C3DFileAdapter: very slow file reading to Tables

[nickbianco]

Reading a c3d file's data to a Table using the C3DFileAdapter is currently very slow. I compared loading a c3d file (1 minute of walking data) using @jimmyDunne's btk_loadc3d() MATLAB script to the C3DFileAdapter and got the following results after 3 runs (Windows 7, 64-bit, i5 2.50 GHz):

btk in MATLAB: 0.39 +/- 0.07 seconds
C3DFileAdapter: 671.96 +/- 20.08 seconds

If you'd like to recreate the test, I can send you the file I used.

import org.opensim.modeling.*

file = 'slk.c3d';

% Using btk directly in MATLAB (need btk MATLAB wrapper)
tic
data = btk_loadc3d(file);
disp('btk in MATLAB: ')
toc

disp(' ')
 
% Using new C3DFileAdapter in 4.0
tic
adapter = C3DFileAdapter();
tables = adapter.read(file);
disp('C3DFileAdapter: ')
toc

[jimmyDunne]

Need to add a benchmark to the test case. Profile each step to see where issue is coming from.

[jimmyDunne]

@aseth1 will profile

[chrisdembia]

I did some profiling and it seems that the issue is the resizing that DataTable_::appendRow() does (this takes up 66% of the time in testC3DFileAdapter). I tried to pre-allocate the matrix underneath the DataTable, but I was not successful. @aseth1 let me know if you want to chat about this.

[chrisdembia]

Here's how I got the number of rows and column:

        int marker_num_frames = marker_pts->GetFrontItem()->GetFrameNumber();
        int marker_num_columns = marker_pts->GetItemNumber();
        marker_table.updMatrix().resize(marker_num_frames, marker_num_columns);

[aseth1]

Thanks @chrisdembia for checking and suggesting a fix. I can confirm your findings in VS2015 profiler:
87.1 % -> _depData.resizeKeep(_depData.nrow() + 1, _depData.ncol());

[chrisdembia]

Ah; it seems like your profiler was more helpful. Let me know if you want to chat more.

[aymanhab]

PR in review