PCDSYSTEM The 2D dynamical system of the Programmed Cell Death Model by Markus Daub. More...

Detailed Description

PCDSYSTEM The 2D dynamical system of the Programmed Cell Death Model by Markus Daub.

For details on properties and components see the Paper "Mathematical Modeling of Programmed Cell Death", Markus Daub, Milestone presentation.

See Also: models.pcd.CoreFun

Author: Daniel Wirtz

Date: 2010-03-15

New in 0.6:: (Daniel Wirtz, 2011-11-27) New property BasePCDSystem.SteadyStates that includes the linearized system's steady states for life and death (From "M. Daub: Death wins against life in a spatially extended apoptosis model"). This property is used in the plot methods for the different models.

New in 0.5:

(Daniel Wirtz, 2011-11-02)

New property ReacCoeff. The coefficients have been removed (commented out) of the system's Params and are inserted manually into the mu parameters in the CoreFunctions in order not to have to change much code. This way, they can be easily reintroduced as true system parameters.
Removed checkCFL method and placed it into the set.h method (directly sets the MaxTimestep property according to CFL conditions)

Change in 0.5:: (Daniel Wirtz, 2011-10-10) Generalized and restructured the models.pcd models and systems as far as possible. Removed the ISimConstants interfaces and added protected, custom models.pcd.BasePCDSystem.newSysDimension methods to propagate changes in geometry (models.pcd.BasePCDSystem.Omega or models.pcd.BasePCDSystem.h) to the systems and core functions.

New in 0.3:: (Daniel Wirtz, 2011-04-21) Integrated this class to the property default value changed supervision system Property classes and levels. This class now inherits from KerMorObject and has an extended constructor registering any user-relevant properties using KerMorObject.registerProps.

Definition at line 19 of file BasePCDSystem.m.

Public Member Functions
	BasePCDSystem (models.BaseFullModel model)

function	setConfig (colvec< double > mu,integer inputidx)

Public Member Functions inherited from models.BaseFirstOrderSystem
	BaseFirstOrderSystem (models.BaseFullModel model)
	Creates a new base dynamical system class instance. More...

function rsys =	getReducedSystemInstance (models.ReducedModel rmodel)
	Creates a reduced system given the current system and the reduced model. More...

function	setConfig (mu, inputidx)
	Sets the dynamical system's configuration. More...

function	prepareSimulation (colvec< double > mu,integer inputidx)

function dx =	ODEFun (double t,colvec< double > x)
	Debug variant for single evaluation. Commented in function above. More...

function y =	computeOutput (matrix< double > x,colvec< double > mu)
	Computes the output \(y(t) = C(t,\mu)Sx(t)\) from a given state result vector \(x(t)\), using the system's time and current mu (if given). More...

function	updateSparsityPattern ()

function J =	getJacobian (double t, xc)
	Computes the global jacobian of the current system. More...

function matrix < double > x0 =	getX0 (rowvec< double > mu)
	Gets the initial state variable at \(t=0\). More...

function M =	getMassMatrix ()
	For first order systems, only algebraic constraints need to be catered for. More...

function ModelParam p =	addParam (char name, default, varargin)
	Adds a parameter with the given values to the parameter collection of the current dynamical system. More...

function pidx =	getParamIndexFromName (paramname)
	Gets the index within the parameter vector \(\mu\) for a given parameter name. More...

function pt =	getParamInfo (colvec< double > mu)

function	plotInputs (pm)

Public Member Functions inherited from KerMorObject
	KerMorObject ()
	Constructs a new KerMor object. More...

function	display ()
	disp(object2str(this)); More...

function bool =	eq (B)
	Checks equality of two KerMor objects. More...

function bool =	ne (B)
	Checks if two KerMorObjects are different. More...

function cn =	getClassName ()
	Returns the simple class name of this object without packages. More...

Public Member Functions inherited from DPCMObject
	DPCMObject ()
	Creates a new DPCM object. More...

	DPCMObject ()

Public Attributes
	h
	Spatial stepwidth (in unscaled size units!) is set in subclasses. More...

	Omega
	The spatial width/area/region (in unscaled size units!) More...

	Diff
	Relative diffusion coefficients ([d2/d1, d3/d1, d4/d1]) More...

	hs
	scaled spatial stepwidth More...

	Dims
	The system's dimensions. More...

	ReacCoeff
	The reaction coefficients. More...

Public Attributes inherited from models.BaseFirstOrderSystem
dscomponents.ACoreFun	f
	The core f function from the dynamical system. More...

dscomponents.LinearCoreFun	A = "[]"
	Represents a linear or affine-linear component of the dynamical system. More...

dscomponents.AInputConv	B = "[]"
	The input conversion. More...

dscomponents.LinearOutputConv	C
	The output conversion Defaults to an LinearOutputConv instance using a 1-matrix, which just forwards the state variables and supports projection. More...

dscomponents.AInitialValue	x0 = "[]"
	Function handle to initial state evaluation. More...

dscomponents.AMassMatrix	M = "[]"
	The system's mass matrix. More...

dscomponents.ACoreFun	g = "[]"
	The system's algebraic constraints function. More...

	Inputs = {""}
	The system's possible input functions. A cell array of function handles, each taking a time argument t. More...

	Params = data.ModelParam.empty
	The parameters usable for the dynamical system. More...

integer	DependentParamIndices = -1
	Indices of the parameter vector that are effectively used in the system's core function. More...

double	MaxTimestep = "[]"
	The maximum timestep allowed for any ODE solvers. More...

colvec	StateScaling = 1
	The scaling for the state vectors. More...

	SparsityPattern
	The global sparsity pattern for the entire RHS. More...

	mu = "[]"
	The current parameter \(\mu\) for simulations, [] is none used. More...

	u = "[]"
	The current input function \(u(t)\) as function handle, [] if none used. More...

	inputidx = "[]"
	The current inputindex of the function \(u(t)\). More...

	NumStateDofs = "[]"

	NumAlgebraicDofs = 0

	NumTotalDofs = "[]"

	InputCount
	The number of inputs available. More...

	ParamCount
	The number of the system's parameters. More...

	Model
	The Model this System is attached to. More...

Public Attributes inherited from DPCMObject
	WorkspaceVariableName = ""
	The workspace variable name of this class. Optional. More...

	ID = "[]"
	An ID that allows to uniquely identify this DPCMObject (at least within the current MatLab session/context). More...

	PropertiesChanged = "[]"
	The Dictionary containing all the property settings as key/value pairs. More...

Public Attributes inherited from handle
	addlistener
	Creates a listener for the specified event and assigns a callback function to execute when the event occurs. More...

	notify
	Broadcast a notice that a specific event is occurring on a specified handle object or array of handle objects. More...

	delete
	Handle object destructor method that is called when the object's lifecycle ends. More...

	disp
	Handle object disp method which is called by the display method. See the MATLAB disp function. More...

	display
	Handle object display method called when MATLAB software interprets an expression returning a handle object that is not terminated by a semicolon. See the MATLAB display function. More...

	findobj
	Finds objects matching the specified conditions from the input array of handle objects. More...

	findprop
	Returns a meta.property objects associated with the specified property name. More...

	fields
	Returns a cell array of string containing the names of public properties. More...

	fieldnames
	Returns a cell array of string containing the names of public properties. See the MATLAB fieldnames function. More...

	isvalid
	Returns a logical array in which elements are true if the corresponding elements in the input array are valid handles. This method is Sealed so you cannot override it in a handle subclass. More...

	eq
	Relational functions example. See details for more information. More...

	transpose
	Transposes the elements of the handle object array. More...

	permute
	Rearranges the dimensions of the handle object array. See the MATLAB permute function. More...

	reshape
	hanges the dimensions of the handle object array to the specified dimensions. See the MATLAB reshape function. More...

	sort
	ort the handle objects in any array in ascending or descending order. More...

Protected Member Functions
function	updateDimensions ()

virtual function	newSysDimension ()
	Custom updates for new system dimension. More...

Protected Member Functions inherited from models.BaseFirstOrderSystem
function	updateDimensions ()

function ad_ic =	getAlgebraicDofsInitialConditions ()
	The default is to return all zeros. More...

function	validateModel (models.BaseFullModel model)
	Validates if the model to be set is a valid BaseModel at least. Extracting this function out of the setter enables subclasses to further restrict the objects that may be passed, as is being done in models.ReducedSystem, for example. More...

Protected Member Functions inherited from KerMorObject
function	checkType (obj, type)
	Object typechecker. More...

Protected Member Functions inherited from DPCMObject
function	registerProps (varargin)
	Call this method at any class that defines DPCM observed properties. More...

function	registerProps (varargin)

Additional Inherited Members
Static Protected Member Functions inherited from DPCMObject
static function obj =	loadobj (obj, from)
	Re-register any registered change listeners! More...

static function obj =	loadobj (obj, from)

Constructor & Destructor Documentation

models.pcd.BasePCDSystem.BasePCDSystem ( models.BaseFullModel model )

Definition at line 149 of file BasePCDSystem.m.

References models.BaseFirstOrderSystem.addParam(), Diff, models.BaseFirstOrderSystem.Model, ReacCoeff, DPCMObject.registerProps(), and t.

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Member Function Documentation

function models.pcd.BasePCDSystem.newSysDimension ( )

protectedpure virtual

Custom updates for new system dimension.

Implemented in models.pcd.PCDSystem3D, models.pcd.PCDSystem1D, and models.pcd.PCDSystem2D.

Referenced by updateDimensions().

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function models.pcd.BasePCDSystem.setConfig	(	colvec< double >	mu,
		integer	inputidx
	)

Definition at line 246 of file BasePCDSystem.m.

References models.BaseFirstOrderSystem.Model, ReacCoeff, and t.

function models.pcd.BasePCDSystem.updateDimensions ( )

protected

Definition at line 258 of file BasePCDSystem.m.

References Dims, models.BaseFirstOrderSystem.f, h, newSysDimension(), models.BaseFirstOrderSystem.NumStateDofs, and models.BaseFirstOrderSystem.StateScaling.

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Member Data Documentation

models.pcd.BasePCDSystem.Diff

Relative diffusion coefficients ([d2/d1, d3/d1, d4/d1])

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.

Definition at line 103 of file BasePCDSystem.m.

Referenced by BasePCDSystem(), models.pcd.PCDSystem2D.newSysDimension(), models.pcd.PCDSystem1D.newSysDimension(), and models.pcd.PCDSystem3D.newSysDimension().

models.pcd.BasePCDSystem.Dims

The system's dimensions.

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.

Definition at line 125 of file BasePCDSystem.m.

Referenced by models.pcd.PCDSystem2D.newSysDimension(), models.pcd.PCDSystem1D.newSysDimension(), models.pcd.PCDSystem3D.newSysDimension(), models.pcd.PCDSystem3D.plotState(), and updateDimensions().

models.pcd.BasePCDSystem.h

Spatial stepwidth (in unscaled size units!) is set in subclasses.

Property class critical:: Determines the spatial resolution of the model.

See Also: L

Note: This property has the MATLAB attribute Dependent set to true.; This property has the MATLAB attribute SetObservable set to true.; Matlab documentation of property attributes.

Definition at line 62 of file BasePCDSystem.m.

Referenced by models.pcd.PCDSystem3D.newSysDimension(), models.pcd.PCDSystem1D.PCDSystem1D(), models.pcd.PCDSystem2D.PCDSystem2D(), models.pcd.PCDSystem3D.PCDSystem3D(), models.pcd.PCDSystem1D.plot(), models.pcd.PCDSystem2D.plot(), models.pcd.PCDSystem3D.plotState(), and updateDimensions().

models.pcd.BasePCDSystem.hs

scaled spatial stepwidth

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.

Definition at line 114 of file BasePCDSystem.m.

Referenced by models.pcd.PCDSystem2D.newSysDimension(), models.pcd.PCDSystem1D.newSysDimension(), and models.pcd.PCDSystem3D.plotState().

models.pcd.BasePCDSystem.Omega

The spatial width/area/region (in unscaled size units!)

Property class data:: The area for the model.

See Also: L

Note: This property has the MATLAB attribute Dependent set to true.; This property has the MATLAB attribute SetObservable set to true.; Matlab documentation of property attributes.

Definition at line 78 of file BasePCDSystem.m.

Referenced by models.pcd.PCDSystem1D.PCDSystem1D(), models.pcd.PCDSystem2D.PCDSystem2D(), models.pcd.PCDSystem3D.PCDSystem3D(), models.pcd.PCDSystem1D.plot(), and models.pcd.PCDSystem3D.plotState().

models.pcd.BasePCDSystem.ReacCoeff

The reaction coefficients.

Note: This property has non-standard access specifiers: SetAccess = Private, GetAccess = Public; Matlab documentation of property attributes.

Definition at line 136 of file BasePCDSystem.m.

Referenced by BasePCDSystem(), and setConfig().

The documentation for this class was generated from the following file:

+models/+pcd/BasePCDSystem.m

Detailed Description

Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation