Commit 906d6487 authored by incardon's avatar incardon
Browse files

Merge branch 'develop' of ssh://git.mpi-cbg.de/openfpm/openfpm_io into develop

parents 8fed0db5 91686e37
Pipeline #3056 failed with stages
in 14 minutes and 57 seconds
...@@ -18,6 +18,7 @@ ...@@ -18,6 +18,7 @@
#include <iostream> #include <iostream>
#include <typeinfo> #include <typeinfo>
#include <cmath> #include <cmath>
#include <sys/stat.h>
#include "Vector/vector_dist.hpp" #include "Vector/vector_dist.hpp"
#include "Grid/grid_dist_id.hpp" #include "Grid/grid_dist_id.hpp"
...@@ -26,6 +27,14 @@ ...@@ -26,6 +27,14 @@
#include "level_set/redistancing_Sussman/HelpFunctionsForGrid.hpp" #include "level_set/redistancing_Sussman/HelpFunctionsForGrid.hpp"
typedef signed char BYTE; typedef signed char BYTE;
inline bool exists_test (const std::string& name) {
struct stat buffer;
return (stat (name.c_str(), &buffer) == 0);
}
/**@brief Read the number of pixels per dimension from a csv-file in order to create a grid with the same size. /**@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 * @param path_to_file Std::string containing the path to the csv file that holds the image/volume size in
...@@ -35,13 +44,15 @@ typedef signed char BYTE; ...@@ -35,13 +44,15 @@ typedef signed char BYTE;
std::vector<size_t> get_size(const std::string & path_to_file) std::vector<size_t> get_size(const std::string & path_to_file)
{ {
std::vector<size_t> stack_dimst_1d; std::vector<size_t> stack_dimst_1d;
// stream input csv file and error check // check if file exists and stream input csv file
std::ifstream file(path_to_file); if(!exists_test(path_to_file)){
if (!file) std::cout << "------------------------------------------------------------------------" << std::endl;
{ std::cout << "Error: file " << path_to_file << " does not exist. Aborting..." << std::endl;
std::cout << "Error opening file" << std::endl; std::cout << "------------------------------------------------------------------------" << std::endl;
exit (EXIT_FAILURE); abort();
} }
std::ifstream file(path_to_file);
// get its size // get its size
std::streampos fileSize; std::streampos fileSize;
...@@ -84,6 +95,13 @@ void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector < ...@@ -84,6 +95,13 @@ void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector <
constexpr size_t y = 1; constexpr size_t y = 1;
constexpr size_t z = 2; constexpr size_t z = 2;
// check if file exists and stream input file
if(!exists_test(file_name)){
std::cout << "------------------------------------------------------------------------" << std::endl;
std::cout << "Error: file " << file_name << " does not exist. Aborting..." << std::endl;
std::cout << "------------------------------------------------------------------------" << std::endl;
abort();
}
std::ifstream file_stream (file_name, std::ifstream::binary); std::ifstream file_stream (file_name, std::ifstream::binary);
auto & v_cl = create_vcluster(); auto & v_cl = create_vcluster();
...@@ -121,17 +139,24 @@ void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector < ...@@ -121,17 +139,24 @@ void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector <
auto key = dom.get(); auto key = dom.get();
auto gkey = grid.getGKey(key); auto gkey = grid.getGKey(key);
// In case a patch starts within a group of nodes to which same pixel-value should be assigned, get the
// respective rest-offset
size_t rest_offset = (size_t) (fmod(gkey.get(0), refinement[x])); // get the remainder
// get l as the length of one x-line of the original image stack for the specific patch on the processor // 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 & gbox = grid.getLocalGridsInfo();
auto & DomBox = gbox.get(key.getSub()).Dbox; auto & DomBox = gbox.get(key.getSub()).Dbox;
int l = (size_t) std::round((DomBox.getHigh(0) - DomBox.getLow(0) + 1) / refinement[x]); size_t patch_size = DomBox.getHigh(0) - DomBox.getLow(0) + 1;
size_t l = (size_t) ceil( (patch_size + rest_offset) / refinement[x]);
// in case that the grid has a different resolution than the underlying image stack: // 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 // 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 // the indices in this key are corrected by the refinement factor
for (size_t d = 0; d < grid_type::dims; d++) for (size_t d = 0; d < grid_type::dims; d++)
{ {
gkey.set_d(d, std::round(gkey.get(d) / refinement[d])); gkey.set_d(d, floor(gkey.get(d) / refinement[d]));
} }
// the offset matches the pixel from the image stack to the corresponding current position of the iterator // the offset matches the pixel from the image stack to the corresponding current position of the iterator
...@@ -147,10 +172,13 @@ void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector < ...@@ -147,10 +172,13 @@ void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector <
// run over a whole grid-line in x and assign pixel values from pixel_line to grid nodes // 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 // if the grid is finer in x as the image stack, the same pixel value from pixel_line is
// assigned refinement[x] times // assigned refinement[x] times
for (size_t i = 0; i < l * refinement[x]; i++) for (size_t k = 0; k < patch_size; ++k)
{ {
auto key = dom.get(); auto key = dom.get();
grid.template get<Phi_0>(key) = (double) pixel_line[(size_t)floor(i / refinement[x])]; // get the correct index of the pixel to be read from pixel_line by considering a potential rest-offset,
// when the patch divides group of nodes that belong to the same pixel
size_t i = (size_t) floor((k + rest_offset) / refinement[x]);
grid.template get<Phi_0>(key) = (double) pixel_line[i];
++dom; ++dom;
} }
// now one grid line in x is finished and the iterator dom has advanced accordingly s.t. next loop continues // now one grid line in x is finished and the iterator dom has advanced accordingly s.t. next loop continues
......
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