===========================================================================**/
// clitk includes
+#include "clitkIO.h"
#include "clitkDicom2Image_ggo.h"
#include "clitkCommon.h"
#include "clitkImageCommon.h"
#include <gdcmFile.h>
#include <vtkVersion.h>
#include <vtkImageChangeInformation.h>
-#if GDCM_MAJOR_VERSION == 2
+#if GDCM_MAJOR_VERSION >= 2
#include <gdcmImageHelper.h>
#include <gdcmAttribute.h>
#include <gdcmReader.h>
{
// init command line
GGO(clitkDicom2Image, args_info);
+ CLITK_INIT;
+
std::vector<std::string> input_files;
///if std_input is given, read the input files from stdin
if (args_info.std_input_given) {
//===========================================
/// Get slices locations ...
- int series_number = -1;
- std::set<int> series_numbers;
- std::map< int, std::vector<double> > theorigin;
- std::map< int, std::vector<double> > sliceLocations;
- std::map< int, std::vector<std::string> > seriesFiles;
+ std::string series_UID = "";
+ std::set<std::string> series_UIDs;
+ std::map< std::string, std::vector<double> > theorigin;
+ std::map< std::string, std::vector<double> > theorientation;
+ std::map< std::string, std::vector<double> > sliceLocations;
+ std::map< std::string, std::vector<std::string> > seriesFiles;
+#if GDCM_MAJOR_VERSION >= 2
+ if (args_info.verbose_flag)
+ std::cout << "Using GDCM-2.x" << std::endl;
+#else
+ if (args_info.verbose_flag) {
+ std::cout << "Not using GDCM-2.x" << std::endl;
+ std::cout<< "The image orientation is not supported with this version of GDCM" <<std::endl;
+ }
+#endif
for(unsigned int i=0; i<args_info.inputs_num; i++) {
- //std::cout << "Reading <" << input_files[i] << std::endl;
-#if GDCM_MAJOR_VERSION == 2
if (args_info.verbose_flag)
- std::cout << "Using GDCM-2.x" << std::endl;
+ std::cout << "Reading <" << input_files[i] << std::endl;
+#if GDCM_MAJOR_VERSION >= 2
gdcm::Reader hreader;
hreader.SetFileName(input_files[i].c_str());
hreader.Read();
gdcm::DataSet& ds = hreader.GetFile().GetDataSet();
if (args_info.extract_series_flag) {
- gdcm::Attribute<0x20,0x11> series_number_att;
- series_number_att.SetFromDataSet(hreader.GetFile().GetDataSet());
- series_number = series_number_att.GetValue();
+ gdcm::Attribute<0x20,0x000e> series_UID_att;
+ series_UID_att.SetFromDataSet(ds);
+ series_UID = series_UID_att.GetValue();
}
-
- series_numbers.insert(series_number);
- theorigin[series_number] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
- sliceLocations[series_number].push_back(theorigin[series_number][2]);
- seriesFiles[series_number].push_back(input_files[i]);
-
+
+ series_UIDs.insert(series_UID);
+ theorigin[series_UID] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
+ theorientation[series_UID] = gdcm::ImageHelper::GetDirectionCosinesValue(hreader.GetFile());
+ if (args_info.patientSystem_flag) {
+ double n1 = theorientation[series_UID][1]*theorientation[series_UID][5]-
+ theorientation[series_UID][2]*theorientation[series_UID][4];
+ double n2 = theorientation[series_UID][3]*theorientation[series_UID][2]-
+ theorientation[series_UID][5]*theorientation[series_UID][0];
+ double n3 = theorientation[series_UID][0]*theorientation[series_UID][4]-
+ theorientation[series_UID][1]*theorientation[series_UID][3];
+ double sloc = theorigin[series_UID][0]*n1+
+ theorigin[series_UID][1]*n2+
+ theorigin[series_UID][2]*n3;
+ sliceLocations[series_UID].push_back(sloc);
+ } else
+ sliceLocations[series_UID].push_back(theorigin[series_UID][2]);
+ seriesFiles[series_UID].push_back(input_files[i]);
+
gdcm::Attribute<0x28, 0x100> pixel_size;
pixel_size.SetFromDataSet(ds);
/* if (pixel_size.GetValue() != 16)
}
*/
#else
- if (args_info.verbose_flag)
- std::cout << "Not using GDCM-2.x" << std::endl;
gdcm::File *header = new gdcm::File();
header->SetFileName(input_files[i]);
header->SetMaxSizeLoadEntry(16384); // required ?
header->Load();
if (args_info.extract_series_flag) {
- series_number = atoi(header->GetEntryValue(0x20,0x11).c_str());
+ series_UID = header->GetEntryValue(0x20,0x000e).c_str();
}
-
- series_numbers.insert(series_number);
- theorigin[series_number].resize(3);
- theorigin[series_number][0] = header->GetXOrigin();
- theorigin[series_number][1] = header->GetYOrigin();
- theorigin[series_number][2] = header->GetZOrigin();
- sliceLocations[series_number].push_back(theorigin[series_number][2]);
- seriesFiles[series_number].push_back(input_files[i]);
+
+ series_UIDs.insert(series_UID);
+ theorigin[series_UID].resize(3);
+ theorigin[series_UID][0] = header->GetXOrigin();
+ theorigin[series_UID][1] = header->GetYOrigin();
+ theorigin[series_UID][2] = header->GetZOrigin();
+ sliceLocations[series_UID].push_back(theorigin[series_UID][2]);
+ seriesFiles[series_UID].push_back(input_files[i]);
/*if (header->GetPixelSize() != 2) {
std::cerr << "Pixel type 2 bytes ! " << std::endl;
std::cerr << "In file " << input_files[i] << std::endl;
//===========================================
// Sort slices locations ...
- std::set<int>::iterator sn = series_numbers.begin();
- while ( sn != series_numbers.end() ) {
+ std::set<std::string>::iterator sn = series_UIDs.begin();
+ while ( sn != series_UIDs.end() ) {
std::vector<double> locs = sliceLocations[*sn];
std::vector<double> origin = theorigin[*sn];
std::vector<std::string> files = seriesFiles[*sn];
std::vector<int> sliceIndex;
clitk::GetSortedIndex(locs, sliceIndex);
- if (args_info.verboseSliceLocation_flag) {
+ if (args_info.verbose_flag) {
std::cout << locs[sliceIndex[0]] << " -> "
<< sliceIndex[0] << " / " << 0 << " => "
<< "0 mm "
// Read write serie
vvImageReader::Pointer reader = vvImageReader::New();
reader->SetInputFilenames(sorted_files);
+ reader->SetPatientCoordinateSystem(args_info.patientSystem_flag);
reader->Update(vvImageReader::DICOM);
if (reader->GetLastError().size() != 0) {
std::cerr << reader->GetLastError() << std::endl;
return 1;
}
-
+
vvImage::Pointer image = reader->GetOutput();
vtkImageData* vtk_image = image->GetFirstVTKImageData();
vtkImageChangeInformation* modifier = vtkImageChangeInformation::New();
}
std::string outfile;
- if (series_numbers.size() == 1)
+ if (series_UIDs.size() == 1)
outfile = args_info.output_arg;
else {
std::ostringstream name;
- name << *sn << "_" << args_info.output_arg;
+ std::vector<std::string> directory = clitk::SplitFilename(args_info.output_arg);
+ if (directory.size() == 2)
+ name << directory[0] << "/" << *sn << "_" << directory[1];
+ else
+ name << *sn << "_" << args_info.output_arg;
outfile = name.str();
}
vvImageWriter::Pointer writer = vvImageWriter::New();
writer->SetInput(image);
+ if (args_info.patientSystem_flag && !image->GetTransform().empty())
+ writer->SetSaveTransform(true);
writer->SetOutputFileName(outfile);
writer->Update();
modifier->Delete();
-
+
sn++;
}
-
+
return 0;
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff