Update version to 1.3

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+/*
+-----------------------------------------------------------------------
+Copyright 2012 iMinds-Vision Lab, University of Antwerp
+
+Contact: astra@ua.ac.be
+Website: http://astra.ua.ac.be
+
+
+This file is part of the
+All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
+
+The ASTRA Toolbox 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 ASTRA Toolbox 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+
+-----------------------------------------------------------------------
+$Id$
+*/
+
+#ifndef _INC_ASTRA_SIRTALGORITHM
+#define _INC_ASTRA_SIRTALGORITHM
+
+#include "Globals.h"
+#include "Config.h"
+
+#include "Algorithm.h"
+#include "ReconstructionAlgorithm2D.h"
+
+#include "Projector2D.h"
+#include "Float32ProjectionData2D.h"
+#include "Float32VolumeData2D.h"
+
+#include "DataProjector.h"
+
+namespace astra {
+
+/**
+ * \brief
+ * This class contains the implementation of the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm.
+ *
+ * The update step of pixel \f$v_j\f$ for iteration \f$k\f$ is given by:
+ * \f[
+ *	v_j^{(k+1)} = v_j^{(k)} + \alpha \sum_{i=1}^{M} \left( \frac{w_{ij}\left( p_i - \sum_{r=1}^{N} w_{ir}v_r^{(k)}\right)}{\sum_{k=1}^{N} w_{ik}} \right) \frac{1}{\sum_{l=1}^{M}w_{lj}}
+ * \f]
+ *
+ * \par XML Configuration
+ * \astra_xml_item{ProjectorId, integer, Identifier of a projector as it is stored in the ProjectorManager.}
+ * \astra_xml_item{ProjectionDataId, integer, Identifier of a projection data object as it is stored in the DataManager.}
+ * \astra_xml_item{ReconstructionDataId, integer, Identifier of a volume data object as it is stored in the DataManager.}
+ * \astra_xml_item_option{ReconstructionMaskId, integer, not used, Identifier of a volume data object that acts as a reconstruction mask. 1 = reconstruct on this pixel. 0 = don't reconstruct on this pixel.}
+ * \astra_xml_item_option{SinogramMaskId, integer, not used, Identifier of a projection data object that acts as a projection mask. 1 = reconstruct using this ray. 0 = don't use this ray while reconstructing.}
+ * \astra_xml_item_option{UseMinConstraint, bool, false, Use minimum value constraint.}
+ * \astra_xml_item_option{MinConstraintValue, float, 0, Minimum constraint value.}
+ * \astra_xml_item_option{UseMaxConstraint, bool, false, Use maximum value constraint.}
+ * \astra_xml_item_option{MaxConstraintValue, float, 255, Maximum constraint value.}
+ *
+ * \par XML Example
+ * \astra_code{
+ *		&lt;Algorithm type="SIRT"&gt;\n
+ *		&lt;ProjectorID&gt;proj_id&lt;/ProjectorID&gt;\n
+ *		&lt;ProjectionDataId&gt;sino_id&lt;/ProjectionDataId&gt;\n
+ *		&lt;ReconstructionDataId&gt;recon_id&lt;/ReconstructionDataId&gt;\n
+ *		&lt;Option key="ReconstructionMaskId" value="3"/&gt;\n
+ *		&lt;Option key="SinogramMaskId" value="4"/&gt;\n
+ *		&lt;Option key="UseMinConstraint" value="yes"/&gt;\n
+ *		&lt;Option key="UseMaxConstraint" value="yes"/&gt;\n
+ *		&lt;Option key="MaxConstraintValue" value="1024"/&gt;\n
+ *		&lt;/Algorithm&gt;
+ * }
+ *
+ * \par MATLAB example
+ * \astra_code{
+ *		cfg = astra_struct('SIRT');\n
+ *		cfg.ProjectorId = proj_id;\n
+ *		cfg.ProjectionDataId = sino_id;\n
+ *		cfg.ReconstructionDataId = recon_id;\n
+ *		cfg.option.SinogramMaskId = smask_id;\n
+ *		cfg.option.ReconstructionMaskId = mask_id;\n
+ *		cfg.option.UseMinConstraint = 'yes';\n 
+ *		cfg.option.UseMaxConstraint = 'yes';\n
+ *		cfg.option.MaxConstraintValue = 1024;\n
+ *		alg_id = astra_mex_algorithm('create'\, cfg);\n
+ *		astra_mex_algorithm('iterate'\, alg_id\, 10);\n
+ *		astra_mex_algorithm('delete'\, alg_id);\n
+ * }
+ *
+ * \par References
+ * [1] "Computational Analysis and Improvement of SIRT", J. Gregor, T. Benson, IEEE Transactions on Medical Imaging, Vol. 22, No. 7, July 2008.
+ */
+class _AstraExport CSirtAlgorithm : public CReconstructionAlgorithm2D {
+
+protected:
+
+	/** Init stuff
+	 */
+	virtual void _init();
+
+	/** Initial clearing. Only to be used by constructors.
+	 */
+	virtual void _clear();
+
+	/** Check the values of this object.  If everything is ok, the object can be set to the initialized state.
+	 * The following statements are then guaranteed to hold:
+	 * - valid projector
+	 * - valid data objects
+	 */
+	virtual bool _check();
+
+	/** Temporary data object for storing the total ray lengths
+	 */
+	CFloat32ProjectionData2D* m_pTotalRayLength;
+	
+	/** Temporary data object for storing the total pixel weigths
+	 */
+	CFloat32VolumeData2D* m_pTotalPixelWeight;
+	
+	/** Temporary data object for storing the difference between the forward projected
+	 * reconstruction, and the measured projection data
+	 */
+	CFloat32ProjectionData2D* m_pDiffSinogram;
+
+	/** Temporary data object for storing volume data
+	*/
+	CFloat32VolumeData2D* m_pTmpVolume;
+
+	/** The number of performed iterations
+	 */
+	int m_iIterationCount;
+
+public:
+	
+	// type of the algorithm, needed to register with CAlgorithmFactory
+	static std::string type;
+	
+	/** Default constructor, containing no code. 
+	 */
+	CSirtAlgorithm();
+
+	/** Default constructor
+	 *
+	 * @param _pProjector		Projector Object.
+	 * @param _pSinogram		ProjectionData2D object containing the sinogram data.
+	 * @param _pReconstruction	VolumeData2D object for storing the reconstructed volume.
+	 */
+	CSirtAlgorithm(CProjector2D* _pProjector, 
+				   CFloat32ProjectionData2D* _pSinogram, 
+				   CFloat32VolumeData2D* _pReconstruction);
+
+	/** Destructor. 
+	 */
+	virtual ~CSirtAlgorithm();
+
+	/** Clear this class.
+	 */
+	virtual void clear();
+
+	/** Initialize the algorithm with a config object.
+	 *
+	 * @param _cfg Configuration Object
+	 * @return Initialization successful?
+	 */
+	virtual bool initialize(const Config& _cfg);
+
+	/** Initialize class.
+	 *
+	 * @param _pProjector		Projector Object.
+	 * @param _pSinogram		ProjectionData2D object containing the sinogram data.
+	 * @param _pReconstruction	VolumeData2D object for storing the reconstructed volume.
+	 * @return Initialization successful?
+	 */
+	bool initialize(CProjector2D* _pProjector, 
+					CFloat32ProjectionData2D* _pSinogram, 
+					CFloat32VolumeData2D* _pReconstruction);
+
+	/** Get all information parameters.
+	 *
+	 * @return Map with all available identifier strings and their values.
+	 */
+	virtual map<string,boost::any> getInformation();
+
+	/** Get a single piece of information represented as a boost::any
+	 *
+	 * @param _sIdentifier Identifier string to specify which piece of information you want.
+	 * @return One piece of information.
+	 */
+	virtual boost::any getInformation(std::string _sIdentifier);
+
+	/** Perform a number of iterations.
+	 *
+	 * @param _iNrIterations amount of iterations to perform.
+	 */
+	virtual void run(int _iNrIterations = 0);
+
+	/** Get a description of the class.
+	 *
+	 * @return description string
+	 */
+	virtual std::string description() const;
+
+};
+
+// inline functions
+inline std::string CSirtAlgorithm::description() const { return CSirtAlgorithm::type; };
+
+
+} // end namespace
+
+#endif