IF(WIN32)
ADD_EXECUTABLE(creaImageIOApp WIN32 main)
- SET_TARGET_PROPERTIES(creaImageIOApp PROPERTIES LINK_FLAGS /subsystem:console )
+
+ IF(MINGW)
+ SET_TARGET_PROPERTIES(creaImageIOApp PROPERTIES LINK_FLAGS -mconsole )
+ ELSE(MINGW)
+ SET_TARGET_PROPERTIES(creaImageIOApp PROPERTIES LINK_FLAGS /subsystem:console )
+ ENDIF(MINGW)
+
ELSE(WIN32)
ADD_EXECUTABLE(creaImageIOApp MACOSX_BUNDLE main)
ENDIF(WIN32)
-TARGET_LINK_LIBRARIES( creaImageIOApp creaImageIO )
+TARGET_LINK_LIBRARIES( creaImageIOApp creaImageIO ${ITK_LIBRARIES} )
INSTALL_TARGETS(/bin/ creaImageIOApp )
BBTK_BEGIN_DESCRIBE_BLACK_BOX(GetDicomAttributesFromMaps,bbtk::AtomicBlackBox);
BBTK_NAME("GetDicomAttributesFromMaps");
-BBTK_AUTHOR("Info-Dev, Eduardo DAVIL");
+BBTK_AUTHOR("Info-Dev, Eduardo DAVILA");
BBTK_DESCRIPTION("eduardo.davila[at]creatis.insa-lyon.fr -");
BBTK_CATEGORY("empty");
BBTK_INPUT(GetDicomAttributesFromMaps,In,"Vector of maps with DICOM attributes",std::vector< mapString >,"");
- BBTK_INPUT(GetDicomAttributesFromMaps,KeyDicom,"Key DICOM",std::string ,"");
+ BBTK_INPUT(GetDicomAttributesFromMaps,KeyDicom,"Key DICOM ex: D0028_0030 ",std::string ,"");
BBTK_OUTPUT(GetDicomAttributesFromMaps,Out,"Vector of the attribute asked.",std::vector <std::string>,"");
BBTK_END_DESCRIBE_BLACK_BOX(GetDicomAttributesFromMaps);
//=====
/*
- # ---------------------------------------------------------------------
- #
- # 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.
- # ------------------------------------------------------------------------
+ # ---------------------------------------------------------------------
+ #
+ # 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.
+ # ------------------------------------------------------------------------
*/
//=====
// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
#include "bbcreaImageIOItkImagesChooserDialogBox.h"
#include "bbcreaImageIOPackage.h"
+#include "itkImage.h"
+#include "itkImportImageFilter.h"
+
+/*
+// -------------------------------------------------------------------------
+// LFV: avoid itk::Concept check on 4d or superior images
+#define BBCREAIMAGEIO_ChooserDlg_Template( t, ty, di ) \
+ if( t == typeid( itk::Image< ty, di >* ) ) \
+ { \
+ this->Export< itk::Image< ty, di > >( ); \
+ this->ExportVTK< itk::Image< ty, di > >( ); \
+ }
+*/
+
+// -------------------------------------------------------------------------
+// LFV: avoid itk::Concept check on 4d or superior images
+#define BBCREAIMAGEIO_ChooserDlg_Template( t, ty, di ) \
+ if( t == typeid( itk::Image< ty, di >* ) ) \
+ { \
+ this->Export< ty , di >( ); \
+ this->ExportVTK< itk::Image< ty, di > >( ); \
+ }
+
+
+// -------------------------------------------------------------------------
+
namespace bbcreaImageIO
{
dlg->ShowModal();
bbtk::TypeInfo typ = bbitk::GetITKImagePtrTypeInfoFromPixelTypeInfoAndDimension(*dlg->getTypes().front(), dlg->getDims().front());
- BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ, Export);
- BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ, ExportVTK);
+
+ BBCREAIMAGEIO_ChooserDlg_Template( typ, char, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, short, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, int, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, long, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, float, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, double, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned char, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned short, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned int, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned long, 1 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, char, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, short, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, int, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, long, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, float, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, double, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned char, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned short, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned int, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned long, 2 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, char, 3 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, short, 3 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, int, 3 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, long, 3 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, float, 3 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, double, 3 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned char, 3 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned short, 3 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned int, 3 )
+ else BBCREAIMAGEIO_ChooserDlg_Template( typ, unsigned long, 3 );
+
+
+ /* Deprecated
+ BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ, Export);
+ BBTK_TEMPLATE_ITK_IMAGE_SWITCH(typ, ExportVTK);
+ */
delete dlg;
}
-template <class TImage>
+
+//template <class TImage>
+template <typename ty, size_t di>
void ItkImagesChooserDialogBox::Export()
{
- if (dlg->getImagesSelected().size() == 1)
- {
+ typedef itk::Image<ty,di> TImage;
+ if (dlg->getImagesSelected().size() == 1)
+ {
bbSetOutputOut( dlg->getTemplatedImagesSelected<TImage>().front().GetPointer() );
- }
- else if (dlg->getImagesSelected().size() > 1)
- {
- OutputImagesITKType outVect;
-
- typename std::vector<typename TImage::Pointer> tempImgs= dlg->getTemplatedImagesSelected<TImage>();
- typename std::vector<typename TImage::Pointer>::iterator it = tempImgs.begin();
- for(;it != tempImgs.end(); ++it)
- {
- outVect.push_back( (*it).GetPointer() );
- }
- bbSetOutputOutIImages( outVect);
- }
- else
- {
+ } else if (dlg->getImagesSelected().size() > 1){
+ OutputImagesITKType outVect;
+ typename std::vector<typename TImage::Pointer> tempImgs= dlg->getTemplatedImagesSelected<TImage>();
+ typename std::vector<typename TImage::Pointer>::iterator it = tempImgs.begin();
+ for(;it != tempImgs.end(); ++it)
+ {
+ outVect.push_back( (*it).GetPointer() );
+ } // for
+ bbSetOutputOutIImages( outVect);
+
+ typedef ty RGBPixelType;
+ typedef itk::ImportImageFilter< ty , di > ImportFilterType;
+ typename ImportFilterType::Pointer importFilter = ImportFilterType::New();
+
+ typename TImage::SizeType imsize;
+ imsize[0] = tempImgs[0].GetPointer()->GetLargestPossibleRegion().GetSize()[0];
+ imsize[1] = tempImgs[0].GetPointer()->GetLargestPossibleRegion().GetSize()[1];
+ imsize[2] = tempImgs.size();
+
+ typename ImportFilterType::IndexType start;
+ start.Fill( 0 );
+ typename ImportFilterType::RegionType region;
+ region.SetIndex( start );
+ region.SetSize( imsize );
+ importFilter->SetRegion( region );
+
+ const itk::SpacePrecisionType origin[ 3 ] = { 0.0, 0.0, 0.0 };
+ importFilter->SetOrigin( origin );
+
+ const itk::SpacePrecisionType spacing[ 3 ] = { 1.0, 1.0, 1.0 };
+ importFilter->SetSpacing( spacing );
+ const unsigned long int numberOfPixels2D = imsize[0]*imsize[1];
+ const unsigned long int numberOfPixels2DInBytes = imsize[0]*imsize[1]*sizeof(ty);
+ const unsigned long int numberOfPixels3D = imsize[0]*imsize[1]*imsize[2]*sizeof(ty);
+
+ RGBPixelType * localBuffer = new RGBPixelType[ numberOfPixels3D ];
+ RGBPixelType * tmpLocalBuffer = localBuffer;
+
+ it = tempImgs.begin();
+ for(;it != tempImgs.end(); ++it)
+ {
+ memcpy(tmpLocalBuffer, (*it).GetPointer()->GetBufferPointer(), numberOfPixels2DInBytes);
+ tmpLocalBuffer = tmpLocalBuffer + numberOfPixels2D;
+ } // for
+
+ const bool importImageFilterWillOwnTheBuffer = true;
+ importFilter->SetImportPointer( localBuffer , numberOfPixels3D , importImageFilterWillOwnTheBuffer );
+ importFilter->Update();
+ importFilter->Register();
+ bbSetOutputOut( importFilter->GetOutput() );
+
+ } else {
// warning: passing NULL to non-pointer
//bbSetOutputOut( NULL);
bbSetOutputOut(0); // JPR
}
- // FCY To test the Output
- //typedef itk::Image <short, 3> ImageType;
- //typedef itk::ImageFileReader< ImageType > itkReaderType;
- // typename itkReaderType::Pointer reader = itkReaderType::New();
- //
- // reader->SetFileName("d:\test.hdr");
- // reader->Update();
- //reader->GetOutput()->Register();
- // this->bbSetOutputOut(reader->GetOutput());
}
+
+
template <class TImage>
void ItkImagesChooserDialogBox::ExportVTK()
{
dlg->split3Din3Dvtk<TImage>( (*it) );
}
bbSetOutputOutVImages( dlg->getVtkImagesSelected() );
- }
- else if (dlg->getDims().front() == 4)
- {
+ } else if (dlg->getDims().front() == 4) {
// To Test
// dlg->split4Din3Dvtk("d:/temp2");
// bbSetOutputOutVImages( dlg->getVtkImagesSelected());
- }
- else
- {
- // NOT IMPLEMENTED YET FOR DIMENSIONS > 4
-
- }
-
+ } else {
+ // NOT IMPLEMENTED YET FOR DIMENSIONS > 4
+ } // if dlg
}
+
//=====
// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
//=====
void ItkImagesChooserDialogBox::bbUserSetDefaultValues()
-{
-
+{
}
+
//=====
// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
//=====
void ItkImagesChooserDialogBox::bbUserInitializeProcessing()
{
-
}
+
//=====
// Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
//=====
void ItkImagesChooserDialogBox::bbUserFinalizeProcessing()
{
-
}
-}
-// EO namespace bbcreaImageIO
+
+} // EO namespace bbcreaImageIO
private:
// Template read method
- template<class TImage> void Export();
+
+//EED template<class TImage> void Export();
+template <typename ty, size_t di> void Export();
// Template export vtk Images
template<class TImage> void ExportVTK();
IF (NOT USE_XERCES)
+
+message("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+message(${VTK_LIBRARIES})
+
TARGET_LINK_LIBRARIES(${LIBRARY_NAME}
${crea_LIBRARIES}
${creaBruker_LIBRARIES}
{
if (mHomeDirectory.size()==0)
{
-#if defined(__GNUC__)
- mHomeDirectory = getenv("HOME");
-#elif defined(_WIN32)
+#if defined(_WIN32)
mHomeDirectory = getenv("USERPROFILE");
+#elif defined(__GNUC__)
+ mHomeDirectory = getenv("HOME");
#endif
}
return mHomeDirectory;
#include <gdcmFileHelper.h>
#include <gdcmUtil.h>
#include <vtkGdcmReader.h>
+
#endif
+#include <vtkMetaImageWriter.h>
+
/*#if defined(USE_GDCM2)
#include <vtkGDCMImageReader.h>
#include "gdcmSystem.h"
// n*2D to 3D
vtkImageData* out = vtkImageData::New();
// out->CopyStructure(first);
- out->SetScalarType(first->GetScalarType());
- out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
int ext[6];
//first->GetExtent(ext); // JPR
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
first->GetWholeExtent(ext); // renvoie egalement 0,0 en Z // JPR
+#else
+ first->GetExtent(ext); // renvoie egalement 0,0 en Z // JPR
+#endif
if(ext[5] == 0)
{
int dim[3];
first->GetDimensions(dim);
-
out->SetDimensions(dim[0], dim[1], (int)im.size() );
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
+ out->SetScalarType(first->GetScalarType());
+ out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
out->AllocateScalars();
out->Update();
+#else
+ out->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents());
+#endif
unsigned long imsize = dim[0] * dim[1];
imsize = imsize * dim[2] ; // deal with multiframes // JPR
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
-
std::vector<std::string>::iterator it;
for (it=im.begin(); it!=im.end(); ++it)
{
OutStrGimmick out;
vtkImageData* first = mReader.GetImage( im.front());
out.img = vtkImageData::New();
- out.img->SetScalarType(first->GetScalarType());
- out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
int ext[6];
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
first->GetWholeExtent(ext); // send also 0,0 in Z
+#else
+ first->GetExtent(ext); // send also 0,0 in Z
+#endif
if(ext[5] == 0)
{
ext[5] = (int)im.size()-1;
first->GetSpacing(spac);
out.img->SetSpacing(spac);
out.img->SetDimensions(dim[0], dim[1], (int)im.size() );
+
+
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
+ out.img->SetScalarType(first->GetScalarType());
+ out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
out.img->AllocateScalars();
out.img->Update();
+#else
+ out.img->AllocateScalars(first->GetScalarType(), first->GetNumberOfScalarComponents());
+#endif
+
+
unsigned long imsize = dim[0] * dim[1];
imsize = imsize * dim[2] ; // deal with multiframes here
// differents formats char , short, etc...
memcpy(out.img->GetScalarPointer(0,0,slice), cur->GetScalarPointer(0,0,0), imsize);
slice++;
}
+
getAttributes(im.front(),out.infos, i_attr);
o_output.push_back(out);
}
{
OutStrGimmick out;
out.img = vtkImageData::New();
- out.img->SetScalarType(first->GetScalarType());
out.img->SetSpacing(spac);
- out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
int ext[6];
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
first->GetWholeExtent(ext); // send also 0,0 in Z
+#else
+ first->GetExtent(ext); // send also 0,0 in Z
+#endif
ext[5] = 0;
out.img->SetExtent(ext);
-
out.img->SetDimensions(dim[0], dim[1], 1 );
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
+ out.img->SetScalarType(first->GetScalarType());
+ out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
out.img->AllocateScalars();
out.img->Update();
+#else
+ out.img->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents());
+#endif
+
+
memcpy(out.img->GetScalarPointer(0,0,0), cur->GetScalarPointer(0,0,slice), imsize);
o_output.push_back(out);
}
{
OutStrGimmick out;
out.img = vtkImageData::New();
- out.img->SetScalarType(first->GetScalarType());
- out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
int ext[6];
- double spac[6];
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
first->GetWholeExtent(ext); // send also 0,0 in Z
+#else
+ first->GetExtent(ext); // send also 0,0 in Z
+#endif
+
+ double spac[6];
ext[5] = 0;
out.img->SetExtent(ext);
first->GetSpacing(spac);
out.img->SetSpacing(spac);
out.img->SetDimensions(dim[0], dim[1], (int)im.size() );
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
+ out.img->SetScalarType(first->GetScalarType());
+ out.img->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
out.img->AllocateScalars();
out.img->Update();
+#else
+ out.img->AllocateScalars(first->GetScalarType(), first->GetNumberOfScalarComponents());
+#endif
+
unsigned long imsize = dim[0] * dim[1];
imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
int index = 0;
dim[0] = dim[1] = 128;
dim[2] = 1;
mUnreadableImage->SetDimensions ( dim );
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
mUnreadableImage->SetScalarTypeToUnsignedChar();
- mUnreadableImage->AllocateScalars();
+ mUnreadableImage->AllocateScalars();
+#else
+ mUnreadableImage->AllocateScalars(VTK_UNSIGNED_CHAR,1);
+#endif
+
for (int i=0;i<dim[0];i++)
for (int j=0;j<dim[1];j++)
mUnreadableImage->SetScalarComponentFromFloat(i,j,0,0,0);
//=====================================================================
bool MultiThreadImageReader::Start()
{
-
// std::cout << "#### MultiThreadImageReader::Start()"
// <<std::endl;
if (mNumberOfThreadedReadersRunning > 0) return true;
// std::cout << "user="<<p->GetUser() <<std::endl;
if ( p->GetUser() == this )
+ {
GetMultiThreadImageReaderUserMutex().Unlock();
+ }
p->GetUser()->MultiThreadImageReaderSendEvent
(p->GetFilename(),
// wxMutexLocker lock(GetMultiThreadImageReaderUserMutex());
mUnloadQueue.insert(p);
+
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
p->GetImage()->UpdateInformation();
p->GetImage()->PropagateUpdateExtent();
long ImMem = p->GetImage()->GetEstimatedMemorySize();
+#else
+ int ext[6];
+ int dim[3];
+ p->GetImage()->GetExtent(ext);
+ dim[0] = ext[1]-ext[0]+1;
+ dim[1] = ext[3]-ext[2]+1;
+ dim[2] = ext[5]-ext[4]+1;
+ long ImMem = dim[0]*dim[1]*dim[2]*p->GetImage()->GetScalarSize();;
+#endif
mTotalMem += ImMem;
GimmickMessage(5,"==> Image in memory = "<<mUnloadQueue.size()<<std::endl);
std::string filename = unload->GetFilename();
GimmickMessage(5,"'" << filename << "'" << std::endl);
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
mTotalMem -= unload->GetImage()->GetEstimatedMemorySize();
+#else
+ int ext[6];
+ int dim[3];
+ unload->GetImage()->GetExtent(ext);
+ dim[0] = ext[1]-ext[0]+1;
+ dim[1] = ext[3]-ext[2]+1;
+ dim[2] = ext[5]-ext[4]+1;
+ mTotalMem -= dim[0]*dim[1]*dim[2]*unload->GetImage()->GetScalarSize();
+#endif
GimmickMessage(5," ==> Total mem = "<<mTotalMem<<" Ko "<<std::endl);
{
delete crea::MessageManager::GetInstance();
}
-
#define GimmickMessage(LEV,MESS) \
- creaMessage("Gimmick!",LEV,"[Gimmick!] "<<MESS);
+ creaMessage( "Gimmick!" , LEV , "[Gimmick!] " << MESS );
+
#define GimmickDebugMessage(LEV,MESS) \
creaDebugMessage("Gimmick! DEBUG",LEV,"[Gimmick!] DEBUG: "<<MESS);
#define GimmickError(MESS) \
#include "creaImageIOSystem.h"
#include "creaImageIOUltrasonixImageReader.h"
+
#include <creaVtk.h>
#include <boost/filesystem/path.hpp>
}
fclose(Ultrasonix_file);
- im = crea::NewVtkImageDataFromRaw( dataRF, h.width, h.height, h.frame);
+ im = crea::NewVtkImageDataFromRaw<short>( dataRF, h.width, h.height, h.frame);
break;
case TYPE_B8:
fclose(Ultrasonix_file);
- im = crea::NewVtkImageDataFromRaw( dataB8, h.width, h.height, h.frame);
+ im = crea::NewVtkImageDataFromRaw<char>( dataB8, h.width, h.height, h.frame);
break;
case TYPE_B32:
fclose(Ultrasonix_file);
- im = crea::NewVtkImageDataFromRaw( dataB32, h.width, h.height, h.frame);
+ im = crea::NewVtkImageDataFromRaw<int>( dataB32, h.width, h.height, h.frame);
break;
}
int outputdims[3];
imageIn->GetDimensions (inputdims);
unsigned short *input = (unsigned short *)(imageIn->GetScalarPointer());
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
imageIn->Update();
+#else
+ // ..
+#endif
+
unsigned int div = (unsigned int)ceil(sqrt( (double)numberOfImagesInMosaic ) );
outputdims[0] = inputdims[0] / div;
vtkImageOut = vtkImageData::New();
vtkImageOut->SetDimensions( outputdims );
vtkImageOut->SetExtent(0,outputdims[0]-1,0,outputdims[1]-1,0,outputdims[2]-1);
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
vtkImageOut->SetWholeExtent(0,outputdims[0]-1,0,outputdims[1]-1,0,outputdims[2]-1);
vtkImageOut->SetNumberOfScalarComponents(1);
//vtkImageOut->SetSpacing( blabla );
vtkImageOut->SetScalarType( VTK_UNSIGNED_SHORT );
vtkImageOut->AllocateScalars();
vtkImageOut->Update();
+#else
+ vtkImageOut->AllocateScalars(VTK_UNSIGNED_SHORT,1);
+#endif
unsigned short *output =(unsigned short *)(vtkImageOut->GetScalarPointer());
#include "creaImageIOWxAnySimpleDlg.h"
#include "creaImageIOWxGimmickReaderDialog.h"
-#include <itkAnalyzeImageIO.h>
+
+#if ITK_VERSION_MAJOR < 4 // : WARNING: deprecated in ITK 4.0
+# include <itkAnalyzeImageIO.h>
+# include <itkDICOMSeriesFileNames.h>
+#else // ITK_VERSION_MAJOR < 4
+# include <itkGDCMSeriesFileNames.h>
+#endif // ITK_VERSION_MAJOR < 4
+
#include <itkImageFileReader.h>
#include <itkImageSeriesReader.h>
#include <itkImage.h>
#include <itkImageSeriesWriter.h>
#include <itkGDCMImageIO.h>
-#include <itkDICOMSeriesFileNames.h>
#include <itkNumericSeriesFileNames.h>
#include <itkVectorImage.h>
#include <itkMetaImageIO.h>
void WxAnySimpleDlg::OnReadFile(wxCommandEvent& event)
{
int resultShowModal;
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
wxFileDialog* fileDlg = new wxFileDialog( 0, _T("Select file"), _T(""), _T(""), crea::std2wx("*"), wxOPEN |wxFD_MULTIPLE, wxDefaultPosition);
+#else
+ wxFileDialog* fileDlg = new wxFileDialog( 0, _T("Select file"), _T(""), _T(""), crea::std2wx("*"), wxFD_OPEN |wxFD_MULTIPLE, wxDefaultPosition);
+#endif
resultShowModal = fileDlg->ShowModal();
if ( resultShowModal==wxID_OK )
std::string name = crea::wx2std(wxArray[i]);
// FOR THE MOMENT ONLY short 3D et short 4D
readImg(name);
- }
- }
- else {
+ } // for
+ } else {
// TO DO WARNING MESSAGES
- }
- }
+ } // if
+ } // if
SetReturnCode( resultShowModal );
// Close();
EndModal( resultShowModal );
}
+
+/////////////////////////////////////////////////////////////////////
+// //
+//////////////////////////////////////////////////////////////////////
void WxAnySimpleDlg::setExts(std::vector<std::string> i_exts)
{
m_exts = i_exts;
}
- /////////////////////////////////////////////////////////////////////
+
+/////////////////////////////////////////////////////////////////////
// //
//////////////////////////////////////////////////////////////////////
-
void WxAnySimpleDlg::OnReadDirectory(wxCommandEvent &event)
{
int resultShowModal;
if ( resultShowModal==wxID_OK )
{
std::string path = crea::wx2std(dirDlg->GetPath());
+
+/*
typedef boost::filesystem::directory_iterator dir_it;
dir_it itr(path);
dir_it end_itr;
- /*if (boost::filesystem::exists(path))
- {*/
+// if (boost::filesystem::exists(path))
+// {
for(;itr != end_itr; ++itr)
{
- bvalid = m_exts.size() == 0? true : false;
- std::vector<std::string>::iterator it = m_exts.begin();
- std::string ext = itr->path().filename().string().substr(itr->path().filename().string().find_last_of("."));
- for(; it != m_exts.end(); it++)
- {
- if(ext == (*it) )
- {
- bvalid = true;
- break;
- }
- }
+//EED
+// All files have the same extention
+// bvalid = m_exts.size() == 0? true : false;
+// std::vector<std::string>::iterator it = m_exts.begin();
+// std::string ext = itr->path().filename().string().substr(itr->path().filename().string().find_last_of("."));
+// for(; it != m_exts.end(); it++)
+// {
+// if(ext == (*it) )
+// {
+// bvalid = true;
+// break;
+// }
+// } // for
+bvalid=true;
if (!boost::filesystem::is_directory(itr->status()) && bvalid)
{
- readImg(itr->path().string().c_str());
- }
- }
- }
+printf("EED WxAnySimpleDlg::OnReadDirectory Each file %s \n", itr->path().string().c_str() );
+ readImg( itr->path().string().c_str() );
+ } // if
+ } // for itr
+*/
+
+ typedef vector<boost::filesystem::path> vec; // store paths
+ vec v; // so we can sort them later
+ copy(boost::filesystem::directory_iterator(path), boost::filesystem::directory_iterator(), back_inserter(v));
+ sort(v.begin(), v.end()); // sort, since directory iteration
+ // is not ordered on some file systems
+ for (vec::const_iterator it (v.begin()); it != v.end(); ++it)
+ {
+ readImg( it->string().c_str() );
+ } // for
+
+
+
+
+ } // if OK
SetReturnCode( resultShowModal );
// Close();
EndModal( resultShowModal );
+
}
//////////////////////////////////////////////////////////////////////
return imageIO->GetNumberOfDimensions();
}
+
void WxAnySimpleDlg::readImg(const std::string &i_name)
{
size_t dims = getNumberOfDimensions(i_name);
+
//const std::type_info *type= &getType(i_name);
switch(dims)
{
}
else
{
+ printf("EED WxAnySimpleDlg::readImg Not type found for DIM 3 \n");
//????FCY, so what the type????
}
break;
}
else
{
+ printf("EED WxAnySimpleDlg::readImg Not type found for DIM 4 \n");
//????FCY, so what the type????
}
break;
{
typedef itk::Image<short,3> TImage;
typedef itk::GDCMImageIO GDCMType;
+#if ITK_VERSION_MAJOR < 4
typedef itk::DICOMSeriesFileNames dicnames;
+#else // ITK_VERSION_MAJOR < 4
+ typedef itk::GDCMSeriesFileNames dicnames;
+#endif // ITK_VERSION_MAJOR < 4
GDCMType::Pointer gdcmIO = GDCMType::New();
dicnames::Pointer generator = dicnames::New();
for(; it != m_AnyImages.end(); it++)
{
imgs.push_back(boost::any_cast<TImage*> (*it));
- }
+ } // for
return imgs;
}
bool AllSameType();
template <class TImage>
void split3Din3Dvtk(TImage* i_Img)
- {
+ {
typedef itk::ImageToVTKImageFilter< TImage > ConnectorType;
typename ConnectorType::Pointer connector = ConnectorType::New();
connector->SetInput(i_Img);
connector->Update();
vtkImageData *im = vtkImageData::New();
im->ShallowCopy(connector->GetOutput());
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
im->Update();
+#else
+ im->Modified();
+#endif
+
+
m_Vresults.push_back(im);
}
-
template <typename TImage>
void split4Din3Dvtk(TImage* i_Img);
-
private:
-
// strange compile error with gcc 4.5.1-4 //JPR
std::vector</*const*/ size_t> m_AnyDims; //comment out const JPR
std::vector</*const*/ std::type_info *> m_AnyType; //comment out const JPR
wxString infoimage;
std::string m_dir;
-
bool m_dicom;
/// interface to read data
SimpleView m_view;
const std::type_info & getType(const std::string &i_name);
};
-
}// namespace creaImageIO
#endif //__creaImageWxAnySimpleDlg_h_INCLUDED__
// RESULT
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
ResultCtrl=new wxTextCtrl(this, ID_EL_CTRL,_T(""), wxPoint(5,150), wxSize(250,310), wxTE_READONLY| wxMac | wxTE_MULTILINE | wxTE_RICH );
+#else
+ ResultCtrl=new wxTextCtrl(this, ID_EL_CTRL,_T(""), wxPoint(5,150), wxSize(250,310), wxTE_READONLY| wxTE_MULTILINE | wxTE_RICH );
+#endif
+
+
wxButton *RemoveCtrl = new wxButton(this, ID_REMOVE_ADD,_T("Remove an entry"), wxPoint(280,200) );
Connect( RemoveCtrl->GetId(), wxEVT_COMMAND_BUTTON_CLICKED , (wxObjectEventFunction) &WxDescriptorPanel::OnRemove );
//////////////////////////////////////////////////
void WxDescriptorPanel::OnLoad(wxCommandEvent &Event)
{
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
long style = wxOPEN | wxFILE_MUST_EXIST;
+#else
+ long style = wxFD_OPEN | wxFD_FILE_MUST_EXIST;
+#endif
LevelCtrl->SetValue(_T("patient"));
ResultCtrl->Clear();
DscpTree.clear();
const std::string WxDescriptorPanel::saveDescriptor()
{
std::string file = "";
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
long style = wxSAVE;
+#else
+ long style = wxFD_SAVE;
+#endif
std::string wc("*.dscp");
wxFileDialog* FD = new wxFileDialog( 0,
_T("Select file"),
wxToolBar *mToolBar = new wxToolBar(this,-1,wxDefaultPosition,wxDefaultSize);
mToolBar->AddTool( DUMP_SAVE_ID,_T("Save"), mIcon->GetBitmap(0), _T("Save Dicom Tags in text file"));
mToolBar->Realize();
+
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
DumpText = new wxTextCtrl( this, wxID_ANY,_T(""), wxPoint(5,30), wxSize(520,510), wxTE_READONLY| wxMac | wxTE_MULTILINE | wxTE_RICH );
+#else
+ DumpText = new wxTextCtrl( this, wxID_ANY,_T(""), wxPoint(5,30), wxSize(520,510), wxTE_READONLY | wxTE_MULTILINE | wxTE_RICH );
+#endif
+
Layout();
Print();
}
///////////////////////////////////////////////////
void WxDumpPanel::SaveInfos(wxCommandEvent& event)
{
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
wxFileDialog* FD = new wxFileDialog( 0,_T("Select file"), _T(""), _T(""),
crea::std2wx("*.txt"), wxOPEN, wxDefaultPosition);
+#else
+ wxFileDialog* FD = new wxFileDialog( 0,_T("Select file"), _T(""), _T(""),
+ crea::std2wx("*.txt"), wxFD_OPEN, wxDefaultPosition);
+#endif
if (FD->ShowModal()==wxID_OK)
{
wxBusyCursor busy;
threads);
mView->Initialize();
// Connect the AddProgress callback
- mView->ConnectValidationObserver
- ( boost::bind( &WxGimmickReaderDialog::OnValid , this, _1 ) );
+ mView->ConnectValidationObserver( boost::bind( &WxGimmickReaderDialog::OnValid , this, _1 ) );
}
catch (crea::Exception e)
{
Connect( _addCheckBox->GetId(), wxEVT_COMMAND_CHECKBOX_CLICKED, (wxObjectEventFunction) &WxGimmickTools::onAddToDatabase );
Connect( _mhdCheckBox->GetId(), wxEVT_COMMAND_CHECKBOX_CLICKED, (wxObjectEventFunction) &WxGimmickTools::onMHD );
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
wxFlexGridSizer *textSizer = new wxFlexGridSizer(1,2);
+#else
+ wxFlexGridSizer *textSizer = new wxFlexGridSizer(2);
+#endif
+
textSizer->Add( new wxStaticText(this, -1, _T("Transform a Bruker 'Serie'/'Study'/'set of Studies' directory into Dicom / MHD format.")), 1, wxGROW );
textSizer->Add( new wxStaticText(this, -1, _T("If checkbox is selected images will be loaded into the DB.")), 1, wxGROW );
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
wxFlexGridSizer *sizer = new wxFlexGridSizer(2,5);
+#else
+ wxFlexGridSizer *sizer = new wxFlexGridSizer(5);
+#endif
sizer->Add( new wxStaticText(this, -1, _T(" ")), 1, wxGROW );
sizer->Add( new wxStaticText(this, -1, _T(" ")), 1, wxGROW );
sizer->Add( _inputPath, 1, wxGROW );
sizer->Add( _addCheckBox, 1, wxGROW );
sizer->Add( _mhdCheckBox, 1, wxGROW );
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
wxFlexGridSizer *topSizer = new wxFlexGridSizer(1, 2);
+#else
+ wxFlexGridSizer *topSizer = new wxFlexGridSizer(2);
+#endif
topSizer->Add( textSizer, 1, wxGROW );
topSizer->Add( sizer, 1, wxGROW );
this->SetSizer( topSizer );
void WxGimmickView::OnAddFiles(wxCommandEvent& event)
{
mViewer->StopPlayer();
+
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
long style = wxOPEN | wxFILE_MUST_EXIST | wxFD_MULTIPLE;
+#else
+ long style = wxFD_OPEN | wxFD_FILE_MUST_EXIST | wxFD_MULTIPLE;
+#endif
+
+
std::string wc("*");
wxFileDialog* FD = new wxFileDialog( 0,
_T("Select file"),
{
ClearSelection();
}*/
- ReadImageThreaded(sel);
+
+ printf("EED Warnning WxGimmickView::OnSelectionChange ....... To avoid threads conflicts//ReadImageThreaded(sel)\n ");
+//EED1 ReadImageThreaded(sel);
+
+
}
//==================================================
//=====================================================================
/// Concrete derivative of GimmickView which implements a wxWidgets-based view
- class WxGimmickView : public wxPanel, virtual public GimmickView
+ class CREAIMAGEIO_EXPORT WxGimmickView : public wxPanel, virtual public GimmickView
{
public:
void WxSimpleDlg::OnReadFile(wxCommandEvent& event)
{
int resultShowModal;
+//EED 2017-09-16 Migration wxWidgets 2.8 to 3.0
+#if wxMAJOR_VERSION <= 2
wxFileDialog* fileDlg = new wxFileDialog( 0, _T("Select file"), _T(""), _T(""), crea::std2wx("*"), wxOPEN |wxFD_MULTIPLE, wxDefaultPosition);
+#else
+ wxFileDialog* fileDlg = new wxFileDialog( 0, _T("Select file"), _T(""), _T(""), crea::std2wx("*"), wxFD_OPEN |wxFD_MULTIPLE, wxDefaultPosition);
+#endif
resultShowModal = fileDlg->ShowModal();
if ( resultShowModal==wxID_OK )
dlg.ShowModal();
if (dlg.GetReturnCode() == wxID_OK)
{
- dlg.stopReading();
- std::vector<creaImageIO::OutStrGimmick> outStrGimmick;
- dlg.getSelected(outStrGimmick, m_attrDicomTags,true,"");
+//EED1 dlg.stopReading();
m_results.clear();
int size=(int)outStrGimmick.size();
int ii;
// {
for (ii=0;ii<size;ii++)
{
- outStrGimmick[ii].img->Modified();
- outStrGimmick[ii].img->Update();
m_results.push_back(outStrGimmick[ii].img);
m_resultsDicomAtr.push_back( outStrGimmick[ii].infos );
}
first->GetDimensions(dim);
if (dim[2]==1)
{
- vtkImageData *out;
- out = vtkImageData::New();
- out->SetScalarType(first->GetScalarType());
- out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
+ vtkImageData *out = vtkImageData::New();
int ext[6];
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
first->GetWholeExtent(ext);
+#else
+ first->GetExtent(ext);
+#endif
if(ext[5] == 0)
{
ext[5] = getImagesSelected().size()-1;
}
out->SetSpacing(spac);
out->SetDimensions(dim[0], dim[1], getImagesSelected().size() );
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
+
+ out->SetScalarType(first->GetScalarType());
+ out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
out->AllocateScalars();
out->Update();
+#else
+ out->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents());
+#endif
+
+
unsigned long imsize = dim[0] * dim[1];
imsize = imsize * dim[2]; // deal with multiframes here
// differents formats char , short, etc...
#include <creaImageIOWxTreeView.h>
#include <creaImageIOGimmickView.h>
-
#include <wx/splitter.h>
#include <wx/gdicmn.h>
#include <boost/date_time/gregorian/gregorian.hpp>
std::vector<tree::Node*>::const_iterator i;
for (i=sel.begin(); i!=sel.end(); ++i)
{
- GimmickMessage(1,
- "deleting '"
- <<(*i)->GetLabel()
- <<"'"<<mLastLevel
- <<std::endl);
+ GimmickMessage(1,"deleting '" << (*i)->GetLabel() << "'" << mLastLevel << std::endl );
if((*i)->GetParent()->GetNumberOfChildren()<2)
{
needRefresh=true;
mLastImageShown = NULL;
// previewer
- mInteractor = new crea::creawxVTKRenderWindowInteractor(this,-1);
+ mInteractor = new crea::wxVTKRenderWindowInteractor(this,-1);
mInteractor->UseCaptureMouseOn();
mViewer = vtkImageViewer2::New();
<<std::endl);
if (im==0) return;
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
mViewer->SetInput(im);
+#else
+ mViewer->SetInputData(im);
+#endif
mViewer->SetSlice( 0 );
int x1,x2,y1,y2,z1,z2;
double spx,spy,spz;
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
im->Update();
+#else
+ // ...
+#endif
+
//std::cout << "in WxViewer::ShowImage PrintSelf() =";
//im->PrintSelf(std::cout, vtkIndent(2));
im->GetSpacing(spx,spy,spz);
//im->GetExtent (x1,x2,y1,y2,z1,z2); // JPR
+
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
im->GetWholeExtent (x1,x2,y1,y2,z1,z2);
+#else
+ im->GetExtent (x1,x2,y1,y2,z1,z2);
+#endif
+
+
/*
std::cout << "in WxViewer::ShowImage GetWholeExtent ext =";
std::cout << " [x1]=" << x1;
class WxViewerPlayer;
- class WxViewer : public wxPanel
+ class CREAIMAGEIO_EXPORT WxViewer : public wxPanel
{
public:
wxCheckBox *mcheck;
/// Associated wxvtk interactor
- crea::creawxVTKRenderWindowInteractor *mInteractor;
+ crea::wxVTKRenderWindowInteractor *mInteractor;
/// Current extent
int mx1,mx2,my1,my2,mz1,mz2;
git://git.creatis.insa-lyon.fr / creaImageIO.git / commitdiff