User/wbodo/reference electrode information (#455)

rec_to_nwb/processing/nwb/components/electrodes/extension/electrode_extension_injector.py

@@ -28,8 +28,7 @@ def inject_extensions(self, nwb_content: NWBFile, fl_electrode_extension: FlElec
             fl_electrode_extension.bad_channels,
             fl_electrode_extension.probe_shank,
             fl_electrode_extension.probe_electrode,
-            fl_electrode_extension.ref_n_trode_id,
-            fl_electrode_extension.ref_chan
+            fl_electrode_extension.ref_elect_id
         )
         self.__join_extensions_to_electrodes(nwb_content, fl_electrode_extension)
 
@@ -81,12 +80,7 @@ def __join_extensions_to_electrodes(nwb_content, fl_electrode_extension):
             data=fl_electrode_extension.probe_electrode
         )
         nwb_content.electrodes.add_column(
-            name='ref_n_trode_id',
+            name='ref_elect_id',
             description='None',
-            data=fl_electrode_extension.ref_n_trode_id
-        )
-        nwb_content.electrodes.add_column(
-            name='ref_chan',
-            description='None',
-            data=fl_electrode_extension.ref_chan
-        )
+            data=fl_electrode_extension.ref_elect_id
+        )

rec_to_nwb/processing/nwb/components/electrodes/extension/fl_electrode_extension.py

@@ -1,7 +1,7 @@
 class FlElectrodeExtension:
 
     def __init__(self, rel_x, rel_y, rel_z, hw_chan, ntrode_id, channel_id, bad_channels, probe_shank, probe_electrode,
-                 ref_n_trode_id, ref_chan):
+                 ref_elect_id):
         self.rel_x = rel_x
         self.rel_y = rel_y
         self.rel_z = rel_z
@@ -11,5 +11,4 @@ def __init__(self, rel_x, rel_y, rel_z, hw_chan, ntrode_id, channel_id, bad_chan
         self.bad_channels = bad_channels
         self.probe_shank = probe_shank
         self.probe_electrode = probe_electrode
-        self.ref_n_trode_id = ref_n_trode_id
-        self.ref_chan = ref_chan
+        self.ref_elect_id = ref_elect_id

rec_to_nwb/processing/nwb/components/electrodes/extension/fl_electrode_extension_builder.py

@@ -7,7 +7,7 @@ class FlElectrodeExtensionBuilder:
     @staticmethod
     @beartype
     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_electrode: list, ref_n_trode_id: list, ref_chan: list
+              bad_channels: list, probe_shank: list, probe_electrode: list, ref_elect_id: list
               ) -> FlElectrodeExtension:
         return FlElectrodeExtension(
             rel_x=rel_x,
@@ -19,6 +19,5 @@ def build(rel_x: list, rel_y: list, rel_z: list, hw_chan: list, ntrode_id: list,
             bad_channels=bad_channels,
             probe_shank=probe_shank,
             probe_electrode=probe_electrode,
-            ref_n_trode_id=ref_n_trode_id,
-            ref_chan=ref_chan
+            ref_elect_id=ref_elect_id
         )

rec_to_nwb/processing/nwb/components/electrodes/extension/fl_electrode_extension_factory.py

@@ -71,23 +71,18 @@ def create_probe_electrode(cls, probes_metadata: list, electrode_groups_metadata
         return probe_electrode
 
     @classmethod
-    def create_ref_n_trode_id(cls, spike_n_trodes: list):
-        ref_n_trode_id = []
-        [
-            ref_n_trode_id.extend(
-                [int(spike_n_trode.ref_n_trode_id)] * len(spike_n_trode.spike_channels)
-            )
-            for spike_n_trode in spike_n_trodes
-        ]
-        return ref_n_trode_id
+    def create_ref_elect_id(cls, spike_n_trodes: list, ntrode_metadata: dict):
+        ref_elect_id = []
+        for spike_n_trode in spike_n_trodes:
+            if not int(spike_n_trode.ref_n_trode_id) == 0:
+                for ntrode in ntrode_metadata:
+                    if ntrode["ntrode_id"] == int(spike_n_trode.ref_n_trode_id):
+                        ref_elect_id.extend(
+                            [ntrode["map"][int(spike_n_trode.ref_chan)]]
+                            * len(spike_n_trode.spike_channels)
+                        )
+            else:
+                ref_elect_id.extend([-1] * len(spike_n_trode.spike_channels))
+        return ref_elect_id
+
 
-    @classmethod
-    def create_ref_chan(cls, spike_n_trodes: list):
-        ref_chan = []
-        [
-            ref_chan.extend(
-                [int(spike_n_trode.ref_chan)] * len(spike_n_trode.spike_channels)
-            )
-            for spike_n_trode in spike_n_trodes
-        ]
-        return ref_chan

rec_to_nwb/processing/nwb/components/electrodes/extension/fl_electrode_extension_manager.py

@@ -56,13 +56,12 @@ def get_fl_electrodes_extension(self, electrodes_valid_map: list) -> FlElectrode
             probes_metadata=probes_metadata,
             electrode_groups_metadata=electrode_groups_metadata
         )
-        ref_n_trode_id = FlElectrodeExtensionFactory.create_ref_n_trode_id(
-            spike_n_trodes=spike_n_trodes,
-        )
-        ref_chan = FlElectrodeExtensionFactory.create_ref_chan(
+        ref_elect_id = FlElectrodeExtensionFactory.create_ref_elect_id(
             spike_n_trodes=spike_n_trodes,
+            ntrode_metadata=ntrode_metadata
         )
 
+
         self.__validate_extension_length(
             electrodes_valid_map,
             rel['rel_x'],
@@ -74,8 +73,7 @@ def get_fl_electrodes_extension(self, electrodes_valid_map: list) -> FlElectrode
             bad_channels,
             probe_shank,
             probe_electrode,
-            ref_n_trode_id,
-            ref_chan
+            ref_elect_id
         )
 
         return FlElectrodeExtensionBuilder.build(
@@ -88,8 +86,7 @@ def get_fl_electrodes_extension(self, electrodes_valid_map: list) -> FlElectrode
             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_electrode=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, probe_electrode),
-            ref_n_trode_id=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, ref_n_trode_id),
-            ref_chan=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, ref_chan),
+            ref_elect_id=self.__filter_extension_list_with_electrodes_valid_map(electrodes_valid_map, ref_elect_id),
         )
 
     @staticmethod

rec_to_nwb/test/processing/electrodes/extension/test_electrodeExtensionInjector.py

@@ -60,8 +60,7 @@ def test_electrode_extension_injector_inject_proper_values_successfully(self):
         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_electrode = [0, 1, 2, 3]
-        mock_fl_electrode_extension.ref_n_trode_id = [0, 1, 2, 2]
-        mock_fl_electrode_extension.ref_chan = [0, 1, 2, 3]
+        mock_fl_electrode_extension.ref_elect_id = [0, 1, 2, 3]
 
         electrode_extension_injector = ElectrodeExtensionInjector()
         electrode_extension_injector.inject_extensions(
@@ -132,19 +131,13 @@ def test_electrode_extension_injector_inject_proper_values_successfully(self):
         self.assertEqual(nwb_file.electrodes[2, 17], 2)
         self.assertEqual(nwb_file.electrodes[3, 17], 3)
 
-        # metadata_extension - ref_n_trode_id
+        # metadata_extension - ref_elect_id
         self.assertIsInstance(nwb_file.electrodes[0, 18], int)
         self.assertEqual(nwb_file.electrodes[0, 18], 0)
         self.assertEqual(nwb_file.electrodes[1, 18], 1)
         self.assertEqual(nwb_file.electrodes[2, 18], 2)
-        self.assertEqual(nwb_file.electrodes[3, 18], 2)
+        self.assertEqual(nwb_file.electrodes[3, 18], 3)
 
-        # metadata_extension - ref_chan
-        self.assertIsInstance(nwb_file.electrodes[0, 19], int)
-        self.assertEqual(nwb_file.electrodes[0, 19], 0)
-        self.assertEqual(nwb_file.electrodes[1, 19], 1)
-        self.assertEqual(nwb_file.electrodes[2, 19], 2)
-        self.assertEqual(nwb_file.electrodes[3, 19], 3)
 
     @should_raise(NoneParamException)
     def test_electrodes_extension_injector_failed_injecting_due_to_None_fl_electrode_attr(self):
@@ -164,8 +157,7 @@ def test_electrodes_extension_injector_failed_injecting_due_to_None_fl_electrode
         mock_fl_electrode_extension.bad_channels = [False, False, False, False]
         mock_fl_electrode_extension.probe_shank = None
         mock_fl_electrode_extension.probe_electrode = [0, 1, 2, 3]
-        mock_fl_electrode_extension.ref_n_trode_id = [0, 1, 2, 2]
-        mock_fl_electrode_extension.ref_chan = [0, 1, 2, 3]
+        mock_fl_electrode_extension.ref_elect_id = [0, 1, 2, 3]
 
         electrode_extension_injector = ElectrodeExtensionInjector()
         electrode_extension_injector.inject_extensions(

rec_to_nwb/test/processing/electrodes/extension/test_flElectrodeExtensionManager.py

@@ -77,8 +77,7 @@ def test_electrode_extension_manager_get_fl_electrode_extension_successfully(sel
         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_electrode, [1, 0, 1, 64, 96])
-        self.assertEqual(fl_electrode_extension.ref_n_trode_id, [0, 1, 1, 1, 1])
-        self.assertEqual(fl_electrode_extension.ref_chan, [1, 2, 2, 3, 3])
+        self.assertEqual(fl_electrode_extension.ref_elect_id, [-1, 2, 2, 34, 34])
 
     @should_raise(NotCompatibleMetadata)
     def test_electrode_extension_manager_failed_due_to_not_equal_extensions_length(self):

rec_to_nwb/test/processing/res/electrodes_extensions/header.xml

@@ -189,7 +189,7 @@
    <SpikeChannel maxDisp="225" triggerOn="1" hwChan="72" thresh="10"/>
    <SpikeChannel maxDisp="225" triggerOn="1" hwChan="76" thresh="10"/>
   </SpikeNTrode>
-  <SpikeNTrode filterOn="1" lowFilter="300" lfpRefOn="0" color="#24c600" highFilter="6000" lfpFilterOn="1" moduleDataOn="0" LFPHighFilter="400" refGroup="0" LFPChan="1" refNTrodeID="1" refChan="3" groupRefOn="0" refOn="0" id="3">
+  <SpikeNTrode filterOn="1" lowFilter="300" lfpRefOn="0" color="#24c600" highFilter="6000" lfpFilterOn="1" moduleDataOn="0" LFPHighFilter="400" refGroup="0" LFPChan="1" refNTrodeID="2" refChan="2" groupRefOn="0" refOn="0" id="3">
    <SpikeChannel maxDisp="225" triggerOn="1" hwChan="98" thresh="10"/>
    <SpikeChannel maxDisp="225" triggerOn="1" hwChan="99" thresh="10"/>
    <SpikeChannel maxDisp="225" triggerOn="1" hwChan="102" thresh="10"/>