fix mass prop in examples. Close #85

Author: modenaxe

Example_bilateral_model.m

@@ -18,6 +18,9 @@
 datasets_folder = 'bone_datasets';
 % datasets that you would like to process
 datasets = {'TLEM2_MRI', 'JIA_MRI'};
+% masses for models
+subj_mass_set = [45,      76.5]; %kg
+
 % format of input geometries
 input_geom_format = 'tri';
 % visualization geometry format (options: 'stl' or 'obj')
@@ -42,24 +45,24 @@
     % folder from which triangulations will be read
     tri_folder = fullfile(datasets_folder, cur_dataset, input_geom_format);
 
+    % log printout
+    log_file = fullfile(output_models_folder, [cur_dataset,'_bilateral.log']);
+    logConsolePrintout('on', log_file);
+    
     for n_side = 1:2
 
         % get current body side
         [sign_side , cur_side] = bodySide2Sign(sides{n_side});
 
         % cell array with the bone geometries that you would like to process
         bones_list = {'pelvis_no_sacrum',  ['femur_', cur_side],...
-                     ['tibia_', cur_side],['talus_', cur_side],...
+                     ['tibia_', cur_side], ['talus_', cur_side],...
                      ['calcn_', cur_side]};
 
         % model and model file naming
         cur_model_name = ['auto_',datasets{n_d},'_',upper(cur_side)];
         model_file_name = [cur_model_name, '.osim'];
 
-        % log printout
-        log_file = fullfile(output_models_folder, [cur_model_name, '.log']);
-        logConsolePrintout('on', log_file);
-        
         % create geometry set structure for all 3D bone geometries in the dataset
         triGeom_set = createTriGeomSet(bones_list, tri_folder);
 
@@ -81,6 +84,10 @@
 
         % create joints
         createOpenSimModelJoints(osimModel, JCS, joint_defs);
+
+        % update mass properties to those estimated using a scale version of
+        % gait2392 with COM based on Winters's book.
+        osimModel = assignMassPropsToSegments(osimModel, JCS, subj_mass_set(n_d));
 
         % add markers to the bones
         addBoneLandmarksAsMarkers(osimModel, BL);
@@ -99,14 +106,16 @@
         disp(['Model geometries saved in folder: ', geometry_folder_path,'.'])
         disp('-------------------------')
         clear triGeom_set JCS BL CS
-        logConsolePrintout('off');
+        
         % store model file (with path) for merging
         osim_model_set(n_side) = {osim_model_file}; %#ok<SAGROW>
     end
     % merge the two sides
     merged_model_file = fullfile(output_models_folder,[cur_dataset,'_bilateral.osim']);
     mergeOpenSimModels(osim_model_set{1}, osim_model_set{2}, merged_model_file);
-
+    
+    % stop logger
+    logConsolePrintout('off');
 end
 % remove paths
 rmpath(genpath('STAPLE'));

Example_full_leg_left.m

@@ -21,6 +21,9 @@
 % datasets that you would like to process
 dataset_set = {'TLEM2_CT', 'TLEM2_MRI'};
 
+% estimated mass of specimen
+mass = 45; % [kg] 
+
 % cell array with the bone geometries that you would like to process
 bones_list = {'pelvis_no_sacrum','femur_l','tibia_l','talus_l', 'calcn_l'};
 
@@ -37,7 +40,7 @@
 % create model folder if required
 if ~isfolder(output_models_folder); mkdir(output_models_folder); end
 
-for n_d = 1%:numel(dataset_set)
+for n_d = 1:numel(dataset_set)
 
     % current dataset being processed
     cur_dataset = dataset_set{n_d};
@@ -78,6 +81,10 @@
     % create joints
     createOpenSimModelJoints(osimModel, JCS, workflow);
 
+    % update mass properties to those estimated using a scale version of
+    % gait2392 with COM based on Winters's book.
+    osimModel = assignMassPropsToSegments(osimModel, JCS, mass);
+    
     % add markers to the bones
     addBoneLandmarksAsMarkers(osimModel, BL);
 

Example_full_leg_right.m

@@ -13,14 +13,17 @@
 %----------%
 % SETTINGS %
 %----------%
-output_models_folder = 'opensim_models_example';
+output_models_folder = 'opensim_models_examples';
 
 % folder where the various datasets (and their geometries) are located.
 datasets_folder = 'bone_datasets';
 
 % datasets that you would like to process
 datasets = {'TLEM2_CT'};
 
+% estimated mass of specimen
+mass = 45; % [kg] 
+
 % body sides
 cur_side = 'r';
 
@@ -82,6 +85,10 @@
 
     % create joints
     createOpenSimModelJoints(osimModel, JCS, workflow);
+
+    % update mass properties to those estimated using a scale version of
+    % gait2392 with COM based on Winters's book.
+    osimModel = assignMassPropsToSegments(osimModel, JCS, mass);
 
     % add markers to the bones
     addBoneLandmarksAsMarkers(osimModel, BL);

Example_hip_model.m

@@ -23,6 +23,7 @@
 % If you add multiple datasets they will be batched processed but you will
 % have to adapt the folder and file namings below.
 dataset_set = {'LHDL_CT'};
+body_mass = 64; %kg
 
 % cell array with the name of the bone geometries to process.
 bones_list = {'pelvis_no_sacrum', 'femur_r'};
@@ -79,6 +80,10 @@
 
     % create joints
     createOpenSimModelJoints(osimModel, JCS, joint_defs);
+
+    % update mass properties to those estimated using a scale version of
+    % gait2392 with COM based on Winters's book.
+    osimModel = assignMassPropsToSegments(osimModel, JCS, body_mass);
 
     % add markers to the bones
     addBoneLandmarksAsMarkers(osimModel, BL);

Example_knee_model.m

@@ -17,6 +17,7 @@
 
 % datasets that you would like to process
 dataset_set = {'ICL_MRI'};
+body_mass = 87; %kg
 
 % cell array with the name of the bone geometries to process
 bones_list = {'femur_r', 'tibia_r'};
@@ -77,9 +78,14 @@
     % add patella to tibia (this will be replaced by a proper joint and
     % dealt with the other joints in the future).
     side = inferBodySideFromAnatomicStruct(geom_set);
-%     improve!
+
+    % temporary approach to improve
     attachPatellaGeom(osimModel, side, tri_folder, geometry_folder_path, geometry_folder_name, vis_geom_format)
 
+    % update mass properties to those estimated using a scale version of
+    % gait2392 with COM based on Winters's book.
+    osimModel = assignMassPropsToSegments(osimModel, JCS, body_mass);
+    
     % add markers to the bones
     addBoneLandmarksAsMarkers(osimModel, BL);
 

STAPLE/anthropometry/assignMassPropsToSegments.m

@@ -102,7 +102,7 @@
 %---------------------------------------------
 
 % map gait2392 properties to the model segments as an initial value
-disp('Mapping segment masses and inertias from gait2392/Rajagopal model.')
+disp('Mapping segment masses and inertias from gait2392 model.')
 osimModel = mapGait2392MassPropToModel(osimModel);
 
 % opensim model total mass (consistent in gait2392 and Rajagopal)