Map2mask (#38)

* added map to mask function

src/ttmask/__init__.py

@@ -16,4 +16,5 @@
 from .cube import cube
 from .cone import cone
 from .ellipsoid import ellipsoid
+from .map2mask import map2mask
 

src/ttmask/map2mask.py

@@ -0,0 +1,30 @@
+import mrcfile
+import numpy as np
+import typer
+from pathlib import Path
+
+from ._cli import cli
+from .soft_edge import add_soft_edge
+
+@cli.command(name='map2mask')
+def map2mask(
+
+    input_map: Path = typer.Option(Path("map.mrc")),
+    binarization_threshold: float = typer.Option(...),
+    output_mask: Path = typer.Option(Path("mask.mrc")),
+    pixel_size: float = typer.Option(...),
+    soft_edge_width: int = typer.Option(0),
+
+):
+    with mrcfile.open(input_map) as mrc:
+        map_data = np.array(mrc.data)
+
+    above_threshold = map_data >= binarization_threshold
+    below_threshold = map_data < binarization_threshold
+
+    map_data[above_threshold] = 1
+    map_data[below_threshold] = 0
+
+    mask = add_soft_edge(map_data, soft_edge_width)
+
+    mrcfile.write(output_mask, mask, voxel_size=pixel_size, overwrite=True)