pyAgrum.lib.notebook¶
pyAgrum.lib.notebook
aims to facilitate the use of pyAgrum with jupyter notebook (or lab).
Visualization of graphical models¶
Important
For many graphical representations functions, the parameter size is directly transferred to graphviz. Hence, Its format is a string containing an int. However if size ends in an exclamation point “!” (such as size=”4!”), then size is taken to be the desired minimum size. In this case, if both dimensions of the drawing are less than size, the drawing is scaled up uniformly until at least one dimension equals its dimension in size.
- pyAgrum.lib.notebook.showBN(bn, size=None, nodeColor=None, arcWidth=None, arcColor=None, cmap=None, cmapArc=None)¶
show a Bayesian network
- Parameters
bn – the Bayesian network
size – size of the rendered graph
nodeColor – a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
arcWidth – a arcMap of values to be shown as width of arcs
arcColor – a arcMap of values (between 0 and 1) to be shown as color of arcs
cmap – color map to show the colors
cmapArc – color map to show the arc color if distinction is needed
- Returns
the graph
- pyAgrum.lib.notebook.getBN(bn, size=None, nodeColor=None, arcWidth=None, arcColor=None, cmap=None, cmapArc=None)¶
get a HTML string for a Bayesian network
- Parameters
bn – the Bayesian network
size – size of the rendered graph
nodeColor – a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
arcWidth – a arcMap of values to be shown as width of arcs
arcColor – a arcMap of values (between 0 and 1) to be shown as color of arcs
cmap – color map to show the colors
cmapArc – color map to show the arc color if distinction is needed
- Returns
the graph
- pyAgrum.lib.notebook.showInfluenceDiagram(diag, size=None)¶
show an influence diagram as a graph
- Parameters
diag – the influence diagram
size – size of the rendered graph
- Returns
the representation of the influence diagram
- pyAgrum.lib.notebook.getInfluenceDiagram(diag, size=None)¶
get a HTML string for an influence diagram as a graph
- Parameters
diag – the influence diagram
size – size of the rendered graph
- Returns
the HTML representation of the influence diagram
- pyAgrum.lib.notebook.showMN(mn, view=None, size=None, nodeColor=None, factorColor=None, edgeWidth=None, edgeColor=None, cmap=None, cmapEdge=None)¶
show a Markov network
- Parameters
mn – the markov network
view – ‘graph’ | ‘factorgraph’ | None (default)
size – size of the rendered graph
nodeColor – a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
factorColor – a function returning a value (beeween 0 and 1) to be shown as a color of factor. (used when view=’factorgraph’)
edgeWidth – a edgeMap of values to be shown as width of edges (used when view=’graph’)
edgeColor – a edgeMap of values (between 0 and 1) to be shown as color of edges (used when view=’graph’)
cmap – color map to show the colors
cmapEdge – color map to show the edge color if distinction is needed
- Returns
the graph
- pyAgrum.lib.notebook.getMN(mn, view=None, size=None, nodeColor=None, factorColor=None, edgeWidth=None, edgeColor=None, cmap=None, cmapEdge=None)¶
get an HTML string for a Markov network
- Parameters
mn – the markov network
view – ‘graph’ | ‘factorgraph’ | None (default)
size – size of the rendered graph
nodeColor – a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
factorColor – a function returning a value (beeween 0 and 1) to be shown as a color of factor. (used when view=’factorgraph’)
edgeWidth – a edgeMap of values to be shown as width of edges (used when view=’graph’)
edgeColor – a edgeMap of values (between 0 and 1) to be shown as color of edges (used when view=’graph’)
cmap – color map to show the colors
cmapEdge – color map to show the edge color if distinction is needed
- Returns
the graph
- pyAgrum.lib.notebook.showCN(cn, size=None, nodeColor=None, arcWidth=None, arcColor=None, cmap=None, cmapArc=None)¶
show a credal network
- Parameters
cn – the credal network
size – size of the rendered graph
nodeColor – a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
arcWidth – a arcMap of values to be shown as width of arcs
arcColor – a arcMap of values (between 0 and 1) to be shown as color of arcs
cmap – color map to show the colors
cmapArc – color map to show the arc color if distinction is needed
- Returns
the graph
- pyAgrum.lib.notebook.getCN(cn, size=None, nodeColor=None, arcWidth=None, arcColor=None, cmap=None, cmapArc=None)¶
get a HTML string for a credal network
- Parameters
cn – the credal network
size – size of the rendered graph
nodeColor – a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
arcWidth – a arcMap of values to be shown as width of arcs
arcColor – a arcMap of values (between 0 and 1) to be shown as color of arcs
cmap – color map to show the colors
cmapArc – color map to show the arc color if distinction is needed
- Returns
the graph
- pyAgrum.lib.notebook.showInference(model, **kwargs)¶
show pydot graph for an inference in a notebook
- Parameters
model (GraphicalModel) – the model in which to infer (pyAgrum.BayesNet, pyAgrum.MarkovNet or pyAgrum.InfluenceDiagram)
engine (gum.Inference) – inference algorithm used. If None, gum.LazyPropagation will be used for BayesNet, gum.ShaferShenoy for gum.MarkovNet and gum.ShaferShenoyLIMIDInference for gum.InfluenceDiagram.
evs (dictionnary) – map of evidence
targets (set) – set of targets
size (string) – size of the rendered graph
nodeColor – a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
factorColor – a nodeMap of values (between 0 and 1) to be shown as color of factors (in MarkovNet representation)
arcWidth – a arcMap of values to be shown as width of arcs
arcColor – a arcMap of values (between 0 and 1) to be shown as color of arcs
cmap – color map to show the color of nodes and arcs
cmapArc – color map to show the vals of Arcs.
graph – only shows nodes that have their id in the graph (and not in the whole BN)
view – graph | factorgraph | None (default) for Markov network
- Returns
the desired representation of the inference
- pyAgrum.lib.notebook.getInference(model, **kwargs)¶
get a HTML string for an inference in a notebook
- Parameters
model (GraphicalModel) – the model in which to infer (pyAgrum.BayesNet, pyAgrum.MarkovNet or pyAgrum.InfluenceDiagram)
engine (gum.Inference) – inference algorithm used. If None, gum.LazyPropagation will be used for BayesNet, gum.ShaferShenoy for gum.MarkovNet and gum.ShaferShenoyLIMIDInference for gum.InfluenceDiagram.
evs (dictionnary) – map of evidence
targets (set) – set of targets
size (string) – size of the rendered graph
nodeColor – a nodeMap of values (between 0 and 1) to be shown as color of nodes (with special colors for 0 and 1)
factorColor – a nodeMap of values (between 0 and 1) to be shown as color of factors (in MarkovNet representation)
arcWidth – a arcMap of values to be shown as width of arcs
arcColor – a arcMap of values (between 0 and 1) to be shown as color of arcs
cmap – color map to show the color of nodes and arcs
cmapArc – color map to show the vals of Arcs.
graph – only shows nodes that have their id in the graph (and not in the whole BN)
view – graph | factorgraph | None (default) for Markov network
- Returns
the desired representation of the inference
- pyAgrum.lib.notebook.showJunctionTree(bn, withNames=True, size=None)¶
Show a junction tree
- Parameters
bn – the Bayesian network
withNames (boolean) – display the variable names or the node id in the clique
size – size of the rendered graph
- Returns
the representation of the graph
- pyAgrum.lib.notebook.getJunctionTree(bn, withNames=True, size=None)¶
get a HTML string for a junction tree (more specifically a join tree)
- Parameters
bn – the Bayesian network
withNames (boolean) – display the variable names or the node id in the clique
size – size of the rendered graph
- Returns
the HTML representation of the graph
Visualization of Potentials¶
- pyAgrum.lib.notebook.showProba(p, scale=1.0)¶
Show a mono-dim Potential
- Parameters
p – the mono-dim Potential
scale – the scale (zoom)
- pyAgrum.lib.notebook.getPosterior(bn, evs, target)¶
shortcut for proba2histo(gum.getPosterior(bn,evs,target))
- Parameters
bn (gum.BayesNet) – the BayesNet
evs (dict(str->int)) – map of evidence
target (str) – name of target variable
- Returns
the matplotlib graph
- pyAgrum.lib.notebook.showPosterior(bn, evs, target)¶
shortcut for showProba(gum.getPosterior(bn,evs,target))
- Parameters
bn – the BayesNet
evs – map of evidence
target – name of target variable
- pyAgrum.lib.notebook.getPotential(pot, digits=None, withColors=None, varnames=None)¶
return a HTML string of a gum.Potential as a HTML table. The first dimension is special (horizontal) due to the representation of conditional probability table
- Parameters
pot (gum.Potential) – the potential to get
digits (int) – number of digits to show
varnames (list of strings) – the aliases for variables name in the table
- Param
boolean withColors : bgcolor for proba cells or not
- Returns
the HTML string
- pyAgrum.lib.notebook.showPotential(pot, digits=None, withColors=None, varnames=None)¶
show a gum.Potential as a HTML table. The first dimension is special (horizontal) due to the representation of conditional probability table
- Parameters
pot (gum.Potential) – the potential to get
digits (int) – number of digits to show
varnames (list of strings) – the aliases for variables name in the table
- Param
boolean withColors : bgcolor for proba cells or not
- Returns
the display of the potential
Visualization of graphs¶
- pyAgrum.lib.notebook.getDot(dotstring, size=None)¶
get a dot string as a HTML string
- Parameters
dotstring – dot string
size – size of the rendered graph
format – render as “png” or “svg”
bg – color for background
- Returns
the HTML representation of the graph
- pyAgrum.lib.notebook.showDot(dotstring, size=None)¶
show a dot string as a graph
- Parameters
dotstring – dot string
size – size of the rendered graph
- Returns
the representation of the graph
- pyAgrum.lib.notebook.getGraph(gr, size=None)¶
get a HTML string representation of pydot graph
- Parameters
gr – pydot graph
size – size of the rendered graph
format – render as “png” or “svg”
- Returns
the HTML representation of the graph as a string
- pyAgrum.lib.notebook.showGraph(gr, size=None)¶
show a pydot graph in a notebook
- Parameters
gr – pydot graph
size – size of the rendered graph
- Returns
the representation of the graph
Visualization of approximation algorithm¶
- pyAgrum.lib.notebook.animApproximationScheme(apsc, scale=<ufunc 'log10'>)¶
show an animated version of an approximation algorithm
- Parameters
apsc – the approximation algorithm
scale – a function to apply to the figure
Helpers¶
- pyAgrum.lib.notebook.configuration()¶
Display the collection of dependance and versions
- pyAgrum.lib.notebook.sideBySide(*args, **kwargs)¶
display side by side args as HMTL fragment (using string, _repr_html_() or str())
- Parameters
args – HMTL fragments as string arg, arg._repr_html_() or str(arg)
captions – list of strings (captions)