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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2011, 2013 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 $
//
*/
#ifndef __cmtkElasticRegistrationCommandLine_h_included_
#define __cmtkElasticRegistrationCommandLine_h_included_
#include <cmtkconfig.h>
#include <Registration/cmtkElasticRegistration.h>
namespace
cmtk
{
/** \addtogroup Registration */
//@{
/** Class for command line controlled voxel registration.
*\author T. Rohlfing
*\version $Revision: 5436 $ $Date: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
*/
class ElasticRegistrationCommandLine :
/// Inherit generic elastic registration.
public ElasticRegistration
{
public:
/// This class.
typedef ElasticRegistrationCommandLine Self;
/// Smart pointer.
typedef SmartPointer<ElasticRegistrationCommandLine> SmartPtr;
/// Parent class.
typedef ElasticRegistration Superclass;
/** Constructor.
*\param argc Number of command line arguments; this should be the argc
* parameter of the main() function.
*\param argv Array of command line arguments; this should be the argv
* parameter of the main() function.
*/
ElasticRegistrationCommandLine ( const int argc, const char *argv[] );
/// Destructor.
~ElasticRegistrationCommandLine ();
/** Perform registration.
*/
virtual CallbackResult Register ();
protected:
/** Initialize registration.
* So far, this function has no effect other than calling the equivalent
* inherited function.
*/
virtual CallbackResult InitRegistration();
/** Output registration result.
*/
virtual void OutputResult ( const CoordinateVector* v, const CallbackResult irq = CALLBACK_OK );
/** Enter resolution level.
* An information is printed to stderr and to the protocol file if one is
* written.
*/
virtual void EnterResolution( CoordinateVector::SmartPtr&, Functional::SmartPtr&, const int, const int );
/** Leave resolution level.
* The transformation found so far is written to a file if desired.
*/
virtual int DoneResolution( CoordinateVector::SmartPtr&, Functional::SmartPtr&, const int, const int );
private:
/** Name of input studylist.
* This is defined by the --inlist command line parameter (not currently
* supported).
*/
std::string InputStudylist;
/** Name of output studylist.
* This is defined by the -o or --outlist command line option.
*/
std::string Studylist;
/** Name of first study to be registered.
* This is given as the first non-option command line paramter.
*/
std::string Study1;
/** Name of second study to be registered.
* This is given as the second non-option command line paramter.
*/
std::string Study2;
#ifdef CMTK_USE_SQLITE
/// Database to update after registration completes.
std::string m_UpdateDB;
#endif
/// Filename for rigidity constraint map.
std::string RigidityConstraintMapFilename;
/** Name of protocol output file.
* This is defined by the -p or --protocol command line option.
*/
std::string Protocol;
/** Name of elapsed time output file.
* This is defined by the -t or --time command line option.
*/
std::string Time;
/** Select whether too create intermediate warp output files (level-xx.list).
*/
bool m_OutputIntermediate;
/// Write deformation to studylist archive.
void OutputWarp ( const std::string& ) const;
/// Name of output transformation file in ITK format.
std::string m_OutputPathITK;
/// Path for reformatted floating image.
std::string m_ReformattedImagePath;
public:
/// Static pointer to this object.
static Self* StaticThis;
/// Counter for intermediate result files.
int IntermediateResultIndex;
/// Write intermediate deformation file.
void OutputIntermediate( const bool incrementCount = true );
};
//@}
} // namespace cmtk
/// Signal handler that writes intermediate result during a level.
extern "C" void cmtkElasticRegistrationCommandLineDispatchSIGUSR1( int sig );
#endif // #ifndef __cmtkElasticRegistrationCommandLine_h_included_
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