Saving lattice visualization to a file

[Egor Dudyrev]

Hello!

I'm trying to improve my FCA libraries performance benchmark (https://github.com/EgorDudyrev/FCApy/tree/feature/benchmarking/notebooks/Performance_Benchmark). But I have some problems saving concepts lattice visualization to a file.

I use the function context.lattice.graphviz('concepts', render=True, ) to save a visualization into a file 'concepts.pdf'. It works for a small context (like 'animal_movement'). But when applied to 'Bob Ross elements-by-episode' dataset it results in a very wide and totally white pdf file.

What is the proper way to save (big) lattice visualization to a file? Can it be png file instead of pdf?

The code to reproduce the error:

import concepts
import pandas as pd

fname = 'bob_ross.csv'
!wget -O {fname} -q https://raw.githubusercontent.com/fivethirtyeight/data/master/bob-ross/elements-by-episode.csv 

df = pd.read_csv(fname)
df['EPISODE_TITLE'] = df['EPISODE']+' '+df['TITLE']
df = df.drop(['EPISODE','TITLE'],1).set_index('EPISODE_TITLE').astype(bool)

context = concepts.Context(df.index, df.columns, df.values)
context.lattice.graphviz('concepts', render=True, );

[Egor Dudyrev]

Upd. Seems like the problem is with the pdf viewer installed in my laptop.

I open the file with https://smallpdf.com/pdf-reader and after zooming in 26 times it finally shows a lattice.

Still, can a lattice visualization be saved to png file instead of pdf?

[Sebastian Bank]

Hi Egor, yep, the issue is probably purely the size.

Still, can a lattice visualization be saved to png file instead of pdf?

Use the format argument, see Lattice.graphviz() and Digraph.render()

AFAICT your code includes the row number as feature (68 instead of 67), here is an adaped version:

import pathlib

import concepts
import pandas as pd

URL = ('https://raw.githubusercontent.com/fivethirtyeight/data/master'
       '/bob-ross/elements-by-episode.csv')

CSV = pathlib.Path('bob_ross.csv')

FORMAT = {'encoding': 'utf-8'}

if not CSV.exists():
    pd.read_csv(URL, **FORMAT).to_csv(CSV, **FORMAT)
    
df = pd.read_csv(CSV, **FORMAT).drop('Unnamed: 0', axis='columns')
df['EPISODE_TITLE'] = df['EPISODE'] + ' ' + df['TITLE']
df = df.drop(['EPISODE','TITLE'], axis='columns')
df = df.set_index('EPISODE_TITLE', drop=True).astype(bool)

context = concepts.Context(df.index, df.columns, df.values)
assert len(context.objects) == 403
assert len(context.properties) == 67
dot = context.lattice.graphviz('bob_ross.gv', render=True, format='png')

[Sebastian Bank]

Closing for now.