%M = csvread('C:\Documents and Settings\dzinovev\Desktop\parsed_xml.csv',1,1);

%data = textread('\\ailab03\NEW_LIDC\LIDC\dataset.csv', '', 'delimiter', ',');

%fid = fopen('\\ailab03\NEW_LIDC\LIDC\dataset.csv');

%C = textscan(fid, '%s /n', 'delimiter', ',', 'treatAsEmpty', {'NA', 'na'}, 'commentStyle', '//');

%M = dlmread('\\ailab03\NEW_LIDC\LIDC\dataset.csv', ',');

A=fopen('\\ailab03\NEW_LIDC\LIDC\dataset.csv');

fid = fopen ('\\ailab03\NEW_LIDC\LIDC\dataset_big.csv', 'wt');

fid1 = fopen ('\\ailab03\NEW_LIDC\LIDC\missing.csv', 'wt');

fid2 = fopen ('\\ailab03\NEW_LIDC\LIDC\pmaps.csv', 'wt');

tline = fgetl(A);

current = 0;

missing = 0;

for r = 1:14927

    tline = fgetl(A);

    B=textscan(A,'%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s /n', 'delimiter',',');

    name = strcat(B{6},B{18},'.dcm');        

    filename = strcat(B{18});    

    noduleid = strcat(B{5});

    pts = strcat(B{19});

    lobul = B{12};

    malig = B{15};

    margin = B{11};

    spher = B{10};

    spicul = B{13};

    subtl = B{7};

    textur = B{14};

    data(r,1)=name;

    data(r,2)=filename;

    data(r,3)=noduleid;

    data(r,4)=pts;

    data(r,5) = lobul;

    data(r,6) = malig;

    data(r,7) = margin;

    data(r,8) = spher;

    data(r,9) = spicul;

    data(r,10) = subtl;

    data(r,11) = textur;

end

check = 1;%need two counters: 1 for going through the list, another for naming purposes

%name = 1;

while (check<14927)

    if (exist(char(data(check,1)),'file'))

        I = dicomread(data{check,1});

        m = data{check,4};

        points = strread(m,'%s','delimiter','*|'); 

        [k,l]=size(points);

        for pts=1:k

            point = strread(points{pts,1},'%d','delimiter','*;');

            xcoord(pts)=point(1);

            ycoord(pts)=point(2);

            %I(point(2),point(1))=2215;

        end;   

        ymax = max(xcoord);    

        ymin = min(xcoord);    

        xmax = max(ycoord);    

        xmin = min(ycoord);

        width = xmax-xmin;

        heigth = ymax-ymin;

        if(width > 4 && heigth > 4)

            current=current+1;

            %cropped = I(xmin:xmax,ymin:ymax);

            BW=zeros(size(I));

            %fprintf(fid,'%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s \n',num2str(current),char(B{1,2}),char(B{1,3}),char(B{1,4}),char(B{1,5}),char(B{1,6}),char(B{1,7}),char(B{1,8}),char(B{1,9}),char(B{1,10}),char(B{1,11}),char(B{1,12}),char(B{1,13}),char(B{1,14}),char(B{1,15}),char(B{1,16}),char(B{1,17}),char(B{1,18}));

            for pts=1:k

                point = strread(points{pts,1},'%d','delimiter','*;');

                BW(point(2),point(1))=1;

            end; 

            pmap = imfill(BW,'holes');

            cntr = 1;

            lob(cntr)=data(check,5);

            mal(cntr)=data(check,6);

            mar(cntr)=data(check,7);

            sph(cntr)=data(check,8);

            spi(cntr)=data(check,9);

            sub(cntr)=data(check,10);

            tex(cntr)=data(check,11);

            for n=1:14927

                if(n~=check)

                    b=1;

                    if((strcmp(data{check,1},data{n,1})==1)&&(strcmp(data{check,3},data{n,3})==1))

                        cntr = cntr+1;

                        lob(cntr)=data(n,5);

                        mal(cntr)=data(n,6);

                        mar(cntr)=data(n,7);

                        sph(cntr)=data(n,8);

                        spi(cntr)=data(n,9);

                        sub(cntr)=data(n,10);

                        tex(cntr)=data(n,11);

                        a='preved!';

                        m = data{n,4};

                        points = strread(m,'%s','delimiter','*|'); 

                        [k,l]=size(points);

                        BW=zeros(size(I));

                        for pts=1:k

                            point = strread(points{pts,1},'%d','delimiter','*;');

                            xcoord(pts)=point(1);

                            ycoord(pts)=point(2);

                            %I(point(2),point(1))=2215;

                            BW(point(2),point(1))=1;

                        end;   

                        BW = imfill(BW,'holes');

                        a

                        pmap=pmap+BW;

                        data(n)=cellstr('NaN');

                    end

                end

            end

            %check=check+1;

             for curthresh=1:4

                 binar = im2bw(pmap/10, (curthresh-1)/10);

                 if(sum(sum(binar))>0);

                     contur = bwmorph(binar,'remove');

                     [r,c]=find(pmap);

                     maxx = max(c);

                     minx = min(c);

                     maxy = max(r);

                     miny = min(r);

                     cropped = I(minx:maxx,miny:maxy);

                     BW = contur(minx:maxx,miny:maxy);

                %BW = imfill(BW,'holes');

                %imshow(BW,[0 1]);

                     [rows,cols]=size(cropped);

                     for m=1:rows

                         for n=1:cols

                             if(BW(m,n)==1)

                                 croppednod(m,n)=cropped(m,n);

                                 croppedback(m,n)=-2000;

                             else

                                 croppednod(m,n)=-2000;

                                 croppedback(m,n)=cropped(m,n);

                             end;

                         end;

                     end;

%                  figure;

%                  imshow(croppednod,[0 2215]);

%                  figure;

%                  imshow(croppedback,[0 2215]);

%                  figure;

%                  imshow(cropped,[0 2215]);

%                  figure;

%                  imshow(contur,[0 1]);

%                  figure;

%                  imshow(I);

                     fname = strcat(data(check,3),'_',data(check,2),'.dcm');

                     dicomwrite(int16(cropped), strcat('\\Ailab03\NEW_LIDC\LIDC\extract LIDC\pmap\',num2str(curthresh),'\crop\',fname{:}));        

                     dicomwrite(int16(croppednod), strcat('\\Ailab03\NEW_LIDC\LIDC\extract LIDC\pmap\',num2str(curthresh),'\segmented_nodules\',fname{:}));        

                     dicomwrite(int16(croppedback), strcat('\\Ailab03\NEW_LIDC\LIDC\extract LIDC\pmap\',num2str(curthresh),'\segmented_background\',fname{:}));            

                     dicomwrite(int16(BW), strcat('\\Ailab03\new_lidc\LIDC\extract LIDC\pmap\',num2str(curthresh),'\contours\',fname{:}));

                 end;

                % ceil(median(lob));

                 if(size(lob,2)>1)

                     fprintf(fid2,'%s,%s,%s,%s,%s,%s,%s,%s \n',fname{:},num2str(ceil(median(str2double(lob)))),num2str(ceil(median(str2double(mal)))),num2str(ceil(median(str2double(mar)))),num2str(ceil(median(str2double(sph)))),num2str(ceil(median(str2double(spi)))),num2str(ceil(median(str2double(sub)))),num2str(ceil(median(str2double(tex)))));

                 else

                     fprintf(fid2,'%s,%s,%s,%s,%s,%s,%s,%s \n',fname{:},str2double(lob{:}),str2double(mal{:}),str2double(mar{:}),str2double(sph{:}),str2double(spi{:}),str2double(sub{:}),str2double(tex{:}));

                 end                     

             end;

             %name=name+1;

        end;

        clear lob;

        clear mal;

        clear mar;

        clear sph;

        clear spi;

        clear sub;

        clear tex;

        clear xcoord;    

        clear ycoord;

        clear cropped;

        clear croppednod;

        clear croppedback;

        clear BW;

    else

        missing = missing + 1;

        fprintf(fid1,'%s,%s,%s \n',num2str(r+1),char(B{1,6}),char(B{1,18}));

    end;

    check=check+1;

    r

end;

missing

fclose(fid);

fclose(fid1);

fclose(fid2);

fclose(A);