%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);
