#if defined(USE_GDCM)
#include <gdcmGlobal.h>
#include <gdcmSerieHelper.h>
+#include <gdcmFileHelper.h>
+#include <gdcmUtil.h>
#include <vtkGdcmReader.h>
#endif
public:
ImageExtent(const std::string& x, const std::string& y, const std::string& z, const std::string& t)
{
- sscanf(x.c_str(),"%d",&mExtent[0]);
- sscanf(y.c_str(),"%d",&mExtent[1]);
- sscanf(z.c_str(),"%d",&mExtent[2]);
- sscanf(t.c_str(),"%d",&mExtent[3]);
- if(x==""){mExtent[0]=1;}
- if(y==""){mExtent[1]=1;}
- if(z==""){mExtent[2]=1;}
- if(t==""){mExtent[3]=1;}
-
- if (mExtent[3]>1) mDim=4;
- else if (mExtent[2]>1) mDim=3;
- else if (mExtent[1]>1) mDim=2;
- else if (mExtent[0]>1) mDim=1;
- else mDim=0;
+ sscanf(x.c_str(),"%d",&mExtent[0]);
+ sscanf(y.c_str(),"%d",&mExtent[1]);
+ sscanf(z.c_str(),"%d",&mExtent[2]);
+ sscanf(t.c_str(),"%d",&mExtent[3]);
+ if(x==""){mExtent[0]=1;}
+ if(y==""){mExtent[1]=1;}
+ if(z==""){mExtent[2]=1;}
+ if(t==""){mExtent[3]=1;}
+
+ if (mExtent[3]>1) mDim=4;
+ else if (mExtent[2]>1) mDim=3;
+ else if (mExtent[1]>1) mDim=2;
+ else if (mExtent[0]>1) mDim=1;
+ else mDim=0;
}
}
else
{
- std::string extentx = (*sel).GetAttribute("D0028_0010");
- std::string extenty = (*sel).GetAttribute("D0028_0011");
- std::string extentz = (*sel).GetAttribute("D0028_0012");
- std::string extentt = (*sel).GetAttribute("D0028_0010");
- if( extentx == "" && extenty == "" && extentz == "")
- {
- // we try to create a vtkImageData just to get dim informations
- // Long method need to improve it!
- std::string name = (*sel).GetAttribute("FullFileName");
- if (name != "")
- {
- int dim[3];
- char c[5];
- mReader.GetImage(name)->GetDimensions(dim);
- sprintf(c,"%d", dim[0]);
- extentx = c;
- sprintf(c,"%d", dim[1]);
- extenty = c;
- sprintf(c,"%d", dim[2]);
- extentz = c;
- }
- }
+ boost::shared_ptr<ImageExtent> ie=boost::shared_ptr<ImageExtent>(new ImageExtent((*sel).GetAttribute("D0028_0010"),
+ (*sel).GetAttribute("D0028_0011"),
+ (*sel).GetAttribute("D0028_0012"),
+ ""));
- boost::shared_ptr<ImageExtent> ie=boost::shared_ptr<ImageExtent>(new ImageExtent(extentx, extenty, extentz,extentt));
if(mImageExtent==0)
{
mImageExtent=ie;
mValidationSignal(ivalid);
}
+ void GimmickView::stopReader()
+ {
+ mReader.Stop();
+ }
+
//======================================================================
///Reads Images (Non Threaded)
void GimmickView::ReadImagesNotThreaded(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
{
- mReader.Stop();
+ stopReader();
/* remember!
#define GIMMICK_NO_IMAGE_SELECTION 0
vtkImageData* first = mReader.GetImage( i_file);
int dim[3];
first->GetDimensions(dim);
- if (dim[3] > 1)
+ if (dim[2] > 1)
{
bres = false;
}
// If we want only one output information structure, we set it outside the loop
if(!i_attr.mult)
{
- getAttributes(im.front(), o_output.front().infos,i_attr);
+ getAttributes(im.front(), o_output.front().infos, i_attr);
}
}
}
out.img->SetExtent(ext);
int dim[3];
+ double spac[3];
first->GetDimensions(dim);
+ first->GetSpacing(spac);
+ out.img->SetSpacing(spac);
out.img->SetDimensions(dim[0], dim[1], im.size() );
out.img->AllocateScalars();
out.img->Update();
{
vtkImageData* first = mReader.GetImage( im.front());
int dim[3];
+ double spac[3];
first->GetDimensions(dim);
+ first->GetSpacing(spac);
// differents formats char , short, etc...
// differents components 1..3 ex. jpg ->RGB 3
unsigned long imsize = dim[0] * dim[1];
OutStrGimmick out;
out.img = vtkImageData::New();
out.img->SetScalarType(first->GetScalarType());
-
+ out.img->SetSpacing(spac);
out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
int ext[6];
first->GetWholeExtent(ext); // send also 0,0 in Z
}
- //////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////
// create an output structure with n entries (T size) = T + n output
//////////////////////////////////////////////////////////
void GimmickView::readImages4(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
int ext[6];
+ double spac[6];
first->GetWholeExtent(ext); // send also 0,0 in Z
ext[5] = 0;
out.img->SetExtent(ext);
-
+ first->GetSpacing(spac);
+ out.img->SetSpacing(spac);
out.img->SetDimensions(dim[0], dim[1], im.size() );
out.img->AllocateScalars();
out.img->Update();
-
void GimmickView::ReadImagesNotThreadedInVector(std::vector<vtkImageData*>& s, std::vector<std::string> im, int dimension)
{
// Create the output data
}
else if (im.size()>1) // Test inutile ? JPR
{
+ /// \TODO fix unused variable 'first'
vtkImageData* first = mReader.GetImage( im.front());
if (dimension == 2)
{
+////////////////////////////////////////////////////////////////////////
+void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
+{
+ bool res = true;
+ std::vector<GDCM_NAME_SPACE::FileHelper *> filesH;
+ std::vector<std::string> suid;
+ std::map<std::string, std::string> msuid;
+ std::string tempuid = GDCM_NAME_SPACE::Util::CreateUniqueUID();
+ int i = 1;
+ std::vector<std::string>::iterator it = i_filenames.begin();
+ for(; it != i_filenames.end(); it++)
+ {
+
+ GDCM_NAME_SPACE::File *file;
+ file = GDCM_NAME_SPACE::File::New( );
+ file->SetLoadMode( GDCM_NAME_SPACE::LD_ALL );
+ file->SetFileName( (*it).c_str() );
+ res = file->Load();
+ if ( !res )
+ {
+ std::cerr << "Sorry, " << (*it).c_str() <<" not a gdcm-readable "
+ << "DICOM / ACR File" <<std::endl;
+ file ->Delete();
+ //return 0;
+ }
+ std::cout << " ... is readable " << std::endl;
+
+ // We need a gdcm::FileHelper, since we want to load the pixels
+ GDCM_NAME_SPACE::FileHelper *fh = GDCM_NAME_SPACE::FileHelper::New(file);
+
+ uint8_t *imageData = fh->GetImageData();
+
+ // Institution name
+ file->AddAnonymizeElement(0x0008, 0x0080, "*");
+ // Patient's name
+ file->AddAnonymizeElement(0x0010, 0x0010, "*");
+ // Patient's ID
+ file->AddAnonymizeElement( 0x0010, 0x0020,"1515" );
+ // Study Instance UID
+ file->AddAnonymizeElement(0x0020, 0x000d, tempuid );
+ // Telephone
+ file->AddAnonymizeElement(0x0010, 0x2154, "3615" );
+
+ // Aware user will add here more fields to anonymize here
+
+ // The gdcm::File is modified in memory
+
+ file->AnonymizeFile();
+
+
+ i++;
+ fh->SetContentType(GDCM_NAME_SPACE::UNMODIFIED_PIXELS_IMAGE);
+
+ fh->WriteDcmExplVR(file->GetFileName() +".ano1" );
+ std::cout << i <<" End Anonymize" << std::cout;
+ file->ClearAnonymizeList();
+ file->Delete();
+ fh->Delete();
+ }
+}
////////////////////////////////////////////////////////////////////////
//void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
//{
// }
//}
//
-} // EO namespace creaImageIO
\ No newline at end of file
+} // EO namespace creaImageIO
git://git.creatis.insa-lyon.fr / creaImageIO.git / blobdiff