#include <creaImageIOImageReader.h>
#include <creaImageIOTreeAttributeDescriptor.h>
+#include <creaImageIOSystem.h>
+#include <creaImageIOVtkImageReader.h>
+#include <creaImageIODicomImageReader.h>
+#include <creaImageIOUltrasonixImageReader.h>
-#include <vtkImageReader2.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);
- }
-
- }
-
-
- //=====================================================================
- class SpecificImageReader
- {
- public:
- SpecificImageReader() {}
- virtual ~SpecificImageReader() {}
-
- void SetName(const std::string& s) { mName = s; }
- const std::string& GetName() const { return mName; }
-
- virtual void PushBackExtensions(std::vector<std::string>&) {}
-
- virtual bool CanRead(const std::string& filename) { return false; }
- virtual vtkImageData* ReadImage(const std::string& filename) { return 0; }
- virtual void ReadAttributes(const std::string& filename,
- std::map<std::string,std::string>& attr) {}
-
- 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* ReadImage(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 ReadAttributes(const std::string& filename,
- std::map<std::string,std::string>& attr)
- {
- // std::cout << "SpecificVtkReader::ReadDicomInfo '"<<filename<<"'"<<std::endl;
- // Get image dimensions
- // How to get the image info without loading it in vtk ?
- mVTKReader->SetFileName(filename.c_str());
- mVTKReader->Update(); //OpenFile();
- int ext[6];
- mVTKReader->GetDataExtent(ext);
- // Columns
- char cols[128];
- sprintf(cols,"%i",ext[1]-ext[0]);
- // Rows
- char rows[128];
- sprintf(rows,"%i",ext[3]-ext[2]);
- // Planes
- char planes[128];
- sprintf(planes,"%i",ext[5]-ext[4]);
-
- //
- std::map<std::string,std::string>::iterator i;
- if ( (i = attr.find("Full File Name")) != attr.end())
- {
- boost::filesystem::path full_path(filename);
- std::string f = full_path.leaf();
- i->second = f;
- }
- if ( (i = attr.find("Columns")) != attr.end())
- {
- i->second = cols;
- }
- if ( (i = attr.find("Rows")) != attr.end())
- {
- i->second = rows;
- }
- if ( (i = attr.find("Planes")) != attr.end())
- {
- i->second = planes;
- }
- }
- //=====================================================================
- 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* ReadImage(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 ReadAttributes(const std::string& filename,
- std::map<std::string,std::string>& attr)
- {
- // std::cout << "DicomReader::ReadDicomInfo '"<<filename<<"'"<<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();
- if (file->IsReadable())
- {
-
- std::map<std::string,std::string>::iterator i;
- for (i=attr.begin();i!=attr.end();++i)
- {
- if ( i->first == "Full File Name" )
- {
- boost::filesystem::path full_path(filename);
- std::string f = full_path.leaf();
- i->second = f;
- }
- else
- {
- tree::AttributeDescriptor a(i->first);
- uint16_t gr = a.GetGroup();
- uint16_t el = a.GetElement();
- if ( ( gr!=0 ) && ( el!=0 ) )
- {
- std::string val = file->GetEntryString(gr,el);
- i->second = irclean(val);
- }
- }
- }
- }
- file->Delete();
- }
-
-
- private:
- vtkGdcmReader* mReader;
- };
- //=====================================================================
-
// 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);
+ Register(new VtkImageReader(vtkPNGReader::New()));
+ Register(new VtkImageReader(vtkTIFFReader::New()));
+ Register(new VtkImageReader(vtkJPEGReader::New()));
+ Register(new VtkImageReader(vtkBMPReader::New()));
+ Register(new VtkImageReader(vtkSLCReader::New()));
+ Register(new VtkImageReader(vtkMetaImageReader::New(),"MHD",".mhd"));
+ // Register(new VtkImageReader(vtkGESignalReader::New()));
+ Register(new DicomImageReader);
+ Register(new UltrasonixImageReader);
- /*
- 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;
- }
- */
- //
+
mUnreadableImage = vtkImageData::New();
int dim[3];
dim[0] = dim[1] = 128;
//=====================================================================
ImageReader::~ImageReader()
{
- // std::cout << "#### ImageReader::~ImageReader()"<<std::endl;
- std::vector<SpecificImageReader*>::iterator i;
+ std::vector<AbstractImageReader*>::iterator i;
for (i=mReader.begin(); i!=mReader.end(); i++)
{
- // std::cout << "#### ImageReader::UnRegister("
- // << (*i)->GetName()<<")"<<std::endl;
delete (*i);
}
mReader.clear();
//=====================================================================
//=====================================================================
- void ImageReader::Register(SpecificImageReader* r)
+ void ImageReader::Register(AbstractImageReader* r)
{
- // std::cout << "#### ImageReader::Register("<<r->GetName()<<")"<<std::endl;
mReader.push_back(r);
- r->PushBackExtensions(mKnownExtensions);
+
}
//=====================================================================
//=====================================================================
// 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;
+ std::vector<AbstractImageReader*>::iterator i;
for (i=mReader.begin(); i!=mReader.end(); i++)
{
- if ((*i)->GetName()==exclude) continue;
ok = (*i)->CanRead(filename);
if (ok)
{
//=====================================================================
// Reads the file (CanRead must be called before : no test here)
- vtkImageData* ImageReader::ReadImage( 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 (!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->ReadImage(mLastFilename);
- // std::cout << "i="<<i<<std::endl;
if (i==0)
{
- // std::cout << "i=UNREAD"<<i<<std::endl;
i = vtkImageData::New();
i->ShallowCopy(mUnreadableImage);
}
- // std::cout << "i="<<i<<std::endl;
return i;
}
//=====================================================================
void ImageReader::ReadAttributes(const std::string& filename,
std::map<std::string,std::string>& attr)
{
- // std::cout << "ImageReader::ReadDicomInfo '"<<filename<<"'"<<std::endl;
- // std::cout << "## ImageReader::Read("<<filename<<")"<<std::endl;
if (mLastFilename!=filename)
{
if (!CanRead(filename))
//=====================================================================
-
+ //=====================================================================
+ /// Pushes back all kwown extensions (without dot) in the vector given
+ void ImageReader::PushBackExtensions(std::vector<std::string>& v)
+ {
+ std::vector<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