Update version to 1.3

1 files changed, 321 insertions, 0 deletions

diff --git a/src/SirtAlgorithm.cpp b/src/SirtAlgorithm.cpp
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+++ b/src/SirtAlgorithm.cpp
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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/>.
+
+-----------------------------------------------------------------------
+$Id$
+*/
+
+#include "astra/SirtAlgorithm.h"
+
+#include <boost/lexical_cast.hpp>
+
+#include "astra/AstraObjectManager.h"
+#include "astra/DataProjectorPolicies.h"
+
+using namespace std;
+
+namespace astra {
+
+#include "astra/Projector2DImpl.inl"
+
+// type of the algorithm, needed to register with CAlgorithmFactory
+std::string CSirtAlgorithm::type = "SIRT";
+
+//----------------------------------------------------------------------------------------
+// Constructor
+CSirtAlgorithm::CSirtAlgorithm() 
+{
+	_clear();
+}
+
+//---------------------------------------------------------------------------------------
+// Initialize - C++
+CSirtAlgorithm::CSirtAlgorithm(CProjector2D* _pProjector, 
+							   CFloat32ProjectionData2D* _pSinogram, 
+							   CFloat32VolumeData2D* _pReconstruction)
+{
+	_clear();
+	initialize(_pProjector, _pSinogram, _pReconstruction);
+}
+
+//----------------------------------------------------------------------------------------
+// Destructor
+CSirtAlgorithm::~CSirtAlgorithm() 
+{
+	clear();
+}
+
+//---------------------------------------------------------------------------------------
+// Clear - Constructors
+void CSirtAlgorithm::_clear()
+{
+	CReconstructionAlgorithm2D::_clear();
+	m_bIsInitialized = false;
+
+	m_pTotalRayLength = NULL;
+	m_pTotalPixelWeight = NULL;
+	m_pDiffSinogram = NULL;
+	m_pTmpVolume = NULL;
+
+	m_iIterationCount = 0;
+}
+
+//---------------------------------------------------------------------------------------
+// Clear - Public
+void CSirtAlgorithm::clear()
+{
+	CReconstructionAlgorithm2D::_clear();
+	m_bIsInitialized = false;
+
+	ASTRA_DELETE(m_pTotalRayLength);
+	ASTRA_DELETE(m_pTotalPixelWeight);
+	ASTRA_DELETE(m_pDiffSinogram);
+	ASTRA_DELETE(m_pTmpVolume);
+
+	m_iIterationCount = 0;
+}
+
+//----------------------------------------------------------------------------------------
+// Check
+bool CSirtAlgorithm::_check()
+{
+	// check base class
+	ASTRA_CONFIG_CHECK(CReconstructionAlgorithm2D::_check(), "SIRT", "Error in ReconstructionAlgorithm2D initialization");
+
+	ASTRA_CONFIG_CHECK(m_pTotalRayLength, "SIRT", "Invalid TotalRayLength Object");
+	ASTRA_CONFIG_CHECK(m_pTotalRayLength->isInitialized(), "SIRT", "Invalid TotalRayLength Object");
+	ASTRA_CONFIG_CHECK(m_pTotalPixelWeight, "SIRT", "Invalid TotalPixelWeight Object");
+	ASTRA_CONFIG_CHECK(m_pTotalPixelWeight->isInitialized(), "SIRT", "Invalid TotalPixelWeight Object");
+	ASTRA_CONFIG_CHECK(m_pDiffSinogram, "SIRT", "Invalid DiffSinogram Object");
+	ASTRA_CONFIG_CHECK(m_pDiffSinogram->isInitialized(), "SIRT", "Invalid DiffSinogram Object");
+
+	return true;
+}
+
+//---------------------------------------------------------------------------------------
+// Initialize - Config
+bool CSirtAlgorithm::initialize(const Config& _cfg)
+{
+	ASTRA_ASSERT(_cfg.self);
+	ConfigStackCheck<CAlgorithm> CC("SirtAlgorithm", this, _cfg);
+
+	// if already initialized, clear first
+	if (m_bIsInitialized) {
+		clear();
+	}
+
+	// initialization of parent class
+	if (!CReconstructionAlgorithm2D::initialize(_cfg)) {
+		return false;
+	}
+
+	// init data objects and data projectors
+	_init();
+
+	// success
+	m_bIsInitialized = _check();
+	return m_bIsInitialized;
+}
+
+//---------------------------------------------------------------------------------------
+// Initialize - C++
+bool CSirtAlgorithm::initialize(CProjector2D* _pProjector, 
+								CFloat32ProjectionData2D* _pSinogram, 
+								CFloat32VolumeData2D* _pReconstruction)
+{
+	// if already initialized, clear first
+	if (m_bIsInitialized) {
+		clear();
+	}
+
+	// required classes
+	m_pProjector = _pProjector;
+	m_pSinogram = _pSinogram;
+	m_pReconstruction = _pReconstruction;
+
+	// init data objects and data projectors
+	_init();
+
+	// success
+	m_bIsInitialized = _check();
+	return m_bIsInitialized;
+}
+
+//---------------------------------------------------------------------------------------
+// Initialize Data Projectors - private
+void CSirtAlgorithm::_init()
+{
+	// create data objects
+	m_pTotalRayLength = new CFloat32ProjectionData2D(m_pProjector->getProjectionGeometry());
+	m_pTotalPixelWeight = new CFloat32VolumeData2D(m_pProjector->getVolumeGeometry());
+	m_pDiffSinogram = new CFloat32ProjectionData2D(m_pProjector->getProjectionGeometry());
+	m_pTmpVolume = new CFloat32VolumeData2D(m_pProjector->getVolumeGeometry());
+}
+
+//---------------------------------------------------------------------------------------
+// Information - All
+map<string,boost::any> CSirtAlgorithm::getInformation() 
+{
+	map<string, boost::any> res;
+	return mergeMap<string,boost::any>(CReconstructionAlgorithm2D::getInformation(), res);
+};
+
+//---------------------------------------------------------------------------------------
+// Information - Specific
+boost::any CSirtAlgorithm::getInformation(std::string _sIdentifier) 
+{
+	return CAlgorithm::getInformation(_sIdentifier);
+};
+
+//----------------------------------------------------------------------------------------
+// Iterate
+void CSirtAlgorithm::run(int _iNrIterations)
+{
+	// check initialized
+	ASTRA_ASSERT(m_bIsInitialized);
+
+	m_bShouldAbort = false;
+
+	int iIteration = 0;
+
+	// data projectors
+	CDataProjectorInterface* pForwardProjector;
+	CDataProjectorInterface* pBackProjector;
+	CDataProjectorInterface* pFirstForwardProjector;
+
+	m_pTotalRayLength->setData(0.0f);
+	m_pTotalPixelWeight->setData(0.0f);
+
+	// forward projection data projector
+	pForwardProjector = dispatchDataProjector(
+		m_pProjector, 
+			SinogramMaskPolicy(m_pSinogramMask),														// sinogram mask
+			ReconstructionMaskPolicy(m_pReconstructionMask),											// reconstruction mask
+			DiffFPPolicy(m_pReconstruction, m_pDiffSinogram, m_pSinogram),								// forward projection with difference calculation
+			m_bUseSinogramMask, m_bUseReconstructionMask, true											// options on/off
+		); 
+
+	// backprojection data projector
+	pBackProjector = dispatchDataProjector(
+			m_pProjector, 
+			SinogramMaskPolicy(m_pSinogramMask),														// sinogram mask
+			ReconstructionMaskPolicy(m_pReconstructionMask),											// reconstruction mask
+			DefaultBPPolicy(m_pTmpVolume, m_pDiffSinogram), // backprojection
+			m_bUseSinogramMask, m_bUseReconstructionMask, true // options on/off
+		); 
+
+	// first time forward projection data projector,
+	// also computes total pixel weight and total ray length
+	pFirstForwardProjector = dispatchDataProjector(
+			m_pProjector, 
+			SinogramMaskPolicy(m_pSinogramMask),														// sinogram mask
+			ReconstructionMaskPolicy(m_pReconstructionMask),											// reconstruction mask
+			Combine3Policy<DiffFPPolicy, TotalPixelWeightPolicy, TotalRayLengthPolicy>(					// 3 basic operations
+				DiffFPPolicy(m_pReconstruction, m_pDiffSinogram, m_pSinogram),								// forward projection with difference calculation
+				TotalPixelWeightPolicy(m_pTotalPixelWeight),												// calculate the total pixel weights
+				TotalRayLengthPolicy(m_pTotalRayLength)),													// calculate the total ray lengths
+			m_bUseSinogramMask, m_bUseReconstructionMask, true											 // options on/off
+		);
+
+
+
+	// forward projection, difference calculation and raylength/pixelweight computation
+	pFirstForwardProjector->project();
+
+	float32* pfT = m_pTotalPixelWeight->getData();
+	for (int i = 0; i < m_pTotalPixelWeight->getSize(); ++i) {
+		float32 x = pfT[i];
+		if (x < -eps || x > eps)
+			x = 1.0f / x;
+		else
+			x = 0.0f;
+		pfT[i] = x;
+	}
+	pfT = m_pTotalRayLength->getData();
+	for (int i = 0; i < m_pTotalRayLength->getSize(); ++i) {
+		float32 x = pfT[i];
+		if (x < -eps || x > eps)
+			x = 1.0f / x;
+		else
+			x = 0.0f;
+		pfT[i] = x;
+	}
+
+	// divide by line weights
+	(*m_pDiffSinogram) *= (*m_pTotalRayLength);
+
+	// backprojection
+	m_pTmpVolume->setData(0.0f);
+	pBackProjector->project();
+
+	// divide by pixel weights
+	(*m_pTmpVolume) *= (*m_pTotalPixelWeight);
+	(*m_pReconstruction) += (*m_pTmpVolume);
+
+	if (m_bUseMinConstraint)
+		m_pReconstruction->clampMin(m_fMinValue);
+	if (m_bUseMaxConstraint)
+		m_pReconstruction->clampMax(m_fMaxValue);
+
+	// update iteration count
+	m_iIterationCount++;
+	iIteration++;
+
+
+	
+
+	// iteration loop
+	for (; iIteration < _iNrIterations && !m_bShouldAbort; ++iIteration) {
+		// forward projection and difference calculation
+		pForwardProjector->project();
+
+		// divide by line weights
+		(*m_pDiffSinogram) *= (*m_pTotalRayLength);
+
+
+		// backprojection
+		m_pTmpVolume->setData(0.0f);
+		pBackProjector->project();
+
+		// divide by pixel weights
+		(*m_pTmpVolume) *= (*m_pTotalPixelWeight);
+		(*m_pReconstruction) += (*m_pTmpVolume);
+
+		if (m_bUseMinConstraint)
+			m_pReconstruction->clampMin(m_fMinValue);
+		if (m_bUseMaxConstraint)
+			m_pReconstruction->clampMax(m_fMaxValue);
+
+		// update iteration count
+		m_iIterationCount++;
+	}
+
+
+	ASTRA_DELETE(pForwardProjector);
+	ASTRA_DELETE(pBackProjector);
+	ASTRA_DELETE(pFirstForwardProjector);
+}
+//----------------------------------------------------------------------------------------
+
+} // namespace astra