CHANGES.txt

JAABA: The Janelia Automatic Animal Behavior Annotator
v. 0.5.0

Copyright 2012, Kristin Branson, HHMI Janelia Farm Resarch Campus
http://jaaba.sourceforge.net/
bransonk@janelia.hhmi.org


CHANGES from 0.6.0:

JAABA:

* Support for multiple classifiers.
* Support for ST features.
* Ethogram and Labelgram.
* Various minor bugfixes.
* Updated project (.jab) file format.
* Substantial internal cleanup/refactoring.

***

CHANGES from 0.5.0:

JAABA:

* Major changes to file management. All JAABA-related data is now stored in a single file with the extension .jab. Previously, this information had all been stored in the JAABA project, JAABA classifier, and JAABA labels files. The parts of the GUI related to file and project management have been restructured to reflect this change. The code was also refactored to some extent during this change. 
* Made plotting trajectories more efficient if there are lots of short-lived trajectories. 

JAABAPlot:

* Lots of new functionality:
 * Tooltips.
 * Options for alignment of different experiments and trajectories when plotting time series. 
 * Time series plotted in seconds/minutes/hours/days instead of frames. 
 * Can no
* Bug fix: Fixed bug in computing intersections of features. 
* Bug fix: Fixed bug in computing mean statistics per bout. 

***

CHANGES from 0.4.1:

JAABA:

* Bug fix: If trans_types in feature config file only had one type, e.g. None, then it was not getting parsed correctly, and the feature was not actually being used. Fixed this issue. 

* More information is now stored in the classifier, labels, and scores files, so that it is possible to reconstruct which classifier was used for what. In particular, labels are now stored in the classifier file, so that versioning of classifiers & labels can be done. 

* Sundry bug fixes and feature requests fullfilled. 

JAABAPlot: 

* Completely redone. 

***

CHANGES from 0.4.0:

* Sped up training. If the number of training samples is less than 
numSamples=2500, this may cause a slight change in the resulting 
classifier. Within findWeakRuleSamples, we now only sample the
training set to numSamples=2500 if the training set size is > 2500. 
Otherwise, we use the weights. Accumulation of the weights is now
done in a mex file. 

* Documentation no longer included within the package. Instead, the
Sourceforge website is referenced. 

* Changed StartJAABA_compiled so that it doesn't complain if user clicks cancel in editfiles gui.

* Made playing the movies smoother. Checks to predict are done every 5000 frames.

***

Documentation and up-to-date versions of the software are available on
our project homepage:

                    http://jaaba.sourceforge.net/

***

JAABA was developed by 
Mayank Kabra, Alice Robie, Marta Rivera-Alba, Steven Branson, 
and Kristin Branson.
All work was funded by the Howard Hughes Medical Institute and 
the Janelia Farm Research Campus. 

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License (version 3 pasted below) for more
details.

***

JAABA contains code from the following sources:

* Ctrax by Kristin Branson et al.: 
  http://ctrax.sourceforge.net/
* Piotr's Image & Video MATLAB Toolbox by Piotr Dollar et al.: 
  http://vision.ucsd.edu/~pdollar/toolbox/doc/
* Netlab by Christopher Bishop et al.: 
  http://www1.aston.ac.uk/eas/research/groups/ncrg/resources/netlab/
* ellipsedraw.m by Lei Wang: 
  http://www.mathworks.com/matlabcentral/fileexchange/3224-ellipsedraw1-0/content/ellipsedraw.m
* savefig.m and eps2pdf.m by Peder Axensten: 
  http://www.mathworks.com/matlabcentral/fileexchange/10889-savefig
* MATLAB and Octave Functions for Computer Vision and Image Processing by Peter Kovesi:
  http://www.csse.uwa.edu.au/~pk/research/matlabfns/
* rotateticklabel.m by Andrew Bliss:
  http://www.mathworks.com/matlabcentral/fileexchange/8722-rotate-tick-label
* findjobj.m by Yair Altman:
  http://www.mathworks.com/matlabcentral/fileexchange/14317-findjobj-find-java-handles-of-matlab-graphic-objects

***

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