用于计算python中的体积或表面积的良好算法
作者:互联网
我正在尝试计算3D numpy数组的体积(或表面积).在许多情况下,体素是各向异性的,并且我在每个方向上具有像素到厘米的转换因子.
有没有人知道找到工具包或包来做上述的好地方?
现在,我有一些内部代码,但我希望在准确性方面升级到更具工业实力的东西.
编辑1:这是一些(差)样本data.这比典型的球体小得多.我可以在生成它时添加更好的数据!它在(自我)肿瘤脑肿瘤中.
解决方法:
一种选择是使用VTK. (我将在这里使用tvtk python绑定…)
至少在某些情况下,获得等值面内的区域会更准确一些.
此外,就表面积而言,tvtk.MassProperties也会计算表面积.它是mass.surface_area(下面代码中的mass对象).
import numpy as np
from tvtk.api import tvtk
def main():
# Generate some data with anisotropic cells...
# x,y,and z will range from -2 to 2, but with a
# different (20, 15, and 5 for x, y, and z) number of steps
x,y,z = np.mgrid[-2:2:20j, -2:2:15j, -2:2:5j]
r = np.sqrt(x**2 + y**2 + z**2)
dx, dy, dz = [np.diff(it, axis=a)[0,0,0] for it, a in zip((x,y,z),(0,1,2))]
# Your actual data is a binary (logical) array
max_radius = 1.5
data = (r <= max_radius).astype(np.int8)
ideal_volume = 4.0 / 3 * max_radius**3 * np.pi
coarse_volume = data.sum() * dx * dy * dz
est_volume = vtk_volume(data, (dx, dy, dz), (x.min(), y.min(), z.min()))
coarse_error = 100 * (coarse_volume - ideal_volume) / ideal_volume
vtk_error = 100 * (est_volume - ideal_volume) / ideal_volume
print 'Ideal volume', ideal_volume
print 'Coarse approximation', coarse_volume, 'Error', coarse_error, '%'
print 'VTK approximation', est_volume, 'Error', vtk_error, '%'
def vtk_volume(data, spacing=(1,1,1), origin=(0,0,0)):
data[data == 0] = -1
grid = tvtk.ImageData(spacing=spacing, origin=origin)
grid.point_data.scalars = data.T.ravel() # It wants fortran order???
grid.point_data.scalars.name = 'scalars'
grid.dimensions = data.shape
iso = tvtk.ImageMarchingCubes(input=grid)
mass = tvtk.MassProperties(input=iso.output)
return mass.volume
main()
这会产生:
Ideal volume 14.1371669412
Coarse approximation 14.7969924812 Error 4.66731094565 %
VTK approximation 14.1954890878 Error 0.412544796894 %
标签:discrete-mathematics,python,numpy,math,volume 来源: https://codeday.me/bug/20190729/1575042.html