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
- m_dicom = true;
- 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)
- {
- 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() );
- }
+ 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()
- {
- return m_Iresults;
- }
-
- template <typename TImage>
- void WxISimpleDlg<TImage>::readImg(const std::string &i_name)
- {
- // FCY : just to check but not needed, we hardly suppose that we load only same type and dim of images
- // uncomment to test
- /*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());
- imageIO->ReadImageInformation();
- ScalarPixelType pixelType = imageIO->GetComponentType();
- const size_t dims = imageIO->GetNumberOfDimensions();*/
-
- typedef itk::ImageFileReader<TImage> ReaderType;
- typename ReaderType::Pointer reader = ReaderType::New();
- 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>::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()
- {
- if ((m_Iresults).size() != 0)
- {
- 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);
- }
- }
- }
-
-
-
- template <typename TImage>
- void WxISimpleDlg<TImage>::split4Din3Dvtk(const std::string &i_dir)
- {
- if ((m_Iresults).size() != 0)
- {
- typename TImage::Pointer image = m_Iresults[0];
-
- if(image->GetImageDimension() == 4)
- {
- // 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();
-
- // 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
- {
- 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;
- }
- }
- }
-
- }
+ template <typename TImage>
+ std::vector<typename TImage::Pointer> WxISimpleDlg<TImage>::getImagesSelected()
+ {
+ return m_Iresults;
+ }
+
+ template <typename TImage>
+ void WxISimpleDlg<TImage>::readImg(const std::string &i_name)
+ {
+ // FCY : just to check but not needed, we hardly suppose that we load only same type and dim of images
+ // uncomment to test
+ /*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());
+ imageIO->ReadImageInformation();
+ ScalarPixelType pixelType = imageIO->GetComponentType();
+ const size_t dims = imageIO->GetNumberOfDimensions();*/
+
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ typename ReaderType::Pointer reader = ReaderType::New();
+ 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>::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()
+ {
+ if ((m_Iresults).size() != 0)
+ {
+ 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);
+ }
+ }
+ }
+
+
+
+ template <typename TImage>
+ void WxISimpleDlg<TImage>::split4Din3Dvtk(const std::string &i_dir)
+ {
+ if ((m_Iresults).size() != 0)
+ {
+ typename TImage::Pointer image = m_Iresults[0];
+
+ if(image->GetImageDimension() == 4)
+ {
+ // 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();
+
+ // 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
+ {
+ 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;
+ }
+ }
+ }
+ }
}// namespace end
git://git.creatis.insa-lyon.fr / creaImageIO.git / commitdiff