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Update osimC3D to deal with empty tables #2645

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Update osimC3D to deal with empty tables #2645

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143 changes: 94 additions & 49 deletions Bindings/Java/Matlab/Utilities/osimC3D.m
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,8 @@
markers
forces
ForceLocation
noMarkers
noForces
end
methods
function self = osimC3D(path2c3d, ForceLocation)
Expand Down Expand Up @@ -80,6 +82,16 @@
location = 'PointOfWrenchApplication';
end
self.ForceLocation = location;

% Set flags if marker or force data tables are empty
if self.markers.getNumColumns() == 0
self.noMarkers = 1; disp('Marker table is empty');
else; self.noMarkers = 0;
end
if self.forces.getNumColumns() == 0
self.noForces = 1; disp('Force table is empty');
else; self.noForces = 0;
end
end
function p = getPath(self)
p = self.path();
Expand All @@ -93,11 +105,15 @@
end
function rate = getRate_marker(self)
% Get the capture rate used for the Marker Data
rate = str2double(self.markers.getTableMetaDataAsString('DataRate'));
if self.noMarkers; disp('No Markers exist'); return; else
rate = str2double(self.markers.getTableMetaDataAsString('DataRate'));
end
end
function rate = getRate_force(self)
% Get the capture rate used for the Force Data
rate = str2double(self.forces.getTableMetaDataAsString('DataRate'));
if self.noForces; disp('No Forces exist'); return; else
rate = str2double(self.forces.getTableMetaDataAsString('DataRate'));
end
end
function n = getNumTrajectories(self)
% Get the number of markers in the c3d file
Expand Down Expand Up @@ -130,7 +146,8 @@
table = self.forces().clone();
end
function [markerStruct, forcesStruct] = getAsStructs(self)
% Convert the OpenSim tables into Matlab Structures
% Convert the OpenSim tables into Matlab Structures.
% If tables are empty, empty Structs are returned.
markerStruct = osimTableToStruct(self.markers);
forcesStruct = osimTableToStruct(self.forces);
disp('Maker and force data returned as Matlab Structs')
Expand All @@ -146,17 +163,35 @@ function rotateData(self,axis,value)
if ~isnumeric(value)
error('value must be numeric (90, -90, 270, ...')
end
% rotate the tables
self.rotateTable(self.markers, axis, value);
self.rotateTable(self.forces, axis, value);
disp('Marker and Force tables have been rotated')

% Rotate the Marker table
if self.noMarkers
disp('No Markers exist');
else
self.rotateTable(self.markers, axis, value);
disp('Marker table rotated');
end

% Rotate the Force table
if self.noForces
disp('No Forces exist');
else
self.rotateTable(self.forces, axis, value);
disp('Forces table rotated');
end
end
function convertMillimeters2Meters(self)
% Function to convert point data (mm) to m and Torque data
% (Nmm) to Nm.

% Check if a force table is non-empty
if self.noForces
disp('No Force table found, no conversion performed');
return
end

import org.opensim.modeling.*

nRows = self.forces.getNumRows();
labels = self.forces.getColumnLabels();

Expand All @@ -179,37 +214,47 @@ function writeTRC(self,varargin)
% osimC3d.writeTRC() Write to dir of input c3d.
% osimC3d.writeTRC('Walking.trc') Write to dir of input c3d with defined file name.
% osimC3d.writeTRC('C:/data/Walking.trc') Write to defined path input path.


% Check if a Marker table is non-empty
if self.noMarkers
disp('No Marker table found, file not written');
return
end
% Compute an output path to use for writing to file
outputPath = generateOutputPath(self,varargin,'.trc');


import org.opensim.modeling.*
% Write to file
TRCFileAdapter().write( self.markers, outputPath)
disp(['Marker file written to ' outputPath]);
end
function writeMOT(self,varargin)
% Write force data to mot file.
% osimC3d.writeMOT() Write to dir of input c3d.
% osimC3d.writeMOT('Walking.mot') Write to dir of input c3d with defined file name.
% osimC3d.writeMOT('C:/data/Walking.mot') Write to defined path input path.
% Write force data to mot file.
% osimC3d.writeMOT() Write to dir of input c3d.
% osimC3d.writeMOT('Walking.mot') Write to dir of input c3d with defined file name.
% osimC3d.writeMOT('C:/data/Walking.mot') Write to defined path input path.

% Compute an output path to use for writing to file
outputPath = generateOutputPath(self,varargin,'.mot');

% Compute an output path to use for writing to file
outputPath = generateOutputPath(self,varargin,'.mot');
% Check if a force table is non-empty
if self.noForces
disp('No Force table found, file not written');
return
end

import org.opensim.modeling.*
% Get the forces table
forces = self.getTable_forces();
% Get the column labels
labels = forces.getColumnLabels();
% Make a copy
updlabels = labels;
import org.opensim.modeling.*
% Get the forces table
forces = self.getTable_forces();
% Get the column labels
labels = forces.getColumnLabels();
% Make a copy
updlabels = labels;

% Labels from C3DFileAdapter are f1, p1, m1, f2,...
% We edit them to be consistent with requirements of viewing
% forces in the GUI (ground_force_vx, ground_force_px,...)
for i = 0 : labels.size() - 1
% Labels from C3DFileAdapter are f1, p1, m1, f2,...
% We edit them to be consistent with requirements of viewing
% forces in the GUI (ground_force_vx, ground_force_px,...)
for i = 0 : labels.size() - 1
% Get the label as a string
label = char(labels.get(i));
% Transform the label depending on force, point, or moment
Expand All @@ -224,38 +269,38 @@ function writeMOT(self,varargin)
label = [label '_m'];
end
% update the label name
updlabels.set(i,label);
end
updlabels.set(i,label);
end

% set the column labels
forces.setColumnLabels(updlabels)
% set the column labels
forces.setColumnLabels(updlabels)

% Flatten the Vec3 force table
postfix = StdVectorString();
postfix.add('x');postfix.add('y');postfix.add('z');
forces_flat = forces.flatten(postfix);
% Flatten the Vec3 force table
postfix = StdVectorString();
postfix.add('x');postfix.add('y');postfix.add('z');
forces_flat = forces.flatten(postfix);

% Change the header in the file to meet Storage conditions
if forces_flat.getTableMetaDataKeys().size() > 0
for i = 0 : forces_flat.getTableMetaDataKeys().size() - 1
% Change the header in the file to meet Storage conditions
if forces_flat.getTableMetaDataKeys().size() > 0
for i = 0 : forces_flat.getTableMetaDataKeys().size() - 1
% Get the metakey string at index zero. Since the array gets smaller on
% each loop, we just need to keep taking the first one in the array.
metakey = char(forces_flat.getTableMetaDataKeys().get(0));
% Remove the key from the meta data
forces_flat.removeTableMetaDataKey(metakey)
end
end
% Add the column and row data to the meta key
forces_flat.addTableMetaDataString('nColumns',num2str(forces_flat.getNumColumns()+1))
forces_flat.addTableMetaDataString('nRows',num2str(forces_flat.getNumRows()));
end
end
% Add the column and row data to the meta key
forces_flat.addTableMetaDataString('nColumns',num2str(forces_flat.getNumColumns()+1))
forces_flat.addTableMetaDataString('nRows',num2str(forces_flat.getNumRows()));

% Write to file
STOFileAdapter().write(forces_flat, outputPath)
disp(['Forces file written to ' outputPath]);
end
end
% Write to file
STOFileAdapter().write(forces_flat, outputPath)
disp(['Forces file written to ' outputPath]);
end
end

methods (Access = private, Hidden = true)
methods (Access = private, Hidden = true)
function setMarkers(self, a)
% Private Method for setting the internal Marker table
self.markers = a;
Expand Down