+/*
+# ---------------------------------------------------------------------
+#
+# Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
+# pour la Santé)
+# Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
+# Previous Authors : Laurent Guigues, Jean-Pierre Roux
+# CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil
+#
+# This software is governed by the CeCILL-B license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL-B
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+# or in the file LICENSE.txt.
+#
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL-B license and that you accept its terms.
+# ------------------------------------------------------------------------
+*/
+
+
#include <creaImageIOGimmickView.h>
-#include <creaImageIOSystem.h>
+
#include "boost/filesystem.hpp"
#if defined(USE_GDCM)
#include <gdcmGlobal.h>
#include <gdcmSerieHelper.h>
+#include <gdcmFileHelper.h>
+#include <gdcmUtil.h>
#include <vtkGdcmReader.h>
#endif
-#if defined(USE_GDCM2)
+/*#if defined(USE_GDCM2)
#include <vtkGDCMImageReader.h>
#include "gdcmSystem.h"
#include "gdcmCryptographicMessageSyntax.h"
#include "gdcmUIDGenerator.h"
#include "gdcmAnonymizer.h"
#include "gdcmGlobal.h"
+#endif*/
+#if defined(_WIN32)
+#pragma warning(disable: 4996)
#endif
-
namespace fs = boost::filesystem;
namespace creaImageIO
{
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;
}
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
if(ext[5] == 0)
{
- ext[5] = im.size()-1;
+ ext[5] = (int)im.size()-1;
}
else
{
- ext[5] = ext[5] * im.size()-1; // to deal with multiframes - JPR
+ ext[5] = ext[5] * (int)im.size()-1; // to deal with multiframes - JPR
}
out->SetExtent(ext);
int dim[3];
first->GetDimensions(dim);
- out->SetDimensions(dim[0], dim[1], im.size() );
+ out->SetDimensions(dim[0], dim[1], (int)im.size() );
out->AllocateScalars();
out->Update();
vtkImageData* first = mReader.GetImage( i_file);
int dim[3];
first->GetDimensions(dim);
- if (dim[3] > 1)
+ if (dim[2] > 1)
{
bres = false;
}
void GimmickView::readImages1(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
OutputAttr i_attr)
{
+
+ i_attr.outside.push_back("D0019_100a"); // simens Number Of Images In Mosaic
+
+//EED Borrame
+ int i,isize=i_attr.outside.size();
+ for (i=0;i<isize;i++)
+ {
+ printf("EED GimmickView::readImages1 A i_attr out %s \n", i_attr.outside[i].c_str());
+ }
+
+
+
std::vector<std::string>::iterator it;
for (it=im.begin(); it!=im.end(); ++it)
{
OutStrGimmick out;
out.img = vtkImageData::New();
out.img->ShallowCopy(mReader.GetImage(*it));
- if(i_attr.mult)
+printf("EED GimmickView::readImages1 A\n ");
+ if(i_attr.mult)
+ {
getAttributes((*it),out.infos,i_attr);
+printf("EED GimmickView::readImages1 B %s \n ", out.infos.find("D0019_100a")->second.c_str() );
+ }
o_output.push_back(out);
}
// 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);
+printf("EED GimmickView::readImages1 C %s \n ", o_output.front().infos.find("D0019_100a")->second.c_str() );
}
}
first->GetWholeExtent(ext); // send also 0,0 in Z
if(ext[5] == 0)
{
- ext[5] = im.size()-1;
- }
- else
- {
- ext[5] = ext[5] * im.size()-1; // to deal with multiframes
+ ext[5] = (int)im.size()-1;
+ } else {
+ ext[5] = ext[5] * (int)im.size()-1; // to deal with multiframes
}
out.img->SetExtent(ext);
int dim[3];
+ double spac[3];
first->GetDimensions(dim);
- out.img->SetDimensions(dim[0], dim[1], im.size() );
+ first->GetSpacing(spac);
+ out.img->SetSpacing(spac);
+ out.img->SetDimensions(dim[0], dim[1], (int)im.size() );
out.img->AllocateScalars();
out.img->Update();
unsigned long imsize = dim[0] * dim[1];
{
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];
std::vector<std::string>::iterator it;
std::vector<OutStrGimmick>::iterator it_out = o_output.begin();
- for (it=im.begin(); it!=im.end(); ++it, it_out += dim[2])
+ for (it=im.begin(); it!=im.end(); ++it)//, it_out ++)
{
vtkImageData* cur = mReader.GetImage( (*it) );
for (int slice= 0 ; slice <dim[2]; slice++)
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
memcpy(out.img->GetScalarPointer(0,0,0), cur->GetScalarPointer(0,0,slice), imsize);
o_output.push_back(out);
}
- if(i_attr.mult)
- getAttributes((*it),(*it_out).infos,i_attr);
+ // if(i_attr.mult)
+ // getAttributes((*it),(*it_out).infos,i_attr);
}
if(!i_attr.mult)
{
}
- //////////////////////////////////////////////////////////
+ //////////////////////////////////////////////////////////
// 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);
-
- out.img->SetDimensions(dim[0], dim[1], im.size() );
+ first->GetSpacing(spac);
+ out.img->SetSpacing(spac);
+ out.img->SetDimensions(dim[0], dim[1], (int)im.size() );
out.img->AllocateScalars();
out.img->Update();
unsigned long imsize = dim[0] * dim[1];
void GimmickView::readImages(std::vector<OutStrGimmick>& o_output, std::vector<std::string> im,
OutputAttr i_attr, int i_dim, double i_zspc)
{
- int size = im.size();
+ int size = (int)im.size();
if ( size == 0)
{
return;
- }
- else if (size == 1)
- {
+ } else if (size == 1) {
// Simplest case
// Only one image : give it
// But take in count multiframe possibility
if ( isSingle(im.front()) || i_dim != 1)
{
readImages1(o_output,im, i_attr);
- }
- else
- {
- readImages2(o_output,im, i_attr,i_zspc);
- }
-
- }
- else
- {
+ } else {
+ readImages2(o_output,im, i_attr,i_zspc);
+ }
+ } else {
// multiple or single frame
if ( isSingle(im.front()) )
{
{
// 2D to 3D
readImages3(o_output,im, i_attr,i_zspc);
- }
- else
- {
+ } else {
readImages1(o_output,im, i_attr);
}
- }
- else
- {
+ } else {
// we deal with multiple frames n x (2D x T)
// Differents outputs are avaialable
if(i_dim == 1)
{
// put all in one output
readImages3(o_output,im, i_attr,i_zspc);
-
- }
- else if( i_dim == 2)
- {
+ } else if( i_dim == 2) {
// put in a vector of n x T (2D)
readImages2(o_output,im, i_attr,i_zspc);
- }
- else if( i_dim == 3)
- {
+ } else if( i_dim == 3) {
// put in a vector of n (2D x T)
// No transformations.
readImages1(o_output,im, i_attr);
- }
- else
- {
+ } else {
// put in a vector of T (2D x n)
readImages4(o_output,im, i_attr);
- }
- }
- }
- }
+ } // i_dim
+ } //isSingle(im.front())
+ } // if size
+//EED UnMosaic step...
+//How to verifie if is a mosaic file , with how many images inside??
+
+ }
}
else if (im.size()>1) // Test inutile ? JPR
{
- vtkImageData* first = mReader.GetImage( im.front());
+ /// \TODO fix unused variable 'first'
+// vtkImageData* first = mReader.GetImage( im.front());
if (dimension == 2)
{
// n3D
vtkImageData* out = vtkImageData::New();
out->ShallowCopy(mReader.GetImage(*it));
s.push_back(out);
- }
- }
- else
- {
+ } // for
+ } else {
// n2D to 3D // NO!
// n *2D + T in a vector :
{
vtkImageData* out = mReader.GetImage( (*it));
s.push_back(out);
- }
- }
- }
+ } // for
+ } // if dimension
+ } // if im.size
}
//======================================================================
}
-
+#if defined(USE_GDCM)
+////////////////////////////////////////////////////////////////////////
+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);
+
+//Borrame
+//EED 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();
+ }
+}
+#endif
+#if defined(USE_GDCM2)
+void GimmickView::Anonymize(std::vector<std::string> i_filenames, int type)
+{
+}
+#endif
////////////////////////////////////////////////////////////////////////
//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