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\f0\b\fs24 \cf0 Mousetracking README 
\b0 - updated Jun 2016, Peter Jones\
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\b\fs28 Overview
\b0\fs24 \
The analyses that are in this folder process the data in stages.  It is designed to work on video files as input.  Each video file is then analyzed (tracked) and the result saved in a MAT file.  Those tracking results are then referenced by scripts and functions that compile results for each mouse over multiple trials and days, and over multiple mice.  Some datasets include recordings of sniffing (thermocouple signals), which are recorded in Igor Pro files and in HD5 format, read by some matlab routines, and integrated/synched with the video records of the behavior.   
\b This MATLAB software runs best on a computer with large amount (>= 16GB) of RAM. 
\b0 This is because of the loading segments of movie, and then saving tracking is pretty memory intensive, as well as processor intensive.  If you have 16GB of RAM you run the processing in parallel with 3 files at once.  \
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\b\fs28 \
Saved Data Files\

\i \
sniffData 
\b0 folder
\i0\b \

\b0\fs24 Contains the mat files of the 5 mice for which there is good behavior/sniff recording data.  These mat files are made by loadSniffExps2014.m.  
\b processedSniffData.mat 
\b0 is a hand saved data file of the workspace after running compilePopSniffdata.m \

\b \
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\fs28 \cf0 Code Files/functions\
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\fs24 \cf0 MouseTrackerKF
\b0  - the currently developed version of the mousetracker object.  This object loads in a video and will process it to generate a mouse trajectory based on the video. It also provides functions to access and visualize the data within it. \
\

\b loadMouseTracking
\b0  - This function loads the files in a specified list.  It is a way to include different files in different multi-day analyses.  Does not load the full paths of all of the tracked videos, but summary statistics.  Returns the info to the calling function.  The data structure name used is 
\b perMouseData.
\b0 \
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\b reviewTracking 
\b0 - GUI and m-file to review a video and manually change the tracking results in an interactive way.\
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\b makeTrainingCurves -
\b0  Script that is used to plot several statistics of behavior over a range of days.\
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\b Xfiles.txt 
\b0 - files that are lists of movies to include in various analyses...generally for a single animal.\
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\b plotDistanceHistComparison
\b0  - function that plots the distribution of distances from the closest point on the trail. Can be used to show \
    	biases in how they follow the trail.\
    \

\b plotFollowingDistanceHistComparison 
\b0 - Plots the histograms of distance traveled while continuously within a certain distance of the trail.\
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\b \
In 'common' folder: 
\b0 \

\b genMovieList 
\b0 - Lists the files in the specified folder, followed by brackets.  Easy format for copying to a text file and saving typing\
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\b igorData folder 
\b0 - A bunch of functions used to process the HD5 file exported by Igor when recording electrophys data (currently thermocouple data for sniffing). They are all documented individually.\
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\b \cf0 igorData/processVideoFolder
\b0  - Processes a folder of videos in the ranges specified by the text file 'tracking_times.txt' contained within the same folder.\
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\cf0     \

\b igorData/processSniffExp
\b0  - Top level function to go through a single experiment file and set of associated video files.  \
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}