def test_manager_fails_creating_FlElectrodes_due_to_None_ElectrodeGroup(
self):
electrode_groups_metadata = []
probes_metadata = []
fl_electrodes_manager = FlElectrodeManager(probes_metadata,
electrode_groups_metadata)
fl_electrodes_manager.get_fl_electrodes(electrode_groups=None)
def test_manager_fails_creating_FlElectrodes_due_to_None_FlElectrodeGroup_attr(
self):
electrode_groups_metadata = []
probes_metadata = []
mock_eg_1 = Mock(spec=ElectrodeGroup)
mock_eg_2 = Mock(spec=ElectrodeGroup)
mock_eg_1.name = None
mock_eg_2.name = 'ElectrodeGroup2'
fl_electrodes_manager = FlElectrodeManager(probes_metadata,
electrode_groups_metadata)
fl_electrodes_manager.get_fl_electrodes(
electrode_groups=[mock_eg_1, mock_eg_2],
electrodes_valid_map=[True, False, True, False],
electrode_groups_valid_map={True, True})
class ElectrodesOriginator:
def __init__(self, probes, metadata):
self.fl_electrode_manager = FlElectrodeManager(probes, metadata['electrode groups'])
self.electrode_creator = ElectrodesCreator()
def make(self, nwb_content, electrode_groups, electrodes_valid_map, electrode_groups_valid_map):
logger.info('Electrodes: Building')
fl_electrodes = self.fl_electrode_manager.get_fl_electrodes(
electrode_groups=electrode_groups,
electrodes_valid_map=electrodes_valid_map,
electrode_groups_valid_map=electrode_groups_valid_map
)
logger.info('Electrodes: Creating&Injecting into NWB')
[self.electrode_creator.create(nwb_content, fl_electrode) for fl_electrode in fl_electrodes]
def test_electrode_failed_creating_and_injecting_inside_nwb_due_to_None_NWB(
self):
electrode_groups_metadata = [{
'id': 0,
'location': 'mPFC',
'device_type': 'tetrode_12.5',
'description': 'Probe 1'
}, {
'id': 1,
'location': 'mPFC',
'device_type': '128c-4s8mm6cm-20um-40um-sl',
'description': 'Probe 2'
}]
probes_metadata = [{
'probe_type':
'tetrode_12.5',
'contact_size':
20.0,
'num_shanks':
1,
'shanks': [{
'shank_id':
0,
'electrodes': [
{
'id': 0,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
},
{
'id': 1,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
},
]
}]
}, {
'probe_type':
'128c-4s8mm6cm-20um-40um-sl',
'contact_size':
20.0,
'num_shanks':
4,
'shanks': [
{
'shank_id':
0,
'electrodes': [{
'id': 0,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}, {
'id': 1,
'rel_x': 40.0,
'rel_y': 0.0,
'rel_z': 0.0
}]
},
{
'shank_id':
1,
'electrodes': [{
'id': 32,
'rel_x': 0.0,
'rel_y': 300.0,
'rel_z': 0.0
}, {
'id': 33,
'rel_x': 40.0,
'rel_y': 300.0,
'rel_z': 0.0
}]
},
]
}]
mock_electrode_groups_valid_map = {0, 1}
mock_eg_1 = Mock(spec=ElectrodeGroup)
mock_eg_2 = Mock(spec=ElectrodeGroup)
mock_eg_1.name = '0'
mock_eg_2.name = '1'
electrode_creator = ElectrodesCreator()
fl_electrodes_manager = FlElectrodeManager(probes_metadata,
electrode_groups_metadata)
fl_electrodes = fl_electrodes_manager.get_fl_electrodes(
electrode_groups=[mock_eg_1, mock_eg_2],
electrodes_valid_map=[True, True, False, False, False, True],
electrode_groups_valid_map=mock_electrode_groups_valid_map)
[
electrode_creator.create(None, fl_electrode)
for fl_electrode in fl_electrodes
]
def test_electrode_create_and_inject_inside_nwb_successfully(self):
electrode_groups_metadata = [{
'id': 0,
'location': 'mPFC',
'device_type': 'tetrode_12.5',
'description': 'Probe 1'
}, {
'id': 1,
'location': 'mPFC',
'device_type': '128c-4s8mm6cm-20um-40um-sl',
'description': 'Probe 2'
}]
probes_metadata = [{
'probe_type':
'tetrode_12.5',
'contact_size':
20.0,
'num_shanks':
1,
'shanks': [{
'shank_id':
0,
'electrodes': [{
'id': 0,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}, {
'id': 1,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}, {
'id': 2,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}, {
'id': 3,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}]
}]
}, {
'probe_type':
'128c-4s8mm6cm-20um-40um-sl',
'contact_size':
20.0,
'num_shanks':
4,
'shanks': [{
'shank_id':
0,
'electrodes': [{
'id': 0,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}, {
'id': 1,
'rel_x': 40.0,
'rel_y': 0.0,
'rel_z': 0.0
}]
}, {
'shank_id':
1,
'electrodes': [{
'id': 32,
'rel_x': 0.0,
'rel_y': 300.0,
'rel_z': 0.0
}, {
'id': 33,
'rel_x': 40.0,
'rel_y': 300.0,
'rel_z': 0.0
}]
}, {
'shank_id':
2,
'electrodes': [
{
'id': 64,
'rel_x': 0.0,
'rel_y': 600.0,
'rel_z': 0.0
},
{
'id': 65,
'rel_x': 40.0,
'rel_y': 600.0,
'rel_z': 0.0
},
]
}, {
'shank_id':
3,
'electrodes': [{
'id': 96,
'rel_x': 0.0,
'rel_y': 900.0,
'rel_z': 0.0
}, {
'id': 97,
'rel_x': 40.0,
'rel_y': 900.0,
'rel_z': 0.0
}]
}]
}]
mock_electrodes_valid_map = [
False, False, False, False, True, True, False, False, True, True,
True, True
]
mock_electrode_groups_valid_map = {1}
mock_eg_1 = Mock(spec=ElectrodeGroup)
mock_eg_2 = Mock(spec=ElectrodeGroup)
mock_eg_1.name = '0'
mock_eg_2.name = '1'
nwb_file = NWBFile(session_description='demonstrate external files',
identifier='NWBE1',
session_start_time=datetime(2017,
4,
3,
11,
tzinfo=tzlocal()),
file_create_date=datetime(2017,
4,
15,
12,
tzinfo=tzlocal()))
electrode_creator = ElectrodesCreator()
fl_electrodes_manager = FlElectrodeManager(probes_metadata,
electrode_groups_metadata)
fl_electrodes = fl_electrodes_manager.get_fl_electrodes(
electrode_groups=[mock_eg_2],
electrodes_valid_map=mock_electrodes_valid_map,
electrode_groups_valid_map=mock_electrode_groups_valid_map)
[
electrode_creator.create(nwb_file, fl_electrode)
for fl_electrode in fl_electrodes
]
self.assertEqual(6, len(fl_electrodes))
self.assertIsInstance(nwb_file.electrodes, DynamicTable)
# id
self.assertEqual(nwb_file.electrodes[0, 0], 4)
self.assertEqual(nwb_file.electrodes[1, 0], 5)
# x
self.assertEqual(nwb_file.electrodes[0, 1], 0.0)
self.assertEqual(nwb_file.electrodes[1, 1], 0.0)
# y
self.assertEqual(nwb_file.electrodes[0, 2], 0.0)
self.assertEqual(nwb_file.electrodes[1, 2], 0.0)
# z
self.assertEqual(nwb_file.electrodes[0, 3], 0.0)
self.assertEqual(nwb_file.electrodes[1, 3], 0.0)
# imp
self.assertEqual(nwb_file.electrodes[0, 4], 0.0)
self.assertEqual(nwb_file.electrodes[1, 4], 0.0)
# location
self.assertEqual(nwb_file.electrodes[0, 5], 'None')
self.assertEqual(nwb_file.electrodes[1, 5], 'None')
# filtering
self.assertEqual(nwb_file.electrodes[0, 6], 'None')
self.assertEqual(nwb_file.electrodes[1, 6], 'None')
# group
self.assertEqual(nwb_file.electrodes[0, 7], mock_eg_2)
self.assertEqual(nwb_file.electrodes[1, 7], mock_eg_2)
# electrode_group name
self.assertEqual(nwb_file.electrodes[0, 8], '1')
self.assertEqual(nwb_file.electrodes[1, 8], '1')
def __init__(self, probes, metadata):
self.fl_electrode_manager = FlElectrodeManager(
probes, metadata['electrode_groups'])
self.electrode_creator = ElectrodesCreator()
def test_manager_fails_creating_FlElectrodes_due_to_None_param(self):
probes_metadata = []
FlElectrodeManager(probes_metadata, None)
def test_manager_builds_FlElectrodes_successfully(self):
electrode_groups_metadata = [{
'id': 0,
'location': 'mPFC',
'device_type': 'tetrode_12.5',
'description': 'Probe 1'
}, {
'id': 1,
'location': 'mPFC',
'device_type': '128c-4s8mm6cm-20um-40um-sl',
'description': 'Probe 2'
}]
probes_metadata = [{
'probe_type':
'tetrode_12.5',
'contact_size':
20.0,
'num_shanks':
1,
'shanks': [{
'shank_id':
0,
'electrodes': [{
'id': 0,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}, {
'id': 1,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}, {
'id': 2,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}, {
'id': 3,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}]
}]
}, {
'probe_type':
'128c-4s8mm6cm-20um-40um-sl',
'contact_size':
20.0,
'num_shanks':
4,
'shanks': [{
'shank_id':
0,
'electrodes': [{
'id': 0,
'rel_x': 0.0,
'rel_y': 0.0,
'rel_z': 0.0
}, {
'id': 1,
'rel_x': 40.0,
'rel_y': 0.0,
'rel_z': 0.0
}]
}, {
'shank_id':
1,
'electrodes': [{
'id': 32,
'rel_x': 0.0,
'rel_y': 300.0,
'rel_z': 0.0
}, {
'id': 33,
'rel_x': 40.0,
'rel_y': 300.0,
'rel_z': 0.0
}]
}, {
'shank_id':
2,
'electrodes': [
{
'id': 64,
'rel_x': 0.0,
'rel_y': 600.0,
'rel_z': 0.0
},
{
'id': 65,
'rel_x': 40.0,
'rel_y': 600.0,
'rel_z': 0.0
},
]
}, {
'shank_id':
3,
'electrodes': [{
'id': 96,
'rel_x': 0.0,
'rel_y': 900.0,
'rel_z': 0.0
}, {
'id': 97,
'rel_x': 40.0,
'rel_y': 900.0,
'rel_z': 0.0
}]
}]
}]
mock_eg_1 = Mock(spec=ElectrodeGroup)
mock_eg_2 = Mock(spec=ElectrodeGroup)
mock_eg_1.name = '0'
mock_eg_2.name = '1'
mock_electrodes_valid_map = [
False, False, False, True, True, True, False, False, True, True,
True, True
]
mock_electrode_groups_valid_map = {0, 1}
fl_electrodes_manager = FlElectrodeManager(probes_metadata,
electrode_groups_metadata)
fl_electrodes = fl_electrodes_manager.get_fl_electrodes(
electrode_groups=[mock_eg_1, mock_eg_2],
electrodes_valid_map=mock_electrodes_valid_map,
electrode_groups_valid_map=mock_electrode_groups_valid_map)
self.assertEqual(7, len(fl_electrodes))
self.assertIsInstance(fl_electrodes, list)
self.assertIsInstance(fl_electrodes[0].electrode_group, ElectrodeGroup)
self.assertEqual(fl_electrodes[0].electrode_group, mock_eg_1)
self.assertEqual(fl_electrodes[0].electrode_id, 3)
self.assertEqual(fl_electrodes[1].electrode_group, mock_eg_2)
self.assertEqual(fl_electrodes[1].electrode_id, 4)
self.assertEqual(fl_electrodes[2].electrode_group, mock_eg_2)
self.assertEqual(fl_electrodes[2].electrode_id, 5)
self.assertEqual(fl_electrodes[3].electrode_group, mock_eg_2)
self.assertEqual(fl_electrodes[3].electrode_id, 8)
self.assertEqual(fl_electrodes[4].electrode_group, mock_eg_2)
self.assertEqual(fl_electrodes[4].electrode_id, 9)
self.assertEqual(fl_electrodes[5].electrode_group, mock_eg_2)
self.assertEqual(fl_electrodes[5].electrode_id, 10)
self.assertEqual(fl_electrodes[6].electrode_group, mock_eg_2)
self.assertEqual(fl_electrodes[6].electrode_id, 11)