markdown for graphs

gtsam/discrete/DecisionTreeFactor.h

@@ -168,7 +168,7 @@ namespace gtsam {
 
     /// Render as markdown table.
     std::string _repr_markdown_(
-        const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
+        const KeyFormatter& keyFormatter = DefaultKeyFormatter) const override;
 
     /// @}
 

gtsam/discrete/DiscreteBayesNet.cpp

@@ -38,7 +38,7 @@ namespace gtsam {
   double DiscreteBayesNet::evaluate(const DiscreteValues & values) const {
     // evaluate all conditionals and multiply
     double result = 1.0;
-    for(DiscreteConditional::shared_ptr conditional: *this)
+    for(const DiscreteConditional::shared_ptr& conditional: *this)
       result *= (*conditional)(values);
     return result;
   }
@@ -61,5 +61,15 @@ namespace gtsam {
     return result;
   }
 
+  /* ************************************************************************* */
+  std::string DiscreteBayesNet::_repr_markdown_(
+      const KeyFormatter& keyFormatter) const {
+    using std::endl;
+    std::stringstream ss;
+    ss << "`DiscreteBayesNet` of size " << size() << endl << endl;
+    for(const DiscreteConditional::shared_ptr& conditional: *this)
+      ss << conditional->_repr_markdown_(keyFormatter) << endl;
+    return ss.str();
+  }
 /* ************************************************************************* */
 } // namespace

gtsam/discrete/DiscreteBayesNet.h

@@ -13,6 +13,7 @@
  * @file DiscreteBayesNet.h
  * @date Feb 15, 2011
  * @author Duy-Nguyen Ta
+ * @author Frank dellaert
  */
 
 #pragma once
@@ -97,6 +98,14 @@ namespace gtsam {
     DiscreteValues sample() const;
 
     ///@}
+    /// @name Wrapper support
+    /// @{
+
+    /// Render as markdown table.
+    std::string _repr_markdown_(
+        const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
+
+    /// @}
 
   private:
     /** Serialization function */

gtsam/discrete/DiscreteBayesTree.cpp

@@ -55,8 +55,21 @@ namespace gtsam {
     return result;
   }
 
-} // \namespace gtsam
-
-
-
+  /* **************************************************************************/
+  std::string DiscreteBayesTree::_repr_markdown_(
+      const KeyFormatter& keyFormatter) const {
+    using std::endl;
+    std::stringstream ss;
+    ss << "`DiscreteBayesTree` of size " << nodes_.size() << endl << endl;
+    auto visitor = [&](const DiscreteBayesTreeClique::shared_ptr& clique,
+                       size_t& indent) {
+      ss << "\n" << clique->conditional()->_repr_markdown_(keyFormatter);
+      return indent + 1;
+    };
+    size_t indent;
+    treeTraversal::DepthFirstForest(*this, indent, visitor);
+    return ss.str();
+  }
 
+  /* **************************************************************************/
+  }  // namespace gtsam

gtsam/discrete/DiscreteBayesTree.h

@@ -72,6 +72,8 @@ class GTSAM_EXPORT DiscreteBayesTree
   typedef DiscreteBayesTree This;
   typedef boost::shared_ptr<This> shared_ptr;
 
+  /// @name Standard interface
+  /// @{
   /** Default constructor, creates an empty Bayes tree */
   DiscreteBayesTree() {}
 
@@ -82,10 +84,19 @@ class GTSAM_EXPORT DiscreteBayesTree
   double evaluate(const DiscreteValues& values) const;
 
   //** (Preferred) sugar for the above for given DiscreteValues */
-  double operator()(const DiscreteValues & values) const {
+  double operator()(const DiscreteValues& values) const {
     return evaluate(values);
   }
 
+  /// @}
+  /// @name Wrapper support
+  /// @{
+
+  /// Render as markdown table.
+  std::string _repr_markdown_(
+      const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
+
+  /// @}
 };
 
 }  // namespace gtsam

gtsam/discrete/DiscreteConditional.cpp

@@ -229,11 +229,22 @@ std::string DiscreteConditional::_repr_markdown_(
 
   // Print out signature.
   ss << " $P(";
-  for(Key key: frontals())
-    ss << keyFormatter(key);
-  if (nrParents() > 0)
-    ss << "|";
   bool first = true;
+  for (Key key : frontals()) {
+    if (!first) ss << ",";
+    ss << keyFormatter(key);
+    first = false;
+  }
+  if (nrParents() == 0) {
+   // We have no parents, call factor method.
+    ss << ")$:" << std::endl;
+    ss << DecisionTreeFactor::_repr_markdown_();
+    return ss.str();
+  }
+
+  // We have parents, continue signature and do custom print.
+  ss << "|";
+  first = true;
   for (Key parent : parents()) {
     if (!first) ss << ",";
     ss << keyFormatter(parent);
@@ -256,9 +267,8 @@ std::string DiscreteConditional::_repr_markdown_(
     pairs.emplace_back(key, k);
     n *= k;
   }
-  size_t nrParents = size() - nrFrontals_;
   std::vector<std::pair<Key, size_t>> slatnorf(pairs.rbegin(),
-                                               pairs.rend() - nrParents);
+                                               pairs.rend() - nrParents());
   const auto frontal_assignments = cartesianProduct(slatnorf);
   for (const auto& a : frontal_assignments) {
     for (it = beginFrontals(); it != endFrontals(); ++it) ss << a.at(*it);
@@ -268,7 +278,7 @@ std::string DiscreteConditional::_repr_markdown_(
 
   // Print out separator with alignment hints.
   ss << "|";
-  for (size_t j = 0; j < nrParents + n; j++) ss << ":-:|";
+  for (size_t j = 0; j < nrParents() + n; j++) ss << ":-:|";
   ss << "\n";
 
   // Print out all rows.

gtsam/discrete/DiscreteConditional.h

@@ -172,7 +172,7 @@ class GTSAM_EXPORT DiscreteConditional: public DecisionTreeFactor,
 
   /// Render as markdown table.
   std::string _repr_markdown_(
-      const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
+      const KeyFormatter& keyFormatter = DefaultKeyFormatter) const override;
 
   /// @}
 };

gtsam/discrete/DiscreteFactor.h

@@ -88,6 +88,14 @@ class GTSAM_EXPORT DiscreteFactor: public Factor {
 
   virtual DecisionTreeFactor toDecisionTreeFactor() const = 0;
 
+  /// @}
+  /// @name Wrapper support
+  /// @{
+
+  /// Render as markdown table.
+  virtual std::string _repr_markdown_(
+      const KeyFormatter& keyFormatter = DefaultKeyFormatter) const = 0;
+
   /// @}
 };
 // DiscreteFactor

gtsam/discrete/DiscreteFactorGraph.cpp

@@ -129,6 +129,18 @@ namespace gtsam {
     return std::make_pair(cond, sum);
   }
 
-/* ************************************************************************* */
-} // namespace
+  /* ************************************************************************* */
+  std::string DiscreteFactorGraph::_repr_markdown_(
+      const KeyFormatter& keyFormatter) const {
+    using std::endl;
+    std::stringstream ss;
+    ss << "`DiscreteFactorGraph` of size " << size() << endl << endl;
+    for (size_t i = 0; i < factors_.size(); i++) {
+      ss << "factor " << i << ":\n";
+      ss << factors_[i]->_repr_markdown_(keyFormatter) << endl;
+    }
+    return ss.str();
+  }
 
+  /* ************************************************************************* */
+  }  // namespace gtsam

gtsam/discrete/DiscreteFactorGraph.h

@@ -154,6 +154,14 @@ public EliminateableFactorGraph<DiscreteFactorGraph> {
 //  /** Apply a reduction, which is a remapping of variable indices. */
 //  GTSAM_EXPORT void reduceWithInverse(const internal::Reduction& inverseReduction);
 
+  /// @name Wrapper support
+  /// @{
+
+  /// Render as markdown table.
+  std::string _repr_markdown_(
+      const KeyFormatter& keyFormatter = DefaultKeyFormatter) const;
+
+  /// @}
 }; // \ DiscreteFactorGraph
 
 /// traits

gtsam/discrete/discrete.i

@@ -93,6 +93,8 @@ class DiscreteBayesNet {
   double operator()(const gtsam::DiscreteValues& values) const;
   gtsam::DiscreteValues optimize() const;
   gtsam::DiscreteValues sample() const;
+  string _repr_markdown_(const gtsam::KeyFormatter& keyFormatter =
+                 gtsam::DefaultKeyFormatter) const;
 };
 
 #include <gtsam/discrete/DiscreteBayesTree.h>
@@ -124,6 +126,9 @@ class DiscreteBayesTree {
                 const gtsam::KeyFormatter& keyFormatter =
                  gtsam::DefaultKeyFormatter) const;
   double operator()(const gtsam::DiscreteValues& values) const;
+
+  string _repr_markdown_(const gtsam::KeyFormatter& keyFormatter =
+                 gtsam::DefaultKeyFormatter) const;
 };
 
 #include <gtsam/inference/DotWriter.h>
@@ -164,6 +169,9 @@ class DiscreteFactorGraph {
   gtsam::DiscreteBayesNet eliminateSequential(const gtsam::Ordering& ordering);
   gtsam::DiscreteBayesTree eliminateMultifrontal();
   gtsam::DiscreteBayesTree eliminateMultifrontal(const gtsam::Ordering& ordering);
+
+  string _repr_markdown_(const gtsam::KeyFormatter& keyFormatter =
+                 gtsam::DefaultKeyFormatter) const;
 };
 
 }  // namespace gtsam

gtsam/discrete/tests/testDiscreteBayesNet.cpp

@@ -38,6 +38,9 @@ using namespace boost::assign;
 using namespace std;
 using namespace gtsam;
 
+static const DiscreteKey Asia(0, 2), Smoking(4, 2), Tuberculosis(3, 2),
+    LungCancer(6, 2), Bronchitis(7, 2), Either(5, 2), XRay(2, 2), Dyspnea(1, 2);
+
 /* ************************************************************************* */
 TEST(DiscreteBayesNet, bayesNet) {
   DiscreteBayesNet bayesNet;
@@ -71,8 +74,6 @@ TEST(DiscreteBayesNet, bayesNet) {
 /* ************************************************************************* */
 TEST(DiscreteBayesNet, Asia) {
   DiscreteBayesNet asia;
-  DiscreteKey Asia(0, 2), Smoking(4, 2), Tuberculosis(3, 2), LungCancer(6, 2),
-      Bronchitis(7, 2), Either(5, 2), XRay(2, 2), Dyspnea(1, 2);
 
   asia.add(Asia % "99/1");
   asia.add(Smoking % "50/50");
@@ -151,9 +152,6 @@ TEST(DiscreteBayesNet, Sugar) {
 
 /* ************************************************************************* */
 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");
@@ -172,6 +170,32 @@ TEST(DiscreteBayesNet, Dot) {
          "}");
 }
 
+/* ************************************************************************* */
+// Check markdown representation looks as expected.
+TEST(DiscreteBayesNet, markdown) {
+  DiscreteBayesNet fragment;
+  fragment.add(Asia % "99/1");
+  fragment.add(Smoking | Asia = "8/2 7/3");
+
+  string expected =
+      "`DiscreteBayesNet` of size 2\n"
+      "\n"
+      " $P(Asia)$:\n"
+      "|0|value|\n"
+      "|:-:|:-:|\n"
+      "|0|0.99|\n"
+      "|1|0.01|\n"
+      "\n"
+      " $P(Smoking|Asia)$:\n"
+      "|Asia|0|1|\n"
+      "|:-:|:-:|:-:|\n"
+      "|0|0.8|0.2|\n"
+      "|1|0.7|0.3|\n\n";
+  auto formatter = [](Key key) { return key == 0 ? "Asia" : "Smoking"; };
+  string actual = fragment._repr_markdown_(formatter);
+  EXPECT(actual == expected);
+}
+
 /* ************************************************************************* */
 int main() {
   TestResult tr;

gtsam/discrete/tests/testDiscreteConditional.cpp

@@ -110,13 +110,15 @@ TEST(DiscreteConditional, Combine) {
 /* ************************************************************************* */
 // Check markdown representation looks as expected, no parents.
 TEST(DiscreteConditional, markdown_prior) {
-  DiscreteKey A(Symbol('x', 1), 2);
-  DiscreteConditional conditional(A % "1/3");
+  DiscreteKey A(Symbol('x', 1), 3);
+  DiscreteConditional conditional(A % "1/2/2");
   string expected =
       " $P(x1)$:\n"
-      "|0|1|\n"
+      "|x1|value|\n"
       "|:-:|:-:|\n"
-      "|0.25|0.75|\n";
+      "|0|0.2|\n"
+      "|1|0.4|\n"
+      "|2|0.4|\n";
   string actual = conditional._repr_markdown_();
   EXPECT(actual == expected);
 }

gtsam/discrete/tests/testDiscreteFactorGraph.cpp

@@ -361,11 +361,9 @@ cout << unicorns;
 
 /* ************************************************************************* */
 TEST(DiscreteFactorGraph, Dot) {
-  // Declare a bunch of keys
-  DiscreteKey C(0, 2), A(1, 2), B(2, 2);
-
   // Create Factor graph
   DiscreteFactorGraph graph;
+  DiscreteKey C(0, 2), A(1, 2), B(2, 2);
   graph.add(C & A, "0.2 0.8 0.3 0.7");
   graph.add(C & B, "0.1 0.9 0.4 0.6");
 
@@ -384,6 +382,44 @@ TEST(DiscreteFactorGraph, Dot) {
   EXPECT(actual == expected);
 }
 
+/* ************************************************************************* */
+// Check markdown representation looks as expected.
+TEST(DiscreteFactorGraph, markdown) {
+  // Create Factor graph
+  DiscreteFactorGraph graph;
+  DiscreteKey C(0, 2), A(1, 2), B(2, 2);
+  graph.add(C & A, "0.2 0.8 0.3 0.7");
+  graph.add(C & B, "0.1 0.9 0.4 0.6");
+
+  string expected =
+      "`DiscreteFactorGraph` of size 2\n"
+      "\n"
+      "factor 0:\n"
+      "|C|A|value|\n"
+      "|:-:|:-:|:-:|\n"
+      "|0|0|0.2|\n"
+      "|0|1|0.8|\n"
+      "|1|0|0.3|\n"
+      "|1|1|0.7|\n"
+      "\n"
+      "factor 1:\n"
+      "|C|B|value|\n"
+      "|:-:|:-:|:-:|\n"
+      "|0|0|0.1|\n"
+      "|0|1|0.9|\n"
+      "|1|0|0.4|\n"
+      "|1|1|0.6|\n\n";
+  vector<string> names{"C", "A", "B"};
+  auto formatter = [names](Key key) { return names[key]; };
+  string actual = graph._repr_markdown_(formatter);
+  EXPECT(actual == expected);
+
+  // Make sure values are correctly displayed.
+  DiscreteValues values;
+  values[0] = 1;
+  values[1] = 0;
+  EXPECT_DOUBLES_EQUAL(0.3, graph[0]->operator()(values), 1e-9);
+}
 /* ************************************************************************* */
 int main() {
 TestResult tr;