channel_id (#327)

fl/datamigration/nwb/components/electrodes/extension/electrode_extension_injector.py

@@ -24,6 +24,7 @@ def inject_extensions(self, nwb_content: NWBFile, fl_electrode_extension: FlElec
             fl_electrode_extension.rel_z,
             fl_electrode_extension.hw_chan,
             fl_electrode_extension.ntrode_id,
+            fl_electrode_extension.channel_id,
             fl_electrode_extension.bad_channels,
             fl_electrode_extension.probe_shank,
             fl_electrode_extension.probe_channel
@@ -42,6 +43,11 @@ def __join_extensions_to_electrodes(nwb_content, fl_electrode_extension):
             description='None',
             data=fl_electrode_extension.ntrode_id
         )
+        nwb_content.electrodes.add_column(
+            name='channel_id',
+            description='None',
+            data=fl_electrode_extension.channel_id
+        )
         nwb_content.electrodes.add_column(
             name='bad_channel',
             description='None',

fl/datamigration/nwb/components/electrodes/extension/fl_electrode_extension.py

@@ -1,11 +1,12 @@
 class FlElectrodeExtension:
 
-    def __init__(self, rel_x, rel_y, rel_z, hw_chan, ntrode_id, bad_channels, probe_shank, probe_channel):
+    def __init__(self, rel_x, rel_y, rel_z, hw_chan, ntrode_id, channel_id, bad_channels, probe_shank, probe_channel):
         self.rel_x = rel_x
         self.rel_y = rel_y
         self.rel_z = rel_z
         self.hw_chan = hw_chan
         self.ntrode_id = ntrode_id
+        self.channel_id = channel_id
         self.bad_channels = bad_channels
         self.probe_shank = probe_shank
         self.probe_channel = probe_channel

fl/datamigration/nwb/components/electrodes/extension/fl_electrode_extension_builder.py

@@ -9,14 +9,15 @@ class FlElectrodeExtensionBuilder:
 
     @staticmethod
     @beartype
-    def build(rel_x: list, rel_y: list, rel_z: list, hw_chan: list, ntrode_id: list, bad_channels: list,
-              probe_shank: list, probe_channel: list):
+    def build(rel_x: list, rel_y: list, rel_z: list, hw_chan: list, ntrode_id: list, channel_id: list,
+              bad_channels: list, probe_shank: list, probe_channel: list):
         return FlElectrodeExtension(
             rel_x=rel_x,
             rel_y=rel_y,
             rel_z=rel_z,
             hw_chan=hw_chan,
             ntrode_id=ntrode_id,
+            channel_id=channel_id,
             bad_channels=bad_channels,
             probe_shank=probe_shank,
             probe_channel=probe_channel

fl/datamigration/nwb/components/electrodes/extension/fl_electrode_extension_factory.py

@@ -28,6 +28,14 @@ def create_ntrode_id(cls, ntrode_metadata):
         [ntrode_id.extend([ntrode['ntrode_id']] * len(ntrode['map'])) for ntrode in ntrode_metadata]
         return ntrode_id
 
+    @classmethod
+    def create_channel_id(cls, ntrode_metadata):
+        validate_parameters_not_none(__name__, ntrode_metadata)
+
+        channel_id = []
+        for ntrode in ntrode_metadata:
+            [channel_id.append(map_index) for map_index in ntrode['map']]
+        return channel_id
 
     @classmethod
     def create_bad_channels(cls, ntrode_metadata):

fl/datamigration/nwb/components/electrodes/extension/fl_electrode_extension_manager.py

@@ -43,6 +43,9 @@ def get_fl_electrodes_extension(self, electrodes_valid_map: list) -> FlElectrode
         ntrode_id = FlElectrodeExtensionFactory.create_ntrode_id(
             ntrode_metadata=ntrode_metadata
         )
+        channel_id = FlElectrodeExtensionFactory.create_channel_id(
+            ntrode_metadata=ntrode_metadata
+        )
         bad_channels = FlElectrodeExtensionFactory.create_bad_channels(
             ntrode_metadata=ntrode_metadata
         )
@@ -61,6 +64,7 @@ def get_fl_electrodes_extension(self, electrodes_valid_map: list) -> FlElectrode
             rel['rel_z'],
             hw_chan,
             ntrode_id,
+            channel_id,
             bad_channels,
             probe_shank,
             probe_channel
@@ -72,6 +76,7 @@ def get_fl_electrodes_extension(self, electrodes_valid_map: list) -> FlElectrode
             rel_z=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, rel['rel_z']),
             hw_chan=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, hw_chan),
             ntrode_id=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, ntrode_id),
+            channel_id=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, channel_id),
             bad_channels=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, bad_channels),
             probe_shank=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, probe_shank),
             probe_channel=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, probe_channel),

fl/test/datamigration/electrodes/extension/test_electrodeExtensionInjector.py

@@ -62,6 +62,7 @@ def test_electrode_extension_injector_inject_proper_values_successfully(self):
         mock_fl_electrode_extension.rel_z = [2, 2, 2, 2]
         mock_fl_electrode_extension.hw_chan = [0, 1, 2, 3]
         mock_fl_electrode_extension.ntrode_id = [11, 11, 22, 22]
+        mock_fl_electrode_extension.channel_id = [1, 1, 2, 3]
         mock_fl_electrode_extension.bad_channels = [False, False, False, False]
         mock_fl_electrode_extension.probe_shank = [0, 0, 1, 2]
         mock_fl_electrode_extension.probe_channel = [0, 1, 2, 3]
@@ -72,15 +73,6 @@ def test_electrode_extension_injector_inject_proper_values_successfully(self):
             fl_electrode_extension=mock_fl_electrode_extension
         )
 
-        self.assertIsInstance(nwb_file.electrodes['rel_x'], VectorData)
-        self.assertIsInstance(nwb_file.electrodes['rel_y'], VectorData)
-        self.assertIsInstance(nwb_file.electrodes['rel_z'], VectorData)
-        self.assertIsInstance(nwb_file.electrodes['ntrode_id'], VectorData)
-        self.assertIsInstance(nwb_file.electrodes['bad_channel'], VectorData)
-        self.assertIsInstance(nwb_file.electrodes['hwChan'], VectorData)
-        self.assertIsInstance(nwb_file.electrodes['probe_shank'], VectorData)
-        self.assertIsInstance(nwb_file.electrodes['probe_channel'], VectorData)
-
         # header_extension - hw_chan
         self.assertIsInstance(nwb_file.electrodes[0, 9], int)
         self.assertEqual(nwb_file.electrodes[0, 9], 0)
@@ -95,47 +87,54 @@ def test_electrode_extension_injector_inject_proper_values_successfully(self):
         self.assertEqual(nwb_file.electrodes[2, 10], 22)
         self.assertEqual(nwb_file.electrodes[3, 10], 22)
 
+        # ntrodes_extension - channel_id
+        self.assertIsInstance(nwb_file.electrodes[0, 11], int)
+        self.assertEqual(nwb_file.electrodes[0, 11], 1)
+        self.assertEqual(nwb_file.electrodes[1, 11], 1)
+        self.assertEqual(nwb_file.electrodes[2, 11], 2)
+        self.assertEqual(nwb_file.electrodes[3, 11], 3)
+
         # ntrodes_extension - bad_channels
-        self.assertIsInstance(nwb_file.electrodes[0, 11], bool)
-        self.assertEqual(nwb_file.electrodes[0, 11], False)
-        self.assertEqual(nwb_file.electrodes[1, 11], False)
-        self.assertEqual(nwb_file.electrodes[2, 11], False)
-        self.assertEqual(nwb_file.electrodes[3, 11], False)
+        self.assertIsInstance(nwb_file.electrodes[0, 12], bool)
+        self.assertEqual(nwb_file.electrodes[0, 12], False)
+        self.assertEqual(nwb_file.electrodes[1, 12], False)
+        self.assertEqual(nwb_file.electrodes[2, 12], False)
+        self.assertEqual(nwb_file.electrodes[3, 12], False)
 
         # metadata_extension - rel_x
-        self.assertIsInstance(nwb_file.electrodes[0, 12], int)
-        self.assertEqual(nwb_file.electrodes[0, 12], 0)
-        self.assertEqual(nwb_file.electrodes[1, 12], 0)
-        self.assertEqual(nwb_file.electrodes[2, 12], 0)
-        self.assertEqual(nwb_file.electrodes[3, 12], 0)
-
-        # metadata_extension - rel_y
         self.assertIsInstance(nwb_file.electrodes[0, 13], int)
-        self.assertEqual(nwb_file.electrodes[0, 13], 1)
-        self.assertEqual(nwb_file.electrodes[1, 13], 1)
-        self.assertEqual(nwb_file.electrodes[2, 13], 1)
-        self.assertEqual(nwb_file.electrodes[3, 13], 1)
+        self.assertEqual(nwb_file.electrodes[0, 13], 0)
+        self.assertEqual(nwb_file.electrodes[1, 13], 0)
+        self.assertEqual(nwb_file.electrodes[2, 13], 0)
+        self.assertEqual(nwb_file.electrodes[3, 13], 0)
 
-        # metadata_extension - rel_z
+        # metadata_extension - rel_y
         self.assertIsInstance(nwb_file.electrodes[0, 14], int)
-        self.assertEqual(nwb_file.electrodes[0, 14], 2)
-        self.assertEqual(nwb_file.electrodes[1, 14], 2)
-        self.assertEqual(nwb_file.electrodes[2, 14], 2)
-        self.assertEqual(nwb_file.electrodes[3, 14], 2)
+        self.assertEqual(nwb_file.electrodes[0, 14], 1)
+        self.assertEqual(nwb_file.electrodes[1, 14], 1)
+        self.assertEqual(nwb_file.electrodes[2, 14], 1)
+        self.assertEqual(nwb_file.electrodes[3, 14], 1)
 
-        # metadata_extension - proba_shank
+        # metadata_extension - rel_z
         self.assertIsInstance(nwb_file.electrodes[0, 15], int)
-        self.assertEqual(nwb_file.electrodes[0, 15], 0)
-        self.assertEqual(nwb_file.electrodes[1, 15], 0)
-        self.assertEqual(nwb_file.electrodes[2, 15], 1)
+        self.assertEqual(nwb_file.electrodes[0, 15], 2)
+        self.assertEqual(nwb_file.electrodes[1, 15], 2)
+        self.assertEqual(nwb_file.electrodes[2, 15], 2)
         self.assertEqual(nwb_file.electrodes[3, 15], 2)
 
-        # metadata_extension - probe_channel
+        # metadata_extension - proba_shank
         self.assertIsInstance(nwb_file.electrodes[0, 16], int)
         self.assertEqual(nwb_file.electrodes[0, 16], 0)
-        self.assertEqual(nwb_file.electrodes[1, 16], 1)
-        self.assertEqual(nwb_file.electrodes[2, 16], 2)
-        self.assertEqual(nwb_file.electrodes[3, 16], 3)
+        self.assertEqual(nwb_file.electrodes[1, 16], 0)
+        self.assertEqual(nwb_file.electrodes[2, 16], 1)
+        self.assertEqual(nwb_file.electrodes[3, 16], 2)
+
+        # metadata_extension - probe_channel
+        self.assertIsInstance(nwb_file.electrodes[0, 17], int)
+        self.assertEqual(nwb_file.electrodes[0, 17], 0)
+        self.assertEqual(nwb_file.electrodes[1, 17], 1)
+        self.assertEqual(nwb_file.electrodes[2, 17], 2)
+        self.assertEqual(nwb_file.electrodes[3, 17], 3)
 
     @should_raise(NoneParamException)
     def test_electrodes_extension_injector_failed_injecting_due_to_None_fl_electrode_attr(self):
@@ -151,6 +150,7 @@ def test_electrodes_extension_injector_failed_injecting_due_to_None_fl_electrode
         mock_fl_electrode_extension.rel_z = [2, 2, 2, 2]
         mock_fl_electrode_extension.hw_chan = [0, 1, 2, 3]
         mock_fl_electrode_extension.ntrode_id = [11, 11, 22, 22]
+        mock_fl_electrode_extension.channel_id = [1, 2, 3, 3]
         mock_fl_electrode_extension.bad_channels = [False, False, False, False]
         mock_fl_electrode_extension.probe_shank = None
         mock_fl_electrode_extension.probe_channel = [0, 1, 2, 3]

fl/test/datamigration/electrodes/extension/test_flElectrodeExtensionManager.py

@@ -75,6 +75,7 @@ def test_electrode_extension_manager_get_fl_electrode_extension_successfully(sel
         self.assertEqual(fl_electrode_extension.hw_chan[0], 85)
         self.assertEqual(fl_electrode_extension.hw_chan[-1], 102)
         self.assertEqual(fl_electrode_extension.ntrode_id, [1, 2, 2, 3, 4])
+        self.assertEqual(fl_electrode_extension.channel_id, [1, 1, 2, 2, 1])
         self.assertEqual(fl_electrode_extension.probe_shank, [0, 0, 0, 2, 3])
         self.assertEqual(fl_electrode_extension.bad_channels, [False, False, False, False, False])
         self.assertEqual(fl_electrode_extension.probe_channel, [1, 33, 34, 66, 97])