doEvalFISHStacksForAll.m

function doEvalFISHStacksForAll(varargin)
    %% ========================================================================
    %   Name:       doEvalFISHStacksForAll.m
    %   Version:    2.0, 5th July 2012
    %   Author:     Allison Wu
    %   Command:    doEvalFISHStacksForAll(toOverWrite*) *Optional Input
    %   Description:
    %       - a wrapper function that do evalFISHStacks on all the segStacks.mat files on the directory.
    %       - toOverWrite=0 (by default), will skip the SegStacks.mat files
    %       that already have corresponding wormGassianFit.mat files
    %       - toOverWrite=1, it will not detect the existence of
    %       wormGaussianFit.mat files and therefore, overwrites all the
    %       wormGausianFit.mat files that exist.
    %% ========================================================================
    
    if isempty(varargin)
        toOverWrite=0;
    else
        toOverWrite=varargin{1};
    end;
    WormGaussianFitDir='';% need this here so that the parfor can run.  it is overwritten by Aro_parameters but the parfor needs to see it here to know about it
    run('Aro_parameters.m');
    
    switch nestedOrFlatDirectoryStructure
        case 'flat'
            d=dir('**_SegStacks.mat');
            
            for k=1:length(d)
                [dye, stackSuffix, wormFitName, ~,~]=parseStackNames(regexprep(d(k).name,'_SegStacks.mat',''));
                if ~any(strcmp(dye,{'dapi','trans'}))
                    if toOverWrite % Will overwrite all the wormGaussianFit.mat files
                        fprintf('Evaluating the image stack %s ....\n', d(k).name)
                        evalFISHStacks(d(k).name);
                    else % detects the existence of wormGaussianFit.mat files and skip the ones already done
                        if exist(wormFitName,'file')
                            fprintf('Position %s in %s channel is already evaluated.\n', stackSuffix,dye)
                        else
                            fprintf('Evaluating the image stack %s ....\n', d(k).name)
                            evalFISHStacks(d(k).name);
                        end
                    end
                end
            end
            
        case 'nested'
            for iD=1:length(dyesUsed)
                d=dir(fullfile(SegStacksDir,dyesUsed{iD},'*_SegStacks.mat'));
                
                parfor k=1:length(d)
                    [dye, stackSuffix, wormFitName, ~,~]=parseStackNames(regexprep(d(k).name,'_SegStacks.mat',''));
                    disp(dye);
                    disp(stackSuffix);
                    disp(wormFitName);
                    disp(d(k).name);
                    if ~any(strcmp(dye,{'dapi','trans'}))
                        if toOverWrite % Will overwrite all the wormGaussianFit.mat files
                            fprintf('Evaluating the image stack %s ....\n', d(k).name)
                            evalFISHStacks(d(k).name);
                        else % detects the existence of wormGaussianFit.mat files and skip the ones already done
                            if exist(fullfile(WormGaussianFitDir,dye,wormFitName),'file')
                                fprintf('Position %s in %s channel is already evaluated.\n', stackSuffix,dye)
                            else
                                fprintf('Evaluating the image stack %s ....\n', d(k).name)
                                evalFISHStacks(d(k).name);
                            end
                        end
                    end
                end
            end;
    end;
            
            
            
            
    end