parseDesignOptimizationSettingsTree.m

% This function is part of the NMSM Pipeline, see file for full license.
%
% This function parses the settings tree resulting from xml2struct of the
% Design Optimizatoin settings XML file.
%
% (struct) -> (struct, struct)
% returns the input values for Design Optimization


function [inputs, params] = ...
    parseDesignOptimizationSettingsTree(settingsTree)
inputs = getInputs(settingsTree);
params = getParams(settingsTree);
inputs = modifyModelForces(inputs);
inputs = updateMuscleModelProperties(inputs);
end

function inputs = getInputs(tree)
import org.opensim.modeling.Storage
inputs = getTreatmentOptimizationInputs(tree);
inputs = getDesignVariableBounds(tree, inputs);
if strcmpi(inputs.controllerType, 'synergy_driven')
inputs.synergyWeights = parseTreatmentOptimizationStandard(...
    {getTextFromField(getFieldByName(tree, 'synergy_vectors_file'))});
end
inputs.systemFns = parseSpaceSeparatedList(tree, "model_functions");
parameterTree = getFieldByNameOrError(tree, "RCNLParameterTermSet");
if isstruct(parameterTree) && isfield(parameterTree, "RCNLParameterTerm")
    inputs.userDefinedVariables = parseRcnlCostTermSet( ...
        parameterTree.RCNLParameterTerm);
else
    inputs.userDefinedVariables = {};
end
end

function inputs = getDesignVariableBounds(tree, inputs)
designVariableTree = getFieldByNameOrError(tree, ...
    'RCNLDesignVariableBoundsTerms');
jointPositionsMultiple = getFieldByNameOrError(designVariableTree, ...
    'joint_positions_multiple');
if(isstruct(jointPositionsMultiple))
    inputs.statePositionsMultiple = getDoubleFromField(jointPositionsMultiple);
end
jointVelocitiesMultiple = getFieldByNameOrError(designVariableTree, ...
    'joint_velocities_multiple');
if(isstruct(jointVelocitiesMultiple))
    inputs.stateVelocitiesMultiple = getDoubleFromField(jointVelocitiesMultiple);
end
jointAccelerationsMultiple = getFieldByNameOrError(designVariableTree, ...
    'joint_accelerations_multiple');
if(isstruct(jointAccelerationsMultiple))
    inputs.stateAccelerationsMultiple = ...
        getDoubleFromField(jointAccelerationsMultiple);
end
jointJerkMultiple = getFieldByNameOrError(designVariableTree, ...
    'joint_jerks_multiple');
if(isstruct(jointJerkMultiple))
    inputs.controlJerksMultiple = getDoubleFromField(jointJerkMultiple);
end
if strcmp(inputs.controllerType, 'synergy_driven')
maxControlSynergyActivations = getFieldByNameOrError(designVariableTree, ...
    'synergy_activations_max');
if(isstruct(maxControlSynergyActivations))
    inputs.maxControlSynergyActivations = ...
        getDoubleFromField(maxControlSynergyActivations);
end
if inputs.optimizeSynergyVectors
    maxParameterSynergyWeights = getFieldByNameOrError(designVariableTree, ...
        'synergy_weights_max');
    if(isstruct(maxParameterSynergyWeights))
        inputs.maxParameterSynergyWeights = ...
            getDoubleFromField(maxParameterSynergyWeights);
    end
end
else 
maxControlTorques = getFieldByName(designVariableTree, ...
    'torque_controls_multiple');
if(isstruct(maxControlTorques))
    inputs.maxControlTorquesMultiple = getDoubleFromField(maxControlTorques);
else
    inputs.maxControlTorquesMultiple = 1;
end
end
finalTimeRange = getFieldByName(designVariableTree, ...
    'final_time_range');
if(isstruct(finalTimeRange))
    inputs.finalTimeRange = getDoubleFromField(finalTimeRange);
end
inputs.enableExternalTorqueControl = getBooleanLogicFromField( ...
    getFieldByName(tree, "enable_external_torque_controls"));
if inputs.enableExternalTorqueControl
    inputs.externalControlTorqueNames = parseSpaceSeparatedList(tree, ...
        "external_control_coordinate_list");
    inputs.numExternalTorqueControls = ...
        length(inputs.externalControlTorqueNames);
    inputs.maxExternalTorqueControls = getDoubleFromField( ...
        getFieldByNameOrError(designVariableTree, ...
        'external_torque_control_multiple'));
end
inputs.toolName = "DesignOptimization";
end

function params = getParams(tree)
params.solverSettings = getOptimalControlSolverSettings(...
    getTextFromField(getFieldByName(tree, 'optimal_control_settings_file')));
end