--- /dev/null
+#include "creaImageIOWxAnySimpleDlg.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 <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
+{
+
+ ///Ctor
+ WxAnySimpleDlg::WxAnySimpleDlg(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))
+ {
+ 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) &WxAnySimpleDlg::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) &WxAnySimpleDlg::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) &WxAnySimpleDlg::OnReadGimmick );
+
+ /// \TODO Button to select Bruker directory
+ m_dicom = true;
+ Layout();
+
+ }
+//////////////////////////////////////////////////////////////////////
+// //
+//////////////////////////////////////////////////////////////////////
+
+ void WxAnySimpleDlg::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++)
+ {
+ std::string name = crea::wx2std(wxArray[i]);
+ // FOR THE MOMENT ONLY short 3D et short 4D
+ readImg(name);
+ }
+ }
+ else {
+ // TO DO WARNING MESSAGES
+ }
+ }
+ 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;
+ 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 );
+ }
+
+ //////////////////////////////////////////////////////////////////////
+// //
+//////////////////////////////////////////////////////////////////////
+
+ void WxAnySimpleDlg::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() );
+ }
+
+
+
+ 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());
+ imageIO->ReadImageInformation();
+ return imageIO->GetComponentTypeInfo();//AsString( imageIO->GetComponentType());
+ }
+
+ 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);
+ imageIO->SetFileName(i_name.c_str());
+ imageIO->ReadImageInformation();
+ 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)
+ {
+ case 3:
+ if (getType(i_name) == typeid(unsigned char))
+ {
+ typedef itk::Image<unsigned char, 3> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ 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->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ else if (getType(i_name) == typeid(short))
+ {
+ typedef itk::Image<short, 3> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ 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();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ else if (getType(i_name) == typeid(unsigned int))
+ {
+ typedef itk::Image<unsigned int, 3> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ else if (getType(i_name) == typeid(signed int))
+ {
+ typedef itk::Image<signed int, 3> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ else if (getType(i_name) == typeid(unsigned long))
+ {
+ typedef itk::Image<unsigned long, 3> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ else if (getType(i_name) == typeid(signed long))
+ {
+ typedef itk::Image<signed long, 3> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ else if (getType(i_name) == typeid(float))
+ {
+ typedef itk::Image<float, 3> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ else if (getType(i_name) == typeid(double))
+ {
+ typedef itk::Image<double, 3> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ }
+ else
+ {
+ //????FCY, so what the type????
+ }
+ break;
+ //assume that we have only one 4D file
+ case 4:
+ if (getType(i_name) == typeid(unsigned char))
+ {
+ typedef itk::Image<unsigned char, 4> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ 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->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ 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->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ else if(getType(i_name) == typeid(short))
+ {
+ typedef itk::Image<short, 4> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ 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;
+ }
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ 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->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ 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->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ 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->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ 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->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ 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->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ else if (getType(i_name) == typeid(float))
+ {
+ typedef itk::Image<float, 4> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ else if (getType(i_name) == typeid(double))
+ {
+ typedef itk::Image<double, 4> TImage;
+ typedef itk::ImageFileReader<TImage> ReaderType;
+ ReaderType::Pointer reader = ReaderType::New();
+ reader->SetFileName( i_name );
+ reader->Update();
+ reader->GetOutput()->Register();
+ m_AnyImages.push_back(reader->GetOutput());
+ split4Din3Dvtk<TImage>(reader->GetOutput());
+ }
+ else
+ {
+ //????FCY, so what the type????
+ }
+ break;
+ }
+
+ // Test to know if we have to add new type
+ bool btest = false;
+ if( m_AnyDims.size() != 0)
+ {
+ btest = true;
+ }
+ else
+ {
+ m_AnyDims.push_back(dims);
+ m_AnyType.push_back(&getType(i_name));
+ }
+ 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));
+ }
+ else{}
+ }
+ else {}
+ }
+
+
+
+
+ void WxAnySimpleDlg::readDicomImg(const std::vector<std::string> &i_names)
+ {
+ typedef itk::Image<short,3> TImage;
+ typedef itk::GDCMImageIO GDCMType;
+ typedef itk::DICOMSeriesFileNames dicnames;
+ GDCMType::Pointer gdcmIO = GDCMType::New();
+ dicnames::Pointer generator = dicnames::New();
+
+
+ typedef itk::ImageSeriesReader<TImage> ReaderType;
+ 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 WxAnySimpleDlg::split3Din3Dvtk(TImage* i_Img)
+ {
+ typedef itk::ImageToVTKImageFilter< TImage > ConnectorType;
+ ConnectorType::Pointer connector = ConnectorType::New();
+ connector->SetInput(i_Img);
+ connector->GetImporter()->SetDataScalarTypeToUnsignedChar();
+ connector->Update();
+ vtkImageData *im = vtkImageData::New();
+ 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;
+ 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;
+ }
+ }
+ }
+
+ bool WxAnySimpleDlg::AllSameType()
+ {
+ if(m_AnyType.size() == 1)
+ {
+ return true;
+ }
+ else
+ {
+ return false;
+ }
+
+ }
+
+ }// namespace end
+
git://git.creatis.insa-lyon.fr / creaImageIO.git / commitdiff