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main_nrrd_to_blocks.m
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main_nrrd_to_blocks.m
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%% main function
clc;
clear;
%% selected patients who have ground truth
selected = {'LIDC-IDRI-0068'
'LIDC-IDRI-0071'
'LIDC-IDRI-0072'
'LIDC-IDRI-0088'
'LIDC-IDRI-0090'
'LIDC-IDRI-0091'
'LIDC-IDRI-0100'
'LIDC-IDRI-0118'
'LIDC-IDRI-0124'
'LIDC-IDRI-0129'
'LIDC-IDRI-0135'
'LIDC-IDRI-0137'
'LIDC-IDRI-0138'
'LIDC-IDRI-0143'
'LIDC-IDRI-0149'
'LIDC-IDRI-0159'
'LIDC-IDRI-0161'
'LIDC-IDRI-0162'
'LIDC-IDRI-0163'
'LIDC-IDRI-0164'
'LIDC-IDRI-0165'
'LIDC-IDRI-0166'
'LIDC-IDRI-0167'
'LIDC-IDRI-0168'
'LIDC-IDRI-0169'
'LIDC-IDRI-0171'
'LIDC-IDRI-0173'
'LIDC-IDRI-0174'
'LIDC-IDRI-0175'
'LIDC-IDRI-0176'
'LIDC-IDRI-0178'
'LIDC-IDRI-0179'
'LIDC-IDRI-0180'
'LIDC-IDRI-0181'
'LIDC-IDRI-0182'
'LIDC-IDRI-0183'
'LIDC-IDRI-0184'
'LIDC-IDRI-0185'
'LIDC-IDRI-0186'
'LIDC-IDRI-0187'
'LIDC-IDRI-0188'
'LIDC-IDRI-0189'
'LIDC-IDRI-0190'
'LIDC-IDRI-0191'
'LIDC-IDRI-0192'
'LIDC-IDRI-0193'
'LIDC-IDRI-0194'
'LIDC-IDRI-0197'
'LIDC-IDRI-0198'
'LIDC-IDRI-0200'
'LIDC-IDRI-0202'
'LIDC-IDRI-0203'
'LIDC-IDRI-0205'
'LIDC-IDRI-0207'
'LIDC-IDRI-0210'
'LIDC-IDRI-0211'
'LIDC-IDRI-0212'
'LIDC-IDRI-0213'
'LIDC-IDRI-0214'
'LIDC-IDRI-0217'
'LIDC-IDRI-0220'
'LIDC-IDRI-0221'
'LIDC-IDRI-0222'
'LIDC-IDRI-0223'
'LIDC-IDRI-0224'
'LIDC-IDRI-0225'
'LIDC-IDRI-0226'
'LIDC-IDRI-0230'
'LIDC-IDRI-0231'
'LIDC-IDRI-0232'
'LIDC-IDRI-0233'
'LIDC-IDRI-0234'
'LIDC-IDRI-0235'
'LIDC-IDRI-0236'
'LIDC-IDRI-0237'
'LIDC-IDRI-0239'
'LIDC-IDRI-0242'
'LIDC-IDRI-0243'
'LIDC-IDRI-0244'
'LIDC-IDRI-0245'
'LIDC-IDRI-0246'
'LIDC-IDRI-0247'
'LIDC-IDRI-0248'
'LIDC-IDRI-0249'
'LIDC-IDRI-0250'
'LIDC-IDRI-0251'
'LIDC-IDRI-0252'
'LIDC-IDRI-0253'
'LIDC-IDRI-0254'
'LIDC-IDRI-0255'
'LIDC-IDRI-0256'
'LIDC-IDRI-0257'
'LIDC-IDRI-0258'
'LIDC-IDRI-0260'
'LIDC-IDRI-0261'
'LIDC-IDRI-0264'
'LIDC-IDRI-0265'
'LIDC-IDRI-0266'
'LIDC-IDRI-0267'
'LIDC-IDRI-0268'
'LIDC-IDRI-0270'
'LIDC-IDRI-0271'
'LIDC-IDRI-0272'
'LIDC-IDRI-0273'
'LIDC-IDRI-0274'
'LIDC-IDRI-0275'
'LIDC-IDRI-0276'
'LIDC-IDRI-0277'
'LIDC-IDRI-0278'
'LIDC-IDRI-0279'
'LIDC-IDRI-0280'
'LIDC-IDRI-0281'
'LIDC-IDRI-0282'
'LIDC-IDRI-0283'
'LIDC-IDRI-0285'
'LIDC-IDRI-0286'
'LIDC-IDRI-0287'
'LIDC-IDRI-0288'
'LIDC-IDRI-0289'
'LIDC-IDRI-0290'
'LIDC-IDRI-0314'
'LIDC-IDRI-0325'
'LIDC-IDRI-0332'
'LIDC-IDRI-0377'
'LIDC-IDRI-0385'
'LIDC-IDRI-0399'
'LIDC-IDRI-0405'
'LIDC-IDRI-0454'
'LIDC-IDRI-0470'
'LIDC-IDRI-0493'
'LIDC-IDRI-0510'
'LIDC-IDRI-0522'
'LIDC-IDRI-0543'
'LIDC-IDRI-0559'
'LIDC-IDRI-0562'
'LIDC-IDRI-0568'
'LIDC-IDRI-0576'
'LIDC-IDRI-0580'
'LIDC-IDRI-0610'
'LIDC-IDRI-0624'
'LIDC-IDRI-0766'
'LIDC-IDRI-0771'
'LIDC-IDRI-0772'
'LIDC-IDRI-0811'
'LIDC-IDRI-0818'
'LIDC-IDRI-0875'
'LIDC-IDRI-0893'
'LIDC-IDRI-0905'
'LIDC-IDRI-0921'
'LIDC-IDRI-0924'
'LIDC-IDRI-0939'
'LIDC-IDRI-0965'
'LIDC-IDRI-0994'
'LIDC-IDRI-1002'
'LIDC-IDRI-1004'
'LIDC-IDRI-1010'
'LIDC-IDRI-1011'};
l_offset = [0, 0, 0;
1, 0, 0;
-1, 0, 0;
0, 1, 0;
0, -1, 0;
0, 0, 1;
0, 0, -1;
1, 1, 0;
-1, 1, 0;
-1, -1, 0;
1, -1, 0;
1, 0, 1;
-1, 0, 1;
-1, 0, -1;
1, 0, -1;
0, 1, 1;
0, -1, 1;
0, -1, -1;
0, 1, -1;
1, 1, 1
-1, 1, 1
-1, -1, 1
-1, 1, -1
-1, -1, -1
1, -1, 1
1, -1, -1
1, 1, -1];
l_sz_blk = [64,32,16];
%% toolbox
addpath(genpath([pwd '/toolbox']))
%% module path values
util_path=[pwd '/util'];
input_path=[pwd '/io'];
%% module addpath
addpath(genpath(util_path));
addpath(genpath(input_path));
%% set global values
global path_nodule;
path_nodule = [pwd '/DATA']; %pwd : returns the current directory
%% set values
iso_px_size=1; % a standard unit ('mm-unit')
%% directory paths
nrrd_img_path=[path_nodule '/nodule_radiomics/'];
dir_nrrd = dir(nrrd_img_path);
pid_list = {dir_nrrd.name};
%% main process
for idx = 1:numel(pid_list)
pid = pid_list{idx};
if sum(strfind(pid,'.')) > 0
continue
end
results = table();
tic % tic starts a stopwatch timer
fprintf('%d %s\n', idx, pid);
%% input part
nodule_info = readtable([nrrd_img_path '/' pid '/' pid '.csv']);
[~, meta_org] = fn_nrrdread([nrrd_img_path '/' pid '/' pid '_CT.nrrd']);
[lung_img_3d, meta_lung_img_3d] = fn_nrrdread([nrrd_img_path '/' pid '/' pid '_CT-1mm.nrrd']);
[o_nodule_img_3d, meta_nodule_img_3d] = fn_nrrdread([nrrd_img_path '/' pid '/' pid '_CT_all-1mm-label.nrrd']);
lung_img_3d(lung_img_3d<-1000) = -1000;
lung_img_3d(lung_img_3d>400) = 400;
lung_img_3d = (double(lung_img_3d)+1000)/1400;
sz_img_3d = size(lung_img_3d);
sz_o_nodule_img_3d = size(o_nodule_img_3d);
offsetXYZ = round((meta_nodule_img_3d.spaceorigin - meta_lung_img_3d.spaceorigin)./meta_lung_img_3d.pixelspacing')+1;
nodule_img_3d = zeros(sz_img_3d);
nodule_img_3d(offsetXYZ(2):offsetXYZ(2)+sz_o_nodule_img_3d(1)-1, ...
offsetXYZ(1):offsetXYZ(1)+sz_o_nodule_img_3d(2)-1, ...
offsetXYZ(3):offsetXYZ(3)+sz_o_nodule_img_3d(3)-1) = o_nodule_img_3d;
meta = struct();
meta.type = 'float';
meta.encoding = 'gzip';
meta.endian = 'little';
meta.spacedirections = meta_lung_img_3d.spacedirections;
if ~isdir(['output/' pid]); mkdir(['output/' pid]); end
non_nodule_count = 0;
for nid = 1:size(nodule_info,1)
o_volume = table2array(nodule_info(nid,4));
o_centroid = table2array(nodule_info(nid,10:12));
if sum(isnan(o_centroid)) > 0; continue; end
o_centroid = ceil((o_centroid-1).*meta_org.pixelspacing'+1);
o_centroid(3) = sz_img_3d(3) - o_centroid(3) + 1;
% nodules
for oid = 1:size(l_offset,1)
break
offset = l_offset(oid,:);
centroid = o_centroid + offset;% one voxel offset
bbox = [centroid-16+1,centroid+16];
if sum(bbox(1:3) < 1) > 0 || sum(bbox(4:6) > sz_img_3d) > 0
continue
end
lung_blk_3d = lung_img_3d(bbox(2):bbox(5),bbox(1):bbox(4),bbox(3):bbox(6));
nodule_blk_3d = nodule_img_3d(bbox(2):bbox(5),bbox(1):bbox(4),bbox(3):bbox(6));
if sum(nodule_blk_3d(:))/o_volume < 0.5
continue
end
%display(mean(lung_blk_3d(:)))
meta.spaceorigin = meta_lung_img_3d.spaceorigin+bbox(1:3)-1;
fn_nrrdwrite(['output/' pid '/' pid sprintf('_%03d_%03d_%03d',centroid([3 1 2])) '_32_N_' num2str(mean(lung_blk_3d(:)),2) '_' num2str(oid-1, '%02d') '.nrrd'], double(lung_blk_3d), meta);
if oid == 1
for rot = 1:3
%fn_nrrdwrite(['output/' pid '/' pid sprintf('_%03d_%03d_%03d',centroid([3 1 2])) '_32_N_' num2str(mean(lung_blk_3d(:)),2) '_r' num2str(rot*90, '%03d') '.nrrd'], double(rot90(lung_blk_3d,rot)), meta);
end
end
end
% non nodules
for a = randn(3,round(rand()*500))
offset = round(a'*32);
centroid = o_centroid + offset;% background sample
bbox = [centroid-16+1,centroid+16];
if sum(bbox(1:3) < 1) > 0 || sum(bbox(4:6) > sz_img_3d) > 0
continue
end
lung_blk_3d = lung_img_3d(bbox(2):bbox(5),bbox(1):bbox(4),bbox(3):bbox(6));
nodule_blk_3d = nodule_img_3d(bbox(2):bbox(5),bbox(1):bbox(4),bbox(3):bbox(6));
if mean(nodule_blk_3d(:)) == 0 && std(lung_blk_3d(:)) ~= 0
%display(mean(lung_blk_3d(:)))
meta.spaceorigin = meta_lung_img_3d.spaceorigin+bbox(1:3)-1;
fn_nrrdwrite(['output/' pid '/' pid sprintf('_%03d_%03d_%03d',centroid([3 1 2])) '_32_B_' num2str(mean(lung_blk_3d(:)),2) '.nrrd'], double(lung_blk_3d), meta);
non_nodule_count = non_nodule_count + 1;
end
if non_nodule_count > 500
break
end
end
end
fprintf('block images saved ... \t\t\t %6.2f sec\n', toc);
fclose all;
end