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Streamlined dot methods #971

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merged 11 commits into from
Dec 21, 2021
Merged

Streamlined dot methods #971

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81b9724
Added dot methods
dellaert Dec 17, 2021
d41ab8a
dot methods
dellaert Dec 19, 2021
3522684
wrap and test dot method
dellaert Dec 19, 2021
d85a1e6
dot methods for Bayes tree
dellaert Dec 19, 2021
46080d7
reversed order of nodes in dot
dellaert Dec 19, 2021
74951be
wrap and notebook
dellaert Dec 19, 2021
e45641e
compilation issue
dellaert Dec 20, 2021
9d2b627
Generic dot export with DotWriter
dellaert Dec 20, 2021
a535113
Show factor graph in notebook
dellaert Dec 20, 2021
cab0dd0
GraphvizFormatting refactor
dellaert Dec 20, 2021
e6ca595
fixed method naming convention
dellaert Dec 20, 2021
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4 changes: 2 additions & 2 deletions gtsam/base/tests/testMatrix.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,7 @@ TEST(Matrix, stack )
{
Matrix A = (Matrix(2, 2) << -5.0, 3.0, 00.0, -5.0).finished();
Matrix B = (Matrix(3, 2) << -0.5, 2.1, 1.1, 3.4, 2.6, 7.1).finished();
Matrix AB = stack(2, &A, &B);
Matrix AB = gtsam::stack(2, &A, &B);
Matrix C(5, 2);
for (int i = 0; i < 2; i++)
for (int j = 0; j < 2; j++)
Expand All @@ -187,7 +187,7 @@ TEST(Matrix, stack )
std::vector<gtsam::Matrix> matrices;
matrices.push_back(A);
matrices.push_back(B);
Matrix AB2 = stack(matrices);
Matrix AB2 = gtsam::stack(matrices);
EQUALITY(C,AB2);
}

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20 changes: 15 additions & 5 deletions gtsam/discrete/DecisionTree-inl.h
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Expand Up @@ -248,8 +248,9 @@ namespace gtsam {
void dot(std::ostream& os, bool showZero) const override {
os << "\"" << this->id() << "\" [shape=circle, label=\"" << label_
<< "\"]\n";
for (size_t i = 0; i < branches_.size(); i++) {
NodePtr branch = branches_[i];
size_t B = branches_.size();
for (size_t i = 0; i < B; i++) {
const NodePtr& branch = branches_[i];

// Check if zero
if (!showZero) {
Expand All @@ -258,8 +259,10 @@ namespace gtsam {
}

os << "\"" << this->id() << "\" -> \"" << branch->id() << "\"";
if (i == 0) os << " [style=dashed]";
if (i > 1) os << " [style=bold]";
if (B == 2) {
if (i == 0) os << " [style=dashed]";
if (i > 1) os << " [style=bold]";
}
os << std::endl;
branch->dot(os, showZero);
}
Expand Down Expand Up @@ -671,7 +674,14 @@ namespace gtsam {
int result = system(
("dot -Tpdf " + name + ".dot -o " + name + ".pdf >& /dev/null").c_str());
if (result==-1) throw std::runtime_error("DecisionTree::dot system call failed");
}
}

template<typename L, typename Y>
std::string DecisionTree<L, Y>::dot(bool showZero) const {
std::stringstream ss;
dot(ss, showZero);
return ss.str();
}

/*********************************************************************************/

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3 changes: 3 additions & 0 deletions gtsam/discrete/DecisionTree.h
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Expand Up @@ -198,6 +198,9 @@ namespace gtsam {
/** output to graphviz format, open a file */
void dot(const std::string& name, bool showZero = true) const;

/** output to graphviz format string */
std::string dot(bool showZero = true) const;

/// @name Advanced Interface
/// @{

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26 changes: 22 additions & 4 deletions gtsam/discrete/discrete.i
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Expand Up @@ -38,7 +38,7 @@ virtual class DecisionTreeFactor: gtsam::DiscreteFactor {
const gtsam::KeyFormatter& keyFormatter =
gtsam::DefaultKeyFormatter) const;
bool equals(const gtsam::DecisionTreeFactor& other, double tol = 1e-9) const;
double operator()(const gtsam::DiscreteValues& values) const; // TODO(dellaert): why do I have to repeat???
string dot(bool showZero = false) const;
};

#include <gtsam/discrete/DiscreteConditional.h>
Expand All @@ -52,8 +52,6 @@ virtual class DiscreteConditional : gtsam::DecisionTreeFactor {
DiscreteConditional(const gtsam::DecisionTreeFactor& joint,
const gtsam::DecisionTreeFactor& marginal,
const gtsam::Ordering& orderedKeys);
size_t size() const; // TODO(dellaert): why do I have to repeat???
double operator()(const gtsam::DiscreteValues& values) const; // TODO(dellaert): why do I have to repeat???
void print(string s = "Discrete Conditional\n",
const gtsam::KeyFormatter& keyFormatter =
gtsam::DefaultKeyFormatter) const;
Expand Down Expand Up @@ -82,6 +80,8 @@ class DiscreteBayesNet {
const gtsam::KeyFormatter& keyFormatter =
gtsam::DefaultKeyFormatter) const;
bool equals(const gtsam::DiscreteBayesNet& other, double tol = 1e-9) const;
string dot(const gtsam::KeyFormatter& keyFormatter =
gtsam::DefaultKeyFormatter) const;
void saveGraph(string s,
const gtsam::KeyFormatter& keyFormatter =
gtsam::DefaultKeyFormatter) const;
Expand All @@ -98,9 +98,19 @@ class DiscreteBayesTree {
const gtsam::KeyFormatter& keyFormatter =
gtsam::DefaultKeyFormatter) const;
bool equals(const gtsam::DiscreteBayesTree& other, double tol = 1e-9) const;
string dot(const gtsam::KeyFormatter& keyFormatter =
gtsam::DefaultKeyFormatter) const;
void saveGraph(string s,
const gtsam::KeyFormatter& keyFormatter =
gtsam::DefaultKeyFormatter) const;
double operator()(const gtsam::DiscreteValues& values) const;
};

#include <gtsam/inference/DotWriter.h>
class DotWriter {
DotWriter();
};

#include <gtsam/discrete/DiscreteFactorGraph.h>
class DiscreteFactorGraph {
DiscreteFactorGraph();
Expand All @@ -117,7 +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;
Expand Down
25 changes: 24 additions & 1 deletion gtsam/discrete/tests/testDiscreteBayesNet.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -135,7 +135,7 @@ TEST(DiscreteBayesNet, Asia) {
}

/* ************************************************************************* */
TEST_UNSAFE(DiscreteBayesNet, Sugar) {
TEST(DiscreteBayesNet, Sugar) {
DiscreteKey T(0, 2), L(1, 2), E(2, 2), C(8, 3), S(7, 2);

DiscreteBayesNet bn;
Expand All @@ -149,6 +149,29 @@ TEST_UNSAFE(DiscreteBayesNet, Sugar) {
bn.add(C | S = "1/1/2 5/2/3");
}

/* ************************************************************************* */
TEST(DiscreteBayesNet, Dot) {
DiscreteKey Asia(0, 2), Smoking(4, 2), Tuberculosis(3, 2), LungCancer(6, 2),
Either(5, 2);

DiscreteBayesNet fragment;
fragment.add(Asia % "99/1");
fragment.add(Smoking % "50/50");

fragment.add(Tuberculosis | Asia = "99/1 95/5");
fragment.add(LungCancer | Smoking = "99/1 90/10");
fragment.add((Either | Tuberculosis, LungCancer) = "F T T T");

string actual = fragment.dot();
EXPECT(actual ==
"digraph G{\n"
"0->3\n"
"4->6\n"
"3->5\n"
"6->5\n"
"}");
}

/* ************************************************************************* */
int main() {
TestResult tr;
Expand Down
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