-#include <creaImageIOImageReader.h>
-//#include <creaImageIOUtilities.h>
+/*
+# ---------------------------------------------------------------------
+#
+# 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 <vtkImageReader2.h>
+#include <creaImageIOImageReader.h>
+#include <creaImageIOTreeAttributeDescriptor.h>
+#include <creaImageIOSystem.h>
+
+#include <creaImageIOVtkImageReader.h>
+#if defined (USE_GDCM)
+ #include <creaImageIODicomImageReader.h>
+#endif
+#if defined(USE_GDCM2)
+ #include <creaImageIODicomImageReader2.h>
+#endif
+#include <creaImageIOUltrasonixImageReader.h>
#include <vtkPNGReader.h>
#include <vtkTIFFReader.h>
#include <vtkJPEGReader.h>
#include <vtkMetaImageReader.h>
//#include <vtkGESignalReader.h>
-#include <gdcmFile.h>
-#include <vtkGdcmReader.h>
-
-
#include "boost/filesystem/path.hpp"
namespace creaImageIO
{
-
- //========================================================================
- std::string irclean(const std::string& str)
- {
- if (str == "GDCM::Unfound")
- {
- return "----";
- }
- if (str[str.size()-1]==' ')
- {
- return str.substr(0,str.size()-1);
- }
- if (str[str.size()-1]==0)
- {
- return str.substr(0,str.size()-1);
- }
-
- return str;
- }
- //========================================================================
-
- void IRSplitString ( const std::string& str,
- const std::string& delimiters,
- std::vector<std::string>& tokens)
- {
- // Skip delimiters at beginning.
- std::string::size_type lastPos = str.find_first_not_of(delimiters, 0);
- // Find first delimiter.
- std::string::size_type pos = str.find_first_of(delimiters, lastPos);
-
- while (std::string::npos != pos || std::string::npos != lastPos)
- {
- // Found a token, add it to the vector.
- // SPECIFIC : REMOVE INITIAL DOT (lastPos + 1)
- tokens.push_back(str.substr(lastPos+1, pos - lastPos));
- // Skip delimiters. Note the "not_of"
- lastPos = str.find_first_not_of(delimiters, pos);
- // Find next delimiter
- pos = str.find_first_of(delimiters, lastPos);
- }
-
- }
-
- //=====================================================================
- // Static members
- /*
- std::vector<SpecificImageReader*> ImageReader::mReader;
- std::vector<std::string>ImageReader::mKnownExtensions;
- vtkImageData* ImageReader::mUnreadableImage = 0;
- std::string ImageReader::mLastFilename("&&&&&&&&&&&&&&&&&&&&&&&&&&&&&");
- SpecificImageReader* ImageReader::mLastReader = 0;
- //=====================================================================
- // Global instance : automatic init / destr
- ImageReader GlobalImageReader;
- //=====================================================================
- */
-
- //=====================================================================
- class SpecificImageReader
- {
- public:
- SpecificImageReader() {}
- virtual ~SpecificImageReader() {}
- void SetName(const std::string& s) { mName = s; }
- const std::string& GetName() const { return mName; }
- virtual bool CanRead(const std::string& filename) { return false; }
- virtual vtkImageData* Read(const std::string& filename) { return 0; }
- virtual void PushBackExtensions(std::vector<std::string>&) {}
- virtual void ReadDicomInfo(const std::string& filename,
- DicomNode* image) {}
- private:
- std::string mName;
- };
- //=====================================================================
-
- //=====================================================================
- class SpecificVtkReader : public SpecificImageReader
- {
- public:
- SpecificVtkReader(vtkImageReader2* r,
- const std::string& name = "",
- const std::string& extensions = "")
- : mVTKReader(r), mExtensions(extensions)
- {
- if (name.size() == 0)
- {
- SetName ( mVTKReader->GetDescriptiveName() );
- }
- else
- {
- SetName ( name );
- }
- };
- ~SpecificVtkReader()
- {
- mVTKReader->Delete();
- }
- bool CanRead(const std::string& filename)
- {
- // std::cout << "## Reader "<<GetName()
- //<<" ::CanRead("<<filename<<")"
- // <<std::endl;
- return (mVTKReader->CanReadFile(filename.c_str())!=0);
- }
- vtkImageData* Read(const std::string& filename)
- {
- // std::cout << "## Reader "<<GetName()
- //<<" ::Read("<<filename<<")"
- // <<std::endl;
- vtkImageData* im = 0;
- try
- {
- mVTKReader->SetFileName(filename.c_str());
- mVTKReader->Update();
- im = vtkImageData::New();
- im->ShallowCopy(mVTKReader->GetOutput());
- }
- catch (...)
- {
- if (im!=0) im->Delete();
- im = 0;
- }
- return im;
- }
-
- void PushBackExtensions(std::vector<std::string>& v)
- {
- std::string ext = mExtensions;
- if (ext.size()==0) ext = mVTKReader->GetFileExtensions ();
-
- IRSplitString(ext," ",v);
- }
-
- void ReadDicomInfo(const std::string& filename,
- DicomNode* image)
- {
- boost::filesystem::path full_path(filename);
- std::string f = full_path.leaf();
- //Utilities::GetFileName(filename));
- // file name
- image->SetFieldValue("A0004_1500",irclean(f));
- // Does not work :
- // How to get the image info without loading it in vtk ?
- /*
- mVTKReader->SetFileName(filename.c_str());
- mVTKReader->OpenFile();
- int ext[6];
- mVTKReader->GetDataExtent(ext);
- // Columns
- char str[128];
- sprintf(str,"%i",ext[1]-ext[0]);
- image->SetFieldValue("A0028_0011",str);
- // Rows
- sprintf(str,"%i",ext[3]-ext[2]);
- image->SetFieldValue("A0028_0010",str);
- */
-
- }
- private:
- vtkImageReader2* mVTKReader;
- std::string mExtensions;
- };
- //=====================================================================
-
- //=====================================================================
- void IRFillFields(DicomNode* node,
- GDCM_NAME_SPACE::File* gdcmFile)
- {
- const DicomNodeTypeDescription::FieldDescriptionMapType& dm
- = node->GetTypeDescription().GetFieldDescriptionMap();
- DicomNodeTypeDescription::FieldDescriptionMapType::const_iterator i;
-
-
- DicomNode::FieldValueMapType& vm = node->GetFieldValueMap();
- for (i=dm.begin(); i!=dm.end(); ++i)
- {
- if ( (i->second.flags==0) &&
- (i->second.group!=0) &&
- (i->second.element!=0) )
- {
- uint16_t gr = i->second.group;
- uint16_t el = i->second.element;
-
- std::string val = gdcmFile->GetEntryString(gr,el);
-
- vm[i->first] = irclean(val);
- }
- else
- {
- vm[i->first] = "";
- }
- }
- }
- //=====================================================================
-
- //=====================================================================
- class DicomReader : public SpecificImageReader
- {
- public:
- DicomReader()
- {
- mReader = vtkGdcmReader::New();
- SetName ( "Dicom" );
- };
- ~DicomReader()
- {
- mReader->Delete();
- }
- bool CanRead(const std::string& filename)
- {
- // std::cout << "## Reader "<<GetName()
- //<<" ::CanRead("<<filename<<")"
- // <<std::endl;
- // return true;
-
-
- // GDCM_NAME_SPACE
- // std::cout << "GDCM_NAME_SPACE = '" << STRINGIFY_SYMBOL(GDCM_NAME_SPACE)
- // << "'"
- // <<std::endl;
-
- GDCM_NAME_SPACE::File* file = GDCM_NAME_SPACE::File::New();
- file->SetLoadMode( GDCM_NAME_SPACE::LD_ALL);
- file->SetFileName(filename.c_str());
- file->Load();
- bool ok = file->IsReadable();
- file->Delete();
- return ok;
- }
- vtkImageData* Read(const std::string& filename)
- {
- // std::cout << "## Reader "<<GetName()
- //<<" ::Read("<<filename<<")"
- // <<std::endl;
-
- vtkImageData* im = 0;
- try
- {
- mReader->SetFileName(filename.c_str());
- mReader->Update();
- im = vtkImageData::New();
- im->ShallowCopy(mReader->GetOutput());
- }
- catch (...)
- {
- if (im!=0) im->Delete();
- im = 0;
- }
- return im;
- }
-
- void PushBackExtensions(std::vector<std::string>& v)
- {
- v.push_back("dcm");
- v.push_back("");
- }
-
- void ReadDicomInfo(const std::string& filename,
- DicomNode* image)
- {
- GDCM_NAME_SPACE::File* file = GDCM_NAME_SPACE::File::New();
- file->SetLoadMode( GDCM_NAME_SPACE::LD_ALL);
- file->SetFileName(filename.c_str());
- file->Load();
- if (file->IsReadable())
- {
-
- DicomNode* cur = image;
- do
- {
- IRFillFields(cur,file);
- cur = cur->GetParent();
- }
- while (cur);
- // File name and full file name
- image->SetFieldValue("FullFileName",filename);
-
- boost::filesystem::path full_path(filename);
-
- image->SetFieldValue("A0004_1500",full_path.leaf());
- //Utilities::GetFileName(filename));
- }
- file->Delete();
- }
-
-
- private:
- vtkGdcmReader* mReader;
- };
- //=====================================================================
-
-
-
-
//=====================================================================
ImageReader::ImageReader()
:
mUnreadableImage(0),
- mLastFilename("&&&&&&&&&&&&&&&&&&&&&&&&&&&&&"),
- mLastReader(0)
-
+ mLastFilename("&&&&&&&&&&&&&&&&&&&&&&&&&&&&&")
{
// std::cout << "#### ImageReader::ImageReader()"<<std::endl;
if (mUnreadableImage!=0) return;
- Register(new SpecificVtkReader(vtkPNGReader::New()));
- Register(new SpecificVtkReader(vtkTIFFReader::New()));
- Register(new SpecificVtkReader(vtkJPEGReader::New()));
- Register(new SpecificVtkReader(vtkBMPReader::New()));
- Register(new SpecificVtkReader(vtkSLCReader::New()));
- Register(new SpecificVtkReader(vtkMetaImageReader::New(),"MHD",".mhd"));
- // Register(new SpecificVtkReader(vtkGESignalReader::New()));
- Register(new DicomReader);
- /*
- std::cout << "## Registered file extensions : "<<std::endl;
- std::vector<std::string>::const_iterator i;
- for (i=GetKnownExtensions().begin();
- i!=GetKnownExtensions().end();
- i++)
- {
- std::cout << "'"<<(*i)<<"'"<<std::endl;
- }
- */
- //
+ Register( boost::shared_ptr<AbstractImageReader>(new VtkImageReader(vtkPNGReader::New() , "PNG", ".png")));
+ Register(boost::shared_ptr<AbstractImageReader>(new VtkImageReader(vtkTIFFReader::New(), "TIFF", ".tiff")));
+ Register(boost::shared_ptr<AbstractImageReader>(new VtkImageReader(vtkJPEGReader::New(), "JPEG", ".jpeg")));
+ Register(boost::shared_ptr<AbstractImageReader>(new VtkImageReader(vtkBMPReader::New(), "BMP", ".bmp")));
+ Register(boost::shared_ptr<AbstractImageReader>(new VtkImageReader(vtkSLCReader::New())));
+ Register(boost::shared_ptr<AbstractImageReader>(new VtkImageReader(vtkMetaImageReader::New(),"MHD",".mhd")));
+ // Register(new VtkImageReader(vtkGESignalReader::New()));
+ Register(boost::shared_ptr<AbstractImageReader>(new DicomImageReader));
+ Register(boost::shared_ptr<AbstractImageReader>(new UltrasonixImageReader));
+
+ UnRegister(".txt");
+
mUnreadableImage = vtkImageData::New();
int dim[3];
- dim[0] = dim[1] = 32;
+ dim[0] = dim[1] = 128;
dim[2] = 1;
mUnreadableImage->SetDimensions ( dim );
mUnreadableImage->SetScalarTypeToUnsignedChar();
mUnreadableImage->SetScalarComponentFromFloat(i,i,0,0,255);
mUnreadableImage->SetScalarComponentFromFloat(dim[0]-1-i,i,0,0,255);
}
-
-
-
}
//=====================================================================
//=====================================================================
ImageReader::~ImageReader()
{
- // std::cout << "#### ImageReader::~ImageReader()"<<std::endl;
- std::vector<SpecificImageReader*>::iterator i;
- for (i=mReader.begin(); i!=mReader.end(); i++)
- {
- // std::cout << "#### ImageReader::UnRegister("
- // << (*i)->GetName()<<")"<<std::endl;
- delete (*i);
- }
- mReader.clear();
+
+ // for (i=mReader.begin(); i!=mReader.end(); i++)
+ // {
+ //delete (*i);
+ // }
+// mReader.clear();
if (mUnreadableImage!=0)
{
mUnreadableImage->Delete();
//=====================================================================
//=====================================================================
- void ImageReader::Register(SpecificImageReader* r)
+ void ImageReader::Register(boost::shared_ptr<AbstractImageReader> r)
{
- // std::cout << "#### ImageReader::Register("<<r->GetName()<<")"<<std::endl;
mReader.push_back(r);
- r->PushBackExtensions(mKnownExtensions);
+
+ }
+
+ void ImageReader::UnRegister(const std::string i_val)
+ {
+ mUnReader.push_back(i_val);
+
}
//=====================================================================
+ //=====================================================================
+ // Returns true iff the file is readable
+ bool ImageReader::ShallNotRead( const std::string& filename )
+ {
+ bool ok = true;
+ if(filename != "")
+ {
+ std::vector<std::string >::iterator i ;
+ for (i=mUnReader.begin(); i!=mUnReader.end(); i++)
+ {
+
+ if ( (*i).c_str() == filename)
+ {
+ ok = false;
+ break;
+ }
+ }
+ }
+ return ok;
+ }
+
//=====================================================================
// Returns true iff the file is readable
- bool ImageReader::CanRead( const std::string& filename,
- const std::string& exclude )
+ bool ImageReader::CanRead( const std::string& filename )
{
- // std::cout << "## ImageReader::CanRead("<<filename<<")"<<std::endl;
bool ok = false;
- std::vector<SpecificImageReader*>::iterator i;
- for (i=mReader.begin(); i!=mReader.end(); i++)
- {
- if ((*i)->GetName()==exclude) continue;
- ok = (*i)->CanRead(filename);
- if (ok)
- {
- mLastFilename = filename;
- mLastReader = *i;
- break;
- }
- }
- return ok;
+
+ if( !ShallNotRead(filename))
+ {
+ return ok;
+ }
+ if(filename != "")
+ {
+ std::vector<boost::shared_ptr<AbstractImageReader> >::iterator i;
+ for (i=mReader.begin(); i!=mReader.end(); i++)
+ {
+ ok = (*i)->CanRead(filename);
+ if (ok)
+ {
+ mLastFilename = filename;
+ mLastReader = *i;
+ break;
+ }
+ }
+ }
+ return ok;
}
//=====================================================================
//=====================================================================
// Reads the file (CanRead must be called before : no test here)
- vtkImageData* ImageReader::Read( const std::string& filename,
- const std::string& exclude )
+ vtkImageData* ImageReader::ReadImage( const std::string& filename)
{
- // std::cout << "## ImageReader::Read("<<filename<<")"<<std::endl;
- if (mLastFilename!=filename)
+ if (mLastFilename!=filename)
{
- if (!CanRead(filename,exclude))
+ if (!CanRead(filename))
{
- // std::cout << " -- Cannot read image "<<std::endl;
vtkImageData* im = vtkImageData::New();
im->ShallowCopy(mUnreadableImage);
return im;
}
}
- vtkImageData* i = mLastReader->Read(mLastFilename);
- // std::cout << "i="<<i<<std::endl;
+ vtkImageData* i = mLastReader->ReadImage(mLastFilename);
if (i==0)
{
- // std::cout << "i=UNREAD"<<i<<std::endl;
i = vtkImageData::New();
i->ShallowCopy(mUnreadableImage);
}
- // std::cout << "i="<<i<<std::endl;
return i;
}
//=====================================================================
-
-
+ // Another function to read attributes for a file
+ void ImageReader::getAttributes(const std::string filename,
+ std::map <std::string , std::string> &infos, std::vector<std::string> i_attr)
+ {
+ if (mLastFilename!=filename)
+ {
+ if (!CanRead(filename))
+ {
+ return;
+ }
+ }
+ mLastReader->getAttributes(filename, infos, i_attr);
+ }
//=====================================================================
- void ImageReader::ReadDicomInfo(const std::string& filename,
- DicomNode* image)
+ void ImageReader::ReadAttributes(const std::string& filename,
+ std::map<std::string,std::string>& attr)
{
- // std::cout << "## ImageReader::Read("<<filename<<")"<<std::endl;
if (mLastFilename!=filename)
{
if (!CanRead(filename))
return;
}
}
- mLastReader->ReadDicomInfo(mLastFilename,image);
+ mLastReader->ReadAttributes(mLastFilename,attr);
}
//=====================================================================
-
+ //=====================================================================
+ /// Pushes back all kwown extensions (without dot) in the vector given
+ void ImageReader::PushBackExtensions(std::vector<std::string>& v)
+ {
+ std::vector<boost::shared_ptr<AbstractImageReader> >::iterator i;
+ for (i=mReader.begin(); i!=mReader.end(); i++)
+ {
+ (*i)->PushBackExtensions(v);
+ }
+ }
+ //=====================================================================
+
} // namespace creaImageIO
git://git.creatis.insa-lyon.fr / creaImageIO.git / blobdiff