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DOC: Change sampling to spacing in skimage.draw.ellipsoid and tests

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Josh Warner (Mac)
2013-10-13 13:11:11 -05:00
parent 1de6d93850
commit a229d19eb0
3 changed files with 15 additions and 17 deletions
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skimage/draw/draw3d.py
+12 -14
View File
@@ -3,10 +3,10 @@ import numpy as np
from scipy.special import (ellipkinc as ellip_F, ellipeinc as ellip_E)
def ellipsoid(a, b, c, sampling=(1., 1., 1.), levelset=False):
def ellipsoid(a, b, c, spacing=(1., 1., 1.), levelset=False):
"""
Generates ellipsoid with semimajor axes aligned with grid dimensions
on grid with specified `sampling`.
on grid with specified `spacing`.
Parameters
----------
@@ -16,8 +16,8 @@ def ellipsoid(a, b, c, sampling=(1., 1., 1.), levelset=False):
Length of semimajor axis aligned with y-axis.
c : float
Length of semimajor axis aligned with z-axis.
sampling : tuple of floats, length 3
Sampling in (x, y, z) spatial dimensions.
spacing : tuple of floats, length 3
spacing in (x, y, z) spatial dimensions.
levelset : bool
If True, returns the level set for this ellipsoid (signed level
set about zero, with positive denoting interior) as np.float64.
@@ -26,7 +26,7 @@ def ellipsoid(a, b, c, sampling=(1., 1., 1.), levelset=False):
Returns
-------
ellip : (N, M, P) array
Ellipsoid centered in a correctly sized array for given `sampling`.
Ellipsoid centered in a correctly sized array for given `spacing`.
Boolean dtype unless `levelset=True`, in which case a float array is
returned with the level set above 0.0 representing the ellipsoid.
@@ -34,7 +34,7 @@ def ellipsoid(a, b, c, sampling=(1., 1., 1.), levelset=False):
if (a <= 0) or (b <= 0) or (c <= 0):
raise ValueError('Parameters a, b, and c must all be > 0')
offset = np.r_[1, 1, 1] * np.r_[sampling]
offset = np.r_[1, 1, 1] * np.r_[spacing]
# Calculate limits, and ensure output volume is odd & symmetric
low = np.ceil((- np.r_[a, b, c] - offset))
@@ -43,14 +43,14 @@ def ellipsoid(a, b, c, sampling=(1., 1., 1.), levelset=False):
for dim in range(3):
if (high[dim] - low[dim]) % 2 == 0:
low[dim] -= 1
num = np.arange(low[dim], high[dim], sampling[dim])
num = np.arange(low[dim], high[dim], spacing[dim])
if 0 not in num:
low[dim] -= np.max(num[num < 0])
# Generate (anisotropic) spatial grid
x, y, z = np.mgrid[low[0]:high[0]:sampling[0],
low[1]:high[1]:sampling[1],
low[2]:high[2]:sampling[2]]
x, y, z = np.mgrid[low[0]:high[0]:spacing[0],
low[1]:high[1]:spacing[1],
low[2]:high[2]:spacing[2]]
if not levelset:
arr = ((x / float(a)) ** 2 +
@@ -64,10 +64,10 @@ def ellipsoid(a, b, c, sampling=(1., 1., 1.), levelset=False):
return arr
def ellipsoid_stats(a, b, c, sampling=(1., 1., 1.)):
def ellipsoid_stats(a, b, c):
"""
Calculates analytical surface area and volume for ellipsoid with
semimajor axes aligned with grid dimensions of specified `sampling`.
semimajor axes aligned with grid dimensions of specified `spacing`.
Parameters
----------
@@ -77,8 +77,6 @@ def ellipsoid_stats(a, b, c, sampling=(1., 1., 1.)):
Length of semimajor axis aligned with y-axis.
c : float
Length of semimajor axis aligned with z-axis.
sampling : tuple of floats, length 3
Sampling in (x, y, z) spatial dimensions.
Returns
-------
skimage/draw/tests/test_draw3d.py
+2 -2
View File
@@ -6,7 +6,7 @@ from skimage.draw import ellipsoid, ellipsoid_stats
def test_ellipsoid_bool():
test = ellipsoid(2, 2, 2)[1:-1, 1:-1, 1:-1]
test_anisotropic = ellipsoid(2, 2, 4, sampling=(1., 1., 2.))
test_anisotropic = ellipsoid(2, 2, 4, spacing=(1., 1., 2.))
test_anisotropic = test_anisotropic[1:-1, 1:-1, 1:-1]
expected = np.array([[[0, 0, 0, 0, 0],
@@ -45,7 +45,7 @@ def test_ellipsoid_bool():
def test_ellipsoid_levelset():
test = ellipsoid(2, 2, 2, levelset=True)[1:-1, 1:-1, 1:-1]
test_anisotropic = ellipsoid(2, 2, 4, sampling=(1., 1., 2.),
test_anisotropic = ellipsoid(2, 2, 4, spacing=(1., 1., 2.),
levelset=True)
test_anisotropic = test_anisotropic[1:-1, 1:-1, 1:-1]
skimage/measure/tests/test_marching_cubes.py
+1 -1
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@@ -19,7 +19,7 @@ def test_marching_cubes_anisotropic():
spacing = (1., 10 / 6., 16 / 6.)
ellipsoid_anisotropic = ellipsoid(6, 10, 16, spacing=spacing,
levelset=True)
_, surf = ellipsoid_stats(6, 10, 16, spacing=spacing)
_, surf = ellipsoid_stats(6, 10, 16)
verts, faces = marching_cubes(ellipsoid_anisotropic, 0.,
spacing=spacing)
surf_calc = mesh_surface_area(verts, faces)