PoreSpy

Porous Media Image Analysis in Python

PoreSpy consists of the following modules:


generators: Routines for generating artificial images of porous materials useful for testing and illustration


filters: Functions that accept an image and return an altered image


metrics: Tools for quantifying properties of images


networks: Tools for obtaining pore network representations of images


visualization: Helper functions for creating useful views of the image


io: Functions for output image data in various formats for use in common software


tools: Various useful tools for working with images


Example Usage

Working with PoreSpy was designed to be a series of function calls, similar to building a macro in ImageJ or using Matlab. A sample workflow is as follows:

Create a test image (or load one using skimage.io.imread)

>>> import porespy as ps
>>> import scipy as sp
>>> import scipy.ndimage as spim
>>> sp.random.seed(0)  # Set number generator for same image each time
>>> im = ps.generators.blobs(shape=[250, 250])

Apply a filter to the image using tools from scipy.ndimage:

>>> dt = spim.distance_transform_edt(im)

Use some filters from PoreSpy:

>>> peaks = ps.filters.snow_partitioning(im=im, dt=dt)
____________________________________________________________
Beginning SNOW Algorithm
Converting supplied image (im) to boolean
Applying Gaussian blur with sigma = 0.4
Initial number of peaks:  77
Peaks after trimming saddle points:  71
Peaks after trimming nearby peaks:  70