From 5492c415e33470d96964c2ddc7943aa2acbb7088 Mon Sep 17 00:00:00 2001
From: Miles Graham <miles.graham98@gmail.com>
Date: Thu, 13 Jun 2024 14:33:30 +0100
Subject: [PATCH 1/2] added map to mask function

---
 src/ttmask/__init__.py |  1 +
 src/ttmask/map2mask.py | 30 ++++++++++++++++++++++++++++++
 2 files changed, 31 insertions(+)
 create mode 100644 src/ttmask/map2mask.py

diff --git a/src/ttmask/__init__.py b/src/ttmask/__init__.py
index e1e99b2..e464458 100644
--- a/src/ttmask/__init__.py
+++ b/src/ttmask/__init__.py
@@ -16,4 +16,5 @@
 from .cube import cube
 from .cone import cone
 from .ellipsoid import ellipsoid
+from .map2mask import map2mask
 
diff --git a/src/ttmask/map2mask.py b/src/ttmask/map2mask.py
new file mode 100644
index 0000000..e543393
--- /dev/null
+++ b/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)

From 0ae13e2036cdc10942f7c3ac0315c503f94e04cc Mon Sep 17 00:00:00 2001
From: Miles Graham <miles.graham98@gmail.com>
Date: Thu, 13 Jun 2024 14:33:59 +0100
Subject: [PATCH 2/2] added map to mask function

---
 src/ttmask/map2mask.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ttmask/map2mask.py b/src/ttmask/map2mask.py
index e543393..5c1010e 100644
--- a/src/ttmask/map2mask.py
+++ b/src/ttmask/map2mask.py
@@ -2,8 +2,8 @@
 import numpy as np
 import typer
 from pathlib import Path
-from ._cli import cli
 
+from ._cli import cli
 from .soft_edge import add_soft_edge
 
 @cli.command(name='map2mask')