gdcm::MediaStorage ms2;
- ms2.SetFromFile( reader.GetFile() );
- if( ms2 != ms1 && ms2 != gdcm::MediaStorage::SecondaryCaptureImageStorage )
- {
- vtkWarningMacro( "SHOULD NOT HAPPEN. Unrecognized Modality: " << this->MedicalImageProperties->GetModality()
- << " Will be set instead to the known one: " << ms2.GetModality() )
- this->MedicalImageProperties->SetModality( ms2.GetModality() );
- }
-#endif
-
- // Add more info:
-
-}
-
-//(3006,0022) ?? (IS) [2 ] # 2,1 ROI Number
-//(3006,0024) ?? (UI) [2.16.840.1.114362.1.759508.1251415878280.193] # 44,1 Referenced Frame of Reference UID
-//(3006,0026) ?? (LO) [Bladder ] # 8,1 ROI Name
-//(3006,0036) ?? (CS) [MANUAL] # 6,1 ROI Generation Algorithm
-
-int vtkGDCMPolyDataReader::RequestData_RTStructureSetStorage(gdcm::Reader const &reader,
- vtkInformationVector *outputVector)
-{
-// This is done in RequestInformation
-// gdcm::MediaStorage ms;
-// ms.SetFromFile( reader.GetFile() );
-// //std::cout << ms << std::endl;
-// if( ms != gdcm::MediaStorage::RTStructureSetStorage )
-// {
-// return 0;
-// }
-
- const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
- // (3006,0010) SQ (Sequence with undefined length #=1) # u/l, 1 ReferencedFrameOfReferenceSequence
- // (3006,0020) SQ (Sequence with explicit length #=4) # 370, 1 StructureSetROISequence
- // (3006,0039) SQ (Sequence with explicit length #=4) # 24216, 1 ROIContourSequence
- gdcm::Tag troicsq(0x3006,0x0039);
- if( !ds.FindDataElement( troicsq ) )
- {
- return 0;
- }
- gdcm::Tag tssroisq(0x3006,0x0020);
- if( !ds.FindDataElement( tssroisq ) )
- {
- return 0;
- }
- gdcm::Tag trefframerefsq(0x3006,0x0010);
- if( !ds.FindDataElement( trefframerefsq ) )
- {
- return 0;
- }
- const gdcm::DataElement &refframerefsq = ds.GetDataElement( trefframerefsq );
- gdcm::SmartPointer<gdcm::SequenceOfItems> sqi0 = refframerefsq.GetValueAsSQ();
- if( !sqi0 || !sqi0->GetNumberOfItems() )
- {
- return 0;
- }
- assert( sqi0->GetNumberOfItems() == 1 );
- for(unsigned int pd = 0; pd < sqi0->GetNumberOfItems(); ++pd)
- {
- const gdcm::Item & item = sqi0->GetItem(pd+1); // Item start at #1
- const gdcm::DataSet& nestedds = item.GetNestedDataSet();
- // (3006,0012) SQ (Sequence with undefined length #=1) # u/l, 1 RTReferencedStudySequence
- gdcm::Attribute<0x0020,0x052> frameofreferenceuid;
- frameofreferenceuid.SetFromDataSet( nestedds );
- this->RTStructSetProperties->SetReferenceFrameOfReferenceUID(
- frameofreferenceuid.GetValue() );
- gdcm::Tag trtrefstudysq(0x3006,0x0012);
- if( !nestedds.FindDataElement( trtrefstudysq) )
- {
- return 0;
- }
- const gdcm::DataElement &rtrefstudysq = nestedds.GetDataElement( trtrefstudysq );
- gdcm::SmartPointer<gdcm::SequenceOfItems> sqi00 = rtrefstudysq.GetValueAsSQ();
- if( !sqi00 || !sqi00->GetNumberOfItems() )
- {
- return 0;
- }
- assert( sqi00->GetNumberOfItems() == 1 );
- for(unsigned int pd0 = 0; pd0 < sqi00->GetNumberOfItems(); ++pd0)
- {
- const gdcm::Item & item = sqi00->GetItem(pd0+1); // Item start at #1
- const gdcm::DataSet& nestedds = item.GetNestedDataSet();
-
- // (3006,0014) SQ (Sequence with undefined length #=1) # u/l, 1 RTReferencedSeriesSequence
- gdcm::Tag trtrefseriessq(0x3006,0x0014);
- if( !nestedds.FindDataElement( trtrefseriessq) )
- {
- return 0;
- }
- const gdcm::DataElement &rtrefseriessq = nestedds.GetDataElement( trtrefseriessq);
-
- gdcm::SmartPointer<gdcm::SequenceOfItems> sqi000 = rtrefseriessq.GetValueAsSQ();
- if( !sqi000 || !sqi000->GetNumberOfItems() )
- {
- return 0;
- }
- assert( sqi000->GetNumberOfItems() == 1 );
- for(unsigned int pd00 = 0; pd00 < sqi000->GetNumberOfItems(); ++pd00)
- {
- const gdcm::Item & item = sqi000->GetItem(pd00+1); // Item start at #1
- const gdcm::DataSet& nestedds = item.GetNestedDataSet();
-
- gdcm::Attribute<0x0020,0x000e> seriesinstanceuid;
- seriesinstanceuid.SetFromDataSet( nestedds );
- this->RTStructSetProperties->SetReferenceSeriesInstanceUID(
- seriesinstanceuid.GetValue() );
-
-
- // (3006,0016) SQ (Sequence with undefined length #=162) # u/l, 1 ContourImageSequence
- gdcm::Tag tcontourimageseq(0x3006,0x0016);
- if( !nestedds.FindDataElement( tcontourimageseq) )
- {
- return 0;
- }
- const gdcm::DataElement &contourimageseq = nestedds.GetDataElement( tcontourimageseq );
- gdcm::SmartPointer<gdcm::SequenceOfItems> sqi0000 = contourimageseq.GetValueAsSQ();
- if( !sqi0000 || !sqi0000->GetNumberOfItems() )
- {
- return 0;
- }
-
- assert( sqi0000->GetNumberOfItems() != 1 );
- for(unsigned int pd000 = 0; pd000 < sqi0000->GetNumberOfItems(); ++pd000)
- {
- const gdcm::Item & item = sqi0000->GetItem(pd000+1); // Item start at #1
- const gdcm::DataSet& nestedds = item.GetNestedDataSet();
- gdcm::Attribute<0x0008,0x1150> refsopclassuid;
- refsopclassuid.SetFromDataSet( nestedds );
- gdcm::Attribute<0x0008,0x1155> refinstanceuid;
- refinstanceuid.SetFromDataSet( nestedds );
- this->RTStructSetProperties->AddReferencedFrameOfReference( refsopclassuid.GetValue().c_str(),
-refinstanceuid.GetValue().c_str() );
- }
-
- }
-
- }
- }
-
- const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
- //std::cout << roicsq << std::endl;
- //const gdcm::SequenceOfItems *sqi_debug = roicsq.GetSequenceOfItems();
- gdcm::SmartPointer<gdcm::SequenceOfItems> sqi = roicsq.GetValueAsSQ();
- if( !sqi || !sqi->GetNumberOfItems() )
- {
- return 0;
- }
- const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
- //const gdcm::SequenceOfItems *ssqi = ssroisq.GetSequenceOfItems();
- gdcm::SmartPointer<gdcm::SequenceOfItems> ssqi = ssroisq.GetValueAsSQ();
- if( !ssqi || !ssqi->GetNumberOfItems() )
- {
- return 0;
- }
-
- // For each Item in the DataSet create a vtkPolyData
- for(unsigned int pd = 0; pd < sqi->GetNumberOfItems(); ++pd)
- {
- //StructureSetROI structuresetroi;
- // get the info object
- vtkInformation *outInfo1 = outputVector->GetInformationObject(pd);
-
- // get the ouptut
- vtkPolyData *output = vtkPolyData::SafeDownCast(
- outInfo1->Get(vtkDataObject::DATA_OBJECT()));
-
-
- const gdcm::Item & item = sqi->GetItem(pd+1); // Item start at #1
- //std::cout << item << std::endl;
- const gdcm::Item & sitem = ssqi->GetItem(pd+1); // Item start at #1
- const gdcm::DataSet& snestedds = sitem.GetNestedDataSet();
- // (3006,0026) ?? (LO) [date] # 4,1 ROI Name
- gdcm::Tag stcsq(0x3006,0x0026);
- if( !snestedds.FindDataElement( stcsq ) )
- {
- continue;
- }
- const gdcm::DataElement &sde = snestedds.GetDataElement( stcsq );
- std::string s(sde.GetByteValue()->GetPointer(), sde.GetByteValue()->GetLength());
- //structuresetroi.ROIName = s;
- gdcm::Attribute<0x3006,0x0022> roinumber;
- roinumber.SetFromDataSet( snestedds );
- //structuresetroi.ROINumber = roinumber.GetValue();
- gdcm::Attribute<0x3006,0x0024> refframeuid;
- refframeuid.SetFromDataSet( snestedds );
- //structuresetroi.RefFrameRefUID = refframeuid.GetValue();
- gdcm::Attribute<0x3006,0x0026> roiname;
- roiname.SetFromDataSet( snestedds );
- assert( s == roiname.GetValue() );
- gdcm::Attribute<0x3006,0x0036> roigenalg;
- roigenalg.SetFromDataSet( snestedds );
- //structuresetroi.ROIGenerationAlgorithm = roigenalg.GetValue();
- //structuresetrois.push_back( structuresetroi );
-
- this->RTStructSetProperties->AddStructureSetROI(
- roinumber.GetValue(),
- refframeuid.GetValue(),
- roiname.GetValue(),
- roigenalg.GetValue()
- );
-
- const gdcm::DataSet& nestedds = item.GetNestedDataSet();
- //std::cout << nestedds << std::endl;
- //(3006,002a) IS [255\192\96] # 10,3 ROI Display Color
- gdcm::Tag troidc(0x3006,0x002a);
- gdcm::Attribute<0x3006,0x002a> color = {};
- if( nestedds.FindDataElement( troidc) )
- {
- const gdcm::DataElement &decolor = nestedds.GetDataElement( troidc );
- color.SetFromDataElement( decolor );
- //std::cout << "color:" << color[0] << "," << color[1] << "," << color[2] << std::endl;
- }
- //(3006,0040) SQ (Sequence with explicit length #=8) # 4326, 1 ContourSequence
- gdcm::Tag tcsq(0x3006,0x0040);
- if( !nestedds.FindDataElement( tcsq ) )
- {
- continue;
- }
- const gdcm::DataElement& csq = nestedds.GetDataElement( tcsq );
- //std::cout << csq << std::endl;
-
- //const gdcm::SequenceOfItems *sqi2 = csq.GetSequenceOfItems();
- gdcm::SmartPointer<gdcm::SequenceOfItems> sqi2 = csq.GetValueAsSQ();
- if( !sqi2 || !sqi2->GetNumberOfItems() )
- {
- continue;
- }
- unsigned int nitems = sqi2->GetNumberOfItems();
- //std::cout << nitems << std::endl;
- //this->SetNumberOfOutputPorts(nitems);
- vtkDoubleArray *scalars = vtkDoubleArray::New();
- scalars->SetNumberOfComponents(3);
-
- vtkPoints *newPts = vtkPoints::New();
- //std::string s(sde.GetByteValue()->GetPointer(), sde.GetByteValue()->GetLength());
- //std::cout << s << std::endl;
- //newPts->GetData()->SetName( s.c_str() );
- // In VTK there is no API to specify the name of a vtkPolyData, you can only specify Name
- // for the scalars (pointdata or celldata), so let's do that...
- //scalars->SetName( structuresetroi.ROIName.c_str() );
- scalars->SetName( roiname.GetValue().c_str() );
- vtkCellArray *polys = vtkCellArray::New();
- for(unsigned int i = 0; i < nitems; ++i)
- {
- const gdcm::Item & item2 = sqi2->GetItem(i+1); // Item start at #1
-
- const gdcm::DataSet& nestedds2 = item2.GetNestedDataSet();
- //std::cout << nestedds2 << std::endl;
- // (3006,0050) DS [43.57636\65.52504\-10.0\46.043102\62.564945\-10.0\49.126537\60.714... # 398,48 ContourData
- gdcm::Tag tcontourdata(0x3006,0x0050);
- const gdcm::DataElement & contourdata = nestedds2.GetDataElement( tcontourdata );
- //std::cout << contourdata << std::endl;
-
- //const gdcm::ByteValue *bv = contourdata.GetByteValue();
- gdcm::Attribute<0x3006,0x0042> contgeotype;
- contgeotype.SetFromDataSet( nestedds2 );
- assert( contgeotype.GetValue() == "CLOSED_PLANAR " );
-
- gdcm::Attribute<0x3006,0x0046> numcontpoints;
- numcontpoints.SetFromDataSet( nestedds2 );
-
- gdcm::Attribute<0x3006,0x0050> at;
- at.SetFromDataElement( contourdata );
-
- {
- assert( nestedds2.FindDataElement( gdcm::Tag(0x3006,0x0016) ) );
- const gdcm::DataElement &contourimagesequence = nestedds2.GetDataElement( gdcm::Tag(0x3006,0x0016) );
- gdcm::SmartPointer<gdcm::SequenceOfItems> contourimagesequence_sqi = contourimagesequence.GetValueAsSQ();
- assert( contourimagesequence_sqi && contourimagesequence_sqi->GetNumberOfItems() == 1 );
- const gdcm::Item & theitem = contourimagesequence_sqi->GetItem(1);
- const gdcm::DataSet& nestedds = theitem.GetNestedDataSet();
-
- gdcm::Attribute<0x0008,0x1150> classat;
- classat.SetFromDataSet( nestedds );
- gdcm::Attribute<0x0008,0x1155> instat;
- instat.SetFromDataSet( nestedds );
-
- this->RTStructSetProperties->AddContourReferencedFrameOfReference( pd,
- classat.GetValue(), instat.GetValue() );
- }
-
- //newPts->SetNumberOfPoints( at.GetNumberOfValues() / 3 );
- //assert( at.GetNumberOfValues() % 3 == 0); // FIXME
- const double* pts = at.GetValues();
- vtkIdType buffer[256];
- vtkIdType *ptIds;
- unsigned int npts = at.GetNumberOfValues() / 3;
- assert( npts == numcontpoints.GetValue() );
- if(npts>256)
- {
- ptIds = new vtkIdType[npts];
- }
- else
- {
- ptIds = buffer;
- }
- for(unsigned int i = 0; i < npts * 3; i+=3)
- {
- float x[3];
- x[0] = pts[i+0];
- x[1] = pts[i+1];
- x[2] = pts[i+2];
- vtkIdType ptId = newPts->InsertNextPoint( x );
- ptIds[i / 3] = ptId;
- }
- // Each Contour Data is in fact a Cell:
- vtkIdType cellId = polys->InsertNextCell( npts , ptIds);
- scalars->InsertTuple3(cellId, (double)color[0]/255.0, (double)color[1]/255.0, (double)color[2]/255.0);
- if(npts>256)
- {
- delete[] ptIds;
- }
- }
- output->SetPoints(newPts);
- newPts->Delete();
- output->SetPolys(polys);
- polys->Delete();
- output->GetCellData()->SetScalars(scalars);
- scalars->Delete();
- }
-
- // Add the Observations:
- // we can only be doing it here once all RT are loaded, since we will
- // attach observation to *existing* rtstruct
- gdcm::Tag trtroiobssq(0x3006,0x0080);
- if( !ds.FindDataElement( trtroiobssq ) )
- {
- return 0;
- }
- const gdcm::DataElement &rtroiobssq = ds.GetDataElement( trtroiobssq );
- gdcm::SmartPointer<gdcm::SequenceOfItems> rtroiobssqsqi = rtroiobssq.GetValueAsSQ();
- if( !rtroiobssqsqi || !rtroiobssqsqi->GetNumberOfItems() )
- {
- return 0;
- }
- for(unsigned int obs = 0; obs < rtroiobssqsqi->GetNumberOfItems(); ++obs)
- {
- const gdcm::Item & item = rtroiobssqsqi->GetItem(obs+1); // Item start at #1
- const gdcm::DataSet& nestedds = item.GetNestedDataSet();
- gdcm::Attribute<0x3006,0x0082> observationnumber;
- observationnumber.SetFromDataSet( nestedds );
- gdcm::Attribute<0x3006,0x0084> referencedroinumber;
- referencedroinumber.SetFromDataSet( nestedds );
- gdcm::Attribute<0x3006,0x00a4> rtroiinterpretedtype;
- rtroiinterpretedtype.SetFromDataSet( nestedds );
- gdcm::Attribute<0x3006,0x00a6> roiinterpreter;
- roiinterpreter.SetFromDataSet( nestedds );
- this->RTStructSetProperties->
- AddStructureSetROIObservation( referencedroinumber.GetValue(),
- observationnumber.GetValue(),
- rtroiinterpretedtype.GetValue(),
- roiinterpreter.GetValue() );
- }
-
- return 1;
-}
-
-int vtkGDCMPolyDataReader::RequestData_HemodynamicWaveformStorage(gdcm::Reader const &reader,
- vtkInformationVector *outputVector)
-{
- const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
- // (5400,0100) SQ (Sequence with undefined length #=1) # u/l, 1 WaveformSequence
- gdcm::Tag twsq(0x5400,0x0100);
- if( !ds.FindDataElement( twsq) )
- {
- return 0;
- }
- const gdcm::DataElement &wsq = ds.GetDataElement( twsq );
- //std::cout << wsq << std::endl;
- //const gdcm::SequenceOfItems *sqi = wsq.GetSequenceOfItems();
- gdcm::SmartPointer<gdcm::SequenceOfItems> sqi = wsq.GetValueAsSQ();
- if( !sqi || !sqi->GetNumberOfItems() )
- {
- return 0;
- }
-
- const gdcm::Item & item = sqi->GetItem(1); // Item start at #1
- const gdcm::DataSet& nestedds = item.GetNestedDataSet();
-
- // (5400,1004) US 16 # 2, 1 WaveformBitsAllocated
- gdcm::Tag twba(0x5400,0x1004);
- if( !nestedds.FindDataElement( twba ) )
- {
- return 0;
- }
- const gdcm::DataElement &wba= nestedds.GetDataElement( twba );
-
- //std::cout << wba << std::endl;
- // (5400,1006) CS [SS] # 2, 1 WaveformSampleInterpretation
- // (5400,1010) OW 00ba\0030\ff76\ff8b\00a2\ffd3\ffae\ff50\0062\00c4\011e\00c2\00ba... # 57600, 1 WaveformData
- gdcm::Tag twd(0x5400,0x1010);
- if( !nestedds.FindDataElement( twd ) )
- {
- return 0;
- }
- const gdcm::DataElement &wd = nestedds.GetDataElement( twd );
- const gdcm::ByteValue *bv = wd.GetByteValue();
- size_t len = bv->GetLength();
- int16_t *p = (int16_t*)bv;
-
- // get the info object
- int pd = 0;
- vtkInformation *outInfo1 = outputVector->GetInformationObject(pd);
-
- // get the ouptut
- vtkPolyData *output = vtkPolyData::SafeDownCast(
- outInfo1->Get(vtkDataObject::DATA_OBJECT()));
-
- vtkPoints *newPts = vtkPoints::New();
- size_t npts = len / 2;
- //npts = 10; // DEBUG !
- for(size_t i = 0; i < npts; ++i )
- {
- float x[3];
- x[0] = (float)p[i] / 8800;
- //std::cout << p[i] << std::endl;
- x[1] = i;
- x[2] = 0;
- vtkIdType ptId = newPts->InsertNextPoint( x );
- }
- output->SetPoints(newPts);
- newPts->Delete();
-
- vtkCellArray* lines = vtkCellArray::New();
- for ( int i = 0; i < newPts->GetNumberOfPoints() - 1; ++i )
- {
- vtkIdType topol[2];
- topol[0] = i;
- topol[1] = i+1;
- lines->InsertNextCell( 2, topol );
- }
-
- output->SetLines(lines);
- lines->Delete();
- output->BuildCells();
- //output->GetCellData()->SetScalars(scalars);
- //scalars->Delete();
-
- return 1;
-}
-
-//----------------------------------------------------------------------------
-int vtkGDCMPolyDataReader::RequestData(
- vtkInformation *vtkNotUsed(request),
- vtkInformationVector **vtkNotUsed(inputVector),
- vtkInformationVector *outputVector)
-{
- vtkInformation *outInfo = outputVector->GetInformationObject(0);
- //vtkPoints *newPts, *mergedPts;
- //vtkCellArray *newPolys, *mergedPolys;
- //vtkFloatArray *newScalars=0, *mergedScalars=0;
-
- // All of the data in the first piece.
- if (outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_PIECE_NUMBER()) > 0)
- {
- return 0;
- }
-
- if ( !this->FileName || !*this->FileName )
- {
- vtkErrorMacro(<<"A FileName must be specified.");
- return 0;
- }
-
- gdcm::Reader reader;
- reader.SetFileName( this->FileName );
- if( !reader.Read() )
- {
- return 0;
- }
-
- gdcm::MediaStorage ms;
- ms.SetFromFile( reader.GetFile() );
-
- int ret;
- if( ms == gdcm::MediaStorage::RTStructureSetStorage )
- {
- ret = this->RequestData_RTStructureSetStorage(reader, outputVector);
- }
- else if( ms == gdcm::MediaStorage::HemodynamicWaveformStorage)
- {
- ret = this->RequestData_HemodynamicWaveformStorage(reader, outputVector);
- }
- else
- {
- // not handled assume error
- ret = 0;
- }
-
- return ret;
-}
-
-int vtkGDCMPolyDataReader::RequestInformation_RTStructureSetStorage(gdcm::Reader const & reader)
-{
- const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
- // (3006,0020) SQ (Sequence with explicit length #=4) # 370, 1 StructureSetROISequence
- gdcm::Tag tssroisq(0x3006,0x0020);
- if( !ds.FindDataElement( tssroisq ) )
- {
- return 0;
- }
-
- const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
- //const gdcm::SequenceOfItems *sqi = ssroisq.GetSequenceOfItems();
- gdcm::SmartPointer<gdcm::SequenceOfItems> sqi = ssroisq.GetValueAsSQ();
- if( !sqi || !sqi->GetNumberOfItems() )
- {
- return 0;
- }
- unsigned int npds = sqi->GetNumberOfItems();
-
- //std::cout << "Nb pd:" << npds << std::endl;
- this->SetNumberOfOutputPorts( npds );
-
- // Allocate
- for(unsigned int i = 1; i < npds; ++i) // first output is allocated for us
- {
- vtkPolyData *output2 = vtkPolyData::New();
- this->GetExecutive()->SetOutputData(i, output2);
- output2->Delete();
- }
- return 1;
-}
-
-int vtkGDCMPolyDataReader::RequestInformation_HemodynamicWaveformStorage(gdcm::Reader const & reader)
-{
- return 1;
-}
-
-//----------------------------------------------------------------------------
-int vtkGDCMPolyDataReader::RequestInformation(
- vtkInformation *vtkNotUsed(request),
- vtkInformationVector **vtkNotUsed(inputVector),
- vtkInformationVector *outputVector)
-{
- // get the info object
-// vtkInformation *outInfo = outputVector->GetInformationObject(0);
-//
-// outInfo->Set(vtkStreamingDemandDrivenPipeline::MAXIMUM_NUMBER_OF_PIECES(),
-// -1);
- gdcm::Reader reader;
- reader.SetFileName( this->FileName );
- if( !reader.Read() )
- {
- return 0;
- }
-
- gdcm::MediaStorage ms;
- ms.SetFromFile( reader.GetFile() );
-
- int ret;
- if( ms == gdcm::MediaStorage::RTStructureSetStorage )
- {
- ret = this->RequestInformation_RTStructureSetStorage(reader);
- }
- else if( ms == gdcm::MediaStorage::HemodynamicWaveformStorage)
- {
- ret = this->RequestInformation_HemodynamicWaveformStorage(reader);
- }
- else
- {
- // not handled assume error
- ret = 0;
- }
-
- if( ret )
- {
- // Ok let's fill in the 'extra' info:
- this->FillMedicalImageInformation(reader);
- }
-
- return ret;
-}
-
-
-//----------------------------------------------------------------------------
-void vtkGDCMPolyDataReader::PrintSelf(ostream& os, vtkIndent indent)
-{
- this->Superclass::PrintSelf(os,indent);
-
- os << indent << "File Name: "
- << (this->FileName ? this->FileName : "(none)") << "\n";
-
-
-}
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff