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Expose flags to include or not data streams #14

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merged 2 commits into from
Nov 11, 2024
Merged

Expose flags to include or not data streams #14

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2404b34
add flags to include datastream
alessandratrapani Nov 1, 2024
c53070c
improve printed messages
alessandratrapani Nov 11, 2024
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67 changes: 45 additions & 22 deletions src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_session.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ def get_miniscope_folder_path(folder_path: Union[str, Path]):
miniscope_name = general_metadata["miniscopes"][0]
return folder_path / miniscope_name.replace(" ", "_")
else:
print("No Miniscope data found at {}".format(folder_path))
print(f"No Miniscope data found at {folder_path}")
return None


Expand All @@ -35,8 +35,13 @@ def session_to_nwb(
time_str: str,
stub_test: bool = False,
verbose: bool = True,
include_imaging: bool = True,
include_freezing_behavior: bool = True,
include_sleep_classification: bool = True,
include_behavioral_video: bool = True,
include_eeg_emg_signals: bool = True,
):
print("Converting session {}".format(session_id))
print(f"Converting session {session_id}")
if verbose:
start = time.time()

Expand All @@ -56,70 +61,88 @@ def session_to_nwb(
experiment_dir_path = data_dir_path / "Ca_EEG_Experiment" / subject_id / (subject_id + "_Offline") / offline_day
else:
experiment_dir_path = data_dir_path / "Ca_EEG_Experiment" / subject_id / (subject_id + "_Sessions") / session_id
include_eeg_emg_signals = False
include_sleep_classification = False

# Add Imaging
folder_path = experiment_dir_path / date_str / time_str
miniscope_folder_path = get_miniscope_folder_path(folder_path)
if miniscope_folder_path is not None:
if miniscope_folder_path is not None and include_imaging:
source_data.update(dict(MiniscopeImaging=dict(folder_path=miniscope_folder_path)))
conversion_options.update(dict(MiniscopeImaging=dict(stub_test=stub_test)))
elif verbose and not include_imaging:
print(f"Miniscope data will not be included for session {session_id}")
elif verbose and miniscope_folder_path is None:
print(f"No Miniscope data found at {miniscope_folder_path}")

# Add Segmentation
minian_folder_path = data_dir_path / "Ca_EEG_Calcium" / subject_id / session_id / "minian"
if minian_folder_path.is_dir():
if minian_folder_path.is_dir() and include_imaging:
source_data.update(dict(MinianSegmentation=dict(folder_path=minian_folder_path)))
conversion_options.update(dict(MinianSegmentation=dict(stub_test=stub_test)))
elif verbose:
print("No Minian data found at {}".format(minian_folder_path))
elif verbose and not include_imaging:
print(f"Minian data will not be included for session {session_id}")
elif verbose and not minian_folder_path.is_dir():
print(f"No Minian data found at {minian_folder_path}")

# Add Motion Correction
motion_corrected_video = minian_folder_path / "minian_mc.mp4"
if motion_corrected_video.is_file():
if motion_corrected_video.is_file() and include_imaging:
source_data.update(
dict(MinianMotionCorrection=dict(folder_path=minian_folder_path, video_file_path=motion_corrected_video))
)
conversion_options.update(dict(MinianMotionCorrection=dict(stub_test=stub_test)))
elif verbose:
print("No motion corrected data found at {}".format(motion_corrected_video))
elif verbose and not include_imaging:
print(f"Minian Motion Correction data will not be included for session {session_id}")
elif verbose and not motion_corrected_video.is_file():
print(f"No motion corrected data found at {motion_corrected_video}")

# Add Behavioral Video
video_file_path = experiment_dir_path / (session_id + ".wmv")
if video_file_path.is_file():
if video_file_path.is_file() and include_behavioral_video:
source_data.update(dict(Video=dict(file_paths=[video_file_path])))
conversion_options.update(dict(Video=dict(stub_test=stub_test)))
elif verbose:
print("No behavioral video found at {}".format(video_file_path))
elif verbose and not include_behavioral_video:
print(f"The behavioral video will not be included for session {session_id}")
elif verbose and not video_file_path.is_file():
print(f"No behavioral video found at {video_file_path}")

# Add Freezing Analysis output
freezing_output_file_path = experiment_dir_path / (session_id + "_FreezingOutput.csv")
if freezing_output_file_path.is_file():
if freezing_output_file_path.is_file() and include_freezing_behavior:
source_data.update(
dict(FreezingBehavior=dict(file_path=freezing_output_file_path, video_sampling_frequency=30.0))
)
elif verbose:
print("No freezing output csv file found at {}".format(freezing_output_file_path))
elif verbose and not include_freezing_behavior:
print(f"The Freezing Analysis output will not be included for session {session_id}")
elif verbose and not freezing_output_file_path.is_file():
print(f"No freezing output csv file found at {freezing_output_file_path}")

# Add EEG, EMG, Temperature and Activity signals
# TODO discuss how to slice this data
datetime_obj = datetime.strptime(date_str, "%Y_%m_%d")
reformatted_date_str = datetime_obj.strftime("_%m%d%y")
edf_file_path = data_dir_path / "Ca_EEG_EDF" / (subject_id + "_EDF") / (subject_id + reformatted_date_str + ".edf")
if edf_file_path.is_file():
if edf_file_path.is_file() and include_eeg_emg_signals:
source_data.update(dict(EDFSignals=dict(file_path=edf_file_path)))
conversion_options.update(dict(EDFSignals=dict(stub_test=stub_test)))
elif verbose:
print("No .edf file found at {}".format(edf_file_path))
elif verbose and not include_eeg_emg_signals:
print(f"The EEG, EMG, Temperature and Activity signals will not be included for session {session_id}")
elif verbose and not edf_file_path.is_file():
print(f"No .edf file found at {edf_file_path}")

# Add Sleep Classification output
sleep_classification_file_path = (
data_dir_path / "Ca_EEG_Sleep" / subject_id / "AlignedSleep" / (session_id + "_AlignedSleep.csv")
)
if sleep_classification_file_path.is_file():
if sleep_classification_file_path.is_file() and include_sleep_classification:
source_data.update(
dict(SleepClassification=dict(file_path=sleep_classification_file_path, video_sampling_frequency=30.0))
)
elif verbose:
print("No sleep classification output csv file found at {}".format(sleep_classification_file_path))
elif verbose and not include_sleep_classification:
print(f"The Sleep Classification output will not be included for session {session_id}")
elif verbose and not sleep_classification_file_path.is_file():
print(f"No sleep classification output csv file found at {sleep_classification_file_path}")

converter = Zaki2024NWBConverter(source_data=source_data)

Expand Down Expand Up @@ -159,7 +182,7 @@ def session_to_nwb(
# Parameters for conversion
data_dir_path = Path("D:/")
subject_id = "Ca_EEG3-4"
task = "OfflineDay1Session1"
task = "NeutralExposure"
session_id = subject_id + "_" + task
output_dir_path = Path("D:/cai_lab_conversion_nwb/")
stub_test = True
Expand Down
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