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geci_loader.py

@@ -4,22 +4,53 @@ import argh
 
 
 # mouse:int = 0, 1, 2, 3, 4
-def loader(mouse:int = 0, fpath:str = "/data_1/hendrik/gevi") -> None:
+def loader(mouse: int = 0, fpath: str = "/data_1/hendrik/gevi") -> None:
 
     mouse_name = [
-        'M_Sert_Cre_41',
+        "M_Sert_Cre_41",
-        'M_Sert_Cre_42',
+        "M_Sert_Cre_42",
-        'M_Sert_Cre_45',
+        "M_Sert_Cre_45",
-        'M_Sert_Cre_46',
+        "M_Sert_Cre_46",
-        'M_Sert_Cre_49'
+        "M_Sert_Cre_49",
     ]
 
     n_tris = [
-        [15, 15, 30, 30, 30, 30,],  # 0 in cond 7
+        [
-        [15, 15, 30, 30, 30, 30,],  # 0 in cond 7
+            15,
-        [15, 15, 30, 30, 30, 30,],  # 0 in cond 7
+            15,
-        [20, 40, 20, 20,],  # 0, 0, 0 in cond 5-7
+            30,
-        [20, 40, 20, 20,],  # 0, 0, 0 in cond 5-7
+            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
     ]
 
     # 41, 42, 45, 46, 49:
@@ -32,11 +63,32 @@ def loader(mouse:int = 0, fpath:str = "/data_1/hendrik/gevi") -> None:
     #               "7": "grating 3s"
 
     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",
-        ['control', 'visual control', 'op20 50 5', 'op20 100 5', 'op20 50 grat', 'op20 100 grat'],
+            "visual control",
-        ['control', 'visual control', 'op20 50 5', 'op20 100 5'],
+            "op20 50 5",
-        ['control', 'visual control', 'op20 50 5', 'op20 100 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"],
     ]
 
     n_exp = len(n_tris[mouse])
@@ -45,9 +97,11 @@ def loader(mouse:int = 0, fpath:str = "/data_1/hendrik/gevi") -> None:
         n_tri = n_tris[mouse][i_exp]
         for i_tri in range(n_tri):
 
-            experiment_name: str = f"Exp{i_exp+1:03d}_Trial{i_tri+1:03d}"
+            experiment_name: str = f"Exp{i_exp + 1:03d}_Trial{i_tri + 1:03d}"
             tmp_fname = os.path.join(
-                fpath, "output_" + mouse_name[mouse], experiment_name + "_acceptor_donor.npz"
+                fpath,
+                "output_" + mouse_name[mouse],
+                experiment_name + "_acceptor_donor.npz",
             )
             print(f'Processing file "{tmp_fname}"...')
             tmp = np.load(tmp_fname)
@@ -67,5 +121,6 @@ def loader(mouse:int = 0, fpath:str = "/data_1/hendrik/gevi") -> None:
     np.save("lsq_" + mouse_name[mouse], light_signal)
     np.save("msq_" + mouse_name[mouse], mask)
 
+
 if __name__ == "__main__":
     argh.dispatch_command(loader)

geci_plot.py

@@ -79,7 +79,7 @@ def plot(
     trials = get_trials(raw_data_path, experiment).numpy()
     assert trials.shape[0] > 0
 
-    with open(os.path.join(raw_data_path, f"Exp{experiment:03d}_Trial{trials[0]:03d}_Part001_meta.txt"), "r") as file:
+    with open(f"meta_{config["mouse_identifier"]}_exp{experiment:03d}.json", "r") as file:
         metadata = json.loads(jsmin(file.read()))
 
     experiment_names = metadata['sessionMetaData']['experimentNames'][str(experiment)]

stage_5_convert_metadata.py

@@ -0,0 +1,52 @@
+import json
+import os
+import argh
+from jsmin import jsmin  # type:ignore
+from functions.get_trials import get_trials
+from functions.get_experiments import get_experiments
+
+
+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()
+
+    experiments = get_experiments(raw_data_path).numpy()
+
+    for experiment in experiments:
+
+        trials = get_trials(raw_data_path, experiment).numpy()
+        assert trials.shape[0] > 0
+
+        with open(
+            os.path.join(
+                raw_data_path,
+                f"Exp{experiment:03d}_Trial{trials[0]:03d}_Part001_meta.txt",
+            ),
+            "r",
+        ) as file:
+            metadata = json.loads(jsmin(file.read()))
+
+        filename_out: str = f"meta_{config["mouse_identifier"]}_exp{experiment:03d}.json"
+
+        with open(filename_out, 'w') as file:
+            json.dump(metadata, file)
+
+
+if __name__ == "__main__":
+    argh.dispatch_command(converter)