Concrete image reader for ultrasonix 'rf' files. More...

#include <creaImageIOUltrasonixImageReader.h>

Inheritance diagram for creaImageIO::UltrasonixImageReader:

Collaboration diagram for creaImageIO::UltrasonixImageReader:

Public Member Functions
	UltrasonixImageReader ()

virtual	~UltrasonixImageReader ()

virtual void	PushBackExtensions (std::vector< std::string > &)
	Add file extensions read by the reader. More...

virtual bool	CanRead (const std::string &filename)
	Test if file is read by this reader. More...

virtual vtkImageData *	ReadImage (const std::string &filename)
	return for a file a 2D VTkImage More...

virtual void	ReadAttributes (const std::string &filename, tree::AttributeMapType &attr)
	Read the attributes for a file. More...

virtual void	getAttributes (const std::string filename, std::map< std::string, std::string > &infos, std::vector< std::string > i_attr)
	Another function to read attributes for a file. More...

const std::string &	GetName () const
	Get the reader's name. More...

Protected Member Functions
void	SetName (const std::string &s)
	Set the reader's name. More...

Detailed Description

Concrete image reader for ultrasonix 'rf' files.

Definition at line 43 of file creaImageIOUltrasonixImageReader.h.

Constructor & Destructor Documentation

creaImageIO::UltrasonixImageReader::UltrasonixImageReader ( )

Definition at line 47 of file creaImageIOUltrasonixImageReader.cpp.

References creaImageIO::AbstractImageReader::SetName().

   {
     SetName("Ultrasonix");
   }

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creaImageIO::UltrasonixImageReader::~UltrasonixImageReader ( )

virtual

Definition at line 54 of file creaImageIOUltrasonixImageReader.cpp.

55 {

56 }

Member Function Documentation

bool creaImageIO::UltrasonixImageReader::CanRead ( const std::string & filename )

virtual

Test if file is read by this reader.

Reimplemented from creaImageIO::AbstractImageReader.

Definition at line 88 of file creaImageIOUltrasonixImageReader.cpp.

References creaImageIO::Ultrasonix_header::frame, HEADER_SIZE, creaImageIO::Ultrasonix_header::height, creaImageIO::ReadHeader(), creaImageIO::Ultrasonix_header::type, TYPE_B32, TYPE_RF, and creaImageIO::Ultrasonix_header::width.

   { 
     long size = -1;
     bool ok = false;
     FILE *Ultrasonix_file=fopen(filename.c_str(), "rb");
     if (Ultrasonix_file) 
     {
         Ultrasonix_header h;
         if (!ReadHeader(Ultrasonix_file, h) )
         {
                 fclose(Ultrasonix_file);
                 std::cout << "cannot read Ultrasonix header for file [" << filename << "]" << std::endl;                                
                 return false;   
         }
 
         fseek(Ultrasonix_file,0,SEEK_END);              // go to end of file
         if (h.type == TYPE_RF)
                 size = (ftell(Ultrasonix_file) - (HEADER_SIZE+h.frame) * sizeof(int)) / sizeof(short);
         else if (h.type == 1)//TYPE_B8)
                 size = (ftell(Ultrasonix_file) - (HEADER_SIZE+h.frame+4) *  sizeof(int)) / sizeof(char);
         else if (h.type == TYPE_B32)
                 size = (ftell(Ultrasonix_file) - HEADER_SIZE * sizeof(int)) / sizeof(int);
 
         // check if the data size corresponds to the dimensions of the images
         if (size == h.width * h.height * h.frame )
                 ok = true;
 
         fclose(Ultrasonix_file);
     }
     return ok;
   }

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void creaImageIO::UltrasonixImageReader::getAttributes	(	const std::string	filename,
		std::map< std::string, std::string > &	infos,
		std::vector< std::string >	i_attr
	)

virtual

Another function to read attributes for a file.

Reimplemented from creaImageIO::AbstractImageReader.

Definition at line 120 of file creaImageIOUltrasonixImageReader.cpp.

   {
           //TO DO
   }

const std::string& creaImageIO::AbstractImageReader::GetName ( ) const

inlineinherited

Get the reader's name.

Definition at line 56 of file creaImageIOAbstractImageReader.h.

References creaImageIO::AbstractImageReader::mName.

Referenced by creaImageIO::VtkImageReader::ReadImage().

56 { return mName; }

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void creaImageIO::UltrasonixImageReader::PushBackExtensions ( std::vector< std::string > & v )

virtual

Add file extensions read by the reader.

Reimplemented from creaImageIO::AbstractImageReader.

Definition at line 213 of file creaImageIOUltrasonixImageReader.cpp.

   {
     v.push_back("Ultrasonix");
   }

void creaImageIO::UltrasonixImageReader::ReadAttributes	(	const std::string &	filename,
		tree::AttributeMapType &	attr
	)

virtual

Read the attributes for a file.

Reimplemented from creaImageIO::AbstractImageReader.

Definition at line 222 of file creaImageIOUltrasonixImageReader.cpp.

References creaImageIO::Ultrasonix_header::frame, creaImageIO::Ultrasonix_header::frequency, GimmickMessage, creaImageIO::Ultrasonix_header::height, creaImageIO::ReadHeader(), creaImageIO::Ultrasonix_header::samplingRate, and creaImageIO::Ultrasonix_header::width.

  {
     GimmickMessage(2,"Reading attributes from '" << filename << std::endl);
 
     FILE *Ultrasonix_file = fopen(filename.c_str(), "rb");
     if (!Ultrasonix_file)
     {
         std::cout << "cannot open RF file [" << filename << "]" << std::endl;
         return;
     }
 
     Ultrasonix_header h;
     if (!ReadHeader(Ultrasonix_file, h)) 
     {
         fclose(Ultrasonix_file);
         std::cout << "cannot read Ultrasonix Attributes for RF file [" << filename << "]" << std::endl;  
         return;
     }
 
     fclose(Ultrasonix_file);  
   
     // Columns
     char cols[128];
     sprintf(cols,"%i", h.width);
     // Rows
     char rows[128];
     sprintf(rows,"%i", h.height);
     // Planes 
     char planes[128];
     sprintf(planes,"%i", h.frame);
     // Sampling frequency
     char samplingFrequency[128];
     sprintf(samplingFrequency,"%i", h.samplingRate);
     // Transducer frequency
     char transducerFrequency[128];
     sprintf(transducerFrequency,"%i", h.frequency);
    
     // 
     std::map<std::string,std::string>::iterator i;
     if ( (i = attr.find("FullFileName")) != attr.end())
     {
            i->second = filename;
     }
     if ( (i = attr.find("D0004_1500")) != attr.end())
     {
            boost::filesystem::path full_path(filename);
            std::string f = full_path.leaf().string();
            i->second = f;
     }
     if ( (i = attr.find("D0028_0010")) != attr.end())
     {
            i->second = rows;
     }
     if ( (i = attr.find("D0028_0011")) != attr.end())
     {
            i->second = cols;
     }
     if ( (i = attr.find("D0028_0012")) != attr.end())
     {
            i->second = planes;
     }
     if ( (i = attr.find("D003a_001a")) != attr.end())
     {
        i->second = samplingFrequency;
     }
     if ( (i = attr.find("D0018_6030")) != attr.end())
     {
            i->second = transducerFrequency;
     }
     
     GimmickMessage(2,"Attributes map:"<<std::endl<<attr<<std::endl);
     return;
 }

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vtkImageData * creaImageIO::UltrasonixImageReader::ReadImage ( const std::string & filename )

virtual

return for a file a 2D VTkImage

Reimplemented from creaImageIO::AbstractImageReader.

Definition at line 127 of file creaImageIOUltrasonixImageReader.cpp.

References creaImageIO::Ultrasonix_header::frame, creaImageIO::Ultrasonix_header::height, creaImageIO::ReadHeader(), creaImageIO::Ultrasonix_header::type, TYPE_B32, TYPE_B8, TYPE_RF, and creaImageIO::Ultrasonix_header::width.

   {
     FILE *Ultrasonix_file=fopen(filename.c_str(),"rb");
     if (!Ultrasonix_file) 
     {
         std::cout << "cannot open file [" << filename << "]" << std::endl;
         return 0;
     }
     Ultrasonix_header h;
     if (!ReadHeader(Ultrasonix_file,h)) 
     {
         std::cout << "cannot read Ultrasonix header for file [" << filename << "]" << std::endl;
         fclose(Ultrasonix_file);  
         return 0;
     }
 
     long frame_size = h.height   * h.width;      
     long im_size    = frame_size * h.frame;
 
     short *dataRF,  *ptrRF;
     char  *dataB8,  *ptrB8;
     int   *dataB32, *ptrB32;
     vtkImageData* im;
     int temp;
 
     switch (h.type)
     {
         case TYPE_RF:
                 dataRF = (short*)malloc(sizeof(short)*im_size);
                 ptrRF  = dataRF;
 
                 for (int k=0; k<h.frame; k++)
                 {
                         int frame_number;
                         fread(&frame_number, sizeof(int), 1, Ultrasonix_file);
                         fread(ptrRF,sizeof(short), frame_size, Ultrasonix_file);
                         ptrRF += frame_size;
                 }
                 fclose(Ultrasonix_file);  
 
                 im = crea::NewVtkImageDataFromRaw( dataRF, h.width, h.height, h.frame);
         break;
 
         case TYPE_B8:
                 dataB8 = (char*)malloc(sizeof(char)*im_size);
                 ptrB8  = dataB8;
                 for (int k=0; k<h.frame; k++)
                 {
                         fread(ptrB8,sizeof(char), frame_size, Ultrasonix_file);
                         ptrB8 += frame_size;
                 }
                 // in mode b frames width and height are inverted
                 temp     = h.width;
                 h.width  = h.height;
                 h.height = temp;
 
                 fclose(Ultrasonix_file);  
 
         im = crea::NewVtkImageDataFromRaw( dataB8, h.width, h.height, h.frame);
         break;
 
         case TYPE_B32:
                 dataB32 = (int*)malloc(sizeof(int)*im_size);
                 ptrB32  = dataB32;
                 for (int k=0; k<h.frame; k++)
                 {
                         fread(ptrB32, sizeof(int), frame_size, Ultrasonix_file);
                         ptrB32 += frame_size;
                 }
                 // in B mode frames width and height are inverted
                 temp     = h.width;
                 h.width  = h.height;
                 h.height = temp;
 
                 fclose(Ultrasonix_file);  
 
                 im = crea::NewVtkImageDataFromRaw( dataB32, h.width, h.height, h.frame);
         break;
     }
 
     return im;
 }

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void creaImageIO::AbstractImageReader::SetName ( const std::string & s )

inlineprotectedinherited

Set the reader's name.

Definition at line 79 of file creaImageIOAbstractImageReader.h.

References creaImageIO::AbstractImageReader::mName.

Referenced by creaImageIO::DicomImageReader::DicomImageReader(), UltrasonixImageReader(), and creaImageIO::VtkImageReader::VtkImageReader().

79 { mName = s; }

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The documentation for this class was generated from the following files:

/home/davila/Creatis/All/creatools_source/creaImageIO/src/creaImageIOUltrasonixImageReader.h
/home/davila/Creatis/All/creatools_source/creaImageIO/src/creaImageIOUltrasonixImageReader.cpp

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation