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geci_loader.py

@@ -1,68 +1,45 @@
 import numpy as np
 import os
+import json
+from jsmin import jsmin  # type:ignore
 import argh
+from functions.get_trials import get_trials
+from functions.get_experiments import get_experiments
 
 
-# mouse:int = 0, 1, 2, 3, 4
+def loader(
-def loader(mouse: int = 0, fpath: str = "/data_1/hendrik/gevi") -> None:
+    filename: str = "config_M_Sert_Cre_49.json", fpath: str = "/data_1/hendrik/gevi"
+) -> None:
 
-    mouse_name = [
+    if os.path.isfile(filename) is False:
-        "M_Sert_Cre_41",
+        print(f"{filename} is missing")
-        "M_Sert_Cre_42",
+        exit()
-        "M_Sert_Cre_45",
-        "M_Sert_Cre_46",
-        "M_Sert_Cre_49",
-    ]
 
-    n_tris = [
+    with open(filename, "r") as file:
-        [
+        config = json.loads(jsmin(file.read()))
-            15,
-            15,
-            30,
-            30,
-            30,
-            30,
-        ],  # 0 in cond 7
-        [
-            15,
-            15,
-            30,
-            30,
-            30,
-            30,
-        ],  # 0 in cond 7
-        [
-            15,
-            15,
-            30,
-            30,
-            30,
-            30,
-        ],  # 0 in cond 7
-        [
-            20,
-            40,
-            20,
-            20,
-        ],  # 0, 0, 0 in cond 5-7
-        [
-            20,
-            40,
-            20,
-            20,
-        ],  # 0, 0, 0 in cond 5-7
-    ]
 
-    n_exp = len(n_tris[mouse])
+    raw_data_path: str = os.path.join(
+        config["basic_path"],
+        config["recoding_data"],
+        config["mouse_identifier"],
+        config["raw_path"],
+    )
 
-    for i_exp in range(n_exp):
+    experiments = get_experiments(raw_data_path).numpy()
-        n_tri = n_tris[mouse][i_exp]
+    n_exp = experiments.shape[0]
-        for i_tri in range(n_tri):
 
-            experiment_name: str = f"Exp{i_exp + 1:03d}_Trial{i_tri + 1:03d}"
+    for i_exp in range(0, n_exp):
+        trials = get_trials(raw_data_path, experiments[i_exp]).numpy()
+        n_tri = trials.shape[0]
+
+        for i_tri in range(0, n_tri):
+
+            experiment_name: str = (
+                f"Exp{experiments[i_exp]:03d}_Trial{trials[i_tri]:03d}"
+            )
             tmp_fname = os.path.join(
                 fpath,
-                "output_" + mouse_name[mouse],
+                "output_" + config["mouse_identifier"],
                 experiment_name + "_acceptor_donor.npz",
             )
             print(f'Processing file "{tmp_fname}"...')
@@ -76,12 +53,14 @@ def loader(mouse: int = 0, fpath: str = "/data_1/hendrik/gevi") -> None:
                 new_shape = [n_exp, *tmp_data_sequence.shape]
                 data_sequence = np.zeros(new_shape)
                 light_signal = np.zeros(new_shape)
+
+            # Here you might want to use the exp fit and removal...
             data_sequence[i_exp] += tmp_data_sequence / n_tri
             light_signal[i_exp] += tmp_light_signal / n_tri
 
-    np.save("dsq_" + mouse_name[mouse], data_sequence)
+    np.save("dsq_" + config["mouse_identifier"], data_sequence)
-    np.save("lsq_" + mouse_name[mouse], light_signal)
+    np.save("lsq_" + config["mouse_identifier"], light_signal)
-    np.save("msq_" + mouse_name[mouse], mask)
+    np.save("msq_" + config["mouse_identifier"], mask)
 
 
 if __name__ == "__main__":

geci_plot.py

@@ -27,35 +27,6 @@ def plot(
     fit_power: bool = False,  # True => -ax^b ; False => exp(-b)
 ) -> None:
 
-    # lbs = [
-    #     [
-    #         "control",
-    #         "visual control",
-    #         "op20 50 5",
-    #         "op20 100 5",
-    #         "op20 50 grat",
-    #         "op20 100 grat",
-    #     ],
-    #     [
-    #         "control",
-    #         "visual control",
-    #         "op20 50 5",
-    #         "op20 100 5",
-    #         "op20 50 grat",
-    #         "op20 100 grat",
-    #     ],
-    #     [
-    #         "control",
-    #         "visual control",
-    #         "op20 50 5",
-    #         "op20 100 5",
-    #         "op20 50 grat",
-    #         "op20 100 grat",
-    #     ],
-    #     ["control", "visual control", "op20 50 5", "op20 100 5"],
-    #     ["control", "visual control", "op20 50 5", "op20 100 5"],
-    # ]
-
     if os.path.isfile(filename) is False:
         print(f"{filename} is missing")
         exit()