Merge branch 'master' into parallel_vec

9 files changed, 54 insertions, 94 deletions

diff --git a/src/CompositeGeometryManager.cpp b/src/CompositeGeometryManager.cpp
index a4dace2..184144c 100644
--- a/src/CompositeGeometryManager.cpp
+++ b/src/CompositeGeometryManager.cpp
@@ -1386,6 +1386,12 @@ static bool doJob(const CCompositeGeometryManager::TJobSet::const_iterator& iter
 	bool ok = dstMem->allocateGPUMemory(outx, outy, outz, zero ? astraCUDA3d::INIT_ZERO : astraCUDA3d::INIT_NO);
 	if (!ok) ASTRA_ERROR("Error allocating GPU memory");
 
+	if (!zero) {
+		// instead of zeroing output memory, copy from host
+		ok = dstMem->copyToGPUMemory(dstdims);
+		if (!ok) ASTRA_ERROR("Error copying output data to GPU");
+	}
+
 	for (CCompositeGeometryManager::TJobList::const_iterator i = L.begin(); i != L.end(); ++i) {
 		const CCompositeGeometryManager::SJob &j = *i;
 
diff --git a/src/CudaDartMaskAlgorithm.cpp b/src/CudaDartMaskAlgorithm.cpp
index 375d565..a2e1ee6 100644
--- a/src/CudaDartMaskAlgorithm.cpp
+++ b/src/CudaDartMaskAlgorithm.cpp
@@ -29,6 +29,7 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 
 #include "astra/CudaDartMaskAlgorithm.h"
 
+#include "../cuda/2d/astra.h"
 #include "../cuda/2d/darthelper.h"
 #include "../cuda/2d/algo.h"
 
diff --git a/src/CudaDartSmoothingAlgorithm.cpp b/src/CudaDartSmoothingAlgorithm.cpp
index 0759ea0..9e586c0 100644
--- a/src/CudaDartSmoothingAlgorithm.cpp
+++ b/src/CudaDartSmoothingAlgorithm.cpp
@@ -29,6 +29,7 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 
 #include "astra/CudaDartSmoothingAlgorithm.h"
 
+#include "../cuda/2d/astra.h"
 #include "../cuda/2d/darthelper.h"
 #include "../cuda/2d/algo.h"
 
diff --git a/src/CudaDataOperationAlgorithm.cpp b/src/CudaDataOperationAlgorithm.cpp
index f9466e2..6c6b27c 100644
--- a/src/CudaDataOperationAlgorithm.cpp
+++ b/src/CudaDataOperationAlgorithm.cpp
@@ -31,6 +31,7 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 
 #include "../cuda/2d/algo.h"
 #include "../cuda/2d/darthelper.h"
+#include "../cuda/2d/astra.h"
 #include "../cuda/2d/arith.h"
 
 #include "astra/AstraObjectManager.h"
diff --git a/src/CudaRoiSelectAlgorithm.cpp b/src/CudaRoiSelectAlgorithm.cpp
index baf8a6f..2b0ba15 100644
--- a/src/CudaRoiSelectAlgorithm.cpp
+++ b/src/CudaRoiSelectAlgorithm.cpp
@@ -29,6 +29,7 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 
 #include "astra/CudaRoiSelectAlgorithm.h"
 
+#include "../cuda/2d/astra.h"
 #include "../cuda/2d/darthelper.h"
 #include "../cuda/2d/algo.h"
 
diff --git a/src/Float32Data3DMemory.cpp b/src/Float32Data3DMemory.cpp
index 5c5c310..017625b 100644
--- a/src/Float32Data3DMemory.cpp
+++ b/src/Float32Data3DMemory.cpp
@@ -71,8 +71,6 @@ bool CFloat32Data3DMemory::_initialize(int _iWidth, int _iHeight, int _iDepth)
 
 	// allocate memory for the data, but do not fill it
 	m_pfData = NULL;
-	m_ppfDataRowInd = NULL;
-	m_pppfDataSliceInd = NULL;
 	m_pCustomMemory = 0;
 	_allocateData();
 
@@ -103,8 +101,6 @@ bool CFloat32Data3DMemory::_initialize(int _iWidth, int _iHeight, int _iDepth, c
 
 	// allocate memory for the data, but do not fill it
 	m_pfData = NULL;
-	m_ppfDataRowInd = NULL;
-	m_pppfDataSliceInd = NULL;
 	m_pCustomMemory = 0;
 	_allocateData();
 
@@ -140,8 +136,6 @@ bool CFloat32Data3DMemory::_initialize(int _iWidth, int _iHeight, int _iDepth, f
 
 	// allocate memory for the data, but do not fill it
 	m_pfData = NULL;
-	m_ppfDataRowInd = NULL;
-	m_pppfDataSliceInd = NULL;
 	m_pCustomMemory = 0;
 	_allocateData();
 
@@ -178,8 +172,6 @@ bool CFloat32Data3DMemory::_initialize(int _iWidth, int _iHeight, int _iDepth, C
 	// allocate memory for the data, but do not fill it
 	m_pCustomMemory = _pCustomMemory;
 	m_pfData = NULL;
-	m_ppfDataRowInd = NULL;
-	m_pppfDataSliceInd = NULL;
 	_allocateData();
 
 	// initialization complete
@@ -198,8 +190,6 @@ void CFloat32Data3DMemory::_allocateData()
 	ASTRA_ASSERT(m_iSize > 0);
 	ASTRA_ASSERT(m_iSize == (size_t)m_iWidth * m_iHeight * m_iDepth);
 	ASTRA_ASSERT(m_pfData == NULL);
-	ASTRA_ASSERT(m_ppfDataRowInd == NULL);
-	ASTRA_ASSERT(m_pppfDataSliceInd == NULL);
 
 	if (!m_pCustomMemory) {
 		// allocate contiguous block
@@ -213,20 +203,6 @@ void CFloat32Data3DMemory::_allocateData()
 	} else {
 		m_pfData = m_pCustomMemory->m_fPtr;
 	}
-
-	// create array of pointers to each row of the data block
-	m_ppfDataRowInd = new float32*[m_iHeight*m_iDepth];
-	for (int iy = 0; iy < m_iHeight*m_iDepth; iy++)
-	{
-		m_ppfDataRowInd[iy] = &(m_pfData[iy * m_iWidth]);
-	}
-
-	// create array of pointers to each row of the data block
-	m_pppfDataSliceInd = new float32**[m_iDepth];
-	for (int iy = 0; iy < m_iDepth; iy++)
-	{
-		m_pppfDataSliceInd[iy] = &(m_ppfDataRowInd[iy * m_iHeight]);
-	}
 }
 
 //----------------------------------------------------------------------------------------
@@ -235,13 +211,6 @@ void CFloat32Data3DMemory::_freeData()
 {
 	// basic checks
 	ASTRA_ASSERT(m_pfData != NULL);
-	ASTRA_ASSERT(m_ppfDataRowInd != NULL);
-	ASTRA_ASSERT(m_pppfDataSliceInd != NULL);
-
-	// free memory for index table
-	delete[] m_pppfDataSliceInd;
-	// free memory for index table
-	delete[] m_ppfDataRowInd;
 
 	if (!m_pCustomMemory) {
 		// free memory for data block
@@ -266,8 +235,6 @@ void CFloat32Data3DMemory::_clear()
 	m_iSize = 0;
 
 	m_pfData = NULL;
-	m_ppfDataRowInd = NULL;
-	m_pppfDataSliceInd = NULL;
 	m_pCustomMemory = NULL;
 }
 
diff --git a/src/Utilities.cpp b/src/Utilities.cpp
index eb06d8b..2ae1b66 100644
--- a/src/Utilities.cpp
+++ b/src/Utilities.cpp
@@ -66,20 +66,44 @@ double stringToDouble(const std::string& s)
 template<> float stringTo(const std::string& s) { return stringToFloat(s); }
 template<> double stringTo(const std::string& s) { return stringToDouble(s); }
 
-std::vector<float> stringToFloatVector(const std::string &s)
+template<typename T>
+std::vector<T> stringToNumericVector(const std::string &s)
 {
-	return stringToVector<float>(s);
+	std::vector<T> out;
+	out.reserve(100);
+	std::istringstream iss;
+	iss.imbue(std::locale::classic());
+	size_t length = s.size();
+	size_t current = 0;
+	size_t next;
+	do {
+		next = s.find_first_of(",;", current);
+		std::string t = s.substr(current, next - current);
+		iss.str(t);
+		iss.clear();
+		T f;
+		iss >> f;
+		out.push_back(f);
+		current = next + 1;
+	} while (next != std::string::npos && current != length);
+
+	return out;
 }
 
+std::vector<float> stringToFloatVector(const std::string &s)
+{
+	return stringToNumericVector<float>(s);
+}
 std::vector<double> stringToDoubleVector(const std::string &s)
 {
-	return stringToVector<double>(s);
+	return stringToNumericVector<double>(s);
 }
 
 template<typename T>
 std::vector<T> stringToVector(const std::string& s)
 {
 	std::vector<T> out;
+	size_t length = s.size();
 	size_t current = 0;
 	size_t next;
 	do {
@@ -87,7 +111,7 @@ std::vector<T> stringToVector(const std::string& s)
 		std::string t = s.substr(current, next - current);
 		out.push_back(stringTo<T>(t));
 		current = next + 1;
-	} while (next != std::string::npos);
+	} while (next != std::string::npos && current != length);
 
 	return out;
 }
@@ -117,13 +141,14 @@ void splitString(std::vector<std::string> &items, const std::string& s,
                  const char *delim)
 {
 	items.clear();
+	size_t length = s.size();
 	size_t current = 0;
 	size_t next;
 	do {
 		next = s.find_first_of(delim, current);
 		items.push_back(s.substr(current, next - current));
 		current = next + 1;
-	} while (next != std::string::npos);
+	} while (next != std::string::npos && current != length);
 }
 
 }
diff --git a/src/XMLNode.cpp b/src/XMLNode.cpp
index 3b7237f..2bf1330 100644
--- a/src/XMLNode.cpp
+++ b/src/XMLNode.cpp
@@ -30,6 +30,9 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 #include "rapidxml/rapidxml.hpp"
 #include "rapidxml/rapidxml_print.hpp"
 
+#include <sstream>
+#include <iomanip>
+
 
 using namespace rapidxml;
 using namespace astra;
@@ -376,9 +379,9 @@ void XMLNode::setContent(float32 _fValue)
 
 template<typename T>
 static std::string setContentList_internal(T* pfList, int _iSize) {
-	std::string str = (_iSize > 0) ? StringUtil::toString(pfList[0]) : "";
-	for (int i = 1; i < _iSize; i++) {
-		str += "," + StringUtil::toString(pfList[i]);
+	std::string str;
+	for (int i = 0; i < _iSize; i++) {
+		str += StringUtil::toString(pfList[i]) + ",";
 	}
 	return str;
 }
@@ -399,8 +402,6 @@ void XMLNode::setContent(double* pfList, int _iSize)
 template<typename T>
 static std::string setContentMatrix_internal(T* _pfMatrix, int _iWidth, int _iHeight, bool transposed)
 {
-	std::string str = "";
-
 	int s1,s2;
 
 	if (!transposed) {
@@ -411,17 +412,20 @@ static std::string setContentMatrix_internal(T* _pfMatrix, int _iWidth, int _iHe
 		s2 = 1;
 	}
 
+	std::ostringstream s;
+	s.imbue(std::locale::classic());
+	s << std::setprecision(17);
+
 	for (int y = 0; y < _iHeight; ++y) {
 		if (_iWidth > 0)
-			str += StringUtil::toString(_pfMatrix[0*s1 + y*s2]);
+			s << _pfMatrix[0*s1 + y*s2];
 		for (int x = 1; x < _iWidth; x++)
-			str += "," + StringUtil::toString(_pfMatrix[x*s1 + y*s2]);
+			s << "," << _pfMatrix[x*s1 + y*s2];
 
-		if (y != _iHeight-1)
-			str += ";";
+		s << ";";
 	}
 
-	return str;
+	return s.str();
 }
 
 void XMLNode::setContent(float32* _pfMatrix, int _iWidth, int _iHeight, bool transposed)
diff --git a/src/swrap.cpp b/src/swrap.cpp
deleted file mode 100644
index c970ab5..0000000
--- a/src/swrap.cpp
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
------------------------------------------------------------------------
-Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
-           2014-2016, CWI, Amsterdam
-
-Contact: astra@uantwerpen.be
-Website: http://www.astra-toolbox.com/
-
-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/>.
-
------------------------------------------------------------------------
-*/
-
-#ifndef _MSC_VER
-
-#include "astra/swrap.h"
-#include <cerrno>
-
-errno_t fopen_s(FILE** pFile, const char* filename, const char* mode)
-{
-	if (!pFile)
-		return EINVAL;
-
-	FILE* x = fopen(filename, mode);
-	if (!x)
-		return errno;
-
-	*pFile = x;
-	return 0;
-}
-
-#endif