- Author:
- JuliaMusgrave <jmus753@aucklanduni.ac.nz>
- Date:
- 2025-07-28 16:16:19+12:00
- Desc:
- Jupyter Notebook and alternate modes of the model to implement work-loop simulations
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d52/rawfile/7a0de368661d5f1fe8812a21e2ba6984aca7e3c3/MATLAB/get_sim_inputs.m
% Function to simplify the length and or calcium inputs to an ode muscle
% model. Gets the right type of variable depending on the simulation
%
% Inputs:
% - t: the t value from the ODE (either a scalar or vector)
% - length_info: the variable that I typically call s in my ode
% functions (sarcomere length input. Either a constant or 2 x n matrix
% with matching time and length points (t in 1st row and L in 2nd)
% - ca_info: a similar variable but instead representing the
% intracellular calcium concentration (either constant or the array
% form)
% - y8(optional) : the value of L found from the dL ode in models
% with internal shortening
% Outputs:
% - L: sarcomere length value or array (depending on form of t and length_info)
% - L0: the initial sarcomere (which is only required if we are doing
% internal shortening)
% - dL: sarcomere velocity found numerically from length input, array
% or scalar. Takes the string value 'iso' if it needs to
% be computed when solving the model
% - Ca: calcium concentration, array or scalar
% Author: Julia Musgrave
% Date last updated:
function [L, L0, dL, Ca] = get_sim_inputs(t,length_info,ca_info,y8)
if length(length_info)>1 % length perturbation
if length(t)==1 % in solver mode (step by step)
% The ODE solver won't take the same steps as the length input so
% we need to interpolate to find the estimated length
L=interp1(length_info(1,:),length_info(2,:),t);
% Use finite difference formulae to get velocity
dL_full=gradient(length_info(2,:),length_info(1,2)-length_info(1,1));
dL=interp1(length_info(1,:),dL_full,t);
else % finding stress for the whole simulation (tvals should match L vals)
L=length_info(2,:)';
if length(L)~=length(t) % weird fitting situation where t is cropped
L=L(1:length(t));
end
dL=gradient(L,t(2)-t(1));
end
L0=length_info(2,1);
else % isometric/isosarcometric simulation (single SL value)
L0=length_info;
if nargin==3 % for models without internal shortening
L=length_info;
dL=0;
else
L=y8; % L is determined by the ODE
dL='iso';
end
end
if length(ca_info)==1
Ca=ca_info;
elseif length(t)==1 % in solver mode (step by step)
% The ODE solver won't take the same steps as the Ca input so
% we need to find closest index and the corresponding Ca
[~,idx]=min(abs(ca_info(1,:)-t));
Ca=ca_info(2,idx);
else % finding stress for the whole simulation (tvals should match C vals)
Ca=ca_info(2,:)';
end
end
