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Generalize midplane point calculation
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Update locations.txt after midplane update
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@Misty-W
Misty-W committed Jun 26, 2024
1 parent a31fecb commit 810a314
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110 changes: 56 additions & 54 deletions aquapointer/analog/example_output/DNA/locations.txt
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@@ -1,54 +1,56 @@
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54 changes: 31 additions & 23 deletions aquapointer/slicing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,27 +56,24 @@ def density_slices_by_planes(
origin = density_origin(density_grid)
endpoint = density_point_boundaries(density_grid)


a = np.zeros_like(normals[0])
a[normals[0].argmax()] = 1
b = np.zeros_like(normals[-1])
b[normals[-1].argmax()] = 1
midplane_points = (
[(origin + slicing_planes[0][0, :]) / 2]
+ [
(slicing_planes[s][0, :] + slicing_planes[s + 1][0, :]) / 2
[_calculate_midplane_points(a, normals[0], origin, slicing_planes[0][0,:])]
+ [_calculate_midplane_points(normals[s], normals[s+1], slicing_planes[s][0,:], slicing_planes[s+1][0,:])
for s in range(len(slicing_planes) - 1)
]
+ [
slicing_planes[-1][0, :]
+ normals[-1][1]
* (endpoint - slicing_planes[-1][0, :]).dot(normals[-1][1])
/ 2
]
+ [_calculate_midplane_points(normals[-1], b, slicing_planes[-1][0, :], endpoint)]
)
midplane_normals = (
[normals[0]]
+ [
np.mean(np.array(normals[n : n + 2]), axis=0)
/ norm(np.mean(np.array(normals[n : n + 2]), axis=0))
[_calculate_midplane_normals(a, normals[0])]
+ [_calculate_midplane_normals(normals[n], normals[n+1])
for n in range(len(normals) - 1)
]
+ [normals[-1]]
+ [_calculate_midplane_normals(normals[-1], b)]
)

for ind in np.ndindex(density_grid.grid.shape):
Expand Down Expand Up @@ -106,15 +103,6 @@ def density_slices_by_planes(
break

idx_lists[s].append(ind)
if s == 0:
a = origin
b = slicing_planes[s][0, :]
elif 0 < s < len(slicing_planes):
a = slicing_planes[s - 1][0, :]
b = slicing_planes[s][0, :]
else:
a = slicing_planes[s - 1][0, :]
b = endpoint

point_lists[s].append(
center
Expand All @@ -139,6 +127,26 @@ def density_slices_by_planes(
return density_canvases


def _calculate_midplane_points(n1, n2, p1, p2):
if n1[0] + n2[0]:
px = (n1[0] * p1[0] + n2[0] * p2[0]) / (n1[0] + n2[0])
else:
px = 0
if n1[1] + n2[1]:
py = (n1[1] * p1[1] + n2[1] * p2[1]) / (n1[1] + n2[1])
else:
py = 0
if n1[2] + n2[2]:
pz = (n1[2] * p1[2] + n2[2] * p2[2]) / (n1[2] + n2[2])
else:
pz = 0
return np.array([px, py, pz])


def _calculate_midplane_normals(n1, n2):
return np.sum(np.array([n1, n2]), axis=0) / norm(np.sum(np.array([n1, n2]), axis=0))


def _generate_slice_rotation_matrix(normal: NDArray):
n = np.cross(np.array([0, 0, 1]), normal)
n1 = n[0]
Expand Down

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