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432 new feature willard chandler density parameter #433

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merged 4 commits into from
Sep 11, 2024
Merged

432 new feature willard chandler density parameter #433

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f01a70e
Delete .travis.yml.
a-ws-m Sep 10, 2024
4114673
Add density cutoff argument to Willard Chandler
a-ws-m Sep 10, 2024
de4a905
Fix import order
a-ws-m Sep 10, 2024
9c619dc
small fix
Marcello-Sega Sep 11, 2024
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61 changes: 0 additions & 61 deletions .travis.yml.
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7 changes: 6 additions & 1 deletion pytim/willard_chandler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,9 @@ class WillardChandler(Interface):
this group
:param float alpha: The width of the Gaussian kernel
:param float mesh: The grid spacing for the density calculation
:param float density_cutoff: The density value used to define the
isosurface. `None` (default) uses the average
of the minimum and maximum density.
:param AtomGroup group: Compute the density using this group
:param dict radii_dict: Dictionary with the atomic radii of
the elements in the group.
Expand Down Expand Up @@ -127,10 +130,12 @@ def __init__(self,
centered=False,
warnings=False,
autoassign=True,
density_cutoff=None,
**kargs):

self.autoassign, self.do_center = autoassign, centered
self.include_zero_radius = include_zero_radius
self.density_cutoff = density_cutoff
sanity = SanityCheck(self, warnings=warnings)
sanity.assign_universe(universe, group)
sanity.assign_alpha(alpha)
Expand Down Expand Up @@ -245,7 +250,7 @@ def _assign_layers(self):
volume = self.density_field.reshape(
tuple(np.array(ngrid[::-1]).astype(int)))
verts, faces, normals, values = marching_cubes(
volume, None, spacing=tuple(spacing))
volume, self.density_cutoff, spacing=tuple(spacing))
# note that len(normals) == len(verts): they are normals
# at the vertices, and not normals of the faces
# verts and normals have x and z flipped because skimage uses zyx ordering
Expand Down
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