Patch environment components

Table of Contents

• Component creation
  • Example: Initializing one environment component
  • Example: Initializing two environment components
• Component parameters
  • Example: Modifying component parameters
• Registration to layers
  • Example: Registering a component to a single layer
  • Example: Registering a component to multiple layers

The component tag defines a single component. Nested tags include component.parameter for parameters and component.register for registration to a layer.

<components>
    <component id="[ID]" class="[CLASS]">
        <component.parameter id="[ID]" value="[VALUE]" scale="[SCALE]" />
        <component.register id="[ID]" />
        ...
    </component>
    ...
</components>

Component creation

The component tag attributes are used to create the component.

• Each component must have a unique id
• Each component must specify a class

Valid options for classes include:

source_sites

Sites for generator based on source layout

pattern_sites

Sites for generator based on pattern layout

graph_sites_simple

Sites for generator based on graph layout with simple hemodynamics

graph_sites_complex

Sites for generator based on graph layout with complex hemodynamics

pulse

Component for pulsing source concentrations

Requires source_sites component

cycle

Component for cycling source concentrations

Requires source_sites component

degrade

Component for degrading graph sites

Requires graph_sites_simple or graph_sites_complex component

remodel

Component for remodeling graph sites

Requires graph_sites_simple or graph_sites_complex component

ATTRIBUTE	DESCRIPTION	TYPE	REQUIRED
id	unique name for the component	string	Y
class	component class option	string	Y

Example: Initializing one environment component

Specifies an environment component, A, with the source sites component class.

<components>
    <component id="A" class="source_sites" />
</components>

Example: Initializing two environment components

Specifies two environment components, A and B. Component A uses the complex graph sites component class, and component B uses the remodeling component class.

<components>
    <component id="A" class="graph_sites_complex" />
    <component id="B" class="remodel" />
</components>

Component parameters

The component.parameter tag defines component parameters. Unless modified, default values are used for all parameters. Defaults are listed in parameter.patch.xml.

• Either or both value and scale attributes can be applied, with value applied first
• Only numeric parameters can be modified using scale

ATTRIBUTE	DESCRIPTION
id	parameter name
value	new parameter value
scale	scaling factor applied to parameter value

Example: Modifying component parameters

The degradation rate parameter is set to the new value 2000.

<component.parameter id="DEGRADATION_RATE" value="2000" />

The default value of the degradation rate parameter is scaled by 2.

<component.parameter id="DEGRADATION_RATE" scale="2" />

The degradation rate parameter is set to the new value 10 * 2 = 20.

<component.parameter id="DEGRADATION_RATE" value="10" scale="2" />

Registration to layers

The component.register tag registers the component to a specific layer. A component may be registered to more than one layer. The registered layer id must match a layer defined in the lattice layer setup.

ATTRIBUTE	DESCRIPTION
id	layer id

Example: Registering a component to a single layer

The component is registered to layer A.

<component.register id="A" />

Example: Registering a component to multiple layers

The component is registered to layer A and layer B.

<component.register id="A" />
<component.register id="B" />