+/*
+# ---------------------------------------------------------------------
+#
+# 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 "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>
-#include <itkOrientedImage.h>
#include <vtkImageReader2.h>
#include <vtkMetaImageReader.h>
#include <boost/filesystem/path.hpp>
#include <boost/filesystem.hpp>
#include <boost/utility.hpp>
#include <creaVtkBasicSlicer.h>
-#include "itkImageToVTKImageFilter.h"
+
namespace creaImageIO
{
}
// Button to select file(s)
wxButton *fileBut = new wxButton(this, -1,_T("Select a file to display"), wxPoint(10,7) );
- Connect( fileBut->GetId(), wxEVT_COMMAND_BUTTON_CLICKED , (wxObjectEventFunction) &WxAnySimpleDlg::OnReadFile );
+ Connect( fileBut->GetId(), wxEVT_COMMAND_BUTTON_CLICKED , (wxObjectEventFunction) &WxAnySimpleDlg::OnReadFile );
// Button to select directory
wxButton *directoryBut = new wxButton(this, -1,_T("Select a directory to display"), wxPoint(10,40) );
Connect( gimmickBut->GetId(), wxEVT_COMMAND_BUTTON_CLICKED , (wxObjectEventFunction) &WxAnySimpleDlg::OnReadGimmick );
/// \TODO Button to select Bruker directory
- m_dicom = true;
+ m_dicom = false;
Layout();
}
+
//////////////////////////////////////////////////////////////////////
// //
//////////////////////////////////////////////////////////////////////
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::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->filename().substr(itr->filename().find_last_of("."));
- for(; it != m_exts.end(); it++)
+//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)
{
- if(ext == (*it) )
- {
- bvalid = true;
- break;
- }
- }
- if (!boost::filesystem::is_directory(itr->status()) && bvalid)
- {
- readImg(itr->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 );
+
}
- //////////////////////////////////////////////////////////////////////
-// //
+//////////////////////////////////////////////////////////////////////
+// //
//////////////////////////////////////////////////////////////////////
void WxAnySimpleDlg::OnReadGimmick(wxCommandEvent &event)
{
// Run Gimmick
- WxGimmickReaderDialog dlg(0,-1,
+ WxGimmickReaderDialog dlg(0,-1,
namedescp,
namedb,
_T("Select image(s) - Gimmick! (c) CREATIS-LRMN 2008"),
- wxString WxAnySimpleDlg::getInfoImage()
+ wxString WxAnySimpleDlg::getInfoImage()
{
return infoimage;
}
// FCY : just to check but not needed, we hardly suppose that we load only same type and dim of images
const std::type_info & WxAnySimpleDlg::getType(const std::string &i_name)
- {
+ {
typedef itk::ImageIOBase::IOComponentType ScalarPixelType;
itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(i_name.c_str(), itk::ImageIOFactory::ReadMode);
imageIO->SetFileName(i_name.c_str());
return imageIO->GetComponentTypeInfo();//AsString( imageIO->GetComponentType());
}
- const size_t WxAnySimpleDlg::getNumberOfDimensions(const std::string &i_name)
+ const size_t WxAnySimpleDlg::getNumberOfDimensions(const std::string &i_name)
{
typedef itk::ImageIOBase::IOComponentType ScalarPixelType;
itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(i_name.c_str(), itk::ImageIOFactory::ReadMode);
return imageIO->GetNumberOfDimensions();
}
- void WxAnySimpleDlg::readImg(const std::string &i_name)
- {
+
+ void WxAnySimpleDlg::readImg(const std::string &i_name)
+ {
size_t dims = getNumberOfDimensions(i_name);
- const std::type_info *type= &getType(i_name);
+
+ //const std::type_info *type= &getType(i_name);
switch(dims)
{
case 3:
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
}
- else if (getType(i_name) == typeid(signed char))
- {
+ else if (getType(i_name) == typeid(signed char))
+ {
typedef itk::Image<signed char, 3> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->Update();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
- }
+ }
else if (getType(i_name) == typeid(short))
{
typedef itk::Image<short, 3> TImage;
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
}
- else if (getType(i_name) == typeid(unsigned short))
- {
+ else if (getType(i_name) == typeid(unsigned short))
+ {
typedef itk::Image<unsigned short, 3> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
}
else
{
+ printf("EED WxAnySimpleDlg::readImg Not type found for DIM 3 \n");
//????FCY, so what the type????
}
break;
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
}
- else if (getType(i_name) == typeid(signed char))
- {
+ else if (getType(i_name) == typeid(signed char))
+ {
typedef itk::Image<signed char, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
- }
- else if (getType(i_name) == typeid(unsigned short))
+ }
+ else if (getType(i_name) == typeid(unsigned short))
{
typedef itk::Image<unsigned short, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
}
- else if(getType(i_name) == typeid(short))
- {
+ else if(getType(i_name) == typeid(short))
+ {
typedef itk::Image<short, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
- }
- else if (getType(i_name) == typeid(unsigned short))
- {
+ }
+ else if (getType(i_name) == typeid(unsigned short))
+ {
typedef itk::Image<unsigned short, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
- }
- else if (getType(i_name) == typeid(unsigned int))
- {
+ }
+ else if (getType(i_name) == typeid(unsigned int))
+ {
typedef itk::Image<unsigned int, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
- }
- else if (getType(i_name) == typeid(signed int))
- {
+ }
+ else if (getType(i_name) == typeid(signed int))
+ {
typedef itk::Image<signed int, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
- }
- else if (getType(i_name) == typeid(unsigned long))
- {
+ }
+ else if (getType(i_name) == typeid(unsigned long))
+ {
typedef itk::Image<unsigned long, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
- }
- else if (getType(i_name) == typeid(signed long))
- {
+ }
+ else if (getType(i_name) == typeid(signed long))
+ {
typedef itk::Image<signed long, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
- }
- else if (getType(i_name) == typeid(float))
- {
+ }
+ else if (getType(i_name) == typeid(float))
+ {
typedef itk::Image<float, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
- }
- else if (getType(i_name) == typeid(double))
- {
+ }
+ else if (getType(i_name) == typeid(double))
+ {
typedef itk::Image<double, 4> TImage;
typedef itk::ImageFileReader<TImage> ReaderType;
ReaderType::Pointer reader = ReaderType::New();
reader->GetOutput()->Register();
m_AnyImages.push_back(reader->GetOutput());
split4Din3Dvtk<TImage>(reader->GetOutput());
- }
- else
- {
+ }
+ else
+ {
+ printf("EED WxAnySimpleDlg::readImg Not type found for DIM 4 \n");
//????FCY, so what the type????
- }
- break;
+ }
+ break;
}
// Test to know if we have to add new type
- bool btest = false;
+ bool btest = false;
if( m_AnyDims.size() != 0)
{
btest = true;
else
{
m_AnyDims.push_back(dims);
- m_AnyType.push_back(&getType(i_name));
+ m_AnyType.push_back((std::type_info*)&getType(i_name)); //JPR cast
}
if (btest)
{
if(m_AnyDims.front() != dims || m_AnyType.front()->before(getType(i_name)))
{
m_AnyDims.push_back(dims);
- m_AnyType.push_back(&getType(i_name));
+ m_AnyType.push_back((std::type_info*)&getType(i_name)); //JPR cast
}
else{}
}
else {}
}
-
-
-
void WxAnySimpleDlg::readDicomImg(const std::vector<std::string> &i_names)
{
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();
}
-
-
-
- template <typename TImage>
+ /* template <typename TImage>
void WxAnySimpleDlg::split3Din3Dvtk(TImage* i_Img)
{
typedef itk::ImageToVTKImageFilter< TImage > ConnectorType;
im->ShallowCopy(connector->GetOutput());
im->Update();
m_Vresults.push_back(im);
- }
+ }*/
template <typename TImage>
void WxAnySimpleDlg::split4Din3Dvtk(TImage* i_Img)
{
- if(i_Img->GetImageDimension() == 4)
- {
- // size of fourth dimension
- int dsize = i_Img->GetLargestPossibleRegion().GetSize(3);
- // Output Type
- typedef itk::Image<unsigned char,3> ImageOutputType;
- typedef itk::ImageSeriesWriter<TImage, ImageOutputType > SeriesWriterType;
- typedef itk::MetaImageIO MetaImageType;
- MetaImageType::Pointer metaIO;
- typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
+ if(i_Img->GetImageDimension() == 4)
+ {
+ // size of fourth dimension
+ int dsize = i_Img->GetLargestPossibleRegion().GetSize(3);
+ // Output Type
+ typedef itk::Image<unsigned char,3> ImageOutputType;
+ typedef itk::ImageSeriesWriter<TImage, ImageOutputType > SeriesWriterType;
+ typedef itk::MetaImageIO MetaImageType;
+ MetaImageType::Pointer metaIO;
+ typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
- // from JPR file to generate output files
- typedef itk::NumericSeriesFileNames NamesGeneratorType;
- NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
- namesGenerator->SetStartIndex(0);
- namesGenerator->SetEndIndex(dsize-1);
- namesGenerator->SetIncrementIndex(1);
- std::string format = m_dir;
- format += "/image%03d.mhd";
- namesGenerator->SetSeriesFormat( format.c_str() );
-
- const std::vector<std::string> names = namesGenerator->GetFileNames();
- seriesWriter->SetFileNames( names );
- seriesWriter->SetInput(i_Img);
- seriesWriter->SetImageIO(metaIO);
- try
- {
- seriesWriter->Update();
- vtkMetaImageReader *vReader = vtkMetaImageReader::New();
- std::vector<std::string>::const_iterator it = names.begin();
- for( ;it != names.end(); ++it)
- {
- vReader->SetFileName((*it).c_str());
- vReader->Update();
- m_Vresults.push_back(vReader->GetOutput());
-
- }
- }
- catch( itk::ExceptionObject & excp )
- {
- std::cerr << "Exception thrown while writing the series " << std::endl;
- std::cerr << excp << std::endl;
- //return EXIT_FAILURE;
- }
+ // from JPR file to generate output files
+ typedef itk::NumericSeriesFileNames NamesGeneratorType;
+ NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
+ namesGenerator->SetStartIndex(0);
+ namesGenerator->SetEndIndex(dsize-1);
+ namesGenerator->SetIncrementIndex(1);
+ std::string format = m_dir;
+ format += "/image%03d.mhd";
+ namesGenerator->SetSeriesFormat( format.c_str() );
+
+ const std::vector<std::string> names = namesGenerator->GetFileNames();
+ seriesWriter->SetFileNames( names );
+ seriesWriter->SetInput(i_Img);
+ seriesWriter->SetImageIO(metaIO);
+ try
+ {
+ seriesWriter->Update();
+ vtkMetaImageReader *vReader = vtkMetaImageReader::New();
+ std::vector<std::string>::const_iterator it = names.begin();
+ for( ;it != names.end(); ++it)
+ {
+ vReader->SetFileName((*it).c_str());
+ vReader->Update();
+ m_Vresults.push_back(vReader->GetOutput());
+
}
+ }
+ catch( itk::ExceptionObject & excp )
+ {
+ std::cerr << "Exception thrown while writing the series " << std::endl;
+ std::cerr << excp << std::endl;
+ //return EXIT_FAILURE;
+ }
+ }
}
- bool WxAnySimpleDlg::AllSameType()
- {
+ bool WxAnySimpleDlg::AllSameType()
+ {
if(m_AnyType.size() == 1)
{
return true;
return false;
}
- }
+ }
- }// namespace end
+ } // namespace end
git://git.creatis.insa-lyon.fr / creaImageIO.git / blobdiff