From 0b9fa6e46d6d83809f95755e8877841e40fa7342 Mon Sep 17 00:00:00 2001
From: Yohai Meiron <sahmes@gmail.com>
Date: Thu, 26 Mar 2020 19:56:12 -0400
Subject: [PATCH] Working on HDF5 reader

---
 io.cpp | 91 ++++++++++++++++++++++++++++++++++++++++++++++++++++------
 1 file changed, 82 insertions(+), 9 deletions(-)

diff --git a/io.cpp b/io.cpp
index 6cacd25..40f009c 100644
--- a/io.cpp
+++ b/io.cpp
@@ -1,5 +1,7 @@
 #include "hdf5.h"
 #include <string>
+#include <vector>
+#include <algorithm>
 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)
@@ -9,9 +11,8 @@ void h5_write(const std::string file_name, const int step_num, const double t, c
     bool write_acc = (write_mode>>1)%2;
     bool write_jrk = (write_mode>>2)%2;
 
-    hid_t file_id, group_id, attribute_id, dataset_id, dataspace_id;  /* identifiers */
+    hid_t file_id, group_id, attribute_id, dataset_id, dataspace_id;
     hsize_t dims[2] = {(hsize_t)N, 3};
-    herr_t status;
 
     hid_t h5_float_type;
     if (use_double_precision) h5_float_type = H5T_IEEE_F64LE;
@@ -23,53 +24,99 @@ void h5_write(const std::string file_name, const int step_num, const double t, c
     dataspace_id = H5Screate(H5S_SCALAR);
     attribute_id = H5Acreate2 (group_id, "Time", H5T_IEEE_F64LE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT);
     H5Awrite(attribute_id, H5T_NATIVE_DOUBLE, &t);
+    H5Sclose(dataspace_id);
 
     dataspace_id = H5Screate_simple(1, dims, NULL);
     sprintf(dataset_path, "%s/MASS", 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, m);
+    H5Dclose(dataset_id);
+    H5Sclose(dataspace_id);
 
     dataspace_id = H5Screate_simple(2, dims, NULL);
     sprintf(dataset_path, "%s/X", 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, x);
+    H5Dclose(dataset_id);
+    H5Sclose(dataspace_id);
 
     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);
     }
-
-    H5Dclose(dataset_id);
     H5Gclose(group_id);
-    H5Sclose(dataspace_id);
+
+    
+    group_id = H5Gcreate2(file_id, "/Step#22", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+    H5Gclose(group_id);
+    
+    
     H5Fclose(file_id);
 }
 
+
+
+
+herr_t file_info(hid_t loc_id, const char *name, void *opdata)
+{
+    H5G_stat_t statbuf;
+
+    /*
+     * Get type of the object and display its name and type.
+     * The name of the object is passed to this function by 
+     * the Library. Some magic :-)
+     */
+    H5Gget_objinfo(loc_id, name, 0, &statbuf);
+    switch (statbuf.type) {
+    case H5G_GROUP: 
+         printf(" Object with name %s is a group \n", name);
+         break;
+    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;
+ }
+
+
+
+
 int main()
 {
-    double3 aaa;
-    double pot;
+//     double3 aaa;
+//     double pot;
     int N = 25;
     double3 x[N];
     for (int i=0; i<N; i++) {
@@ -78,4 +125,30 @@ int main()
         x[i].z=i+0.03;
     }
     h5_write("new_file.h5", 34, 987.654, N, (double*)x, x, x, (double*)x, x, x, 7);
+    
+    auto file_id = H5Fopen("new_file.h5", H5F_ACC_RDONLY, H5P_DEFAULT);
+    auto group_id = H5Gopen2(file_id, "/", H5P_DEFAULT);
+    H5G_info_t object_info;
+    H5Gget_info(group_id, &object_info);
+    std::vector<int> step_num;
+    for (int i=0; i<object_info.nlinks; i++) {
+        char name_cstr[256];
+        H5Gget_objname_by_idx(group_id, i, name_cstr, 256);
+        std::string name(name_cstr);
+        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);
 }