From a5351137ab8b09adb7eeeb972989a9e97736e292 Mon Sep 17 00:00:00 2001 From: Frank Dellaert Date: Mon, 20 Dec 2021 00:19:35 -0500 Subject: [PATCH] Show factor graph in notebook --- gtsam/discrete/discrete.i | 15 +- .../gtsam/notebooks/DiscreteBayesTree.ipynb | 33 +++- .../gtsam/notebooks/DiscreteSwitching.ipynb | 176 ++++++++++++++++++ 3 files changed, 218 insertions(+), 6 deletions(-) create mode 100644 python/gtsam/notebooks/DiscreteSwitching.ipynb diff --git a/gtsam/discrete/discrete.i b/gtsam/discrete/discrete.i index e802d3db8..87fdca72c 100644 --- a/gtsam/discrete/discrete.i +++ b/gtsam/discrete/discrete.i @@ -106,6 +106,11 @@ class DiscreteBayesTree { double operator()(const gtsam::DiscreteValues& values) const; }; +#include +class DotWriter { + DotWriter(); +}; + #include class DiscreteFactorGraph { DiscreteFactorGraph(); @@ -122,7 +127,15 @@ class DiscreteFactorGraph { void print(string s = "") const; bool equals(const gtsam::DiscreteFactorGraph& fg, double tol = 1e-9) const; - + + string dot(const gtsam::DotWriter& dotWriter = gtsam::DotWriter(), + const gtsam::KeyFormatter& keyFormatter = + gtsam::DefaultKeyFormatter) const; + void saveGraph(string s, + const gtsam::DotWriter& dotWriter = gtsam::DotWriter(), + const gtsam::KeyFormatter& keyFormatter = + gtsam::DefaultKeyFormatter) const; + gtsam::DecisionTreeFactor product() const; double operator()(const gtsam::DiscreteValues& values) const; gtsam::DiscreteValues optimize() const; diff --git a/python/gtsam/notebooks/DiscreteBayesTree.ipynb b/python/gtsam/notebooks/DiscreteBayesTree.ipynb index a678e0d1b..066c31d6a 100644 --- a/python/gtsam/notebooks/DiscreteBayesTree.ipynb +++ b/python/gtsam/notebooks/DiscreteBayesTree.ipynb @@ -61,7 +61,7 @@ "data": { "image/svg+xml": "\n\n\n\n\n\nG\n\n\n\n8\n\n8\n\n\n\n0\n\n0\n\n\n\n8->0\n\n\n\n\n\n1\n\n1\n\n\n\n8->1\n\n\n\n\n\n12\n\n12\n\n\n\n12->8\n\n\n\n\n\n12->0\n\n\n\n\n\n12->1\n\n\n\n\n\n9\n\n9\n\n\n\n12->9\n\n\n\n\n\n2\n\n2\n\n\n\n12->2\n\n\n\n\n\n3\n\n3\n\n\n\n12->3\n\n\n\n\n\n9->2\n\n\n\n\n\n9->3\n\n\n\n\n\n10\n\n10\n\n\n\n4\n\n4\n\n\n\n10->4\n\n\n\n\n\n5\n\n5\n\n\n\n10->5\n\n\n\n\n\n13\n\n13\n\n\n\n13->10\n\n\n\n\n\n13->4\n\n\n\n\n\n13->5\n\n\n\n\n\n11\n\n11\n\n\n\n13->11\n\n\n\n\n\n6\n\n6\n\n\n\n13->6\n\n\n\n\n\n7\n\n7\n\n\n\n13->7\n\n\n\n\n\n11->6\n\n\n\n\n\n11->7\n\n\n\n\n\n14\n\n14\n\n\n\n14->8\n\n\n\n\n\n14->12\n\n\n\n\n\n14->9\n\n\n\n\n\n14->10\n\n\n\n\n\n14->13\n\n\n\n\n\n14->11\n\n\n\n\n\n", "text/plain": [ - "<__main__.show at 0x1051c05b0>" + "<__main__.show at 0x109c615b0>" ] }, "execution_count": 4, @@ -130,9 +130,9 @@ "outputs": [ { "data": { - "image/svg+xml": "\n\n\n\n\n\nG\n\n\n\n0\n\n8,12,14\n\n\n\n1\n\n0 : 8,12\n\n\n\n0->1\n\n\n\n\n\n2\n\n1 : 8,12\n\n\n\n0->2\n\n\n\n\n\n3\n\n9 : 12,14\n\n\n\n0->3\n\n\n\n\n\n6\n\n10,13 : 14\n\n\n\n0->6\n\n\n\n\n\n4\n\n2 : 9,12\n\n\n\n3->4\n\n\n\n\n\n5\n\n3 : 9,12\n\n\n\n3->5\n\n\n\n\n\n7\n\n4 : 10,13\n\n\n\n6->7\n\n\n\n\n\n8\n\n5 : 10,13\n\n\n\n6->8\n\n\n\n\n\n9\n\n11 : 13,14\n\n\n\n6->9\n\n\n\n\n\n10\n\n6 : 11,13\n\n\n\n9->10\n\n\n\n\n\n11\n\n7 : 11,13\n\n\n\n9->11\n\n\n\n\n\n", + "image/svg+xml": "\n\n\n\n\n\n\n\n\nvar0\n\n0\n\n\n\nfactor0\n\n\n\n\nvar0--factor0\n\n\n\n\nvar1\n\n1\n\n\n\nfactor1\n\n\n\n\nvar1--factor1\n\n\n\n\nvar2\n\n2\n\n\n\nfactor2\n\n\n\n\nvar2--factor2\n\n\n\n\nvar3\n\n3\n\n\n\nfactor3\n\n\n\n\nvar3--factor3\n\n\n\n\nvar4\n\n4\n\n\n\nfactor4\n\n\n\n\nvar4--factor4\n\n\n\n\nvar5\n\n5\n\n\n\nfactor5\n\n\n\n\nvar5--factor5\n\n\n\n\nvar6\n\n6\n\n\n\nfactor6\n\n\n\n\nvar6--factor6\n\n\n\n\nvar7\n\n7\n\n\n\nfactor7\n\n\n\n\nvar7--factor7\n\n\n\n\nvar8\n\n8\n\n\n\nvar8--factor0\n\n\n\n\nvar8--factor1\n\n\n\n\nfactor8\n\n\n\n\nvar8--factor8\n\n\n\n\nvar9\n\n9\n\n\n\nvar9--factor2\n\n\n\n\nvar9--factor3\n\n\n\n\nfactor9\n\n\n\n\nvar9--factor9\n\n\n\n\nvar10\n\n10\n\n\n\nvar10--factor4\n\n\n\n\nvar10--factor5\n\n\n\n\nfactor10\n\n\n\n\nvar10--factor10\n\n\n\n\nvar11\n\n11\n\n\n\nvar11--factor6\n\n\n\n\nvar11--factor7\n\n\n\n\nfactor11\n\n\n\n\nvar11--factor11\n\n\n\n\nvar12\n\n12\n\n\n\nvar14\n\n14\n\n\n\nvar12--var14\n\n\n\n\nvar12--factor0\n\n\n\n\nvar12--factor1\n\n\n\n\nvar12--factor2\n\n\n\n\nvar12--factor3\n\n\n\n\nvar12--factor8\n\n\n\n\nvar12--factor9\n\n\n\n\nvar13\n\n13\n\n\n\nvar13--var14\n\n\n\n\nvar13--factor4\n\n\n\n\nvar13--factor5\n\n\n\n\nvar13--factor6\n\n\n\n\nvar13--factor7\n\n\n\n\nvar13--factor10\n\n\n\n\nvar13--factor11\n\n\n\n\nvar14--factor8\n\n\n\n\nvar14--factor9\n\n\n\n\nvar14--factor10\n\n\n\n\nvar14--factor11\n\n\n\n\nfactor14\n\n\n\n\nvar14--factor14\n\n\n\n\n", "text/plain": [ - "<__main__.show at 0x1051c00d0>" + "<__main__.show at 0x109c61f10>" ] }, "execution_count": 6, @@ -141,10 +141,33 @@ } ], "source": [ - "# Create a BayesTree out of the Bayes net.\n", + "# Create a factor graph out of the Bayes net.\n", + "factorGraph = DiscreteFactorGraph(bayesNet)\n", + "show(factorGraph)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": "\n\n\n\n\n\nG\n\n\n\n0\n\n8,12,14\n\n\n\n1\n\n0 : 8,12\n\n\n\n0->1\n\n\n\n\n\n2\n\n1 : 8,12\n\n\n\n0->2\n\n\n\n\n\n3\n\n9 : 12,14\n\n\n\n0->3\n\n\n\n\n\n6\n\n10,13 : 14\n\n\n\n0->6\n\n\n\n\n\n4\n\n2 : 9,12\n\n\n\n3->4\n\n\n\n\n\n5\n\n3 : 9,12\n\n\n\n3->5\n\n\n\n\n\n7\n\n4 : 10,13\n\n\n\n6->7\n\n\n\n\n\n8\n\n5 : 10,13\n\n\n\n6->8\n\n\n\n\n\n9\n\n11 : 13,14\n\n\n\n6->9\n\n\n\n\n\n10\n\n6 : 11,13\n\n\n\n9->10\n\n\n\n\n\n11\n\n7 : 11,13\n\n\n\n9->11\n\n\n\n\n\n", + "text/plain": [ + "<__main__.show at 0x109c61b50>" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Create a BayesTree out of the factor graph.\n", "ordering = Ordering()\n", "for j in range(15): ordering.push_back(j)\n", - "bayesTree = DiscreteFactorGraph(bayesNet).eliminateMultifrontal(ordering)\n", + "bayesTree = factorGraph.eliminateMultifrontal(ordering)\n", "show(bayesTree)" ] } diff --git a/python/gtsam/notebooks/DiscreteSwitching.ipynb b/python/gtsam/notebooks/DiscreteSwitching.ipynb new file mode 100644 index 000000000..0707cbd3b --- /dev/null +++ b/python/gtsam/notebooks/DiscreteSwitching.ipynb @@ -0,0 +1,176 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# A Discrete Switching System\n", + "\n", + "A la MHS, but all discrete.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "from gtsam import DiscreteBayesNet, DiscreteKeys, DiscreteFactorGraph, Ordering\n", + "from gtsam.symbol_shorthand import S\n", + "from gtsam.symbol_shorthand import M\n" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "def P(*args):\n", + " \"\"\" Create a DiscreteKeys instances from a variable number of DiscreteKey pairs.\"\"\"\n", + " # TODO: We can make life easier by providing variable argument functions in C++ itself.\n", + " dks = DiscreteKeys()\n", + " for key in args:\n", + " dks.push_back(key)\n", + " return dks\n" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "import graphviz\n", + "\n", + "\n", + "class show(graphviz.Source):\n", + " \"\"\" Display an object with a dot method as a graph.\"\"\"\n", + "\n", + " def __init__(self, obj):\n", + " \"\"\"Construct from object with 'dot' method.\"\"\"\n", + " # This small class takes an object, calls its dot function, and uses the\n", + " # resulting string to initialize a graphviz.Source instance. This in turn\n", + " # has a _repr_mimebundle_ method, which then renders it in the notebook.\n", + " super().__init__(obj.dot())\n" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": "\n\n\n\n\n\nG\n\n\n\ns1\n\ns1\n\n\n\ns2\n\ns2\n\n\n\ns1->s2\n\n\n\n\n\ns3\n\ns3\n\n\n\ns2->s3\n\n\n\n\n\nm1\n\nm1\n\n\n\nm1->s2\n\n\n\n\n\ns4\n\ns4\n\n\n\ns3->s4\n\n\n\n\n\nm2\n\nm2\n\n\n\nm2->s3\n\n\n\n\n\ns5\n\ns5\n\n\n\ns4->s5\n\n\n\n\n\nm3\n\nm3\n\n\n\nm3->s4\n\n\n\n\n\nm4\n\nm4\n\n\n\nm4->s5\n\n\n\n\n\n", + "text/plain": [ + "<__main__.show at 0x119a80d90>" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "nrStates = 3\n", + "K = 5\n", + "\n", + "bayesNet = DiscreteBayesNet()\n", + "for k in range(1, K):\n", + " key = S(k), nrStates\n", + " key_plus = S(k+1), nrStates\n", + " mode = M(k), 2\n", + " bayesNet.add(key_plus, P(key, mode), \"1/1/1 1/2/1 3/2/3 1/1/1 1/2/1 3/2/3\")\n", + "\n", + "show(bayesNet)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "image/svg+xml": "\n\n\n\n\n\n\n\n\nvar7854277750134145025\n\nm1\n\n\n\nfactor0\n\n\n\n\nvar7854277750134145025--factor0\n\n\n\n\nvar7854277750134145026\n\nm2\n\n\n\nfactor1\n\n\n\n\nvar7854277750134145026--factor1\n\n\n\n\nvar7854277750134145027\n\nm3\n\n\n\nfactor2\n\n\n\n\nvar7854277750134145027--factor2\n\n\n\n\nvar7854277750134145028\n\nm4\n\n\n\nfactor3\n\n\n\n\nvar7854277750134145028--factor3\n\n\n\n\nvar8286623314361712641\n\ns1\n\n\n\nvar8286623314361712641--factor0\n\n\n\n\nvar8286623314361712642\n\ns2\n\n\n\nvar8286623314361712642--factor0\n\n\n\n\nvar8286623314361712642--factor1\n\n\n\n\nvar8286623314361712643\n\ns3\n\n\n\nvar8286623314361712643--factor1\n\n\n\n\nvar8286623314361712643--factor2\n\n\n\n\nvar8286623314361712644\n\ns4\n\n\n\nvar8286623314361712644--factor2\n\n\n\n\nvar8286623314361712644--factor3\n\n\n\n\nvar8286623314361712645\n\ns5\n\n\n\nvar8286623314361712645--factor3\n\n\n\n\n", + "text/plain": [ + "<__main__.show at 0x119a80820>" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Create a factor graph out of the Bayes net.\n", + "factorGraph = DiscreteFactorGraph(bayesNet)\n", + "show(factorGraph)\n" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Position 0: s1, s2, s3, s4, s5, m1, m2, m3, m4\n", + "\n" + ] + }, + { + "data": { + "image/svg+xml": "\n\n\n\n\n\nG\n\n\n\n0\n\ns4,s5,m1,m2,m3,m4\n\n\n\n1\n\ns3 : m1,m2,m3,s4\n\n\n\n0->1\n\n\n\n\n\n2\n\ns2 : m1,m2,s3\n\n\n\n1->2\n\n\n\n\n\n3\n\ns1 : m1,s2\n\n\n\n2->3\n\n\n\n\n\n", + "text/plain": [ + "<__main__.show at 0x119a76b80>" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Create a BayesTree out of the factor graph.\n", + "ordering = Ordering()\n", + "# First eliminate \"continuous\" states in time order\n", + "for k in range(1, K+1):\n", + " ordering.push_back(S(k))\n", + "for k in range(1, K):\n", + " ordering.push_back(M(k))\n", + "print(ordering)\n", + "bayesTree = factorGraph.eliminateMultifrontal(ordering)\n", + "show(bayesTree)\n" + ] + } + ], + "metadata": { + "interpreter": { + "hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6" + }, + "kernelspec": { + "display_name": "Python 3.8.9 64-bit", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.7" + }, + "orig_nbformat": 4 + }, + "nbformat": 4, + "nbformat_minor": 2 +}