Exemplo n.º 1
0
    def test__cut_block_by_epochs(self):
        epoch = Epoch([0.5, 10.0, 25.2] * pq.s,
                      durations=[5.1, 4.8, 5.0] * pq.s,
                      t_start=.1 * pq.s)
        epoch.annotate(epoch_type='a', pick='me')
        epoch.array_annotate(trial_id=[1, 2, 3])

        epoch2 = Epoch([0.6, 9.5, 16.8, 34.1] * pq.s,
                       durations=[4.5, 4.8, 5.0, 5.0] * pq.s,
                       t_start=.1 * pq.s)
        epoch2.annotate(epoch_type='b')
        epoch2.array_annotate(trial_id=[1, 2, 3, 4])

        event = Event(times=[0.5, 10.0, 25.2] * pq.s, t_start=.1 * pq.s)
        event.annotate(event_type='trial start')
        event.array_annotate(trial_id=[1, 2, 3])

        anasig = AnalogSignal(np.arange(50.0) * pq.mV,
                              t_start=.1 * pq.s,
                              sampling_rate=1.0 * pq.Hz)
        irrsig = IrregularlySampledSignal(signal=np.arange(50.0) * pq.mV,
                                          times=anasig.times,
                                          t_start=.1 * pq.s)
        st = SpikeTrain(
            np.arange(0.5, 50, 7) * pq.s,
            t_start=.1 * pq.s,
            t_stop=50.0 * pq.s,
            waveforms=np.array(
                [[[0., 1.], [0.1, 1.1]], [[2., 3.], [2.1, 3.1]],
                 [[4., 5.], [4.1, 5.1]], [[6., 7.], [6.1, 7.1]],
                 [[8., 9.], [8.1, 9.1]], [[12., 13.], [12.1, 13.1]],
                 [[14., 15.], [14.1, 15.1]], [[16., 17.], [16.1, 17.1]]]) *
            pq.mV,
            array_annotations={'spikenum': np.arange(1, 9)})

        seg = Segment()
        seg2 = Segment(name='NoCut')
        seg.epochs = [epoch, epoch2]
        seg.events = [event]
        seg.analogsignals = [anasig]
        seg.irregularlysampledsignals = [irrsig]
        seg.spiketrains = [st]

        block = Block()
        block.segments = [seg, seg2]
        block.create_many_to_one_relationship()

        # test without resetting the time
        cut_block_by_epochs(block, properties={'pick': 'me'})

        assert_neo_object_is_compliant(block)
        self.assertEqual(len(block.segments), 3)

        for epoch_idx in range(len(epoch)):
            self.assertEqual(len(block.segments[epoch_idx].events), 1)
            self.assertEqual(len(block.segments[epoch_idx].spiketrains), 1)
            self.assertEqual(len(block.segments[epoch_idx].analogsignals), 1)
            self.assertEqual(
                len(block.segments[epoch_idx].irregularlysampledsignals), 1)

            if epoch_idx != 0:
                self.assertEqual(len(block.segments[epoch_idx].epochs), 1)
            else:
                self.assertEqual(len(block.segments[epoch_idx].epochs), 2)

            assert_same_attributes(
                block.segments[epoch_idx].spiketrains[0],
                st.time_slice(t_start=epoch.times[epoch_idx],
                              t_stop=epoch.times[epoch_idx] +
                              epoch.durations[epoch_idx]))
            assert_same_attributes(
                block.segments[epoch_idx].analogsignals[0],
                anasig.time_slice(t_start=epoch.times[epoch_idx],
                                  t_stop=epoch.times[epoch_idx] +
                                  epoch.durations[epoch_idx]))
            assert_same_attributes(
                block.segments[epoch_idx].irregularlysampledsignals[0],
                irrsig.time_slice(t_start=epoch.times[epoch_idx],
                                  t_stop=epoch.times[epoch_idx] +
                                  epoch.durations[epoch_idx]))
            assert_same_attributes(
                block.segments[epoch_idx].events[0],
                event.time_slice(t_start=epoch.times[epoch_idx],
                                 t_stop=epoch.times[epoch_idx] +
                                 epoch.durations[epoch_idx]))
        assert_same_attributes(
            block.segments[0].epochs[0],
            epoch.time_slice(t_start=epoch.times[0],
                             t_stop=epoch.times[0] + epoch.durations[0]))
        assert_same_attributes(
            block.segments[0].epochs[1],
            epoch2.time_slice(t_start=epoch.times[0],
                              t_stop=epoch.times[0] + epoch.durations[0]))

        seg = Segment()
        seg2 = Segment(name='NoCut')
        seg.epochs = [epoch, epoch2]
        seg.events = [event]
        seg.analogsignals = [anasig]
        seg.irregularlysampledsignals = [irrsig]
        seg.spiketrains = [st]

        block = Block()
        block.segments = [seg, seg2]
        block.create_many_to_one_relationship()

        # test with resetting the time
        cut_block_by_epochs(block, properties={'pick': 'me'}, reset_time=True)

        assert_neo_object_is_compliant(block)
        self.assertEqual(len(block.segments), 3)

        for epoch_idx in range(len(epoch)):
            self.assertEqual(len(block.segments[epoch_idx].events), 1)
            self.assertEqual(len(block.segments[epoch_idx].spiketrains), 1)
            self.assertEqual(len(block.segments[epoch_idx].analogsignals), 1)
            self.assertEqual(
                len(block.segments[epoch_idx].irregularlysampledsignals), 1)
            if epoch_idx != 0:
                self.assertEqual(len(block.segments[epoch_idx].epochs), 1)
            else:
                self.assertEqual(len(block.segments[epoch_idx].epochs), 2)

            assert_same_attributes(
                block.segments[epoch_idx].spiketrains[0],
                st.time_shift(-epoch.times[epoch_idx]).time_slice(
                    t_start=0 * pq.s, t_stop=epoch.durations[epoch_idx]))

            anasig_target = anasig.time_shift(-epoch.times[epoch_idx])
            anasig_target = anasig_target.time_slice(
                t_start=0 * pq.s, t_stop=epoch.durations[epoch_idx])
            assert_same_attributes(block.segments[epoch_idx].analogsignals[0],
                                   anasig_target)
            irrsig_target = irrsig.time_shift(-epoch.times[epoch_idx])
            irrsig_target = irrsig_target.time_slice(
                t_start=0 * pq.s, t_stop=epoch.durations[epoch_idx])
            assert_same_attributes(
                block.segments[epoch_idx].irregularlysampledsignals[0],
                irrsig_target)
            assert_same_attributes(
                block.segments[epoch_idx].events[0],
                event.time_shift(-epoch.times[epoch_idx]).time_slice(
                    t_start=0 * pq.s, t_stop=epoch.durations[epoch_idx]))

        assert_same_attributes(
            block.segments[0].epochs[0],
            epoch.time_shift(-epoch.times[0]).time_slice(
                t_start=0 * pq.s, t_stop=epoch.durations[0]))
        assert_same_attributes(
            block.segments[0].epochs[1],
            epoch2.time_shift(-epoch.times[0]).time_slice(
                t_start=0 * pq.s, t_stop=epoch.durations[0]))
Exemplo n.º 2
0
    def test__time_slice(self):
        time_slice = [.5, 5.6] * pq.s

        epoch2 = Epoch([0.6, 9.5, 16.8, 34.1] * pq.s,
                       durations=[4.5, 4.8, 5.0, 5.0] * pq.s,
                       t_start=.1 * pq.s)
        epoch2.annotate(epoch_type='b')
        epoch2.array_annotate(trial_id=[1, 2, 3, 4])

        event = Event(times=[0.5, 10.0, 25.2] * pq.s, t_start=.1 * pq.s)
        event.annotate(event_type='trial start')
        event.array_annotate(trial_id=[1, 2, 3])

        anasig = AnalogSignal(np.arange(50.0) * pq.mV,
                              t_start=.1 * pq.s,
                              sampling_rate=1.0 * pq.Hz)
        irrsig = IrregularlySampledSignal(signal=np.arange(50.0) * pq.mV,
                                          times=anasig.times,
                                          t_start=.1 * pq.s)
        st = SpikeTrain(
            np.arange(0.5, 50, 7) * pq.s,
            t_start=.1 * pq.s,
            t_stop=50.0 * pq.s,
            waveforms=np.array(
                [[[0., 1.], [0.1, 1.1]], [[2., 3.], [2.1, 3.1]],
                 [[4., 5.], [4.1, 5.1]], [[6., 7.], [6.1, 7.1]],
                 [[8., 9.], [8.1, 9.1]], [[12., 13.], [12.1, 13.1]],
                 [[14., 15.], [14.1, 15.1]], [[16., 17.], [16.1, 17.1]]]) *
            pq.mV,
            array_annotations={'spikenum': np.arange(1, 9)})

        seg = Segment()
        seg.epochs = [epoch2]
        seg.events = [event]
        seg.analogsignals = [anasig]
        seg.irregularlysampledsignals = [irrsig]
        seg.spiketrains = [st]

        block = Block()
        block.segments = [seg]
        block.create_many_to_one_relationship()

        # test without resetting the time
        sliced = seg.time_slice(time_slice[0], time_slice[1])

        assert_neo_object_is_compliant(sliced)

        self.assertEqual(len(sliced.events), 1)
        self.assertEqual(len(sliced.spiketrains), 1)
        self.assertEqual(len(sliced.analogsignals), 1)
        self.assertEqual(len(sliced.irregularlysampledsignals), 1)
        self.assertEqual(len(sliced.epochs), 1)

        assert_same_attributes(
            sliced.spiketrains[0],
            st.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))
        assert_same_attributes(
            sliced.analogsignals[0],
            anasig.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))
        assert_same_attributes(
            sliced.irregularlysampledsignals[0],
            irrsig.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))
        assert_same_attributes(
            sliced.events[0],
            event.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))
        assert_same_attributes(
            sliced.epochs[0],
            epoch2.time_slice(t_start=time_slice[0], t_stop=time_slice[1]))

        seg = Segment()
        seg.epochs = [epoch2]
        seg.events = [event]
        seg.analogsignals = [anasig]
        seg.irregularlysampledsignals = [irrsig]
        seg.spiketrains = [st]

        block = Block()
        block.segments = [seg]
        block.create_many_to_one_relationship()

        # test with resetting the time
        sliced = seg.time_slice(time_slice[0], time_slice[1], reset_time=True)

        assert_neo_object_is_compliant(sliced)

        self.assertEqual(len(sliced.events), 1)
        self.assertEqual(len(sliced.spiketrains), 1)
        self.assertEqual(len(sliced.analogsignals), 1)
        self.assertEqual(len(sliced.irregularlysampledsignals), 1)
        self.assertEqual(len(sliced.epochs), 1)

        assert_same_attributes(
            sliced.spiketrains[0],
            st.time_shift(-time_slice[0]).time_slice(t_start=0 * pq.s,
                                                     t_stop=time_slice[1] -
                                                     time_slice[0]))

        anasig_target = anasig.copy()
        anasig_target = anasig_target.time_shift(-time_slice[0]).time_slice(
            t_start=0 * pq.s, t_stop=time_slice[1] - time_slice[0])
        assert_same_attributes(sliced.analogsignals[0], anasig_target)
        irrsig_target = irrsig.copy()
        irrsig_target = irrsig_target.time_shift(-time_slice[0]).time_slice(
            t_start=0 * pq.s, t_stop=time_slice[1] - time_slice[0])
        assert_same_attributes(sliced.irregularlysampledsignals[0],
                               irrsig_target)
        assert_same_attributes(
            sliced.events[0],
            event.time_shift(-time_slice[0]).time_slice(t_start=0 * pq.s,
                                                        t_stop=time_slice[1] -
                                                        time_slice[0]))
        assert_same_attributes(
            sliced.epochs[0],
            epoch2.time_shift(-time_slice[0]).time_slice(t_start=0 * pq.s,
                                                         t_stop=time_slice[1] -
                                                         time_slice[0]))

        seg = Segment()

        reader = ExampleRawIO(filename='my_filename.fake')
        reader.parse_header()

        proxy_anasig = AnalogSignalProxy(rawio=reader,
                                         stream_index=0,
                                         inner_stream_channels=None,
                                         block_index=0,
                                         seg_index=0)
        seg.analogsignals.append(proxy_anasig)

        proxy_st = SpikeTrainProxy(rawio=reader,
                                   spike_channel_index=0,
                                   block_index=0,
                                   seg_index=0)
        seg.spiketrains.append(proxy_st)

        proxy_event = EventProxy(rawio=reader,
                                 event_channel_index=0,
                                 block_index=0,
                                 seg_index=0)
        seg.events.append(proxy_event)

        proxy_epoch = EpochProxy(rawio=reader,
                                 event_channel_index=1,
                                 block_index=0,
                                 seg_index=0)
        proxy_epoch.annotate(pick='me')
        seg.epochs.append(proxy_epoch)

        loaded_epoch = proxy_epoch.load()
        loaded_event = proxy_event.load()
        loaded_st = proxy_st.load()
        loaded_anasig = proxy_anasig.load()

        block = Block()
        block.segments = [seg]
        block.create_many_to_one_relationship()

        # test with proxy objects
        sliced = seg.time_slice(time_slice[0], time_slice[1])

        assert_neo_object_is_compliant(sliced)

        sliced_event = loaded_event.time_slice(t_start=time_slice[0],
                                               t_stop=time_slice[1])
        has_event = len(sliced_event) > 0

        sliced_anasig = loaded_anasig.time_slice(t_start=time_slice[0],
                                                 t_stop=time_slice[1])

        sliced_st = loaded_st.time_slice(t_start=time_slice[0],
                                         t_stop=time_slice[1])

        self.assertEqual(len(sliced.events), int(has_event))
        self.assertEqual(len(sliced.spiketrains), 1)
        self.assertEqual(len(sliced.analogsignals), 1)

        self.assertTrue(isinstance(sliced.spiketrains[0], SpikeTrain))
        assert_same_attributes(sliced.spiketrains[0], sliced_st)

        self.assertTrue(isinstance(sliced.analogsignals[0], AnalogSignal))
        assert_same_attributes(sliced.analogsignals[0], sliced_anasig)

        if has_event:
            self.assertTrue(isinstance(sliced.events[0], Event))
            assert_same_attributes(sliced.events[0], sliced_event)