celldetective 1.4.2__py3-none-any.whl → 1.5.0b0__py3-none-any.whl

celldetective/scripts/train_signal_model.py

@@ -9,71 +9,113 @@ from glob import glob
 import numpy as np
 from art import tprint
 from celldetective.signals import SignalDetectionModel
-from celldetective.io import locate_signal_model
+from celldetective.utils.model_loaders import locate_signal_model
 
 tprint("Train")
 
-parser = argparse.ArgumentParser(description="Train a signal model from instructions.",
-								formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-parser.add_argument('-c',"--config", required=True,help="Training instructions")
+parser = argparse.ArgumentParser(
+    description="Train a signal model from instructions.",
+    formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+)
+parser.add_argument("-c", "--config", required=True, help="Training instructions")
 
 args = parser.parse_args()
 process_arguments = vars(args)
-instructions = str(process_arguments['config'])
+instructions = str(process_arguments["config"])
 
 if os.path.exists(instructions):
-	with open(instructions, 'r') as f:
-		threshold_instructions = json.load(f)
-		threshold_instructions.update({'n_channels': len(threshold_instructions['channel_option'])})
-		if threshold_instructions['augmentation_factor']>1.0:
-			threshold_instructions.update({'augment': True})
-		else:
-			threshold_instructions.update({'augment': False})
-		threshold_instructions.update({'test_split': 0.})
+    with open(instructions, "r") as f:
+        threshold_instructions = json.load(f)
+        threshold_instructions.update(
+            {"n_channels": len(threshold_instructions["channel_option"])}
+        )
+        if threshold_instructions["augmentation_factor"] > 1.0:
+            threshold_instructions.update({"augment": True})
+        else:
+            threshold_instructions.update({"augment": False})
+        threshold_instructions.update({"test_split": 0.0})
 else:
-	print('The configuration path is not valid. Abort.')
-	os.abort()
+    print("The configuration path is not valid. Abort.")
+    os.abort()
 
 all_classes = []
 for d in threshold_instructions["ds"]:
-	datasets = glob(d+os.sep+"*.npy")
-	for dd in datasets:
-		data = np.load(dd, allow_pickle=True)
-		classes = np.unique([ddd["class"] for ddd in data])
-		all_classes.extend(classes)
+    datasets = glob(d + os.sep + "*.npy")
+    for dd in datasets:
+        data = np.load(dd, allow_pickle=True)
+        classes = np.unique([ddd["class"] for ddd in data])
+        all_classes.extend(classes)
 all_classes = np.unique(all_classes)
-print(all_classes,len(all_classes))
+print(all_classes, len(all_classes))
 
 n_classes = len(all_classes)
 
-model_params = {k:threshold_instructions[k] for k in ('pretrained', 'model_signal_length', 'channel_option', 'n_channels', 'label') if k in threshold_instructions}
-model_params.update({'n_classes': n_classes})
+model_params = {
+    k: threshold_instructions[k]
+    for k in (
+        "pretrained",
+        "model_signal_length",
+        "channel_option",
+        "n_channels",
+        "label",
+    )
+    if k in threshold_instructions
+}
+model_params.update({"n_classes": n_classes})
 
-train_params = {k:threshold_instructions[k] for k in ('model_name', 'target_directory', 'channel_option','recompile_pretrained', 'test_split', 'augment', 'epochs', 'learning_rate', 'batch_size', 'validation_split','normalization_percentile','normalization_values','normalization_clip') if k in threshold_instructions}
+train_params = {
+    k: threshold_instructions[k]
+    for k in (
+        "model_name",
+        "target_directory",
+        "channel_option",
+        "recompile_pretrained",
+        "test_split",
+        "augment",
+        "epochs",
+        "learning_rate",
+        "batch_size",
+        "validation_split",
+        "normalization_percentile",
+        "normalization_values",
+        "normalization_clip",
+    )
+    if k in threshold_instructions
+}
 
-print(f'model params {model_params}')
-print(f'train params {train_params}')
+print(f"model params {model_params}")
+print(f"train params {train_params}")
 
 model = SignalDetectionModel(**model_params)
-print(threshold_instructions['ds'])
-model.fit_from_directory(threshold_instructions['ds'], **train_params)
+print(threshold_instructions["ds"])
+model.fit_from_directory(threshold_instructions["ds"], **train_params)
 
 
 # if neighborhood of interest in training instructions, write it in config!
-if 'neighborhood_of_interest' in threshold_instructions:
-	if threshold_instructions['neighborhood_of_interest'] is not None:
-		
-		model_path = locate_signal_model(threshold_instructions['model_name'], path=None, pairs=True)
-		complete_path = model_path #+model
-		complete_path = rf"{complete_path}"
-		model_config_path = os.sep.join([complete_path,'config_input.json'])
-		model_config_path = rf"{model_config_path}"
-
-		f = open(model_config_path)
-		config = json.load(f)
-		config.update({'neighborhood_of_interest': threshold_instructions['neighborhood_of_interest'], 'reference_population': threshold_instructions['reference_population'], 'neighbor_population': threshold_instructions['neighbor_population']})
-		json_string = json.dumps(config)
-		with open(model_config_path, 'w') as outfile:
-			outfile.write(json_string)
-
-print('Done.')
+if "neighborhood_of_interest" in threshold_instructions:
+    if threshold_instructions["neighborhood_of_interest"] is not None:
+
+        model_path = locate_signal_model(
+            threshold_instructions["model_name"], path=None, pairs=True
+        )
+        complete_path = model_path  # +model
+        complete_path = rf"{complete_path}"
+        model_config_path = os.sep.join([complete_path, "config_input.json"])
+        model_config_path = rf"{model_config_path}"
+
+        f = open(model_config_path)
+        config = json.load(f)
+        config.update(
+            {
+                "neighborhood_of_interest": threshold_instructions[
+                    "neighborhood_of_interest"
+                ],
+                "reference_population": threshold_instructions["reference_population"],
+                "neighbor_population": threshold_instructions["neighbor_population"],
+            }
+        )
+        json_string = json.dumps(config)
+        with open(model_config_path, "w") as outfile:
+            outfile.write(json_string)
+
+print("Done.")