pytme 0.3b0__cp311-cp311-macosx_15_0_arm64.whl → 0.3b0.post1__cp311-cp311-macosx_15_0_arm64.whl

scripts/eval.py

@@ -0,0 +1,93 @@
+#!python3
+""" Apply tme.preprocessor.Preprocessor methods to an input file based
+    on a provided yaml configuration obtaiend from preprocessor_gui.py.
+
+    Copyright (c) 2023 European Molecular Biology Laboratory
+
+    Author: Valentin Maurer <valentin.maurer@embl-hamburg.de>
+"""
+import yaml
+import argparse
+import textwrap
+from tme import Preprocessor, Density
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(
+        description=textwrap.dedent(
+            """
+        Apply preprocessing to an input file based on a provided YAML configuration.
+
+        Expected YAML file format:
+        ```yaml
+        <method_name>:
+            <parameter1>: <value1>
+            <parameter2>: <value2>
+            ...
+        ```
+        """
+        ),
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    parser.add_argument(
+        "-i",
+        "--input_file",
+        type=str,
+        required=True,
+        help="Path to the input data file in CCP4/MRC format.",
+    )
+    parser.add_argument(
+        "-y",
+        "--yaml_file",
+        type=str,
+        required=True,
+        help="Path to the YAML configuration file.",
+    )
+    parser.add_argument(
+        "-o",
+        "--output_file",
+        type=str,
+        required=True,
+        help="Path to output file in CPP4/MRC format..",
+    )
+    parser.add_argument(
+        "--compress", action="store_true", help="Compress the output file using gzip."
+    )
+
+    args = parser.parse_args()
+
+    return args
+
+
+def main():
+    args = parse_args()
+    with open(args.yaml_file, "r") as f:
+        preprocess_settings = yaml.safe_load(f)
+
+    if len(preprocess_settings) > 1:
+        raise NotImplementedError(
+            "Multiple preprocessing methods specified. "
+            "The script currently supports one method at a time."
+        )
+
+    method_name = list(preprocess_settings.keys())[0]
+    if not hasattr(Preprocessor, method_name):
+        raise ValueError(f"Method {method_name} does not exist in Preprocessor.")
+
+    density = Density.from_file(args.input_file)
+    output = density.empty
+
+    method_params = preprocess_settings[method_name]
+    preprocessor = Preprocessor()
+    method = getattr(preprocessor, method_name, None)
+    if not method:
+        raise ValueError(
+            f"{method} does not exist in dge.preprocessor.Preprocessor class."
+        )
+
+    output.data = method(template=density.data, **method_params)
+    output.to_file(args.output_file, gzip=args.compress)
+
+
+if __name__ == "__main__":
+    main()