parameters.txt

    
A listing of all parameters and their default values.  Default values can be altered within setRunParameters.m.  How to change parameters on a run-by-run basis is shown in runExample.m.




    %%%%%%%% General Parameters %%%%%%%%


    %number of processors to use in parallel code
    numProcessors = 12;
    
    %whether or not to close the matlabpool after running a routine
    closeMatPool = false;
    
    
    
    
    
    %%%%%%%% Segmentation and Alignment Parameters %%%%%%%%
    
    %angle spacing for alignement Radon transform
    alignment_angle_spacing = 1;
    
    %tolerance for translational alignment
    pixelTol = .1;
    
    %minimum area for use in image dilation/erosion
    minArea = 3500;
    
    %asymmetry threshold used in eliminating rotational degeneracy
    asymThreshold = 150;
    
    %line about which directional symmetry is 
    %determined for eliminating rotational degeneracy
    symLine = 110;
    
    %initial guess for rotation angle
    initialPhi = 0;

    %initial dilation size for image segmentation
    dilateSize = 5;

    %parameter for Canny edge detection
    cannyParameter = .1;

   %threshold for image segmentation
    imageThreshold = 40;

    %largest allowed percentage reduction in area from frame to frame
    maxAreaDifference = .15;

    %toggle switch for image segmentation (alignment still performed)
    segmentationOff = false;
    
    %threshold for seperating body from background
    bodyThreshold = 150;

    
    
    
    %%%%%%%% PCA Parameters %%%%%%%% 
    
    %number of angles in radon transform
    num_Radon_Thetas = 90;
    
    %image scaling factor
    rescaleSize = 10/7;
    
    %batch size for running online PCA
    pca_batchSize = 20000;
    
    %number of projections to find in PCA
    numProjections = 100;
    
    %number of PCA modes to use in later analyses
    pcaModes = 50;
    
    
    
    %%%%%%%% Wavelet Parameters %%%%%%%%
    
    %number of wavelet frequencies to use
    numPeriods = 25;
    
    %dimensionless Morlet wavelet parameter
    omega0 = 5;
    
    %sampling frequency (Hz)
    samplingFreq = 100;
        
    %minimum frequency for wavelet transform (Hz)
    minF = 1;
    
    %maximum frequency for wavelet transform (Hz)
    maxF = 50;
    
    
    
    
    
    
    %%%%%%%% t-SNE Parameters %%%%%%%%
    
    
    %2^H (H is the transition entropy)
    perplexity = 32;
    
    %relative convergence criterium for t-SNE
    relTol = 1e-4;
    
    %number of dimensions for use in t-SNE
    num_tsne_dim = 2;
    
    %binary search tolerance for finding pointwise transition region
    sigmaTolerance = 1e-5;
    
    %maximum number of non-zero neighbors in P
    maxNeighbors = 200;
    
    %initial momentum
    momentum = .5;
    
    %value to which momentum is changed
    final_momentum = 0.8;    
    
    %iteration at which momentum is changed
    mom_switch_iter = 250;      
    
    %iteration at which lying about P-values is stopped
    stop_lying_iter = 125;      
    
    %degree of P-value expansion at early iterations
    lie_multiplier = 4;
    
    %maximum number of iterations
    max_iter = 1000;  
    
    %initial learning rate
    epsilon = 500;  
    
    %minimum gain for delta-bar-delta
    min_gain = .01;   

    %readout variable for t-SNE
    tsne_readout = 1;
    
    %embedding batchsize
    embedding_batchSize = 20000;
    
    %maximum number of iterations for the Nelder-Mead algorithm
    maxOptimIter = 100;
    
    %number of points in the training set
    trainingSetSize = 35000;
    
    %local neighborhood definition in training set creation
    kdNeighbors = 5;
    
    %t-SNE training set stopping critereon
    training_relTol = 2e-3;
    
    %t-SNE training set perplexity
    training_perplexity = 20;
    
    %number of points to evaluate in each training set file
    training_numPoints = 10000;
    
    %minimum training set template length
    minTemplateLength = 1;