Update units.raw_structure description and remove raw_location

AllenInstitute · May 29, 2024 · 3ba11c6 · 3ba11c6
1 parent 02f9676
commit 3ba11c6
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Showing 2 changed files with 9 additions and 11 deletions.
diff --git a/src/npc_sessions/sessions.py b/src/npc_sessions/sessions.py
@@ -1323,15 +1323,13 @@ def electrodes(self) -> pynwb.core.DynamicTable:
                 "z",
             ) + column_names
             ccf_df = utils.get_tissuecyte_electrodes_table(self.id)
-            if "raw_location" in ccf_df:
+            if "raw_structure" in ccf_df:
                 column_names = column_names + (
-                    "raw_location",
                     "raw_structure",
                 )
         column_description = {
             "structure": "acronym for the Allen CCF structure that the electrode recorded from - less-specific than `location`",
-            "raw_location": "raw non-processed (for white matter areas (lowercase), will be different than location) acronym for the Allen CCF strucutre that the electrode recorded from",
-            "raw_structure": "raw non-processed (for white matter areas (lowercase), will be different than structure) acronym for the Allen CCF strucutre that the electrode recorded from - less specific than location",
+            "raw_structure": "same as `structure`, except white matter areas (lowercase names) have not been reassigned",
             "x": "x coordinate in the Allen CCF, +x is posterior",
             "y": "y coordinate in the Allen CCF, +y is inferior",
             "z": "z coordinate in the Allen CCF, +z is right",
@@ -1356,7 +1354,7 @@ def electrodes(self) -> pynwb.core.DynamicTable:
             group = self.electrode_groups[f"probe{probe_letter}"]
             for channel_label, (x, y) in channel_pos_xy.items():
                 channel_idx = int(channel_label.strip("CH"))
-                kwargs: dict[str, str | float] = {
+                row_kwargs: dict[str, str | float] = {
                     "group": group,
                     "group_name": group.name,
                     "rel_x": x,
@@ -1373,13 +1371,14 @@ def electrodes(self) -> pynwb.core.DynamicTable:
                         )
                     ).any()
                 ):
-                    kwargs |= (
-                        annotated_probes.query(f"channel == {channel_idx}")
+                    row_kwargs |= (
+                        annotated_probes
+                        .query(f"channel == {channel_idx}")
                         .iloc[0]
                         .to_dict()
                     )
                 electrodes.add_row(
-                    **kwargs,
+                    **row_kwargs,
                 )
 
         return electrodes

diff --git a/src/npc_sessions/utils/electrodes.py b/src/npc_sessions/utils/electrodes.py
@@ -20,7 +20,7 @@ def get_tissuecyte_electrodes_table(
     >>> df = get_tissuecyte_electrodes_table('626791_2022-08-16')
     >>> df.columns
     Index(['group_name', 'channel', 'location', 'structure', 'x', 'y', 'z',
-           'raw_location', 'raw_structure'],
+           'raw_structure'],
           dtype='object')
     """
     electrode_files = npc_lims.get_tissuecyte_annotation_files_from_s3(session)
@@ -62,10 +62,9 @@ def get_tissuecyte_electrodes_table(
         ]
         + (
             [
-                "raw_location",
                 "raw_structure",
             ]
-            if "raw_location" in session_electrodes.columns
+            if "raw_structure" in session_electrodes.columns
             else []
         )
     ]