def test_construction_from_sources():
aux_arrays = ('test1', 'test2')
files = [_create_hdf5(aux_arrays=aux_arrays) for i in range(3)]
shape = files[0]['data'].shape
shape = (shape[0], 3 * shape[1])
map_source = MappedSource.from_hdf_sources(files,
'data',
aligned_arrays=aux_arrays)
assert map_source.shape == shape, 'Shape wrong'
assert map_source.binary_channel_mask.sum(
) == shape[0], 'Wrong number of active channels'
for field in aux_arrays:
assert hasattr(map_source,
field), 'Aux field {} not preserved'.format(field)
assert getattr(
map_source, field
).shape[1] == shape[1], 'aligned field {} wrong length'.format(field)
# repeat for transpose: now sources are stacked on axis=0, but the resulting shape is transposed per vector
# timeseries convention (channels X samples)
shape = files[0]['data'].shape
shape = (shape[0] * 3, shape[1])
map_source = MappedSource.from_hdf_sources(files,
'data',
aligned_arrays=aux_arrays,
transpose=True)
assert map_source.shape == shape[::-1], 'Shape wrong in transpose'
assert map_source.binary_channel_mask.sum(
) == shape[1], 'Wrong number of active channels in transpose'
for field in aux_arrays:
assert hasattr(map_source,
field), 'Aux field {} not preserved'.format(field)
assert getattr(
map_source, field
).shape[0] == shape[0], 'aligned field {} wrong length'.format(field)
def test_scaling():
f = _create_hdf5()
float_data = f['data'][:, 500:1000].astype('d')
map_source = MappedSource.from_hdf_sources(f, 'data', units_scale=2.0)
assert np.all(map_source[:, 500:1000] == float_data *
2).all(), 'scalar scaling wrong'
map_source = MappedSource.from_hdf_sources(f,
'data',
units_scale=(-100, 2.0))
assert np.all(map_source[:, 500:1000] == (float_data - 100) *
2).all(), 'affine scaling wrong'
def test_basic_construction_binder():
buffer, data = _create_binder(axis=1)
map_source = MappedSource(buffer)
shape = data.shape
assert map_source.shape == shape, 'Shape wrong'
assert map_source.binary_channel_mask.sum(
) == shape[0], 'Wrong number of active channels'
# repeat for transpose
map_source = MappedSource(buffer, transpose=True)
assert map_source.shape == shape[::-1], 'Shape wrong in transpose'
assert map_source.binary_channel_mask.sum(
) == shape[1], 'Wrong number of active channels in transpose'
def test_basic_mirror():
try:
f = _create_hdf5(n_rows=25, n_cols=500)
electrode_channels = [2, 4, 6, 8]
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels)
temp_files = []
clone1 = map_source.mirror(new_rate_ratio=None,
writeable=True,
mapped=True,
channel_compatible=False,
filename='foo.h5')
temp_files.append(clone1.data_buffer._array.file)
assert clone1.shape == (len(electrode_channels),
500), 'wrong # of channels'
assert clone1.writeable, 'Should be writeable'
assert isinstance(clone1, MappedSource), 'Clone is not a MappedSource'
clone2 = map_source.mirror(new_rate_ratio=None,
mapped=False,
channel_compatible=False)
assert isinstance(
clone2,
PlainArraySource), 'Not-mapped file should be PlainArraySource'
except Exception as e:
raise e
finally:
_clean_up_hdf_files(temp_files)
def test_electrode_subset():
f = _create_hdf5()
electrode_channels = [2, 4, 6, 8]
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels)
data = f['data'][:, :][electrode_channels]
assert np.all(
data[:, 100:200] == map_source[:, 100:200]), 'electrode subset failed'
def test_direct_mapped():
f = _create_hdf5()
mapped_source = MappedSource.from_hdf_sources(f, 'data')
assert mapped_source.is_direct_map, 'direct map should be true'
mapped_source = MappedSource.from_hdf_sources(f,
'data',
electrode_channels=range(4))
assert not mapped_source.is_direct_map, 'direct map should be false'
# for transposed disk arrays
f = _create_hdf5(transpose=True)
mapped_source = MappedSource.from_hdf_sources(f, 'data', transpose=True)
assert mapped_source.is_direct_map, 'direct map should be true'
mapped_source = MappedSource.from_hdf_sources(f,
'data',
transpose=True,
electrode_channels=range(4))
assert not mapped_source.is_direct_map, 'direct map should be false'
def test_joining():
aux_arrays = ('test1', 'test2')
files = [_create_hdf5(aux_arrays=aux_arrays) for i in range(3)]
map_source1 = MappedSource.from_hdf_sources(files,
'data',
aligned_arrays=aux_arrays)
next_file = _create_hdf5(aux_arrays=aux_arrays)
map_source2 = MappedSource.from_hdf_sources(next_file,
'data',
aligned_arrays=aux_arrays)
full_map = map_source1.join(map_source2)
assert full_map.shape == (
len(map_source1), map_source1.shape[1] +
map_source2.shape[1]), 'binder to buffer appending failed'
full_map = map_source2.join(map_source1)
assert full_map.shape == (
len(map_source1), map_source1.shape[1] +
map_source2.shape[1]), 'buffer to binder appending failed'
def test_electrode_subsetT():
f = _create_hdf5(transpose=True)
electrode_channels = [2, 4, 6, 8]
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels, transpose=True)
data = f['data'][:, :][:, electrode_channels].T
assert np.all(data[:, 100:200] ==
map_source[:,
100:200]), 'electrode subset failed in transpose'
def test_iter_channelsT():
f = _create_hdf5(n_rows=10, n_cols=100, transpose=True)
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=[2, 4, 6, 8, 9], transpose=True)
data = f['data'][:].T
channel_blocks = []
for chans in map_source.iter_channels(chans_per_block=2):
channel_blocks.append(chans)
for n, chans in enumerate(np.array_split(data[[2, 4, 6, 8, 9]], 3)):
assert np.array_equal(channel_blocks[n],
chans), 'channel block {} not equal'.format(n)
def test_mirror_modes():
f = _create_hdf5(n_rows=25, n_cols=500)
electrode_channels = [2, 4, 6, 8]
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels)
clone1 = map_source.mirror(writeable=True,
mapped=True,
channel_compatible=False)
assert clone1.shape == (len(electrode_channels), 500), 'wrong # of samples'
clone2 = map_source.mirror(writeable=True,
mapped=True,
channel_compatible=True)
assert clone2.data_buffer.shape == (
25, 500), 'wrong # of channels for channel-compat'
f = _create_hdf5(n_rows=25, n_cols=500, transpose=True)
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels, transpose=True)
clone3 = map_source.mirror(mapped=True, channel_compatible=True)
assert clone3.data_buffer.shape == (
25, 500), 'mapped mirror did not reverse the source transpose'
def test_iterT_binder():
files = [_create_hdf5(transpose=True, n_cols=100) for i in range(3)]
data = np.concatenate([f['data'][:] for f in files], axis=0).T
electrode_channels = [2, 4, 6, 8]
block_size = data.shape[1] // 2 + 20
map_source = MappedSource.from_hdf_sources(
files, 'data', electrode_channels=electrode_channels, transpose=True)
blocks = list(map_source.iter_blocks(block_size))
assert (data[electrode_channels][:, :block_size] == blocks[0]
).all(), 'first block wrong in transpose'
assert (data[electrode_channels][:, block_size:] == blocks[1]
).all(), 'second block wrong in transpose'
def test_iterT():
f = _create_hdf5(transpose=True)
electrode_channels = [2, 4, 6, 8]
data = f['data'][:].T
block_size = data.shape[1] // 2 + 100
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels, transpose=True)
blocks = list(map_source.iter_blocks(block_size))
assert (data[electrode_channels][:, :block_size] == blocks[0]
).all(), 'first block wrong in transpose'
assert (data[electrode_channels][:, block_size:] == blocks[1]
).all(), 'second block wrong in transpose'
def test_basic_construction():
aux_arrays = ('test1', 'test2')
buffer, data = _create_buffer(aux_arrays=aux_arrays)
# hacky way to get h5py.File object...
hdf = buffer.file_array.file
aligned = dict([(k, HDF5Buffer(hdf[k])) for k in aux_arrays])
map_source = MappedSource(buffer, aligned_arrays=aligned)
shape = data.shape
assert map_source.shape == shape, 'Shape wrong'
assert map_source.binary_channel_mask.sum(
) == shape[0], 'Wrong number of active channels'
for field in aux_arrays:
assert hasattr(map_source,
field), 'Aux field {} not preserved'.format(field)
assert getattr(
map_source, field
).shape[1] == shape[1], 'aligned field {} wrong length'.format(field)
# repeat for transpose
map_source = MappedSource(buffer, aligned_arrays=aligned, transpose=True)
assert map_source.shape == shape[::-1], 'Shape wrong in transpose'
assert map_source.binary_channel_mask.sum(
) == shape[1], 'Wrong number of active channels in transpose'
def test_big_slicing_allowed():
import ecogdata.expconfig.global_config as globalconfig
f = _create_hdf5()
data = f['data']
globalconfig.OVERRIDE[
'memory_limit'] = data.size * data.dtype.itemsize / 2.0
map_source = MappedSource.from_hdf_sources(f, 'data')
try:
with map_source.big_slices(True):
_ = map_source[:, :]
except MemoryBlowOutError as e:
assert False, 'Big slicing context failed'
finally:
globalconfig.OVERRIDE.pop('memory_limit')
def test_big_slicing_exception():
import ecogdata.expconfig.global_config as globalconfig
f = _create_hdf5()
data = f['data']
globalconfig.OVERRIDE[
'memory_limit'] = data.size * data.dtype.itemsize / 2.0
map_source = MappedSource.from_hdf_sources(f, 'data')
with pytest.raises(MemoryBlowOutError):
try:
map_source[:, :]
except Exception as e:
raise e
finally:
globalconfig.OVERRIDE.pop('memory_limit')
def test_reductions(reduction, axis, keepdims):
f = _create_hdf5(rand=True, dtype='f')
arr = f['data'][()]
data = MappedSource.from_hdf_sources(f, 'data')
# make this just small enough to force iteration
OVERRIDE['memory_limit'] = int(
arr.shape[0] * arr.shape[1] * 0.8) * arr.dtype.itemsize
r_method = getattr(data, reduction)
val1 = r_method(axis=axis, keepdims=keepdims)
val2 = getattr(arr, reduction)(axis=axis, keepdims=keepdims)
try:
assert np.allclose(val1, val2)
finally:
del OVERRIDE['memory_limit']
def test_construction_from_single_source():
aux_arrays = ('test1', 'test2')
f = _create_hdf5(aux_arrays=aux_arrays)
shape = f['data'].shape
map_source = MappedSource.from_hdf_sources(f,
'data',
aligned_arrays=aux_arrays)
assert map_source.shape == shape, 'Shape wrong'
assert map_source.binary_channel_mask.sum(
) == shape[0], 'Wrong number of active channels'
for field in aux_arrays:
assert hasattr(map_source,
field), 'Aux field {} not preserved'.format(field)
assert getattr(
map_source, field
).shape[1] == shape[1], 'aligned field {} wrong length'.format(field)
# repeat for transpose
map_source = MappedSource.from_hdf_sources(f,
'data',
aligned_arrays=aux_arrays,
transpose=True)
assert map_source.shape == shape[::-1], 'Shape wrong in transpose'
assert map_source.binary_channel_mask.sum(
) == shape[1], 'Wrong number of active channels in transpose'
def test_channel_slicing():
f = _create_hdf5()
electrode_channels = list(range(6, 17))
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels, units_scale=5.0)
data_first_channels = map_source[:3, :]
with map_source.channels_are_maps(True):
first_channels = map_source[:3]
assert isinstance(first_channels,
MappedSource), 'slice did not return new map'
assert np.array_equal(data_first_channels,
first_channels[:, :]), 'new map data mis-mapped'
first_channels = map_source[:3]
assert isinstance(first_channels, np.ndarray), 'slice-as-array failed'
assert np.array_equal(data_first_channels,
first_channels), 'slice-as-array wrong data'
def test_iter():
f = _create_hdf5()
electrode_channels = [2, 4, 6, 8]
data = f['data'][:]
block_size = data.shape[1] // 2 + 100
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels)
blocks = list(map_source.iter_blocks(block_size))
assert (data[electrode_channels][:, :block_size] == blocks[0]
).all(), 'first block wrong'
assert (data[electrode_channels][:, block_size:] == blocks[1]
).all(), 'second block wrong'
blocks = list(map_source.iter_blocks(block_size, reverse=True))
assert (data[electrode_channels][:, block_size:][:, ::-1] == blocks[0]
).all(), 'first rev block wrong'
assert (data[electrode_channels][:, :block_size][:, ::-1] == blocks[1]
).all(), 'second rev block wrong'
def test_write():
f = _create_hdf5()
electrode_channels = list(range(10))
binary_mask = np.ones(10, '?')
binary_mask[:5] = False
# so channels 5, 6, 7, 8, 9 should be active
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels)
shp = map_source.shape
rand_pattern = np.random.randint(0, 100, size=(2, shp[1]))
map_source[:2] = rand_pattern
# use full-slice syntax to get data
assert np.array_equal(map_source[:2, :],
rand_pattern), 'write failed (map subset)'
map_source.set_channel_mask(binary_mask)
# write again
map_source[:2] = rand_pattern
assert np.array_equal(map_source[:2, :],
rand_pattern), 'write failed (map subset and mask)'
def test_write_to_binder():
files = [_create_hdf5() for i in range(3)]
electrode_channels = list(range(10))
binary_mask = np.ones(10, '?')
binary_mask[:5] = False
# so channels 5, 6, 7, 8, 9 should be active
map_source = MappedSource.from_hdf_sources(
files, 'data', electrode_channels=electrode_channels)
# make a write that spans buffers
single_length = files[0]['data'].shape[1]
rand_pattern = np.random.randint(0, 100, size=(2, 205))
sl = np.s_[:2, single_length - 100:single_length + 105]
map_source[sl] = rand_pattern
# use full-slice syntax to get data
assert np.array_equal(map_source[sl],
rand_pattern), 'write failed to binder (map subset)'
map_source.set_channel_mask(binary_mask)
# write again
map_source[sl] = rand_pattern
assert np.array_equal(
map_source[sl],
rand_pattern), 'write failed to binder (map subset and mask)'
def test_channel_map():
f = _create_hdf5()
electrode_channels = list(range(10))
binary_mask = np.ones(10, '?')
binary_mask[:5] = False
# so channels 5, 6, 7, 8, 9 should be active
map_source = MappedSource.from_hdf_sources(
f, 'data', electrode_channels=electrode_channels)
map_source.set_channel_mask(binary_mask)
assert (map_source.binary_channel_mask == binary_mask
).all(), 'binary mask wrong'
data = f['data'][:, :][electrode_channels, :]
assert np.all(
data[5:, 100:200] == map_source[:, 100:200]), 'channel masking failed'
# unmask
map_source.set_channel_mask(None)
binary_mask[:] = True
assert (map_source.binary_channel_mask == binary_mask
).all(), 'binary mask wrong'
data = f['data'][:, :][electrode_channels, :]
assert np.all(
data[:, 100:200] == map_source[:, 100:200]), 'channel masking failed'
def test_iter_overlap():
f = _create_hdf5(n_cols=100)
data = f['data'][:]
block_size = 20
overlap = 10
map_source = MappedSource.from_hdf_sources(f, 'data')
blocks = list(map_source.iter_blocks(block_size, overlap=overlap))
assert (data[:, :block_size] == blocks[0]).all(), 'first block wrong'
assert (data[:,
(block_size -
overlap):(2 * block_size -
overlap)] == blocks[1]).all(), 'second block wrong'
# last block is a partial, starting at index 90
assert (data[:, -10:] == blocks[-1]).all(), 'last block wrong'
blocks = list(
map_source.iter_blocks(block_size, reverse=True, overlap=overlap))
assert (
data[:, :block_size] == blocks[-1][:, ::-1]).all(), 'first block wrong'
assert (data[:, (block_size - overlap):(
2 * block_size -
overlap)] == blocks[-2][:, ::-1]).all(), 'second block wrong'
assert (data[:, -10:] == blocks[0][:, ::-1]).all(), 'last block wrong'
def test_iter_overlap_binder():
files = [_create_hdf5(n_cols=100) for i in range(3)]
data = np.concatenate([f['data'][:] for f in files], axis=1)
block_size = 20
overlap = 10
map_source = MappedSource.from_hdf_sources(files, 'data')
blocks = list(map_source.iter_blocks(block_size, overlap=overlap))
assert (data[:, :block_size] == blocks[0]).all(), 'first block wrong'
assert (data[:,
(block_size -
overlap):(2 * block_size -
overlap)] == blocks[1]).all(), 'second block wrong'
# last block is a partial, starting at index 90
assert (data[:, -10:] == blocks[-1]).all(), 'last block wrong'
blocks = list(
map_source.iter_blocks(block_size, reverse=True, overlap=overlap))
assert (
data[:, :block_size] == blocks[-1][:, ::-1]).all(), 'first block wrong'
assert (data[:, (block_size - overlap):(
2 * block_size -
overlap)] == blocks[-2][:, ::-1]).all(), 'second block wrong'
assert (data[:, -10:] == blocks[0][:, ::-1]).all(), 'last block wrong'
