genesisR.h

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/* This software and supporting documentation are distributed by
 *     Institut Federatif de Recherche 49
 *     CEA/NeuroSpin, Batiment 145,
 *     91191 Gif-sur-Yvette cedex
 *     France
 *
 * 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".
 *
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 * modify and redistribute granted by the license, users are provided only
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 * economic rights,  and the successive licensors  have only  limited
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 */
 
/*
 *  Data reader class
 */
 
#ifndef AIMS_IO_GENESISR_H
#define AIMS_IO_GENESISR_H
 
#include <aims/config/aimsdata_config.h>
#include <aims/io/defaultItemR.h>
#include <aims/io/genesisheader.h>
#include <aims/io/datatypecode.h>
#include <aims/data/data.h>
#include <cartobase/stream/directory.h>
#include <cartobase/stream/fileutil.h>
#include <cartobase/exception/file.h>
#include <cartobase/exception/format.h>
#include <soma-io/datasource/filedatasource.h>
 
namespace aims
{
 
  template<class T> class GenesisReader
  {
  public:
    GenesisReader( const std::string & name ) : _name( name ) {}
    ~GenesisReader() {}
 
    void read( AimsData<T> & thing, const carto::AllocatorContext & context, 
               carto::Object options );
 
  private:
    std::string         _name;
  };
 
  template <class T>
  inline GenesisReader<T> & 
  operator >> ( GenesisReader<T> & reader, AimsData<T> & thing )
  {
    reader.read( thing );
    return reader;
  }
 
  template <class T>
  inline
  void GenesisReader<T>::read( AimsData<T>& thing, 
                               const carto::AllocatorContext & context, 
                               carto::Object options )
  {
    GenesisHeader  *hdr = new GenesisHeader( _name );
    try
      {
        hdr->read();
      }
    catch( std::exception & e )
      {
        delete hdr;
        throw;
      }
 
    carto::DataTypeCode<T>        dtc;
    if( hdr->dataType() != dtc.dataType() )
      throw carto::datatype_format_error
        ( std::string( "data type / reader type mismatch : file is " ) 
          + hdr->dataType() + ", expecting " + dtc.dataType(), _name );
 
    int frame = -1, border = 0;
    options->getProperty( "frame", frame );
    options->getProperty( "border", border );
 
    int dimt;
    if( frame >= 0 )
      {
        if( frame >= hdr->dimT() )
          {
            delete hdr;
            throw std::domain_error( "frame higher than file dimT" );
          }
        dimt = 1;
      }
    else
      {
        dimt = hdr->dimT();
      }
 
    /*cout << "dimensions: " << hdr->dimX() << ", " << hdr->dimY() << ", " 
      << hdr->dimZ() << ", " << dimt << endl;*/
 
    carto::AllocatorContext 
      ac( context.accessMode(), 
          carto::rc_ptr<carto::DataSource>
          ( new carto::FileDataSource( _name, 0, carto::DataSource::Read ) ), 
          false, context.useFactor() );
 
    AimsData<T> data( hdr->dimX(), hdr->dimY(), hdr->dimZ(), dimt, 
                      border, ac );
 
    data.setSizeX( hdr->sizeX() );
    data.setSizeY( hdr->sizeY() );
    data.setSizeZ( hdr->sizeZ() );
    data.setSizeT( hdr->sizeT() );
    data.setHeader( hdr );
 
    // we must scandir to obtain a files list
 
    char        s = carto::FileUtil::separator();
    std::string::size_type      pos = _name.rfind( s );
    std::string dirname;
    if( pos == std::string::npos )
      dirname = ".";
    else
      dirname = _name.substr( 0, pos );
 
    carto::Directory                            dir( dirname );
    std::set<std::string>               names = dir.files();
    std::set<std::string>::iterator     in, en = names.end();
    std::string                         name;
    int                                 z, t, ss = 0, es = 0;
    std::vector<bool>                   reads( data.dimT() * data.dimZ() );
 
    z = data.dimZ();        // temp
    for( in=names.begin(); in!=en; ++in )
      {
        name = dirname + s + *in;
        //cout << "read " << name << endl;
        GenesisHeader      h( name );      // (re)read each header
 
    //std::cout << "read " << name << "(byte swapping: " << h.byteSwapping() << ")" << std::endl;
        try
          {
            h.read();
            std::ifstream       is( name.c_str(), 
                                    std::ios::in | std::ios::binary );
            if( !is )
              carto::io_error::launchErrnoExcept( name );
            is.unsetf( std::ios::skipws );
            is.seekg( h.dataOffset() );
            if( !is )
              carto::io_error::launchErrnoExcept( name );
            if( h.compressCode() != 1 )
              throw 
                carto::format_mismatch_error( "Genesis reader can't deal with "
                                              "compressed data", name );
            t = 0;      // temporarily
            h.getProperty( "slice", z );
            h.getProperty( "start_slice", ss );
            h.getProperty( "end_slice", es );
            z = abs(es - z);
            if( (z >= 0) && (z < data.dimZ()) /*&& (t >= 0) && (t < data.dimT())*/ ) //FR: unuseful checks
              {
                if( reads[ t*data.dimZ() + z ] )
                {
                  std::cerr << "warning: slice z=" << z << ", t=" << t 
                            << " already read" << std::endl;
                }
                else
                {
                  std::cerr << "........reading slice z=" << z << ", t=" << t << std::endl;
                  reads[ t*data.dimZ() + z ] = true;
                
                  DefaultItemReader<T>      ib1;
                  ItemReader<T>    *ir = ib1.reader( "binar", h.byteSwapping() );
                  for( int y=0; y<data.dimY(); ++y )  
                    ir->read( is, &data(0,y,z,t), data.dimX() );
 
                  delete ir;
                }
              }
          }
        catch( std::exception & )
          {
            std::cout << name << " not part of genesis volume\n";
          }
      }
 
    //cout << "read finished, checking if we've got all slices...\n";
    for( t=0; t<data.dimT(); ++t )
      for( z=0; z<data.dimZ(); ++z )
        if( !reads[ t*data.dimZ() + z ] )
          std::cerr << "warning: missing slice " << z << ", t=" << t 
                    << std::endl;
    thing = data;
  }
}
 
#endif