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Quanfima (quantitativeanalysis offibrousmaterials)is a collection of useful functions for morphological analysis and visualizationof 2D/3D data from various areas of material science. The aim is to simplifythe analysis process by providing functionality for frequently required tasksin 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 inpandas.DataFrame format.
• Calculation of porosity measure for each material in 2D / 3D datasets.
• Visualization in 2D / 3D using matplotlib, visvis packages.

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

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

importnumpyasnpfromskimageimportio,filtersfromquanfimaimportmorphologyasmrphfromquanfimaimportvisualizationasvisfromquanfimaimportutilsimg=io.imread('../data/polymer_slice.tif')th_val=filters.threshold_otsu(img)img_seg= (img>th_val).astype(np.uint8)# estimate porositypr=mrph.calc_porosity(img_seg)fork,vinpr.items():print'Porosity ({}): {}'.format(k,v)# prepare data and analyze fibersdata,skeleton,skeleton_thick=utils.prepare_data(img_seg)cskel,fskel,omap,dmap,ovals,dvals= \mrph.estimate_fiber_properties(data,skeleton)# plot resultsvis.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 (Material1):0.845488888889