add "require_size" hdf5 functionality

bfps/_base.py

@@ -175,9 +175,12 @@ class _base(object):
     def rewrite_par(
             self,
             group = None,
-            parameters = None):
+            parameters = None,
+            file_name = None):
         assert(group != 'parameters')
-        ofile = h5py.File(os.path.join(self.work_dir, self.simname + '.h5'), 'r+')
+        if type(file_name) == None:
+            file_name = os.path.join(self.work_dir, self.simname + '.h5')
+        ofile = h5py.File(file_name, 'a')
         for k in parameters.keys():
             if group not in ofile.keys():
                 ofile.create_group(group)

bfps/cpp/hdf5_tools.cpp

 #include "hdf5_tools.hpp"
 
+int hdf5_tools::require_size_single_dataset(hid_t dset, int tsize)
+{
+    int ndims;
+    hsize_t space;
+    space = H5Dget_space(dset);
+    ndims = H5Sget_simple_extent_ndims(space);
+    hsize_t *dims = new hsize_t[ndims];
+    H5Sget_simple_extent_dims(space, dims, NULL);
+    if (dims[0] < tsize)
+    {
+        dims[0] = tsize;
+        H5Dset_extent(dset, dims);
+    }
+    H5Sclose(space);
+    delete[] dims;
+    return EXIT_SUCCESS;
+}
+
 int hdf5_tools::grow_single_dataset(hid_t dset, int tincrement)
 {
     int ndims;
@@ -15,6 +33,21 @@ int hdf5_tools::grow_single_dataset(hid_t dset, int tincrement)
     return EXIT_SUCCESS;
 }
 
+herr_t hdf5_tools::require_size_dataset_visitor(
+    hid_t o_id,
+    const char *name,
+    const H5O_info_t *info,
+    void *op_data)
+{
+    if (info->type == H5O_TYPE_DATASET)
+    {
+        hsize_t dset = H5Dopen(o_id, name, H5P_DEFAULT);
+        require_size_single_dataset(dset, *((int*)(op_data)));
+        H5Dclose(dset);
+    }
+    return EXIT_SUCCESS;
+}
+
 herr_t hdf5_tools::grow_dataset_visitor(
     hid_t o_id,
     const char *name,
@@ -50,6 +83,26 @@ int hdf5_tools::grow_file_datasets(
     return file_problems;
 }
 
+
+int hdf5_tools::require_size_file_datasets(
+        const hid_t stat_file,
+        const std::string group_name,
+        int tsize)
+{
+    int file_problems = 0;
+
+    hid_t group;
+    group = H5Gopen(stat_file, group_name.c_str(), H5P_DEFAULT);
+    H5Ovisit(
+            group,
+            H5_INDEX_NAME,
+            H5_ITER_NATIVE,
+            require_size_dataset_visitor,
+            &tsize);
+    H5Gclose(group);
+    return file_problems;
+}
+
 template <typename number>
 std::vector<number> hdf5_tools::read_vector(
         const hid_t group,

bfps/cpp/hdf5_tools.hpp

@@ -48,6 +48,21 @@ namespace hdf5_tools
             const std::string group_name,
             int tincrement);
 
+    int require_size_single_dataset(
+            hid_t dset,
+            int tincrement);
+
+    herr_t require_size_dataset_visitor(
+        hid_t o_id,
+        const char *name,
+        const H5O_info_t *info,
+        void *op_data);
+
+    int require_size_file_datasets(
+            const hid_t stat_file,
+            const std::string group_name,
+            int tincrement);
+
     template <typename number>
     std::vector<number> read_vector(
             const hid_t group,