Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.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
- 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>
+#if GDCM_MAJOR_VERSION >= 2
+// IMPLEMENTATION NOTE:
+// The following has been done without the use of vtkGDCMImageReader which directly
+// handle RTDOSE image. Another approach would have been to use gdcm::ImageReader
+// which also properly recognize RTDOSE
+ #include <gdcmReader.h>
+ #include <gdcmAttribute.h>
+#else
+ #include <gdcmFileHelper.h>
+#endif
#define GFOV_SPACING_TOL (1e-1)
// Read Image Information
void clitk::DicomRTDoseIO::ReadImageInformation()
{
+#if GDCM_MAJOR_VERSION < 2
if(m_GdcmFile)
delete m_GdcmFile;
m_GdcmFile = new gdcm::File;
+#endif
- int i, rc;
+ int i;
std::string tmp;
float ipp[3];
int dim[3];
float spacing[3];
- float *gfov; /* gfov = GridFrameOffsetVector */
+ double *gfov; /* gfov = GridFrameOffsetVector */
int gfov_len;
+#if GDCM_MAJOR_VERSION < 2
const char *gfov_str;
-
+ int rc;
+#endif
+
+#if GDCM_MAJOR_VERSION >= 2
+ m_GdcmImageReader.SetFileName(m_FileName.c_str());
+ m_GdcmImageReader.Read();
+ gdcm::File* m_GdcmFile = &m_GdcmImageReader.GetFile();
+#else
m_GdcmFile->SetMaxSizeLoadEntry (0xffff);
m_GdcmFile->SetFileName (m_FileName.c_str());
m_GdcmFile->SetLoadMode (0);
m_GdcmFile->Load();
+#endif
/* Modality -- better be RTSTRUCT */
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::DataSet &ds = m_GdcmFile->GetDataSet();
+
+ gdcm::Attribute<0x8,0x60> at1;
+ at1.SetFromDataSet(ds);
+ tmp = at1.GetValue();
+#else
tmp = m_GdcmFile->GetEntryValue (0x0008, 0x0060);
+#endif
if (strncmp (tmp.c_str(), "RTDOSE", strlen("RTDOSE"))) {
itkExceptionMacro(<< "Error. Input file not RTDOSE: " << m_FileName);
}
/* ImagePositionPatient */
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Attribute<0x20,0x32> at2;
+ at2.SetFromDataSet(ds);
+ ipp[0] = at2.GetValue(0);
+ ipp[1] = at2.GetValue(1);
+ ipp[2] = at2.GetValue(2);
+#else
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.");
}
+#endif
/* Rows */
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Attribute<0x28,0x10> at3;
+ at3.SetFromDataSet(ds);
+ dim[1] = at3.GetValue();
+#else
tmp = m_GdcmFile->GetEntryValue (0x0028, 0x0010);
rc = sscanf (tmp.c_str(), "%d", &dim[1]);
if (rc != 1) {
itkExceptionMacro(<< "Error parsing RTDOSE rows.");
}
+#endif
/* Columns */
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Attribute<0x28,0x11> at4;
+ at4.SetFromDataSet(ds);
+ dim[0] = at4.GetValue();
+#else
tmp = m_GdcmFile->GetEntryValue (0x0028, 0x0011);
rc = sscanf (tmp.c_str(), "%d", &dim[0]);
if (rc != 1) {
itkExceptionMacro(<< "Error parsing RTDOSE columns.");
}
+#endif
/* PixelSpacing */
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Attribute<0x28,0x30> at5;
+ at5.SetFromDataSet(ds);
+ spacing[0] = at5.GetValue(0);
+ spacing[1] = at5.GetValue(1);
+#else
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.");
}
+#endif
/* GridFrameOffsetVector */
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Attribute<0x3004,0x000C> at6;
+ const gdcm::DataElement& de6 = ds.GetDataElement( at6.GetTag() );
+ at6.SetFromDataElement(de6);
+ gfov = (double*) at6.GetValues();
+ gfov_len = at6.GetNumberOfValues();
+#else
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);
+ gfov = (double*) realloc (gfov, (gfov_len + 1) * sizeof(double));
+ rc = sscanf (gfov_str, "%lf%n", &gfov[gfov_len], &len);
if (rc != 1) {
break;
}
gfov_str ++;
}
}
+#endif
+
dim[2] = gfov_len;
if (gfov_len == 0) {
itkExceptionMacro(<< "Error parsing RTDOSE gfov.");
if (i == 1) {
spacing[2] = gfov[1] - gfov[0];
} else {
- float sp = gfov[i] - gfov[i-1];
+ double 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]);
}
}
+#if GDCM_MAJOR_VERSION < 2
free (gfov);
+#endif
/* DoseGridScaling */
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Attribute<0x3004,0x000E> at7 = { 1. } ;
+ at7.SetFromDataSet(ds);
+ m_DoseScaling = at7.GetValue();
+#else
m_DoseScaling = 1.0;
tmp = m_GdcmFile->GetEntryValue (0x3004, 0x000E);
rc = sscanf (tmp.c_str(), "%f", &m_DoseScaling);
+#endif
/* If element doesn't exist, scaling is 1.0 */
// set dimension values
// Read Image Information
bool clitk::DicomRTDoseIO::CanReadFile(const char* FileNameToRead)
{
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Reader creader;
+ creader.SetFileName(FileNameToRead);
+ if (!creader.Read())
+ return false;
+
+ gdcm::DataSet &ds = creader.GetFile().GetDataSet();
+ gdcm::Attribute<0x8,0x60> at1;
+ at1.SetFromDataSet(ds);
+ std::string tmp = at1.GetValue();
+#else
// opening dicom input file
gdcm::File dcmFile;
dcmFile.SetFileName(FileNameToRead);
/* Modality -- better be RTDOSE */
std::string tmp = dcmFile.GetEntryValue (0x0008, 0x0060);
+#endif
if (!strncmp (tmp.c_str(), "RTDOSE", strlen("RTDOSE"))) {
return true;
}
// 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 */
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Image &i = m_GdcmImageReader.GetImage();
+
+ char* image_data = new char[i.GetBufferLength()];
+ i.GetBuffer(image_data);
+
+ gdcm::DataSet& ds = m_GdcmImageReader.GetFile().GetDataSet();
+ float *img = (float*) buffer;
+
+ gdcm::Attribute<0x28, 0x100> pixel_size;
+ pixel_size.SetFromDataSet(ds);
+ if (pixel_size.GetValue() == 16) {
+ unsigned short* image_data2 = (unsigned short*) image_data ;
+ dose_copy_raw (img, image_data2, npix, m_DoseScaling);
+ }
+ else if (pixel_size.GetValue() == 32) {
+ unsigned long* image_data2 = (unsigned long*) image_data;
+ dose_copy_raw (img, image_data2, npix, m_DoseScaling);
+ } else {
+ itkExceptionMacro(<< "Error RTDOSE not type 16U and 32U (type="
+ << pixel_size.GetValue() << ")");
+ }
+
+ delete [] image_data;
+#else
+ float *img = (float*) buffer;
+
gdcm::FileHelper m_GdcmFile_helper (m_GdcmFile);
//size_t image_data_size = m_GdcmFile_helper.GetImageDataSize();
itkExceptionMacro(<< "Error RTDOSE not type 16U and 32U (type="
<< m_GdcmFile->GetPixelType().c_str() << ")");
}
+ delete m_GdcmFile;
+#endif
/* GCS FIX: Do I need to do something about endian-ness? */
// for (i = 0; i < vol->npix; i++) {
//img[i] = image_data[i] * m_DoseScaling;
// }
-
- delete m_GdcmFile;
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff