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Enhance error checking for szip H5DataIO settings #168

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merged 2 commits into from
Oct 15, 2019
Merged

Enhance error checking for szip H5DataIO settings #168

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c11f42a
Enhance error checking for szip H5DataIO settings
oruebel Oct 9, 2019
2471f85
Merge branch 'dev' into enh/szipchecks
oruebel Oct 15, 2019
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24 changes: 17 additions & 7 deletions src/hdmf/backends/hdf5/h5_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -310,20 +310,30 @@ def _check_compression_options(self):
if 'compression_opts' in self.__iosettings:
if self.__iosettings['compression'] == 'gzip':
if self.__iosettings['compression_opts'] not in range(10):
raise ValueError("GZIP compression_opts setting must be an integer from 0-9, " +
raise ValueError("GZIP compression_opts setting must be an integer from 0-9, "
"not " + str(self.__iosettings['compression_opts']))
elif self.__iosettings['compression'] == 'lzf':
if self.__iosettings['compression_opts'] is not None:
raise ValueError("LZF compression filter accepts no compression_opts")
elif self.__iosettings['compression'] == 'szip':
if not isinstance(self.__iosettings['compression_opts'], tuple) or \
len(self.__iosettings['compression_opts']) != 2:
raise ValueError("SZIP compression filter compression_opts" +
" must be a 2-tuple ('ec'|'nn', even integer 0-32")
szip_opts_error = False
# Check that we have a tuple
szip_opts_error |= not isinstance(self.__iosettings['compression_opts'], tuple)
# Check that we have a tuple of the right length and correct settings
if not szip_opts_error:
try:
szmethod, szpix = self.__iosettings['compression_opts']
szip_opts_error |= (szmethod not in ('ec', 'nn'))
szip_opts_error |= (not (0 < szpix <= 32 and szpix % 2 == 0))
except ValueError: # ValueError is raised if tuple does not have the right length to unpack
szip_opts_error = True
if szip_opts_error:
raise ValueError("SZIP compression filter compression_opts"
" must be a 2-tuple ('ec'|'nn', even integer 0-32).")
# Warn if compressor other than gzip is being used
if self.__iosettings['compression'] != 'gzip':
warnings.warn(str(self.__iosettings['compression']) + " compression may not be available" +
"on all installations of HDF5. Use of gzip is recommended to ensure portability of" +
warnings.warn(str(self.__iosettings['compression']) + " compression may not be available"
"on all installations of HDF5. Use of gzip is recommended to ensure portability of"
"the generated HDF5 files.")

@staticmethod
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10 changes: 8 additions & 2 deletions tests/unit/test_io_hdf5_h5tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -441,7 +441,7 @@ def test_warning_on_non_gzip_compression(self):
compression='gzip')
self.assertEqual(len(w), 0)
self.assertEqual(dset.io_settings['compression'], 'gzip')
# Make sure no warning is issued when using szip (if installed)
# Make sure a warning is issued when using szip (even if installed)
if "szip" in h5py_filters.encode:
with warnings.catch_warnings(record=True) as w:
dset = H5DataIO(np.arange(30),
Expand All @@ -452,7 +452,7 @@ def test_warning_on_non_gzip_compression(self):
else:
with self.assertRaises(ValueError):
H5DataIO(np.arange(30), compression='szip', compression_opts=('ec', 16))
# Make sure no warning is issued when using lzf
# Make sure a warning is issued when using lzf compression
with warnings.catch_warnings(record=True) as w:
dset = H5DataIO(np.arange(30),
compression='lzf')
Expand Down Expand Up @@ -494,6 +494,12 @@ def test_value_error_on_incompatible_compression_opts(self):
# Make sure we warn if szip with gzip compression option is used
with self.assertRaises(ValueError):
H5DataIO(np.arange(30), compression='szip', compression_opts=4)
# Make sure szip raises a ValueError if bad options are used (odd compression option)
with self.assertRaises(ValueError):
H5DataIO(np.arange(30), compression='szip', compression_opts=('ec', 3))
# Make sure szip raises a ValueError if bad options are used (bad methos)
with self.assertRaises(ValueError):
H5DataIO(np.arange(30), compression='szip', compression_opts=('bad_method', 16))

def test_warning_on_linking_of_regular_array(self):
with warnings.catch_warnings(record=True) as w:
Expand Down