--- /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://oncora1.lyon.fnclcc.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
+======================================================================-====*/
+
+// clitk include
+#include "clitkDicomRTDoseIO.h"
+#include "clitkCommon.h"
+
+// itk include
+#include <gdcmFileHelper.h>
+
+#define GFOV_SPACING_TOL (1e-1)
+
+//--------------------------------------------------------------------
+// Read Image Information
+void clitk::DicomRTDoseIO::ReadImageInformation()
+{
+ if(m_GdcmFile)
+ delete m_GdcmFile;
+ m_GdcmFile = new gdcm::File;
+
+ int i, rc;
+ std::string tmp;
+ float ipp[3];
+ int dim[3];
+ float spacing[3];
+ float *gfov; /* gfov = GridFrameOffsetVector */
+ int gfov_len;
+ const char *gfov_str;
+
+ m_GdcmFile->SetMaxSizeLoadEntry (0xffff);
+ m_GdcmFile->SetFileName (m_FileName.c_str());
+ m_GdcmFile->SetLoadMode (0);
+ m_GdcmFile->Load();
+
+ /* Modality -- better be RTSTRUCT */
+ tmp = m_GdcmFile->GetEntryValue (0x0008, 0x0060);
+ if (strncmp (tmp.c_str(), "RTDOSE", strlen("RTDOSE"))) {
+ itkExceptionMacro(<< "Error. Input file not RTDOSE: " << m_FileName);
+ }
+
+ /* ImagePositionPatient */
+ tmp = m_GdcmFile->GetEntryValue (0x0020, 0x0032);
+ rc = sscanf (tmp.c_str(), "%f\\%f\\%f", &ipp[0], &ipp[1], &ipp[2]);
+ if (rc != 3) {
+ itkExceptionMacro(<< "Error parsing RTDOSE ipp.");
+ }
+
+ /* Rows */
+ tmp = m_GdcmFile->GetEntryValue (0x0028, 0x0010);
+ rc = sscanf (tmp.c_str(), "%d", &dim[1]);
+ if (rc != 1) {
+ itkExceptionMacro(<< "Error parsing RTDOSE rows.");
+ }
+
+ /* Columns */
+ tmp = m_GdcmFile->GetEntryValue (0x0028, 0x0011);
+ rc = sscanf (tmp.c_str(), "%d", &dim[0]);
+ if (rc != 1) {
+ itkExceptionMacro(<< "Error parsing RTDOSE columns.");
+ }
+
+ /* PixelSpacing */
+ tmp = m_GdcmFile->GetEntryValue (0x0028, 0x0030);
+ rc = sscanf (tmp.c_str(), "%g\\%g", &spacing[0], &spacing[1]);
+
+ if (rc != 2) {
+ itkExceptionMacro(<< "Error parsing RTDOSE pixel spacing.");
+ }
+
+ /* GridFrameOffsetVector */
+ tmp = m_GdcmFile->GetEntryValue (0x3004, 0x000C);
+ gfov = 0;
+ gfov_len = 0;
+ gfov_str = tmp.c_str();
+ while (1) {
+ int len;
+ gfov = (float*) realloc (gfov, (gfov_len + 1) * sizeof(float));
+ rc = sscanf (gfov_str, "%g%n", &gfov[gfov_len], &len);
+ if (rc != 1) {
+ break;
+ }
+ gfov_len ++;
+ gfov_str += len;
+ if (gfov_str[0] == '\\') {
+ gfov_str ++;
+ }
+ }
+ dim[2] = gfov_len;
+ if (gfov_len == 0) {
+ itkExceptionMacro(<< "Error parsing RTDOSE gfov.");
+ }
+
+ /* --- Analyze GridFrameOffsetVector --- */
+
+ /* (1) Make sure first element is 0. */
+ if (gfov[0] != 0.) {
+ itkExceptionMacro(<< "Error RTDOSE gfov[0] is not 0.");
+ }
+
+ /* (2) Handle case where gfov_len == 1 (only one slice). */
+ if (gfov_len == 1) {
+ spacing[2] = spacing[0];
+ }
+
+ /* (3) Check to make sure spacing is regular. */
+ for (i = 1; i < gfov_len; i++) {
+ if (i == 1) {
+ spacing[2] = gfov[1] - gfov[0];
+ } else {
+ float sp = gfov[i] - gfov[i-1];
+ if (fabs(sp - spacing[2]) > GFOV_SPACING_TOL) {
+ itkExceptionMacro(<< "Error RTDOSE grid has irregular spacing:"
+ << sp << " vs " << spacing[2]);
+ }
+ }
+ }
+
+ free (gfov);
+
+ /* DoseGridScaling */
+ m_DoseScaling = 1.0;
+ tmp = m_GdcmFile->GetEntryValue (0x3004, 0x000E);
+ rc = sscanf (tmp.c_str(), "%f", &m_DoseScaling);
+ /* If element doesn't exist, scaling is 1.0 */
+
+ // set dimension values
+ SetNumberOfDimensions(3);
+ for(int i=0; i<3; i++) {
+ SetDimensions(i, dim[i]);
+ SetSpacing(i, spacing[i]);
+ SetOrigin(i, ipp[i]);
+ }
+
+ // set other information
+ SetByteOrderToLittleEndian();
+ SetPixelType(itk::ImageIOBase::SCALAR);
+ SetNumberOfComponents(1);
+ SetComponentType(itk::ImageIOBase::FLOAT);
+}
+
+//--------------------------------------------------------------------
+// Read Image Information
+bool clitk::DicomRTDoseIO::CanReadFile(const char* FileNameToRead)
+{
+ // opening dicom input file
+ gdcm::File dcmFile;
+ dcmFile.SetFileName(FileNameToRead);
+ if (!dcmFile.OpenFile())
+ return false;
+
+ //Taken from plastimatch
+ dcmFile.SetMaxSizeLoadEntry (0xffff);
+ dcmFile.SetLoadMode (0);
+ dcmFile.Load();
+
+ /* Modality -- better be RTDOSE */
+ std::string tmp = dcmFile.GetEntryValue (0x0008, 0x0060);
+ if (!strncmp (tmp.c_str(), "RTDOSE", strlen("RTDOSE"))) {
+ return true;
+ }
+
+ return false;
+}
+
+//--------------------------------------------------------------------
+template <class T>
+void
+clitk::DicomRTDoseIO::dose_copy_raw (float *img_out, T *img_in, int nvox, float scale)
+{
+ for (int i = 0; i < nvox; i++) {
+ img_out[i] = img_in[i] * scale;
+ }
+}
+
+//--------------------------------------------------------------------
+// Read Image Content
+void clitk::DicomRTDoseIO::Read(void * buffer)
+{
+ float *img = (float*) buffer;
+
+ unsigned long npix = 1;
+ for(unsigned int i=0; i<GetNumberOfDimensions(); i++)
+ npix *= GetDimensions(i);
+
+ /* PixelData */
+ gdcm::FileHelper m_GdcmFile_helper (m_GdcmFile);
+
+ //size_t image_data_size = m_GdcmFile_helper.GetImageDataSize();
+ if (strcmp (m_GdcmFile->GetPixelType().c_str(), "16U")==0) {
+ unsigned short* image_data = (unsigned short*) m_GdcmFile_helper.GetImageData();
+ dose_copy_raw (img, image_data, npix, m_DoseScaling);
+ } else if (strcmp(m_GdcmFile->GetPixelType().c_str(),"32U")==0) {
+ unsigned long* image_data = (unsigned long*) m_GdcmFile_helper.GetImageData ();
+ dose_copy_raw (img, image_data, npix, m_DoseScaling);
+ } else {
+ itkExceptionMacro(<< "Error RTDOSE not type 16U and 32U (type="
+ << m_GdcmFile->GetPixelType().c_str() << ")");
+ }
+
+ /* GCS FIX: Do I need to do something about endian-ness? */
+
+
+
+ /* Copy data to volume */
+// float *img = (float*) vol->img;
+// for (i = 0; i < vol->npix; i++) {
+ //img[i] = image_data[i] * m_DoseScaling;
+// }
+
+ delete m_GdcmFile;
+}
+
+//--------------------------------------------------------------------
+// Write Image Information
+void clitk::DicomRTDoseIO::WriteImageInformation(bool keepOfStream)
+{
+}
+
+//--------------------------------------------------------------------
+// Write Image Information
+bool clitk::DicomRTDoseIO::CanWriteFile(const char* FileNameToWrite)
+{
+ return false;
+}
+
+//--------------------------------------------------------------------
+// Write Image
+void clitk::DicomRTDoseIO::Write(const void * buffer)
+{
+}
+
--- /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://oncora1.lyon.fnclcc.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 clitkDicomRTDoseIO_h
+#define clitkDicomRTDoseIO_h
+
+// clitk include
+#include "clitkCommon.h"
+
+// itk include
+#include <itkImageIOBase.h>
+#include <gdcmFile.h>
+
+// std include
+#include <fstream>
+
+namespace clitk
+{
+
+//====================================================================
+// Class for reading Vox Image file format
+class DicomRTDoseIO: public itk::ImageIOBase
+{
+public:
+ /** Standard class typedefs. */
+ typedef DicomRTDoseIO Self;
+ typedef itk::ImageIOBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef signed short int PixelType;
+
+ DicomRTDoseIO():Superclass() {
+ mustWriteHeader = false;
+ m_GdcmFile=NULL;
+ }
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(DicomRTDoseIO, ImageIOBase);
+
+ /*-------- This part of the interface deals with reading data. ------ */
+ virtual void ReadImageInformation();
+ virtual bool CanReadFile( const char* FileNameToRead );
+ virtual void Read(void * buffer);
+
+ /*-------- This part of the interfaces deals with writing data. ----- */
+ virtual void WriteImageInformation(bool keepOfStream);
+ virtual void WriteImageInformation() {
+ WriteImageInformation(false);
+ }
+ virtual bool CanWriteFile(const char* filename);
+ virtual void Write(const void* buffer);
+
+protected:
+ template <class T> void dose_copy_raw (float *img_out, T *img_in, int nvox, float scale);
+
+ bool mustWriteHeader;
+ int m_HeaderSize;
+ std::ofstream file;
+ gdcm::File *m_GdcmFile;
+ float m_DoseScaling;
+}; // end class DicomRTDoseIO
+
+} // end namespace
+
+#endif /* end #define clitkDicomRTDoseIO_h */
+
--- /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://oncora1.lyon.fnclcc.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 clitkDicomRTDoseIOFactory_h
+#define clitkDicomRTDoseIOFactory_h
+
+// clitk include
+#include "clitkDicomRTDoseIO.h"
+
+// itk include
+#include "itkImageIOBase.h"
+#include "itkObjectFactoryBase.h"
+#include "itkVersion.h"
+
+namespace clitk
+{
+
+//====================================================================
+// Factory for reading Dicom RT Dose file
+class DicomRTDoseIOFactory: public itk::ObjectFactoryBase
+{
+public:
+ /** Standard class typedefs. */
+ typedef DicomRTDoseIOFactory Self;
+ typedef itk::ObjectFactoryBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Class methods used to interface with the registered factories. */
+ const char* GetITKSourceVersion(void) const {
+ return ITK_SOURCE_VERSION;
+ }
+
+ const char* GetDescription(void) const {
+ return "Dicom RT Dose IO factory";
+ }
+
+ /** Method for class instantiation. */
+ itkFactorylessNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(DicomRTDoseIOFactory, ObjectFactoryBase);
+
+ /** Register one factory of this type */
+ static void RegisterOneFactory(void) {
+ ObjectFactoryBase::RegisterFactory( Self::New() );
+ }
+
+protected:
+ DicomRTDoseIOFactory();
+ ~DicomRTDoseIOFactory() {};
+
+private:
+ DicomRTDoseIOFactory(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+};
+
+} // end namespace
+
+#endif /* end #define clitkDicomRTDoseIOFactory_h */
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff