How to use the pynwb.base.TimeSeries function in pynwb

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github NeurodataWithoutBorders / pynwb / tests / unit / test_base.py View on Github external
def test_init_data(self):
        dat = [0, 1, 2, 3, 4]
        ts = TimeSeries('test_ts', dat, 'volts', timestamps=[0.1, 0.2, 0.3, 0.4])
        self.assertIs(ts.data, dat)
        self.assertEqual(ts.conversion, 1.0)
        self.assertEqual(ts.resolution, 0.0)
        self.assertEqual(ts.unit, 'volts')
github NeurodataWithoutBorders / pynwb / tests / unit / test_base.py View on Github external
def test_deprecated_get_data_interface(self):
        ts = TimeSeries('test_ts', [0, 1, 2, 3, 4, 5],
                        'grams', timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
        self.pm.add(ts)
        with self.assertWarnsRegex(PendingDeprecationWarning, r'get_data_interface will be replaced by get'):
            tmp = self.pm.get_data_interface('test_ts')
        self.assertIs(tmp, ts)
github NeurodataWithoutBorders / pynwb / tests / unit / test_base.py View on Github external
def test_timestamps_timeseries(self):
        ts1 = TimeSeries('test_ts1', [0, 1, 2, 3, 4, 5],
                         'grams', timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
        ts2 = TimeSeries('test_ts2', [10, 11, 12, 13, 14, 15],
                         'grams', timestamps=ts1)
        self.assertEqual(ts2.timestamps, [0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
github NeurodataWithoutBorders / pynwb / tests / unit / test_ophys.py View on Github external
external_file=['external_file'],
            starting_frame=[1, 2, 3],
            format='tiff',
            timestamps=[1., 2.]
        )
        is2 = ImageSeries(
            name='is2',
            data=np.ones((2, 2, 2)),
            unit='unit',
            external_file=['external_file'],
            starting_frame=[1, 2, 3],
            format='tiff',
            timestamps=[1., 2.]
        )
        tstamps = np.arange(1.0, 100.0, 0.1, dtype=np.float)
        ts = TimeSeries(
            name="test_ts",
            data=list(range(len(tstamps))),
            unit='unit',
            timestamps=tstamps
        )
        cis = CorrectedImageStack(
            corrected=is1,
            original=is2,
            xy_translation=ts
        )
        self.assertEqual(cis.corrected, is1)
        self.assertEqual(cis.original, is2)
        self.assertEqual(cis.xy_translation, ts)
github NeurodataWithoutBorders / pynwb / tests / integration / ui_write / test_modular_storage.py View on Github external
with HDF5IO(self.data_filename, 'w', manager=get_manager()) as data_write_io:
            data_write_io.write(data_file)

        # read data file
        with HDF5IO(self.data_filename, 'r', manager=get_manager()) as self.data_read_io:
            data_file_obt = self.data_read_io.read()

            # write "link file" with timeseries.data that is an external link to the timeseries in "data file"
            # also link timeseries.timestamps.data to the timeseries.timestamps in "data file"
            with HDF5IO(self.link_filename, 'w', manager=get_manager()) as link_write_io:
                link_file = NWBFile(
                    session_description='a test file',
                    identifier='link_file',
                    session_start_time=self.start_time
                )
                self.link_container = TimeSeries(
                    name='test_mod_ts',
                    unit='V',
                    data=data_file_obt.get_acquisition('data_ts'),  # test direct link
                    timestamps=H5DataIO(
                        data=data_file_obt.get_acquisition('data_ts').timestamps,
                        link_data=True  # test with setting link data
                    )
                )
                link_file.add_acquisition(self.link_container)
                link_write_io.write(link_file)

        # note that self.link_container contains a link to a dataset that is now closed

        # read the link file
        self.link_read_io = HDF5IO(self.link_filename, 'r', manager=get_manager())
        self.read_nwbfile = self.link_read_io.read()
github NeurodataWithoutBorders / pynwb / tests / unit / test_base.py View on Github external
def test_init_timestampslink_set(self):
        ts = TimeSeries('test_ts', list(), 'unit', timestamps=list())
        self.assertIsInstance(ts.timestamp_link, set)
        self.assertEqual(len(ts.timestamp_link), 0)
github NeurodataWithoutBorders / pynwb / tests / unit / test_base.py View on Github external
def test_no_starting_time(self):
        # if no starting_time is given, 0.0 is assumed
        ts1 = TimeSeries('test_ts1', rate=0.1)
        self.assertEqual(ts1.starting_time, 0.0)
github NeurodataWithoutBorders / pynwb / tests / unit / test_base.py View on Github external
def test_add_data_interface(self):
        ts = TimeSeries('test_ts', [0, 1, 2, 3, 4, 5],
                        'grams', timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
        self.pm.add(ts)
        self.assertIn(ts.name, self.pm.containers)
        self.assertIs(ts, self.pm.containers[ts.name])
github NeurodataWithoutBorders / pynwb / tests / unit / test_base.py View on Github external
def test_get_data_interface(self):
        ts = TimeSeries('test_ts', [0, 1, 2, 3, 4, 5],
                        'grams', timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
        self.pm.add(ts)
        tmp = self.pm.get('test_ts')
        self.assertIs(tmp, ts)
        self.assertIs(self.pm['test_ts'], self.pm.get('test_ts'))
github NeurodataWithoutBorders / pynwb / tests / unit / test_base.py View on Github external
def test_deprecated_add_data_interface(self):
        ts = TimeSeries('test_ts', [0, 1, 2, 3, 4, 5],
                        'grams', timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
        with self.assertWarnsRegex(PendingDeprecationWarning, r'add_data_interface will be replaced by add'):
            self.pm.add_data_interface(ts)
        self.assertIn(ts.name, self.pm.containers)
        self.assertIs(ts, self.pm.containers[ts.name])