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https://github.com/rshkarin/quanfima
Quanfima (Quantitative Analysis of Fibrous Materials)
https://github.com/rshkarin/quanfima
data-analysis material-science morphological-analysis volumetric-data
Last synced: about 12 hours ago
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Quanfima (Quantitative Analysis of Fibrous Materials)
- Host: GitHub
- URL: https://github.com/rshkarin/quanfima
- Owner: rshkarin
- License: mit
- Created: 2018-04-02T18:27:36.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2024-02-03T22:20:10.000Z (9 months ago)
- Last Synced: 2024-08-09T01:06:09.423Z (3 months ago)
- Topics: data-analysis, material-science, morphological-analysis, volumetric-data
- Language: Python
- Homepage: http://quanfima.readthedocs.io
- Size: 4.55 MB
- Stars: 28
- Watchers: 2
- Forks: 16
- Open Issues: 6
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
Awesome Lists containing this project
- awesome-biological-image-analysis - Quanfima - Quantitative Analysis of Fibrous Materials: A collection of useful functions for morphological analysis and visualization of 2D/3D data from various areas of material science. (Other)
README
.. image:: docs/source/_static/logo.png
:align: left
-----------
.. image:: https://travis-ci.org/rshkarin/quanfima.svg?branch=master
:target: https://travis-ci.org/rshkarin/quanfima
.. image:: https://readthedocs.org/projects/quanfima/badge/?version=latest
:target: http://quanfima.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://zenodo.org/badge/127795855.svg
:target: https://zenodo.org/badge/latestdoi/127795855
*Quanfima* (**qu**\ antitative **an**\ alysis of **fi**\ brous **ma**\ terials)
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.
.. code-block:: python
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')
.. code-block:: python
>> Porosity (Material 1): 0.845488888889
.. image:: docs/source/_static/2d_polymer_data.png
:align: center
.. image:: docs/source/_static/2d_polymer_orientation_map_600px.png
:align: center
.. image:: docs/source/_static/2d_polymer_diameter_map_600px.png
:align: center