Python nestio.NestIO類代碼示例

    def test_notimeid(self):
        """
        Test for warning, when no time column id was provided.
        """

        filename = get_test_file_full_path(
                ioclass=NestIO,
                filename='0gid-1time-2gex-1262-0.dat',
                directory=self.local_test_dir, clean=False)
        r = NestIO(filenames=filename)

        t_start_targ = 450. * pq.ms
        t_stop_targ = 460. * pq.ms
        sampling_period = pq.CompoundUnit('5*ms')

        with warnings.catch_warnings(record=True) as w:
            # Cause all warnings to always be triggered.
            warnings.simplefilter("always")
            seg = r.read_segment(gid_list=[], t_start=t_start_targ,
                                 sampling_period=sampling_period,
                                 t_stop=t_stop_targ, lazy=False,
                                 id_column_dat=0, time_column_dat=None,
                                 value_columns_dat=2, value_types='V_m')
            # Verify number and content of warning
            self.assertEqual(len(w), 1)
            self.assertIn("no time column id", str(w[0].message))
        sts = seg.analogsignals
        for st in sts:
            self.assertTrue(st.t_start == 1 * 5 * pq.ms)
            self.assertTrue(
                    st.t_stop == len(st) * sampling_period + 1 * 5 * pq.ms)

    def test_read_segment(self):
        """
        Tests if signals are correctly stored in a segment.
        """

        filename = get_test_file_full_path(
                ioclass=NestIO,
                filename='0gid-1time-2gex-1262-0.dat',
                directory=self.local_test_dir, clean=False)
        r = NestIO(filenames=filename)

        id_list_to_test = range(1, 10)
        seg = r.read_segment(gid_list=id_list_to_test,
                             t_stop=1000. * pq.ms,
                             sampling_period=pq.ms, lazy=False,
                             id_column_dat=0, time_column_dat=1,
                             value_columns_dat=2, value_types='V_m')

        self.assertTrue(len(seg.analogsignals) == len(id_list_to_test))

        id_list_to_test = []
        seg = r.read_segment(gid_list=id_list_to_test,
                             t_stop=1000. * pq.ms,
                             sampling_period=pq.ms, lazy=False,
                             id_column_dat=0, time_column_dat=1,
                             value_columns_dat=2, value_types='V_m')

        self.assertEqual(len(seg.analogsignals), 50)

    def test_wrong_input(self):
        """
        Tests two cases of wrong user input, namely
        - User does not specify a value column
        - User does not make any specifications
        - User does not define sampling_period as a unit
        - User specifies a non-default value type without
          specifying a value_unit
        - User specifies t_start < 1.*sampling_period
        """

        filename = get_test_file_full_path(
                ioclass=NestIO,
                filename='0gid-1time-2gex-1262-0.dat',
                directory=self.local_test_dir, clean=False)
        r = NestIO(filenames=filename)
        with self.assertRaises(ValueError):
            r.read_segment(t_stop=1000. * pq.ms, lazy=False,
                           id_column_dat=0, time_column_dat=1)
        with self.assertRaises(ValueError):
            r.read_segment()
        with self.assertRaises(ValueError):
            r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
                           sampling_period=1. * pq.ms, lazy=False,
                           id_column_dat=0, time_column_dat=1,
                           value_columns_dat=2, value_types='V_m')

        with self.assertRaises(ValueError):
            r.read_segment(gid_list=[1], t_stop=1000. * pq.ms,
                           sampling_period=pq.ms, lazy=False,
                           id_column_dat=0, time_column_dat=1,
                           value_columns_dat=2, value_types='U_mem')

 def test_no_gid_no_time(self):
     filename = get_test_file_full_path(
             ioclass=NestIO,
             filename='N1-0Vm-1267-0.dat',
             directory=self.local_test_dir, clean=False)
     r = NestIO(filenames=filename)
     anasig = r.read_analogsignal(gid=None,
                                  sampling_period=pq.ms, lazy=False,
                                  id_column=None, time_column=None,
                                  value_column=0, value_type='V_m')
     self.assertEqual(anasig.annotations['id'], None)
     self.assertEqual(len(anasig), 19)

 def test_single_gid(self):
     filename = get_test_file_full_path(
             ioclass=NestIO,
             filename='N1-0gid-1time-2Vm-1265-0.dat',
             directory=self.local_test_dir, clean=False)
     r = NestIO(filenames=filename)
     anasig = r.read_analogsignal(gid=1, t_stop=1000. * pq.ms,
                                  time_unit=pq.CompoundUnit('0.1*ms'),
                                  sampling_period=pq.ms, lazy=False,
                                  id_column=0, time_column=1,
                                  value_column=2, value_type='V_m')
     assert anasig.annotations['id'] == 1

 def test_read_spiketrain_annotates(self):
     """
     Tests if correct annotation is added when reading a spike train.
     """
     filename = get_test_file_full_path(
             ioclass=NestIO,
             filename='0gid-1time-1256-0.gdf',
             directory=self.local_test_dir, clean=False)
     r = NestIO(filenames=filename)
     ID = 7
     st = r.read_spiketrain(gdf_id=ID, t_start=400. * pq.ms,
                            t_stop=500. * pq.ms)
     self.assertEqual(ID, st.annotations['id'])

 def test_no_gid(self):
     filename = get_test_file_full_path(
             ioclass=NestIO,
             filename='N1-0time-1Vm-1266-0.dat',
             directory=self.local_test_dir, clean=False)
     r = NestIO(filenames=filename)
     anasig = r.read_analogsignal(gid=None, t_stop=1000. * pq.ms,
                                  time_unit=pq.CompoundUnit('0.1*ms'),
                                  sampling_period=pq.ms, lazy=False,
                                  id_column=None, time_column=0,
                                  value_column=1, value_type='V_m')
     self.assertEqual(anasig.annotations['id'], None)
     self.assertEqual(len(anasig), 19)

 def test_read_spiketrain_can_return_empty_spiketrain(self):
     """
     Tests if read_spiketrain returns an empty SpikeTrain if no spikes are in
     time range.
     """
     filename = get_test_file_full_path(
             ioclass=NestIO,
             filename='0gid-1time-1256-0.gdf',
             directory=self.local_test_dir, clean=False)
     r = NestIO(filenames=filename)
     st = r.read_spiketrain(gdf_id=0, t_start=400. * pq.ms,
                            t_stop=1. * pq.ms)
     self.assertEqual(st.size, 0)

    def test_read_segment_accepts_range(self):
        """
        Tests if spiketrains can be retrieved by specifying a range of GDF IDs.
        """
        filename = get_test_file_full_path(
                ioclass=NestIO,
                filename='0gid-1time-1256-0.gdf',
                directory=self.local_test_dir, clean=False)
        r = NestIO(filenames=filename)

        seg = r.read_segment(gid_list=(10, 39), t_start=400. * pq.ms,
                             t_stop=500. * pq.ms, lazy=False,
                             id_column_gdf=0, time_column_gdf=1)
        self.assertEqual(len(seg.spiketrains), 30)

 def test_read_segment_can_return_empty_spiketrains(self):
     """
     Tests if read_segment makes sure that only non-zero spike trains are
     returned.
     """
     filename = get_test_file_full_path(
             ioclass=NestIO,
             filename='0gid-1time-1256-0.gdf',
             directory=self.local_test_dir, clean=False)
     r = NestIO(filenames=filename)
     seg = r.read_segment(gid_list=[], t_start=400. * pq.ms,
                          t_stop=1. * pq.ms)
     for st in seg.spiketrains:
         self.assertEqual(st.size, 0)

 def test_read_segment_annotates(self):
     """
     Tests if correct annotation is added when reading a segment.
     """
     filename = get_test_file_full_path(
             ioclass=NestIO,
             filename='0gid-1time-1256-0.gdf',
             directory=self.local_test_dir, clean=False)
     r = NestIO(filenames=filename)
     IDs = (5, 11)
     sts = r.read_segment(gid_list=(5, 11), t_start=400. * pq.ms,
                          t_stop=500. * pq.ms)
     for ID in np.arange(5, 12):
         self.assertEqual(ID, sts.spiketrains[ID - 5].annotations['id'])

 def test_t_stop_undefined_raises_error(self):
     """
     Tests if undefined t_stop, i.e., t_stop=None raises error.
     """
     filename = get_test_file_full_path(
             ioclass=NestIO,
             filename='0gid-1time-1256-0.gdf',
             directory=self.local_test_dir, clean=False)
     r = NestIO(filenames=filename)
     with self.assertRaises(ValueError):
         r.read_spiketrain(gdf_id=1, t_start=400. * pq.ms, lazy=False,
                           id_column=0, time_column=1)
     with self.assertRaises(ValueError):
         r.read_segment(gid_list=[1, 2, 3], t_start=400. * pq.ms, lazy=False,
                        id_column_gdf=0, time_column_gdf=1)

 def test_adding_custom_annotation(self):
     """
     Tests if custom annotation is correctly added.
     """
     filename = get_test_file_full_path(
             ioclass=NestIO,
             filename='0gid-1time-1256-0.gdf',
             directory=self.local_test_dir, clean=False)
     r = NestIO(filenames=filename)
     st = r.read_spiketrain(gdf_id=0, t_start=400. * pq.ms,
                            t_stop=500. * pq.ms,
                            layer='L23', population='I')
     self.assertEqual(0, st.annotations.pop('id'))
     self.assertEqual('L23', st.annotations.pop('layer'))
     self.assertEqual('I', st.annotations.pop('population'))
     self.assertEqual({}, st.annotations)

    def test_multiple_value_columns(self):
        """
        Test for simultaneous loading of multiple columns from dat file.
        """

        filename = get_test_file_full_path(
                ioclass=NestIO,
                filename='0gid-1time-2Vm-3Iex-4Iin-1264-0.dat',
                directory=self.local_test_dir, clean=False)
        r = NestIO(filenames=filename)

        sampling_period = pq.CompoundUnit('5*ms')
        seg = r.read_segment(gid_list=[1001],
                             value_columns_dat=[2, 3],
                             sampling_period=sampling_period)
        anasigs = seg.analogsignals
        self.assertEqual(len(anasigs), 2)

 def test_read_analogsignal_and_spiketrain(self):
     """
     Test if spiketrains and analogsignals can be read simultaneously
     using read_segment
     """
     files = ['0gid-1time-2gex-3Vm-1261-0.dat',
              '0gid-1time_in_steps-1258-0.gdf']
     filenames = [get_test_file_full_path(ioclass=NestIO, filename=file,
                                          directory=self.local_test_dir,
                                          clean=False)
                  for file in files]
     r = NestIO(filenames=filenames)
     seg = r.read_segment(gid_list=[], t_start=400 * pq.ms,
                          t_stop=600 * pq.ms,
                          id_column_gdf=0, time_column_gdf=1,
                          id_column_dat=0, time_column_dat=1,
                          value_columns_dat=2)
     self.assertEqual(len(seg.spiketrains), 50)
     self.assertEqual(len(seg.analogsignals), 50)