Installation

The easiest way to install the latest version is by using pip:

$ pip install quanfima

You may also use Git to clone the repository and install it manually:

$ git clone https://github.com/rshkarin/quanfima.git
$ cd quanfima
$ python setup.py install

Usage

Open a grayscale image, perform segmentation, estimate porosity, analyze fiber orientation and diameters, and plot the results.

import numpy as np
from skimage import io, filters
from quanfima import morphology as mrph
from quanfima import visualization as vis
from quanfima import utils

img = io.imread('../data/polymer_slice.tif')

th_val = filters.threshold_otsu(img)
img_seg = (img > th_val).astype(np.uint8)

# estimate porosity
pr = mrph.calc_porosity(img_seg)
for k,v in pr.items():
  print 'Porosity ({}): {}'.format(k, v)

# prepare data and analyze fibers
data, skeleton, skeleton_thick = utils.prepare_data(img_seg)
cskel, fskel, omap, dmap, ovals, dvals = \
                    mrph.estimate_fiber_properties(data, skeleton)

# plot results
vis.plot_orientation_map(omap, fskel, min_label=u'0°', max_label=u'180°',
                         figsize=(10,10),
                         name='2d_polymer',
                         output_dir='/path/to/output/dir')
vis.plot_diameter_map(dmap, cskel, figsize=(10,10), cmap='gist_rainbow',
                      name='2d_polymer',
                      output_dir='/path/to/output/dir')

>> Porosity (Material 1): 0.845488888889