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Added sex map to complete missing metadata #89

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Nov 2, 2023
Merged

Added sex map to complete missing metadata #89

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214 changes: 196 additions & 18 deletions src/datta_lab_to_nwb/markowitz_gillis_nature_2023/preconversion/extract_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,195 @@
from neuroconv.utils import dict_deep_update


sex_map = {
"1520": "F",
"1515": "F",
"1521": "F",
"1519": "F",
"1524": "M",
"1525": "M",
"1529": "F",
"1527": "M",
"1528": "M",
"1546": "M",
"1544": "M",
"1561": "F",
"1562": "F",
"1778": "M",
"197": "M",
"200": "M",
"208": "F",
"209": "F",
"184": "F",
"185": "F",
"186": "F",
"189": "F",
"194": "M",
"1738": "M",
"1734": "M",
"1737": "M",
"1736": "M",
"15809": "F",
"15814": "F",
"15825": "F",
"15817": "F",
"15827": "F",
"15816": "F",
"15847": "F",
"15848": "F",
"15836": "F",
"15839": "F",
"15822": "M",
"15823": "M",
"211": "M",
"12": "M",
"10": "M",
"8": "M",
"357": "F",
"358": "F",
"355": "F",
"356": "F",
"361": "M",
"363": "M",
"414": "F",
"413": "F",
"416": "F",
"417": "F",
"368": "M",
"364": "M",
"408": "M",
"410": "M",
"429": "F",
"427": "F",
"428": "F",
"810": "M",
"136": "F",
"137": "F",
"133": "F",
"806": "M",
"807": "F",
"768": "M",
"770": "M",
"769": "M",
"767": "M",
"779": "F",
"778": "F",
"776": "F",
"127": "M",
"126": "M",
"780": "F",
"784": "F",
"781": "F",
"782": "F",
"138": "F",
"2273": "F",
"2275": "F",
"2274": "F",
"2270": "M",
"2269": "M",
"2271": "M",
"2272": "F",
"240": "F",
"239": "F",
"242": "F",
"241": "F",
"snc-acr-1": "F",
"vta-acr-1": "F",
"vta-acr-2": "F",
"snc-acr-2": "F",
"snc-acr-3": "F",
"vta-acr-3": "F",
"snc-acr-4": "M",
"snc-acr-5": "M",
"vta-acr-4": "M",
"vta-acr-5": "M",
"snc-acr-6": "M",
"snc-acr-7": "M",
"vta-acr-6": "M",
"vta-acr-7": "M",
"3172": "F",
"3169": "F",
"3173": "F",
"2865": "F",
"2860": "F",
"2859": "F",
"2863": "F",
"2864": "F",
"2862": "F",
"3158": "F",
"3155": "F",
"3157": "F",
"3214": "M",
"3216": "M",
"3439": "F",
"3440": "F",
"3441": "F",
"3442": "F",
"3474": "M",
"3472": "M",
"3473": "M",
"3475": "M",
"vta-nacc-ctrl-6": "M",
"snc-dls-ctrl-6": "F",
"dlight-chrimson-1": "F",
"dlight-chrimson-2": "F",
"dlight-chrimson-3": "M",
"dlight-chrimson-4": "M",
"dlight-chrimson-5": "F",
"dlight-chrimson-6": "M",
"dlight-chrimson-7": "M",
"dlight-chrimson-8": "M",
"dlight-chrimson-9": "M",
"dls-ai32jr-1": "M",
"dls-ai32jr-2": "M",
"dls-ai32jr-3": "M",
"dls-ai32jr-4": "F",
"dls-ai32jr-5": "F",
"dms-ai32-1": "M",
"dms-ai32-2": "M",
"dms-ai32-3": "F",
"dms-ai32-4": "F",
"dms-ai32-5": "F",
"dms-ai32-6": "M",
"dms-ai32-7": "M",
"dms-ai32-8": "M",
"dms-ai32-9": "M",
"dms-ai32-10": "F",
"dms-ai32-11": "F",
"snc-dls-ctrl-7": "M",
"vta-nacc-ai32-18": "M",
"vta-nacc-ai32-19": "M",
"vta-nacc-ai32-20": "F",
"dls-dlight-1": "M",
"dls-dlight-2": "M",
"dls-dlight-3": "M",
"dls-dlight-4": "M",
"dls-dlight-5": "M",
"dls-dlight-6": "M",
"dls-dlight-7": "M",
"dls-dlight-8": "M",
"dls-dlight-9": "M",
"dls-dlight-10": "M",
"dls-dlight-11": "M",
"dls-dlight-12": "M",
"dls-dlight-13": "M",
"dms-dlight-1": "M",
"dms-dlight-2": "M",
"dms-dlight-3": "M",
"dms-dlight-4": "M",
"dms-dlight-5": "F",
"dms-dlight-6": "F",
"dms-dlight-7": "M",
"dms-dlight-8": "M",
"dms-dlight-9": "M",
"dms-dlight-10": "M",
"dms-dlight-11": "M",
"dms-dlight-12": "M",
"dms-dlight-13": "M",
"dms-dlight-14": "M",
}


def extract_photometry_metadata(
data_path: str,
example_uuids: str = None,
Expand Down Expand Up @@ -89,7 +278,7 @@ def extract_photometry_metadata(
for mouse_id in tqdm(subject_ids, desc="Extracting photometry subject metadata"):
extract_subject_metadata(subject_columns, photometry_data_path, subject_metadata, mouse_id)
subject_metadata[mouse_id]["photometry_area"] = subject_metadata[mouse_id].pop("area")
subject_metadata[mouse_id]["sex"] = "U"
subject_metadata[mouse_id]["sex"] = sex_map[mouse_id]

return session_metadata, subject_metadata

Expand Down Expand Up @@ -131,7 +320,6 @@ def extract_reinforcement_metadata(
)
subject_columns = (
"mouse_id",
"sex",
"opsin",
"genotype",
"area",
Expand Down Expand Up @@ -174,12 +362,7 @@ def extract_reinforcement_metadata(
for mouse_id in tqdm(subject_ids, desc="Extracting reinforcement subject metadata"):
extract_subject_metadata(subject_columns, reinforcement_data_path, subject_metadata, mouse_id)
subject_metadata[mouse_id]["optogenetic_area"] = subject_metadata[mouse_id].pop("area")
if subject_metadata[mouse_id]["sex"] == "male":
subject_metadata[mouse_id]["sex"] = "M"
elif subject_metadata[mouse_id]["sex"] == "female":
subject_metadata[mouse_id]["sex"] = "F"
else:
subject_metadata[mouse_id]["sex"] = "U"
subject_metadata[mouse_id]["sex"] = sex_map[mouse_id]

return session_metadata, subject_metadata

Expand Down Expand Up @@ -246,7 +429,7 @@ def extract_velocity_modulation_metadata(
for mouse_id in tqdm(subject_ids, desc="Extracting reinforcement subject metadata"):
extract_subject_metadata(subject_columns, velocity_data_path, subject_metadata, mouse_id)
subject_metadata[mouse_id]["optogenetic_area"] = "snc (axon)" # from paper
subject_metadata[mouse_id]["sex"] = "U"
subject_metadata[mouse_id]["sex"] = sex_map[mouse_id]

return session_metadata, subject_metadata

Expand Down Expand Up @@ -308,7 +491,7 @@ def extract_keypoint_metadata(data_path: str):
genotype="dls-dlight",
opsin="n/a",
photometry_area="dls",
sex="U",
sex=sex_map[subject],
)
return session_metadata, subject_metadata

Expand All @@ -333,14 +516,9 @@ def _resolve_duplicates(resolved_dict, ids1, dict1, ids2, dict2):
resolved_dict[id1] = {}
for key1 in dict1[id1].keys():
if key1 in dict2[id1].keys():
try:
assert (
dict1[id1][key1] == dict2[id1][key1]
), f"dict1 and dict2 don't match (dict1[{id1}][{key1}]: {dict1[id1][key1]}, dict2[{id1}][{key1}]: {dict2[id1][key1]})"
except AssertionError:
assert key1 == "sex"
if dict1[id1][key1] == "U":
dict1[id1][key1] = dict2[id1][key1]
assert (
dict1[id1][key1] == dict2[id1][key1]
), f"dict1 and dict2 don't match (dict1[{id1}][{key1}]: {dict1[id1][key1]}, dict2[{id1}][{key1}]: {dict2[id1][key1]})"
resolved_dict[id1][key1] = dict1[id1][key1]


Expand Down