initial commit

+astra/ASTRA_GPU_wrapper/astra/GeometryUtil3D.h

@@ -0,0 +1,143 @@
+/*
+-----------------------------------------------------------------------
+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/>.
+
+-----------------------------------------------------------------------
+$Id$
+*/
+
+#ifndef _INC_ASTRA_GEOMETRYUTIL3D
+#define _INC_ASTRA_GEOMETRYUTIL3D
+
+namespace astra {
+
+struct SConeProjection {
+	// the source
+	double fSrcX, fSrcY, fSrcZ;
+
+	// the origin ("bottom left") of the (flat-panel) detector
+	double fDetSX, fDetSY, fDetSZ;
+
+	// the U-edge of a detector pixel
+	double fDetUX, fDetUY, fDetUZ;
+
+	// the V-edge of a detector pixel
+	double fDetVX, fDetVY, fDetVZ;
+
+
+
+
+	void translate(double dx, double dy, double dz) {
+		fSrcX += dx;
+		fSrcY += dy;
+		fSrcZ += dz;
+		fDetSX += dx;
+		fDetSY += dy;
+		fDetSZ += dz;
+
+	}
+	void scale(double factor) {
+		fSrcX *= factor;
+		fSrcY *= factor;
+		fSrcZ *= factor;
+		fDetSX *= factor;
+		fDetSY *= factor;
+		fDetSZ *= factor;
+		fDetUX *= factor;
+		fDetUY *= factor;
+		fDetUZ *= factor;
+		fDetVX *= factor;
+		fDetVY *= factor;
+		fDetVZ *= factor;
+	}
+};
+
+struct SPar3DProjection {
+	// the ray direction
+	double fRayX, fRayY, fRayZ;
+
+	// the origin ("bottom left") of the (flat-panel) detector
+	double fDetSX, fDetSY, fDetSZ;
+
+	// the U-edge of a detector pixel
+	double fDetUX, fDetUY, fDetUZ;
+
+	// the V-edge of a detector pixel
+	double fDetVX, fDetVY, fDetVZ;
+
+
+
+
+	void translate(double dx, double dy, double dz) {
+		fDetSX += dx;
+		fDetSY += dy;
+		fDetSZ += dz;
+	}
+	void scale(double factor) {
+		fRayX *= factor;
+		fRayY *= factor;
+		fRayZ *= factor;
+		fDetSX *= factor;
+		fDetSY *= factor;
+		fDetSZ *= factor;
+		fDetUX *= factor;
+		fDetUY *= factor;
+		fDetUZ *= factor;
+		fDetVX *= factor;
+		fDetVY *= factor;
+		fDetVZ *= factor;
+	}
+};
+
+void computeBP_UV_Coeffs(const SPar3DProjection& proj,
+                         double &fUX, double &fUY, double &fUZ, double &fUC,
+                         double &fVX, double &fVY, double &fVZ, double &fVC);
+
+void computeBP_UV_Coeffs(const SConeProjection& proj,
+                         double &fUX, double &fUY, double &fUZ, double &fUC,
+                         double &fVX, double &fVY, double &fVZ, double &fVC,
+                         double &fDX, double &fDY, double &fDZ, double &fDC);
+
+
+SConeProjection* genConeProjections(unsigned int iProjAngles,
+                                    unsigned int iProjU,
+                                    unsigned int iProjV,
+                                    double fOriginSourceDistance,
+                                    double fOriginDetectorDistance,
+                                    double fDetUSize,
+                                    double fDetVSize,
+                                    const float *pfAngles);
+
+SPar3DProjection* genPar3DProjections(unsigned int iProjAngles,
+                                      unsigned int iProjU,
+                                      unsigned int iProjV,
+                                      double fDetUSize,
+                                      double fDetVSize,
+                                      const float *pfAngles);
+
+
+
+
+}
+
+#endif

+astra/ASTRA_GPU_wrapper/astra/Globals.h

@@ -0,0 +1,318 @@
+/*
+-----------------------------------------------------------------------
+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/>.
+
+-----------------------------------------------------------------------
+$Id$
+*/
+
+#ifndef _INC_ASTRA_GLOBALS
+#define _INC_ASTRA_GLOBALS
+
+/*! \mainpage The ASTRA-toolbox 
+ *
+ * <img src="../images/logo_big.png"/>
+ */
+
+
+//----------------------------------------------------------------------------------------
+
+#ifdef _MSC_VER
+
+// disable warning: 'fopen' was declared deprecated
+#pragma warning (disable : 4996)
+// disable warning: C++ exception handler used, but unwind semantics are not enables
+#pragma warning (disable : 4530)
+// disable warning: no suitable definition provided for explicit template instantiation request
+#pragma warning (disable : 4661)
+
+#endif
+
+//----------------------------------------------------------------------------------------
+// standard includes
+#include <cassert>
+#include <iostream>
+#include <fstream>
+#include <math.h>
+//#include <boost/static_assert.hpp>
+//#include <boost/throw_exception.hpp>
+
+//----------------------------------------------------------------------------------------
+// macro's
+
+#define ASTRA_TOOLBOXVERSION_MAJOR 1
+#define ASTRA_TOOLBOXVERSION_MINOR 7
+#define ASTRA_TOOLBOXVERSION ((ASTRA_TOOLBOXVERSION_MAJOR)*100 + (ASTRA_TOOLBOXVERSION_MINOR))
+#define ASTRA_TOOLBOXVERSION_STRING "1.7.1"
+
+
+#define ASTRA_ASSERT(a) assert(a)
+
+#define ASTRA_CONFIG_CHECK(value, type, msg) if (!(value)) { cout << "Configuration Error in " << type << ": " << msg << endl; return false; }
+
+#define ASTRA_CONFIG_WARNING(type, msg) { cout << "Warning in " << type << ": " << msg << endl; }
+
+
+#define ASTRA_DELETE(a) if (a) { delete a; a = NULL; }
+#define ASTRA_DELETE_ARRAY(a) if (a) { delete[] a; a = NULL; }
+
+#ifdef _MSC_VER
+
+#ifdef DLL_EXPORTS
+#define _AstraExport __declspec(dllexport)
+#define EXPIMP_TEMPLATE
+#else
+#define _AstraExport __declspec(dllimport)
+#define EXPIMP_TEMPLATE extern
+#endif
+
+#else
+
+#define _AstraExport
+
+#endif
+
+
+//----------------------------------------------------------------------------------------
+// typedefs
+namespace astra {
+	typedef float float32;
+	typedef double float64;
+	typedef unsigned short int uint16;
+	typedef signed short int sint16;
+	typedef unsigned char uchar8;
+	typedef signed char schar8;
+
+	typedef int int32;
+	typedef short int int16;
+}
+
+//----------------------------------------------------------------------------------------
+// globals vars & functions
+//namespace astra {
+//#define ToolboxVersion 0.1f;
+
+//float32 getVersion() { return ToolboxVersion; }
+
+//_AstraExport bool cudaEnabled() { 
+//#ifdef ASTRA_CUDA	
+//	return true; 
+//#else
+//	return false;
+//#endif
+//}
+//}
+
+//----------------------------------------------------------------------------------------
+// errors
+namespace astra {
+
+typedef enum {ASTRA_SUCCESS, 
+			  ASTRA_ERROR_NOT_INITIALIZED,
+			  ASTRA_ERROR_INVALID_FILE,
+			  ASTRA_ERROR_OUT_OF_RANGE,
+			  ASTRA_ERROR_DIMENSION_MISMATCH,
+			  ASTRA_ERROR_EXTERNAL_LIBRARY,
+			  ASTRA_ERROR_ALLOCATION,
+			  ASTRA_ERROR_NOT_IMPLEMENTED} AstraError;
+}
+
+
+//----------------------------------------------------------------------------------------
+// variables
+namespace astra {
+	const float32 PI = 3.14159265358979323846264338328f;
+	const float32 PI32 = 3.14159265358979323846264338328f;
+	const float32 PIdiv2 = PI / 2;
+	const float32 PIdiv4 = PI / 4;
+	const float32 eps = 1e-7f;
+	
+	extern _AstraExport bool running_in_matlab;
+}
+
+//----------------------------------------------------------------------------------------
+// math
+namespace astra {
+
+	inline float32 cos_73s(float32 x) 
+	{ 
+		/*
+		const float32 c1 =  0.999999953464f;
+		const float32 c2 = -0.4999999053455f;
+		const float32 c3 =  0.0416635846769f;
+		const float32 c4 = -0.0013853704264f;
+		const float32 c5 =  0.000023233f;
+		*/
+		const float c1= (float)0.99940307;
+		const float c2= (float)-0.49558072;
+		const float c3= (float)0.03679168;
+
+		float32 x2;
+		x2 = x * x;
+		//return (c1 + x2*(c2 + x2*(c3 + x2*(c4 + c5*x2))));
+		return (c1 + x2*(c2 + c3 * x2));
+	}
+
+	inline float32 fast_cos(float32 x) 
+	{
+		int quad; 
+
+		//x = fmod(x, 2*PI);		// Get rid of values > 2* pi
+		if (x < 0) x = -x;		// cos(-x) = cos(x)
+		quad = int(x/PIdiv2);	// Get quadrant # (0 to 3) 
+		switch (quad) {
+			case 0: return  cos_73s(x);
+			case 1: return -cos_73s(PI-x);
+			case 2: return -cos_73s(x-PI);
+			case 3: return  cos_73s(2*PI-x);
+		}
+		return 0.0f;
+	}
+
+	inline float32 fast_sin(float32 x){
+		return fast_cos(PIdiv2-x);
+	}
+
+}
+
+//----------------------------------------------------------------------------------------
+// structs
+namespace astra {
+	/**
+	 * Struct for storing pixel weigths
+	 **/
+	struct SPixelWeight
+	{
+		int m_iIndex;
+		float32 m_fWeight;
+	};
+
+	/**
+	 * Struct combining some properties of a detector in 1D detector row
+	 **/
+	struct SDetector2D
+	{
+		int m_iIndex;
+		int m_iAngleIndex;
+		int m_iDetectorIndex;
+	};
+	
+	/**
+	 * Struct combining some properties of a detector in 2D detector array
+	 **/
+	struct SDetector3D
+	{
+		int m_iIndex;
+		int m_iAngleIndex;
+		int m_iDetectorIndex;
+		int m_iSliceIndex;
+	};
+}
+//----------------------------------------------------------------------------------------
+// some toys
+
+// safe reinterpret cast
+// template <class To, class From>
+// To safe_reinterpret_cast(From from)
+// {
+// 	BOOST_STATIC_ASSERT(sizeof(From) <= sizeof(To));
+// 	return reinterpret_cast<To>(from);
+// }
+
+//----------------------------------------------------------------------------------------
+// functions for testing
+template<typename T>
+inline void writeArray(T*** arr, int dim1, int dim2, int dim3, const std::string& filename)
+{
+	std::ofstream out(filename.c_str());
+	int i1, i2, i3;
+	for (i1 = 0; i1 < dim1; ++i1) {
+		for (i2 = 0; i2 < dim2; ++i2) {
+			for (i3 = 0; i3 < dim3; ++i3) {
+				out << arr[i1][i2][i3] << " ";
+			}
+			out << std::endl;
+		}
+		out << std::endl;
+	}
+	out.close();
+}
+
+template<typename T>
+inline void writeArray(T** arr, int dim1, int dim2, const std::string& filename)
+{
+	std::ofstream out(filename.c_str());
+	for (int i1 = 0; i1 < dim1; i1++) {
+		for (int i2 = 0; i2 < dim2; i2++) {
+			out << arr[i1][i2] << " ";
+		}
+		out << std::endl;
+	}
+	out.close();
+}
+
+template<typename T>
+inline void writeArray(T* arr, int dim1, const std::string& filename)
+{
+	std::ofstream out(filename.c_str());
+	for (int i1 = 0; i1 < dim1; i1++) {
+		out << arr[i1] << " ";
+	}
+	out.close();
+}
+namespace astra {
+_AstraExport inline int getVersion() { return ASTRA_TOOLBOXVERSION; }
+_AstraExport inline const char* getVersionString() { return ASTRA_TOOLBOXVERSION_STRING; }
+#ifdef ASTRA_CUDA
+_AstraExport inline bool cudaEnabled() { return true; }
+#else
+_AstraExport inline bool cudaEnabled() { return false; }
+#endif
+}
+//----------------------------------------------------------------------------------------
+// portability between MSVC and Linux/gcc
+
+#ifndef _MSC_VER
+// #include "swrap.h"
+#define EXPIMP_TEMPLATE
+
+#if !defined(FORCEINLINE) && (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
+#define FORCEINLINE inline __attribute__((__always_inline__))
+#else
+#define FORCEINLINE inline
+#endif
+
+#else
+
+#define FORCEINLINE __forceinline
+
+#endif
+
+//----------------------------------------------------------------------------------------
+// use pthreads on Linux and OSX
+#if defined(__linux__) || defined(__MACH__)
+#define USE_PTHREADS
+#endif
+
+
+#endif

+astra/ASTRA_GPU_wrapper/astra/Logging.cpp

@@ -0,0 +1,212 @@
+/*
+-----------------------------------------------------------------------
+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 "clog.h"
+
+#include "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, apf;
+	if(m_bEnabledScreen){
+        va_start(ap, fmt);
+        clog_debug(sfile,sline,0,fmt,ap);
+        va_end(ap);
+    }
+	if(m_bEnabledFile && m_bFileProvided){
+        va_start(apf, fmt);
+        clog_debug(sfile,sline,1,fmt,apf);
+        va_end(apf);
+    }
+}
+
+void CLogger::info(const char *sfile, int sline, const char *fmt, ...)
+{
+	_assureIsInitialized();
+	va_list ap, apf;
+	if(m_bEnabledScreen){
+        va_start(ap, fmt);
+        clog_info(sfile,sline,0,fmt,ap);
+        va_end(ap);
+    }
+	if(m_bEnabledFile && m_bFileProvided){
+        va_start(apf, fmt);
+        clog_info(sfile,sline,1,fmt,apf);
+        va_end(apf);
+    }
+}
+
+void CLogger::warn(const char *sfile, int sline, const char *fmt, ...)
+{
+	_assureIsInitialized();
+	va_list ap, apf;
+	if(m_bEnabledScreen){
+        va_start(ap, fmt);
+        clog_warn(sfile,sline,0,fmt,ap);
+        va_end(ap);
+    }
+	if(m_bEnabledFile && m_bFileProvided){
+        va_start(apf, fmt);
+        clog_warn(sfile,sline,1,fmt,apf);
+        va_end(apf);
+    }
+}
+
+void CLogger::error(const char *sfile, int sline, const char *fmt, ...)
+{
+	_assureIsInitialized();
+	va_list ap, apf;
+	if(m_bEnabledScreen){
+        va_start(ap, fmt);
+        clog_error(sfile,sline,0,fmt,ap);
+        va_end(ap);
+    }
+	if(m_bEnabledFile && m_bFileProvided){
+        va_start(apf, fmt);
+        clog_error(sfile,sline,1,fmt,apf);
+        va_end(apf);
+    }
+}
+
+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;

+astra/ASTRA_GPU_wrapper/astra/Logging.h

@@ -0,0 +1,164 @@
+/*
+-----------------------------------------------------------------------
+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/>.
+
+-----------------------------------------------------------------------
+$Id$
+*/
+
+#ifndef _INC_ASTRA_LOGGING
+#define _INC_ASTRA_LOGGING
+
+#include "Globals.h"
+
+//#define ASTRA_DEBUG(...) astra::CLogger::debug(__FILE__,__LINE__, __VA_ARGS__)
+//#define ASTRA_INFO(...) astra::CLogger::info(__FILE__,__LINE__, __VA_ARGS__)
+//#define ASTRA_WARN(...) astra::CLogger::warn(__FILE__,__LINE__, __VA_ARGS__)
+//#define ASTRA_ERROR(...) astra::CLogger::error(__FILE__,__LINE__, __VA_ARGS__)
+
+// FIXME !!!!!!
+#define ASTRA_DEBUG(...) 
+#define ASTRA_INFO(...) 
+#define ASTRA_WARN(...) 
+#define ASTRA_ERROR(...) 
+
+namespace astra
+{
+
+enum log_level {
+    LOG_DEBUG,
+    LOG_INFO,
+    LOG_WARN,
+    LOG_ERROR
+};
+
+class _AstraExport CLogger
+{
+	CLogger();
+  ~CLogger();
+  static bool m_bEnabledFile;
+  static bool m_bEnabledScreen;
+  static bool m_bFileProvided;
+  static bool m_bInitialized;
+  static void _assureIsInitialized();
+  static void _setLevel(int id, log_level m_eLevel);
+
+public:
+
+	/**
+	 * Writes a line to the log file (newline is added). Ignored if logging is turned off.
+	 *
+	 * @param sfile
+   * The name of the source file making this log call (e.g. __FILE__).
+   *
+   * @param sline
+   * The line number of the call in the source code (e.g. __LINE__).
+   *
+   * @param id
+   * The id of the logger to write to.
+   *
+   * @param fmt
+   * The format string for the message (printf formatting).
+   *
+   * @param ...
+   * Any additional format arguments.
+	 */
+  static void debug(const char *sfile, int sline, const char *fmt, ...);
+  static void info(const char *sfile, int sline, const char *fmt, ...);
+  static void warn(const char *sfile, int sline, const char *fmt, ...);
+  static void error(const char *sfile, int sline, const char *fmt, ...);
+
+  /**
+	 * Sets the file to log to, with logging level.
+   *
+   * @param filename
+   * File to log to.
+	 *
+	 * @param m_eLevel
+   * Logging level (LOG_DEBUG, LOG_WARN, LOG_INFO, LOG_ERROR).
+   *
+	 */
+  static void setOutputFile(const char *filename, log_level m_eLevel);
+
+  /**
+	 * Sets the screen to log to, with logging level.
+   *
+   * @param screen_fd
+   * Screen file descriptor (1 for stdout, 2 for stderr)
+	 *
+	 * @param m_eLevel
+   * Logging level (LOG_DEBUG, LOG_WARN, LOG_INFO, LOG_ERROR).
+   *
+	 */
+  static void setOutputScreen(int fd, log_level m_eLevel);
+  
+  /**
+   * Set the format string for log messages.  Here are the substitutions you may
+   * use:
+   *
+   *     %f: Source file name generating the log call.
+   *     %n: Source line number where the log call was made.
+   *     %m: The message text sent to the logger (after printf formatting).
+   *     %d: The current date, formatted using the logger's date format.
+   *     %t: The current time, formatted using the logger's time format.
+   *     %l: The log level (one of "DEBUG", "INFO", "WARN", or "ERROR").
+   *     %%: A literal percent sign.
+   *
+   * The default format string is "%d %t %f(%n): %l: %m\n".
+   *
+   * @param fmt
+   * The new format string, which must be less than 256 bytes.
+   * You probably will want to end this with a newline (\n).
+   *
+   */
+  static void setFormatFile(const char *fmt);
+  static void setFormatScreen(const char *fmt);
+
+
+  /**
+   * Enable logging.
+   *
+   */
+  static void enable();
+  static void enableScreen();
+  static void enableFile();
+
+  /**
+   * Disable logging.
+   *
+   */
+  static void disable();
+  static void disableScreen();
+  static void disableFile();
+
+  /**
+   * Set callback function for logging to screen.
+   * @return whether callback was set succesfully.
+   *
+   */
+  static bool setCallbackScreen(void (*cb)(const char *msg, size_t len));
+
+};
+
+}
+
+#endif /* _INC_ASTRA_LOGGING */

+astra/ASTRA_GPU_wrapper/astra/clog.h

@@ -0,0 +1,693 @@
+/* clog: Extremely simple logger for C.
+ *
+ * Features:
+ * - Implemented purely as a single header file.
+ * - Create multiple loggers.
+ * - Four log levels (debug, info, warn, error).
+ * - Custom formats.
+ * - Fast.
+ *
+ * Dependencies:
+ * - Should conform to C89, C++98 (but requires vsnprintf, unfortunately).
+ * - POSIX environment.
+ *
+ * USAGE:
+ *
+ * Include this header in any file that wishes to write to logger(s).  In
+ * exactly one file (per executable), define CLOG_MAIN first (e.g. in your
+ * main .c file).
+ *
+ *     #define CLOG_MAIN
+ *     #include "clog.h"
+ *
+ * This will define the actual objects that all the other units will use.
+ *
+ * Loggers are identified by integers (0 - 15).  It's expected that you'll
+ * create meaningful constants and then refer to the loggers as such.
+ *
+ * Example:
+ *
+ *  const int MY_LOGGER = 0;
+ *
+ *  int main() {
+ *      int r;
+ *      r = clog_init_path(MY_LOGGER, "my_log.txt");
+ *      if (r != 0) {
+ *          fprintf(stderr, "Logger initialization failed.\n");
+ *          return 1;
+ *      }
+ *      clog_info(CLOG(MY_LOGGER), "Hello, world!");
+ *      clog_free(MY_LOGGER);
+ *      return 0;
+ *  }
+ *
+ * The CLOG macro used in the call to clog_info is a helper that passes the
+ * __FILE__ and __LINE__ parameters for you, so you don't have to type them
+ * every time. (It could be prettier with variadic macros, but that requires
+ * C99 or C++11 to be standards compliant.)
+ *
+ * Errors encountered by clog will be printed to stderr.  You can suppress
+ * these by defining a macro called CLOG_SILENT before including clog.h.
+ *
+ * License: Do whatever you want. It would be nice if you contribute
+ * improvements as pull requests here:
+ *
+ *   https://github.com/mmueller/clog
+ *
+ * Copyright 2013 Mike Mueller <mike@subfocal.net>.
+ *
+ * As is; no warranty is provided; use at your own risk.
+ */
+
+#ifndef __CLOG_H__
+#define __CLOG_H__
+
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+#include <fcntl.h>
+#include <stdarg.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <time.h>
+#ifndef _MSC_VER
+#include <unistd.h>
+#else
+#define WIN32_LEAN_AND_MEAN
+#include <windows.h>
+#include <io.h>
+#define open _open
+#define close _close
+#define write _write
+#define snprintf _snprintf
+#endif
+
+/* Number of loggers that can be defined. */
+#define CLOG_MAX_LOGGERS 16
+
+/* Format strings cannot be longer than this. */
+#define CLOG_FORMAT_LENGTH 256
+
+/* Formatted times and dates should be less than this length. If they are not,
+ * they will not appear in the log. */
+#define CLOG_DATETIME_LENGTH 256
+
+/* Default format strings. */
+#define CLOG_DEFAULT_FORMAT "%d %t %f(%n): %l: %m\n"
+#define CLOG_DEFAULT_DATE_FORMAT "%Y-%m-%d"
+#define CLOG_DEFAULT_TIME_FORMAT "%H:%M:%S"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+enum clog_level {
+    CLOG_DEBUG,
+    CLOG_INFO,
+    CLOG_WARN,
+    CLOG_ERROR
+};
+
+struct clog;
+
+/**
+ * Create a new logger writing to the given file path.  The file will always
+ * be opened in append mode.
+ *
+ * @param id
+ * A constant integer between 0 and 15 that uniquely identifies this logger.
+ *
+ * @param path
+ * Path to the file where log messages will be written.
+ *
+ * @return
+ * Zero on success, non-zero on failure.
+ */
+int clog_init_path(int id, const char *const path);
+
+/**
+ * Create a new logger writing to a file descriptor.
+ *
+ * @param id
+ * A constant integer between 0 and 15 that uniquely identifies this logger.
+ *
+ * @param fd
+ * The file descriptor where log messages will be written.
+ *
+ * @return
+ * Zero on success, non-zero on failure.
+ */
+int clog_init_fd(int id, int fd);
+
+/**
+ * Destroy (clean up) a logger.  You should do this at the end of execution,
+ * or when you are done using the logger.
+ *
+ * @param id
+ * The id of the logger to destroy.
+ */
+void clog_free(int id);
+
+#define CLOG(id) __FILE__, __LINE__, id
+
+/**
+ * Log functions (one per level).  Call these to write messages to the log
+ * file.  The first three arguments can be replaced with a call to the CLOG
+ * macro defined above, e.g.:
+ *
+ *     clog_debug(CLOG(MY_LOGGER_ID), "This is a log message.");
+ *
+ * @param sfile
+ * The name of the source file making this log call (e.g. __FILE__).
+ *
+ * @param sline
+ * The line number of the call in the source code (e.g. __LINE__).
+ *
+ * @param id
+ * The id of the logger to write to.
+ *
+ * @param fmt
+ * The format string for the message (printf formatting).
+ *
+ * @param ...
+ * Any additional format arguments.
+ */
+void clog_debug(const char *sfile, int sline, int id, const char *fmt, va_list ap);
+void clog_info(const char *sfile, int sline, int id, const char *fmt, va_list ap);
+void clog_warn(const char *sfile, int sline, int id, const char *fmt, va_list ap);
+void clog_error(const char *sfile, int sline, int id, const char *fmt, va_list ap);
+
+/**
+ * Set the minimum level of messages that should be written to the log.
+ * Messages below this level will not be written.  By default, loggers are
+ * created with level == CLOG_DEBUG.
+ *
+ * @param id
+ * The identifier of the logger.
+ *
+ * @param level
+ * The new minimum log level.
+ *
+ * @return
+ * Zero on success, non-zero on failure.
+ */
+int clog_set_level(int id, enum clog_level level);
+
+/**
+ * Set the format string used for times.  See strftime(3) for how this string
+ * should be defined.  The default format string is CLOG_DEFAULT_TIME_FORMAT.
+ *
+ * @param fmt
+ * The new format string, which must be less than CLOG_FORMAT_LENGTH bytes.
+ *
+ * @return
+ * Zero on success, non-zero on failure.
+ */
+int clog_set_time_fmt(int id, const char *fmt);
+
+/**
+ * Set the format string used for dates.  See strftime(3) for how this string
+ * should be defined.  The default format string is CLOG_DEFAULT_DATE_FORMAT.
+ *
+ * @param fmt
+ * The new format string, which must be less than CLOG_FORMAT_LENGTH bytes.
+ *
+ * @return
+ * Zero on success, non-zero on failure.
+ */
+int clog_set_date_fmt(int id, const char *fmt);
+
+/**
+ * Set the format string for log messages.  Here are the substitutions you may
+ * use:
+ *
+ *     %f: Source file name generating the log call.
+ *     %n: Source line number where the log call was made.
+ *     %m: The message text sent to the logger (after printf formatting).
+ *     %d: The current date, formatted using the logger's date format.
+ *     %t: The current time, formatted using the logger's time format.
+ *     %l: The log level (one of "DEBUG", "INFO", "WARN", or "ERROR").
+ *     %%: A literal percent sign.
+ *
+ * The default format string is CLOG_DEFAULT_FORMAT.
+ *
+ * @param fmt
+ * The new format string, which must be less than CLOG_FORMAT_LENGTH bytes.
+ * You probably will want to end this with a newline (\n).
+ *
+ * @return
+ * Zero on success, non-zero on failure.
+ */
+int clog_set_fmt(int id, const char *fmt);
+
+/**
+ * Set the callback function.
+ *
+ * @param cb
+ * The new callback function.
+ *
+ * @return
+ * Zero on success, non-zero on failure.
+ */
+int clog_set_cb(int id, void (*cb)(const char *msg, size_t len));
+
+/**
+ * Set the file descriptor.
+ *
+ * @param id
+ * The identifier of the logger.
+ *
+ * @param fd
+ * The new file descriptor.
+ *
+ * @return
+ * Zero on success, non-zero on failure.
+ */
+int clog_set_fd(int id, int fd);
+
+
+/*
+ * No need to read below this point.
+ */
+
+/**
+ * The C logger structure.
+ */
+struct clog {
+
+    /* The current level of this logger. Messages below it will be dropped. */
+    enum clog_level level;
+
+    /* The file being written. */
+    int fd;
+
+    /* The format specifier. */
+    char fmt[CLOG_FORMAT_LENGTH];
+
+    /* Date format */
+    char date_fmt[CLOG_FORMAT_LENGTH];
+
+    /* Time format */
+    char time_fmt[CLOG_FORMAT_LENGTH];
+
+    /* Tracks whether the fd needs to be closed eventually. */
+    int opened;
+
+    /* Callback function for each log message. */
+    void (*cb)(const char *msg, size_t len);
+};
+
+void _clog_err(const char *fmt, ...);
+
+#ifdef CLOG_MAIN
+struct clog *_clog_loggers[CLOG_MAX_LOGGERS] = { 0 };
+#else
+extern struct clog *_clog_loggers[CLOG_MAX_LOGGERS];
+#endif
+
+#ifdef CLOG_MAIN
+
+const char *const CLOG_LEVEL_NAMES[] = {
+    "Debug",
+    "Info",
+    "Warning",
+    "Error",
+};
+
+int
+clog_init_path(int id, const char *const path)
+{
+    int fd = open(path, O_CREAT | O_WRONLY | O_APPEND, 0666);
+    if (fd == -1) {
+        _clog_err("Unable to open %s: %s\n", path, strerror(errno));
+        return 1;
+    }
+    if (clog_init_fd(id, fd)) {
+        close(fd);
+        return 1;
+    }
+    _clog_loggers[id]->opened = 1;
+    return 0;
+}
+
+int
+clog_init_fd(int id, int fd)
+{
+    struct clog *logger;
+
+    if (_clog_loggers[id] != NULL) {
+        _clog_err("Logger %d already initialized.\n", id);
+        return 1;
+    }
+
+    logger = (struct clog *) malloc(sizeof(struct clog));
+    if (logger == NULL) {
+        _clog_err("Failed to allocate logger: %s\n", strerror(errno));
+        return 1;
+    }
+
+    logger->level = CLOG_DEBUG;
+    logger->fd = fd;
+    logger->opened = 0;
+    strcpy(logger->fmt, CLOG_DEFAULT_FORMAT);
+    strcpy(logger->date_fmt, CLOG_DEFAULT_DATE_FORMAT);
+    strcpy(logger->time_fmt, CLOG_DEFAULT_TIME_FORMAT);
+    logger->cb = NULL;
+
+    _clog_loggers[id] = logger;
+    return 0;
+}
+
+void
+clog_free(int id)
+{
+    if (_clog_loggers[id]) {
+        if (_clog_loggers[id]->opened) {
+            close(_clog_loggers[id]->fd);
+        }
+        free(_clog_loggers[id]);
+        _clog_loggers[id]=NULL;
+    }
+}
+
+int
+clog_set_level(int id, enum clog_level level)
+{
+    if (_clog_loggers[id] == NULL) {
+        return 1;
+    }
+    if ((unsigned) level > CLOG_ERROR) {
+        return 1;
+    }
+    _clog_loggers[id]->level = level;
+    return 0;
+}
+
+int
+clog_set_fd(int id, int fd)
+{
+    if (_clog_loggers[id] == NULL) {
+        return 1;
+    }
+    _clog_loggers[id]->fd = fd;
+    return 0;
+}
+
+int
+clog_set_time_fmt(int id, const char *fmt)
+{
+    struct clog *logger = _clog_loggers[id];
+    if (logger == NULL) {
+        _clog_err("clog_set_time_fmt: No such logger: %d\n", id);
+        return 1;
+    }
+    if (strlen(fmt) >= CLOG_FORMAT_LENGTH) {
+        _clog_err("clog_set_time_fmt: Format specifier too long.\n");
+        return 1;
+    }
+    strcpy(logger->time_fmt, fmt);
+    return 0;
+}
+
+int
+clog_set_date_fmt(int id, const char *fmt)
+{
+    struct clog *logger = _clog_loggers[id];
+    if (logger == NULL) {
+        _clog_err("clog_set_date_fmt: No such logger: %d\n", id);
+        return 1;
+    }
+    if (strlen(fmt) >= CLOG_FORMAT_LENGTH) {
+        _clog_err("clog_set_date_fmt: Format specifier too long.\n");
+        return 1;
+    }
+    strcpy(logger->date_fmt, fmt);
+    return 0;
+}
+
+int
+clog_set_fmt(int id, const char *fmt)
+{
+    struct clog *logger = _clog_loggers[id];
+    if (logger == NULL) {
+        _clog_err("clog_set_fmt: No such logger: %d\n", id);
+        return 1;
+    }
+    if (strlen(fmt) >= CLOG_FORMAT_LENGTH) {
+        _clog_err("clog_set_fmt: Format specifier too long.\n");
+        return 1;
+    }
+    strcpy(logger->fmt, fmt);
+    return 0;
+}
+
+int
+clog_set_cb(int id, void (*cb)(const char *msg, size_t len))
+{
+    struct clog *logger = _clog_loggers[id];
+    if (logger == NULL) {
+        _clog_err("clog_set_cb: No such logger: %d\n", id);
+        return 1;
+    }
+    logger->cb = cb;
+    return 0;
+}
+
+/* Internal functions */
+
+size_t
+_clog_append_str(char **dst, char *orig_buf, const char *src, size_t cur_size)
+{
+    size_t new_size = cur_size;
+
+    while (strlen(*dst) + strlen(src) >= new_size) {
+        new_size *= 2;
+    }
+    if (new_size != cur_size) {
+        if (*dst == orig_buf) {
+            *dst = (char *) malloc(new_size);
+            strcpy(*dst, orig_buf);
+        } else {
+            *dst = (char *) realloc(*dst, new_size);
+        }
+    }
+
+    strcat(*dst, src);
+    return new_size;
+}
+
+size_t
+_clog_append_int(char **dst, char *orig_buf, long int d, size_t cur_size)
+{
+    char buf[40]; /* Enough for 128-bit decimal */
+    if (snprintf(buf, 40, "%ld", d) >= 40) {
+        return cur_size;
+    }
+    return _clog_append_str(dst, orig_buf, buf, cur_size);
+}
+
+size_t
+_clog_append_time(char **dst, char *orig_buf, struct tm *lt,
+                  const char *fmt, size_t cur_size)
+{
+    char buf[CLOG_DATETIME_LENGTH];
+    size_t result = strftime(buf, CLOG_DATETIME_LENGTH, fmt, lt);
+
+    if (result > 0) {
+        return _clog_append_str(dst, orig_buf, buf, cur_size);
+    }
+
+    return cur_size;
+}
+
+const char *
+_clog_basename(const char *path)
+{
+    const char *slash = strrchr(path, '/');
+    if (slash) {
+        path = slash + 1;
+    }
+#ifdef _WIN32
+    slash = strrchr(path, '\\');
+    if (slash) {
+        path = slash + 1;
+    }
+#endif
+    return path;
+}
+
+char *
+_clog_format(const struct clog *logger, char buf[], size_t buf_size,
+             const char *sfile, int sline, const char *level,
+             const char *message)
+{
+    size_t cur_size = buf_size;
+    char *result = buf;
+    enum { NORMAL, SUBST } state = NORMAL;
+    size_t fmtlen = strlen(logger->fmt);
+    size_t i;
+    time_t t = time(NULL);
+    struct tm *lt = localtime(&t);
+
+    sfile = _clog_basename(sfile);
+    result[0] = 0;
+    for (i = 0; i < fmtlen; ++i) {
+        if (state == NORMAL) {
+            if (logger->fmt[i] == '%') {
+                state = SUBST;
+            } else {
+                char str[2] = { 0 };
+                str[0] = logger->fmt[i];
+                cur_size = _clog_append_str(&result, buf, str, cur_size);
+            }
+        } else {
+            switch (logger->fmt[i]) {
+                case '%':
+                    cur_size = _clog_append_str(&result, buf, "%", cur_size);
+                    break;
+                case 't':
+                    cur_size = _clog_append_time(&result, buf, lt,
+                                                 logger->time_fmt, cur_size);
+                    break;
+                case 'd':
+                    cur_size = _clog_append_time(&result, buf, lt,
+                                                 logger->date_fmt, cur_size);
+                    break;
+                case 'l':
+                    cur_size = _clog_append_str(&result, buf, level, cur_size);
+                    break;
+                case 'n':
+                    cur_size = _clog_append_int(&result, buf, sline, cur_size);
+                    break;
+                case 'f':
+                    cur_size = _clog_append_str(&result, buf, sfile, cur_size);
+                    break;
+                case 'm':
+                    cur_size = _clog_append_str(&result, buf, message,
+                                                cur_size);
+                    break;
+            }
+            state = NORMAL;
+        }
+    }
+
+    return result;
+}
+
+void
+_clog_log(const char *sfile, int sline, enum clog_level level,
+          int id, const char *fmt, va_list ap)
+{
+    /* For speed: Use a stack buffer until message exceeds 4096, then switch
+     * to dynamically allocated.  This should greatly reduce the number of
+     * memory allocations (and subsequent fragmentation). */
+    char buf[4096];
+    size_t buf_size = 4096;
+    char *dynbuf = buf;
+    char *message;
+    int result;
+    struct clog *logger = _clog_loggers[id];
+
+    if (!logger) {
+        _clog_err("No such logger: %d\n", id);
+        return;
+    }
+
+    if (level < logger->level) {
+        return;
+    }
+
+    /* Format the message text with the argument list. */
+    result = vsnprintf(dynbuf, buf_size, fmt, ap);
+    if ((size_t) result >= buf_size) {
+        buf_size = result + 1;
+        dynbuf = (char *) malloc(buf_size);
+        result = vsnprintf(dynbuf, buf_size, fmt, ap);
+        if ((size_t) result >= buf_size) {
+            /* Formatting failed -- too large */
+            _clog_err("Formatting failed (1).\n");
+            free(dynbuf);
+            return;
+        }
+    }
+
+    /* Format according to log format and write to log */
+    {
+        char message_buf[4096];
+        message = _clog_format(logger, message_buf, 4096, sfile, sline,
+                               CLOG_LEVEL_NAMES[level], dynbuf);
+        if (!message) {
+            _clog_err("Formatting failed (2).\n");
+            if (dynbuf != buf) {
+                free(dynbuf);
+            }
+            return;
+        }
+        result = write(logger->fd, message, strlen(message));
+        if (logger->cb) logger->cb(message,strlen(message));
+        if (result == -1) {
+            _clog_err("Unable to write to log file: %s\n", strerror(errno));
+        }
+        if (message != message_buf) {
+            free(message);
+        }
+        if (dynbuf != buf) {
+            free(dynbuf);
+        }
+#ifndef _MSC_VER
+        fsync(logger->fd);
+#else
+        HANDLE h = (HANDLE) _get_osfhandle(logger->fd);
+        if (h != INVALID_HANDLE_VALUE) {
+            // This call will fail on a console fd, but that's ok.
+            FlushFileBuffers(h);
+        }
+#endif
+    }
+}
+
+void
+clog_debug(const char *sfile, int sline, int id, const char *fmt, va_list ap)
+{
+    _clog_log(sfile, sline, CLOG_DEBUG, id, fmt, ap);
+}
+
+void
+clog_info(const char *sfile, int sline, int id, const char *fmt, va_list ap)
+{
+    _clog_log(sfile, sline, CLOG_INFO, id, fmt, ap);
+}
+
+void
+clog_warn(const char *sfile, int sline, int id, const char *fmt, va_list ap)
+{
+    _clog_log(sfile, sline, CLOG_WARN, id, fmt, ap);
+}
+
+void
+clog_error(const char *sfile, int sline, int id, const char *fmt, va_list ap)
+{
+    _clog_log(sfile, sline, CLOG_ERROR, id, fmt, ap);
+}
+
+void
+_clog_err(const char *fmt, ...)
+{
+#ifdef CLOG_SILENT
+    (void) fmt;
+#else
+    va_list ap;
+
+    va_start(ap, fmt);
+    vfprintf(stderr, fmt, ap);
+#endif
+}
+
+#endif /* CLOG_MAIN */
+
+#ifdef __cplusplus
+} /* extern "C" */
+#endif
+
+#endif /* __CLOG_H__ */