Basic usage¶

This Jupyter notebook gives an overview of the Python package mevis. The .ipynb file can be found here.

[1]:

import mevis as mv
from opencog.type_constructors import *

Create an AtomSpace¶

[2]:

atomspace1 = mv.create()

n1 = ConceptNode('Vertebrates')
n2 = ConceptNode('Fish')
n3 = ConceptNode('Tetrapods')
n4 = ConceptNode('Amphibians')
n5 = ConceptNode('Reptiles')
n6 = ConceptNode('Mammals')
n7 = ConceptNode('Birds')
n8 = ConceptNode('Marsupialia')
n9 = ConceptNode('Placentalia')

e1 = InheritanceLink(n2, n1)
e2 = InheritanceLink(n3, n1)
e3 = InheritanceLink(n4, n3)
e4 = InheritanceLink(n5, n3)
e5 = InheritanceLink(n6, n3)
e6 = InheritanceLink(n7, n3)
e7 = InheritanceLink(n8, n6)
e8 = InheritanceLink(n9, n6)
e9 = ListLink(n3, n4, n5, n6, n7)
e10 = ListLink(n8, n9)

Load an AtomSpace¶

[3]:

atomspace2 = mv.load('moses.scm')

Store an AtomSpace¶

[4]:

mv.store(atomspace1, 'vertebrates.scm', overwrite=True)

Inspect an AtomSpace¶

[5]:

mv.inspect(atomspace1)

[5]:

{'atoms': 19,
 'nodes': 9,
 'links': 10,
 'types': {'ConceptNode': 9, 'ListLink': 2, 'InheritanceLink': 8}}

[6]:

mv.inspect(atomspace2, count_details=False)

[6]:

{'atoms': 16, 'nodes': 5, 'links': 11}

Convert an AtomSpace to a graph¶

[7]:

graph1 = mv.convert(atomspace1)

[8]:

graph2 = mv.convert(
    atomspace2,
    node_color='blue',
    node_size=lambda atom: 20 if atom.is_link() else 10,
    node_shape='hexagon')

Inspect a graph¶

[9]:

mv.inspect(graph1)

[9]:

{'nodes': 19,
 'edges': 23,
 'node_properties': {'label': 11, 'color': 1, 'shape': 1, 'hover': 19},
 'edge_properties': {'color': 1}}

[10]:

mv.inspect(graph2, count_details=False)

[10]:

{'nodes': 16, 'edges': 21}

Export a graph¶

[11]:

mv.export(graph2, 'vertebrates.gml', overwrite=True)
mv.export(graph2, 'vertebrates.gml.gz', overwrite=True)
mv.export(graph2, 'vertebrates.gml.bz2', overwrite=True)

Plot an AtomSpace¶

When plot is the last command in a cell, the figure is automatically displayed as output of the cell.

[12]:

mv.plot(atomspace1, node_click='b')

It is also possible to display multiple figures as output of one cell. Other outputs such as text can be put in between.

[13]:

fig1 = mv.plot(atomspace1)
fig2 = mv.plot(atomspace2)

print('AtomSpace 1')
fig1.display(inline=True)

print('AtomSpace 2')
fig2.display(inline=True)

AtomSpace 1

AtomSpace 2

There are three JavaScript backends (d3.js, three.js, vis.js) and various layout algorithms available.

[14]:

mv.plot(atomspace1, 'd3', 'bipartite')

[15]:

mv.plot(atomspace2, 'vis', 'dot')

[16]:

mv.plot(atomspace2, 'three')

Graph annotations can be used to change visual elements of the plot.

[17]:

def calc_node_color(atom):
    if atom.type_name == 'AndLink':
        return 'blue'
    elif atom.type_name == 'OrLink':
        return 'green'
    elif atom.type_name == 'NotLink':
        return 'black'
    else:
        return 'red'

def calc_node_shape(atom):
    if atom.is_node():
        return 'rectangle'
    elif atom.type_name in ('AndLink', 'OrLink'):
        return 'hexagon'
    else:
        return 'circle'

mv.plot(atomspace2, layout_method='dot', filter_target='$2', filter_context=('in', 3),
        node_color=calc_node_color, node_shape=calc_node_shape)

Export a plot¶

A plot can be exported as standalone HTML file that contains an interactive visualization, or as JPG/PNG/SVG file that contains a static image captured with Selenium, which is an optional dependency of mevis. Note that only plots with d3 support the SVG format.

[18]:

fig = mv.plot(atomspace2, 'd3', 'dot', zoom_factor=0.5)

fig.export_html('moses.html')

fig.export_jpg('moses.jpg')
fig.export_png('moses.png')
fig.export_svg('moses.svg')