SC_CellLevelFeatures.asv

function SC_CellLevelFeatures(method)
%function sc_yeastfeatcalc(har_intbins, downsamplerate,featset)
%SC_YEASTFEATCALC  A function for cell/field feature calculation
%   22-Nov-2005 Initial write T. Zhao
%   09-Aug-2006 Modified S.C. Chen

% count = 1
% while license('checkout','statistics_toolbox')==0
%     fprintf(1,'The statistics_toolbox is not avaiable...  Waiting(%d)...', count);  count = count + 1 ;
%     pause(30);
% end

imglist = load(method.procfilesmatname);
nprocfiles = length(imglist.procfiles{1});

if method.celllevel == 1
    resultdir180feat = [method.resultdir filesep method.thresmethod 'feat_b256_d1'];
    resultdir = [method.resultdir filesep method.thresmethod 'feat_b' num2str(method.har_intbins) '_d' num2str(method.downsamplerate)];
    segdirpath = [method.resultdir filesep 'handseg'];
else
    fprintf(1,'error\n');
end

for n=1:nprocfiles
    segImagePath = imglist.procfiles{1}{n};

    featFileName = ['Cell' num2str(n) '_features'];        
    controlDirectory = [resultdir filesep featFileName];
    [s,msg] = mkdir(resultdir,featFileName);
    %% Check if the job has been taken over
    if strfind(msg,'exist')
        continue;
    end

    
    fprintf(1, 'Processing %dth image(%s)...\n',n,segImagePath);
    resultfile = [resultdir filesep featFileName '.mat'];

    if ~exist(resultfile,'file') & method.celllevel == 1
        if ~exist([segdirpath filesep 'handmask' num2str(n) '_1.mat'],'file')
            fprintf(1,'The segmentation file does not exist\n');
            continue;
        else
            % this can be modified to accomodate more than one masks in one image
            tmp = load([segdirpath filesep 'handmask' num2str(n) '_1.mat']);
            fprintf(1,'Reading segmentation file...\n');

            normreg=tz_normreg(tmp.mask_cell);
            if sum(tmp.mask_cell(:)) == 0
                fprintf(1, 'No feature can be calculated from empty masks\n');
                continue;
            end
        end

        dnaimgname = imglist.procfiles{1}{n};
        if ~exist(dnaimgname,'file')
            fprintf(1,'DNA image %s does not exist. Skip it...\n',dnaimgname);
            continue;
        else
            fprintf(1,'Reading DNA image...\n');
            dnaimg=imread(dnaimgname);
        end

        gfpimgname = imglist.procfiles{2}{n};
        if ~exist(gfpimgname,'file')
            fprintf(1,'GFP image %s does not exist. Skip it...\n',gfpimgname);
            continue;
        else
            fprintf(1,'Reading GFP image...\n');
            gfpimg=imread(gfpimgname);
        end

        feats = [];
%         if method.har_intbins == 256
%             keyboard;            
        [feats,names,slfnames]=sc_regionfeatmat(gfpimg,dnaimg,normreg,'mcell_mor',method.har_intbins,method.downsamplerate,method.thresmethod);
                [feats,names,slfnames]=sc_regionfeatmat(gfpimg,dnaimg,normreg,'mcell_mor',method.har_intbins,method.downsamplerate,method.thresmethod);

        
%         else
%             resultfile180feat = [resultdir180feat filesep featFileName '.mat'];
%             if ~exist(resultfile180feat,'file')
%                 feats=sc_regionfeatmat(gfpimg,dnaimg,normreg,'all180',method.har_intbins,method.downsamplerate,method.thresmethod);
%             else
%                 harfeats=sc_regionfeatmat(gfpimg,dnaimg,normreg,'har',method.har_intbins,method.downsamplerate,method.thresmethod);
%                 load(resultfile180feat);
%                 feats(:,73:85) = harfeats;
%             end
%         end

        save(resultfile,'feats','names','slfnames');
        fprintf(1,'%s saved\n\n', resultfile);

        unix(['rm -rf ' controlDirectory]);
    end
end