Dynamic graph creation and manipulation

Alejandro Morales Sierra

Centre for Crop Systems Analysis - Wageningen University


March 22, 2023

Graphs, Rules and Queries

A model in VPL is a (discrete) dynamical model that describes the time evolution of one or more entities (i.e. objects of type graph). Each graph (usually assumed to be an individual plant) is characterized by a series of nodes (usually organs) that are represented by nodes in a graph. Each node is defined by its own state, including (if applicable) a description of its geometry, color, optical propertes, etc. The dynamic simulation of a graph consists of the creation and destruction of nodes via graph rewriting rules, and changes to the internal state of its nodes with the help of queries.

The 3D structure of a graph is generated by processing its nodes using a Turtle procedural geometry approach (i.e. inspired on Logo’s turtle graphs as used in L-systems) and following the topology of the graph. This 3D structure may be used for visualization using a 3D renderer or for simulating spatial processes.

VPL does not provide a domain-specific language to implement rules and queries. Rather, they are defined by functions which are stored in objects of types Rule and Query, respectively. Similarly, the nodes of a graph can be of any user-defined type, as long as the user defines the necessary methods to support specific functionality (e.g. the feed! method to generate geometry).

VPL is designed around data types and methods. Building a model in VPL typically requires:

  • Defining types for the different classes of nodes of a graph
  • Creating rules and queries based on these types
  • Creating graphs by combining rules and the initial states of the graphs
  • Creating additional elements in the scene (e.g. soil)

A simulation in VPL consists of executing rules iteratively and, within each iteration:

  • Use queries to select subset of nodes and modify their states.
  • Modify graph-level variables directly.
  • Use algorithms in VPL to simulate interactions among nodes or between nodes and their environment.

In addition, VPL allows visualizing the results of a simulation by: * 3D rendering of the generated scenes * Network graph representing the nodes in the graph

VPL is designed to facilitate modular model development, such as using different types of graphs in the same simulation, alternative visualizations of the same scene by mapping internal states of nodes to colors, or including multiple ray tracers in the same simulation. Users may also create their own data types that include graphs as fields or to nest graphs within other graphs.


A graph is the basic unit of a model in VPL. Three types of data are stored inside a graph:

  • Components of the graph.
  • Graph rewriting rules.
  • An user-defined object that characterizes the state of a graph besides its nodes (i.e. graph-level variables).

The nodes of a graph are objects created by the user that inherit from the abstract type Node. This abstract type enables describing the relationship between nodes using a simple algebra for graph construction (see below). A graph always needs to be initialized by at least one node (i.e. analogous to the axiom of L-Systems), as otherwise graph rewriting rules could not be applied.

The creation of a graph is achieved with the constructor graph(axiom, rules[, vars]) where axiom, rules and vars are the axiom, a tuple with the graph rewriting rules and an user-defined object that stores all graph-level variables, respectively. Note that the last argument is optional. The method rewrite!(graph) takes a graph as input and executes the graph rewriting rules, updating the internal state of the graph in-place. Note that this method will not be called implicitly: it is the responsability of the user to decide when to call this method.

The system is designed to allow rewriting of graphs in parallel, including shared memory approaches such as multi-threading with the Threads.@threads macro. This is ensured by deep-copying axiom, rules and vars so that changes in one graph do not affect other graphs that may be built from the same axioms and rules. If the user wants some state to be shared across graphs, they should define a global variable that is modified during execution of rules. If such approach is used, it is the responsibility of the user to ensure that updates to such global variables are properly locked or executed atomatically.

Graph-construction algebra

When initializing a graph and when specifying a graph rewriting rule it is necessary to indicate the topological relationship between the nodes being added to a graph (i.e. effectively we build graphs by appending sub-graphs). In order to facilitate the description of these relationships, a simple algebra is defined for all objects that inherit from Node.

The + operator indicates a linear parent-child dependency between the operands. For example, M() + L() indicates that the object generated by L() is a child of M(). A branching point is introduced by enclosing the children of a node within () and separating the different branches with “,”. For example, (M(1) + (L(2), L(3)) + M(4) + L(5)) creates a tree that starts with M(1), has 3 children (L(2), L(3) and M(4)) and M(4) has a child L(5).

A graph always keep tracks of two special nodes: the root and the insertion point. The root is the node that has no parent. When you use a graph rewriting rule (see below) to replace a node a with a graph that has a root node b, the result is that node a is replaced by node b and will inherit all the children and parent from node a (plus the children that b already had in the replacement graph).

An insertion point is the node of a graph where new nodes will be connected to when using the + operator. Branches do not modify the insertion point of an existing graph, but linear addition of nodes will always update the insertion point to the last node. Thus, these two expressions produce the same tree structure but with different insertion points: M(1) + (L(2), L(3)) + M(4) + L(5) and M(1) + (L(2), L(3), M(4) + L(5)). In the first case, the insertion point becomes the node L(5) but in the second case it remains at M(1). Keeping track of the insertion point of a graph is important when building a graph in several steps.


Rules consist of directives that define the dynamic evolution of the nodes that form a graph, by replacing a subset of the nodes by one or more nodes. Rules are not executed directly by the user. Instead, they are stored in the graph and executed by the method rewrite!. A rule is made of three parts:

  • The type of node to be replaced.
  • A function to determine whether a candidate node is to be replaced or not (lhs function)
  • A function that generates a node or subgraph to use as replacement (rhs function).

The first part must always be present, as it represents the minimum information required to match the rule against nodes inside a graph. This type must be the concrete type of the node rather an abstract type or union type from which the node may inherit. The lhs and rhs functions are optional with the following default values if missing:

  • lhs: x -> true
  • rhs: x -> nothing

A rule with a missing lhs will match all the nodes of the specified type. A rule without an rhs will remove any matched node and all of its children (recursively, such that the topological tree is pruned).

A Context object includes the data stored inside a node plus its relationship with other nodes in the graph, as well as a reference to the graph-level variables. In order to extract the data stored in the node use the function data(). In order to extract the object containing all the graph-level variables, use the method vars. The Context object may also be used to access other nodes by walking through the graph (see below).

For rules that do not capture the context of a node, the lhs part is a function that takes an object of type Context and returns true or false, whereas the rhs part is a function that takes a Context object and returns a node or subgraph.

Although rules may also be used to update the internal state of a node (i.e.  by creating a new node of the same type but with a different state), this is only required when the node is an immutable type. Otherwise, one can also (and it is recommended to) use a query for better performance (see below).

Matching relationships among nodes

Sometimes the lhs function needs to check the relationships between nodes inside a graph (e.g. match all leaves that belong to a particular branch of a graph). In order achieve that, one can use the functions hasParent() and hasChildren() to check for inmediate connections (i.e. effectively to check whether the node is a root or a leaf in the graph) whereas hasAncestor() and hasDescendant() allow traversing the graph and finding any connected node that matches a specific query. If we need to extract the contents of the node, we may use the corresponding functions parent(), children(), ancestor() and descendant(). Note that children() will return all the children nodes as a tuple, but the rest of functions only return one node at a time. All these functions take a Context object as input and return either true or false (for the functions that start with has) or a Context or tuple of Context objects for the functions that extract the actual connected node. These methods may also be used inside the rhs function of rules. However, to avoid code repetition (and for performance reasons), it is recommended to capture the Context objects of connected in the lhs function and pass them to the rhs as described below (see below).

Capturing the context of a node

In some scenarios, knowing the relationship between nodes in the graph is not sufficient, because data stored inside those related nodes is required in the rhs function of a rule. In those cases, an extra argument to the constructor for a Rule is required (captures = true) to indicate that this rule will pass additional data from the lhs to the rhs function. Then, the lhs function should return a tuple, where the first element is still true or false (to indicate whether the rule matches a node) and the second element is a tuple of Context objects associated to the nodes being matched. If no match occurs, it is sufficient to return (false, ()), where () indicates an empty tuple. The rhs function should then be a function that takes as first argument the Context object of the node being replaced, and an additional argument for every Context object being captured on the lhs function and passed to the rhs function.

Execution of rules

Rules are executed in the same order in which they are added to the graph object. Then, the lhs part of each rule is tested against all nodes of the specified type in the same order in which they were added to the graph. Similarly, the rhs part of a rule will be applied to those nodes that matched the lhs part, in the same order as in the matching.

The lhs part of all the rules are executed first and VPL will check that each node is not matched by more than rule. In case there is more than one match, an error will be generated. After all the lhs pars are executed, then the rhs parts are executed on the matched nodes. Although generating an error may seem restrictive, the reasoning for this approach is as follows:

  • Graph rewriting is, conceptually, a parallel operation, so two rules cannot replace the same node as that would mean the result depends on the order in which the rules are executed.

  • New nodes will be generated by graph rewriting rules that could be matched by the lhs of other graph rewriting rules. To guarantee that all rules rewrite the same graph, all nodes that need to be replaced are identified before any rhs function is executed.

In essence, you need to program your model such that it does not rely on any specific order of execution of the graph rewriting rules.

Query and apply

The apply() function will apply a Query object to a graph and return a list of nodes that match the query. The main differences between rules and queries is that queries do not have an rhs part,they are not stored inside the graph and the user decides when to apply them. Note that that a query does not modify a graph, it simply returns a collection of nodes matched by it. Another difference is that a query always return a reference to the data stored inside the node, rather than a Context object (so no need to use data()). Note that if a query is used to modify the data stored in a node, then the node needs to be a mutable type.

For nodes of immutable type, a graph rewriting rule must be used to replace the node. This may seem like a limitation but the fact is that, if one needs to modify the state of an object after it has been created then, by definition, that object should be of mutable type. If immutability is required for some reason, one may keep track of associated variables at the graph level, but such kind of manual book-keeping is not recommended.

A query is useful when the data stored inside the nodes of a graph need to be modified or when these data are used as input for some function. Unlike in rules, the order in which queries are applied in the code will affect the result of the simulation, especially whether they are applied before or after a call to rewrite!. The reasoning for this is that queries are not altering the structure of a graph (since they do not remove nor create nodes) and multiple queries can (and often do) match the same node. For example, one query will alter an internal variable that is then need as input by another query. Thus, whereas rules implicitly follow a parallel programming paradigm, queries follow a sequential programming paradigm.

Direct access to nodes

It is possible to access nodes directly by their internal ID. This should be done carefully as the internal ID depends on the internal state of VPL and may not be reproducible across different runs, so only use it for interactive exploration of a model. It is possible to identify the internal ID of a node by using the method draw() with the default node_label method (see section on Visualization).

The internal ID is generated by a counter inside VPL which can be reset by using VPL.Core.resetID(). Once the ID of a node is known, it is possible to access using bracket notation [] on a Graph object or any subgraph generated with the graph construction algebra.

module L
    using VPL

    struct N <: Node 
import .L
using VPL
axiom = L.N(1) + (L.N(3), L.N(4)) + L.N(2) + (L.N(5), L.N(6))

The bracket notation will return the Node object that wraps the data stored by the user. Notice how the internal ID does not match the value stored in the node, but rather the order in which the nodes were processed during the construction of the axiom. In this case that order coincides with reading the code left-to-right but that will not always be the case. If we create the Graph object that contains the axiom, we can access the node with the same syntax.

graph = Graph(axiom = axiom)