Source code for alogos._grammar.visualization.tree_with_graphviz
import os as _os
from ..._utilities import argument_processing as _ap
from ..._utilities import operating_system as _operating_system
[docs]def create_graphviz_tree(
tree,
show_node_indices=None,
layout_engine=None,
fontname=None,
fontsize=None,
shape_nt=None,
shape_unexpanded_nt=None,
shape_t=None,
fontcolor_nt=None,
fontcolor_unexpanded_nt=None,
fontcolor_t=None,
fillcolor_nt=None,
fillcolor_unexpanded_nt=None,
fillcolor_t=None,
):
"""Represent the derivation tree as Digraph in GraphViz.
References
----------
- `Graphviz <https://www.graphviz.org>`__
- `An inofficial Python wrapper for Graphviz <https://pypi.org/project/graphviz>`__ used here
"""
from graphviz import Digraph
# Argument processing
# Node shapes from http://www.graphviz.org/doc/info/shapes.html
shapes = [
"Mcircle",
"Mdiamond",
"Msquare",
"assembly",
"box",
"box3d",
"cds",
"circle",
"component",
"cylinder",
"diamond",
"doublecircle",
"doubleoctagon",
"egg",
"ellipse",
"fivepoverhang",
"folder",
"hexagon",
"house",
"insulator",
"invhouse",
"invtrapezium",
"invtriangle",
"larrow",
"lpromoter",
"none",
"note",
"noverhang",
"octagon",
"oval",
"parallelogram",
"pentagon",
"plain",
"plaintext",
"point",
"polygon",
"primersite",
"promoter",
"proteasesite",
"proteinstab",
"rarrow",
"rect",
"rectangle",
"restrictionsite",
"ribosite",
"rnastab",
"rpromoter",
"septagon",
"signature",
"square",
"star",
"tab",
"terminator",
"threepoverhang",
"trapezium",
"triangle",
"tripleoctagon",
"underline",
"utr",
None,
]
show_node_indices = _ap.bool_arg(
"show_node_indices", show_node_indices, default=False
)
layout_engine = _ap.str_arg(
"layout_engine",
layout_engine,
default="dot",
vals=[
"circo",
"dot",
"fdp",
"neato",
"osage",
"patchwork",
"sfdp",
"twopi",
None,
],
)
fontname = _ap.str_arg("fontname", fontname, default="Mono")
fontsize = _ap.int_arg("fontsize", fontsize, default=12)
shape_nt = _ap.str_arg("shape_nt", shape_nt, vals=shapes, default="box")
shape_unexpanded_nt = _ap.str_arg(
"shape_unexpanded_nt", shape_unexpanded_nt, vals=shapes, default="box"
)
shape_t = _ap.str_arg("shape_t", shape_t, vals=shapes, default="ellipse")
fontcolor_nt = _ap.str_arg("fontcolor_nt", fontcolor_nt, default="black")
fontcolor_unexpanded_nt = _ap.str_arg(
"fontcolor_unexpanded_nt", fontcolor_unexpanded_nt, default="white"
)
fontcolor_t = _ap.str_arg("fontcolor_t", fontcolor_t, default="white")
fillcolor_nt = _ap.str_arg("fillcolor_nt", fillcolor_nt, default="white")
fillcolor_unexpanded_nt = _ap.str_arg(
"fillcolor_unexpanded_nt", fillcolor_unexpanded_nt, default="#b81118"
)
fillcolor_t = _ap.str_arg("fillcolor_t", fillcolor_t, default="#00864b")
# Graph construction
digraph = Digraph(
engine=layout_engine,
node_attr=dict(fontname=fontname, fontsize=str(fontsize)),
encoding="utf-8",
)
stack = [tree.root_node]
cnt = _AutoCounter()
while stack:
# Get node
current_node = stack.pop(0)
if current_node.children:
stack = current_node.children + stack
child_nodes = current_node.children
else:
child_nodes = []
# Determine node style
node_id = str(cnt[current_node])
if show_node_indices:
node_label = "{}: {}".format(node_id, current_node.symbol)
else:
node_label = current_node.symbol.text
if node_label == "":
node_label = "ɛ"
if current_node.contains_nonterminal():
if not current_node.children:
node_shape = shape_unexpanded_nt
node_fillcolor = fillcolor_unexpanded_nt
node_fontcolor = fontcolor_unexpanded_nt
else:
node_shape = shape_nt
node_fillcolor = fillcolor_nt
node_fontcolor = fontcolor_nt
else:
node_shape = shape_t
node_fillcolor = fillcolor_t
node_fontcolor = fontcolor_t
# Create node in visualized graph
digraph.node(
node_id,
node_label,
shape=node_shape,
fontcolor=node_fontcolor,
style="filled",
fillcolor=node_fillcolor,
)
# Create edges in visualized graph
for child_node in child_nodes:
child_node_id = str(cnt[child_node])
digraph.edge(node_id, child_node_id)
fig = DerivationTreeFigure(digraph)
return fig
[docs]class DerivationTreeFigure:
"""Data structure for wrapping, displaying and exporting a Graphviz graph of a tree."""
# Initialization
[docs] def __init__(self, given_graph):
"""Initialize a figure with a Graphviz graph object."""
self.fig = given_graph
# Representations
def __repr__(self):
"""Compute the "official" string representation of the figure."""
return "<{} object at {}>".format(self.__class__.__name__, hex(id(self)))
def _repr_html_(self):
"""Provide rich display representation in HTML format for Jupyter notebooks."""
return self.html_text_partial
# Display in browser or notebook
[docs] def display(self, inline=False):
"""Display the plot in a webbrowser or as IPython rich display representation.
Parameters
----------
inline : bool
If True, the plot will be shown inline in a Jupyter notebook.
"""
if inline:
from IPython.display import HTML, display
display(HTML(self.html_text_standalone))
else:
_operating_system.open_in_webbrowser(self.html_text_standalone)
# Further representations
@property
def html_text(self):
"""Create a HTML text representation."""
return self.html_text_standalone
@property
def html_text_standalone(self):
"""Create a standalone HTML text representation."""
html_text = _HTML.format(self.svg_text)
return html_text
@property
def html_text_partial(self):
"""Create a partial HTML text representation without html, head and body tags."""
return self.svg_text
@property
def svg_text(self):
"""Create an SVG text representation of the plot, usable in HTML context or SVG file."""
try:
svg_text = self.fig._repr_svg_()
except AttributeError:
# API change: https://graphviz.readthedocs.io/en/latest/changelog.html#version-0-19
mime_type = "image/svg+xml"
data = self.fig._repr_mimebundle_(include=[mime_type])
svg_text = data[mime_type]
lines = svg_text.splitlines()
for _i, line in enumerate(lines):
if line.startswith("<svg"):
break
svg_text = "".join(lines[_i:])
return svg_text
# Export as HTML file
[docs] def export_html(self, filepath):
"""Export the plot as text file in HTML format.
Parameters
----------
filepath : str
Filepath of the created HTML file.
If the file exists it will be overwritten without warning.
If the path does not end with ".html" it will be changed to do so.
If the parent directory does not exist it will be created.
Returns
-------
filepath_used : str
Filepath of the generated HTML file, guaranteed to end with ".html".
"""
# Argument processing
used_filepath = _operating_system.ensure_file_extension(filepath, "html")
# Create HTML file
with open(used_filepath, "w", encoding="utf-8") as file_handle:
file_handle.write(self.html_text)
return used_filepath
# Export in various other file formats
def _export(self, filepath, fileformat):
"""Export the digraph in various formats.
References
----------
- https://graphviz.readthedocs.io/en/stable/api.html#digraph
- https://www.graphviz.org/doc/info/output.html
"""
# Argument processing
filepath = _ap.str_arg("filepath", filepath)
filepath = _ap.ensure_no_file_extension(filepath, fileformat)
# Check if file already exists, only to prevent deletion
did_not_exist = not _os.path.exists(filepath)
# Create image file
used_filepath = self.fig.render(filename=filepath, format=fileformat)
# Remove side product generated by GraphViz
if _os.path.isfile(filepath) and did_not_exist:
_operating_system.delete_file(filepath)
return used_filepath
[docs] def export_dot(self, filepath):
"""Export the plot as text file in DOT format.
Parameters
----------
filepath : str
Filepath of the created DOT file.
If the file exists it will be overwritten without warning.
If the path does not end with ".dot" it will be changed to do so.
If the parent directory does not exist it will be created.
Returns
-------
filepath_used : str
Filepath of the generated DOT file, guaranteed to end with ".dot".
"""
return self._export(filepath, "dot")
[docs] def export_eps(self, filepath):
"""Export the plot as vector graphic in EPS format.
Parameters
----------
filepath : str
Filepath of the created EPS file.
If the file exists it will be overwritten without warning.
If the path does not end with ".eps" it will be changed to do so.
If the parent directory does not exist it will be created.
Returns
-------
filepath_used : str
Filepath of the generated EPS file, guaranteed to end with ".eps".
"""
return self._export(filepath, "eps")
[docs] def export_gv(self, filepath):
"""Export the plot as text file in GV format.
Parameters
----------
filepath : str
Filepath of the created GV file.
If the file exists it will be overwritten without warning.
If the path does not end with ".gv" it will be changed to do so.
If the parent directory does not exist it will be created.
Returns
-------
filepath_used : str
Filepath of the generated GV file, guaranteed to end with ".gv".
"""
return self._export(filepath, "gv")
[docs] def export_pdf(self, filepath):
"""Export the plot as vector graphic in PDF format.
Parameters
----------
filepath : str
Filepath of the created PDF file.
If the file exists it will be overwritten without warning.
If the path does not end with ".pdf" it will be changed to do so.
If the parent directory does not exist it will be created.
Returns
-------
filepath_used : str
Filepath of the generated PDF file, guaranteed to end with ".pdf".
"""
return self._export(filepath, "pdf")
[docs] def export_png(self, filepath):
"""Export the plot as raster graphic in PNG format.
Parameters
----------
filepath : str
Filepath of the created PNG file.
If the file exists it will be overwritten without warning.
If the path does not end with ".png" it will be changed to do so.
If the parent directory does not exist it will be created.
Returns
-------
filepath_used : str
Filepath of the generated PNG file, guaranteed to end with ".png".
"""
return self._export(filepath, "png")
[docs] def export_ps(self, filepath):
"""Export the plot as vector graphic in PS format.
Parameters
----------
filepath : str
Filepath of the created PS file.
If the file exists it will be overwritten without warning.
If the path does not end with ".ps" it will be changed to do so.
If the parent directory does not exist it will be created.
Returns
-------
filepath_used : str
Filepath of the generated PS file, guaranteed to end with ".ps".
"""
return self._export(filepath, "ps")
[docs] def export_svg(self, filepath):
"""Export the plot as vector graphic in SVG format.
Parameters
----------
filepath : str
Filepath of the created SVG file.
If the file exists it will be overwritten without warning.
If the path does not end with ".svg" it will be changed to do so.
If the parent directory does not exist it will be created.
Returns
-------
filepath_used : str
Filepath of the generated SVG file, guaranteed to end with ".svg".
"""
return self._export(filepath, "svg")
_HTML = """<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
</head>
<body>
{}
</body>
</html>"""
class _AutoCounter:
def __init__(self):
self.map = dict()
self.cnt = 0
def __getitem__(self, key):
if key not in self.map:
self.map[key] = self.cnt
self.cnt += 1
return self.map[key]