Glossary#
Algorithm
An Algorithm is an operation that transforms a Form (or more) into another or other Forms. Some Algorithms serve as a source (no input Form) or a sink (no output Form).
Input Form(s)
Algorithm
Output Form(s)
It is implemented by Plugins, and can be controlled through Parameters.
Form
A Form is a temporal sequence representing the evolution of a biological object, using a given computational representation. It consists of a time-indexed set of instances of an archetypal data structure (e.g. Image, Mesh, Tree…).
The different types of Forms that Gnomon manipulates are listed here
Parameter
A Parameter is a typed variable proceeding from an atomic type (boolean, number, character string) or from a more complex one (range, color, 2D curve) whose value can be manipulated by the user through a graphical editor.
Pipeline
A Pipeline is a graph composed of Nodes that represent Algorithms and directed Edges corresponding to Forms.
Pipeline Nodes carry input and output Ports that are mapped to the input and output Forms of the Algorithm, and a Pipeline Edge connects an output Port of a given Node to an input Port of another Node if the corresponding output Form of the first Algorithm is used as an input Form of the other.
Plugin
A Plugin is an inherited object conforming with the API of one type of Algorithm, Form or Visualization, and generally relying on a third-party software library providing the functionality.
Available Plugin packages are listed here.
Project
A Project corresponds to a local directory in your file system that gathers the pipelines, custom plugins, data and other resources files constituting a digital experiment.
The Gnomon application manages the Project in order to keep track of the various files required to replay the computations.
Reader
A Reader is a specific type of Algorithm that is used to load Forms from data files. It has no input Form and no Parameters apart from a mandatory path, and returns a single type of output Form.
Path
Reader
Output Form
Reader Plugins declare the list of file extensions they support.
Session
A Session is the result of the interaction of a user with the Gnomon application after opening a Project. The state of the Session includes all the Forms, Workspaces and the subsequent Pipeline that have been generated by the user.
View
A View is an object dedicated to the materialization of Forms in the GUI through a third-party rendering framework. It relies on Visualizations to control the way a particular Form is rendered in a given View.
Visualization
A Visualization is an operation that defines how a Form is rendered in a View. It is implemented by specific Plugins relying on the View’s rendering framework, and can be controlled through Parameters.
Form
Visualization
View
Workspace
A Workspace is the graphical counterpart of an Algorithm, where the user is able to set Forms as inputs through an input View, tune the values of the Parameters and retrieve Forms as outputs in an output View.
Visualization
Input View
Output View
Algorithm
Workspace
Available Workspaces are listed here.
Writer
A Writer is a specific type of Algorithm that is used to save Forms as local files. It has no output Form and no Parameters apart from a mandatory path, and takes a single type of Form as input.
Input Form
Writer
Path
Writer Plugins declare the list of file extensions corresponding to the formats they are able to write.