Skip to main content

The package for morphological analysis and visualization of fibrous materials.

Project description

docs/source/_static/logo.png
https://travis-ci.org/rshkarin/quanfima.svg?branch=master Documentation Status https://zenodo.org/badge/127795855.svg

Quanfima (quantitative analysis of fibrous materials) is a collection of useful functions for morphological analysis and visualization of 2D/3D data from various areas of material science. The aim is to simplify the analysis process by providing functionality for frequently required tasks in the same place.

More examples of usage you can find in the documentation.

  • Analysis of fibrous structures by tensor-based method in 2D / 3D datasets.

  • Estimation of structure diameters in 2D / 3D by a ray-casting method.

  • Counting of particles in 2D / 3D datasets and providing a detailed report in pandas.DataFrame format.

  • Calculation of porosity measure for each material in 2D / 3D datasets.

  • Visualization in 2D / 3D using matplotlib, visvis packages.

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
docs/source/_static/2d_polymer_data.png docs/source/_static/2d_polymer_orientation_map_600px.png docs/source/_static/2d_polymer_diameter_map_600px.png

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distributions

No source distribution files available for this release.See tutorial on generating distribution archives.

Built Distribution

quanfima-0.1a3-py2-none-any.whl (5.0 MB view details)

Uploaded Python 2

File details

Details for the file quanfima-0.1a3-py2-none-any.whl.

File metadata

File hashes

Hashes for quanfima-0.1a3-py2-none-any.whl
Algorithm Hash digest
SHA256 5047e4b4abe726ebd05b98fe5cb4132c824265b97b1af37f13dfe58423c47d7c
MD5 dc2183e395057acd2fff316456a9dafd
BLAKE2b-256 2fde94930d6ea2922cbabe982764974632ea8e26003e9cbb3d17b9e7ad915e17

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page