surface¶

Module author: Adam Gagorik <adam.gagorik@gmail.com>

surface.make_3D(array)[source]¶

Force the numpy array passed to be 3D via np.expand_dims().

Parameters:	array (numpy.ndarray) – numpy array

surface.load_ascii(handle, square=False, cube=False, shape=None, **kwargs)[source]¶

Wrapper around np.loadtxt. Forces data to be at least 3 dimensions.

Parameters:	square – reshape as if data is NxN cube – reshape as if data is NxNxN square – bool cube – bool shape – list
Parm shape:	reshape data

surface.load_chk(handle)[source]¶

Load checkpoint file and convert traps into a surface.

surface.load(handle, rot90=-1, **kwargs)[source]¶

Load surface from file. Takes into account the file extension.

ext	func
pkl	common.load_pkl()
npy	numpy.load()
chk	surface.load_chk()
inp	surface.load_chk()
csv	surface.load_ascii()
txt	surface.load_ascii()
dat	surface.load_ascii()
png	scipy.ndimage.imread()
jpg	scipy.ndimage.imread()
jpeg	scipy.ndimage.imread()

Parameters:	handle (str) – filename rot90 (int) – number of times to rotate image by 90 degrees
Returns:	image
Return type:	numpy.ndarray

Warning

image file (png, jpg, etc) data is forced into range [0,255].

Warning

data is always made 3D via numpy.expand_dims()

Warning

image data is rotated by -90 degrees.

surface.save_vti(handle, array, **kwargs)[source]¶

Save numpy array to vtkImageData XML file. You can open it in paraview.

Parameters:	handle (str) – filename array (numpy.ndarray) – data

surface.save_chk(handle, array)[source]¶

Save numpy array to Langmuir checkpoint file.

Parameters:	handle (str) – filename array (numpy.ndarray) – data

surface.save(handle, obj, zlevel=0, **kwargs)[source]¶

Save object to a file. Takes into account the file extension.

ext	func
pkl	common.load_pkl()
npy	numpy.load()
vti	surface.save_cti()
csv	np.savetxt()
txt	np.savetxt()
dat	np.savetxt()
png	scipy.misc.imsave()
jpg	scipy.misc.imsave()
jpeg	scipy.misc.imsave()

Parameters:	handle (str) – filename obj – object to save zlevel (int) – slice z-index

Warning

image file (png, jpg, etc) data is forced into range [0,255].

Warning

if ndims is 3 and an image file is being saved, only a slice is saved.

surface.threshold(a, v=0, v0=0, v1=1, copy=False)[source]¶

Set values in array above {v} to {v1}, and below {v} to {v0}.

Parameters:	v (float) – threshold value v0 (float) – lower value v1 (float) – upper value copy (bool) – copy array

surface.linear_mapping(array, n=0.0, m=1.0)[source]¶

Map values in array to fall in the range [n,m].

Parameters:	array – array like object n (float) – lower bound m (float) – upper bound

surface.rfunc(size=None)[source]¶

Produces numbers in the range [-0.5, 0.5].

Parameters:	size – shape of output
Type:	int

class surface.WaveDimensions(L=6.283185307179586, n=1)[source]¶

Compute wavelength, wavenumber, etc from an interval length (L) and number of waves (n).

Parameters:	L (float) – interval length n (int) – number of waves in interval

>>> wx = WaveDimensions(10, 2)
>>> print wx
[Wave Dimensions]
    L      = 10
    n      = 2
    lambda = 5.00000e+00
    nubar  = 2.00000e-01
    k      = 1.25664e+00

calc(L=None, n=None)[source]¶

Perform calculations to compute wavelength, wavenumber, etc. Called automatically in constructor.

Parameters:	L (float) – interval length n (int) – number of waves in interval

surface.f_gyroid(x, y, z, kx, ky, kz)[source]¶

Surface function f(x,y,z) for gyroid.

Parameters:	x (float) – x-value(s) y (float) – y-value(s) z (float) – z-value(s) kx (float) – 2 pi nx / Lx ky (float) – 2 pi ny / Ly kz (float) – 2 pi nz / Lz

>>> w = WaveDimensions(10, 2)
>>> x, y, z = np.mgrid[0:10:100j,0:10:100j,0:10:100j]
>>> gyroid(x, y, z, w.k, w.k, w.k)

surface.gyroid(x, y, z, wx, wy, wz)[source]¶

Wrapper around f_* that uses WaveDimensions.

surface.f_scherk_first_surface(x, y, z, kx, ky, kz)[source]¶

Surface function f(x,y,z) for scherk.

Parameters:	x (float) – x-value(s) y (float) – y-value(s) z (float) – z-value(s) kx (float) – 2 pi nx / Lx ky (float) – 2 pi ny / Ly kz (float) – 2 pi nz / Lz

>>> w = WaveDimensions(10, 2)
>>> x, y, z = np.mgrid[0:10:100j,0:10:100j,0:10:100j]
>>> scherk_first_surface(x, y, z, w.k, w.k, w.k)

surface.scherk_first_surface(x, y, z, wx, wy, wz)[source]¶

Wrapper around f_* that uses WaveDimensions.

surface.f_schwarz_p_surface(x, y, z, kx, ky, kz)[source]¶

Surface function f(x,y,z) for psurface.

Parameters:	x (float) – x-value(s) y (float) – y-value(s) z (float) – z-value(s) kx (float) – 2 pi nx / Lx ky (float) – 2 pi ny / Ly kz (float) – 2 pi nz / Lz

>>> w = WaveDimensions(10, 2)
>>> x, y, z = np.mgrid[0:10:100j,0:10:100j,0:10:100j]
>>> schwarz_p_surface(x, y, z, w.k, w.k, w.k)

surface.schwarz_p_surface(x, y, z, wx, wy, wz)[source]¶

Wrapper around f_* that uses WaveDimensions.

surface.f_schwarz_d_surface(x, y, z, kx, ky, kz)[source]¶

Surface function f(x,y,z) for dsurface.

Parameters:	x (float) – x-value(s) y (float) – y-value(s) z (float) – z-value(s) kx (float) – 2 pi nx / Lx ky (float) – 2 pi ny / Ly kz (float) – 2 pi nz / Lz

>>> w = WaveDimensions(10, 2)
>>> x, y, z = np.mgrid[0:10:100j,0:10:100j,0:10:100j]
>>> schwarz_d_surface(x, y, z, w.k, w.k, w.k)

surface.schwarz_d_surface(x, y, z, wx, wy, wz)[source]¶

Wrapper around f_* that uses WaveDimensions.

surface.f_bandXY(x, y, z, kx, ky, kz)[source]¶

Surface function f(x,y,z) for bands that run along z-direction.

Parameters:	x (float) – x-value(s) y (float) – y-value(s) z (float) – z-value(s) kx (float) – 2 pi nx / Lx ky (float) – 2 pi ny / Ly kz (float) – 2 pi nz / Lz

>>> w = WaveDimensions(10, 2)
>>> x, y, z = np.mgrid[0:10:100j,0:10:100j,0:10:100j]
>>> bandXY(x, y, z, w.k, w.k, w.k)

surface.bandXY(x, y, z, wx, wy, wz)[source]¶

Wrapper around f_* that uses WaveDimensions.

surface.f_bandXZ(x, y, z, kx, ky, kz)[source]¶

Surface function f(x,y,z) for bands that run along y-direction.

Parameters:	x (float) – x-value(s) y (float) – y-value(s) z (float) – z-value(s) kx (float) – 2 pi nx / Lx ky (float) – 2 pi ny / Ly kz (float) – 2 pi nz / Lz

>>> w = WaveDimensions(10, 2)
>>> x, y, z = np.mgrid[0:10:100j,0:10:100j,0:10:100j]
>>> bandXZ(x, y, z, w.k, w.k, w.k)

surface.bandXZ(x, y, z, wx, wy, wz)[source]¶

Wrapper around f_* that uses WaveDimensions.

surface.f_bandYZ(x, y, z, kx, ky, kz)[source]¶

Surface function f(x,y,z) for bands that run along x-direction.

Parameters:	x (float) – x-value(s) y (float) – y-value(s) z (float) – z-value(s) kx (float) – 2 pi nx / Lx ky (float) – 2 pi ny / Ly kz (float) – 2 pi nz / Lz

>>> w = WaveDimensions(10, 2)
>>> x, y, z = np.mgrid[0:10:100j,0:10:100j,0:10:100j]
>>> bandYZ(x, y, z, w.k, w.k, w.k)

surface.bandYZ(x, y, z, wx, wy, wz)[source]¶

Wrapper around f_* that uses WaveDimensions.

class surface.Kernel(xmin, xmax, ymin, ymax, zmin, zmax, spacing=1.0)[source]¶

An x, y, z, v mgrid.

Parameters:	xmin (float) – lower x xmax (float) – upper x ymin (float) – lower y ymax (float) – upper y zmin (float) – lower z zmax (float) – upper z spacing (float) – grid spacing

class surface.FuncKernel(func, *args, **kwargs)[source]¶

An x, y, z, v mgrid. Computes v using the function = f(x, y, z) passed. See Kernel for more parameters.

class surface.SimpleKernel(func, nx=3, ny=3, nz=3, spacing=1.0)[source]¶

An x, y, z, v mgrid. Computes v using the function = f(x, y, z) passed. Creates x, y, z domain using spacing and number of points.

Parameters:	func (func) – function of x, y, z nx (int) – x-direction has 2*nx + 1 points ny (int) – y-direction has 2*ny + 1 points nz (int) – z-direction has 2*nz + 1 points spacing (double) – grid spacing

class surface.RandomKernel(*args, **kwargs)[source]¶

An x, y, z, v mgrid. Computes v using random noise. Creates x, y, z domain using spacing and number of points. See SimpleKernel for more parameters.

class surface.GaussianKernel(sx, sy, sz, mx=0.0, my=0.0, mz=0.0, spacing=1.0)[source]¶

An x, y, z, v mgrid. The size of the grid is determined using the stdev of the Gaussian PDF.

Parameters:	sx (float) – sigma x sy (float) – sigma y sz (float) – sigma z mx (float) – mean x my (float) – mean y mz (float) – mean z spacing (float) – grid spacing

class surface.Isotropic(grid, kernel, rfunc=<function rfunc at 0x7fef9ab9dc80>, v=0.0, mode='same', verbose=False)[source]¶

Performs convolution of random noise with a kernel to make morphology.

Parameters:	grid (surface.Grid) – grid kernel (Kernel) – Kernel instance rfunc (func) – function that produces random numbers in range [-0.5,0.5]

surface.f_isotropic(x, y, z, sx, sy, sz, full=False)[source]¶

Surface function f(x,y,z) for isotropic morphology according to Jake.

Parameters:	x (float) – x-value(s) y (float) – y-value(s) z (float) – z-value(s) sx (float) – sigma x sy (float) – sigma y sz (float) – sigma z

>>> x, y, z = np.mgrid[0:10:100j,0:10:100j,0:10:100j]
>>> isotropic(x, y, z, 1, 1, 1)