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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2012 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: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include <IO/cmtkClassStreamInput.h>
#include <IO/cmtkClassStreamOutput.h>
#include <IO/cmtkClassStreamAffineXform.h>
namespace
cmtk
{
ClassStreamOutput&
ClassStreamOutput::operator << ( const WarpXform *warpXform )
{
return this->PutWarp( warpXform );
}
ClassStreamOutput&
ClassStreamOutput::PutWarp
( const WarpXform *warpXform )
{
const Types::Coordinate *nCoeff = warpXform->m_Parameters;
if ( dynamic_cast<const SplineWarpXform*>( warpXform ) )
this->Begin( "spline_warp" );
if ( warpXform->GetInitialAffineXform() )
*this << (*warpXform->GetInitialAffineXform());
this->WriteBool ( "absolute", true );
this->WriteIntArray( "dims", warpXform->m_Dims.begin(), 3 );
this->WriteCoordinateArray( "domain", warpXform->m_Domain.begin(), 3 );
this->WriteCoordinateArray( "origin", warpXform->m_Offset.begin(), 3 );
this->WriteCoordinateArray( "coefficients", nCoeff, warpXform->m_NumberOfParameters, 3 );
const BitVector* activeFlags = warpXform->GetActiveFlags();
if ( activeFlags )
{
this->WriteBoolArray( "active", activeFlags->GetBitVector(), warpXform->m_NumberOfParameters, 30 );
}
this->End();
return *this;
}
ClassStreamInput&
ClassStreamInput::Get
( WarpXform::SmartPtr& warpXform, const AffineXform* initialXform )
{
WarpXform* warp;
this->Get( warp, initialXform );
warpXform = WarpXform::SmartPtr( warp );
return *this;
}
ClassStreamInput&
ClassStreamInput::Get
( WarpXform*& warpXform, const AffineXform* initialXform )
{
warpXform = NULL;
int WarpType = -1;
if ( this->Seek( "spline_warp" ) == TypedStream::CONDITION_OK )
WarpType = 1;
else
if ( this->Seek( "linear_warp" ) == TypedStream::CONDITION_OK )
WarpType = 0;
else
{
this->Rewind();
if ( this->Seek( "registration", true /*forward*/ ) != TypedStream::CONDITION_OK )
{
return *this;
}
if ( this->Seek( "spline_warp" ) == TypedStream::CONDITION_OK )
WarpType = 1;
else
if ( this->Seek( "linear_warp" ) == TypedStream::CONDITION_OK )
WarpType = 0;
else
return *this;
}
AffineXform::SmartPtr initialInverse( NULL );
if ( initialXform == NULL )
{
AffineXform::SmartPtr newInitialXform;
*this >> newInitialXform;
initialInverse = AffineXform::SmartPtr( newInitialXform );
}
else
{
initialInverse = AffineXform::SmartPtr( initialXform->MakeInverse() );
}
int absolute = this->ReadBool( "absolute", 0 );
int dims[3];
if ( TypedStream::CONDITION_OK != this->ReadIntArray( "dims", dims, 3 ) )
{
return *this;
}
int numControlPoints = dims[0] * dims[1] * dims[2];
int numberOfParameters = 3 * numControlPoints;
CoordinateVector::SmartPtr parameters( new CoordinateVector( numberOfParameters ) );
Types::Coordinate *Coefficients = parameters->Elements;
Vector3D domain;
Vector3D origin;
if ( this->ReadCoordinateArray( "domain", domain.begin(), 3 ) != TypedStream::CONDITION_OK )
this->ReadCoordinateArray( "extent", domain.begin(), 3 );
int readOrigin = this->ReadCoordinateArray( "origin", origin.begin(), 3 );
this->ReadCoordinateArray( "coefficients", Coefficients, numberOfParameters );
if ( !absolute && (readOrigin == TypedStream::CONDITION_OK) )
{
Types::Coordinate *p = Coefficients;
for ( int z=0; z<dims[2]; ++z )
for ( int y=0; y<dims[1]; ++y )
for ( int x=0; x<dims[0]; ++x, p+=3 )
{
if ( WarpType == 0 )
{
p[0] += (origin[0] + x * domain[0]/(dims[0]-1));
p[1] += (origin[1] + y * domain[1]/(dims[1]-1));
p[2] += (origin[2] + z * domain[2]/(dims[2]-1));
}
else
{
p[0] += (origin[0] + x * domain[0]/(dims[0]-3));
p[1] += (origin[1] + y * domain[1]/(dims[1]-3));
p[2] += (origin[2] + z * domain[2]/(dims[2]-3));
}
}
}
switch ( WarpType )
{
case 0:
warpXform = NULL; // linear warp no longer supported
break;
case 1:
warpXform = new SplineWarpXform( domain, SplineWarpXform::ControlPointIndexType::FromPointer( dims ), parameters, initialInverse );
break;
};
byte *active = Memory::ArrayC::Allocate<byte>( (numberOfParameters / 8)+1 );
if ( this->ReadBoolArray( "active", active, numberOfParameters ) == TypedStream::CONDITION_OK )
{
BitVector::SmartPtr bitSet( new BitVector( numberOfParameters, active ) );
warpXform->SetActiveFlags( bitSet );
}
else
{
Memory::ArrayC::Delete( active );
}
this->End();
if ( warpXform )
{
warpXform->SetMetaInfo( META_SPACE, AnatomicalOrientation::ORIENTATION_STANDARD );
}
return *this;
}
ClassStreamInput&
ClassStreamInput::operator >> ( WarpXform::SmartPtr& warpXform )
{
this->Get( warpXform );
return *this;
}
ClassStreamInput&
ClassStreamInput::operator >> ( WarpXform*& warpXform )
{
this->Get( warpXform );
return *this;
}
} // namespace cmtk
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