reader_d.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".
 *
 * 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.
 *
 * In this respect, the user's attention is drawn to the risks associated
 * with loading,  using,  modifying and/or developing or reproducing the
 * software by the user in light of its specific status of free software,
 * that may mean  that it is complicated to manipulate,  and  that  also
 * therefore means  that it is reserved for developers  and  experienced
 * professionals having in-depth computer knowledge. Users are therefore
 * encouraged to load and test the software's suitability as regards their
 * requirements in conditions enabling the security of their systems and/or
 * data to be ensured and,  more generally, to use and operate it in the
 * same conditions as regards security.
 *
 * 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.
 */
 
#ifndef AIMS_IO_READER_D_H
#define AIMS_IO_READER_D_H
 
#include <aims/io/reader.h>
#include <aims/io/fileFormat.h>
#include <aims/def/settings.h>
#include <aims/io/finder.h>
#include <cartobase/type/string_conversion.h>
#include <cartobase/exception/ioexcept.h>
#include <cartobase/stream/fileutil.h>
#include <set>
#include <soma-io/io/reader.h>
#include <soma-io/io/formatdictionary.h>
 
#define localMsg( message ) cartoCondMsg( 4, message, "AIMS::READER" )
 
#define AIMS_INSTANTIATE_READER( T ) \
  namespace aims { \
    template class aims::Reader< T >; \
  } \
  namespace soma { \
    template class soma::FormatDictionary< T >; \
    template class soma::Reader< T >; \
  }
#define AIMS_INSTANTIATE_AIMS_READER( T ) \
  namespace aims { \
    template class aims::Reader< T >; \
  }
 
 
namespace aims
{
 
  template<class T> Reader<T>::Reader()
    : _mode( carto::AllocatorStrategy::Memory )
  {
  }
 
  template<class T> Reader<T>::Reader( const std::string& filename )
    : _filename( filename ), _mode( carto::AllocatorStrategy::Memory )
  {
  }
 
 
  template<class T>
  void Reader<T>::setMode( carto::AllocatorStrategy::MappingMode mode )
  {
    _mode = mode;
    // compatibility with new AllocatorContext
    switch( mode )
      {
      case carto::AllocatorStrategy::Memory:
      case carto::AllocatorStrategy::MAP:
      case carto::AllocatorStrategy::CopyMap:
        _alloccontext.setAccessMode( carto::AllocatorStrategy::InternalModif );
        break;
      case carto::AllocatorStrategy::ReadOnlyMap:
        _alloccontext.setAccessMode( carto::AllocatorStrategy::ReadOnly );
        break;
      case carto::AllocatorStrategy::ReadWriteMap:
        _alloccontext.setAccessMode( carto::AllocatorStrategy::ReadWrite );
        break;
      case carto::AllocatorStrategy::Unallocated:
        _alloccontext.setAccessMode( carto::AllocatorStrategy::NotOwner );
        break;
      default:
        _alloccontext.setAccessMode( carto::AllocatorStrategy::InternalModif );
        break;
      }
  }
 
  template <typename T>
  void Reader<T>::setAllocatorContext( const carto::AllocatorContext & ac )
  {
    _alloccontext = ac;
  }
 
  template <typename T>
  const carto::AllocatorContext & Reader<T>::allocatorContext() const
  {
    return _alloccontext;
  }
 
  template<class T>
  void Reader<T>::setFileName( const std::string &fileName )
  {
    _filename = fileName;
  }
 
  template<class T>
  void Reader<T>::setOptions( carto::Object options )
  {
    _options = options;
  }
 
  template<class T>
  carto::Object Reader<T>::options() const
  {
    return _options;
  }
 
  template<class T>
  carto::Object & Reader<T>::options()
  {
    return _options;
  }
 
  template<class T>
  bool Reader<T>::read( T & obj, int border, const std::string* format, 
                        int frame )
  {
#ifdef AIMS_DEBUG_IO
    localMsg("void Reader<" + carto::DataTypeCode<T>::name() + ">::read( obj )");
#endif
 
    carto::Object read_options = carto::Object::value( carto::PropertySet() );
      
    // Copy aims settings to read options
    read_options->copyProperties(
      carto::Object::reference( 
        Settings::settings().getValue() ) );
 
    // take care of old-style options
    if( !_options.get() )
      _options = carto::Object::value( carto::PropertySet() );
    if( frame >= 0 )
      {
        _options->setProperty( "frame", frame );
        // (for graphs)
        _options->setProperty( "subobjectsfilter", frame );
      }
    if( border > 0 )
      _options->setProperty( "border", border );
 
    std::string _format;
    if( !format )
    {
      try
      {
        carto::Object oformat = _options->getProperty( "format" );
        _format = oformat->getString();
        format = &_format;
      }
      catch( ... )
      {
      }
    }
    else
      _options->setProperty( "format", *format );
 
    // update read options using reader object options
    read_options->copyProperties(_options);
    
    // try first soma-io reader (since 2013)
    // try first 3 passes
    try
    {
      // building uri
      std::string uri = _filename;
      if( border != 0 || frame != -1 )
        uri += "?";
      if( border != 0 )
        uri += ( "border=" + carto::toString( border ) );
      if( border != 0 && frame != -1 )
        uri += "&";
      if ( frame != -1 )
        uri += ( "ot=" + carto::toString( frame ) + "&st=1" );
 
      soma::Reader<T> reader( uri );
      // set conversion option to invoque Carto2AimsHeaderTranslator
      carto::Object options = read_options;
      if( options.isNull() )
        options = carto::Object::value( carto::Dictionary() );
      options->setProperty( "convert_to_aims", true );
      reader.setOptions( options );
      reader.setAllocatorContext( allocatorContext() );
      const carto::Object & n = carto::none();
#ifdef AIMS_DEBUG_IO
    localMsg("0. Try soma::Reader ...") ;
#endif
      return reader.read( obj, n, 1, 3 );
    }
#ifdef AIMS_DEBUG_IO
    catch( std::exception & e )
    {
      localMsg("0. soma::Reader failed: " + carto::toString(e.what()));
    }
#else
    catch( ... ) {}
#endif
 
    // if it failed, continue with aims reader.
 
    std::set<std::string>               tried;
    std::set<FileFormat<T> *>           triedf;
    FileFormat<T>                       *reader;
    std::set<std::string>::iterator     notyet = tried.end();
    typename std::set<FileFormat<T> *>::iterator        notyetf = triedf.end();
    int                                 excp = 0;
    int                                 exct = -1;
    std::string                         excm;
 
    // parse/split query-string part or URI
    std::string filename = carto::FileUtil::uriFilename( _filename );
    carto::Object uri_opt = carto::FileUtil::uriOptions( _filename );
    if( uri_opt )
    {
      if( read_options.isNull() )
        read_options = carto::Object::value( carto::Dictionary() );
      read_options->copyProperties( uri_opt );
    }
 
    if( format )        // priority to format hint
    {
      reader = FileFormatDictionary<T>::fileFormat( *format );
      if( reader )
      {
        try
        {
#ifdef AIMS_DEBUG_IO
          localMsg("1. try reader " + *format);
#endif
          if( reader->read( filename, obj, _alloccontext, read_options ) )
          {
#ifdef AIMS_DEBUG_IO
            localMsg("1. " + *format + " OK");
#endif
            carto::Object h = carto::getObjectHeader( obj );
            if( h )
              Finder::postProcessHeader( h );
            return true;
          }
        }
        catch( std::exception & e )
        {
#ifdef AIMS_DEBUG_IO
          localMsg("1. failed: " + carto::toString(e.what()));
#endif
          carto::io_error::keepExceptionPriority( e, excp, exct, excm,
                                                  5 );
        }
        tried.insert( *format );
        triedf.insert( reader );
      }
    }
 
    std::string                bname = carto::FileUtil::basename( filename );
    std::string::size_type     pos = bname.find( '.' );
    std::string::size_type     dlen = filename.length() - bname.length();
    std::string                ext;
 
    if( pos != std::string::npos )
      ext = filename.substr( dlen+pos+1, filename.length() - pos - 1 );
 
    const std::map<std::string, std::list<std::string> >        & extensions
      = FileFormatDictionary<T>::extensions();
 
    std::map<std::string, std::list<std::string> >::const_iterator iext
        = extensions.find( ext ),
    eext = extensions.end();
    std::list<std::string>::const_iterator ie, ee;
 
    while( iext == eext && (pos=bname.find( '.', pos+1 ))!=std::string::npos )
    {
      ext = filename.substr( dlen+pos+1, filename.length() - pos - 1 );
      iext = extensions.find( ext );
    }
 
    // try every matching format until one works
    if( iext != eext )
      for( ie=iext->second.begin(), ee=iext->second.end(); ie!=ee; ++ie )
        if( tried.find( *ie ) == notyet )
        {
          reader = FileFormatDictionary<T>::fileFormat( *ie );
          if( reader && triedf.find( reader ) == notyetf )
          {
            try
            {
#ifdef AIMS_DEBUG_IO
              localMsg("2. try reader " + *ie);
#endif
              if( reader->read( filename, obj, _alloccontext, read_options ) )
              {
#ifdef AIMS_DEBUG_IO
                localMsg("2. " + *ie + " OK");
#endif
                carto::Object h = carto::getObjectHeader( obj );
                if( h )
                  Finder::postProcessHeader( h );
                return true;
              }
            }
            catch( std::exception & e )
            {
#ifdef AIMS_DEBUG_IO
              localMsg("2. failed: " + carto::toString(e.what()));
#endif
              carto::io_error::keepExceptionPriority( e, excp, exct,
                                                      excm );
            }
#ifdef AIMS_DEBUG_IO
            localMsg("2. unsuccessfully tried " + *ie);
#endif
            tried.insert( *ie );
            triedf.insert( reader );
          }
        }
 
    if( !ext.empty() )
    {
      // not found or none works: try readers with no extension
      iext = extensions.find( "" );
 
      if( iext != eext )
        for( ie=iext->second.begin(), ee=iext->second.end(); ie!=ee; ++ie )
          if( tried.find( *ie ) == notyet )
          {
            reader = FileFormatDictionary<T>::fileFormat( *ie );
            if( reader && triedf.find( reader ) == notyetf )
            {
              try
              {
#ifdef AIMS_DEBUG_IO
                localMsg("3. try reader " + *ie);
#endif
                if( reader->read( filename, obj, _alloccontext, read_options ) )
                {
#ifdef AIMS_DEBUG_IO
                  localMsg("3. " + *ie + " OK");
#endif
                  carto::Object h = carto::getObjectHeader( obj );
                  if( h )
                    Finder::postProcessHeader( h );
                  return true;
                }
              }
              catch( std::exception & e )
              {
#ifdef AIMS_DEBUG_IO
                localMsg("3. failed: " + carto::toString(e.what()));
#endif
                carto::io_error::keepExceptionPriority( e, excp, exct,
                                                        excm );
              }
              tried.insert( *ie );
              triedf.insert( reader );
            }
          }
      }
 
    // still not found ? well, try EVERY format this time...
    for( iext=extensions.begin(); iext!=eext; ++iext )
      for( ie=iext->second.begin(), ee=iext->second.end(); ie!=ee; ++ie )
        if( tried.find( *ie ) == notyet )
        {
          reader = FileFormatDictionary<T>::fileFormat( *ie );
          if( reader && triedf.find( reader ) == notyetf )
          {
            try
            {
#ifdef AIMS_DEBUG_IO
              localMsg("4. try reader " + *ie);
#endif
              if( reader->read( filename, obj, _alloccontext, read_options ) )
              {
#ifdef AIMS_DEBUG_IO
                localMsg("4. " + *ie + " OK");
#endif
                carto::Object h = carto::getObjectHeader( obj );
                if( h )
                  Finder::postProcessHeader( h );
                return true;
              }
            }
            catch( std::exception & e )
            {
#ifdef AIMS_DEBUG_IO
              localMsg("4. failed: " + carto::toString(e.what()));
#endif
              carto::io_error::keepExceptionPriority( e, excp, exct,
                                                      excm );
            }
            tried.insert( *ie );
            triedf.insert( reader );
          }
        }
 
    // try first soma-io reader (since 2013)
    // try pass 4
    try
    {
      // building uri
      std::string uri = filename;
      if( border != 0 || frame != -1 )
        uri += "?";
      if( border != 0 )
        uri += ( "border=" + carto::toString( border ) );
      if( border != 0 && frame != -1 )
        uri += "&";
      if ( frame != -1 )
        uri += ( "ot=" + carto::toString( frame ) + "&st=1" );
 
      soma::Reader<T> reader( uri );
      reader.setOptions( read_options );
      const carto::Object & n = carto::none();
      return reader.read( obj, n, 4, 4 );
    } catch( ... ) {}
    // if it failed, it's hopeless.
 
    // still not succeeded, it's hopeless...
    carto::io_error::launchExcept( exct, excm, 
                                   filename + " : no matching format" );
    return( false );
  }
 
 
  template<class T>
  T* Reader<T>::read( int border, const std::string* format, int frame )
  {
#ifdef AIMS_DEBUG_IO
    localMsg(carto::DataTypeCode<T>::name() + "* Reader<"
      + carto::DataTypeCode<T>::name() + ">::read()");
#endif
 
    carto::Object read_options = carto::Object::value( carto::PropertySet() );
      
    // Copy aims settings to read options
    read_options->copyProperties(
      carto::Object::reference( 
        Settings::settings().getValue() ) );
    
    // take care of old-style options
    if( !_options.get() )
      _options = carto::Object::value( carto::PropertySet() );
    if( frame >= 0 )
      {
        _options->setProperty( "frame", frame );
        // (for graphs)
        _options->setProperty( "subobjectsfilter", frame );
      }
    if( border > 0 )
      _options->setProperty( "border", border );
 
    std::string _format;
    if( !format )
    {
      try
      {
        carto::Object oformat = _options->getProperty( "format" );
        _format = oformat->getString();
        format = &_format;
      }
      catch( ... )
      {
      }
    }
    else
      _options->setProperty( "format", *format );
 
    // update read options using reader object options
    read_options->copyProperties(_options);
    
    // try first soma-io reader (since 2013)
    // try first 3 passes
    try
    {
      // building uri
      std::string uri = _filename;
      if( border != 0 || frame != -1 )
        uri += "?";
      if( border != 0 )
        uri += ( "border=" + carto::toString( border ) );
      if( border != 0 && frame != -1 )
        uri += "&";
      if ( frame != -1 )
        uri += ( "ot=" + carto::toString( frame ) + "&st=1" );
 
#ifdef AIMS_DEBUG_IO
    localMsg("building soma::Reader using uri: " + uri);
#endif
      soma::Reader<T> reader( uri );
      // set conversion option to invoque Carto2AimsHeaderTranslator
      carto::Object options = read_options;
      if( options.isNull() )
        options = carto::Object::value( carto::Dictionary() );
      options->setProperty( "convert_to_aims", true );
      reader.setOptions( options );
      reader.setAllocatorContext( allocatorContext() );
#ifdef AIMS_DEBUG_IO
    localMsg("0. Try soma::Reader ...");
#endif
      return reader.read( carto::none(), 1, 3 );
    }
#ifdef AIMS_DEBUG_IO
    catch( std::exception & e )
    {
      localMsg("0. soma::Reader failed: " + carto::toString(e.what()));
    }
#else
    catch( ... ) {}
#endif
 
    // if it failed, continue with aims reader.
 
    std::set<std::string>               tried;
    std::set<FileFormat<T> *>           triedf;
    FileFormat<T>                       *reader;
    std::set<std::string>::iterator     notyet = tried.end();
    typename std::set<FileFormat<T> *>::iterator        notyetf = triedf.end();
    T                                   *obj;
    int                                 excp = 0;
    int                                 exct = -1;
    std::string                         excm;
 
    // parse/split query-string part or URI
    std::string filename = carto::FileUtil::uriFilename( _filename );
    carto::Object uri_opt = carto::FileUtil::uriOptions( _filename );
    if( uri_opt )
    {
      if( read_options.isNull() )
        read_options = carto::Object::value( carto::Dictionary() );
      read_options->copyProperties( uri_opt );
    }
 
    if( format )        // priority to format hint
    {
      reader = FileFormatDictionary<T>::fileFormat( *format );
      if( reader )
      {
        try
        {
#ifdef AIMS_DEBUG_IO
          localMsg("1. try reader " + *format);
#endif
          obj = reader->read( filename, _alloccontext, read_options );
          if( obj )
          {
#ifdef AIMS_DEBUG_IO
            localMsg("1. " + *format + " OK");
#endif
            carto::Object h = carto::getObjectHeader( obj );
            if( h )
              Finder::postProcessHeader( h );
            return( obj );
          }
        }
        catch( std::exception & e )
        {
#ifdef AIMS_DEBUG_IO
          localMsg("1. failed: " + carto::toString(e.what()));
#endif
          carto::io_error::keepExceptionPriority( e, excp, exct, excm,
                                                  5 );
        }
        tried.insert( *format );
        triedf.insert( reader );
      }
    }
 
    std::string ext = carto::FileUtil::extension( filename );
 
    const std::map<std::string, std::list<std::string> >        & extensions
        = FileFormatDictionary<T>::extensions();
 
    std::map<std::string, std::list<std::string> >::const_iterator iext
        = extensions.find( ext ),
    eext = extensions.end();
    std::list<std::string>::const_iterator ie, ee;
 
    // try every matching format until one works
    if( iext != eext )
      for( ie=iext->second.begin(), ee=iext->second.end(); ie!=ee; ++ie )
        if( tried.find( *ie ) == notyet )
        {
          reader = FileFormatDictionary<T>::fileFormat( *ie );
          if( reader && triedf.find( reader ) == notyetf )
          {
            try
            {
#ifdef AIMS_DEBUG_IO
              localMsg("2. try reader " + *ie);
#endif
              obj = reader->read( filename, _alloccontext, read_options );
              if( obj )
              {
#ifdef AIMS_DEBUG_IO
                localMsg("2. " + *ie + " OK");
#endif
                carto::Object h = carto::getObjectHeader( obj );
                if( h )
                  Finder::postProcessHeader( h );
                return( obj );
              }
            }
            catch( std::exception & e )
            {
#ifdef AIMS_DEBUG_IO
              localMsg("2. failed: " + carto::toString(e.what()));
#endif
              carto::io_error::keepExceptionPriority( e, excp, exct,
                                                      excm );
            }
#ifdef AIMS_DEBUG_IO
            localMsg("2. unsuccessfully tried " + *ie);
#endif
            tried.insert( *ie );
            triedf.insert( reader );
          }
        }
 
    if( !ext.empty() )
    {
      // not found or none works: try readers with no extension
      iext = extensions.find( "" );
 
      if( iext != eext )
        for( ie=iext->second.begin(), ee=iext->second.end(); ie!=ee; ++ie )
          if( tried.find( *ie ) == notyet )
          {
            reader = FileFormatDictionary<T>::fileFormat( *ie );
            if( reader && triedf.find( reader ) == notyetf )
            {
              try
              {
#ifdef AIMS_DEBUG_IO
                localMsg("3. try reader " + *ie);
#endif
                obj = reader->read( filename, _alloccontext, read_options );
                if( obj )
                {
#ifdef AIMS_DEBUG_IO
                  localMsg("3. " + *ie + " OK");
#endif
                  carto::Object h = carto::getObjectHeader( obj );
                  if( h )
                    Finder::postProcessHeader( h );
                  return( obj );
                }
              }
              catch( std::exception & e )
              {
#ifdef AIMS_DEBUG_IO
                localMsg("3. failed: " + carto::toString(e.what()));
#endif
                carto::io_error::keepExceptionPriority( e, excp, exct,
                                                        excm );
              }
              tried.insert( *ie );
              triedf.insert( reader );
            }
          }
    }
 
    // still not found ? well, try EVERY format this time...
    for( iext=extensions.begin(); iext!=eext; ++iext )
      for( ie=iext->second.begin(), ee=iext->second.end(); ie!=ee; ++ie )
        if( tried.find( *ie ) == notyet )
        {
          reader = FileFormatDictionary<T>::fileFormat( *ie );
          if( reader && triedf.find( reader ) == notyetf )
          {
            try
            {
#ifdef AIMS_DEBUG_IO
              localMsg("4. try reader " + *ie);
#endif
              obj = reader->read( filename, _alloccontext, read_options );
              if( obj )
              {
#ifdef AIMS_DEBUG_IO
                localMsg("4. " + *ie + " OK");
#endif
                carto::Object h = carto::getObjectHeader( obj );
                if( h )
                  Finder::postProcessHeader( h );
                return( obj );
              }
            }
            catch( std::exception & e )
            {
#ifdef AIMS_DEBUG_IO
              localMsg("4. failed: " + carto::toString(e.what()));
#endif
              carto::io_error::keepExceptionPriority( e, excp, exct,
                                                      excm );
            }
            tried.insert( *ie );
            triedf.insert( reader );
          }
        }
 
    // try first soma-io reader (since 2013)
    // try pass 4
    try
    {
      // building uri
      std::string uri = filename;
      if( border != 0 || frame != -1 )
        uri += "?";
      if( border != 0 )
        uri += ( "border=" + carto::toString( border ) );
      if( border != 0 && frame != -1 )
        uri += "&";
      if ( frame != -1 )
        uri += ( "ot=" + carto::toString( frame ) + "&st=1" );
 
      soma::Reader<T> reader( uri );
      reader.setOptions( read_options );
      return reader.read( carto::none(), 4, 4 );
    } catch( ... ) {}
    // if it failed, it's hopeless
 
    // still not succeeded, it's hopeless...
    carto::io_error::launchExcept( exct, excm, 
                                   filename + " : no matching format" );
    return( 0 );
  }
 
}
 
 
#undef localMsg
 
#endif