def setup(self): self.file_v1 = 'v1.0.h5' self.file_v2 = 'v1.1.h5' self.teardown() # in case files already exist, remove it items, times, features = generate.full(20,10) h5f_1_0.write(self.file_v1, 'features', items, times, features) h5f_1_1.write(self.file_v2, 'features', items, times, features)
def test_bad_file2(self): with open(self.filename, 'w') as f: f.write('This is not a HDF5 file') with pytest.raises(IOError) as ioerror: h5f.write(self.filename, 'group', [], [], []) msg = str(ioerror.value) assert self.filename in msg assert 'not a HDF5 file' in msg
def test_bad_file2(self): with open(self.filename, 'w') as f: f.write('This is not a HDF5 file') data = generate.full(1) with pytest.raises(IOError) as ioerror: h5f.write(self.filename, 'group', data[0], data[1], data[2]) msg = str(ioerror.value) assert self.filename in msg assert 'not a HDF5 file' in msg
def test_bad_file2(self): with open(self.filename, 'w') as f: f.write('This is not a HDF5 file') data = generate.full(1) with pytest.raises(IOError) as ioerror: h5f.write(self.filename, 'group', data[0], data[1], data[2]) msg = str(ioerror.value) assert self.filename in msg assert 'not a HDF5 file' in msg
def test_write(self): files, times, features = generate.full(10, 2, 5) h5f.write(self.filename, 'f', files, times, features) with h5py.File(self.filename, 'r') as f: assert ['f'] == list(f.keys()) g = f.get('f') assert list(g.keys()) == ['features', 'index', 'items', 'labels'] assert g.get('features').shape[1] == 2 assert g.get('index').shape == (10,) assert g.get('items').shape == (10,) assert g.get('features').shape[0] == g.get('labels').shape[0]
def test_write(self): files, times, features = generate.full(10, 2, 5) h5f.write(self.filename, 'f', files, times, features) with h5py.File(self.filename, 'r') as f: assert ['f'] == list(f.keys()) g = f.get('f') assert list(g.keys()) == ['features', 'index', 'items', 'labels'] assert g.get('features').shape[1] == 2 assert g.get('index').shape == (10, ) assert g.get('items').shape == (10, ) assert g.get('features').shape[0] == g.get('labels').shape[0]
def _test_wr(self, time_format): """Test retrieving times and files after a write/read operation.""" items, t_gold, feat = generate.full(self.nbitems, tformat=time_format) write(self.filename, self.group, items, t_gold, feat) t, _ = read(self.filename, self.group) assert len(t) == self.nbitems if time_format == 2: assert all([tt.shape[1] == time_format for tt in t.values()]) # build a dict from gold to compare with t d = {} for k, v in zip(items, t_gold): d[k] = v # compare the two dicts for dd, tt in zip(d, t): assert tt == dd
def setup(self): # init default parameters self.filename = 'test.h5' self.group = 'features' # create a simple feature file items, times, feat = generate.full(10) self.features = Features(feat) self.times = Times(times) self.items = Items(items) self.items2 = Items([i+'2' for i in items]) write(self.filename, self.group, items, times, feat) # read it with h5py self.f = h5py.File(self.filename, 'r') self.g = self.f.get(self.group)
def test_concat(self): """Concatenate new data to an existing item in an existing file.""" # write a single item named 'item_0' data1 = generate.full(1, self.dim, 10, items_root='item') h5f.write(self.filename, 'group1', data1[0], data1[1], data1[2]) h5f.write(self.filename, 'group3', data1[0], data1[1], data1[2]) # concatenate new data to 'item_0' data2 = generate.full(1, self.dim, 20, items_root='item') h5f.write(self.filename, 'group2', data2[0], data2[1], data2[2]) with pytest.raises(IOError): h5f.write(self.filename, 'group3', data2[0], data2[1], data2[2])
def test_concat(self): """Concatenate new data to an existing item in an existing file.""" # write a single item named 'item_0' data1 = generate.full(1, self.dim, 10, items_root='item') h5f.write(self.filename, 'group1', data1[0], data1[1], data1[2]) h5f.write(self.filename, 'group3', data1[0], data1[1], data1[2]) # concatenate new data to 'item_0' data2 = generate.full(1, self.dim, 20, items_root='item') h5f.write(self.filename, 'group2', data2[0], data2[1], data2[2]) with pytest.raises(IOError): h5f.write(self.filename, 'group3', data2[0], data2[1], data2[2])
def test_append(self): """Append a new item to an existing dataset.""" i, t, f = generate.full(30, self.dim, 40, items_root='File') h5f.write(self.filename, 'group', i, t, f) # append new item to existing dataset features_added = np.zeros(shape=(1, self.dim)) times_added = np.linspace(0, 2, 1) h5f.write(self.filename, 'group', ['File_31'], [times_added], [features_added]) with pytest.raises(IOError) as err: h5f.write(self.filename, 'group', ['File_3'], [times_added], [features_added]) assert 'data is not appendable to the group' in str(err.value) # read it times_r, features_r = h5f.read(self.filename, 'group') assert set(times_r.keys()) == set(i+['File_31']) assert set(features_r.keys()) == set(i+['File_31']) assert all(times_r['File_31'] == times_added) assert (features_r['File_31'] == features_added).all()
def test_append(self): """Append a new item to an existing dataset.""" i, t, f = generate.full(30, self.dim, 40, items_root='File') h5f.write(self.filename, 'group', i, t, f) # append new item to existing dataset features_added = np.zeros(shape=(1, self.dim)) times_added = np.linspace(0, 2, 1) h5f.write(self.filename, 'group', ['File_31'], [times_added], [features_added]) with pytest.raises(IOError) as err: h5f.write(self.filename, 'group', ['File_3'], [times_added], [features_added]) assert 'data is not appendable to the group' in str(err.value) # read it times_r, features_r = h5f.read(self.filename, 'group') assert set(times_r.keys()) == set(i + ['File_31']) assert set(features_r.keys()) == set(i + ['File_31']) assert all(times_r['File_31'] == times_added) assert (features_r['File_31'] == features_added).all()
def test_bad_file(self): a, b, c = generate.full(2) with pytest.raises(IOError) as ioerror: h5f.write('/silly/path/to/no/where.h5', 'group', a, b, c) assert all([s in str(ioerror.value)] for s in ['/silly/path', 'No such file'])
def setup(self): items, self.data, feats = generate.full(10,tformat=1) self.filename = 'test.h5' self.teardown() write(self.filename, 'group', items, self.data, feats) self.group = h5py.File(self.filename, 'a')['group']
def test_bad_file(self): a, b, c = generate.full(2) with pytest.raises(IOError) as ioerror: h5f.write('/silly/path/to/no/where.h5', 'group', a, b, c) assert all([s in str(ioerror.value)] for s in ['/silly/path', 'No such file'])
def test_bad_data(self): with pytest.raises(IOError) as ioerror: h5f.write('/silly/path/to/no/where.h5', 'group', [], [], []) assert 'data is empty' == str(ioerror.value)
def test_raise_on_write_sparse(): a, b, c = generate.full(1) with pytest.raises(NotImplementedError) as ioerror: h5f.write('test.h5', 'group', a, b, c, dformat='sparse') assert 'sparse' in str(ioerror.value)
def test_bad_data(self): with pytest.raises(IOError) as ioerror: h5f.write('/silly/path/to/no/where.h5', 'group', [], [], []) assert 'data is empty' == str(ioerror.value)
def test_raise_on_write_sparse(): a, b, c = generate.full(1) with pytest.raises(NotImplementedError) as ioerror: h5f.write('test.h5', 'group', a, b, c, dformat='sparse') assert 'sparse' in str(ioerror.value)