Fix order of raw data to electrode table mapping (#178)

* Fix order of raw data to electrode table mapping
* Update ephys tests

Author: calderast

src/jdb_to_nwb/convert_raw_ephys.py

@@ -1152,9 +1152,16 @@ def add_raw_ephys(
     logger.debug(f"There are {len(nwbfile.electrodes)} electrodes in the nwbfile "
                  "(same as number of channels in traces_as_iterator)")
 
+    # Get electrodes table (added to nwb in `add_electrode_data_berke_probe`)
+    electrodes = nwbfile.electrodes
+    # Get the mapping of electrode to channel number (0-indexed)
+    electrode_table_row_to_raw_data_row = electrodes['intan_channel_number'].data[:]
+    # Get the reverse mapping of row in the raw ElectricalSeries to row in the electrode table
+    raw_data_row_to_electrode_table_row = np.argsort(electrode_table_row_to_raw_data_row)
+
     # Create the electrode table region encompassing all electrodes
     electrode_table_region = nwbfile.create_electrode_table_region(
-        region=list(range(len(nwbfile.electrodes))),
+        region=list(raw_data_row_to_electrode_table_row),
         description="Electrodes used in raw ElectricalSeries recording",
     )
 

tests/test_convert_raw_ephys.py

@@ -81,9 +81,9 @@ def test_add_electrode_data_berke_probe(dummy_logger):
     metadata["ephys"] = {}
     metadata["ephys"]["impedance_file_path"] = "tests/test_data/processed_ephys/impedance.csv"
     metadata["ephys"]["electrodes_location"] = "Hippocampus CA1"
-    metadata["ephys"]["targeted_x"] = 4.5  # AP in mm
-    metadata["ephys"]["targeted_y"] = 2.2  # ML in mm
-    metadata["ephys"]["targeted_z"] = 2.0  # DV in mm
+    metadata["ephys"]["targeted_x"] = 4.5   # AP in mm
+    metadata["ephys"]["targeted_y"] = 2.2   # ML in mm
+    metadata["ephys"]["targeted_z"] = -2.0  # DV in mm
     metadata["ephys"]["probe"] = ["256-ch Silicon Probe, 3mm length, 66um pitch"]
     metadata["ephys"]["plug_order"] = "chip_first"
 
@@ -146,7 +146,7 @@ def test_add_electrode_data_berke_probe(dummy_logger):
         assert egroup.location == "Hippocampus CA1"
         assert egroup.targeted_x == 4.5
         assert egroup.targeted_y == 2.2
-        assert egroup.targeted_z == 2.0
+        assert egroup.targeted_z == -2.0
         assert egroup.device is probe
 
         # Electrode group description should be "Electrodes on shank {shank_index}"
@@ -250,10 +250,25 @@ def test_add_raw_ephys(dummy_logger):
     metadata["ephys"]["openephys_folder_path"] = "tests/test_data/raw_ephys/2022-07-25_15-30-00"
     metadata["ephys"]["impedance_file_path"] = "tests/test_data/processed_ephys/impedance.csv"
     metadata["ephys"]["electrodes_location"] = "Hippocampus CA1"
-    metadata["ephys"]["targeted_x"] = 4.5  # AP in mm
-    metadata["ephys"]["targeted_y"] = 2.2  # ML in mm
-    metadata["ephys"]["targeted_z"] = 2.0  # DV in mm
+    metadata["ephys"]["targeted_x"] = 4.5   # AP in mm
+    metadata["ephys"]["targeted_y"] = 2.2   # ML in mm
+    metadata["ephys"]["targeted_z"] = -2.0  # DV in mm
     metadata["ephys"]["probe"] = ["256-ch Silicon Probe, 3mm length, 66um pitch"]
+    
+    # Mapping from probe electrode to channel number
+    intan_channel_numbers = np.array([
+        191,190,189,188,187,186,185,184,183,182,181,180,179,178,177,176,175,174,173,172,171,170,169,128,129,130,
+        131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,
+        157,158,159,160,161,162,163,164,165,166,167,168,192,193,194,195,196,197,198,199,200,201,202,203,204,205,
+        206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,
+        232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,64,65,66,
+        67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,
+        101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,
+        127,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,
+        56,57,58,59,60,61,62,63,22,21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4,3,2,1,0
+    ])
+    # Reverse mapping from channel (aka row in ElectricalSeries) to row in electrode table
+    expected_electrode_data_mapping = list(np.argsort(intan_channel_numbers))
 
     ephys_data_dict = add_raw_ephys(nwbfile=nwbfile, metadata=metadata, logger=dummy_logger)
 
@@ -267,7 +282,7 @@ def test_add_raw_ephys(dummy_logger):
     )
     assert es.data.maxshape == (3_000, 256)
     assert es.data.dtype == np.int16
-    assert es.electrodes.data == list(range(256))
+    assert es.electrodes.data == expected_electrode_data_mapping
     assert es.timestamps.shape == (3_000,)
     assert es.conversion == 0.19499999284744263 * 1e-6
 
@@ -354,9 +369,9 @@ def test_add_raw_ephys_complete_data():
     metadata["ephys"]["openephys_folder_path"] = "/Users/rly/Documents/NWB/berke-lab-to-nwb/data/2022-07-25_15-30-00"
     metadata["ephys"]["impedance_file_path"] = "tests/test_data/processed_ephys/impedance.csv"
     metadata["ephys"]["electrodes_location"] = "Hippocampus CA1"
-    metadata["ephys"]["targeted_x"] = 4.5  # AP in mm
-    metadata["ephys"]["targeted_y"] = 2.2  # ML in mm
-    metadata["ephys"]["targeted_z"] = 2.0  # DV in mm
+    metadata["ephys"]["targeted_x"] = 4.5   # AP in mm
+    metadata["ephys"]["targeted_y"] = 2.2   # ML in mm
+    metadata["ephys"]["targeted_z"] = -2.0  # DV in mm
     metadata["ephys"]["probe"] = ["256-ch Silicon Probe, 3mm length, 66um pitch"]
 
     ephys_data_dict = add_raw_ephys(nwbfile=nwbfile, metadata=metadata)