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Improve com crop #350

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b6bcfd5
use radius instead of square mask region in v0 of com_sparse
ercius Dec 9, 2025
f5f2909
use radius in com_v1_kernel
ercius Dec 9, 2025
e03737d
fix code where init_center is not supplied
ercius Dec 9, 2025
6bb18c5
change tests to use int
ercius Dec 9, 2025
6f9714d
int aren't tuples
ercius Dec 10, 2025
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27 changes: 9 additions & 18 deletions python/stempy/image/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -404,7 +404,7 @@ def com_v1_kernel(
position_indices: np.ndarray,
scan_shape: Tuple[int, int],
frame_shape: Tuple[int, int],
crop_to: Union[Tuple[int, int], None] = None,
crop_to: Union[int, None] = None,
init_center: Union[Tuple[int, int], None] = None,
replace_nans: bool = True,
) -> np.ndarray:
Expand Down Expand Up @@ -432,12 +432,8 @@ def com_v1_kernel(
# Cropping
if crop_to is not None:
if init_center is not None:
xmin = init_center[0] - crop_to[0]
xmax = init_center[0] + crop_to[0]
ymin = init_center[1] - crop_to[1]
ymax = init_center[1] + crop_to[1]

mask = (x > xmin) & (x <= xmax) & (y > ymin) & (y <= ymax)
r = np.sqrt((x - init_center[0])**2 + (y - init_center[1])**2)
mask = (r < crop_to)
position_indices = position_indices[mask]
x = x[mask]
y = y[mask]
Expand All @@ -454,13 +450,8 @@ def com_v1_kernel(

event_center_x = centers_x[position_indices]
event_center_y = centers_y[position_indices]

mask = (
(x > event_center_x - crop_to[0])
& (x <= event_center_x + crop_to[0])
& (y > event_center_y - crop_to[1])
& (y <= event_center_y + crop_to[1])
)
r = np.sqrt((x - event_center_x)**2 + (y - event_center_y)**2)
mask = (r < crop_to)
position_indices = position_indices[mask]
x = x[mask]
y = y[mask]
Expand Down Expand Up @@ -552,8 +543,8 @@ def _com_sparse_v0(array, crop_to=None, init_center=None, replace_nans=True):

if crop_to is not None:
# Crop around the initial center
keep = (x > comx0 - crop_to[0]) & (x <= comx0 + crop_to[0]) & (y > comy0 - crop_to[1]) & (
y <= comy0 + crop_to[1])
r = np.sqrt((x - comx0)**2 + (y - comy0)**2)
keep = (r < crop_to)
x = x[keep]
y = y[keep]
mm = len(x)
Expand Down Expand Up @@ -594,9 +585,9 @@ def com_sparse(

:param array: A SparseArray of the electron counted data
:type array: stempy.io.SparseArray
:param crop_to: optional; The size of the region to crop around initial full frame COM for improved COM near
:param crop_to: optional; The radius from the center to crop around initial full frame COM for improved COM near
the zero beam
:type crop_to: tuple of ints of length 2
:type crop_to: int
:param init_center: optional; The initial center to use before cropping. If this is not set then cropping will be applied around
the center of mass of the each full frame.
:type init_center: tuple of ints of length 2
Expand Down
10 changes: 5 additions & 5 deletions tests/test_image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -58,12 +58,12 @@ def test_com_sparse_parameters(simulate_sparse_array, version):
assert round(com0[0,].mean()) == 30

# Test crop_to input. Initial COM should be full frame COM
com1 = com_sparse(sp, crop_to=(10, 10), version=version)
com1 = com_sparse(sp, crop_to=10, version=version)
assert round(com1[0,].mean()) == 30

# Test crop_to and init_center input.
# No counts will be in the center so all positions will be np.nan
com2 = com_sparse(sp, crop_to=(10, 10), init_center=(1, 1), version=version)
com2 = com_sparse(sp, crop_to=10, init_center=(1, 1), version=version)
assert np.isnan(com2[0,0,0])


Expand All @@ -75,17 +75,17 @@ def test_com_sparse_version_comparison(sparse_array_small):
{"crop_to": None, "init_center": None, "replace_nans": True},
{"crop_to": None, "init_center": None, "replace_nans": False},
{
"crop_to": (frame_x // 2, frame_y // 2),
"crop_to": frame_x // 2,
"init_center": None,
"replace_nans": True,
},
{
"crop_to": (frame_x // 2, frame_y // 2),
"crop_to": frame_x // 2,
"init_center": (frame_x // 2, frame_y // 2),
"replace_nans": True,
},
{
"crop_to": (frame_x // 2, frame_y // 2),
"crop_to": frame_x // 2,
"init_center": (frame_x // 2, frame_y // 2),
"replace_nans": False,
},
Expand Down
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