MotionMapper_mouse/runAlignment.m at master · gordonberman/MotionMapper_mouse · GitHub

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function outputStruct = runAlignment(fileName,outputPath,startImage,finalImage,parameters)
%runAlignment runs the alignment and segmentation routines on a .avi file
%   and saves the output files to a directorty
%
%   Input variables:
%
%       fileName -> avi file to be analyzed
%       outputPath -> path to which files are saved
%       startImage -> first image in path to be analyzed
%       finalImage -> last image in path to be analyzed
%       parameters -> struct containing non-default choices for parameters
%
%
%   Output variable:
%
%       outputStruct -> struct containing found alignment variables
%
% (C) Gordon J. Berman, 2016
%     Emory University


    addpath(genpath('./utilities/'));
    addpath(genpath('./segmentation_alignment/'));


    if ~exist(outputPath,'dir')
        mkdir(outputPath);
    end


    if nargin < 3 || isempty(startImage)
        startImage = 1;
    end


    if nargin < 4 || isempty(finalImage)
        finalImage = [];
    end


    if nargin < 5 || isempty(parameters)
        parameters = [];
    end

    parameters = setRunParameters(parameters);
    numProcessors = 1;%parameters.numProcessors;

    p = gcp('nocreate');
    c = parcluster;
    numAvailableProcessors = c.NumWorkers;

    if numProcessors > 1 && isempty(p)

        if numAvailableProcessors > numProcessors
            numProcessors = numAvailableProcessors;
            parameters.numProcessors = numAvailableProcessors;
        end

        if numProcessors > 1
            p = parpool(numProcessors);
        end


    else

        if numProcessors > 1
            currentNumProcessors = p.NumWorkers;
            numProcessors = min([numProcessors,numAvailableProcessors]);
            if numProcessors ~= currentNumProcessors
                delete(p);
                p = parpool(numProcessors);
            end
        end

    end


    outputStruct = ...
        alignImages_Radon_parallel_avi(fileName,startImage,finalImage,...
                                        outputPath,parameters);

    outputStruct.parameters = parameters;


    if ~isempty(p) && parameters.closeMatPool
        delete(p);
    end