[python-hdf5storage] 79/84: Fixed bug where a structured ndarray with a field having the name 'O' was always written as an HDF5 Group.

[Ghislain Vaillant]

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ghisvail-guest pushed a commit to annotated tag 0.1.10
in repository python-hdf5storage.

commit 987c893457258316c3beb22d81ad2b7a22089735
Author: Freja Nordsiek <fnordsie at gmail.com>
Date:   Mon Sep 7 20:09:35 2015 -0400

    Fixed bug where a structured ndarray with a field having the name 'O' was always written as an HDF5 Group.
---
 README.rst                    |  8 +++-
 hdf5storage/Marshallers.py    |  6 +--
 tests/test_ndarray_O_field.py | 98 +++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 108 insertions(+), 4 deletions(-)

diff --git a/README.rst b/README.rst
index 8681015..ebf765d 100644
--- a/README.rst
+++ b/README.rst
@@ -213,7 +213,13 @@ canonical empty  0.1      ``np.float64([])``
 Versions
 ========
 
-0.1.9. Minor feature release adding optional data compression and the storage of data checksums. Controlled by several new options.
+0.1.9. Bugfix and minor feature release doing the following.
+       * Issue #23. Fixed bug where a structured ``np.ndarray`` with
+         a field name of ``'O'`` could never be written as an
+         HDF5 COMPOUND Dataset (falsely thought a field's dtype was
+         object).
+       * Issue #6. Added optional data compression and the storage of
+         data checksums. Controlled by several new options.
 
 0.1.8. Bugfix release fixing the following two bugs.
        * Issue #21. Fixed bug where the ``'MATLAB_class'`` Attribute is
diff --git a/hdf5storage/Marshallers.py b/hdf5storage/Marshallers.py
index b64ec14..55541f0 100644
--- a/hdf5storage/Marshallers.py
+++ b/hdf5storage/Marshallers.py
@@ -678,15 +678,15 @@ class NumpyScalarArrayMarshaller(TypeMarshaller):
         # those have to be excluded too. Also, if any of its fields are
         # an object time (no matter how nested), then rather than
         # converting that field to a HDF5 Reference types, it will just
-        # be written as a Group instead (just have to see if "'O'" is in
-        # str(data_to_store.dtype).
+        # be written as a Group instead (just have to see if ", 'O'" is
+        # in str(data_to_store.dtype).
         
         if data_to_store.dtype.fields is not None \
                 and h5py.check_dtype(ref=data_to_store.dtype) \
                 is not h5py.Reference \
                 and not np.iscomplexobj(data) \
                 and (options.structured_numpy_ndarray_as_struct \
-                or "'O'" in str(data_to_store.dtype) \
+                or ", 'O'" in str(data_to_store.dtype) \
                 or not all(data_to_store.shape) \
                 or not all([all(data_to_store[n].shape) \
                 for n in data_to_store.dtype.names])):
diff --git a/tests/test_ndarray_O_field.py b/tests/test_ndarray_O_field.py
new file mode 100644
index 0000000..f4af940
--- /dev/null
+++ b/tests/test_ndarray_O_field.py
@@ -0,0 +1,98 @@
+# Copyright (c) 2013-2015, Freja Nordsiek
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+#
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice, this list of conditions and the following disclaimer in the
+# documentation and/or other materials provided with the distribution.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+import os
+import os.path
+
+import numpy as np
+import h5py
+
+import hdf5storage
+
+
+filename = 'data.mat'
+
+
+# A series of tests to make sure that structured ndarrays with a field
+# that has an object dtype are written like structs (are HDF5 Groups)
+# but are written as an HDF5 COMPOUND Dataset otherwise (even in the
+# case that a field's name is 'O').
+
+
+def test_O_field_compound():
+    name = '/a'
+    data = np.empty(shape=(1, ), dtype=[('O', 'int8'), ('a', 'uint16')])
+    if os.path.exists(filename):
+        os.remove(filename)
+    try:
+        hdf5storage.write(data, path=name, filename=filename,
+                          matlab_compatible=False,
+                          structured_numpy_ndarray_as_struct=False)
+        with h5py.File(filename) as f:
+            assert isinstance(f[name], h5py.Dataset)
+    except:
+        raise
+    finally:
+        if os.path.exists(filename):
+            os.remove(filename)
+
+
+def test_object_field_group():
+    name = '/a'
+    data = np.empty(shape=(1, ), dtype=[('a', 'O'), ('b', 'uint16')])
+    data['a'][0] = [1, 2]
+    if os.path.exists(filename):
+        os.remove(filename)
+    try:
+        hdf5storage.write(data, path=name, filename=filename,
+                          matlab_compatible=False,
+                          structured_numpy_ndarray_as_struct=False)
+        with h5py.File(filename) as f:
+            assert isinstance(f[name], h5py.Group)
+    except:
+        raise
+    finally:
+        if os.path.exists(filename):
+            os.remove(filename)
+
+
+def test_O_and_object_field_group():
+    name = '/a'
+    data = np.empty(shape=(1, ), dtype=[('a', 'O'), ('O', 'uint16')])
+    data['a'][0] = [1, 2]
+    if os.path.exists(filename):
+        os.remove(filename)
+    try:
+        hdf5storage.write(data, path=name, filename=filename,
+                          matlab_compatible=False,
+                          structured_numpy_ndarray_as_struct=False)
+        with h5py.File(filename) as f:
+            assert isinstance(f[name], h5py.Group)
+    except:
+        raise
+    finally:
+        if os.path.exists(filename):
+            os.remove(filename)

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