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stage_6_convert_roi.py
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stage_6_convert_roi.py
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import json
import os
import argh
from jsmin import jsmin # type:ignore
import numpy as np
import h5py
def converter(filename: str = "config_M_Sert_Cre_49.json") -> None:
if os.path.isfile(filename) is False:
print(f"{filename} is missing")
exit()
with open(filename, "r") as file:
config = json.loads(jsmin(file.read()))
raw_data_path: str = os.path.join(
config["basic_path"],
config["recoding_data"],
config["mouse_identifier"],
config["raw_path"],
)
if os.path.isdir(raw_data_path) is False:
print(f"ERROR: could not find raw directory {raw_data_path}!!!!")
exit()
roi_path: str = os.path.join(
config["basic_path"], config["recoding_data"], config["mouse_identifier"]
)
roi_control_mat: str = os.path.join(roi_path, "ROI_control.mat")
roi_sdarken_mat: str = os.path.join(roi_path, "ROI_sDarken.mat")
if os.path.isfile(roi_control_mat):
hf = h5py.File(roi_control_mat, "r")
roi_control = np.array(hf["roi"]).T
filename_out: str = f"roi_control{config["mouse_identifier"]}.npy"
np.save(filename_out, roi_control)
else:
print("ROI Control not found")
if os.path.isfile(roi_sdarken_mat):
hf = h5py.File(roi_sdarken_mat, "r")
roi_darken = np.array(hf["roi"]).T
filename_out = f"roi_sdarken{config["mouse_identifier"]}.npy"
np.save(filename_out, roi_darken)
else:
print("ROI sDarken not found")
if __name__ == "__main__":
argh.dispatch_command(converter)