Improve parameter handling in prepareDatahandle, update optionlists, use absolute paths

ComputeSensitivities/generateFDstep.m

@@ -28,24 +28,24 @@
    p_typ = ones(dim_p, 1);
    t_typ = 1;
 
-   if hasOption(varargin, 'hy'), hy = getOption(varargin, 'hy'); end
-   if hasOption(varargin, 'hp'), hp = getOption(varargin, 'hp'); end
-   if hasOption(varargin, 'ht'), ht = getOption(varargin, 'ht'); end
-   if hasOption(varargin, 'h_dir'), h_dir = getOption(varargin, 'h_dir'); end
-   if hasOption(varargin, 'hy_rel_flag'), hy_rel_flag = getOption(varargin, 'hy_rel_flag'); end
-   if hasOption(varargin, 'hp_rel_flag'), hp_rel_flag = getOption(varargin, 'hp_rel_flag'); end
-   if hasOption(varargin, 'ht_rel_flag'), ht_rel_flag = getOption(varargin, 'ht_rel_flag'); end
-   if hasOption(varargin, 'y_typ'), y_typ = getOption(varargin, 'y_typ'); end
-   if hasOption(varargin, 'p_typ'), p_typ = getOption(varargin, 'p_typ'); end
-   if hasOption(varargin, 't_typ'), t_typ = getOption(varargin, 't_typ'); end
+   if olHasOption(varargin, 'hy'), hy = olGetOption(varargin, 'hy'); end
+   if olHasOption(varargin, 'hp'), hp = olGetOption(varargin, 'hp'); end
+   if olHasOption(varargin, 'ht'), ht = olGetOption(varargin, 'ht'); end
+   if olHasOption(varargin, 'h_dir'), h_dir = olGetOption(varargin, 'h_dir'); end
+   if olHasOption(varargin, 'hy_rel_flag'), hy_rel_flag = olGetOption(varargin, 'hy_rel_flag'); end
+   if olHasOption(varargin, 'hp_rel_flag'), hp_rel_flag = olGetOption(varargin, 'hp_rel_flag'); end
+   if olHasOption(varargin, 'ht_rel_flag'), ht_rel_flag = olGetOption(varargin, 'ht_rel_flag'); end
+   if olHasOption(varargin, 'y_typ'), y_typ = olGetOption(varargin, 'y_typ'); end
+   if olHasOption(varargin, 'p_typ'), p_typ = olGetOption(varargin, 'p_typ'); end
+   if olHasOption(varargin, 't_typ'), t_typ = olGetOption(varargin, 't_typ'); end
 
    hy_min = y_typ * 1e-10;
    hp_min = p_typ * 1e-10;
    ht_min = t_typ * 1e-10;
 
-  if hasOption(varargin, 'hy_min'), hy_min = getOption(varargin, 'hy_min'); end
-  if hasOption(varargin, 'hp_min'), hp_min = getOption(varargin, 'hp_min'); end
-  if hasOption(varargin, 'ht_min'), ht_min = getOption(varargin, 'ht_min'); end
+  if olHasOption(varargin, 'hy_min'), hy_min = olGetOption(varargin, 'hy_min'); end
+  if olHasOption(varargin, 'hp_min'), hp_min = olGetOption(varargin, 'hp_min'); end
+  if olHasOption(varargin, 'ht_min'), ht_min = olGetOption(varargin, 'ht_min'); end
 
 
    if (length(hy) == 1) && (dim_y > 1)

ComputeSensitivities/generateSensitivityFunction.m

@@ -41,12 +41,12 @@
    method                      = 'VDE';
    save_intermediates          = true;
 
-   if hasOption(varargin, 'integrator'),                 integrator = getOption(varargin, 'integrator'); end
-   if hasOption(varargin, 'integrator_options'), integrator_options = getOption(varargin, 'integrator_options'); end
-   if hasOption(varargin, 'calcGy'),                        Gy_flag = getOption(varargin, 'calcGy'); end
-   if hasOption(varargin, 'calcGp'),                        Gp_flag = getOption(varargin, 'calcGp'); end
-   if hasOption(varargin, 'method'),                         method = getOption(varargin, 'method'); end
-   if hasOption(varargin, 'save_intermediates'), save_intermediates = getOption(varargin, 'save_intermediates'); end
+   if olHasOption(varargin, 'integrator'),                 integrator = olGetOption(varargin, 'integrator'); end
+   if olHasOption(varargin, 'integrator_options'), integrator_options = olGetOption(varargin, 'integrator_options'); end
+   if olHasOption(varargin, 'calcGy'),                        Gy_flag = olGetOption(varargin, 'calcGy'); end
+   if olHasOption(varargin, 'calcGp'),                        Gp_flag = olGetOption(varargin, 'calcGp'); end
+   if olHasOption(varargin, 'method'),                         method = olGetOption(varargin, 'method'); end
+   if olHasOption(varargin, 'save_intermediates'), save_intermediates = olGetOption(varargin, 'save_intermediates'); end
 
 
    methodCoded.END_piecewise = 1;
@@ -60,7 +60,7 @@
    % As for the calculation with END_full no intermediate matrices are generated, the flag for the output for the intermediates 
    % can only be set to true if another method is chosen (END_piecewise or VDE)
    if ~(method == methodCoded.END_full)
-      if hasOption(varargin, 'Gmatrices_intermediate'), Gmatrices_intermediate_flag = getOption(varargin, 'Gmatrices_intermediate'); end
+      if olHasOption(varargin, 'Gmatrices_intermediate'), Gmatrices_intermediate_flag = olGetOption(varargin, 'Gmatrices_intermediate'); end
    end
 
    % switches includes tspan(1) and tspan(end)
@@ -113,16 +113,16 @@
 
          if Gy_flag
             directions_y = 0;
-            if hasOption(varargin, 'directions_y')
-               directions_y = getOption(varargin, 'directions_y');
+            if olHasOption(varargin, 'directions_y')
+               directions_y = olGetOption(varargin, 'directions_y');
             end
             sensData.Gy = compute_sensitivity_ENDfull_y(datahandle, sol, t_sort_unique, FDstep, directions_y);
          end
 
          if Gp_flag
             directions_p = 0;
-            if hasOption(varargin, 'directions_p')
-               directions_p = getOption(varargin, 'directions_p');
+            if olHasOption(varargin, 'directions_p')
+               directions_p = olGetOption(varargin, 'directions_p');
             end
             sensData.Gp = compute_sensitivity_ENDfull_p(datahandle, sol, t_sort_unique, FDstep, directions_p);
          end

Examples/ParameterEstimation_WhiteCabbage/generateResidualFunction.m

@@ -7,7 +7,7 @@
 
    integrator_solveODE = @ode45;
    odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-6);
-   datahandle    = prepareDatahandleForIntegration('whiteCabbageRHS','solver', func2str(integrator_solveODE), 'options', odeoptionsrhs_test);
+   datahandle    = prepareDatahandleForIntegration('whiteCabbageRHS', 'integrator', func2str(integrator_solveODE), 'options', odeoptionsrhs_test);
 
    return
 

Examples/ParameterEstimation_WhiteCabbage/plot_sensitivities_cabbage.m

@@ -2,7 +2,7 @@
 initPaths();
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
-datahandle    = prepareDatahandleForIntegration('whiteCabbageRHS','solver', func2str(integrator), 'options', odeoptionsrhs_test);
+datahandle    = prepareDatahandleForIntegration('whiteCabbageRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);
 
 tspan         = [0 118];
 initialvalues = [2.48252;0;0];

Examples/ParameterEstimation_WhiteCabbage/test_Cabbage.m

@@ -2,7 +2,7 @@
 initPaths();
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
-datahandle    = prepareDatahandleForIntegration('whiteCabbageRHS','solver', func2str(integrator), 'options', odeoptionsrhs_test);
+datahandle    = prepareDatahandleForIntegration('whiteCabbageRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);
 
 tspan         = [0 118];
 initialvalues = [2.48252;0;0];

Examples/bounceball/bounceball_test.m

@@ -9,7 +9,7 @@
 odeoptions = odeset( 'AbsTol', 1e-14, 'RelTol', 1e-12);
 filename = 'bounceball_rhs';
 tic
-handlerhs_test = prepareDatahandleForIntegration(filename, 'solver', func2str(integrator), 'options', odeoptions);
+handlerhs_test = prepareDatahandleForIntegration(filename, 'integrator', func2str(integrator), 'options', odeoptions);
 toc
 
 fprintf('Integration with ifdiff/%s...\n  ', func2str(integrator));

Examples/canonicalExample/AnalyticalSensitivities/Gmatrices_VDE_df_exact.m

@@ -2,7 +2,7 @@
 initPaths();
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
-datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS','solver', func2str(integrator), 'options', odeoptionsrhs_test);
+datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);
 
 tspan         = [0 20];
 initialvalues = [1;0];

Examples/canonicalExample/AnalyticalSensitivities/analyticalSensitivities_test.m

@@ -2,7 +2,7 @@
 %initPaths();
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
-datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS','solver', func2str(integrator), 'options', odeoptionsrhs_test);
+datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);
 
 tspan         = [0 20];
 initialvalues = [1;0];

Examples/canonicalExample/analyticalSolution.m

@@ -31,7 +31,7 @@
 initPaths();
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
-datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS','solver', func2str(integrator), 'options', odeoptionsrhs_test);
+datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);
 
 tspan         = [0 20];
 initialvalues = [1;0];

Examples/canonicalExample/canonicalExampleRHS_extended_test.m

@@ -11,7 +11,7 @@
 filename = 'canonicalExampleRHS_extended';
 clc
 tic
-hdlrhs_test = prepareDatahandleForIntegration(filename, 'solver', func2str(integrator), 'options', options);
+hdlrhs_test = prepareDatahandleForIntegration(filename, 'integrator', func2str(integrator), 'options', options);
 toc
 
 

Examples/canonicalExample/canonicalExampleRHS_test.m

@@ -10,7 +10,7 @@
 odeoptions = odeset( 'AbsTol', 1e-20, 'RelTol', 1e-12);
 filename = 'canonicalExampleRHS';
 tic
-hdlrhs_test = prepareDatahandleForIntegration(filename, 'solver', func2str(integrator), 'options', odeoptions);
+hdlrhs_test = prepareDatahandleForIntegration(filename, 'integrator', func2str(integrator), 'options', odeoptions);
 toc
 
 %%

Examples/canonicalExample/sensitivities_CanonicalExample.m

@@ -2,7 +2,7 @@
 initPaths();
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
-datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS','solver', func2str(integrator), 'options', odeoptionsrhs_test);
+datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);
 
 tspan         = [0 20];
 initialvalues = [1;0];

Examples/funfun/funinif_test.m

@@ -22,7 +22,7 @@
 
 % ifdiff
 tic
-hdl = prepareDatahandleForIntegration(rhs_name, 'solver', func2str(odesolver), 'options', options);
+hdl = prepareDatahandleForIntegration(rhs_name, 'integrator', func2str(odesolver), 'options', options);
 fprintf('Ifdiff handle preparation took %g seconds.\n', toc());
 tic
 [solif, dataif] = solveODE(hdl, tspan, x0, []);

Examples/sensExampleIntegration.m

@@ -5,7 +5,7 @@
 odeoptions = odeset( 'AbsTol', 1e-06, 'RelTol', 1e-04);   
 
 tic
-hdlsens = prepareDatahandleForIntegration('sensExample', 'solver', 'ode23', 'options', odeoptions);
+hdlsens = prepareDatahandleForIntegration('sensExample', 'integrator', 'ode23', 'options', odeoptions);
 preptime = toc
 
 tic

Examples/sign/sign_inconsistent_test.m

@@ -10,7 +10,7 @@
 filename = 'sign_inconsistent_rhs';
 tic
 datahandle = prepareDatahandleForIntegration(filename, ...
-    'solver', func2str(integrator), 'options', odeoptions);
+    'integrator', func2str(integrator), 'options', odeoptions);
 toc
 
 fprintf('Integration with ifdiff/%s...\n  ', func2str(integrator));

Examples/spiral/spiral_test.m

@@ -9,7 +9,7 @@
 odeoptions = odeset( 'AbsTol', 1e-8, 'RelTol', 1e-6, 'MaxStep', 10000);
 filename = 'spiral_rhs';
 tic
-handlerhs_test = prepareDatahandleForIntegration(filename, 'solver', func2str(integrator), 'options', odeoptions);
+handlerhs_test = prepareDatahandleForIntegration(filename, 'integrator', func2str(integrator), 'options', odeoptions);
 toc
 
 % solution

Examples/stickslip/stickslip_inconsistent_test_highfreq.m

@@ -15,7 +15,7 @@
 filename = 'stickslip_inconsistent_rhs_highfreq';
 integrator = @ode45;
 odeopts = odeset('RelTol',1e-10, 'AbsTol',1e-12); % defaults
-datahandle = prepareDatahandleForIntegration(filename, 'solver', func2str(integrator), 'options', odeopts);
+datahandle = prepareDatahandleForIntegration(filename, 'integrator', func2str(integrator), 'options', odeopts);
 % integrate with ifdiff
 fprintf('Integration with ifdiff/%s...\n  ', func2str(integrator));
 tic

Examples/stickslip/stickslip_test.m

@@ -18,7 +18,7 @@
 
 fprintf('Preparing...\n  ');
 tic
-hdlrhs_test = prepareDatahandleForIntegration('stickslip_rhs', 'solver', func2str(odesolver), 'options', odeoptions);
+hdlrhs_test = prepareDatahandleForIntegration('stickslip_rhs', 'integrator', func2str(odesolver), 'options', odeoptions);
 toc
 %%
 fprintf('Solving using ifdiff...\n  ');

Examples/subway/Sensitivities/Plot_Sensitivities_NewYork.m

@@ -5,7 +5,7 @@
 parameters = nysscc_getPhysicsParameters_vector();
 odeoptionssubwaymodel = odeset( 'AbsTol', 1e-20, 'RelTol', 1e-10);
 
-datahandle = prepareDatahandleForIntegration('newYorkCitySubwayModelRhs_wrapped', 'solver', func2str(integrator), 'options', odeoptionssubwaymodel);
+datahandle = prepareDatahandleForIntegration('newYorkCitySubwayModelRhs_wrapped', 'integrator', func2str(integrator), 'options', odeoptionssubwaymodel);
 sol = solveODE(datahandle, tspan, initValues, parameters);
 
 sol_ode45 = ode45(@(t,x) newYorkCitySubwayModelRhs(t,x, nysscc_getPhysicsParameters()),tspan, initValues,odeoptionssubwaymodel);

Examples/subway/Sensitivities/sensitivities_NewYorkSubway.m

@@ -5,7 +5,7 @@
 parameters = nysscc_getPhysicsParameters_vector();
 odeoptionssubwaymodel = odeset( 'AbsTol', 1e-20, 'RelTol', 1e-10);
 
-datahandle = prepareDatahandleForIntegration('newYorkCitySubwayModelRhs_wrapped', 'solver', func2str(integrator), 'options', odeoptionssubwaymodel);
+datahandle = prepareDatahandleForIntegration('newYorkCitySubwayModelRhs_wrapped', 'integrator', func2str(integrator), 'options', odeoptionssubwaymodel);
 sol = solveODE(datahandle, tspan, initValues, parameters);
 
 %% Precalculations for sensitivities

Examples/subway/newYorkCityExampleIntegrationForThesis.m

@@ -9,7 +9,7 @@
 
 tic
 hdlnyc = prepareDatahandleForIntegration('newYorkCitySubwayModelRhs', ...
-    'solver', func2str(integrator), 'options', odeoptionssubwaymodel);
+    'integrator', func2str(integrator), 'options', odeoptionssubwaymodel);
 toc
 
 %%

README.md

@@ -46,7 +46,7 @@ We set ODE solver and its options as usual. If not set, default values are used.
       initPaths();  % Initialise the paths for ifdiff
       integrator = @ode45; 
       odeoptions = odeset('AbsTol', 1e-14, 'RelTol', 1e-12);
-      datahandle = prepareDatahandleForIntegration('canonicalExampleRHS', 'solver', func2str(integrator), 'options', odeoptions);
+      datahandle = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptions);
    ```
 
 

Readme_Example.m

@@ -13,7 +13,7 @@
 odeoptions = odeset('AbsTol', 1e-8, 'RelTol', 1e-6);
 
 datahandle = prepareDatahandleForIntegration('canonicalExampleRHS', ...
-                                             'solver', func2str(integrator), ...
+                                             'integrator', func2str(integrator), ...
                                              'options', odeoptions);
 tspan         = [0 20];
 initialvalues = [1; 0];

Tools/assertOptionlist.m → Tools/optionlists/olAssertOptionlist.m

@@ -1,5 +1,5 @@
-function answer = assertOptionlist(object)
-   % assertOptionlist(object);
+function answer = olAssertOptionlist(object)
+   % olAssertOptionlist(object);
    %
    % Asserts that the given object is an optionlist and returns true.
    % Otherwise, an error is thrown.
@@ -8,12 +8,14 @@
    %
    % OUTPUT:    answer  -  true if object is a valid optionlist.
    %
-   % Copyright (c) 2016, Andreas Sommer
+   % Author:  Andreas Sommer, 2016
    % andreas.sommer@iwr.uni-heidelberg.de
-   % mail@andreas-sommer.eu
+   % code@andreas-sommer.eu
+   %
+   % History:     Jul2024 --> renamed to ol* scheme
 
    % ensure optionlist is an optionlist
-   [passed, problem] = isOptionlist(object);
+   [passed, problem] = olIsOptionlist(object);
    if ~passed
       error('Not a valid optionlist! Problem: %s', problem);
    end