I have a dot file generated from my code and want to render it in my output. For this i have seen on the net that the command is something like this on cmd
dot -Tpng InputFile.dot -o OutputFile.png for Graphviz
But my problem is that I want to use this inbuilt in my python program.
How can i do so ??
I looked at pydot but can't seem to find an answer in there.....
Load the file with pydot.graph_from_dot_file to get a pydot.Dot class instance. Then write it to a PNG file with the write_png method.
import pydot
(graph,) = pydot.graph_from_dot_file('somefile.dot')
graph.write_png('somefile.png')
pydot needs the GraphViz binaries to be installed anyway, so if you've already generated your dot file you might as well just invoke dot directly yourself. For example:
from subprocess import check_call
check_call(['dot','-Tpng','InputFile.dot','-o','OutputFile.png'])
You can use pygraphviz. Once you have a graph loaded, you can do
graph.draw('file.png')
You can try:
import os
os.environ["PATH"] += os.pathsep + 'C:/Program Files (x86)/Graphviz2.38/bin/'
os.system('dot -Tpng random.dot -o random.png')
1st Solution)
Going further with the approach of @Mauricio Carrero by setting the PATH inside the script (the same PATH set in the environment variables does not have this effect!):
import os
import pydotplus
from sklearn.tree import export_graphviz
os.environ['PATH'] = os.environ['PATH']+';' + r'C:\Users\Admin\Anaconda3\Library\bin\graphviz'
# first export the dot file only if needed
export_graphviz(clf, out_file=filename + ".dot", feature_names = feature_names)
# now generate the dot_data again
dot_data = export_graphviz(clf, out_file=None, feature_names = feature_names)
graph = pydotplus.graphviz.graph_from_dot_data(dot_data)
graph.write_png(filename + "_gv.png")
This made it possible to save the dot_data to png. Choose your own local paths, you might also have installed graphviz in `C:/Program Files (x86)/Graphviz2.38/bin/
This solution also came from Sarunas answer here: https://datascience.stackexchange.com/questions/37428/graphviz-not-working-when-imported-inside-pydotplus-graphvizs-executables-not
2nd Solution)
You can also avoid the error
Exception has occurred: InvocationException
GraphViz's executables not found
by simply giving it what it wants, as it asks for the executables of the graphviz object:
graph = pydotplus.graphviz.graph_from_dot_data(dot_data)
# graph is now a new Dot object!
# That is why we need to set_graphviz_executables for every new instance
# This cannot be set globally but must be set again and again
# that is why the PATH solution (1st Solution) above seems much better to me
# see the docs in https://pydotplus.readthedocs.io/reference.html
pathCur = 'C:\\Program Files (x86)\\Graphviz2.38\\bin\\'
graph.set_graphviz_executables({'dot': pathCur+'dot.exe', 'twopi': pathCur +'twopi.exe', 'neato': pathCur+'neato.exe', 'circo': pathCur+'circo.exe', 'fdp': pathCur+'fdp.exe'})
graph.write_png(filename + "_gv.png")
p.s: These 2 approaches were the only solutions working for me after 2 hours of calibrating erroneuos installations and full uninstall and install again, all varieties of PATH variables, external and internal graphviz installation, python-graphviz, pygraphviz and all of the solutions I could find in here, or in Convert decision tree directly to png or in https://datascience.stackexchange.com/questions/37428/graphviz-not-working-when-imported-inside-pydotplus-graphvizs-executables-not?newreg=a789aadc5d4b4975949afadd3919fe55
For conda python-graphviz, I got constant installation errors like
InvalidArchiveError('Error with archive C:\\Users\\Admin\\Anaconda3\\pkgs\\openssl-1.1.1d-he774522_20ffr2kor\\pkg-openssl-1.1.1d-he774522_2.tar.zst. You probably need to delete and re-download or re-create this file. Message from libarchive was:\n\nCould not unlink')
For conda install graphviz, I got
InvalidArchiveError('Error with archive C:\\Users\\Admin\\Anaconda3\\pkgs\\openssl-1.1.1d-he774522_21ww0bpcs\\pkg-openssl-1.1.1d-he774522_2.tar.zst. You probably need to delete and re-download or re-create this file. Message from libarchive was:\n\nCould not unlink')
pygraphviz needs MS Visual C++ which I did not want to install:
error: Microsoft Visual C++ 14.0 is required. Get it with "Microsoft Visual C++ Build Tools": https://visualstudio.microsoft.com/downloads/
In the end, no guide was working to really set the PATH variables correctly except for the 1st Solution approach.
You can use graphviz:
# Convert a .dot file to .png
from graphviz import render
render('dot', 'png', 'fname.dot')
# To render an existing file in a notebook
from graphviz import Source
Source.from_file("fname.dot")