X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=src2%2FcreaImageIOImageReader.cpp;h=b1f9279e47a7412c525c21ba847a8abc6698ba3e;hb=96ca5a0d7b7ccd6b4291160c19afd48e3207db2a;hp=2480a47d921ebe5a19747a0b3c68bcf3c04ccadb;hpb=cbf693fa62cd51f4ca5c881838bbb609edc447b0;p=creaImageIO.git

diff --git a/src2/creaImageIOImageReader.cpp b/src2/creaImageIOImageReader.cpp
index 2480a47..b1f9279 100644
--- a/src2/creaImageIOImageReader.cpp
+++ b/src2/creaImageIOImageReader.cpp
@@ -1,8 +1,11 @@
 #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>
@@ -11,8 +14,6 @@
 #include <vtkMetaImageReader.h>
 //#include <vtkGESignalReader.h>
 
-#include <gdcmFile.h> 
-#include <vtkGdcmReader.h>
 
 
 #include "boost/filesystem/path.hpp"
@@ -20,331 +21,6 @@
 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;
-  };
-  //=====================================================================
- 
 
 
 
@@ -360,26 +36,17 @@ namespace creaImageIO
     //    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; 
@@ -404,12 +71,9 @@ namespace creaImageIO
   //=====================================================================
   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();
@@ -422,25 +86,21 @@ namespace creaImageIO
   //=====================================================================
 
   //=====================================================================
-  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) 
 	  {
@@ -455,29 +115,23 @@ namespace creaImageIO
 
   //=====================================================================
   // 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;
   }
   //=====================================================================
@@ -487,8 +141,6 @@ namespace creaImageIO
    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)) 
@@ -501,5 +153,16 @@ namespace creaImageIO
   //=====================================================================
 
 
-
+  //=====================================================================
+  /// 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