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added partial subject handling to fp and dls excitatory
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@pauladkisson
pauladkisson committed May 24, 2024
1 parent 97c8849 commit d50e75b
Showing 1 changed file with 89 additions and 28 deletions.
117 changes: 89 additions & 28 deletions src/lerner_lab_to_nwb/seiler_2024/seiler_2024_convert_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,34 +55,51 @@ def dataset_to_nwb(
verbose=verbose,
)
session_to_nwb_args_per_session = fp_session_to_nwb_args_per_session + opto_session_to_nwb_args_per_session

futures = []
with ProcessPoolExecutor(max_workers=max_workers) as executor:
for session_to_nwb_kwargs in session_to_nwb_args_per_session:
experiment_type = session_to_nwb_kwargs["experiment_type"]
experimental_group = session_to_nwb_kwargs["experimental_group"]
subject_id = session_to_nwb_kwargs["subject_id"]
start_datetime = session_to_nwb_kwargs["start_datetime"]
optogenetic_treatment = session_to_nwb_kwargs.get("optogenetic_treatment", None)
if experiment_type == "FP":
exception_file_path = (
output_dir_path
/ f"ERROR_{experiment_type}_{experimental_group}_{subject_id}_{start_datetime.isoformat().replace(':', '-')}.txt"
)
elif experiment_type == "Opto":
exception_file_path = (
output_dir_path
/ f"ERROR_{experiment_type}_{experimental_group}_{optogenetic_treatment}_{subject_id}_{start_datetime.isoformat().replace(':', '-')}.txt"
)
futures.append(
executor.submit(
safe_session_to_nwb,
session_to_nwb_kwargs=session_to_nwb_kwargs,
exception_file_path=exception_file_path,
)
)
for _ in tqdm(as_completed(futures), total=len(futures)):
pass
unique_subject_ids = set()
for session_to_nwb_kwargs in session_to_nwb_args_per_session:
subject_id = session_to_nwb_kwargs["subject_id"]
unique_subject_ids.add(subject_id)
metadata_path = Path(data_dir_path / "MouseDemographics.xlsx")
df = pd.read_excel(
metadata_path,
sheet_name="Mouse Demographics",
dtype={"Mouse ID": str},
)
df["DNL"] = df["Mouse ID"].str.contains("(DNL)", regex=False)
df["Mouse ID"] = df["Mouse ID"].str.replace("(DNL)", "")
df["Mouse ID"] = df["Mouse ID"].str.strip()
mouse_ids = set(df["Mouse ID"])
missing_subject_ids = unique_subject_ids - mouse_ids
for missing_subject_id in missing_subject_ids:
print(f"Missing metadata for {missing_subject_id}")

# futures = []
# with ProcessPoolExecutor(max_workers=max_workers) as executor:
# for session_to_nwb_kwargs in session_to_nwb_args_per_session:
# experiment_type = session_to_nwb_kwargs["experiment_type"]
# experimental_group = session_to_nwb_kwargs["experimental_group"]
# subject_id = session_to_nwb_kwargs["subject_id"]
# start_datetime = session_to_nwb_kwargs["start_datetime"]
# optogenetic_treatment = session_to_nwb_kwargs.get("optogenetic_treatment", None)
# if experiment_type == "FP":
# exception_file_path = (
# output_dir_path
# / f"ERROR_{experiment_type}_{experimental_group}_{subject_id}_{start_datetime.isoformat().replace(':', '-')}.txt"
# )
# elif experiment_type == "Opto":
# exception_file_path = (
# output_dir_path
# / f"ERROR_{experiment_type}_{experimental_group}_{optogenetic_treatment}_{subject_id}_{start_datetime.isoformat().replace(':', '-')}.txt"
# )
# futures.append(
# executor.submit(
# safe_session_to_nwb,
# session_to_nwb_kwargs=session_to_nwb_kwargs,
# exception_file_path=exception_file_path,
# )
# )
# for _ in tqdm(as_completed(futures), total=len(futures)):
# pass


def safe_session_to_nwb(*, session_to_nwb_kwargs: dict, exception_file_path: Union[Path, str]):
Expand Down Expand Up @@ -186,6 +203,12 @@ def fp_to_nwb(
"Photo_140_306-190809-121107",
"Photo_271_396-200707-125117",
}
partial_subject_ids_to_subject_id = {
"300": "300.405",
"418": "418.404",
"299": "299.405",
"276": "276.405",
}
raw_file_to_info = get_raw_info(behavior_path)

# Iterate through file system to get necessary information for converting each session
Expand Down Expand Up @@ -313,6 +336,8 @@ def fp_to_nwb(
if box_number is not None:
session_conditions["Box"] = box_number
start_datetime = datetime.strptime(f"{start_date} {start_time}", "%m/%d/%y %H:%M:%S")
if photometry_subject_id in partial_subject_ids_to_subject_id:
photometry_subject_id = partial_subject_ids_to_subject_id[photometry_subject_id]
session_to_nwb_args = dict(
data_dir_path=data_dir_path,
output_dir_path=output_dir_path,
Expand Down Expand Up @@ -385,6 +410,8 @@ def fp_to_nwb(
if box_number is not None:
session_conditions["Box"] = box_number
start_datetime = datetime.strptime(f"{start_date} {start_time}", "%m/%d/%y %H:%M:%S")
if subject_id in partial_subject_ids_to_subject_id:
subject_id = partial_subject_ids_to_subject_id[subject_id]
session_to_nwb_args = dict(
data_dir_path=data_dir_path,
output_dir_path=output_dir_path,
Expand Down Expand Up @@ -432,6 +459,35 @@ def opto_to_nwb(
list[dict]
A list of dictionaries containing the arguments for session_to_nwb for each session.
"""
partial_subject_ids_to_subject_id = {
"268": "268.476",
"266": "266.477",
"244": "244.465",
"343": "343.483",
"419": "419.404",
"245": "245.464",
"342": "342.483",
"202": "202.465",
"313": "313.403",
"418": "418.404",
"340": "340.483",
"259": "259.478",
"264": "264.478",
"421": "421.404",
"417": "417.404",
"233": "233.469",
"261": "261.478",
"265": "265.476",
"311": "311.403",
"206": "206.468",
"243": "243.468",
"263": "263.477",
"338": "338.398",
"414": "414.405",
"300": "300.405",
"299": "299.405",
"276": "276.405",
}
experiment_type = "Opto"
experimental_group_to_optogenetic_treatments = {
"DLS-Excitatory": ["ChR2", "EYFP", "ChR2Scrambled"],
Expand Down Expand Up @@ -553,6 +609,8 @@ def opto_to_nwb(
"Box": box_number,
}
start_datetime = datetime.strptime(f"{start_date} {start_time}", "%m/%d/%y %H:%M:%S")
if subject in partial_subject_ids_to_subject_id:
subject = partial_subject_ids_to_subject_id[subject]
session_to_nwb_args = dict(
data_dir_path=data_dir_path,
output_dir_path=output_dir_path,
Expand Down Expand Up @@ -613,6 +671,9 @@ def get_opto_subject_id(subject_path: Path):
"263": "263.477",
"338": "338.398",
"414": "414.405",
"300": "300.405",
"299": "299.405",
"276": "276.405",
}

# fmt: off
Expand Down

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