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FIX: correct other instance of np.linalg.norm, clarify comments

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Josh Warner (Mac)
2014-03-14 14:15:45 -05:00
parent 48ca44bf16
commit 5ac910b0b8
1 changed files with 11 additions and 4 deletions
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skimage/measure/_marching_cubes.py
+11 -4
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@@ -68,6 +68,12 @@ def marching_cubes(volume, level, spacing=(1., 1., 1.)):
lexicographical order) coordinate in the contour. This is a side-effect
of how the input array is traversed, but can be relied upon.
The generated mesh does not guarantee coherent orientation because of how
symmetry is used in the algorithm. If this is required, e.g. due to a
particular visualization package or for generating 3D printing STL files,
the utility ``skimage.measure.correct_mesh_orientation`` is available to
fix this in post-processing.
To quantify the area of an isosurface generated by this algorithm, pass
the outputs directly into `skimage.measure.mesh_surface_area`.
@@ -240,11 +246,12 @@ def correct_mesh_orientation(volume, verts, faces, spacing=(1., 1., 1.),
grad_centroids = np.c_[grad_centroids_x, grad_centroids_y,
grad_centroids_z]
grad_centroids = (grad_centroids /
np.linalg.norm(grad_centroids, axis=1)[:, np.newaxis])
(np.sum(grad_centroids ** 2,
axis=1) ** 0.5)[:, np.newaxis])
# Calculate and normalize cross products for each face
# Find normal vectors for each face via cross product
crosses = np.cross(a, b)
crosses = crosses / np.sum(crosses ** 2, axis=1) ** (0.5)[:, np.newaxis]
crosses = crosses / (np.sum(crosses ** 2, axis=1) ** (0.5))[:, np.newaxis]
# Take dot product
dotproducts = (grad_centroids * crosses).sum(axis=1)
@@ -260,7 +267,7 @@ def correct_mesh_orientation(volume, verts, faces, spacing=(1., 1., 1.),
raise ValueError("Incorrect input %s in `gradient_direction`, see "
"docstring." % (gradient_direction))
# Swap orientation and return, without modifying original data
# Correct orientation and return, without modifying original data
faces_corrected = faces.copy()
faces_corrected[indices] = faces_corrected[indices, ::-1]