Customizing and exporting graphical models and CPTs as image (pdf, png)

from pylab import *
import matplotlib.pyplot as plt

import pyagrum as gum
import pyagrum.lib.notebook as gnb

bn = gum.fastBN("a->b->c->d;b->e->d->f;g->c")
gnb.flow.row(bn, gnb.getInference(bn))

customizing colours and width for model and inference

def nodevalue(n):
  return 0.5 if n in "aeiou" else 0.7


def arcvalue(a):
  return (10 - a[0]) * a[1]


def arcvalue2(a):
  return (a[0] + a[1] + 5) / 22


gnb.showBN(
  bn,
  nodeColor={n: nodevalue(n) for n in bn.names()},
  arcWidth={a: arcvalue(a) for a in bn.arcs()},
  arcLabel={a: f"v={arcvalue(a):02d}" for a in bn.arcs()},
  arcColor={a: arcvalue2(a) for a in bn.arcs()},
)

gnb.showInference(
  bn,
  targets={"a", "g", "f", "b"},
  evs={"e": 0},
  nodeColor={n: nodevalue(n) for n in bn.names()},
  arcWidth={a: arcvalue(a) for a in bn.arcs()},
)

gnb.flow.row(
  gnb.getBN(bn, nodeColor={n: nodevalue(n) for n in bn.names()}, arcWidth={a: arcvalue(a) for a in bn.arcs()}),
  gnb.getInference(bn, nodeColor={n: nodevalue(n) for n in bn.names()}, arcWidth={a: arcvalue(a) for a in bn.arcs()}),
)

mycmap = plt.get_cmap("Reds")
formyarcs = plt.get_cmap("winter")
gnb.flow.row(
  gnb.getBN(
    bn,
    nodeColor={n: nodevalue(n) for n in bn.names()},
    arcColor={a: arcvalue2(a) for a in bn.arcs()},
    cmapNode=mycmap,
    cmapArc=formyarcs,
  ),
  gnb.getInference(
    bn,
    nodeColor={n: nodevalue(n) for n in bn.names()},
    arcColor={a: arcvalue2(a) for a in bn.arcs()},
    arcWidth={a: arcvalue(a) for a in bn.arcs()},
    cmapNode=mycmap,
    cmapArc=formyarcs,
  ),
)

Modifying graph’s layout

Every graph or graphical models can be translated into a pyDot’s representaton (a pydot.Dot object). In this graphical representation, it is possible to manipulate the positions of the node. pyAgrum proposes two functions gum.utils.dot_layout to help modifying this layout.

Layout for Bayesian network

import pyagrum as gum
import pyagrum.lib.notebook as gnb
import pyagrum.lib.utils as gutils
import pyagrum.lib.bn2graph as gumb2g

bn = gum.fastBN("A->B<-C<-D")
bn2 = gum.fastBN("A->B->C<-D")

graph = gumb2g.BN2dot(bn)

graph2 = gumb2g.BN2dot(bn2)
l = gutils.dot_layout(graph)
print(f"Layout proposed by dot for BN :{l}")
gutils.apply_dot_layout(graph2, l)

graph3 = gumb2g.BN2dot(bn2)
## l["C"],l["A"]=l["A"],l["C"]
l["D"], l["C"], l["B"], l["A"] = (
  gutils.DotPoint(0, 0),
  gutils.DotPoint(1, 1),
  gutils.DotPoint(2, 2),
  gutils.DotPoint(3, 3),
)
gutils.apply_dot_layout(graph3, l)
gnb.flow.row(bn, bn2, graph2, graph3, captions=["BN", "BN2", "BN2 with the same layoutas BN", "Layout changed by hand"])

Layout proposed by dot for BN :{'D': DotPoint(x=0.375, y=2.25), 'A': DotPoint(x=1.375, y=1.25), 'B': DotPoint(x=0.875, y=0.25), 'C': DotPoint(x=0.375, y=1.25)}

BN

BN2

BN2 with the same layoutas BN

Layout changed by hand

Layout for other graphical models and for inference

import pyagrum as gum
import pyagrum.lib.notebook as gnb
import pyagrum.lib.utils as gutils
import pyagrum.lib.id2graph as gum2gr

model = gum.fastID("*D->$L<-E<-H->L;E->D")
gnb.flow.add(model)
gum.config.push()
gum.config["influenceDiagram", "utility_shape"] = "diamond"

figure = gum2gr.ID2dot(model)
l = gutils.dot_layout(figure)

## changing LAYOUT
## making some horizontal space
for i, p in l.items():
  l[i] = gutils.DotPoint(1.5 * p.x, p.y)
## E at the vertical of L, at the horizontal of D
l["E"] = gutils.DotPoint(l["L"].x, l["D"].y)
## H symetric of D w.r.t (EL)
l["H"] = gutils.DotPoint(2 * l["E"].x - l["D"].x, l["D"].y)

gutils.apply_dot_layout(figure, l)
gnb.flow.add(figure)

gnb.flow.display()
gum.config.pop()

BN

BN2

BN2 with the same layoutas BN

Layout changed by hand

import pyagrum as gum
import pyagrum.lib.notebook as gnb
import pyagrum.lib.utils as gutils
import pyagrum.lib.id2graph as gum2gr

model = gum.fastID("*D->$L<-E<-H->L;E->D")
gnb.flow.add(gnb.getInference(model))

figure = gum2gr.LIMIDinference2dot(model, evs={}, targets={}, size=None, engine=None)
l = gutils.dot_layout(figure)

## changing LAYOUT
## making some horizontal space
for i, p in l.items():
  l[i] = gutils.DotPoint(3 * p.x, p.y)
## E at the vertical of L, at the horizontal of D
l["E"] = gutils.DotPoint(l["L"].x, l["D"].y)
l["D"] = gutils.DotPoint(l["D"].x / 2, l["D"].y)
l["H"] = gutils.DotPoint(l["L"].x * 3 / 2, l["D"].y)

gutils.apply_dot_layout(figure, l)
gnb.flow.add(figure)

gnb.flow.display()

Exporting model and inference as image

Exporting as image (pdf, png, etc.) has been gathered in 2 functions : pyagrum.lib.image.export() and pyagrum.lib.image.exportInference(). The argument are the same as for pyagrum.notebook.show{Model} and pyagrum.notebook.show{Inference}.

import os
import pyagrum.lib.image as gumimage
from IPython.display import Image  # to display the exported images

os.makedirs("out/export", exist_ok=True)

gumimage.export(bn, "out/export/test_export.png")

Image(filename="out/export/test_export.png")

bn = gum.fastBN("a->b->d;a->c->d[3]->e;f->b")
gumimage.export(
  bn,
  "out/export/test_export.png",
  nodeColor={"a": 1, "b": 0.3, "c": 0.4, "d": 0.1, "e": 0.2, "f": 0.5},
  arcColor={(0, 1): 0.2, (1, 2): 0.5},
  arcWidth={(0, 3): 0.4, (3, 2): 0.5, (2, 4): 0.6},
)

Image(filename="out/export/test_export.png")

gumimage.exportInference(bn, "out/export/test_export.png")

Image(filename="out/export/test_export.png")

gumimage.export(bn, "out/export/test_export.pdf")

Link to out/export/test_export.pdf

exporting inference with evidence

bn = gum.loadBN("res/alarm.bgum")
gumimage.exportInference(
  bn,
  "out/export/test_export.pdf",
  evs={"CO": 1, "VENTLUNG": 1},
  targets={
    "VENTALV",
    "CATECHOL",
    "HR",
    "MINVOLSET",
    "ANAPHYLAXIS",
    "STROKEVOLUME",
    "ERRLOWOUTPUT",
    "HBR",
    "PULMEMBOLUS",
    "HISTORY",
    "BP",
    "PRESS",
    "CO",
  },
  size="15!",
)

Link to out/export/test_export.pdf

Other models

Other models can also use these functions.

infdiag = gum.loadID("res/OilWildcatter.bgum")
gumimage.export(infdiag, "out/export/test_export.pdf")

Link to out/export/test_export.pdf

gumimage.exportInference(infdiag, "out/export/test_export.pdf")

Link to out/export/test_export.pdf

Exporting any object with toDot() method

obs1 = gum.fastBN("Smoking->Cancer")
modele3 = gum.CausalModel(obs1, [("Genotype", ["Smoking", "Cancer"])], True)
gumimage.export(modele3, "out/export/test_export.png")  # a causal model has a toDot method.
Image(filename="out/export/test_export.png")

bn = gum.fastBN("a->b->c->d;b->e->d->f;g->c")
ie = gum.LazyPropagation(bn)
jt = ie.junctionTree()
gumimage.export(jt, "out/export/test_export.png")  # a JunctionTree has a method jt.toDot()
Image(filename="out/export/test_export.png")

… or even a string in dot syntax

gumimage.export(
  jt.toDotWithNames(bn), "out/export/test_export.png"
)  # jt.toDotWithNames(bn) creates a dot-string for a junction tree with names of variables
Image(filename="out/export/test_export.png")

Exporting to pyplot

import matplotlib.pyplot as plt

bn = gum.fastBN("A->B->C<-D")

plt.imshow(gumimage.export(bn))
plt.show()

plt.imshow(gumimage.exportInference(bn, size="15!"))
plt.show()

plt.figure(figsize=(10, 10))
plt.imshow(gumimage.exportInference(bn, size="15!"))
plt.show()

Exporting CPTs and HTML views

pyagrum.lib.image.export() handles any object with a _repr_html_() method (CPTs, inspectBN, sideBySide, explain.Information…) in addition to graphical models.

bn = gum.fastBN("A->B<-C", 3)
gumimage.export(bn.cpt("B"), "out/export/cpt_B_.pdf")

gumimage.export(gnb.getSideBySide(bn, bn.cpt("A"), bn.cpt("B"), bn.cpt("C")), "out/export/sideBySide.pdf")

import pyagrum.explain as gexplain

gumimage.export(gexplain.getInformation(bn), "out/export/informationBN.pdf")

gumimage.export(gnb.inspectBN(bn), "out/export/inspectBN.pdf")

Adjusting PDF margins

PDF export adds margins around the content (default: 50px horizontal, 37px vertical). These can be changed via gum.config — using push/pop to restore defaults afterwards.

gum.config.push()
gum.config.typed["notebook", "export_pdf_margin_x"] = 10
gum.config.typed["notebook", "export_pdf_margin_y"] = 10
gumimage.export(bn.cpt("B"), "out/export/cpt_B_tight.pdf")
gum.config.pop()

gum.config.push()
gum.config.typed["notebook", "export_pdf_margin_x"] = 30
gum.config.typed["notebook", "export_pdf_margin_y"] = 30
gumimage.export(gnb.inspectBN(bn), "out/export/tootight_inspectBN.pdf")
gum.config.pop()