Add LIF to TIFF conversion command line tool

Author: d-j-hatton

pyproject.toml

@@ -79,6 +79,7 @@ murfey = "murfey.client:run"
 "murfey.decrypt_password" = "murfey.cli.decrypt_db_password:run"
 "murfey.generate_key" = "murfey.cli.generate_crypto_key:run"
 "murfey.generate_password" = "murfey.cli.generate_db_password:run"
+"murfey.lif_to_tiff" = "murfey.cli.lif_to_tiff:run"
 "murfey.server" = "murfey.server:run"
 "murfey.sessions" = "murfey.cli.db_sessions:run"
 "murfey.simulate" = "murfey.cli.dummy:run"

src/murfey/cli/lif_to_tiff.py

@@ -0,0 +1,29 @@
+import argparse
+from pathlib import Path
+
+from murfey.util.lif import convert_lif_to_tiff
+
+
+def run():
+    parser = argparse.ArgumentParser(description="Convert LIF to TIFF")
+
+    parser.add_argument(
+        nargs=1, dest="lif_path", help="Path to LIF file for conversion"
+    )
+    parser.add_argument(
+        "--root-dir",
+        default="images",
+        type=str,
+        help="Top subdirectory that LIF files are stored in. Used to determine destination of TIFFs",
+    )
+    parser.add_argument(
+        "-n", "--num-procs", default=1, type=int, help="Number of processes"
+    )
+
+    args = parser.parse_args()
+
+    convert_lif_to_tiff(
+        Path(args.lif_path),
+        root_folder=args.root_dir,
+        number_of_processes=args.num_procs,
+    )