===========================================================================**/
// clitk includes
+#include "clitkIO.h"
#include "clitkDicom2Image_ggo.h"
#include "clitkCommon.h"
#include "clitkImageCommon.h"
#include "vvImageReader.h"
#include "vvImageWriter.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>
#endif
+#include <set>
+
//====================================================================
int main(int argc, char * argv[])
{
// 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 ...
- std::vector<double> theorigin(3);
- std::vector<double> sliceLocations;
+ 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 << "Reading <" << input_files[i] << std::endl;
+#if GDCM_MAJOR_VERSION >= 2
gdcm::Reader hreader;
hreader.SetFileName(input_files[i].c_str());
hreader.Read();
- theorigin = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
- sliceLocations.push_back(theorigin[2]);
- gdcm::Attribute<0x28, 0x100> pixel_size;
gdcm::DataSet& ds = hreader.GetFile().GetDataSet();
- pixel_size.SetFromDataSet(ds);
- if (pixel_size.GetValue() != 16)
- {
- std::cerr << "Pixel type 2 bytes ! " << std::endl;
- std::cerr << "In file " << input_files[i] << std::endl;
- exit(0);
+
+ if (args_info.extract_series_flag) {
+ gdcm::Attribute<0x20,0x000e> series_UID_att;
+ series_UID_att.SetFromDataSet(ds);
+ series_UID = series_UID_att.GetValue();
}
+
+ 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)
+ {
+ std::cerr << "Pixel type not 2 bytes ! " << std::endl;
+ std::cerr << "In file " << input_files[i] << std::endl;
+ exit(0);
+ }
+ */
#else
gdcm::File *header = new gdcm::File();
header->SetFileName(input_files[i]);
header->SetMaxSizeLoadEntry(16384); // required ?
header->Load();
- theorigin[0] = header->GetXOrigin();
- theorigin[1] = header->GetYOrigin();
- theorigin[2] = header->GetZOrigin();
- sliceLocations.push_back(theorigin[2]);
- if (header->GetPixelSize() != 2) {
+
+ if (args_info.extract_series_flag) {
+ series_UID = header->GetEntryValue(0x20,0x000e).c_str();
+ }
+
+ 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;
exit(0);
}
+ */
#endif
}
//===========================================
// Sort slices locations ...
- std::vector<int> sliceIndex;
- clitk::GetSortedIndex(sliceLocations, sliceIndex);
- if (args_info.verboseSliceLocation_flag) {
- std::cout << sliceLocations[sliceIndex[0]] << " -> "
- << sliceIndex[0] << " / " << 0 << " => "
- << "0 mm "
- << input_files[sliceIndex[0]]
- << std::endl;
- for(unsigned int i=1; i<sliceIndex.size(); i++) {
- std::cout << sliceLocations[sliceIndex[i]] << " -> "
- << sliceIndex[i] << " / " << i << " => "
- << sliceLocations[sliceIndex[i]] - sliceLocations[sliceIndex[i-1]]
- << "mm "
- << input_files[sliceIndex[i]]
+ 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.verbose_flag) {
+ std::cout << locs[sliceIndex[0]] << " -> "
+ << sliceIndex[0] << " / " << 0 << " => "
+ << "0 mm "
+ << files[sliceIndex[0]]
<< std::endl;
+ for(unsigned int i=1; i<sliceIndex.size(); i++) {
+ std::cout << locs[sliceIndex[i]] << " -> "
+ << sliceIndex[i] << " / " << i << " => "
+ << locs[sliceIndex[i]] - locs[sliceIndex[i-1]]
+ << "mm "
+ << files[sliceIndex[i]]
+ << std::endl;
+ }
}
- }
- //===========================================
- // Analyze slices locations ...
- double currentDist;
- double dist=0;
- double tolerance = args_info.tolerance_arg;
- double previous = sliceLocations[sliceIndex[0]];
- for(unsigned int i=1; i<sliceIndex.size(); i++) {
- currentDist = sliceLocations[sliceIndex[i]]-previous;
- if (i!=1) {
- if (fabs(dist-currentDist) > tolerance) {
- std::cout << "ERROR : " << std::endl
- << "Current slice pos is = " << sliceLocations[sliceIndex[i]] << std::endl
- << "Previous slice pos is = " << previous << std::endl
- << "Current file is = " << input_files[sliceIndex[i]] << std::endl
- << "Current index is = " << i << std::endl
- << "Current sortindex is = " << sliceIndex[i] << std::endl
- << "Current slice diff = " << dist << std::endl
- << "Current error = " << fabs(dist-currentDist) << std::endl;
- exit(1);
- }
- } else dist = currentDist;
- previous = sliceLocations[sliceIndex[i]];
- }
+ //===========================================
+ // Analyze slices locations ...
+ double currentDist;
+ double dist=0;
+ double tolerance = args_info.tolerance_arg;
+ double previous = locs[sliceIndex[0]];
+ for(unsigned int i=1; i<sliceIndex.size(); i++) {
+ currentDist = locs[sliceIndex[i]]-previous;
+ if (i!=1) {
+ if (fabs(dist-currentDist) > tolerance) {
+ std::cout << "ERROR : " << std::endl
+ << "Current slice pos is = " << locs[sliceIndex[i]] << std::endl
+ << "Previous slice pos is = " << previous << std::endl
+ << "Current file is = " << files[sliceIndex[i]] << std::endl
+ << "Current index is = " << i << std::endl
+ << "Current sortindex is = " << sliceIndex[i] << std::endl
+ << "Current slice diff = " << dist << std::endl
+ << "Current error = " << fabs(dist-currentDist) << std::endl;
+ exit(1);
+ }
+ } else dist = currentDist;
+ previous = locs[sliceIndex[i]];
+ }
- //===========================================
- // Create ordered vector of filenames
- std::vector<std::string> sorted_files;
- sorted_files.resize(sliceIndex.size());
- for(unsigned int i=0; i<sliceIndex.size(); i++)
- sorted_files[i] = input_files[ sliceIndex[i] ];
+ //===========================================
+ // Create ordered vector of filenames
+ std::vector<std::string> sorted_files;
+ sorted_files.resize(sliceIndex.size());
+ for(unsigned int i=0; i<sliceIndex.size(); i++)
+ sorted_files[i] = files[ sliceIndex[i] ];
- //===========================================
- // Read write serie
- vvImageReader::Pointer reader = vvImageReader::New();
- reader->SetInputFilenames(sorted_files);
- 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();
- if (args_info.focal_origin_given) {
- std::vector<double> spacing = image->GetSpacing();
- std::vector<int> size = image->GetSize();
- theorigin[0] = -spacing[0]*size[0]/2.0;
- theorigin[1] = -spacing[1]*size[1]/2.0;
- modifier->SetInput(vtk_image);
- modifier->SetOutputOrigin(theorigin[0], theorigin[1], sliceLocations[sliceIndex[0]]);
- modifier->Update();
- vvImage::Pointer focal_image = vvImage::New();
- focal_image->AddVtkImage(modifier->GetOutput());
- image = focal_image;
- }
+ //===========================================
+ // 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();
+ if (args_info.focal_origin_given) {
+ std::vector<double> spacing = image->GetSpacing();
+ std::vector<int> size = image->GetSize();
+ origin[0] = -spacing[0]*size[0]/2.0;
+ origin[1] = -spacing[1]*size[1]/2.0;
+#if VTK_MAJOR_VERSION <= 5
+ modifier->SetInput(vtk_image);
+#else
+ modifier->SetInputData(vtk_image);
+#endif
+ modifier->SetOutputOrigin(origin[0], origin[1], locs[sliceIndex[0]]);
+ modifier->Update();
+ vvImage::Pointer focal_image = vvImage::New();
+ focal_image->AddVtkImage(modifier->GetOutput());
+ image = focal_image;
+ }
+
+ std::string outfile;
+ if (series_UIDs.size() == 1)
+ outfile = args_info.output_arg;
+ else {
+ std::ostringstream name;
+ 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();
- vvImageWriter::Pointer writer = vvImageWriter::New();
- writer->SetInput(image);
- writer->SetOutputFileName(args_info.output_arg);
- writer->Update();
+ modifier->Delete();
- modifier->Delete();
+ sn++;
+ }
return 0;
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff