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Continued working on HDF5 plugin

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Yohai Meiron 2020-03-27 16:53:01 -04:00
parent 0b9fa6e46d
commit ba5546534f
1 changed files with 84 additions and 102 deletions
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186
io.cpp
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@ -2,11 +2,13 @@
#include <string> #include <string>
#include <vector> #include <vector>
#include <algorithm> #include <algorithm>
struct double3 {double x,y,z;}; #include <stdexcept>
struct double3 {double x,y,z;
};
void h5_write(const std::string file_name, const int step_num, const double t, const int N, const double *m, const double3 *x, const double3 *v, const double *pot, const double3 *acc, const double3 *jrk, const int write_mode=0, const bool use_double_precision=true)
void h5_write(const std::string file_name, const int step_num, const int N, const double t, const double *m, const double3 *x, const double3 *v, const double *pot, const double3 *acc, const double3 *jrk, const int write_mode=0, const bool use_double_precision=true)
{ {
char group_name[32], dataset_path[32];
bool write_pot = (write_mode )%2; bool write_pot = (write_mode )%2;
bool write_acc = (write_mode>>1)%2; bool write_acc = (write_mode>>1)%2;
bool write_jrk = (write_mode>>2)%2; bool write_jrk = (write_mode>>2)%2;
@ -19,6 +21,7 @@ void h5_write(const std::string file_name, const int step_num, const double t, c
else h5_float_type = H5T_IEEE_F32LE; else h5_float_type = H5T_IEEE_F32LE;
file_id = H5Fcreate(file_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); file_id = H5Fcreate(file_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
char group_name[32];
sprintf(group_name, "/Step#%d", step_num); sprintf(group_name, "/Step#%d", step_num);
group_id = H5Gcreate2(file_id, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); group_id = H5Gcreate2(file_id, group_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
dataspace_id = H5Screate(H5S_SCALAR); dataspace_id = H5Screate(H5S_SCALAR);
@ -26,97 +29,89 @@ void h5_write(const std::string file_name, const int step_num, const double t, c
H5Awrite(attribute_id, H5T_NATIVE_DOUBLE, &t); H5Awrite(attribute_id, H5T_NATIVE_DOUBLE, &t);
H5Sclose(dataspace_id); H5Sclose(dataspace_id);
dataspace_id = H5Screate_simple(1, dims, NULL); auto write_dataset = [&](const char dataset_name[], int ndims, double *data) {
sprintf(dataset_path, "%s/MASS", group_name); hid_t dataspace_id = H5Screate_simple(ndims, dims, NULL);
dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); char dataset_path[32];
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, m); sprintf(dataset_path, "%s/%s", group_name, dataset_name);
hid_t dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
H5Dclose(dataset_id); H5Dclose(dataset_id);
H5Sclose(dataspace_id); H5Sclose(dataspace_id);
};
dataspace_id = H5Screate_simple(2, dims, NULL); write_dataset("MASS", 1, (double*)m);
sprintf(dataset_path, "%s/X", group_name); write_dataset("X", 2, (double*)x);
dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); write_dataset("V", 2, (double*)v);
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x); if (write_pot) write_dataset("POT", 1, (double*)pot);
H5Dclose(dataset_id); if (write_acc) write_dataset("ACC", 2, (double*)acc);
H5Sclose(dataspace_id); if (write_jrk) write_dataset("JRK", 2, (double*)jrk);
dataspace_id = H5Screate_simple(2, dims, NULL);
sprintf(dataset_path, "%s/V", group_name);
dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, v);
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
if (write_pot) {
dataspace_id = H5Screate_simple(1, dims, NULL);
sprintf(dataset_path, "%s/POT", group_name);
dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, pot);
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
}
if (write_acc) {
dataspace_id = H5Screate_simple(2, dims, NULL);
sprintf(dataset_path, "%s/ACC", group_name);
dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, acc);
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
}
if (write_jrk) {
dataspace_id = H5Screate_simple(2, dims, NULL);
sprintf(dataset_path, "%s/JRK", group_name);
dataset_id = H5Dcreate2(file_id, dataset_path, h5_float_type, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, jrk);
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
}
H5Gclose(group_id); H5Gclose(group_id);
group_id = H5Gcreate2(file_id, "/Step#22", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group_id);
H5Fclose(file_id); H5Fclose(file_id);
} }
void h5_read(const std::string file_name, int *step_num, int *N, double *t, double m[], double3 x[], double3 v[])
herr_t file_info(hid_t loc_id, const char *name, void *opdata)
{ {
H5G_stat_t statbuf; // Open file and root group; count number of top level objects
hid_t file_id = H5Fopen(file_name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
/* hid_t group_id = H5Gopen2(file_id, "/", H5P_DEFAULT);
* Get type of the object and display its name and type. H5G_info_t object_info;
* The name of the object is passed to this function by H5Gget_info(group_id, &object_info);
* the Library. Some magic :-) // Iterate over objects and add the number of each "step" group into a vector
*/ std::vector<int> step_num_arr;
H5Gget_objinfo(loc_id, name, 0, &statbuf); for (int i=0; i<object_info.nlinks; i++) {
switch (statbuf.type) { char name_cstr[256];
case H5G_GROUP: H5Gget_objname_by_idx(group_id, i, name_cstr, 256);
printf(" Object with name %s is a group \n", name); std::string name(name_cstr);
break; if (name.substr(0, 5) == "Step#") step_num_arr.push_back(std::stoi(name.substr(5, std::string::npos)));
case H5G_DATASET:
printf(" Object with name %s is a dataset \n", name);
break;
case H5G_TYPE:
printf(" Object with name %s is a named datatype \n", name);
break;
default:
printf(" Unable to identify an object ");
} }
return 0; // Find the highest step in the file
*step_num = *max_element(step_num_arr.begin(), step_num_arr.end());
// Prepare to read the data sets dimensionality data.
char dataset_path[256];
hid_t dataset_id, dataspace_id;
int ndims;
hsize_t dims[2];
sprintf(dataset_path, "/Step#%d/MASS", *step_num);
dataset_id = H5Dopen2(file_id, dataset_path, H5P_DEFAULT);
dataspace_id = H5Dget_space(dataset_id);
ndims = H5Sget_simple_extent_ndims(dataspace_id);
if (ndims != 1)
throw std::runtime_error("Dataset MASS in Step#" + std::to_string(*step_num) + " of file " + file_name + " is " + std::to_string(ndims) + "-dimensional (expected 1-dimensional)");
H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, m);
*N = dims[0];
sprintf(dataset_path, "/Step#%d/X", *step_num);
dataset_id = H5Dopen2(file_id, dataset_path, H5P_DEFAULT);
dataspace_id = H5Dget_space(dataset_id);
ndims = H5Sget_simple_extent_ndims(dataspace_id);
if (ndims != 2) throw std::runtime_error("Dataset X in Step#" + std::to_string(*step_num) + " of file " + file_name + " is " + std::to_string(ndims) + "-dimensional (expected 2-dimensional)");
H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
if (dims[0] != *N) throw std::runtime_error("Expected " + std::to_string(*N) + "rows in Dataset X in Step#" + std::to_string(*step_num) + " of file " + file_name + " (based on MASS)");
if (dims[1] != 3) throw std::runtime_error("Dataset X in Step#" + std::to_string(*step_num) + " of file " + file_name + " has " + std::to_string(dims[1]) + " columns (expected 3 columns)");
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, (double*)x);
sprintf(dataset_path, "/Step#%d/V", *step_num);
dataset_id = H5Dopen2(file_id, dataset_path, H5P_DEFAULT);
dataspace_id = H5Dget_space(dataset_id);
ndims = H5Sget_simple_extent_ndims(dataspace_id);
if (ndims != 2) throw std::runtime_error("Dataset V in Step#" + std::to_string(*step_num) + " of file " + file_name + " is " + std::to_string(ndims) + "-dimensional (expected 2-dimensional)");
H5Sget_simple_extent_dims(dataspace_id, dims, NULL);
if (dims[0] != *N) throw std::runtime_error("Expected " + std::to_string(*N) + "rows in Dataset V in Step#" + std::to_string(*step_num) + " of file " + file_name + " (based on MASS)");
if (dims[1] != 3) throw std::runtime_error("Dataset V in Step#" + std::to_string(*step_num) + " of file " + file_name + " has " + std::to_string(dims[1]) + " columns (expected 3 columns)");
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, (double*)v);
} }
int main() int main()
{ {
// double3 aaa; // double3 aaa;
// double pot; // double pot;
std::string file_name = "new_file.h5";
int N = 25; int N = 25;
double3 x[N]; double3 x[N];
for (int i=0; i<N; i++) { for (int i=0; i<N; i++) {
@ -124,31 +119,18 @@ int main()
x[i].y=i+0.02; x[i].y=i+0.02;
x[i].z=i+0.03; x[i].z=i+0.03;
} }
h5_write("new_file.h5", 34, 987.654, N, (double*)x, x, x, (double*)x, x, x, 7); double m[N];
double3 v[N];
int step_num;
double t;
auto file_id = H5Fopen("new_file.h5", H5F_ACC_RDONLY, H5P_DEFAULT); h5_write("123.h5", 17, N, 123.987, (double*)x, x, x, (double*)x, x, x, 7, true);
auto group_id = H5Gopen2(file_id, "/", H5P_DEFAULT); h5_read("123.h5", &step_num, &N, &t, m, x, v);
H5G_info_t object_info; printf("%d %d %f\n", step_num, N, t);
H5Gget_info(group_id, &object_info); #error still havent implemented reading the time attribute
std::vector<int> step_num;
for (int i=0; i<object_info.nlinks; i++) { // h5_write(file_name, 34, 987.654, N, (double*)x, x, x, (double*)x, x, x, 7);
char name_cstr[256];
H5Gget_objname_by_idx(group_id, i, name_cstr, 256); // h5_read(file_name, &N, (double*)x, x, x);
std::string name(name_cstr); // printf("aaaa %d %d %d\n", ndims, dims[0], dims[1]);
if (name.substr(0, 5) == "Step#") step_num.push_back(std::stoi(name.substr(5, std::string::npos)));
}
int step_num_max = *max_element(step_num.begin(), step_num.end());
char dataset_path[256];
sprintf(dataset_path, "/Step#%d/X", step_num_max);
double dset_data[1024*1024];
auto dataset_id = H5Dopen2(file_id, dataset_path, H5P_DEFAULT);
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset_data);
// printf("aaaa %d\n", step_num_max);
} }