Merge branch 'master' into volgeom3d

14 files changed, 272 insertions, 92 deletions

diff --git a/src/ConeProjectionGeometry3D.cpp b/src/ConeProjectionGeometry3D.cpp
index eb9adcf..1976901 100644
--- a/src/ConeProjectionGeometry3D.cpp
+++ b/src/ConeProjectionGeometry3D.cpp
@@ -28,6 +28,8 @@ $Id$
 
 #include "astra/ConeProjectionGeometry3D.h"
 
+#include "astra/Logging.h"
+
 #include <boost/lexical_cast.hpp>
 #include <cstring>
 
@@ -257,7 +259,7 @@ void CConeProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ,
 	// Scale fS to detector plane
 	fU = detectorOffsetXToColIndexFloat( (fS * (m_fOriginSourceDistance + m_fOriginDetectorDistance)) / fD );
 
-	fprintf(stderr, "alpha: %f, D: %f, V: %f, S: %f, U: %f\n", alpha, fD, fV, fS, fU);
+	ASTRA_DEBUG("alpha: %f, D: %f, V: %f, S: %f, U: %f", alpha, fD, fV, fS, fU);
 
 }
 
diff --git a/src/Config.cpp b/src/Config.cpp
index 653935e..d860638 100644
--- a/src/Config.cpp
+++ b/src/Config.cpp
@@ -37,6 +37,9 @@ $Id$
 #include "astra/Projector2D.h"
 #include "astra/Projector3D.h"
 
+#include "astra/Logging.h"
+#include <sstream>
+
 using namespace astra;
 using namespace std;
 
@@ -144,7 +147,9 @@ bool ConfigStackCheck<T>::stopParsing()
 	nodes.clear();
 
 	if (!errors.empty()) {
-		cout << "Warning: " << name << ": unused configuration options: " << errors << std::endl;
+		ostringstream os;
+		os << name << ": unused configuration options: " << errors;
+		ASTRA_WARN(os.str().c_str());
 		return false;
 	}
 
diff --git a/src/CudaFilteredBackProjectionAlgorithm.cpp b/src/CudaFilteredBackProjectionAlgorithm.cpp
index fcdf860..0badc20 100644
--- a/src/CudaFilteredBackProjectionAlgorithm.cpp
+++ b/src/CudaFilteredBackProjectionAlgorithm.cpp
@@ -34,7 +34,7 @@ $Id$
 #include "astra/AstraObjectManager.h"
 #include "../cuda/2d/astra.h"
 
-#include <astra/Logger.h>
+#include "astra/Logging.h"
 
 using namespace std;
 using namespace astra;
@@ -105,7 +105,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg)
 	}
 	CC.markNodeParsed("FilterType");
 	ASTRA_DELETE(node);
-	
+
 	// filter
 	node = _cfg.self->getSingleNode("FilterSinogramId");
 	if(node != NULL)
@@ -168,7 +168,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg)
 		CC.markOptionParsed("ShortScan");
 	}
 
-	
+
 
 
 	m_pFBP = new AstraFBP;
@@ -186,7 +186,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(CFloat32ProjectionData2D *
 	{
 		clear();
 	}
-	
+
 	// required classes
 	m_pSinogram = _pSinogram;
 	m_pReconstruction = _pReconstruction;
@@ -326,7 +326,7 @@ void CCudaFilteredBackProjectionAlgorithm::run(int _iNrIterations /* = 0 */)
 
 	const CVolumeGeometry2D& volgeom = *m_pReconstruction->getGeometry();
 	ok &= m_pFBP->getReconstruction(m_pReconstruction->getData(), volgeom.getGridColCount());
-	
+
 	ASTRA_ASSERT(ok);
 }
 
@@ -335,7 +335,7 @@ bool CCudaFilteredBackProjectionAlgorithm::check()
 	// check pointers
 	ASTRA_CONFIG_CHECK(m_pSinogram, "FBP_CUDA", "Invalid Projection Data Object.");
 	ASTRA_CONFIG_CHECK(m_pReconstruction, "FBP_CUDA", "Invalid Reconstruction Data Object.");
-	
+
 	if((m_eFilter == FILTER_PROJECTION) || (m_eFilter == FILTER_SINOGRAM) || (m_eFilter == FILTER_RPROJECTION) || (m_eFilter == FILTER_RSINOGRAM))
 	{
 		ASTRA_CONFIG_CHECK(m_pfFilter, "FBP_CUDA", "Invalid filter pointer.");
@@ -387,7 +387,7 @@ static bool stringCompareLowerCase(const char * _stringA, const char * _stringB)
 #else
 	iCmpReturn = strcasecmp(_stringA, _stringB);
 #endif
-	
+
 	return (iCmpReturn == 0);
 }
 
@@ -485,7 +485,7 @@ E_FBPFILTER CCudaFilteredBackProjectionAlgorithm::_convertStringToFilter(const c
 	}
 	else
 	{
-		cerr << "Failed to convert \"" << _filterType << "\" into a filter." << endl;
+		ASTRA_ERROR("Failed to convert \"%s\" into a filter.",_filterType);
 	}
 
 	return output;
diff --git a/src/CudaForwardProjectionAlgorithm.cpp b/src/CudaForwardProjectionAlgorithm.cpp
index ab0d643..95abb62 100644
--- a/src/CudaForwardProjectionAlgorithm.cpp
+++ b/src/CudaForwardProjectionAlgorithm.cpp
@@ -42,6 +42,8 @@ $Id$
 #include "astra/FanFlatVecProjectionGeometry2D.h"
 #include "astra/CudaProjector2D.h"
 
+#include "astra/Logging.h"
+
 using namespace std;
 
 namespace astra {
@@ -104,7 +106,7 @@ bool CCudaForwardProjectionAlgorithm::initialize(const Config& _cfg)
 		id = boost::lexical_cast<int>(node->getContent());
 		CProjector2D *projector = CProjector2DManager::getSingleton().get(id);
 		if (!dynamic_cast<CCudaProjector2D*>(projector)) {
-			cout << "Warning: non-CUDA Projector2D passed to FP_CUDA" << std::endl;
+			ASTRA_WARN("non-CUDA Projector2D passed to FP_CUDA");
 		}
 		delete node;
 	}
diff --git a/src/CudaForwardProjectionAlgorithm3D.cpp b/src/CudaForwardProjectionAlgorithm3D.cpp
index 914ee2f..aa36715 100644
--- a/src/CudaForwardProjectionAlgorithm3D.cpp
+++ b/src/CudaForwardProjectionAlgorithm3D.cpp
@@ -40,6 +40,8 @@ $Id$
 #include "astra/ParallelVecProjectionGeometry3D.h"
 #include "astra/ConeVecProjectionGeometry3D.h"
 
+#include "astra/Logging.h"
+
 #include "../cuda/3d/astra3d.h"
 
 using namespace std;
@@ -261,7 +263,7 @@ void CCudaForwardProjectionAlgorithm3D::run(int)
 		for (int k = 0; k < 2; ++k) {
 			float fU, fV;
 			projgeom->projectPoint(fX[i], fY[j], fZ[k], a, fU, fV);
-			fprintf(stderr, "%3d %c1,%c1,%c1 -> %12f %12f\n", a, i ? ' ' : '-', j ? ' ' : '-', k ? ' ' : '-', fU, fV);
+			ASTRA_DEBUG("%3d %c1,%c1,%c1 -> %12f %12f", a, i ? ' ' : '-', j ? ' ' : '-', k ? ' ' : '-', fU, fV);
 		}
 	}
 #endif
diff --git a/src/CudaReconstructionAlgorithm2D.cpp b/src/CudaReconstructionAlgorithm2D.cpp
index d3dedc5..1c6b763 100644
--- a/src/CudaReconstructionAlgorithm2D.cpp
+++ b/src/CudaReconstructionAlgorithm2D.cpp
@@ -37,6 +37,8 @@ $Id$
 #include "astra/FanFlatVecProjectionGeometry2D.h"
 #include "astra/CudaProjector2D.h"
 
+#include "astra/Logging.h"
+
 #include "../cuda/2d/algo.h"
 
 #include <ctime>
@@ -176,7 +178,7 @@ bool CCudaReconstructionAlgorithm2D::initialize(const Config& _cfg)
 		id = boost::lexical_cast<int>(node->getContent());
 		CProjector2D *projector = CProjector2DManager::getSingleton().get(id);
 		if (!dynamic_cast<CCudaProjector2D*>(projector)) {
-			cout << "Warning: non-CUDA Projector2D passed" << std::endl;
+			ASTRA_WARN("non-CUDA Projector2D passed");
 		}
 		delete node;
 	}
diff --git a/src/FilteredBackProjectionAlgorithm.cpp b/src/FilteredBackProjectionAlgorithm.cpp
index 50cf939..4a8e5ac 100644
--- a/src/FilteredBackProjectionAlgorithm.cpp
+++ b/src/FilteredBackProjectionAlgorithm.cpp
@@ -39,6 +39,8 @@ $Id$
 #include "astra/Fourier.h"
 #include "astra/DataProjector.h"
 
+#include "astra/Logging.h"
+
 using namespace std;
 
 namespace astra {
@@ -133,7 +135,7 @@ bool CFilteredBackProjectionAlgorithm::initialize(const Config& _cfg)
 		for (int i = 0; i < angleCount; i ++) {
 			if (projectionIndex[i] > m_pProjector->getProjectionGeometry()->getProjectionAngleCount() -1 )
 			{
-				cout << "Invalid Projection Index" << endl;
+				ASTRA_ERROR("Invalid Projection Index");
 				return false;
 			} else {
 				int orgIndex = (int)projectionIndex[i];
diff --git a/src/Float32ProjectionData2D.cpp b/src/Float32ProjectionData2D.cpp
index 85e0cdd..f7f83e3 100644
--- a/src/Float32ProjectionData2D.cpp
+++ b/src/Float32ProjectionData2D.cpp
@@ -75,6 +75,16 @@ CFloat32ProjectionData2D::CFloat32ProjectionData2D(const CFloat32ProjectionData2
 	m_bInitialized = true;
 }
 
+//----------------------------------------------------------------------------------------
+// Create an instance of the CFloat32ProjectionData2D class with pre-allocated data
+CFloat32ProjectionData2D::CFloat32ProjectionData2D(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory)
+{
+	m_bInitialized = false;
+	m_bInitialized = initialize(_pGeometry, _pCustomMemory);
+}
+ 
+
+
 // Assignment operator
 
 CFloat32ProjectionData2D& CFloat32ProjectionData2D::operator=(const CFloat32ProjectionData2D& _other)
@@ -119,6 +129,15 @@ bool CFloat32ProjectionData2D::initialize(CProjectionGeometry2D* _pGeometry, flo
 }
 
 //----------------------------------------------------------------------------------------
+// Initialization
+bool CFloat32ProjectionData2D::initialize(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory) 
+{
+	m_pGeometry = _pGeometry->clone();
+	m_bInitialized = _initialize(m_pGeometry->getDetectorCount(), m_pGeometry->getProjectionAngleCount(), _pCustomMemory);
+	return m_bInitialized;
+}
+
+//----------------------------------------------------------------------------------------
 // Destructor
 CFloat32ProjectionData2D::~CFloat32ProjectionData2D() 
 {
diff --git a/src/Float32ProjectionData3D.cpp b/src/Float32ProjectionData3D.cpp
index d039c83..2bd0447 100644
--- a/src/Float32ProjectionData3D.cpp
+++ b/src/Float32ProjectionData3D.cpp
@@ -270,4 +270,13 @@ CFloat32ProjectionData3D& CFloat32ProjectionData3D::operator-=(const float32& _f
 	return *this;
 }
 
+void CFloat32ProjectionData3D::changeGeometry(CProjectionGeometry3D* _pGeometry)
+{
+	if (!m_bInitialized) return;
+
+	delete m_pGeometry;
+	m_pGeometry = _pGeometry->clone();
+}
+
+
 } // end namespace astra
diff --git a/src/Float32VolumeData2D.cpp b/src/Float32VolumeData2D.cpp
index e11c4e4..c903c66 100644
--- a/src/Float32VolumeData2D.cpp
+++ b/src/Float32VolumeData2D.cpp
@@ -72,6 +72,15 @@ CFloat32VolumeData2D::CFloat32VolumeData2D(const CFloat32VolumeData2D& _other) :
 	m_bInitialized = true;
 }
 
+//----------------------------------------------------------------------------------------
+// Create an instance of the CFloat32VolumeData2D class with pre-allocated data
+CFloat32VolumeData2D::CFloat32VolumeData2D(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory)
+{
+	m_bInitialized = false;
+	m_bInitialized = initialize(_pGeometry, _pCustomMemory);
+}
+
+
 // Assignment operator
 
 CFloat32VolumeData2D& CFloat32VolumeData2D::operator=(const CFloat32VolumeData2D& _other)
@@ -122,6 +131,17 @@ bool CFloat32VolumeData2D::initialize(CVolumeGeometry2D* _pGeometry, float32 _fS
 	m_bInitialized = _initialize(m_pGeometry->getGridColCount(), m_pGeometry->getGridRowCount(), _fScalar);
 	return m_bInitialized;
 }
+
+//----------------------------------------------------------------------------------------
+// Initialization
+bool CFloat32VolumeData2D::initialize(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory) 
+{
+	m_pGeometry = _pGeometry->clone();
+	m_bInitialized = _initialize(m_pGeometry->getGridColCount(), m_pGeometry->getGridRowCount(), _pCustomMemory);
+	return m_bInitialized;
+}
+
+
 //----------------------------------------------------------------------------------------
 void CFloat32VolumeData2D::changeGeometry(CVolumeGeometry2D* _pGeometry)
 {
diff --git a/src/Float32VolumeData3D.cpp b/src/Float32VolumeData3D.cpp
index ce00a10..bd78001 100644
--- a/src/Float32VolumeData3D.cpp
+++ b/src/Float32VolumeData3D.cpp
@@ -266,4 +266,13 @@ CFloat32VolumeData3D& CFloat32VolumeData3D::operator-=(const float32& _fScalar)
 	return *this;
 }
 
+void CFloat32VolumeData3D::changeGeometry(CVolumeGeometry3D* _pGeometry)
+{
+	if (!m_bInitialized) return;
+
+	delete m_pGeometry;
+	m_pGeometry = _pGeometry->clone();
+}
+
+
 } // end namespace astra
diff --git a/src/Logger.cpp b/src/Logger.cpp
deleted file mode 100644
index 148e18c..0000000
--- a/src/Logger.cpp
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
-           2014-2015, CWI, Amsterdam
-
-Contact: astra@uantwerpen.be
-Website: http://sf.net/projects/astra-toolbox
-
-This file is part of the 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/Logger.h>
-
-using namespace astra;
-
-const char * g_loggerFileName = "astra_logger.txt";
-
-void CLogger::_assureIsInitialized()
-{
-	if(!m_bInitialized)
-	{
-		m_pOutFile = fopen(g_loggerFileName, "r");
-		if(m_pOutFile != NULL)
-		{
-			// file exists, users wants to log
-			fclose(m_pOutFile);
-			m_pOutFile = fopen(g_loggerFileName, "w");
-		}
-
-		m_bInitialized = true;
-	}
-}
-
-void CLogger::writeLine(const char * _text)
-{
-	_assureIsInitialized();
-
-	if(m_pOutFile != NULL)
-	{
-		fprintf(m_pOutFile, "%s\n", _text);
-		fflush(m_pOutFile);
-	}
-}
-
-void CLogger::writeTerminalCUDAError(const char * _fileName, int _iLine, const char * _errString)
-{
-	char buffer[256];
-
-	sprintf(buffer, "Cuda error in file '%s' in line %i : %s.", _fileName, _iLine, _errString);
-
-	writeLine(buffer);
-}
-
-CLogger::CLogger()
-{
-	;
-}
-
-FILE * CLogger::m_pOutFile = NULL;
-bool CLogger::m_bInitialized = false;
diff --git a/src/Logging.cpp b/src/Logging.cpp
new file mode 100644
index 0000000..8290ca0
--- /dev/null
+++ b/src/Logging.cpp
@@ -0,0 +1,184 @@
+/*
+-----------------------------------------------------------------------
+Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
+           2014-2015, CWI, Amsterdam
+
+Contact: astra@uantwerpen.be
+Website: http://sf.net/projects/astra-toolbox
+
+This file is part of the 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/>.
+
+-----------------------------------------------------------------------
+$Id$
+*/
+
+#define CLOG_MAIN
+#include <astra/clog.h>
+
+#include <astra/Logging.h>
+
+#include <cstdio>
+
+using namespace astra;
+
+void CLogger::enableScreen()
+{
+	m_bEnabledScreen = true;
+}
+
+void CLogger::enableFile()
+{
+	m_bEnabledFile = true;
+}
+
+void CLogger::enable()
+{
+	enableScreen();
+	enableFile();
+}
+
+void CLogger::disableScreen()
+{
+	m_bEnabledScreen = false;
+}
+
+void CLogger::disableFile()
+{
+	m_bEnabledFile = false;
+}
+
+void CLogger::disable()
+{
+	disableScreen();
+	disableFile();
+}
+
+void CLogger::debug(const char *sfile, int sline, const char *fmt, ...)
+{
+	_assureIsInitialized();
+	va_list ap;
+	va_start(ap, fmt);
+	if(m_bEnabledScreen) clog_debug(sfile,sline,0,fmt,ap);
+	if(m_bEnabledFile && m_bFileProvided) clog_debug(sfile,sline,1,fmt,ap);
+}
+
+void CLogger::info(const char *sfile, int sline, const char *fmt, ...)
+{
+	_assureIsInitialized();
+	va_list ap;
+	va_start(ap, fmt);
+	if(m_bEnabledScreen) clog_info(sfile,sline,0,fmt,ap);
+	if(m_bEnabledFile && m_bFileProvided) clog_info(sfile,sline,1,fmt,ap);
+}
+
+void CLogger::warn(const char *sfile, int sline, const char *fmt, ...)
+{
+	_assureIsInitialized();
+	va_list ap;
+	va_start(ap, fmt);
+	if(m_bEnabledScreen) clog_warn(sfile,sline,0,fmt,ap);
+	if(m_bEnabledFile && m_bFileProvided) clog_warn(sfile,sline,1,fmt,ap);
+}
+
+void CLogger::error(const char *sfile, int sline, const char *fmt, ...)
+{
+	_assureIsInitialized();
+	va_list ap;
+	va_start(ap, fmt);
+	if(m_bEnabledScreen) clog_error(sfile,sline,0,fmt,ap);
+	if(m_bEnabledFile && m_bFileProvided) clog_error(sfile,sline,1,fmt,ap);
+}
+
+void CLogger::_setLevel(int id, log_level m_eLevel)
+{
+	switch(m_eLevel){
+		case LOG_DEBUG:
+			clog_set_level(id,CLOG_DEBUG);
+			break;
+		case LOG_INFO:
+			clog_set_level(id,CLOG_INFO);
+			break;
+		case LOG_WARN:
+			clog_set_level(id,CLOG_WARN);
+			break;
+		case LOG_ERROR:
+			clog_set_level(id,CLOG_ERROR);
+			break;
+	}
+}
+
+void CLogger::setOutputScreen(int fd, log_level m_eLevel)
+{
+	_assureIsInitialized();
+	if(fd==1||fd==2){
+		clog_set_fd(0, fd);
+	}else{
+		error(__FILE__,__LINE__,"Invalid file descriptor");
+	}
+	_setLevel(0,m_eLevel);
+}
+
+void CLogger::setOutputFile(const char *filename, log_level m_eLevel)
+{
+	if(m_bFileProvided){
+		clog_free(1);
+		m_bFileProvided=false;
+	}
+	if(!clog_init_path(1,filename)){
+		m_bFileProvided=true;
+		_setLevel(1,m_eLevel);
+	}
+}
+
+void CLogger::_assureIsInitialized()
+{
+	if(!m_bInitialized)
+	{
+		clog_init_fd(0, 2);
+		clog_set_level(0, CLOG_INFO);
+		clog_set_fmt(0, "%l: %m\n");
+		m_bInitialized = true;
+	}
+}
+
+void CLogger::setFormatFile(const char *fmt)
+{
+	if(m_bFileProvided){
+		clog_set_fmt(1,fmt);
+	}else{
+		error(__FILE__,__LINE__,"No log file specified");
+	}
+}
+void CLogger::setFormatScreen(const char *fmt)
+{
+	clog_set_fmt(0,fmt);
+}
+
+CLogger::CLogger()
+{
+	;
+}
+
+bool CLogger::setCallbackScreen(void (*cb)(const char *msg, size_t len)){
+	_assureIsInitialized();
+	return clog_set_cb(0,cb)==0;
+}
+
+bool CLogger::m_bEnabledScreen = true;
+bool CLogger::m_bEnabledFile = true;
+bool CLogger::m_bFileProvided = false;
+bool CLogger::m_bInitialized = false;
diff --git a/src/Projector3D.cpp b/src/Projector3D.cpp
index b546ee9..14cb16a 100644
--- a/src/Projector3D.cpp
+++ b/src/Projector3D.cpp
@@ -108,6 +108,7 @@ bool CProjector3D::initialize(const Config& _cfg)
 		pProjGeometry = new CConeVecProjectionGeometry3D();
 	} else {
 		// Invalid geometry type
+		ASTRA_CONFIG_CHECK(false, "Projector3D", "Invalid projection geometry type specified.");
 	}
 	pProjGeometry->initialize(Config(node)); // this deletes node
 	m_pProjectionGeometry = pProjGeometry;
@@ -119,7 +120,7 @@ bool CProjector3D::initialize(const Config& _cfg)
 	CVolumeGeometry3D* pVolGeometry = new CVolumeGeometry3D();
 	pVolGeometry->initialize(Config(node)); // this deletes node
 	m_pVolumeGeometry = pVolGeometry;
-	ASTRA_CONFIG_CHECK(m_pVolumeGeometry->isInitialized(), "Projector2D", "VolumeGeometry not initialized.");
+	ASTRA_CONFIG_CHECK(m_pVolumeGeometry->isInitialized(), "Projector3D", "VolumeGeometry not initialized.");
 	CC.markNodeParsed("VolumeGeometry");
 
 	return true;