def test_read_empty_array_via_path(self):
res = {'a': np.array([[], []])}
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = h5w.load_h5(fn, path='a')
assert_array_equal(res, [[], []])
self.assertEqual(np.shape(res), (2, 0))
def test_store_and_load_simpledata(self):
res = self.construct_simpledata()
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = h5w.load_h5(fn)
for key, val in zip(simpledata_str, simpledata_val):
self.assertEqual(res[key], val)
def test_store_and_load_simpledata(self):
res = self.construct_simpledata()
wrapper.add_to_h5(fn, res, write_mode='w')
res.clear()
res = wrapper.load_h5(fn)
for key, val in zip(simpledata_str, simpledata_val):
assert(res[key] == val)
def test_load_lazy_simple(self):
res = self.construct_simpledata()
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = h5w.load_h5(fn, lazy=True)
for key, obj in res.items():
self.assertIsNone(obj)
def test_load_lazy_simple(self):
res = self.construct_simpledata()
wrapper.add_to_h5(fn, res, write_mode='w')
res.clear()
res = wrapper.load_h5(fn, lazy=True)
for key, obj in res.items():
assert(obj is None)
def test_read_empty_array_via_path(self):
res = {'a': numpy.array([[], []])}
wrapper.add_to_h5(fn, res, write_mode='w')
res.clear()
res = wrapper.load_h5(fn, path='a')
assert_array_equal(res, [[], []])
assert(numpy.shape(res) == (2, 0))
def test_write_empty_array(self):
res = {'a': [], 'b': np.array([])}
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = h5w.load_h5(fn)
assert_array_equal(res['a'], [])
assert_array_equal(res['b'], [])
def test_store_and_load_quantities_array(self):
data = {'times': np.array([1, 2, 3]) * pq.ms, 'positions':
np.array([1, 2, 3]) * pq.cm}
h5w.add_to_h5(fn, data, overwrite_dataset=True)
# loading the whole data
res = h5w.load_h5(fn)
self.assertEqual(res['times'].dimensionality,
data['times'].dimensionality)
def test_store_and_test_key_types(self):
data = {'a': 1, (1, 2): 2., 4.: 3.}
wrapper.add_to_h5(fn, data, write_mode='w', compression='gzip')
res = wrapper.load_h5(fn)
keys = ['a', (1, 2), 4.]
for k in keys:
assert(k in res.keys())
def test_store_and_load_quantities_array(self):
import quantities as pq
data = {'times': numpy.array(
[1, 2, 3]) * pq.ms, 'positions': numpy.array([1, 2, 3]) * pq.cm}
wrapper.add_to_h5(fn, data, overwrite_dataset=True)
# loading the whole data
res = wrapper.load_h5(fn)
assert(res['times'].dimensionality == data['times'].dimensionality)
def test_load_lazy_nested(self):
res = {'a': 1, 'test1': {'b': 2}, 'test2': {
'test3': {'c': numpy.array([1, 2, 3])}}}
wrapper.add_to_h5(fn, res, write_mode='w')
res.clear()
res = wrapper.load_h5(fn, lazy=True)
assert(res['a'] is None)
assert(res['test1']['b'] is None)
assert(res['test2']['test3']['c'] is None)
def test_check_for_node(self):
res = {'a': 1, 'test1': {'b': 2}, 'test2': {'test3': {'c': 3}}}
wrapper.add_to_h5(fn, res, write_mode='w')
assert(wrapper.node_exists(fn, '/a'))
assert(wrapper.node_exists(fn, '/nota') is False)
assert(wrapper.node_exists(fn, '/test1/b'))
assert(wrapper.node_exists(fn, '/test1/notb') is False)
assert(wrapper.node_exists(fn, '/test2/test3/c'))
assert(wrapper.node_exists(fn, '/test2/test3/notc') is False)
def test_store_and_load_arraydata(self):
res = {}
for key, val in zip(arraydata_str, arraydata_val):
res[key] = val
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = h5w.load_h5(fn)
for key, val in zip(arraydata_str, arraydata_val):
assert_array_equal(res[key], val)
def test_load_lazy_nested(self):
res = {'a': 1, 'test1': {'b': 2}, 'test2': {
'test3': {'c': np.array([1, 2, 3])}}}
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = h5w.load_h5(fn, lazy=True)
self.assertIsNone(res['a'])
self.assertIsNone(res['test1']['b'])
self.assertIsNone(res['test2']['test3']['c'])
def test_write_nested_empty_array(self):
res = {'a': [[], []], 'b': np.array([[], []])}
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = h5w.load_h5(fn)
assert_array_equal(res['a'], [[], []])
self.assertEqual(np.shape(res['a']), (2, 0))
assert_array_equal(res['b'], [[], []])
self.assertEqual(np.shape(res['b']), (2, 0))
def test_write_nested_empty_array(self):
res = {'a': [[], []], 'b': numpy.array([[], []])}
wrapper.add_to_h5(fn, res, write_mode='w')
res.clear()
res = wrapper.load_h5(fn)
assert_array_equal(res['a'], [[], []])
assert(numpy.shape(res['a']) == (2, 0))
assert_array_equal(res['b'], [[], []])
assert(numpy.shape(res['b']) == (2, 0))
def test_store_and_test_key_types(self):
data = {'a': 1, (1, 2): {4: 2.}, 4.: 3.}
h5w.add_to_h5(fn, data, write_mode='w')
res = h5w.load_h5(fn)
keys = ['a', (1, 2), 4.]
for k in keys:
self.assertIn(k, res.keys())
self.assertIn(4, res[(1, 2)].keys())
def test_store_and_load_dictdata(self):
res = {}
for key, val in zip(dictdata_str, dictdata_val):
res[key] = val
wrapper.add_to_h5(fn, res, write_mode='w')
res.clear()
res = wrapper.load_h5(fn)
for dkey, dval in zip(dictdata_str, dictdata_val):
for key, val in dval.items():
assert(res[dkey][key] == val)
def test_store_and_load_dictdata(self):
res = {}
for key, val in zip(dictdata_str, dictdata_val):
res[key] = val
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = h5w.load_h5(fn)
for dkey, dval in zip(dictdata_str, dictdata_val):
for key, val in dval.items():
self.assertEqual(res[dkey][key], val)
def test_store_and_load_custom_array(self):
a = [[1, 2, 3, 4], [6, 7]]
h5w.add_to_h5(fn, {'a': a}, overwrite_dataset=True)
# loading the whole data
res = h5w.load_h5(fn)
for i in xrange(len(a)):
self.assertLess(np.sum(a[i] - res['a'][i]), 1e-12)
# loading path directly
res = h5w.load_h5(fn, path='a/')
for i in xrange(len(a)):
self.assertLess(np.sum(a[i] - res[i]), 1e-12)
def test_store_and_load_custom_array(self):
a = [[1, 2, 3, 4], [6, 7]]
wrapper.add_to_h5(fn, {'a': a}, overwrite_dataset=True)
# loading the whole data
res = wrapper.load_h5(fn)
for i in xrange(len(a)):
assert(numpy.sum(a[i] - res['a'][i]) < 1e-12)
# loading path directly
res = wrapper.load_h5(fn, path='a/')
for i in xrange(len(a)):
assert(numpy.sum(a[i] - res[i]) < 1e-12)
def test_handle_nonexisting_path(self):
res = {}
stest = 'this is a test'
h5w.add_to_h5(fn, res, write_mode='w')
try:
res = h5w.load_h5(fn, path='test/')
raise Exception() # should not get until here
except KeyError:
res['test'] = stest
h5w.add_to_h5(fn, res)
res.clear()
res = h5w.load_h5(fn, path='test/')
self.assertEqual(res, stest)
def test_overwrite_dataset(self):
res = {'a': 5}
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = {'a': 6}
self.assertRaises(KeyError, h5w.add_to_h5,
fn, res, write_mode='a', overwrite_dataset=False)
res.clear()
res = h5w.load_h5(fn)
self.assertEqual(res['a'], 5) # dataset should still contain old value
res.clear()
res = {'a': 6}
h5w.add_to_h5(
fn, res, write_mode='a', overwrite_dataset=True)
res.clear()
res = h5w.load_h5(fn)
self.assertEqual(res['a'], 6) # dataset should contain new value
def test_overwrite_dataset(self):
res = {'a': 5}
wrapper.add_to_h5(fn, res, write_mode='w')
res.clear()
res = {'a': 6}
wrapper.add_to_h5(
fn, res, write_mode='a', overwrite_dataset=False)
res.clear()
res = wrapper.load_h5(fn)
assert(res['a'] == 5) # dataset should still contain old value
res.clear()
res = {'a': 6}
wrapper.add_to_h5(
fn, res, write_mode='a', overwrite_dataset=True)
res.clear()
res = wrapper.load_h5(fn)
assert(res['a'] == 6) # dataset should contain new value
def test_store_and_load_dataset_directly(self):
res = self.construct_simpledata()
wrapper.add_to_h5(fn, res, write_mode='w')
for key, val in zip(simpledata_str, simpledata_val):
assert(wrapper.load_h5(fn, '/' + key) == val)
def test_store_none(self):
res = {'a1': None}
h5w.add_to_h5(fn, res, write_mode='w')
res.clear()
res = h5w.load_h5(fn)
self.assertIsNone(res['a1'])
def test_store_and_load_dataset_directly(self):
res = self.construct_simpledata()
h5w.add_to_h5(fn, res, write_mode='w')
for key, val in zip(simpledata_str, simpledata_val):
self.assertEqual(h5w.load_h5(fn, '/' + key), val)
def test_write_and_load_with_label(self):
res = self.construct_simpledata()
h5w.add_to_h5(fn, res, write_mode='w', dict_label='test_label')
for key, val in zip(simpledata_str, simpledata_val):
self.assertEqual(h5w.load_h5(fn, 'test_label/' + key), val)
def test_store_and_load_with_compression(self):
data = {'a': 1, 'test1': {'b': 2}, 'test2': {
'test3': {'c': np.array([1, 2, 3])}}}
h5w.add_to_h5(fn, data, write_mode='w', compression='gzip')
h5w.load_h5(fn)
def test_write_and_load_with_label(self):
res = self.construct_simpledata()
wrapper.add_to_h5(fn, res, write_mode='w', dict_label='test_label')
for key, val in zip(simpledata_str, simpledata_val):
assert(wrapper.load_h5(fn, 'test_label/' + key) == val)
