%% generateSegmentations.m

%Patrick Stein 8/20/2013

%This will run both otsu and region growing segmentations and create the

%appropriate masks for both otsu and RG.

%

% Before you run this script make sure to 

%% Clear workspace 

    clear all;

    close all;

    clc;

%% Setup workspace for image segmentation

    %The folder with all of your DICOM images you wish to segment

    folderWithImages = '\\ailab03\WeakSegmentation\2k largest slice crops';

    %The number of classes you want for Otsu

    otsuClassNumber = 5;

    %Start threshold for RG

    rgStart = 0.0005;

    %Ending threshold

    rgEnd = 0.0021;

    %In what increments should the threshold be increased.

    rgInc = 0.0003;

    %add paths to utility functions and segmentations

    addpath(genpath('..\Image Segmentation'));

    %Open Matlab pool for multi-threading

    if(matlabpool('size') == 0) %checking to see if my pool is already open

       matlabpool open 4

    end

    %start timer

    tic

    %Turn off warnings briefly because parfor loop will get very angry at

    %variables being declared even though they are temporary

    warning('off','all');

%% Generate segmentations

    disp('Beginning Otsu...');

    [otsuImages] = runOtsu(folderWithImages,otsuClassNumber);

    disp('Otsu complete! Beginning Region Growing...');

    [rgImages] = runRegionGrowing(folderWithImages,rgStart,rgEnd,rgInc);

    disp('Region Growing Complete!');

%% Wrap up after segmentation

    %close matlab pool

    matlabpool close;

    %turn warnings back on

    warning('on','all');

 %% Generate masks

    disp('Generating masks...');

    otsuImages = createMasks(otsuImages);

    rgImages = createMasks(rgImages);

    disp('Mask generation complete!');

%% Wrap up

    toc

    %send a message out

    matlabMail('Pinkjello92@gmail.com','Segmentation Complete');