Treatment Optimization parse space separated lists

src/TreatmentOptimization/Analysis/plotTreatmentOptimizationGroundReactions.m

@@ -47,7 +47,7 @@ function plotTreatmentOptimizationGroundReactions(trackedDataFile, ...
 if trackedDataTime(1) ~= 0
     trackedDataTime = trackedDataTime - trackedDataTime(1);
 end
-trackedDataTime = trackedDataTime / trackedDataTime(end);
+% trackedDataTime = trackedDataTime / trackedDataTime(end);
 for j = 1 : numel(modelDataFiles)
     modelDataStorage = Storage(modelDataFiles(j));
     modelData{j} = storageToDoubleMatrix(modelDataStorage)';
@@ -56,7 +56,7 @@ function plotTreatmentOptimizationGroundReactions(trackedDataFile, ...
     if modelDataTime{j} ~= 0
         modelDataTime{j} = modelDataTime{j} - modelDataTime{j}(1);
     end
-    modelDataTime{j} = modelDataTime{j} / modelDataTime{j}(end);
+    % modelDataTime{j} = modelDataTime{j} / modelDataTime{j}(end);
 end
 
 experimentalMomentIndices = contains(trackedDataLabels, ["_m", "M"]);
@@ -120,10 +120,10 @@ function plotTreatmentOptimizationGroundReactions(trackedDataFile, ...
     end
     nexttile(subplotNumber);
     hold on
-    plot(trackedDataTime*100, trackedData(:, i), LineWidth=2, ...
+    plot(trackedDataTime, trackedData(:, i), LineWidth=2, ...
         Color = colors(1));
     for j = 1 : numel(modelDataFiles)
-        plot(modelDataTime{j}*100, modelData{j}(:, i), LineWidth=2, ...
+        plot(modelDataTime{j}, modelData{j}(:, i), LineWidth=2, ...
             Color = colors(j+1));
     end
     hold off

src/TreatmentOptimization/Analysis/plotTreatmentOptimizationJointLoads.m

@@ -47,7 +47,7 @@ function plotTreatmentOptimizationJointLoads(trackedDataFile, ...
 if trackedDataTime(1) ~= 0
     trackedDataTime = trackedDataTime - trackedDataTime(1);
 end
-trackedDataTime = trackedDataTime / trackedDataTime(end);
+% trackedDataTime = trackedDataTime / trackedDataTime(end);
 % Crop data to get rid of edge effects
 trackedDataTime = trackedDataTime(1:end-1);
 trackedData = trackedData(1:end-1, :);
@@ -58,7 +58,7 @@ function plotTreatmentOptimizationJointLoads(trackedDataFile, ...
     if modelDataTime{j} ~= 0
         modelDataTime{j} = modelDataTime{j} - modelDataTime{j}(1);
     end
-    modelDataTime{j} = modelDataTime{j} / modelDataTime{j}(end);
+    % modelDataTime{j} = modelDataTime{j} / modelDataTime{j}(end);
     % Crop data to get rid of edge effects
     modelDataTime{j} = modelDataTime{j}(1:end-1);
     modelData{j} = modelData{j}(1:end-1, :);
@@ -102,9 +102,9 @@ function plotTreatmentOptimizationJointLoads(trackedDataFile, ...
     end
     nexttile(subplotNumber);
     hold on
-    plot(trackedDataTime*100, trackedData(:, i), LineWidth=2, Color = colors(1));
+    plot(trackedDataTime, trackedData(:, i), LineWidth=2, Color = colors(1));
     for j = 1 : numel(modelDataFiles)
-        plot(modelDataTime{j}*100, modelData{j}(:, i), LineWidth=2, Color = colors(j+1));
+        plot(modelDataTime{j}, modelData{j}(:, i), LineWidth=2, Color = colors(j+1));
     end
     hold off
     if contains(jointLoadLabels(i), "moment")

src/core/parse/parseRcnlConstraintTermSet.m

@@ -39,6 +39,7 @@
         currentTerm = tree{term};
     end
     % Find general cost term elements
+    tempTerm = struct();
     tempTerm.type = getTextFromField(getFieldByNameOrError( ...
         currentTerm, 'type'));
     [isValid, isPath] = isTypeValid(tempTerm.type, toolName, controllerType);
@@ -57,6 +58,9 @@
     % Find other cost term elements
     termElements = fieldnames(currentTerm);
     for element = 1:length(termElements)
+        if strcmp(termElements{element}, "Attributes")
+            continue
+        end
         if isempty(intersect(termElements{element}, ["type" ...
                 "is_enabled" "max_error" "min_error"]))
             contents = getTextFromField(getFieldByNameOrError( ...
@@ -67,6 +71,9 @@
                 contents = false;
             elseif ~isnan(str2double(contents))
                 contents = str2double(contents);
+            elseif any(isspace(convertStringsToChars(contents)))
+                contents = parseSpaceSeparatedList(currentTerm, ...
+                    termElements{element});
             end
             tempTerm.(termElements{element}) = contents;
         end

src/core/parse/parseRcnlCostTermSet.m

@@ -55,6 +55,10 @@
     % Find other cost term elements
     termElements = fieldnames(currentTerm);
     for element = 1:length(termElements)
+
+        if strcmp(termElements{element}, "Attributes")
+            continue
+        end
         if isempty(intersect(termElements{element}, ["type" ...
                 "is_enabled" "max_allowable_error" "error_center"]))
             contents = getTextFromField(getFieldByNameOrError( ...
@@ -65,10 +69,13 @@
                 contents = false;
             elseif ~isnan(str2double(contents))
                 contents = str2double(contents);
+            elseif any(isspace(convertStringsToChars(contents)))
+                contents = parseSpaceSeparatedList(currentTerm, ...
+                    termElements{element});
             end
             costTerms{term}.(termElements{element}) = contents;
         end
-    end 
+    end
 end
 end
 

src/core/parse/parseTreatmentOptimizationInputs.m

@@ -37,6 +37,7 @@
 inputs = parseOptimalControlSolverSettings(tree, inputs);
 inputs.costTerms = parseRcnlCostTermSetHelper( ...
     getFieldByNameOrError(tree, 'RCNLCostTermSet'));
+inputs.costTerms = splitListTerms(inputs.costTerms);
 if isequal(mexext, 'mexw64') 
     inputs.calculateAngularMomentum = any(all([ ...
         strcmp(cellfun(@(term) term.type, inputs.costTerms, ...
@@ -74,6 +75,8 @@
 [inputs.path, inputs.terminal] = parseRcnlConstraintTermSetHelper( ...
     getFieldByNameOrError(tree, 'RCNLConstraintTermSet'), ...
     inputs.controllerType, inputs.toolName);
+inputs.path = splitListTerms(inputs.path);
+inputs.terminal = splitListTerms(inputs.terminal);
 end
 
 function inputs = parseBasicInputs(tree)
@@ -125,3 +128,34 @@
 end
 end
 
+function splitTerms = splitListTerms(originalTerms)
+splitTerms = {};
+listTypes = ["coordinate_list", "load_list", "muscle_list", ...
+    "force_list", "moment_list", "marker_list", "controller_list", ...
+    "synergy_group_list"];
+unlistTypes = ["coordinate", "load", "muscle", ...
+    "force", "moment", "marker", "controller", "synergy_group"];
+for i = 1 : length(originalTerms)
+    termElements = fieldnames(originalTerms{i});
+    hasBeenSplit = false;
+    for element = 1:length(termElements)
+        typeIndex = find(termElements{element} == listTypes, 1);
+        if ~isempty(typeIndex)
+            newTermTemplate = originalTerms{i};
+            newTermTemplate = rmfield(newTermTemplate, termElements{element});
+            elementsList = convertCharsToStrings(split(originalTerms{i} ...
+                .(termElements{element})));
+            for j = 1 : length(elementsList)
+                newTerm = newTermTemplate;
+                newTerm.(unlistTypes(typeIndex)) = ...
+                    convertStringsToChars(elementsList(j));
+                splitTerms{end + 1} = newTerm;
+            end
+            hasBeenSplit = true;
+        end
+    end
+    if ~hasBeenSplit
+        splitTerms{end + 1} = originalTerms{i};
+    end
+end
+end