Shorten.m

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namespace models{
namespace motorunit{


/* (Autoinserted by mtoc++)
 * This source code has been filtered by the mtoc++ executable,
 * which generates code that can be processed by the doxygen documentation tool.
 *
 * On the other hand, it can neither be interpreted by MATLAB, nor can it be compiled with a C++ compiler.
 * Except for the comments, the function bodies of your M-file functions are untouched.
 * Consequently, the FILTER_SOURCE_FILES doxygen switch (default in our Doxyfile.template) will produce
 * attached source files that are highly readable by humans.
 *
 * Additionally, links in the doxygen generated documentation to the source code of functions and class members refer to
 * the correct locations in the source code browser.
 * However, the line numbers most likely do not correspond to the line numbers in the original MATLAB source files.
 */

class Shorten
  :public models.BaseFullModel {
    public: /* ( Dependent ) */

        UseNoise;

        
    public:

        logical SinglePeakMode = false;
        logical DynamicInitialConditions = true;
        logical SingleTwitchOutputForceScaling = true;
    public:

        Shorten(dynamic_ic,logical singlepeakmode,outputscaling) {

            if nargin < 3
                outputscaling = true;
                if nargin < 2
                    singlepeakmode = false;
                    if nargin < 1
                        dynamic_ic = true;
                    end
                end
            end
            this.SinglePeakMode= singlepeakmode;
            this.DynamicInitialConditions= dynamic_ic;
            this.SingleTwitchOutputForceScaling= outputscaling;

            this.dt= .1;
            if singlepeakmode
                this.T= 2000; /*  [ms] */

            else
                this.T= 150; /*  [ms] */

            end
            /*  DO NOT INCREASE! Peaks from Motoneuron are not correctly
             * resolved (at least visually) if larger timesteps are used. */
            this.dt= .1; /*  [ms] */


            this.SaveTag= sprintf(" motorunit_shorten_sp%d_dynic%d ",singlepeakmode,dynamic_ic);
            this.Data= data.ModelData(this);
            this.Data.useFileTrajectoryData;

            this.Name= sprintf(" Motor unit model: Single peak mode: %d, Dynamic Initial Conditions: %d ",singlepeakmode,dynamic_ic);
            this.System= models.motorunit.SHSystem(this);
            this.TrainingInputs= 1;
            this.EnableTrajectoryCaching= true;

            s = solvers.MLWrapper(@ode15s);
            if singlepeakmode
                sys = this.System;
                s.odeopts.OutputFcn= @sys.singlePeakModeOutputFcn;
            end
            this.ODESolver= s;

            /*  Set parameter domain already */
            s = sampling.RandomSampler;
            s.Domain= models.motoneuron.ParamDomain;
            this.Sampler= s;

            this.DefaultMu= [.1; 3];
            this.DefaultInput= 1;
        }
/* mtoc++ warning: Optional parameter 'outputscaling' of method 'Shorten' has no specified default value
 */
        function pm = plotMotoSacroLinkFactorCurve() {
            x = 0:.1:80;
            pm = PlotManager;
            pm.LeaveOpen= true;
            h = pm.nextPlot(" moto_sarco_link_factor "," Factor for motoneuro to sarcomere link "," Moto V_s "," Factor ");
            f = this.System.f;
            fx = f.MSLink_MaxFactor*ones(1,length(x));
            dynfac = x < f.MSLink_MaxFactorSignal;
            fx(dynfac) = f.getLinkFactor(x(dynfac));
            plot(h,x,fx);
            pm.done;
        }


        function  plotOutputForceScaling(colvec<double> x) {
            if nargin < 2
                x = 0:.01:1;
            end
            plot(x,polyval(this.System.ForceOutputScalingPolyCoeff,x));
            title(" Force scaling curve for different fibre types ");
            xlabel(" Fibre type parameter ");
            ylabel(" Peak force for single excitation ");
        }


        function pm = plotState(double t,colvec<double> x,pm) {
            if nargin < 4
                pm = PlotManager(false,3,1);
                pm.LeaveOpen= true;
            end
            h = pm.nextPlot(" moto "," Motoneuron V_s "," time "," value ");
            plot(h,t,x(2,:));
            h = pm.nextPlot(" sarco "," Linked sarcomere: V_s "," time "," V_s ");
            plot(h,t,x(this.System.dm+1,:));
            h = pm.nextPlot(" sarco ",sprintf(" Linked sarcomere: A_2\nMu=[%s] ",num2str(this.System.mu" )), "time" , "A_2^t);
            plot(h,t,x(this.System.dm+53,:));

            if nargin < 4
                pm.done;
            end
        }


        function pm = plot(double t,matrix<double> y,pm) {
            if nargin < 4
                pm = PlotManager(false,2,1);
                pm.LeaveOpen= true;
            end
            h = pm.nextPlot(" sarco "," Linked sarcomere: V_s "," time "," V_s ");
            plot(h,t,y(1,:));
            h = pm.nextPlot(" sarco ",sprintf(" Linked sarcomere: A_2\nMu=[%s] ",num2str(this.System.mu" )), "time" , "A_2^t);
            plot(h,t,y(2,:));

            if nargin < 4
                pm.done;
            end
        }

    
    public:

        
#if 0 //mtoc++: 'get.UseNoise'
function value = UseNoise() {
            value = ~this.System.noiseGen.DisableNoise;
        }

#endif


        
#if 0 //mtoc++: 'set.UseNoise'
function  UseNoise(value) {
            this.System.noiseGen.DisableNoise= ~value;
        }

#endif

    
    public: /* ( Static ) */

        static function res = test_Shorten() {
            m = models.motorunit.Shorten;
            [t,y] = m.simulate;
            m.plot(t,y);
            res = 1;
        }

    
    protected: /* ( Static ) */

        static function this = loadobj() {
            if ~isa(this, " models.motorunit.Shorten ")
                sobj = this;
                this = models.motorunit.Shorten;
                this = loadobj@models.BaseFullModel(this, sobj);
            else
                this = loadobj@models.BaseFullModel(this);
            end
        }

};
}
}