diff --git a/CMakeLists.txt b/CMakeLists.txt
index d2530cc7992bbdba69149f6d619e3fb5e80ed9b0..a6cdbe933661ea578da1772f4e08bf9d512caa0e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -14,7 +14,6 @@ endif()
set(BOOST_INCLUDE ${Boost_INCLUDE_DIR} CACHE PATH "Include directory for BOOST")
set(HDF5_ROOT CACHE PATH "HDF5 root path")
set(SE_CLASS1 CACHE BOOL "Activate compilation with SE_CLASS1")
-set(SE_CLASS2 CACHE BOOL "Activate compilation with SE_CLASS2")
set(SE_CLASS3 CACHE BOOL "Activate compilation with SE_CLASS3")
set(ENV{HDF5_ROOT} ${HDF5_ROOT})
set(OPENFPM_PDATA_DIR CACHE PATH "OpenFPM_pdata dirs")
@@ -45,7 +44,10 @@ if(ENABLE_GPU)
elseif ( CUDA_VERSION_MAJOR EQUAL 10 AND CUDA_VERSION_MINOR EQUAL 2 )
message("CUDA is compatible")
set(WARNING_SUPPRESSION_AND_OPTION_NVCC -Xcudafe "--display_error_number --diag_suppress=2977 --diag_suppress=2976 --diag_suppress=2979 --diag_suppress=186" --expt-extended-lambda)
- else()
+ elseif ( CUDA_VERSION_MAJOR EQUAL 11 AND CUDA_VERSION_MINOR EQUAL 0 )
+ message("CUDA is compatible 11.0")
+ set(WARNING_SUPPRESSION_AND_OPTION_NVCC -Xcudafe "--display_error_number --diag_suppress=3059 --diag_suppress=3058 --diag_suppress=3057 --diag_suppress=3056 --diag_suppress=611 --diag_suppress=186" --expt-extended-lambda)
+ else()
message(FATAL_ERROR "CUDA is incompatible, version 9.2 10.1 and 10.2 is only supported")
endif()
endif()
@@ -68,10 +70,6 @@ if(SE_CLASS1)
set(DEFINE_SE_CLASS1 "#define SE_CLASS1")
endif()
-if(SE_CLASS2)
- set(DEFINE_SE_CLASS2 "#define SE_CLASS2")
-endif()
-
if(SE_CLASS3)
set(DEFINE_SE_CLASS3 "#define SE_CLASS3")
endif()
diff --git a/configure b/configure
index 58a970ce6f68fb305ca1699444b61d7e9cd02c7d..8b284b8e6a6ff5af329ad0a1da39ed79cad353c9 100755
--- a/configure
+++ b/configure
@@ -104,7 +104,6 @@ enable_test_performance
enable_test_coverage
with_parmetis
enable_se_class1
-enable_se_class2
enable_se_class3
with_action_on_error
with_boost
@@ -220,9 +219,6 @@ do
se_class1)
conf_options="$conf_options -DSE_CLASS1=ON"
;;
- se_class2)
- conf_options="$conf_options -DSE_CLASS2=ON"
- ;;
se_class3)
conf_options="$conf_options -DSE_CLASS3=ON"
;;
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 87dafed2448824d29b617e398601b3c855f883a6..49d873c2ec77003be5667d7d4bb2d41bcff39a4c 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -9,7 +9,6 @@ add_executable(io main.cpp
../../openfpm_vcluster/src/VCluster/VCluster.cpp
../../openfpm_devices/src/memory/CudaMemory.cu
../../openfpm_devices/src/memory/HeapMemory.cpp
- ../../openfpm_devices/src/Memleak_check.cpp
../../openfpm_devices/src/memory/PtrMemory.cpp)
if ( CMAKE_COMPILER_IS_GNUCC )
@@ -106,6 +105,12 @@ install(FILES HDF5_wr/HDF5_wr.hpp
HDF5_wr/HDF5_reader_vd.hpp
DESTINATION openfpm_io/include/HDF5_wr)
+install(FILES RawReader/InitGridWithPixel.hpp
+ DESTINATION openfpm_io/include/RawReader/)
+
+install(FILES util/PathsAndFiles.hpp
+ DESTINATION openfpm_io/include/util)
+
install(FILES Plot/GoogleChart.hpp Plot/util.hpp
DESTINATION openfpm_io/include/Plot )
diff --git a/src/HDF5_wr/HDF5_writer_gd.hpp b/src/HDF5_wr/HDF5_writer_gd.hpp
index 8a1b98e78d433c6975940e2373287c893e0f30c1..f41de0fec8f6c888a78e2f2118c7f1b0e6048576 100644
--- a/src/HDF5_wr/HDF5_writer_gd.hpp
+++ b/src/HDF5_wr/HDF5_writer_gd.hpp
@@ -173,6 +173,9 @@ public:
H5Sclose(file_dataspace_id_2);
H5Pclose(plist_id);
H5Fclose(file);
+
+ mem.decRef();
+ delete &mem;
}
};
diff --git a/src/HDF5_wr/HDF5_writer_vd.hpp b/src/HDF5_wr/HDF5_writer_vd.hpp
index 70015ba6f6acff2f6aab85634032bfff6e78d2c2..f6bd869a75ee2bb1897f6cb9ab982ca85ab50a9e 100644
--- a/src/HDF5_wr/HDF5_writer_vd.hpp
+++ b/src/HDF5_wr/HDF5_writer_vd.hpp
@@ -156,6 +156,8 @@ public:
H5Sclose(mem_dataspace_id);
H5Pclose(plist_id);
H5Fclose(file);
+ mem.decRef();
+ delete &mem;
}
/*! \brief Return the equivalent HDF5 type for T
diff --git a/src/RawReader/InitGridWithPixel.hpp b/src/RawReader/InitGridWithPixel.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..01e23eca25bbc21394d28f9271d57de82afee39e
--- /dev/null
+++ b/src/RawReader/InitGridWithPixel.hpp
@@ -0,0 +1,165 @@
+//
+// Created by jstark on 2019-11-07.
+//
+/**
+ * @file InitGridWithPixel.hpp
+ *
+ * @brief Header file containing functions for loading pixel values from 2D image or 3D image stack (volume) stored
+ * in a binary file onto an openFPM grid.
+ *
+ * @details Can be run in parallel.
+ *
+ * @author Justina Stark
+ * @date November 2019 - August 2020
+ */
+#ifndef IMAGE_BASED_RECONSTRUCTION_GETINITIALGRID_HPP
+#define IMAGE_BASED_RECONSTRUCTION_GETINITIALGRID_HPP
+
+#include <iostream>
+#include <typeinfo>
+#include <cmath>
+
+#include "Vector/vector_dist.hpp"
+#include "Grid/grid_dist_id.hpp"
+#include "data_type/aggregate.hpp"
+#include "Decomposition/CartDecomposition.hpp"
+
+#include "level_set/redistancing_Sussman/HelpFunctionsForGrid.hpp"
+typedef signed char BYTE;
+/**@brief Read the number of pixels per dimension from a csv-file in order to create a grid with the same size.
+ *
+ * @param path_to_file Std::string containing the path to the csv file that holds the image/volume size in
+ * #pixels per dimension.
+ * @return Std::vector containing the count of pixels for each dimension as it was read from the csv file.
+ */
+std::vector<size_t> get_size(const std::string & path_to_file)
+{
+ std::vector<size_t> stack_dimst_1d;
+ // stream input csv file and error check
+ std::ifstream file(path_to_file);
+ if (!file)
+ {
+ std::cout << "Error opening file" << std::endl;
+ exit (EXIT_FAILURE);
+ }
+
+ // get its size
+ std::streampos fileSize;
+ file.seekg(0, std::ios::end);
+ fileSize = file.tellg();
+ file.seekg(0, std::ios::beg);
+
+ // reserve capacity
+ stack_dimst_1d.reserve(fileSize);
+
+ std::string field;
+ while ( getline(file, field) ) // 1 field per axis
+ {
+ std::istringstream iss(field);
+ size_t val;
+ iss >> val;
+ stack_dimst_1d.push_back(val); // add the #pixels for current axis to the array
+ }
+
+ // reverse order to compensate reverse reading
+ std::reverse(std::begin(stack_dimst_1d), std::end(stack_dimst_1d));
+
+ return stack_dimst_1d;
+}
+
+
+/**@brief Converts the pixel values stored in a binary file into doubles and loads them onto an OpenFPM grid.
+ *
+ * @tparam Phi_0 Index of property in which pixel value should be stored.
+ * @tparam grid_type Type of OpenFPM grid.
+ * @param grid Grid of type grid_type, on which image / image-stack should be loaded.
+ * @param file_name Std::string containing the path + name of the binary file that stores the pixel values.
+ * @param stack_dims Size_t variable that contains the dimensionality of the image / image stack. Can be given
+ * manually or loaded from a csv file before (see: #get_size())
+ */
+template <size_t Phi_0, typename grid_type>
+void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector <size_t> & stack_dims)
+{
+ constexpr size_t x = 0;
+ constexpr size_t y = 1;
+ constexpr size_t z = 2;
+
+ std::ifstream file_stream (file_name, std::ifstream::binary);
+
+ auto & v_cl = create_vcluster();
+ if (v_cl.rank() == 0)
+ {
+ for (size_t d = 0; d < grid_type::dims; d++)
+ {
+ std::cout << "# grid points in dimension " << d << " = " << grid.size(d) << std::endl;
+ }
+ }
+
+ // initialize complete grid including ghost layer with -1
+ init_grid_and_ghost<Phi_0>(grid, -1.0);
+
+ // assign pixel values to domain. For each pixel get factor_refinement number of grid points with corresponding value
+ auto dom = grid.getDomainIterator();
+ std::vector<BYTE> pixel_line; // one x-line of the image stack which will be read
+
+ size_t sz_img[grid_type::dims];
+ for (size_t d = 0; d < grid_type::dims; d++)
+ {
+ sz_img[d] = stack_dims[d];
+ }
+ grid_sm<grid_type::dims,void> ginfo_image(sz_img); // in order to get the image related key later on
+
+ double refinement[grid_type::dims];
+ for (size_t d = 0; d < grid_type::dims; d++)
+ {
+ refinement[d] = (double) grid.size(d) / (double)stack_dims[d]; // get the factor, by which the grid resolution differs from the image stack resolution
+ if (v_cl.rank() == 0) std::cout << "effective refinement in dimension " << d << " = " << refinement[d] << std::endl;
+ }
+
+ while(dom.isNext())
+ {
+ auto key = dom.get();
+ auto gkey = grid.getGKey(key);
+
+ // get l as the length of one x-line of the original image stack for the specific patch on the processor
+ auto & gbox = grid.getLocalGridsInfo();
+ auto & DomBox = gbox.get(key.getSub()).Dbox;
+ int l = (size_t) std::round((DomBox.getHigh(0) - DomBox.getLow(0) + 1) / refinement[x]);
+
+ // in case that the grid has a different resolution than the underlying image stack:
+ // create a key which is used to get the offset for the file reading
+ // the indices in this key are corrected by the refinement factor
+ for (size_t d = 1; d < grid_type::dims; d++)
+ {
+ gkey.set_d(d, std::round(gkey.get(d) / refinement[d]));
+ }
+
+ // the offset matches the pixel from the image stack to the corresponding current position of the iterator
+ // in the grid
+ size_t offset = ginfo_image.LinId(gkey);
+ file_stream.seekg(offset); // jump to the correct position in the file
+
+ // prepare space for the pixel values of one x-line in the original image stack
+ pixel_line.resize(l);
+ // stream the file and fill pixel values into pixel_line
+ file_stream.read((char*) & pixel_line[0], l);
+
+ // run over a whole grid-line in x and assign pixel values from pixel_line to grid nodes
+ // if the grid is finer in x as the image stack, the same pixel value from pixel_line is
+ // assigned refinement[x] times
+ for (size_t i = 0; i < l * refinement[x]; i++)
+ {
+ auto key = dom.get();
+ grid.template get<Phi_0>(key) = (double) pixel_line[(size_t)floor(i / refinement[x])];
+ ++dom;
+ }
+ // now one grid line in x is finished and the iterator dom has advanced accordingly s.t. next loop continues
+ // with next line, meaning that y increased by 1 (or z respectivley, when y = ymax + 1)
+ }
+
+ grid.template ghost_get<Phi_0>();
+}
+
+
+
+#endif //IMAGE_BASED_RECONSTRUCTION_GETINITIALGRID_HPP
diff --git a/src/config/config_cmake.h.in b/src/config/config_cmake.h.in
index 02de32fc4b93d79ac946dbb08127a707b6f7de44..85840022fcec2c75463a60a05aa6c09b76ea448e 100644
--- a/src/config/config_cmake.h.in
+++ b/src/config/config_cmake.h.in
@@ -140,9 +140,6 @@ ${DEFINE_PERFORMANCE_TEST}
/* Security enhancement class 1 */
${DEFINE_SE_CLASS1}
-/* Security enhancement class 2 */
-${DEFINE_SE_CLASS2}
-
/* Security enhancement class 3 */
${DEFINE_SE_CLASS3}
diff --git a/src/util/PathsAndFiles.hpp b/src/util/PathsAndFiles.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..e5cd27e52a1ef26b3c5bb9aa249438b4a5a8c1c8
--- /dev/null
+++ b/src/util/PathsAndFiles.hpp
@@ -0,0 +1,122 @@
+//
+// Created by jstark on 2019-12-03.
+//
+/**
+ * @file PathsAndFiles.hpp
+ *
+ * @brief Header file containing functions for creating files and folders.
+ *
+ * @author Justina Stark
+ * @date December 2019
+ */
+
+#ifndef FILES_READ_AND_WRITE_PATHSANDFILES_HPP
+#define FILES_READ_AND_WRITE_PATHSANDFILES_HPP
+#include <unistd.h>
+#include <iostream>
+#include <fstream>
+#include <boost/filesystem.hpp>
+/**@brief Gets the current working directory and returns path as string.
+ *
+ * @return Std::string of path to current working directory.
+ */
+std::string get_cwd()
+{
+ char *cwd = nullptr;
+ size_t size;
+ cwd = getcwd(cwd, size);
+
+ // convert current directory to string
+ std::string s_cwd;
+ s_cwd = cwd;
+
+ // std::cout << "The current working directory is: " << dir << std::endl;
+ return s_cwd;
+}
+/**@brief Checks if a file already exists.
+ *
+ * @param path Std::string with path of file for which existence should be checked.
+ * @return True, if file exists, false if not.
+ */
+bool check_if_file_exists(std::string path)
+{
+ try
+ {
+ // Create a filesystem::path object from given path string
+ boost::filesystem::path pathObj(path);
+ if (boost::filesystem::exists(pathObj) && boost::filesystem::is_regular_file(pathObj))
+ {
+ return true;
+// BOOST_LOG_TRIVIAL(info) << path << " -> File exists.";
+ }
+
+ }
+ catch (boost::filesystem::filesystem_error & e)
+ {
+ std::cerr << e.what() << std::endl;
+// BOOST_LOG_TRIVIAL(error) << "Error when checking existence of file ( " << path << " ): " << e.what();
+ }
+ return false;
+}
+/**@brief Creates a file if not already existent.
+ *
+ * @param path Std::string that contains path including filename of the file that should be created.
+ */
+void create_file_if_not_exist(std::string path)
+{
+ auto & v_cl = create_vcluster();
+ if (v_cl.rank() == 0)
+ {
+ if ( ! check_if_file_exists(path))
+ {
+ std::ofstream outfile (path);
+// BOOST_LOG_TRIVIAL(info) << "Created file with name: " << path;
+ }
+ }
+}
+
+
+/**@brief Checks if a directory already exists.
+ *
+ * @param path Std::string with path of directory for which existence should be checked.
+ * @return True, if directory exists, false if not.
+ */
+bool check_if_directory_exists(std::string path)
+{
+ try
+ {
+ // Create a filesystem::path object from given path string
+ boost::filesystem::path pathObj(path);
+ if (boost::filesystem::exists(pathObj) && boost::filesystem::is_directory(pathObj)) return true;
+ }
+ catch (boost::filesystem::filesystem_error & e)
+ {
+ std::cerr << e.what() << std::endl;
+ }
+ return false;
+}
+/**@brief Creates a directory if not already existent.
+ *
+ * @param path Std::string that contains path including name of the folder that should be created.
+ */
+void create_directory_if_not_exist(std::string path)
+{
+ auto & v_cl = create_vcluster();
+ if (v_cl.rank() == 0)
+ {
+ if ( ! check_if_directory_exists(path))
+ {
+ boost::filesystem::create_directory(path);
+// BOOST_LOG_TRIVIAL(info) << "Created directory with name: " << path;
+ }
+ else std::cout << "Folder for current settings ( '" << path << "' ) already exists. New files will be saved to this folder." << std::endl;
+// BOOST_LOG_TRIVIAL(info) << "Folder for current settings ( '" << path << "' ) already exists. New files will be saved to this folder.";
+ }
+}
+
+
+
+
+
+#endif //FILES_READ_AND_WRITE_PATHSANDFILES_HPP
+