cmtkTypedStreamStudylist.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: 2584 $
//
//  $LastChangedDate: 2010-12-02 14:37:48 -0800 (Thu, 02 Dec 2010) $
//
//  $LastChangedBy: torstenrohlfing $
//
*/

#include "cmtkTypedStreamStudylist.h"

#include <Base/cmtkTypes.h>

#include <System/cmtkConsole.h>
#include <System/cmtkStrUtility.h>
#include <System/cmtkConsole.h>
#include <System/cmtkCompressedStream.h>
#include <System/cmtkMountPoints.h>

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

namespace
cmtk
{


TypedStreamStudylist::TypedStreamStudylist()
{
  this->Clear();
}

void TypedStreamStudylist::Clear()
{
  StudyPath[0] = StudyPath[1] = NULL;
  ReferenceStudyIndex = 0;
  this->m_AffineXform = AffineXform::SmartPtr( NULL );
  this->m_WarpXform = WarpXform::SmartPtr( NULL );
}

TypedStreamStudylist::~TypedStreamStudylist()
{
  if ( StudyPath[0] ) free( StudyPath[0] );
  if ( StudyPath[1] ) free( StudyPath[1] );
}

bool
TypedStreamStudylist::Read( const char *studylistpath )
{
  char archive[PATH_MAX];

  snprintf( archive, sizeof( archive ), "%s/studylist", MountPoints::Translate( studylistpath ) );
  ClassStream classStream( archive, ClassStream::READ );
  if ( ! classStream.IsValid() ) 
    {
    StdErr.printf( "Could not open studylist archive %s.\n", archive );
    return false;
    }
  
  if ( StudyPath[0] ) free( StudyPath[0] );
  classStream.Seek ( "source" );
  StudyPath[0] = classStream.ReadString( "studyname", "<unknown>" );
  
  if ( StudyPath[1] ) free( StudyPath[1] );
  classStream.Seek ( "source" );
  StudyPath[1] = classStream.ReadString( "studyname", "<unknown>" );
  classStream.Close();
  
  snprintf( archive, sizeof( archive ), "%s/registration", MountPoints::Translate(studylistpath) );
  classStream.Open( archive, ClassStream::READ );
  if ( ! classStream.IsValid() ) 
    {
    StdErr.printf( "Could not open studylist archive %s.\n", archive );
    return false;
    }
  
  classStream.Seek ( "registration" );
  char *referenceStudy = classStream.ReadString( "reference_study" );
  ReferenceStudyIndex = ( StrCmp( referenceStudy, StudyPath[0] ) ) ? 1 : 0;

  bool legacy = false;
  char *floatingStudy = classStream.ReadString( "floating_study" );
  if ( !floatingStudy )
    {
    classStream.Begin();
    floatingStudy = classStream.ReadString( "model_study" );
    if ( floatingStudy )
      {
      legacy = true;
      }
    else
      {
      StdErr.printf( "WARNING: Studylist %s/registration apparently has neither new 'floating_study' nor old 'model_study' entry\n", archive );
      }
    }
  
  classStream >> this->m_AffineXform;

  if ( referenceStudy )
    {
    this->m_AffineXform->SetMetaInfo( META_XFORM_FIXED_IMAGE_PATH, referenceStudy );
    }
  if ( floatingStudy )
    {
    this->m_AffineXform->SetMetaInfo( META_XFORM_MOVING_IMAGE_PATH, floatingStudy );
    }

  if ( legacy )
    {
    this->m_AffineXform = AffineXform::SmartPtr( this->m_AffineXform->MakeInverse() );
    }

  classStream.Get( this->m_WarpXform );
  if ( this->m_WarpXform )
    {
    if ( referenceStudy )
      {
      this->m_WarpXform->SetMetaInfo( META_XFORM_FIXED_IMAGE_PATH, referenceStudy );
      }
    if ( floatingStudy )
      {
      this->m_WarpXform->SetMetaInfo( META_XFORM_MOVING_IMAGE_PATH, floatingStudy );
      }
    }
  
  classStream.Close();
  return true;
}

void
TypedStreamStudylist::Write
( const char *path, const char* referenceStudy, const char* floatingStudy, const Xform* xform )
{
  ClassStream classStream( path, "studylist", ClassStream::WRITE );
  if ( ! classStream.IsValid() ) return;
  
  classStream.Begin( "studylist" );
  classStream.WriteInt( "num_sources", 2 );
  classStream.End();

  classStream.Begin( "source" );
  classStream.WriteString( "studyname", CompressedStream::GetBaseName( referenceStudy ) );
  classStream.End();

  classStream.Begin( "source" );
  classStream.WriteString( "studyname", CompressedStream::GetBaseName( floatingStudy ) );
  classStream.End();

  classStream.Close();

  classStream.Open( path, "registration", ClassStream::WRITE );
  if ( classStream.IsValid() ) 
    {    
    classStream.Begin( "registration" );
    classStream.WriteString( "reference_study", CompressedStream::GetBaseName( referenceStudy ) );
    classStream.WriteString( "floating_study", CompressedStream::GetBaseName( floatingStudy ) );
    
    const WarpXform* warp = dynamic_cast<const WarpXform*>( xform );
    if ( warp ) 
      {
      if ( warp->GetInitialAffineXform() ) 
        {
        classStream << (*warp->GetInitialAffineXform()->GetInverse());
        }
      classStream << warp;
      } 
    else 
      {
      const AffineXform* affine = dynamic_cast<const AffineXform*>( xform );
      if ( affine )
        classStream << (*affine->GetInverse());
      }
    
    classStream.End();
  }
  classStream.Close();
}

} // namespace