def read_block(self, lazy=False, cascade=True):
"""
"""
blk = Block()
if cascade:
seg = Segment(file_origin=self._absolute_filename)
blk.channel_indexes = self._channel_indexes
blk.segments += [seg]
seg.analogsignals = self.read_analogsignal(lazy=lazy,
cascade=cascade)
try:
seg.irregularlysampledsignals = self.read_tracking()
except Exception as e:
print('Warning: unable to read tracking')
print(e)
seg.spiketrains = self.read_spiketrain()
# TODO Call all other read functions
seg.duration = self._duration
# TODO May need to "populate_RecordingChannel"
# spiketrain = self.read_spiketrain()
# seg.spiketrains.append()
blk.create_many_to_one_relationship()
return blk
def test__construct_subsegment_by_unit(self):
nb_seg = 3
nb_unit = 7
unit_with_sig = np.array([0, 2, 5])
signal_types = ['Vm', 'Conductances']
sig_len = 100
# channelindexes
chxs = [ChannelIndex(name='Vm',
index=unit_with_sig),
ChannelIndex(name='Conductance',
index=unit_with_sig)]
# Unit
all_unit = []
for u in range(nb_unit):
un = Unit(name='Unit #%d' % u, channel_indexes=np.array([u]))
assert_neo_object_is_compliant(un)
all_unit.append(un)
blk = Block()
blk.channel_indexes = chxs
for s in range(nb_seg):
seg = Segment(name='Simulation %s' % s)
for j in range(nb_unit):
st = SpikeTrain([1, 2], units='ms',
t_start=0., t_stop=10)
st.unit = all_unit[j]
for t in signal_types:
anasigarr = AnalogSignal(np.zeros((sig_len,
len(unit_with_sig))),
units='nA',
sampling_rate=1000. * pq.Hz,
channel_indexes=unit_with_sig)
seg.analogsignals.append(anasigarr)
blk.create_many_to_one_relationship()
for unit in all_unit:
assert_neo_object_is_compliant(unit)
for chx in chxs:
assert_neo_object_is_compliant(chx)
assert_neo_object_is_compliant(blk)
# what you want
newseg = seg.construct_subsegment_by_unit(all_unit[:4])
assert_neo_object_is_compliant(newseg)
def test__construct_subsegment_by_unit(self):
nb_seg = 3
nb_unit = 7
unit_with_sig = np.array([0, 2, 5])
signal_types = ['Vm', 'Conductances']
sig_len = 100
# channelindexes
chxs = [ChannelIndex(name='Vm',
index=unit_with_sig),
ChannelIndex(name='Conductance',
index=unit_with_sig)]
# Unit
all_unit = []
for u in range(nb_unit):
un = Unit(name='Unit #%d' % u, channel_indexes=np.array([u]))
assert_neo_object_is_compliant(un)
all_unit.append(un)
blk = Block()
blk.channel_indexes = chxs
for s in range(nb_seg):
seg = Segment(name='Simulation %s' % s)
for j in range(nb_unit):
st = SpikeTrain([1, 2], units='ms',
t_start=0., t_stop=10)
st.unit = all_unit[j]
for t in signal_types:
anasigarr = AnalogSignal(np.zeros((sig_len,
len(unit_with_sig))),
units='nA',
sampling_rate=1000.*pq.Hz,
channel_indexes=unit_with_sig)
seg.analogsignals.append(anasigarr)
blk.create_many_to_one_relationship()
for unit in all_unit:
assert_neo_object_is_compliant(unit)
for chx in chxs:
assert_neo_object_is_compliant(chx)
assert_neo_object_is_compliant(blk)
# what you want
newseg = seg.construct_subsegment_by_unit(all_unit[:4])
assert_neo_object_is_compliant(newseg)
def test__children(self):
blk = Block(name='block1')
blk.channel_indexes = [self.chx1]
blk.create_many_to_one_relationship()
self.assertEqual(self.chx1._container_child_objects, ('Unit', ))
self.assertEqual(self.chx1._data_child_objects,
('AnalogSignal', 'IrregularlySampledSignal'))
self.assertEqual(self.chx1._single_parent_objects, ('Block', ))
self.assertEqual(self.chx1._multi_child_objects, tuple())
self.assertEqual(self.chx1._multi_parent_objects, ())
self.assertEqual(self.chx1._child_properties, ())
self.assertEqual(self.chx1._single_child_objects,
('Unit', 'AnalogSignal', 'IrregularlySampledSignal'))
self.assertEqual(self.chx1._container_child_containers, ('units', ))
self.assertEqual(self.chx1._data_child_containers,
('analogsignals', 'irregularlysampledsignals'))
self.assertEqual(
self.chx1._single_child_containers,
('units', 'analogsignals', 'irregularlysampledsignals'))
self.assertEqual(self.chx1._single_parent_containers, ('block', ))
self.assertEqual(self.chx1._multi_child_containers, tuple())
self.assertEqual(self.chx1._multi_parent_containers, ())
self.assertEqual(self.chx1._child_objects,
('Unit', 'AnalogSignal', 'IrregularlySampledSignal'))
self.assertEqual(
self.chx1._child_containers,
('units', 'analogsignals', 'irregularlysampledsignals'))
self.assertEqual(self.chx1._parent_objects, ('Block', ))
self.assertEqual(self.chx1._parent_containers, ('block', ))
self.assertEqual(len(self.chx1._single_children), 3 * self.nchildren)
self.assertEqual(len(self.chx1._multi_children), 0)
self.assertEqual(len(self.chx1.data_children), 2 * self.nchildren)
self.assertEqual(len(self.chx1.data_children_recur),
2 * self.nchildren + 1 * self.nchildren**2)
self.assertEqual(len(self.chx1.container_children), 1 * self.nchildren)
self.assertEqual(len(self.chx1.container_children_recur),
1 * self.nchildren)
self.assertEqual(len(self.chx1.children), 3 * self.nchildren)
self.assertEqual(len(self.chx1.children_recur),
3 * self.nchildren + 1 * self.nchildren**2)
assert_same_sub_schema(list(self.chx1._single_children),
self.units1a + self.sigarrs1a + self.irrsig1a,
exclude=['channel_index'])
assert_same_sub_schema(list(self.chx1.data_children),
self.sigarrs1a + self.irrsig1a,
exclude=['channel_index'])
assert_same_sub_schema(list(self.chx1.data_children_recur),
self.sigarrs1a + self.irrsig1a +
self.trains1[:2] + self.trains1[2:],
exclude=['channel_index'])
assert_same_sub_schema(list(self.chx1.children),
self.sigarrs1a + self.irrsig1a + self.units1a,
exclude=['channel_index'])
assert_same_sub_schema(list(self.chx1.children_recur),
self.sigarrs1a + self.irrsig1a +
self.trains1[:2] + self.trains1[2:] +
self.units1a,
exclude=['channel_index'])
self.assertEqual(len(self.chx1.parents), 1)
self.assertEqual(self.chx1.parents[0].name, 'block1')
def test__children(self):
blk = Block(name='block1')
blk.channel_indexes = [self.chx1]
blk.create_many_to_one_relationship()
self.assertEqual(self.chx1._container_child_objects, ('Unit',))
self.assertEqual(self.chx1._data_child_objects, ('AnalogSignal', 'IrregularlySampledSignal'))
self.assertEqual(self.chx1._single_parent_objects, ('Block',))
self.assertEqual(self.chx1._multi_child_objects, tuple())
self.assertEqual(self.chx1._multi_parent_objects, ())
self.assertEqual(self.chx1._child_properties, ())
self.assertEqual(self.chx1._single_child_objects,
('Unit', 'AnalogSignal', 'IrregularlySampledSignal'))
self.assertEqual(self.chx1._container_child_containers, ('units',))
self.assertEqual(self.chx1._data_child_containers,
('analogsignals', 'irregularlysampledsignals'))
self.assertEqual(self.chx1._single_child_containers,
('units', 'analogsignals', 'irregularlysampledsignals'))
self.assertEqual(self.chx1._single_parent_containers, ('block',))
self.assertEqual(self.chx1._multi_child_containers,
tuple())
self.assertEqual(self.chx1._multi_parent_containers, ())
self.assertEqual(self.chx1._child_objects,
('Unit', 'AnalogSignal', 'IrregularlySampledSignal'))
self.assertEqual(self.chx1._child_containers,
('units', 'analogsignals', 'irregularlysampledsignals'))
self.assertEqual(self.chx1._parent_objects, ('Block',))
self.assertEqual(self.chx1._parent_containers, ('block',))
self.assertEqual(len(self.chx1._single_children), 3*self.nchildren)
self.assertEqual(len(self.chx1._multi_children), 0)
self.assertEqual(len(self.chx1.data_children), 2*self.nchildren)
self.assertEqual(len(self.chx1.data_children_recur),
2*self.nchildren + 1*self.nchildren**2)
self.assertEqual(len(self.chx1.container_children), 1*self.nchildren)
self.assertEqual(len(self.chx1.container_children_recur),
1*self.nchildren)
self.assertEqual(len(self.chx1.children), 3*self.nchildren)
self.assertEqual(len(self.chx1.children_recur),
3*self.nchildren + 1*self.nchildren**2)
assert_same_sub_schema(list(self.chx1._single_children),
self.units1a + self.sigarrs1a + self.irrsig1a,
exclude=['channel_index'])
assert_same_sub_schema(list(self.chx1.data_children), self.sigarrs1a + self.irrsig1a,
exclude=['channel_index'])
assert_same_sub_schema(list(self.chx1.data_children_recur),
self.sigarrs1a + self.irrsig1a +
self.trains1[:2] + self.trains1[2:],
exclude=['channel_index'])
assert_same_sub_schema(list(self.chx1.children),
self.sigarrs1a + self.irrsig1a + self.units1a,
exclude=['channel_index'])
assert_same_sub_schema(list(self.chx1.children_recur),
self.sigarrs1a + self.irrsig1a +
self.trains1[:2] + self.trains1[2:] +
self.units1a,
exclude=['channel_index'])
self.assertEqual(len(self.chx1.parents), 1)
self.assertEqual(self.chx1.parents[0].name, 'block1')
