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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)