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/* -*- mia-c++  -*-
 *
 * This file is part of MIA - a toolbox for medical image analysis 
 * Copyright (c) Leipzig, Madrid 1999-2016 Gert Wollny
 *
 * MIA 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.
 *
 * This program 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 MIA; if not, see <http://www.gnu.org/licenses/>.
 *
 */

#ifndef SegSet_h
#define SegSet_h

#include <mia/core/ioplugin.hh>
#include <mia/2d/segframe.hh>
#include <mia/2d/boundingbox.hh>

namespace xmlpp {
	class Document;
};

NS_MIA_BEGIN

/**
   @ingroup perf 
   \brief A set of segmentation of a 2D series of perfusion images 
   
   A set of slices containing segmentation information specifically designed for 
   myocardial perfusion image series. 
*/
class EXPORT_2D CSegSet: public CIOData {
public:
	/// convenience typedef for the frames comprising a segmentation set 
	typedef std::vector<CSegFrame> Frames;

	/// Standard constructor 
	CSegSet();
	/**
	   Construct the segmentation set by reading from a file 
	   \param src_filename file name to read set from 
	 */
	CSegSet(const std::string& src_filename);

	/**
	   Construct a segmentation set by reading from a XML document
	   \param node the root node of the XML document 
	 */
	CSegSet(const xmlpp::Document& node);


	CSegSet(int version);
	/**
	   Append a segmentation frame 
	   \param frame 
	 */
	void add_frame(const CSegFrame& frame);

	/**
	   Write the segmentation information to an XML tree 
	   \returns root node of xml tree. 
	 */
	xmlpp::Document *write() const;


	/// \returns read-only vector of the segmentation frames 
	const Frames& get_frames()const;

	/** 
	    \returns a reference to the read-write vector of the segmentation frames 
	    Changing this vector changes the segmentation set 
	*/ 
	Frames& get_frames();

	/**
	   \returns the box of minimal size that includes the segmentation 
	 */
	const C2DBoundingBox get_boundingbox() const;

	/**
	   Rename the base of the image file names for all frames on a frame by frame basis. 
	   \param new_base new base name 
	*/
	void rename_base(const std::string& new_base); 


	/**
	   This function renames the images files, shifts the origin of the segmentation and 
	   removes frames from the beginning of the set 
	   \param skip number of frames to skipĆ¼ at the beginning 
	   \param shift new origin of segmentation 
	   \param  new_filename_base new file name base
	   \remark This function does too many things at once. 
	 */
	CSegSet  shift_and_rename(size_t skip, const C2DFVector&  shift, const std::string& new_filename_base)const;

	/**
	   Transform the segmentations slice wise by using the given transformation 
	   Wroks in-place. 
	   \param t tranformation 
	 */
	void transform(const C2DTransformation& t);


	/**
	   Set the frame number of the RV peak enhancement
	   \param peak 
	*/
	void set_RV_peak(int peak); 
	
	/**
	   \\returns the frame number of the RV peak enhancement (-1 if not set)
	*/
	int get_RV_peak() const; 

	/**
	   Set the frame number of the LV peak enhancement
	   \param peak 
	*/
	void set_LV_peak(int peak); 

	/**
	   \\returns the frame number of the LV peak enhancement (-1 if not set)
	*/
	int get_LV_peak() const; 

	/**
	   \\returns the frame number of the image that should be used as reference frame 
	   for time-intensity analysis after motion compensation - if the used motion compensation 
	   algorithm provides some (like quasiperiodic, one2many, or serial do). Returns -1 if no values is given. 
	*/
	int get_preferred_reference() const; 


	/**
	   Set the preferred reference frame for this segmentation set. 
	   \param value 
	 */
	void  set_preferred_reference(int value); 

private:
	void read(const xmlpp::Document& node);
	Frames m_frames;
	int m_RV_peak; 
	int m_LV_peak; 
	int m_preferred_reference; 
	int m_version; 
};


NS_MIA_END

#endif