Fix compatibility for read_nested_dict_from_hdf() (#61)

* Fix compatibility for read_nested_dict_from_hdf()

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---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

h5io_browser/base.py

@@ -21,6 +21,7 @@
     "csr_matrix",
     "csc_array",
     "csr_array",
+    "dict",
     "multiarray",
 )
 
@@ -81,19 +82,9 @@ def read_dict_from_hdf(file_name, h5_path, recursive=False, slash="ignore"):
              any type supported by ``write_hdf5``.
     """
     with h5py.File(file_name, "r") as hdf:
-        if recursive:
-            nodes_lst = _get_hdf_content(
-                hdf=hdf[h5_path], recursive=recursive, only_nodes=True
-            )
-        else:
-            nodes_lst = [h5_path]
-        if len(nodes_lst) > 0 and nodes_lst[0] != "/":
-            return {
-                n: _read_hdf(hdf_filehandle=hdf, h5_path=n, slash=slash)
-                for n in nodes_lst
-            }
-        else:
-            return {}
+        return _read_dict_from_open_hdf(
+            hdf_filehandle=hdf, h5_path=h5_path, recursive=recursive, slash=slash
+        )
 
 
 def read_nested_dict_from_hdf(
@@ -119,32 +110,44 @@ def read_nested_dict_from_hdf(
     if h5_path[0] != "/":
         h5_path = "/" + h5_path
     with h5py.File(file_name, "r") as hdf:
-        nodes_lst = _get_hdf_content(
-            hdf=hdf[h5_path], recursive=recursive, only_nodes=True
-        )
-        if not recursive and len(nodes_lst) == 0 and h5_path != "/":
-            nodes_lst += [h5_path]
-        if len(group_paths) > 0:
-            for group in group_paths:
-                nodes_lst += _get_hdf_content(
-                    hdf=hdf[posixpath.join(h5_path, group)],
-                    recursive=recursive,
-                    only_nodes=True,
-                )
-        if len(nodes_lst) > 0:
-            return_dict = {}
-            for n in nodes_lst:
-                return_dict = _merge_nested_dict(
-                    main_dict=return_dict,
-                    add_dict=_get_nested_dict_item(
-                        key=n,
-                        value=_read_hdf(hdf_filehandle=hdf, h5_path=n, slash=slash),
-                        h5_path=h5_path,
-                    ),
-                )
-            return return_dict
+        group_attrs_dict = hdf[h5_path].attrs
+        if (
+            "TITLE" in group_attrs_dict.keys()
+            and group_attrs_dict["TITLE"] in H5IO_GROUP_TYPES
+        ):
+            return _read_dict_from_open_hdf(
+                hdf_filehandle=hdf,
+                h5_path=h5_path[1:],
+                recursive=recursive,
+                slash=slash,
+            )
         else:
-            return {}
+            nodes_lst = _get_hdf_content(
+                hdf=hdf[h5_path], recursive=recursive, only_nodes=True
+            )
+            if not recursive and len(nodes_lst) == 0 and h5_path != "/":
+                nodes_lst += [h5_path]
+            if len(group_paths) > 0:
+                for group in group_paths:
+                    nodes_lst += _get_hdf_content(
+                        hdf=hdf[posixpath.join(h5_path, group)],
+                        recursive=recursive,
+                        only_nodes=True,
+                    )
+            if len(nodes_lst) > 0:
+                return_dict = {}
+                for n in nodes_lst:
+                    return_dict = _merge_nested_dict(
+                        main_dict=return_dict,
+                        add_dict=_get_nested_dict_item(
+                            key=n,
+                            value=_read_hdf(hdf_filehandle=hdf, h5_path=n, slash=slash),
+                            h5_path=h5_path,
+                        ),
+                    )
+                return return_dict
+            else:
+                return {}
 
 
 def write_dict_to_hdf(file_name, data_dict, compression=4, slash="error"):
@@ -293,6 +296,37 @@ def _read_hdf(hdf_filehandle, h5_path, slash="ignore"):
     )
 
 
+def _read_dict_from_open_hdf(hdf_filehandle, h5_path, recursive=False, slash="ignore"):
+    """
+    Read data from an open HDF5 file into a dictionary - by default only the nodes are converted to dictionaries,
+    additional sub groups can be converted using the recursive parameter.
+
+    Args:
+       hdf_filehandle (h5py.File): Open HDF5 file
+       h5_path (str): Path to a group in the HDF5 file from where the data is read
+       recursive (bool/int): Recursively browse through the HDF5 file, either a boolean flag or an integer
+                              which specifies the level of recursion.
+       slash (str): 'ignore' | 'replace' Whether to replace the string {FWDSLASH} with the value /. This does
+                    not apply to the top level name (title). If 'ignore', nothing will be replaced.
+    Returns:
+       dict: The loaded data as dictionary, with the keys being the path inside the HDF5 file. The values can be of
+             any type supported by ``write_hdf5``.
+    """
+    if recursive:
+        nodes_lst = _get_hdf_content(
+            hdf=hdf_filehandle[h5_path], recursive=recursive, only_nodes=True
+        )
+    else:
+        nodes_lst = [h5_path]
+    if len(nodes_lst) > 0 and nodes_lst[0] != "/":
+        return {
+            n: _read_hdf(hdf_filehandle=hdf_filehandle, h5_path=n, slash=slash)
+            for n in nodes_lst
+        }
+    else:
+        return {}
+
+
 def _write_hdf(
     hdf_filehandle,
     h5_path,

tests/test_base.py

@@ -3,6 +3,7 @@
 import h5py
 from unittest import TestCase
 import posixpath
+import h5io
 from h5io_browser import (
     delete_item,
     list_hdf,
@@ -398,3 +399,41 @@ def test_delete(self):
         nodes, groups = list_hdf(file_name=self.file_name, h5_path="/data_json")
         self.assertEqual(groups, [])
         self.assertEqual(nodes, ["/data_json/a"])
+
+
+class TestCompatibility(TestCase):
+    def setUp(self):
+        self.file_name = "testcomp.h5"
+        self.data = {
+            "array": np.ones(4) * 42,
+            "b": 42,
+        }
+        self.h5_path = "h5io"
+        h5io.write_hdf5("testcomp.h5", self.data)
+
+    def test_h5io(self):
+        dataread = h5io.read_hdf5(self.file_name, self.h5_path)
+        for k, v in self.data.items():
+            if isinstance(v, np.ndarray):
+                self.assertTrue(all(np.equal(v, dataread[k])))
+            else:
+                self.assertTrue(v == dataread[k])
+
+    def test_read_dict_from_hdf(self):
+        dataread = read_dict_from_hdf(self.file_name, self.h5_path)
+        for k, v in self.data.items():
+            if isinstance(v, np.ndarray):
+                self.assertTrue(all(np.equal(v, dataread[self.h5_path][k])))
+            else:
+                self.assertTrue(v == dataread[self.h5_path][k])
+
+    def test_read_nested_dict_from_hdf(self):
+        dataread = read_nested_dict_from_hdf(self.file_name, self.h5_path)
+        for k, v in self.data.items():
+            if isinstance(v, np.ndarray):
+                self.assertTrue(all(np.equal(v, dataread[self.h5_path][k])))
+            else:
+                self.assertTrue(v == dataread[self.h5_path][k])
+
+    def tearDown(self):
+        os.remove(self.file_name)