cmtkClassStreamStudyList.cxx

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/*
//
//  Copyright 1997-2009 Torsten Rohlfing
//
//  Copyright 2004-2010 SRI International
//
//  This file is part of the Computational Morphometry Toolkit.
//
//  http://www.nitrc.org/projects/cmtk/
//
//  The Computational Morphometry Toolkit is free software: you can
//  redistribute it and/or modify it under the terms of the GNU General Public
//  License as published by the Free Software Foundation, either version 3 of
//  the License, or (at your option) any later version.
//
//  The Computational Morphometry Toolkit is distributed in the hope that it
//  will be useful, but WITHOUT ANY WARRANTY; without even the implied
//  warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
//  GNU General Public License for more details.
//
//  You should have received a copy of the GNU General Public License along
//  with the Computational Morphometry Toolkit.  If not, see
//  <http://www.gnu.org/licenses/>.
//
//  $Revision: 2399 $
//
//  $LastChangedDate: 2010-10-05 15:39:13 -0700 (Tue, 05 Oct 2010) $
//
//  $LastChangedBy: torstenrohlfing $
//
*/

#include "cmtkClassStreamStudyList.h"

#include <System/cmtkMountPoints.h>

#include <IO/cmtkClassStream.h>
#include <IO/cmtkClassStreamAffineXform.h>

namespace
cmtk
{


StudyList* 
ClassStreamStudyList::Read
( const char *path )
{
  return Merge( new StudyList, path );
}

StudyList* 
ClassStreamStudyList::Merge
( const StudyList& studyList, const char *path )
{
  return Merge( new StudyList( studyList ), path );
}

StudyList* 
ClassStreamStudyList::Merge
( StudyList* const studyList, const char *path )
{
  ClassStream classStream( MountPoints::Translate( path ), "studylist", ClassStream::READ );
  if ( ! classStream.IsValid() ) 
    {
    return NULL;
    }
  
  StudyList *newStudyList = studyList;
  if ( ! newStudyList ) 
    newStudyList = new StudyList;
  
  while ( classStream.Seek ( "source" ) ) 
    {
    char *fileSystemPath = classStream.ReadString( "studyname", NULL );
    if ( fileSystemPath ) 
      {
      newStudyList->AddStudy( fileSystemPath );
      }
    }
  classStream.Close();
  
  classStream.Open( MountPoints::Translate( path ), "registration", ClassStream::READ );
  if ( ! classStream.IsValid() ) 
    {
    return newStudyList;
    }
  
  while ( classStream.Seek ( "registration" ) ) 
    {
    char *referenceStudy = classStream.ReadString( "reference_study", NULL );
    
    bool legacy = false;
    char *floatingStudy = classStream.ReadString( "floating_study", NULL );
    if ( !floatingStudy ) 
      {
      // check outdated "model_study" entry.
      floatingStudy = classStream.ReadString( "model_study", NULL );
      legacy = true;
      }
    
    if ( referenceStudy && floatingStudy ) 
      {
      AffineXform::SmartPtr affineXform;
      classStream >> affineXform;      

      affineXform->SetMetaInfo( META_XFORM_FIXED_IMAGE_PATH, referenceStudy );
      affineXform->SetMetaInfo( META_XFORM_MOVING_IMAGE_PATH, floatingStudy );
      
      WarpXform::SmartPtr warpXform;
      classStream.Get( warpXform, affineXform );
      
      warpXform->SetMetaInfo( META_XFORM_FIXED_IMAGE_PATH, referenceStudy );
      warpXform->SetMetaInfo( META_XFORM_MOVING_IMAGE_PATH, floatingStudy );
      
      AffineXform::SmartPtr inverse = affineXform->GetInverse();
      
      WarpXform::SmartPtr nullWarp( NULL );
      if ( !legacy )
        {
        newStudyList->AddXform( referenceStudy, floatingStudy, affineXform, warpXform );
        newStudyList->AddXform( floatingStudy, referenceStudy, inverse, nullWarp );
        } 
      else
        {
        newStudyList->AddXform( referenceStudy, floatingStudy, inverse, warpXform );
        newStudyList->AddXform( floatingStudy, referenceStudy, affineXform, nullWarp );
        }
      }
    }
  classStream.Close();
  
  return newStudyList;
}

void 
ClassStreamStudyList::Write
( const char *path, const StudyList* studyList )
{
  ClassStream stream;

  stream.Open( path, "studylist", ClassStream::WRITE );

  StudyList::const_iterator it = studyList->begin();
  while ( it != studyList->end() ) 
    {
    stream.Begin( "source" );
    stream.WriteString( "studyname", it->first->GetFileSystemPath() );
    stream.End();
    ++it;
    }
  
  stream.Close();
  
  stream.Open( path, "registration", ClassStream::WRITE );

  it = studyList->begin();
  while ( it != studyList->end() ) 
    {
    StudyToXform targetList = it->second;
    
    std::map<Study::SmartPtr,bool> seen;

    StudyToXform::const_iterator tit;
    for ( tit = targetList.begin(); tit != targetList.end(); ++tit ) 
      {
      if ( seen.find( tit->first ) == seen.end() )
        {
        seen[tit->first] = true;
        
        stream.Begin( "registration" );
        stream.WriteString( "reference_study", it->first->GetFileSystemPath() );
        stream.WriteString( "floating_study", tit->first->GetFileSystemPath() );
        
        StudyToXform::const_iterator tit2;
        for ( tit2 = targetList.begin(); tit2 != targetList.end(); ++tit2 ) 
          {
          if ( tit2->first == tit->first )
            {
            Xform::SmartPtr xform = tit2->second;
            
            AffineXform::SmartPtr affine = AffineXform::SmartPtr::DynamicCastFrom( xform );
            if ( affine )
              {
              stream << (*affine);
              }
            
            WarpXform::SmartPtr warp = WarpXform::SmartPtr::DynamicCastFrom( xform );
            if ( warp ) 
              {
              stream << warp;
              }
            }
          }
        stream.End();
        }
      }
    ++it;
    }
  
  stream.Close();
}

} // namespace cmtk