findRadonPixels.m

function [pixels,thetas,means,stDevs,vidObjs] = findRadonPixels(filePath,numToTest,parameters)
%findRadonPixels finds a set of pixels that contain much of the observed
%variance in the images given a set of aligned .tiff files.  A gui will
%pop-up asking the user to select a cut-off point.  The left-most minimum
%of the distribution is usually optimal for this
%
%   Input variables:
%
%       filePath -> directory containing aligned .tiff files
%       numToTest -> number of images from which to calculate values
%       parameters -> struct containing non-default choices for parameters
%
%
%   Output variables:
%
%       pixels -> list of the chosen high-variance pixels
%       thetas -> list of the thetas used in the Radon transform
%       means -> double array containing the mean radon-transform values
%       stDevs -> double array containing the standard deviation of the
%                   radon-transform values
%       vidObjs -> VideoReader objects for each of the aligned avi files
%
% (C) Gordon J. Berman, 2014
%     Princeton University

    if nargin < 3
        parameters = [];
    end
    parameters = setRunParameters(parameters);
    
    
    setup_parpool(parameters.numProcessors)

    
    numThetas = parameters.num_Radon_Thetas;
    spacing = 180/numThetas;
    thetas = linspace(0,180-spacing,numThetas);
    scale = parameters.rescaleSize;
    
    
    
    [means,stDevs,vidObjs] = findImageSubsetStatistics(filePath,numToTest,thetas,scale);
    
    
    [Y,X] = hist(stDevs(:),100);
    figure
    test = true;
    
    semilogy(X,Y,'o-')
    title('Select Truncation Point (Best if at Local Minimum)','fontsize',16,'fontweight','bold');
    xlabel('Standard Deviation','fontsize',14,'fontweight','bold')
    ylabel('Number of Counts','fontsize',14,'fontweight','bold')
    while test
        
        [x,~] = ginput(1);
        pixels = find(stDevs(:) > x);
        title(['# of Pixels = ' num2str(length(pixels)) '.  Is this OK? [y/n]'],'fontsize',16,'fontweight','bold');
        
        [~,~,button] = ginput(1);
        while isempty(button)
            [~,~,button] = ginput(1);
        end
        
        while button ~= 121 && button ~= 110 && button ~= 89 && button ~= 78
            [~,~,button] = ginput(1);
        end
        
        if button == 121 || button == 89
            test = false;
        end
                  
    end
    
    
    if parameters.numProcessors > 1 && parameters.closeMatPool
        close_parpool
    end