Using JAABA with my own tracking algorithm

[qga...@gmail.com]

Hello JAABA community,

I have been going through all of the JAABA tutorials and have it running beautifully with the sample experiments and data sets. We use a tracking program that I whipped up in the lab and I am having a tough time getting it to work with JAABA. It is really close as all of the files load, but the videos and tracking just don't look quite right once it's imported into JAABA, even though the tracking works well within our programs own display. Is there anyway to make JAABA compatible with my files? I have generated registered_trx.mat files and an uncompressed video to run JAABA on new mac machines.

Any help is greatly appreciated,

Quentin

[Kristin Branson]

Dear Quentin,

It should be possible to get JAABA to be compatible with your tracker.
If you want to share a video and trajectory file with me via Dropbox,
I can try to see what is going wrong.

KB

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[flytracker]

Dear Kristin,

I am trying to use the results of my tracking algorithm in JAABA, but some how I am getting error, which I have attached as an image. As shown in tutorial, JAABA requires, two important files, the movie(in ufmf format), the tracks obtained from CTRAX (which is basically a structure with 14 fields) .Apart from these files, there needs to be a directory names perframe, which computes all the per frame features and a Metadata file(which I believe is not that important).

 

So, I tracked my flies using my algorithm and copied the entire results (in proper format) into the structure(registered_trx.mat) which JAABA can read. Still i am getting the Warning Dialog named:

 

MATLAB undefined Function:MATLAB undefined function or variable 'msg1'. This also freezes JAABA and MATLAB .Therefore I cannot close. The only option to close MATLAB is to start the task manager and then close it. 

 

I am a bit confused of, from where is JAABA able to find this 'msg1' variable/function? However, when I try to use CTrax results, there is no such error. Could you please help in integrating my tracking results in JAABA?

 

Also, one basic question on the methodology of JAABA, is it a binary classifier, where we can classify only one behavior at a time and cannot treat it as a multi classifier?

 

Please reply.

 

Thanks

[Kristin Branson]

Could you share the current version of your data with me via Dropbox? I can try to see if I can figure out the error. 

Thanks!
Kristin

[Tanmay]

Hi Kristin,

 

Please find attached my tracking result as a mat file. It is only for the first 1000 frames which I am interested in.

 

please let me know how can I integrate it in JAABA.

 

Thanks

[Kristin Branson]

It looks like the _mm fields are missing:

x_mm

y_mm

a_mm

b_mm

theta_mm

These are the positions of the animals in real coordinates. See

http://jaaba.sourceforge.net/DataFormatting.html#TracksFileStructure

for a bit more information. 

I added these fields using the pxpermm value stored in your trx file for converting, and the file did load into JAABA. I've attached the updated version. I'm not sure if the trajectories look like what you want them to -- the orientations seem to not be very correlated with velocity direction -- are your angles in degrees instead of radians? 

KB

[Tanmay]

Dear Kristin,

Thanks for the reply. Indeed I also noticed that the files were missing!

Although, now it is able to load it into JAABA, but why is it so that the triangles corresponding to the fly position do not correlate to the actual fly position? I believe that the center of triangle corresponds to x, y coordinates of the fly.

There is a complete shift of the these triangles with the fly position?

Is it a problem of setting origin? My origin is by default (top left corner of the image).  I have also changed the arena parameters according to mine.

Yes, my angles are in degrees in the range of 0 to 360.

[tracker]

Hi,

Sorry to bother you.I fixed the issue. It was some scaling issue.

Thanks for the help!

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