+/*
+# ---------------------------------------------------------------------
+#
+# 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.
+# ------------------------------------------------------------------------
+*/
+
+
+#ifndef __creaImageIOWxSimpleDlg_hpp_INCLUDED__
+#define __creaImageIOWxSimpleDlg_hpp_INCLUDED__
+
+
//#include "creaImageIOWxISimpleDlg.h"
#include "creaImageIOWxGimmickReaderDialog.h"
#include <itkAnalyzeImageIO.h>
#include <itkImageFileReader.h>
+#include <itkImageSeriesReader.h>
#include <itkImage.h>
#include <itkImageSeriesWriter.h>
+#include <itkGDCMImageIO.h>
+#include <itkDICOMSeriesFileNames.h>
#include <itkNumericSeriesFileNames.h>
-#include "itkImageToVTKImageFilter.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>
namespace creaImageIO
{
- template <typename TImage2>
+ template <typename TImage2>
typename TImage2::Pointer ReadImage( const std::string &fileName)
{
-
-
-
typename TImage2::Pointer image;
typedef itk::ImageFileReader<TImage2> ReaderType;
}
- ///Ctor
+ ///Ctor
template <typename TImage>
WxISimpleDlg<TImage>::WxISimpleDlg(wxWindow *parent,
- wxString i_title,
- const std::string i_namedescp ,
- const std::string i_namedb)
- : wxDialog(parent, -1,_T("DISPLAY IMAGES"), wxDefaultPosition, wxSize(230,150))
+ wxString i_title,
+ const std::string i_namedescp ,
+ const std::string i_namedb)
+ : wxDialog(parent, -1,_T("SELECT IMAGE(S)"), wxDefaultPosition, wxSize(230,150))
{
- namedescp = i_namedescp;
- namedb = i_namedb;
-
- if(!i_title.empty())
- {
- this->SetTitle(i_title);
- }
- // 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) &WxISimpleDlg::OnReadFile );
-
- // Button to select directory
- wxButton *directoryBut = new wxButton(this, -1,_T("Select a directory to display"), wxPoint(10,40) );
- Connect( directoryBut->GetId(), wxEVT_COMMAND_BUTTON_CLICKED , (wxObjectEventFunction) &WxISimpleDlg::OnReadDirectory );
-
- // button to select creaImageIO
- wxButton *gimmickBut = new wxButton(this, -1,_T("Select Gimmick"), wxPoint(10,70) );
- Connect( gimmickBut->GetId(), wxEVT_COMMAND_BUTTON_CLICKED , (wxObjectEventFunction) &WxISimpleDlg::OnReadGimmick );
-
- /// \TODO Button to select Bruker directory
-
- Layout();
-
- }
+ namedescp = i_namedescp;
+ namedb = i_namedb;
+
+ if(!i_title.empty())
+ {
+ this->SetTitle(i_title);
+ }
+ // 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) &WxISimpleDlg::OnReadFile );
+
+ // Button to select directory
+ wxButton *directoryBut = new wxButton(this, -1,_T("Select a directory to display"), wxPoint(10,40) );
+ Connect( directoryBut->GetId(), wxEVT_COMMAND_BUTTON_CLICKED , (wxObjectEventFunction) &WxISimpleDlg::OnReadDirectory );
+
+ // button to select creaImageIO
+ wxButton *gimmickBut = new wxButton(this, -1,_T("Select Gimmick"), wxPoint(10,70) );
+ Connect( gimmickBut->GetId(), wxEVT_COMMAND_BUTTON_CLICKED , (wxObjectEventFunction) &WxISimpleDlg::OnReadGimmick );
+
+ /// \TODO Button to select Bruker directory
+ m_dicom = true;
+ Layout();
+
+ }
//////////////////////////////////////////////////////////////////////
// //
//////////////////////////////////////////////////////////////////////
template <typename TImage>
- void WxISimpleDlg<TImage>::OnReadFile(wxCommandEvent& event)
- {
- int resultShowModal;
- wxFileDialog* fileDlg = new wxFileDialog( 0, _T("Select file"), _T(""), _T(""), crea::std2wx("*"), wxOPEN |wxFD_MULTIPLE, wxDefaultPosition);
+ void WxISimpleDlg<TImage>::OnReadFile(wxCommandEvent& event)
+ {
+ int resultShowModal;
+ wxFileDialog* fileDlg = new wxFileDialog( 0, _T("Select file"), _T(""), _T(""), crea::std2wx("*"), wxOPEN |wxFD_MULTIPLE, wxDefaultPosition);
- resultShowModal = fileDlg->ShowModal();
- if ( resultShowModal==wxID_OK )
- {
- wxArrayString wxArray;
- fileDlg->GetPaths(wxArray);
- if(wxArray.size() >0)
- {
- for( int i = 0; i < wxArray.GetCount(); i++)
- {
- readImg( crea::wx2std(wxArray[i]));
- }
- }
- else {
- // TO DO WARNING MESSAGES
- }
- }
- SetReturnCode( resultShowModal );
-// Close();
- EndModal( resultShowModal );
- }
-
-
- template <typename TImage>
- void WxISimpleDlg<TImage>::setExts(std::vector<std::string> i_exts)
- {
- m_exts = i_exts;
- }
- //////////////////////////////////////////////////////////////////////
-// //
+ resultShowModal = fileDlg->ShowModal();
+ if ( resultShowModal==wxID_OK )
+ {
+ wxArrayString wxArray;
+ fileDlg->GetPaths(wxArray);
+ if(wxArray.size() >0)
+ {
+ for( int i = 0; i < wxArray.GetCount(); i++)
+ {
+ readImg( crea::wx2std(wxArray[i]));
+ }
+ }
+ else {
+ /// \TODO WARNING MESSAGES
+ }
+ }
+ SetReturnCode( resultShowModal );
+// Close();
+ EndModal( resultShowModal );
+ }
+
+
+ template <typename TImage>
+ void WxISimpleDlg<TImage>::setExts(std::vector<std::string> i_exts)
+ {
+ m_exts = i_exts;
+ }
//////////////////////////////////////////////////////////////////////
- template <typename TImage>
- void WxISimpleDlg<TImage>::OnReadDirectory(wxCommandEvent &event)
- {
- int resultShowModal;
- bool bvalid = false;
- long style = wxDD_DEFAULT_STYLE | wxDD_DIR_MUST_EXIST;
- wxDirDialog* dirDlg = new wxDirDialog( 0, _T("Select the directory to display"), _T(""), style);
-
- resultShowModal = dirDlg->ShowModal();
- 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))
- {*/
- 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++)
- {
- if(ext == (*it) )
- {
- bvalid = true;
- break;
- }
- }
- if (!boost::filesystem::is_directory(itr->status()) && bvalid)
- {
- readImg(itr->string().c_str());
- }
- }
- }
- SetReturnCode( resultShowModal );
-// Close();
- EndModal( resultShowModal );
- }
+// //
+//////////////////////////////////////////////////////////////////////
+ template <typename TImage>
+ void WxISimpleDlg<TImage>::OnReadDirectory(wxCommandEvent &event)
+ {
+ int resultShowModal;
+ bool bvalid = false;
+ long style = wxDD_DEFAULT_STYLE | wxDD_DIR_MUST_EXIST;
+ wxDirDialog* dirDlg = new wxDirDialog( 0, _T("Select the directory to display"), _T(""), style);
+
+ resultShowModal = dirDlg->ShowModal();
+ 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))
+ {*/
+ 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++)
+ {
+ if(ext == (*it) )
+ {
+ bvalid = true;
+ break;
+ }
+ }
+ if (!boost::filesystem::is_directory(itr->status()) && bvalid)
+ {
+ readImg(itr->string().c_str());
+ }
+ }
+ }
+ SetReturnCode( resultShowModal );
+// Close();
+ EndModal( resultShowModal );
+ }
- //////////////////////////////////////////////////////////////////////
-// //
//////////////////////////////////////////////////////////////////////
- template <typename TImage>
- void WxISimpleDlg<TImage>::OnReadGimmick(wxCommandEvent &event)
- {
- // Run Gimmick
- WxGimmickReaderDialog dlg(0,-1,
- namedescp,
- namedb,
- _T("Select image(s) - Gimmick! (c) CREATIS-LRMN 2008"),
+// //
+//////////////////////////////////////////////////////////////////////
+ template <typename TImage>
+ void WxISimpleDlg<TImage>::OnReadGimmick(wxCommandEvent &event)
+ {
+ // Run Gimmick
+ WxGimmickReaderDialog dlg(0,-1,
+ namedescp,
+ namedb,
+ _T("Select image(s) - Gimmick! (c) CREATIS-LRMN 2008"),
wxDefaultPosition,
wxSize(810,750),
GIMMICK_2D_IMAGE_SELECTION,
GIMMICK_3D_IMAGE_SELECTION,
_3D,
- 1);
- dlg.ShowModal();
- if (dlg.GetReturnCode() == wxID_OK)
- {
- // infoimage=_T("DICOM: ???_EED_???");
-//EED 07JUIN2010 dlg.GetSelectedImages(m_results,3);
- std::vector<creaImageIO::OutStrGimmick> out;
- std::vector<std::string> attr;
-// attr.push_back("D0028_0010");
-// attr.push_back("D0008_0023");
-// attr.push_back("D0008_1070");
- dlg.stopReading();
- dlg.getSelected(out, attr,true,"");
-// crea::VtkBasicSlicer(out.front().img);
- //m_results.clear();
- int size=out.size();
- int ii;
- //for (ii=0;ii<size;ii++)
- //{
- //m_results.push_back(out[ii].img);
- //}
-
- dlg.OnExit();
- }
- SetReturnCode( dlg.GetReturnCode() );
-// Close();
- EndModal( dlg.GetReturnCode() );
- }
+ 1);
+ dlg.ShowModal();
+ if (dlg.GetReturnCode() == wxID_OK)
+ {
+ std::vector<std::string> out;
+ dlg.stopReading();
+ dlg.GetSelectedFiles(out);
+ if(m_dicom)
+ {
+ readDicomImg( out);
+ }
+ else
+ {
+ std::vector<std::string>::iterator ii = out.begin();
+ for (;ii != out.end();ii++)
+ {
+ readImg( (*ii).c_str() );
+ }
+ }
+ dlg.OnExit();
+ }
+ SetReturnCode( dlg.GetReturnCode() );
+// Close();
+ EndModal( dlg.GetReturnCode() );
+ }
template <typename TImage>
- wxString WxISimpleDlg<TImage>::getInfoImage()
- {
- return infoimage;
- }
+ wxString WxISimpleDlg<TImage>::getInfoImage()
+ {
+ return infoimage;
+ }
//////////////////////////////////////////////////////////////////////
- // Return the results vector //
+ // Return the results vector //
//////////////////////////////////////////////////////////////////////
template <typename TImage>
std::vector<typename TImage::Pointer> WxISimpleDlg<TImage>::getImagesSelected()
+ template <typename TImage>
+ void WxISimpleDlg<TImage>::readDicomImg(const std::vector<std::string> &i_names)
+ {
+ typedef itk::GDCMImageIO GDCMType;
+ typedef itk::DICOMSeriesFileNames dicnames;
+ GDCMType::Pointer gdcmIO = GDCMType::New();
+ dicnames::Pointer generator = dicnames::New();
+// generator->SetInput(i_names);
+ typedef itk::ImageSeriesReader<TImage> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetImageIO(gdcmIO);
+ reader->SetFileNames(i_names);
+ // reader->SetFileName( i_name );
+ try
+ {
+ reader->Update();
+ }
+ catch( itk::ExceptionObject & err )
+ {
+ // std::cout << "Caught an exception reading" << i_name << ": " << std::endl;
+ std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
+ throw err;
+ }
+ catch(...)
+ {
+ //std::cout << "Error while reading image " << i_name << std::endl;
+ throw;
+ }
+ m_Iresults.push_back(reader->GetOutput());
+
+ }
+
+
+
+
template <typename TImage>
void WxISimpleDlg<TImage>::split3Din3Dvtk()
{
-
- int ii;
if ((m_Iresults).size() != 0)
{
-
- typename TImage::Pointer image = m_Iresults[0];
- image->GetImageDimension();
- typedef itk::ImageToVTKImageFilter< TImage > ConnectorType;
- ConnectorType::Pointer connector = ConnectorType::New();
- for(unsigned int i = 0 ;i < m_Iresults.size(); i++)
- {
- connector->SetInput(m_Iresults[i]);
- connector->Update();
- vtkImageData *im = vtkImageData::New();
- im->ShallowCopy(connector->GetOutput());
- m_Vresults.push_back(im);
- }
+ typedef itk::ImageToVTKImageFilter< TImage > ConnectorType;
+ ConnectorType::Pointer connector = ConnectorType::New();
+ for(unsigned int i = 0 ;i < m_Iresults.size(); i++)
+ {
+ connector->SetInput(m_Iresults[i]);
+ connector->GetImporter()->SetDataScalarTypeToUnsignedChar();
+ connector->Update();
+ vtkImageData *im = vtkImageData::New();
+ im->ShallowCopy(connector->GetOutput());
+ im->Update();
+ m_Vresults.push_back(im);
+ }
}
}
{
typename TImage::Pointer image = m_Iresults[0];
- // Size and dims for Input Image
- typedef itk::Size<4> iSize;
- typedef const itk::Size<4>::SizeValueType iSizeVal;
- iSize size = image->GetLargestPossibleRegion().GetSize();
- iSizeVal *dims_size = size.GetSize();
-
- // Output Type
- typedef itk::Image<short,3> ImageOutputType;
- typedef itk::ImageSeriesWriter<TImage, ImageOutputType > SeriesWriterType;
-
- SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
- seriesWriter->SetInput( image);
-
- // from JPR file to generate output files
- typedef itk::NumericSeriesFileNames NamesGeneratorType;
- NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
- namesGenerator->SetStartIndex(0);
- namesGenerator->SetEndIndex(dims_size[3]-1);
- namesGenerator->SetIncrementIndex(1);
- std::string format = i_dir;
- format += "/image%03d.vtk";
- namesGenerator->SetSeriesFormat( format.c_str() );
-
- seriesWriter->SetFileNames( namesGenerator->GetFileNames() );
+ if(image->GetImageDimension() == 4)
+ {
+ boost::any a1(image);
+ m_AnyImages.push_back(a1);
+ // size of fourth dimension
+ int dsize = image->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;
+ SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
- try
- {
- seriesWriter->Update();
- vtkImageReader2 *vReader =vtkImageReader2::New();
- for(unsigned int i = 0 ;i < dims_size[3]; i++)
+ // 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 = i_dir;
+ format += "/image%03d.mhd";
+ namesGenerator->SetSeriesFormat( format.c_str() );
+
+ const std::vector<std::string> names = namesGenerator->GetFileNames();
+ seriesWriter->SetFileNames( names );
+ seriesWriter->SetInput(image);
+ seriesWriter->SetImageIO(metaIO);
+ try
{
- vReader->SetFileName(namesGenerator->GetFileNames()[i].c_str());
- vReader->Update();
- m_Vresults.push_back(vReader->GetOutput());
+ 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;
- }
-
- }
+ catch( itk::ExceptionObject & excp )
+ {
+ std::cerr << "Exception thrown while writing the series " << std::endl;
+ std::cerr << excp << std::endl;
+ //return EXIT_FAILURE;
+ }
+ }
+ }
}
}// namespace end
+#endif //__creaImageIOWxSimpleDlg_hpp_INCLUDED__
+
git://git.creatis.insa-lyon.fr / creaImageIO.git / blobdiff