Metadata-Version: 1.2
Name: quanfima
Version: 0.1a1
Summary: The package for morphological analysis and visualization of fibrous materials.
Home-page: http://github.com/rshkarin/quanfima
Author: Roman Shkarin, Andrei Shkarin
Author-email: roman.v.shkarin@gmail.com, andrei.shkarin@gmail.com
License: MIT
Description: .. image:: docs/source/_static/logo.png
            :align: left
            
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        .. 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
        
Keywords: biomaterials fiber analysis material science visualization
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Requires-Python: >=2.6,<3
