GDCM 3.2.1

gdcmrtionplan.cxx
/*=========================================================================
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 "vtkImageData.h"
#include "vtkPointData.h"
#include "vtkPolyData.h"
#include "vtkProperty.h"
#include "vtkPolyDataMapper.h"
#include "vtkActor.h"
#include "vtkRenderer.h"
#include "vtkCellArray.h"
#include "vtkPoints.h"
#include "vtkDoubleArray.h"
#include <vtkXMLImageDataWriter.h>
#include <vtkXMLPolyDataWriter.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkImageColorViewer.h>
#include "vtkVersion.h"
#include "gdcmReader.h"
#include "gdcmAttribute.h"
/*
This example is just for fun. We found a RT Ion Plan Storage and simply extracted the viz stuff for VTK
RTIonPlanStorage, // 1.2.840.10008.5.1.4.1.1.481.8
*/
int main(int argc, char *argv[])
{
if( argc < 3 )
{
std::cerr << argv[0] << " filename.dcm outfile.vti\n";
return 1;
}
const char * filename = argv[1];
const char * outfilename = argv[2];
const char * outfilename2 = argv[3];
gdcm::Reader reader;
reader.SetFileName( filename );
if( !reader.Read() )
{
return 1;
}
gdcm::MediaStorage ms;
ms.SetFromFile( reader.GetFile() );
if( ms != gdcm::MediaStorage::RTIonPlanStorage )
{
return 1;
}
/*
(300a,03a2) SQ # u/l,1 Ion Beam Sequence
(fffe,e000) na (Item with undefined length)
(0008,1040) LO [Test] # 4,1 Institutional Department Name
(300a,00b2) SH (no value) # 0,1 Treatment Machine Name
(300a,00b3) CS [MU] # 2,1 Primary Dosimeter Unit
(300a,00c0) IS [1 ] # 2,1 Beam Number
(300a,00c2) LO [1 ] # 2,1 Beam Name
(300a,00c4) CS [STATIC] # 6,1 Beam Type
(300a,00c6) CS [PROTON] # 6,1 Radiation Type
(300a,00ce) CS [TREATMENT ] # 10,1 Treatment Delivery Type
(300a,00d0) IS [0 ] # 2,1 Number of Wedges
(300a,00e0) IS [1 ] # 2,1 Number of Compensators
(300a,00ed) IS [0 ] # 2,1 Number of Boli
(300a,00f0) IS [1 ] # 2,1 Number of Blocks
(300a,0110) IS [2 ] # 2,1 Number of Control Points
(300a,02ea) SQ # u/l,1 Ion Range Compensator Sequence
(fffe,e000) na (Item with undefined length)
(300a,00e1) SH [lucite] # 6,1 Material ID
(300a,00e4) IS [1 ] # 2,1 Compensator Number
(300a,00e5) SH [75hdhe5 ] # 8,1 Compensator ID
(300a,00e7) IS [35] # 2,1 Compensator Rows
(300a,00e8) IS [37] # 2,1 Compensator Columns
(300a,00e9) DS [3.679991\4.249288 ] # 18,2 Compensator Pixel Spacing
(300a,00ea) DS [-76.00\62.50] # 12,2 Compensator Position
(300a,00ec) DS [52.13\52.13\52.13\53.18\54.04\54.04\47.11\40.06\40.06\38.79\34.87\33.28\33.28\33.28\33.28\35.43\35.43\34.54\34.54\34.71\36.10\38.62\44.88\44.88\44.88\45.00\45.00\45.00\45.66\45.66\46.42\39.77\39.77\39.77\39.77\39.77\43.52\52.13\52.13\52.13\53.18\53.52\54.0] # 7618,1-n Compensator Thickness Data
(300a,02e0) CS [ABSENT] # 6,1 Compensator Divergence
(300a,02e1) CS [SOURCE_SIDE ] # 12,1 Compensator Mounting Position
(300a,02e4) FL 39.2 # 4,1 Isocenter to Compensator Tray Distance
(300a,02e5) FL 2.12 # 4,1 Compensator Column Offset
(300a,02e8) FL 4.76 # 4,1 Compensator Milling Tool Diameter
(fffe,e00d)
*/
const gdcm::DataSet& ds = reader.GetFile().GetDataSet();
gdcm::Tag tbeamsq(0x300a,0x03a2);
if( !ds.FindDataElement( tbeamsq ) )
{
return 1;
}
const gdcm::DataElement &beamsq = ds.GetDataElement( tbeamsq );
//std::cout << beamsq << std::endl;
gdcm::SmartPointer<gdcm::SequenceOfItems> sqi = beamsq.GetValueAsSQ();
if( !sqi || !sqi->GetNumberOfItems() )
{
return 1;
}
//for(unsigned int pd = 0; pd < sqi->GetNumberOfItems(); ++pd)
// {
//const gdcm::Item & item = sqi->GetItem(1); // Item start at #1
const gdcm::Item & item = sqi->GetItem(1); // Item start at #1
const gdcm::DataSet& nestedds = item.GetNestedDataSet();
//std::cout << nestedds << std::endl;
gdcm::Tag tcompensatorsq(0x300a,0x02ea);
if( !nestedds.FindDataElement( tcompensatorsq ) )
{
return 1;
}
const gdcm::DataElement &compensatorsq = nestedds.GetDataElement( tcompensatorsq );
//std::cout << compensatorsq << std::endl;
gdcm::SmartPointer<gdcm::SequenceOfItems> ssqi = compensatorsq.GetValueAsSQ();
const gdcm::Item & item2 = ssqi->GetItem(1); // Item start at #1
const gdcm::DataSet& nestedds2 = item2.GetNestedDataSet();
//std::cout << nestedds2 << std::endl;
gdcm::Tag tcompensatorthicknessdata(0x300a,0x00ec);
if( !nestedds2.FindDataElement( tcompensatorthicknessdata ) )
{
return 1;
}
const gdcm::DataElement &compensatorthicknessdata = nestedds2.GetDataElement( tcompensatorthicknessdata );
// std::cout << compensatorthicknessdata << std::endl;
gdcm::Attribute<0x300a,0x00ec> at;
at.SetFromDataElement( compensatorthicknessdata );
const double* pts = at.GetValues();
// (300a,00e7) IS [35] # 2,1 Compensator Rows
gdcm::Attribute<0x300a,0x00e7> at1;
const gdcm::DataElement &compensatorrows = nestedds2.GetDataElement( at1.GetTag() );
at1.SetFromDataElement( compensatorrows );
std::cout << at1.GetValue() << std::endl;
// (300a,00e8) IS [37] # 2,1 Compensator Columns
gdcm::Attribute<0x300a,0x00e8> at2;
const gdcm::DataElement &compensatorcols = nestedds2.GetDataElement( at2.GetTag() );
at2.SetFromDataElement( compensatorcols );
std::cout << at2.GetValue() << std::endl;
// (300a,00e9) DS [3.679991\4.249288 ] # 18,2 Compensator Pixel Spacing
gdcm::Attribute<0x300a,0x00e9> at3;
const gdcm::DataElement &compensatorpixelspacing = nestedds2.GetDataElement( at3.GetTag() );
at3.SetFromDataElement( compensatorpixelspacing );
std::cout << at3.GetValue(0) << std::endl;
// (300a,00ea) DS [-76.00\62.50] # 12,2 Compensator Position
gdcm::Attribute<0x300a,0x00ea> at4;
const gdcm::DataElement &compensatorposition = nestedds2.GetDataElement( at4.GetTag() );
at4.SetFromDataElement( compensatorposition );
std::cout << at4.GetValue(0) << std::endl;
vtkDoubleArray *d = vtkDoubleArray::New();
d->SetArray( const_cast<double*>(pts) , at1.GetValue() * at2.GetValue() , 0 );
vtkImageData *img = vtkImageData::New();
img->Initialize();
img->SetDimensions( at2.GetValue(), at1.GetValue(), 1 );
//imgb->SetExtent(1, xdim, 1, ydim, 1, zdim);
#if (VTK_MAJOR_VERSION >= 6)
assert(0);
#else
img->SetScalarTypeToDouble();
#endif
img->SetSpacing( at3.GetValue(1), at3.GetValue(0), 1); // FIXME image is upside down
img->SetOrigin( at4.GetValue(0), at4.GetValue(1), 1);
#if (VTK_MAJOR_VERSION >= 6)
assert(0);
#else
img->SetNumberOfScalarComponents(1);
#endif
img->GetPointData()->SetScalars(d);
#if (VTK_MAJOR_VERSION >= 6)
#else
img->Update();
#endif
img->Print(std::cout);
vtkXMLImageDataWriter *writeb= vtkXMLImageDataWriter::New();
#if (VTK_MAJOR_VERSION >= 6)
writeb->SetInputData( img );
#else
writeb->SetInput( img );
#endif
writeb->SetFileName( outfilename );
writeb->Write( );
/*
(300a,03a6) SQ # u/l,1 Ion Block Sequence
(fffe,e000) na (Item with undefined length)
(300a,00e1) SH [brass ] # 6,1 Material ID
(300a,00f7) FL 95.03 # 4,1 Isocenter to Block Tray Distance
(300a,00f8) CS [APERTURE] # 8,1 Block Type
(300a,00fa) CS [ABSENT] # 6,1 Block Divergence
(300a,00fb) CS [SOURCE_SIDE ] # 12,1 Block Mounting Position
(300a,00fc) IS [1 ] # 2,1 Block Number
(300a,0100) DS [50.00 ] # 6,1 Block Thickness
(300a,0104) IS [179 ] # 4,1 Block Number of Points
(300a,0106) DS [1.7\50.0\14.3\50.0\16.7\49.4\18.7\48.2\19.4\47.7\20.1\47.1\21.0\47.0\22.3\47.0\23.7\46.8\25.7\46.2\27.0\45.6\27.2\45.4\28.2\44.6\28.9\44.2\29.7\43.9\31.5\43.5\33.0\42.8\33.7\42.4\35.2\41.3\38.2\40.4\39.6\39.7\40.0\39.5\41.5\37.9\42
2\37.4\43.0\37.1\44.7\36] # 1934,2-2n Block Data
(fffe,e00d)
(fffe,e0dd)
*/
gdcm::Tag tblocksq(0x300a,0x03a6);
if( !nestedds.FindDataElement( tblocksq ) )
{
return 1;
}
const gdcm::DataElement &blocksq = nestedds.GetDataElement( tblocksq );
//std::cout << blocksq << std::endl;
gdcm::SmartPointer<gdcm::SequenceOfItems> sssqi = blocksq.GetValueAsSQ();
const gdcm::Item & item3 = sssqi->GetItem(1); // Item start at #1
const gdcm::DataSet& nestedds3 = item3.GetNestedDataSet();
gdcm::Tag tblockdata(0x300a,0x0106);
if( !nestedds3.FindDataElement( tblockdata ) )
{
return 1;
}
const gdcm::DataElement &blockdata = nestedds3.GetDataElement( tblockdata );
// std::cout << blockdata << std::endl;
gdcm::Attribute<0x300a,0x0106> at_;
at_.SetFromDataElement( blockdata );
vtkDoubleArray *scalars = vtkDoubleArray::New();
scalars->SetNumberOfComponents(3);
gdcm::Attribute<0x300a,0x0104> bnpts; // IS [179 ] # 4,1 Block Number of Points
if( !nestedds3.FindDataElement( bnpts.GetTag() ) )
{
return 1;
}
const gdcm::DataElement &blocknpts = nestedds3.GetDataElement( bnpts.GetTag() );
bnpts.SetFromDataElement( blocknpts );
//std::cout << bnpts.GetValue() << std::endl;
vtkPolyData *output = vtkPolyData::New();
vtkPoints *newPts = vtkPoints::New();
vtkCellArray *polys = vtkCellArray::New();
const double *ptr = at_.GetValues();
//unsigned int npts = bnpts.GetNumberOfValues() / 2;
unsigned int npts = bnpts.GetValue();
vtkIdType *ptIds = new vtkIdType[npts];
for(unsigned int i = 0; i < npts; ++i)
{
float x[3] = {};
x[0] = (float)ptr[2*i+0];
x[1] = (float)ptr[2*i+1];
//x[2] = pts[i+2];
vtkIdType ptId = newPts->InsertNextPoint( x );
//std::cout << x[0] << "," << x[1] << "," << x[2] << std::endl;
ptIds[i ] = ptId;
}
vtkIdType cellId = polys->InsertNextCell(npts , ptIds);
(void)cellId;
delete[] ptIds;
output->SetPoints(newPts);
newPts->Delete();
output->SetPolys(polys);
polys->Delete();
//output->GetCellData()->SetScalars(scalars);
//scalars->Delete();
#if (VTK_MAJOR_VERSION >= 6)
#else
output->Update();
#endif
output->Print( std::cout );
// }
vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
vtkImageColorViewer *viewer = vtkImageColorViewer::New();
#if (VTK_MAJOR_VERSION >= 6)
viewer->SetInputData(img);
#else
viewer->SetInput(img);
#endif
viewer->SetupInteractor(iren);
viewer->SetSize(600, 600);
viewer->GetRenderer()->ResetCameraClippingRange();
viewer->Render();
viewer->GetRenderer()->ResetCameraClippingRange();
vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
//vtkPolyDataMapper2D* cubeMapper = vtkPolyDataMapper2D::New();
#if (VTK_MAJOR_VERSION >= 6)
cubeMapper->SetInputData( output );
#else
cubeMapper->SetInput( output );
#endif
cubeMapper->SetScalarRange(0,7);
vtkActor *cubeActor = vtkActor::New();
//vtkActor2D* cubeActor = vtkActor2D::New();
cubeActor->SetMapper(cubeMapper);
vtkProperty * property = cubeActor->GetProperty();
property->SetRepresentationToWireframe();
viewer->GetRenderer()->AddActor( cubeActor );
vtkXMLPolyDataWriter *writec= vtkXMLPolyDataWriter::New();
#if (VTK_MAJOR_VERSION >= 6)
writec->SetInputData( output );
#else
writec->SetInput( output );
#endif
writec->SetFileName( outfilename2 );
writec->Write( );
iren->Initialize();
iren->Start();
return 0;
}
gdcm::Attribute
Attribute class This class use template metaprograming tricks to let the user know when the template ...
Definition gdcmAttribute.h:86
gdcm::Attribute::GetValues
const ArrayType * GetValues() const
Definition gdcmAttribute.h:178
gdcm::Attribute::GetValue
ArrayType & GetValue(unsigned int idx=0)
Definition gdcmAttribute.h:154
gdcm::Attribute::GetTag
static Tag GetTag()
Definition gdcmAttribute.h:98
gdcm::Attribute::SetFromDataElement
void SetFromDataElement(DataElement const &de)
Definition gdcmAttribute.h:206
gdcm::DataElement
Class to represent a Data Element either Implicit or Explicit.
Definition gdcmDataElement.h:59
gdcm::DataElement::GetValueAsSQ
SmartPointer< SequenceOfItems > GetValueAsSQ() const
gdcm::DataSet
Class to represent a Data Set (which contains Data Elements)
Definition gdcmDataSet.h:56
gdcm::DataSet::GetDataElement
const DataElement & GetDataElement(const Tag &t) const
Definition gdcmDataSet.h:188
gdcm::DataSet::FindDataElement
bool FindDataElement(const PrivateTag &t) const
Look up if private tag 't' is present in the dataset:
gdcm::File::GetDataSet
const DataSet & GetDataSet() const
Get Data Set.
Definition gdcmFile.h:57
gdcm::Item
Class to represent an Item.
Definition gdcmItem.h:46
gdcm::Item::GetNestedDataSet
const DataSet & GetNestedDataSet() const
Definition gdcmItem.h:80
gdcm::MediaStorage
MediaStorage.
Definition gdcmMediaStorage.h:44
gdcm::MediaStorage::RTIonPlanStorage
@ RTIonPlanStorage
Definition gdcmMediaStorage.h:116
gdcm::MediaStorage::SetFromFile
bool SetFromFile(File const &file)
gdcm::Reader
Reader ala DOM (Document Object Model)
Definition gdcmReader.h:54
gdcm::Reader::GetFile
const File & GetFile() const
Set/Get File.
Definition gdcmReader.h:72
gdcm::Reader::Read
virtual bool Read()
Main function to read a file.
gdcm::Reader::SetFileName
void SetFileName(const char *filename_native)
gdcm::SmartPointer
Class for Smart Pointer.
Definition gdcmSmartPointer.h:40
gdcm::Tag
Class to represent a DICOM Data Element (Attribute) Tag (Group, Element).
Definition gdcmTag.h:39
vtkImageColorViewer
Definition vtkImageColorViewer.h:73
vtkImageColorViewer::Render
virtual void Render(void)
vtkImageColorViewer::SetInput
virtual void SetInput(vtkImageData *in)
vtkImageColorViewer::SetupInteractor
virtual void SetupInteractor(vtkRenderWindowInteractor *)
vtkImageColorViewer::SetSize
virtual void SetSize(int a, int b)
vtkImageColorViewer::New
static vtkImageColorViewer * New()
gdcmAttribute.h
gdcmReader.h
vtkImageColorViewer.h