Implement CLI WIP

Author: constantinpape

setup.py

@@ -13,7 +13,7 @@
     license="MIT",
     entry_points={
         "console_scripts": [
-            # TODO add segmentation CLI
+            "synapse_net.run_segmentation = synaptic_reconstruction:tools.cli:segmentation_cli"
         ],
         "napari.manifest": [
             "synaptic_reconstruction = synaptic_reconstruction:napari.yaml",

synaptic_reconstruction/tools/cli.py

@@ -0,0 +1,51 @@
+import argparse
+from functools import partial
+
+from .util import run_segmentation
+from ..inference.util import inference_helper, parse_tiling
+
+
+def segmentation_cli():
+    parser = argparse.ArgumentParser(description="Run segmentation.")
+    parser.add_argument(
+        "--input_path", "-i", required=True,
+        help="The filepath to the mrc file or the directory containing the tomogram data."
+    )
+    parser.add_argument(
+        "--output_path", "-o", required=True,
+        help="The filepath to directory where the segmentations will be saved."
+    )
+    parser.add_argument(
+        "--model_path", "-m", required=True, help="The filepath to the vesicle model."
+    )
+    parser.add_argument(
+        "--mask_path", help="The filepath to a tif file with a mask that will be used to restrict the segmentation."
+        "Can also be a directory with tifs if the filestructure matches input_path."
+    )
+    parser.add_argument("--input_key", "-k", required=False)
+    parser.add_argument(
+        "--force", action="store_true",
+        help="Whether to over-write already present segmentation results."
+    )
+    parser.add_argument(
+        "--tile_shape", type=int, nargs=3,
+        help="The tile shape for prediction. Lower the tile shape if GPU memory is insufficient."
+    )
+    parser.add_argument(
+        "--halo", type=int, nargs=3,
+        help="The halo for prediction. Increase the halo to minimize boundary artifacts."
+    )
+    parser.add_argument(
+        "--data_ext", default=".mrc", help="The extension of the tomogram data. By default .mrc."
+    )
+    args = parser.parse_args()
+
+    # TODO: preload the model!
+    tiling = parse_tiling(args.tile_shape, args.halo)
+    segmentation_function = partial(
+        run_segmentation, model_path=args.model_path, verbose=False, tiling=tiling,
+    )
+    inference_helper(
+        args.input_path, args.output_path, segmentation_function,
+        mask_input_path=args.mask_path, force=args.force, data_ext=args.data_ext,
+    )