Feature/metadata (#21)

* add graph metadata object

* skip networkx tests if not available

* add python metadata interface

* add node and edge metadata

* use nodesymbol as primary arg type and add implicit conversion

* add node and edge metadata bindings

.flake8

@@ -1,3 +1,5 @@
 [flake8]
 max-line-length = 88
 extend-ignore = E203, W503
+per-file-ignores =
+    *__init__.py:F401,F403

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.14)
-project(spark_dsg VERSION 1.0.5)
+project(spark_dsg VERSION 1.0.6)
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)

include/spark_dsg/dynamic_scene_graph.h

@@ -34,6 +34,7 @@
  * -------------------------------------------------------------------------- */
 #pragma once
 #include <Eigen/Core>
+#include <nlohmann/json.hpp>
 #include <type_traits>
 
 #include "spark_dsg/dynamic_scene_graph_layer.h"
@@ -410,20 +411,20 @@ class DynamicSceneGraph {
 
   /**
    * @brief Get number of static edges in the graph
-   * @return number of static edges in the graph
+   * @return Number of static edges in the graph
    */
   size_t numStaticEdges() const;
 
   /**
    * @brief Get number of dynamic edges in the graph
-   * @return number of dynamic edges in the graph
+   * @return Number of dynamic edges in the graph
    */
   size_t numDynamicEdges() const;
 
   /**
    * @brief Get whether or not the scene graph is empty
-   * @note the scene graph invariants make it so only nodes have to be checked
-   * @return true if the scene graph is empty
+   * @note The scene graph invariants make it so only nodes have to be checked
+   * @return True if the scene graph is empty
    */
   bool empty() const;
 
@@ -435,10 +436,10 @@ class DynamicSceneGraph {
   Eigen::Vector3d getPosition(NodeId node) const;
 
   /**
-   * @brief merge two nodes
-   * @param node_from node to remove
-   * @param node_to node to merge to
-   * @returns true if operation succeeded
+   * @brief Merge two nodes
+   * @param node_from Node to remove
+   * @param node_to Node to merge to
+   * @returns True if operation succeeded
    */
   bool mergeNodes(NodeId node_from, NodeId node_to);
 
@@ -457,7 +458,7 @@ class DynamicSceneGraph {
    * @note Will add the nodes and edges not previously added in current graph
    * @param other other graph to update from
    * @param config Configuration controlling merge behavior
-   * @returns true if merge was successful
+   * @returns True if merge was successful
    */
   bool mergeGraph(const DynamicSceneGraph& other, const GraphMergeConfig& config = {});
 
@@ -471,7 +472,7 @@ class DynamicSceneGraph {
   /**
    * @brief Get all new nodes in the graph
    * @param clear_new Clear new status for all new nodes up until this point
-   * @returns list of all new nodes
+   * @returns List of all new nodes
    */
   std::vector<NodeId> getNewNodes(bool clear_new = false);
 
@@ -490,12 +491,12 @@ class DynamicSceneGraph {
   std::vector<EdgeKey> getNewEdges(bool clear_new = false);
 
   /**
-   * @brief track which edges get used during a serialization update
+   * @brief Track which edges get used during a serialization update
    */
   void markEdgesAsStale();
 
   /**
-   * @brief remove edges that do not appear in serialization update
+   * @brief Remove edges that do not appear in serialization update
    */
   void removeAllStaleEdges();
 
@@ -514,7 +515,7 @@ class DynamicSceneGraph {
   void save(std::string filepath, bool include_mesh = true) const;
 
   /**
-   * @brief parse graph from binary or JSON file
+   * @brief Parse graph from binary or JSON file
    * @param filepath Complete path to file to read, including extension.
    * @returns Resulting parsed scene graph
    */
@@ -526,9 +527,12 @@ class DynamicSceneGraph {
 
   std::shared_ptr<Mesh> mesh() const;
 
-  //! current static layer ids in the graph
+  //! Current static layer ids in the graph
   const LayerIds layer_ids;
 
+  //! Any extra information about the graph
+  nlohmann::json metadata;
+
  protected:
   BaseLayer& layerFromKey(const LayerKey& key);
 

include/spark_dsg/edge_attributes.h

@@ -34,6 +34,7 @@
  * -------------------------------------------------------------------------- */
 #pragma once
 #include <memory>
+#include <nlohmann/json.hpp>
 #include <ostream>
 
 #include "spark_dsg/serialization/attribute_registry.h"
@@ -76,6 +77,8 @@ struct EdgeAttributes {
   bool weighted;
   //! the weight of the edge
   double weight;
+  //! Arbitrary metadata about the edge
+  nlohmann::json metadata;
 
   /**
    * @brief output attribute information

include/spark_dsg/node_attributes.h

@@ -38,6 +38,7 @@
 #include <list>
 #include <map>
 #include <memory>
+#include <nlohmann/json.hpp>
 #include <optional>
 #include <ostream>
 #include <string>
@@ -113,6 +114,8 @@ struct NodeAttributes {
   bool is_active;
   //! whether the node was observed by Hydra, or added as a prediction
   bool is_predicted;
+  //! Arbitrary node metadata
+  nlohmann::json metadata;
 
   /**
    * @brief output attribute information

include/spark_dsg/serialization/attribute_serialization.h

@@ -36,9 +36,11 @@
 
 #include <map>
 #include <nlohmann/json.hpp>
+#include <sstream>
 
 #include "spark_dsg/serialization/attribute_registry.h"
 #include "spark_dsg/serialization/binary_serialization.h"
+#include "spark_dsg/serialization/versioning.h"
 
 namespace spark_dsg::serialization {
 
@@ -170,6 +172,7 @@ void Visitor::to(nlohmann::json& record, const Attrs& attrs) {
   visitor.type_ = Type::JSON_WRITE;
   visitor.impl_ = std::make_unique<JsonWriter>(&record);
   record["type"] = attrs.registration().name;
+  record["metadata"] = attrs.metadata;
   attrs.serialization_info();
   visitor.impl_.reset();
 }
@@ -180,6 +183,12 @@ void Visitor::to(BinarySerializer& serializer, const Attrs& attrs) {
   visitor.type_ = Type::BINARY_WRITE;
   visitor.impl_ = std::make_unique<BinaryWriter>(&serializer);
   serializer.write(attrs.registration().type_id);
+
+  // serialize metadata
+  std::stringstream ss;
+  ss << attrs.metadata;
+  serializer.write(ss.str());
+
   attrs.serialization_info();
   visitor.impl_.reset();
 }
@@ -196,6 +205,10 @@ std::unique_ptr<Attrs> Visitor::from(const AttributeFactory<Attrs>& factory,
     return nullptr;
   }
 
+  if (record.contains("metadata")) {
+    attrs->metadata = record["metadata"];
+  }
+
   attrs->serialization_info();
   visitor.impl_.reset();
   return attrs;
@@ -215,6 +228,13 @@ std::unique_ptr<Attrs> Visitor::from(const AttributeFactory<Attrs>& factory,
     return nullptr;
   }
 
+  const auto& header = io::GlobalInfo::loadedHeader();
+  if (header.version >= io::Version(1, 0, 6)) {
+    std::string metadata_json;
+    deserializer.read(metadata_json);
+    attrs->metadata = nlohmann::json::parse(metadata_json);
+  }
+
   attrs->serialization_info();
   visitor.impl_.reset();
   return attrs;

package.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <package format="2">
   <name>spark_dsg</name>
-  <version>1.0.5</version>
+  <version>1.0.6</version>
   <description>Dynamic Scene Graph (DSG) type definitions and core library code</description>
 
   <author email="[email protected]">Nathan Hughes</author>

python/bindings/include/spark_dsg/python/python_layer_view.h

@@ -34,6 +34,7 @@
  * -------------------------------------------------------------------------- */
 #pragma once
 #include <spark_dsg/dynamic_scene_graph.h>
+#include <spark_dsg/node_symbol.h>
 
 #include "spark_dsg/python/scene_graph_iterators.h"
 
@@ -46,11 +47,11 @@ class LayerView {
   EdgeIter edges() const;
   size_t numNodes() const;
   size_t numEdges() const;
-  bool hasNode(NodeId node_id) const;
-  bool hasEdge(NodeId source, NodeId target) const;
-  const SceneGraphNode& getNode(NodeId node_id) const;
-  const SceneGraphEdge& getEdge(NodeId source, NodeId target) const;
-  Eigen::Vector3d getPosition(NodeId node_id) const;
+  bool hasNode(NodeSymbol node_id) const;
+  bool hasEdge(NodeSymbol source, NodeSymbol target) const;
+  const SceneGraphNode& getNode(NodeSymbol node_id) const;
+  const SceneGraphEdge& getEdge(NodeSymbol source, NodeSymbol target) const;
+  Eigen::Vector3d getPosition(NodeSymbol node_id) const;
 
   const LayerId id;
 

python/bindings/src/python_layer_view.cpp

@@ -48,21 +48,21 @@ size_t LayerView::numNodes() const { return layer_ref_.numNodes(); }
 
 size_t LayerView::numEdges() const { return layer_ref_.numEdges(); }
 
-bool LayerView::hasNode(NodeId node_id) const { return layer_ref_.hasNode(node_id); }
+bool LayerView::hasNode(NodeSymbol node_id) const { return layer_ref_.hasNode(node_id); }
 
-bool LayerView::hasEdge(NodeId source, NodeId target) const {
+bool LayerView::hasEdge(NodeSymbol source, NodeSymbol target) const {
   return layer_ref_.hasEdge(source, target);
 }
 
-const SceneGraphNode& LayerView::getNode(NodeId node_id) const {
+const SceneGraphNode& LayerView::getNode(NodeSymbol node_id) const {
   return layer_ref_.getNode(node_id);
 }
 
-const SceneGraphEdge& LayerView::getEdge(NodeId source, NodeId target) const {
+const SceneGraphEdge& LayerView::getEdge(NodeSymbol source, NodeSymbol target) const {
   return layer_ref_.getEdge(source, target);
 }
 
-Eigen::Vector3d LayerView::getPosition(NodeId node_id) const {
+Eigen::Vector3d LayerView::getPosition(NodeSymbol node_id) const {
   return layer_ref_.getNode(node_id).attributes().position;
 }