def test_append_simple():
"""Test appending without regard to dimensions."""
points = 100
data1 = np.random.random(points)
data2 = np.random.random(points)
coords1 = {'time': np.linspace(0, points, points)}
coords2 = {'time': np.linspace(points, points * 2, points)}
dims = ["time"]
samplerate = 10.
# Base case: everything should Just Work
ts1 = TimeSeriesX.create(data1, samplerate, coords=coords1, dims=dims)
ts2 = TimeSeriesX.create(data2, samplerate, coords=coords2, dims=dims)
combined = ts1.append(ts2)
assert combined.samplerate == samplerate
assert (combined.data == np.concatenate([data1, data2])).all()
assert combined.dims == ts1.dims
assert combined.dims == ts2.dims
assert (combined.coords['time'] == np.concatenate(
[coords1['time'], coords2['time']])).all()
# Incompatible sample rates
ts1 = TimeSeriesX.create(data1, samplerate, coords=coords1, dims=dims)
ts2 = TimeSeriesX.create(data2, samplerate + 1, coords=coords2, dims=dims)
with pytest.raises(ConcatenationError):
ts1.append(ts2)
def test_mean():
"""tests various ways to compute mean - collapsing different combination of axes"""
data = np.arange(100).reshape(10,10)
ts_1 = TimeSeriesX.create(data, None, dims=['x','y'], coords={'x':np.arange(10)*2,
'y':np.arange(10),
'samplerate': 1})
grand_mean = ts_1.mean()
assert grand_mean == 49.5
x_mean = ts_1.mean(dim='x')
assert (x_mean == np.arange(45,55,1, dtype=np.float)).all()
# checking axes
assert(ts_1.y == x_mean.y).all()
y_mean = ts_1.mean(dim='y')
assert (y_mean == np.arange(4.5,95,10, dtype=np.float)).all()
# checking axes
assert (y_mean.x == ts_1.x).all()
# test mean NaN
data_2 = np.arange(100, dtype=np.float).reshape(10,10)
np.fill_diagonal(data_2,np.NaN)
# data_2[9,9] = 99
ts_2 = TimeSeriesX.create(data_2, None, dims=['x','y'], coords={'x':np.arange(10)*2,
'y':np.arange(10),
'samplerate': 1})
grand_mean = ts_2.mean(skipna=True)
assert grand_mean == 49.5
def test_concatenate():
"""make sure we can concatenate easily time series x - test it with rec
array as one of the coords.
This fails for xarray > 0.7. See https://github.com/pydata/xarray/issues/1434
for details.
"""
p1 = np.array([('John', 180), ('Stacy', 150), ('Dick',200)], dtype=[('name', '|S256'), ('height', int)])
p2 = np.array([('Bernie', 170), ('Donald', 250), ('Hillary',150)], dtype=[('name', '|S256'), ('height', int)])
data = np.arange(50, 80, 1, dtype=np.float)
dims = ['measurement', 'participant']
ts1 = TimeSeriesX.create(data.reshape(10, 3), None, dims=dims,
coords={
'measurement': np.arange(10),
'participant': p1,
'samplerate': 1
})
ts2 = TimeSeriesX.create(data.reshape(10, 3)*2, None, dims=dims,
coords={
'measurement': np.arange(10),
'participant': p2,
'samplerate': 1
})
combined = xr.concat((ts1, ts2), dim='participant')
assert isinstance(combined, TimeSeriesX)
assert (combined.participant.data['height'] ==
np.array([180, 150, 200, 170, 250, 150])).all()
assert (combined.participant.data['name'] ==
np.array(['John', 'Stacy', 'Dick', 'Bernie', 'Donald', 'Hillary'])).all()
def test_append_simple():
"""Test appending without regard to dimensions."""
points = 100
data1 = np.random.random(points)
data2 = np.random.random(points)
coords1 = {'time': np.linspace(0, points, points)}
coords2 = {'time': np.linspace(points, points*2, points)}
dims = ["time"]
samplerate = 10.
# Base case: everything should Just Work
ts1 = TimeSeriesX.create(data1, samplerate, coords=coords1, dims=dims)
ts2 = TimeSeriesX.create(data2, samplerate, coords=coords2, dims=dims)
combined = ts1.append(ts2)
assert combined.samplerate == samplerate
assert (combined.data == np.concatenate([data1, data2])).all()
assert combined.dims == ts1.dims
assert combined.dims == ts2.dims
assert (combined.coords['time'] == np.concatenate([coords1['time'], coords2['time']])).all()
# Incompatible sample rates
ts1 = TimeSeriesX.create(data1, samplerate, coords=coords1, dims=dims)
ts2 = TimeSeriesX.create(data2, samplerate + 1, coords=coords2, dims=dims)
with pytest.raises(ConcatenationError):
ts1.append(ts2)
def test_coords_ops():
data = np.arange(1000).reshape(10, 10, 10)
ts_1 = TimeSeriesX.create(data,
None,
dims=['x', 'y', 'z'],
coords={
'x': np.arange(10),
'y': np.arange(10),
'z': np.arange(10) * 2,
'samplerate': 1
})
ts_2 = TimeSeriesX.create(data,
None,
dims=['x', 'y', 'z'],
coords={
'x': np.arange(10),
'y': np.arange(10),
'z': np.arange(10),
'samplerate': 1
})
ts_out = ts_1 + ts_2
assert ts_out.z.shape[0] == 5
ts_out_1 = ts_1 + ts_2[..., ::2]
assert (ts_out_1 == ts_out).all()
ts_out_2 = ts_2[..., 1::2] + ts_2[..., ::2]
assert ts_out_2.shape[-1] == 0
ts_out_3 = ts_2[..., [0, 2, 3, 4, 8]] + ts_2[..., [3, 4, 8, 9]]
assert (ts_out_3.z.data == np.array([3, 4, 8])).all()
def test_coords_ops():
data = np.arange(1000).reshape(10,10,10)
ts_1 = TimeSeriesX.create(data, None, dims=['x','y','z'], coords={'x':np.arange(10),
'y':np.arange(10),
'z':np.arange(10)*2,
'samplerate': 1})
ts_2 = TimeSeriesX.create(data, None, dims=['x','y','z'], coords={'x':np.arange(10),
'y':np.arange(10),
'z':np.arange(10),
'samplerate': 1})
ts_out = ts_1 + ts_2
assert ts_out.z.shape[0] == 5
ts_out_1 = ts_1 + ts_2[...,::2]
assert (ts_out_1 == ts_out).all()
ts_out_2 = ts_2[...,1::2] + ts_2[...,::2]
assert ts_out_2.shape[-1] ==0
ts_out_3 = ts_2[...,[0,2,3,4,8]] + ts_2[...,[3,4,8,9]]
assert (ts_out_3.z.data == np.array([3,4,8])).all()
def test_hdf(tempdir):
"""Test saving/loading with HDF5."""
data = np.random.random((10, 10, 10, 10))
dims = ('time', 'x', 'y', 'z')
coords = {label: np.linspace(0, 1, 10) for label in dims}
rate = 1
ts = TimeSeriesX.create(data, rate, coords=coords, dims=dims, name="test")
filename = osp.join(tempdir, "timeseries.h5")
ts.to_hdf(filename)
with h5py.File(filename, 'r') as hfile:
assert "data" in hfile
assert "dims" in hfile
assert "coords" in hfile
assert "name" in list(hfile['/'].attrs.keys())
assert "ptsa_version" in hfile.attrs
assert "created" in hfile.attrs
loaded = TimeSeriesX.from_hdf(filename)
assert (loaded.data == data).all()
for coord in loaded.coords:
assert (loaded.coords[coord] == ts.coords[coord]).all()
for n, dim in enumerate(dims):
assert loaded.dims[n] == dim
assert loaded.name == "test"
ts_with_attrs = TimeSeriesX.create(data, rate, coords=coords, dims=dims,
name="test", attrs=dict(a=1, b=[1, 2]))
ts_with_attrs.to_hdf(filename)
loaded = TimeSeriesX.from_hdf(filename)
for key in ts_with_attrs.attrs:
assert ts_with_attrs.attrs[key] == loaded.attrs[key]
def test_addition(i, j, k, expected):
data = np.arange(1000).reshape(10,10,10)
rate = 1000
ts_1 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_2 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_out = ts_1 + ts_2
assert ts_out[i,j,k] == expected
def test_samplerate_prop():
data = np.arange(1000).reshape(10, 10, 10)
rate = 1000
ts_1 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_2 = TimeSeriesX.create(data, None, coords={'samplerate': 2})
with pytest.raises(AssertionError):
ts_out = ts_1 + ts_2
def test_addition(i, j, k, expected):
data = np.arange(1000).reshape(10, 10, 10)
rate = 1000
ts_1 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_2 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_out = ts_1 + ts_2
assert ts_out[i, j, k] == expected
def test_samplerate_prop():
data = np.arange(1000).reshape(10,10,10)
rate = 1000
ts_1 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_2 = TimeSeriesX.create(data, None, coords={'samplerate': 2})
with pytest.raises(AssertionError):
ts_out = ts_1 + ts_2
def test_arithmetic_operations():
data = np.arange(1000).reshape(10, 10, 10)
rate = 1000
ts_1 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_2 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_out = ts_1 + ts_2
print('ts_out=', ts_out)
def test_arithmetic_operations():
data = np.arange(1000).reshape(10,10,10)
rate = 1000
ts_1 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_2 = TimeSeriesX.create(data, None, coords={'samplerate': 1})
ts_out = ts_1 + ts_2
print('ts_out=', ts_out)
def test_append_recarray():
"""Test appending along a dimension with a recarray."""
p1 = np.array([('John', 180), ('Stacy', 150), ('Dick',200)], dtype=[('name', '|S256'), ('height', int)])
p2 = np.array([('Bernie', 170), ('Donald', 250), ('Hillary',150)], dtype=[('name', '|S256'), ('height', int)])
data = np.arange(50, 80, 1, dtype=np.float)
dims = ['measurement', 'participant']
ts1 = TimeSeriesX.create(data.reshape(10, 3), None, dims=dims,
coords={
'measurement': np.arange(10),
'participant': p1,
'samplerate': 1
})
ts2 = TimeSeriesX.create(data.reshape(10, 3)*2, None, dims=dims,
coords={
'measurement': np.arange(10),
'participant': p2,
'samplerate': 1
})
ts3 = TimeSeriesX.create(data.reshape(10, 3)*2, None, dims=dims,
coords={
'measurement': np.arange(10),
'participant': p2,
'samplerate': 2
})
ts4 = TimeSeriesX.create(data.reshape(10, 3)*2, None, dims=dims,
coords={
'measurement': np.linspace(0, 1, 10),
'participant': p2,
'samplerate': 2
})
combined = ts1.append(ts2, dim='participant')
assert isinstance(combined, TimeSeriesX)
assert (combined.participant.data['height'] == np.array([180, 150, 200, 170, 250, 150])).all()
names = np.array([b'John', b'Stacy', b'Dick', b'Bernie', b'Donald', b'Hillary'])
assert (combined.participant.data['name'] == names).all()
# incompatible sample rates
with pytest.raises(ConcatenationError):
ts1.append(ts3)
# incompatible other dimensions (measurement)
with pytest.raises(ConcatenationError):
ts1.append(ts4)
def filter(self):
"""
Chops session into chunks corresponding to events
:return: timeSeriesX object with chopped session
"""
chop_on_start_offsets_flag = bool(len(self.start_offsets))
if chop_on_start_offsets_flag:
start_offsets = self.start_offsets
chopping_axis_name = 'start_offsets'
chopping_axis_data = start_offsets
else:
evs = self.events[self.events.eegfile == self.session_data.attrs['dataroot']]
start_offsets = evs.eegoffset
chopping_axis_name = 'events'
chopping_axis_data = evs
# samplerate = self.session_data.attrs['samplerate']
samplerate = float(self.session_data['samplerate'])
offset_time_array = self.session_data['offsets']
event_chunk_size, start_point_shift = self.get_event_chunk_size_and_start_point_shift(
eegoffset=start_offsets[0],
samplerate=samplerate,
offset_time_array=offset_time_array)
event_time_axis = np.arange(event_chunk_size)*(1.0/samplerate)+(self.start_time-self.buffer_time)
data_list = []
for i, eegoffset in enumerate(start_offsets):
start_chop_pos = np.where(offset_time_array >= eegoffset)[0][0]
start_chop_pos += start_point_shift
selector_array = np.arange(start=start_chop_pos, stop=start_chop_pos + event_chunk_size)
chopped_data_array = self.session_data.isel(time=selector_array)
chopped_data_array['time'] = event_time_axis
chopped_data_array['start_offsets'] = [i]
data_list.append(chopped_data_array)
ev_concat_data = xr.concat(data_list, dim='start_offsets')
ev_concat_data = ev_concat_data.rename({'start_offsets':chopping_axis_name})
ev_concat_data[chopping_axis_name] = chopping_axis_data
attrs = {
"start_time": self.start_time,
"end_time": self.end_time,
"buffer_time": self.buffer_time
}
ev_concat_data['samplerate'] = samplerate
return TimeSeriesX.create(ev_concat_data, samplerate, attrs=attrs)
def test_init():
"""Test that everything is initialized properly."""
data = np.random.random((10, 10, 10))
rate = 1000
with pytest.raises(AssertionError):
TimeSeriesX(data, {})
with pytest.raises(AssertionError):
TimeSeriesX.create(data, None, coords={})
assert TimeSeriesX.create(data, None, coords={'samplerate': 1}).samplerate == 1
ts = TimeSeriesX(data, dict(samplerate=rate))
assert isinstance(ts, xr.DataArray)
assert ts.shape == (10, 10, 10)
assert ts['samplerate'] == rate
def test_init():
"""Test that everything is initialized properly."""
data = np.random.random((10, 10, 10))
rate = 1000
with pytest.raises(AssertionError):
TimeSeriesX(data, {})
with pytest.raises(AssertionError):
TimeSeriesX.create(data, None, coords={})
assert TimeSeriesX.create(data, None, coords={
'samplerate': 1
}).samplerate == 1
ts = TimeSeriesX(data, dict(samplerate=rate))
assert isinstance(ts, xr.DataArray)
assert ts.shape == (10, 10, 10)
assert ts['samplerate'] == rate
def test_baseline_corrected():
t = np.linspace(0, 10, 100)
values = np.array([1] * 50 + [2] * 50)
coords = {"time": t}
ts = TimeSeriesX.create(values, 10., coords, dims=("time", ))
corrected = ts.baseline_corrected((0, 5))
assert all(ts['time'] == corrected['time'])
assert ts['samplerate'] == corrected['samplerate']
assert all(corrected.data[:50] == 0)
assert all(corrected.data[50:] == 1)
def test_resampled():
ts = TimeSeriesX.create(np.linspace(0, 100, 100), 10., dims=['time'])
resampled = ts.resampled(20.)
assert resampled.data.shape == (200,)
assert resampled['samplerate'] == 20
resampled = ts.resampled(5)
assert resampled.data.shape == (50,)
assert resampled['samplerate'] == 5
def test_baseline_corrected():
t = np.linspace(0, 10, 100)
values = np.array([1]*50 + [2]*50)
coords = {"time": t}
ts = TimeSeriesX.create(values, 10., coords, dims=("time",))
corrected = ts.baseline_corrected((0, 5))
assert all(ts['time'] == corrected['time'])
assert ts['samplerate'] == corrected['samplerate']
assert all(corrected.data[:50] == 0)
assert all(corrected.data[50:] == 1)
def test_resampled():
ts = TimeSeriesX.create(np.linspace(0, 100, 100), 10., dims=['time'])
resampled = ts.resampled(20.)
assert resampled.data.shape == (200, )
assert resampled['samplerate'] == 20
resampled = ts.resampled(5)
assert resampled.data.shape == (50, )
assert resampled['samplerate'] == 5
def test_mean():
"""tests various ways to compute mean - collapsing different combination of axes"""
data = np.arange(100).reshape(10, 10)
ts_1 = TimeSeriesX.create(data,
None,
dims=['x', 'y'],
coords={
'x': np.arange(10) * 2,
'y': np.arange(10),
'samplerate': 1
})
grand_mean = ts_1.mean()
assert grand_mean == 49.5
x_mean = ts_1.mean(dim='x')
assert (x_mean == np.arange(45, 55, 1, dtype=np.float)).all()
# checking axes
assert (ts_1.y == x_mean.y).all()
y_mean = ts_1.mean(dim='y')
assert (y_mean == np.arange(4.5, 95, 10, dtype=np.float)).all()
# checking axes
assert (y_mean.x == ts_1.x).all()
# test mean NaN
data_2 = np.arange(100, dtype=np.float).reshape(10, 10)
np.fill_diagonal(data_2, np.NaN)
# data_2[9,9] = 99
ts_2 = TimeSeriesX.create(data_2,
None,
dims=['x', 'y'],
coords={
'x': np.arange(10) * 2,
'y': np.arange(10),
'samplerate': 1
})
grand_mean = ts_2.mean(skipna=True)
assert grand_mean == 49.5
def test_concatenate():
"""make sure we can concatenate easily time series x - test it with rec
array as one of the coords.
This fails for xarray > 0.7. See https://github.com/pydata/xarray/issues/1434
for details.
"""
p1 = np.array([('John', 180), ('Stacy', 150), ('Dick', 200)],
dtype=[('name', '|S256'), ('height', int)])
p2 = np.array([('Bernie', 170), ('Donald', 250), ('Hillary', 150)],
dtype=[('name', '|S256'), ('height', int)])
data = np.arange(50, 80, 1, dtype=np.float)
dims = ['measurement', 'participant']
ts1 = TimeSeriesX.create(data.reshape(10, 3),
None,
dims=dims,
coords={
'measurement': np.arange(10),
'participant': p1,
'samplerate': 1
})
ts2 = TimeSeriesX.create(data.reshape(10, 3) * 2,
None,
dims=dims,
coords={
'measurement': np.arange(10),
'participant': p2,
'samplerate': 1
})
combined = xr.concat((ts1, ts2), dim='participant')
assert isinstance(combined, TimeSeriesX)
assert (combined.participant.data['height'] == np.array(
[180, 150, 200, 170, 250, 150])).all()
assert (combined.participant.data['name'] == np.array(
['John', 'Stacy', 'Dick', 'Bernie', 'Donald', 'Hillary'])).all()
def test_hdf(tempdir):
"""Test saving/loading with HDF5."""
data = np.random.random((10, 10, 10, 10))
dims = ('time', 'x', 'y', 'z')
coords = {label: np.linspace(0, 1, 10) for label in dims}
rate = 1
ts = TimeSeriesX.create(data, rate, coords=coords, dims=dims, name="test")
filename = osp.join(tempdir, "timeseries.h5")
ts.to_hdf(filename)
with h5py.File(filename, 'r') as hfile:
assert "data" in hfile
assert "dims" in hfile
assert "coords" in hfile
assert "name" in list(hfile['/'].attrs.keys())
loaded = TimeSeriesX.from_hdf(filename)
assert (loaded.data == data).all()
for coord in loaded.coords:
assert (loaded.coords[coord] == ts.coords[coord]).all()
for n, dim in enumerate(dims):
assert loaded.dims[n] == dim
assert loaded.name == "test"
ts_with_attrs = TimeSeriesX.create(data,
rate,
coords=coords,
dims=dims,
name="test",
attrs=dict(a=1, b=[1, 2]))
ts_with_attrs.to_hdf(filename)
loaded = TimeSeriesX.from_hdf(filename)
for key in ts_with_attrs.attrs:
assert ts_with_attrs.attrs[key] == loaded.attrs[key]
def test_add_mirror_buffer():
points = 100
data = np.array([-1] * points + [1] * points)
samplerate = 10.
coords = {'time': np.linspace(-1, 1, points * 2)}
dims = ['time']
ts = TimeSeriesX.create(data, samplerate, coords=coords, dims=dims)
duration = 10
buffered = ts.add_mirror_buffer(duration)
assert len(buffered.data) == len(data) + 2 * duration * samplerate
with pytest.raises(ValueError):
# 100 s is longer than the length of data
ts.add_mirror_buffer(100)
def test_add_mirror_buffer():
points = 100
data = np.array([-1] * points + [1] * points)
samplerate = 10.
coords = {'time': np.linspace(-1, 1, points*2)}
dims = ['time']
ts = TimeSeriesX.create(data, samplerate, coords=coords, dims=dims)
duration = 10
buffered = ts.add_mirror_buffer(duration)
assert len(buffered.data) == len(data) + 2 * duration * samplerate
with pytest.raises(ValueError):
# 100 s is longer than the length of data
ts.add_mirror_buffer(100)
def test_filtered():
data = np.random.random(1000)
dims = ['time']
ts = TimeSeriesX.create(data, 10, dims=dims)
# TODO: real test (i.e., actually care about the filtering)
with warnings.catch_warnings(record=True) as w:
new_ts = ts.filtered([1, 2])
assert len(w) == 1
assert ts['samplerate'] == new_ts['samplerate']
assert all(ts.data != new_ts.data)
for key, attr in ts.attrs.items():
assert attr == new_ts[key]
assert ts.name == new_ts.name
assert ts.dims == new_ts.dims
def test_filtered():
data = np.random.random(1000)
dims = ['time']
ts = TimeSeriesX.create(data, 10, dims=dims)
# TODO: real test (i.e., actually care about the filtering)
with warnings.catch_warnings(record=True) as w:
new_ts = ts.filtered([1, 2])
assert len(w) == 1
assert ts['samplerate'] == new_ts['samplerate']
assert all(ts.data != new_ts.data)
for key, attr in ts.attrs.items():
assert attr == new_ts[key]
assert ts.name == new_ts.name
assert ts.dims == new_ts.dims
def test_remove_buffer():
length = 100
data = np.array([0] * length)
samplerate = 10.
coords = {'time': np.linspace(-1, 1, length)}
dims = ['time']
ts = TimeSeriesX.create(data, samplerate, coords=coords, dims=dims)
with pytest.raises(ValueError):
# We can't remove this much
ts.remove_buffer(int(samplerate * length + 1))
buffer_dur = 0.1
buffered = ts.add_mirror_buffer(buffer_dur)
unbuffered = buffered.remove_buffer(buffer_dur)
assert len(unbuffered.data) == len(ts.data)
assert (unbuffered.data == ts.data).all()
def test_remove_buffer():
length = 100
data = np.array([0]*length)
samplerate = 10.
coords = {'time': np.linspace(-1, 1, length)}
dims = ['time']
ts = TimeSeriesX.create(data, samplerate, coords=coords, dims=dims)
with pytest.raises(ValueError):
# We can't remove this much
ts.remove_buffer(int(samplerate * length + 1))
buffer_dur = 0.1
buffered = ts.add_mirror_buffer(buffer_dur)
unbuffered = buffered.remove_buffer(buffer_dur)
assert len(unbuffered.data) == len(ts.data)
assert (unbuffered.data == ts.data).all()
def filter(self):
"""
Chops session into chunks corresponding to events
:return: timeSeriesX object with chopped session
"""
chop_on_start_offsets_flag = bool(len(self.start_offsets))
if chop_on_start_offsets_flag:
start_offsets = self.start_offsets
chopping_axis_name = 'start_offsets'
chopping_axis_data = start_offsets
else:
evs = self.events[self.events.eegfile ==
self.session_data.attrs['dataroot']]
start_offsets = evs.eegoffset
chopping_axis_name = 'events'
chopping_axis_data = evs
# samplerate = self.session_data.attrs['samplerate']
samplerate = float(self.session_data['samplerate'])
offset_time_array = self.session_data['offsets']
event_chunk_size, start_point_shift = self.get_event_chunk_size_and_start_point_shift(
eegoffset=start_offsets[0],
samplerate=samplerate,
offset_time_array=offset_time_array)
event_time_axis = np.arange(event_chunk_size) * (1.0 / samplerate) + (
self.start_time - self.buffer_time)
data_list = []
for i, eegoffset in enumerate(start_offsets):
start_chop_pos = np.where(offset_time_array >= eegoffset)[0][0]
start_chop_pos += start_point_shift
selector_array = np.arange(start=start_chop_pos,
stop=start_chop_pos + event_chunk_size)
chopped_data_array = self.session_data.isel(time=selector_array)
chopped_data_array['time'] = event_time_axis
chopped_data_array['start_offsets'] = [i]
data_list.append(chopped_data_array)
ev_concat_data = xr.concat(data_list, dim='start_offsets')
ev_concat_data = ev_concat_data.rename(
{'start_offsets': chopping_axis_name})
ev_concat_data[chopping_axis_name] = chopping_axis_data
attrs = {
"start_time": self.start_time,
"end_time": self.end_time,
"buffer_time": self.buffer_time
}
ev_concat_data['samplerate'] = samplerate
return TimeSeriesX.create(ev_concat_data, samplerate, attrs=attrs)
def test_append_recarray():
"""Test appending along a dimension with a recarray."""
p1 = np.array([('John', 180), ('Stacy', 150), ('Dick', 200)],
dtype=[('name', '|S256'), ('height', int)])
p2 = np.array([('Bernie', 170), ('Donald', 250), ('Hillary', 150)],
dtype=[('name', '|S256'), ('height', int)])
data = np.arange(50, 80, 1, dtype=np.float)
dims = ['measurement', 'participant']
ts1 = TimeSeriesX.create(data.reshape(10, 3),
None,
dims=dims,
coords={
'measurement': np.arange(10),
'participant': p1,
'samplerate': 1
})
ts2 = TimeSeriesX.create(data.reshape(10, 3) * 2,
None,
dims=dims,
coords={
'measurement': np.arange(10),
'participant': p2,
'samplerate': 1
})
ts3 = TimeSeriesX.create(data.reshape(10, 3) * 2,
None,
dims=dims,
coords={
'measurement': np.arange(10),
'participant': p2,
'samplerate': 2
})
ts4 = TimeSeriesX.create(data.reshape(10, 3) * 2,
None,
dims=dims,
coords={
'measurement': np.linspace(0, 1, 10),
'participant': p2,
'samplerate': 2
})
combined = ts1.append(ts2, dim='participant')
assert isinstance(combined, TimeSeriesX)
assert (combined.participant.data['height'] == np.array(
[180, 150, 200, 170, 250, 150])).all()
names = np.array(
[b'John', b'Stacy', b'Dick', b'Bernie', b'Donald', b'Hillary'])
assert (combined.participant.data['name'] == names).all()
# incompatible sample rates
with pytest.raises(ConcatenationError):
ts1.append(ts3)
# incompatible other dimensions (measurement)
with pytest.raises(ConcatenationError):
ts1.append(ts4)
def test_append(self):
"""make sure we can concatenate easily time series x - test it with rec array as one of the coords"""
p_data_1 = np.array([('John', 180), ('Stacy', 150), ('Dick',200)], dtype=[('name', '|S256'), ('height', int)])
p_data_2 = np.array([('Bernie', 170), ('Donald', 250), ('Hillary',150)], dtype=[('name', '|S256'), ('height', int)])
weights_data = np.arange(50,80,1,dtype=np.float)
weights_ts_1 = TimeSeriesX.create(weights_data.reshape(10,3),
None,
dims=['measurement','participant'],
coords={'measurement':np.arange(10),
'participant':p_data_1,
'samplerate': 1}
)
weights_ts_2 = TimeSeriesX.create(weights_data.reshape(10,3)*2,
None,
dims=['measurement','participant'],
coords={'measurement':np.arange(10),
'participant':p_data_2,
'samplerate': 1}
)
weights_ts_3 = TimeSeriesX.create(weights_data.reshape(3,10)*2,
None,
dims=['participant','measurement'],
coords={'measurement':np.arange(10),
'participant':p_data_2,
'samplerate': 1}
)
weights_ts_4 = TimeSeriesX.create(np.arange(50,83,1,dtype=np.float).reshape(11,3),
None,
dims=['measurement','participant'],
coords={'measurement':np.arange(11),
'participant':p_data_2,
'samplerate': 1}
)
weights_ts_5 = TimeSeriesX.create(weights_data.reshape(10,3)*2,
None,
dims=['measurement','participant'],
coords={'measurement':np.arange(10)*2,
'participant':p_data_2,
'samplerate': 1}
)
with self.assertRaises(ValueError) as context:
weights_ts_1.append(dim='measurement', ts=np.arange(1000))
self.assertTrue(isinstance(context.exception,ValueError))
with self.assertRaises(ValueError) as context:
weights_ts_1.append(dim='measurement', ts=weights_ts_3)
self.assertTrue(isinstance(context.exception,ValueError))
self.assertTrue('Dimensions' in str(context.exception))
with self.assertRaises(ValueError) as context:
weights_ts_1.append(dim='participant', ts=weights_ts_4)
self.assertTrue(isinstance(context.exception,ValueError))
self.assertTrue('Dimension mismatch' in str(context.exception))
weights_ts_1.append(dim='participant', ts=weights_ts_5)