Help with integrating OPTOTRAK 3020 and Matlab

[Justin Fine]

Hello all! This is my first post on here. I was hoping someone more experienced with programming, and such, might be able to help me with an issue I am having. I am not familiar with the C language, and I am just mildly seasoned in Matlab. I am trying to use the optotoolbox of functions created for Matlab to write incoming marker data to a variable, that is, rather than using the fprintf function to write to a text file. If anybody here might be able to help with this, well, I would greatly appreciate it.

Justin Fine

[Andrew Wilson]

Re: Help with integrating OPTOTRAK 3020 and Matlab

If all you're trying to do is save data out in Matlab format, then it's just a matter of assigning the output of the function that is reading the marker to a Matlab variable and saving it out using the 'save' function. I don't know the Optotrak tool box per se, but this is a fairly standard Matlab operation.

[Jason Friedman]

Re: Help with integrating OPTOTRAK 3020 and Matlab

Hi Justin,

Can you post a few lines of the relevant code, then I'm sure that someone will be able to help you.

Jason

[Justin Fine]

Re: Help with integrating OPTOTRAK 3020 and Matlab

Here is the portion of the code that is giving me trouble. I am trying to write to the variable, A, matlab is only writing the last sampled value repeatedly instead of appending each sample to the variable. Any help would be appreciated.

%Loop around spooling data to file and displaying realtime 3d data.
SpoolComplete=0;
while(~SpoolComplete)
%Write data if there is any to write.
[RealtimeDataReady,SpoolComplete,SpoolStatus,Frames Buffered]=optotrak('DataBufferWriteData');

%Display realtime if there is any to display.
if(RealtimeDataReady)
%Receive the 3D data.
data=optotrak('DataReceiveLatest3D',coll.NumMarker s);
for MarkerCnt = 1:coll.NumMarkers
for sampleIndex = 1:samples
A(1:sampleIndex,1) = data.Markers{MarkerCnt}(1);
A(1:sampleIndex,2) = data.Markers{MarkerCnt}(2);
A(1:sampleIndex,3) = data.Markers{MarkerCnt}(3);
end
end
end
%Request a new frame of realtime 3D data.
optotrak('RequestLatest3D')
RealtimeDataReady = 0;
end

[Jason Friedman]

Re: Help with integrating OPTOTRAK 3020 and Matlab

Hi Justin,

If you just want to save to a variable, then you don't need to call "DataBufferWriteData"

I think you want to do something like this (where samples is the number of samples you want to collect) [not tested]:

for sampleIndex=1:samples
data=optotrak('DataReceiveLatest3D',coll.NumMarker s);
for MarkerCnt=1:coll.NumMarkers
A(sampleIndex,1) = data.Markers{MarkerCnt}(1);
A(sampleIndex,2) = data.Markers{MarkerCnt}(2);
A(sampleIndex,3) = data.Markers{MarkerCnt}(3);
end
end

Note that every time in the outer loop, you need to call "DataReceiveLatest3D" to get a new piece of data.
Also, if you write A(1:sampleindex,1) then you overwrite all the data with the latest sample, whereas
A(sampleIndex,1) will only set the last value (as I assume you actually want).

Jason

Every time you want a new sample, you need to make a call to DataReceiveLatest3D

[Tim Wrigley]

Re: Help with integrating OPTOTRAK 3020 and Matlab

Edited to avoid confusion with Jason's message ... written while I was writing mine .... :-)

Firstly, 'samples' has no defined value in Justin's code snippet.
One of the first steps in troubleshooting should be to check the values of all variables to see if they makes sense. I assume that the number of samples returned from the optotrak('DataReceiveLatest3D') function can vary ? You will need to test for that.
Secondly, 'for' loops are rarely the best way to do things in Matlab, esp for real-time code. Look up 'vectorization'. All the marker data should probably be able to be dumped into A in one operation, without one if not both of the 'for' loops. Also '1:sampleIndex' looks wrong (redundant) for the for loop but could be on the right track in a vectorized version.
Good luck
Tim

[Tim Haswell]

Re: Help with integrating OPTOTRAK 3020 and Matlab

Hi Justin,

The function DataBufferWriteData is a non-blocking (does not prevent code execution until all the data is collected) function for writing data to file, while DataReceiveLatest3D is for capturing a single frame of data. So Jason is correct in stating that the sample index should be incremented for each call to DataReceiveLatest3D. The toolbox you are using is simply a wrapper around the NDI Optotrak API and has no vectorization, to my knowledge.

In short, your problem is the result of precisely the problem Jason pointed out. You were over-writing the first frame of data with each new frame of data. However, I don't think that you will need to use a for-loop to increment sampleIndex, since the while(~SpoolComplete)-loop will continue to iterate through your code until all the requested data is spooled to disk. You just need to initialize sampleIndex to 0 before the while-loop and increment it at the end of the code within the while-loop. I also noticed, you will probably need to add a MarketCnt index to A or you will only end up with the last marker's data (it having been over-written by each marker's data as it goes through that MarkerCnt for-loop). I would also recommend pre-allocating A before this code runs to avoid memory fragmentation. I haven't tested any of the code below, its just to illustrate my comments.

A = zeros(samples, coll.NumMarkers, 3); % Pre-allocate A to avoid memory fragmentation
SpoolComplete = 0;
sampleIndex = 0;

%Loop around spooling data to file and displaying realtime 3d data.
while(~SpoolComplete)
%Write data if there is any to write.
[RealtimeDataReady,SpoolComplete,SpoolStatus,Frames Buffered]=optotrak('DataBufferWriteData');

%Display realtime if there is any to display.
if(RealtimeDataReady)
%Receive the 3D data.
data=optotrak('DataReceiveLatest3D',coll.NumMarker s);
for MarkerCnt = 1:coll.NumMarkers
A(sampleIndex, MarkerCnt, 1) = data.Markers{MarkerCnt}(1);
A(sampleIndex, MarkerCnt, 2) = data.Markers{MarkerCnt}(2);
A(sampleIndex, MarkerCnt, 3) = data.Markers{MarkerCnt}(3);
end
end
sampleIndex = sampleIndex + 1;
%Request a new frame of realtime 3D data.
optotrak('RequestLatest3D')
RealtimeDataReady = 0;
end