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main_image_to_nrrd.m
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main_image_to_nrrd.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'};
selected = {'LIDC-IDRI-0072'
'LIDC-IDRI-0090'
'LIDC-IDRI-0138'
'LIDC-IDRI-0149'
'LIDC-IDRI-0162'
'LIDC-IDRI-0163'
'LIDC-IDRI-0166'
'LIDC-IDRI-0167'
'LIDC-IDRI-0168'
'LIDC-IDRI-0171'
'LIDC-IDRI-0178'
'LIDC-IDRI-0180'
'LIDC-IDRI-0183'
'LIDC-IDRI-0185'
'LIDC-IDRI-0186'
'LIDC-IDRI-0187'
'LIDC-IDRI-0191'
'LIDC-IDRI-0203'
'LIDC-IDRI-0211'
'LIDC-IDRI-0212'
'LIDC-IDRI-0233'
'LIDC-IDRI-0234'
'LIDC-IDRI-0242'
'LIDC-IDRI-0246'
'LIDC-IDRI-0247'
'LIDC-IDRI-0249'
'LIDC-IDRI-0256'
'LIDC-IDRI-0257'
'LIDC-IDRI-0265'
'LIDC-IDRI-0267'
'LIDC-IDRI-0268'
'LIDC-IDRI-0270'
'LIDC-IDRI-0271'
'LIDC-IDRI-0273'
'LIDC-IDRI-0275'
'LIDC-IDRI-0276'
'LIDC-IDRI-0277'
'LIDC-IDRI-0283'
'LIDC-IDRI-0286'
'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-0580'
'LIDC-IDRI-0610'
'LIDC-IDRI-0624'
'LIDC-IDRI-0766'
'LIDC-IDRI-0771'
'LIDC-IDRI-0811'
'LIDC-IDRI-0875'
'LIDC-IDRI-0905'
'LIDC-IDRI-0921'
'LIDC-IDRI-0924'
'LIDC-IDRI-0939'
'LIDC-IDRI-0965'
'LIDC-IDRI-0994'
'LIDC-IDRI-1002'
'LIDC-IDRI-1004'};
%% 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;
global path_data;
path_nodule = [pwd '/DATA']; %pwd : returns the current directory
path_data = [pwd '/DATA/LIDC-IDRI/']; %dcm files directory
%% set values
iso_px_size=1; % a standard unit ('mm-unit')
%% directory paths
ct_img_path=[path_nodule '/nodule-radiomics_72/'];
%% make directory
if ~isdir(ct_img_path); mkdir(ct_img_path); end
%% saved data load or not
load_input = true;
%% get pids
filename_pid_list = [path_nodule '/dicom_pid_list.mat'];
if(fn_check_load_data(filename_pid_list, load_input))
[dicom_path_list,pid_list]=fn_scan_pid(path_data);
save(filename_pid_list, 'dicom_path_list', 'pid_list');
else
load(filename_pid_list);
end
all_parameters = table();
%% main process
for idx = 1:numel(pid_list)
pid = pid_list{idx};
if sum(strcmp(selected, pid)) == 0
continue
end
tic % tic starts a stopwatch timer
fprintf('%d %s\n', idx, pid);
%% input part
dicom_path = dicom_path_list{idx};
[lung_img_3d, nodule_img_3d, dicom_tags, thick, pixelsize, nodule_info] = fn_dicom_read(dicom_path,pid);
fprintf('dicom images loaded ... \t\t\t %6.2f sec\n', toc);
if numel(nodule_info) == 0
continue
end
[nodule_img_3d, nodule_info] = fn_nodule_info_update(lung_img_3d,nodule_img_3d,nodule_info,thick,pixelsize);
meta = struct();
meta.type = 'int16';
meta.encoding = 'gzip';
meta.spaceorigin = dicom_tags{1}.ImagePositionPatient';
meta.spacedirections = [reshape(dicom_tags{1}.ImageOrientationPatient,3,2),[0;0;1]]*diag([pixelsize; thick]);
meta.endian = 'little';
parameters = table();
parameters.PID = {pid};
try
parameters.PatientAge = dicom_tags{1}.PatientAge;
catch
parameters.PatientAge = '000Y';
end
try
parameters.PatientSex = dicom_tags{1}.PatientSex;
catch
parameters.PatientSex = ' ';
end
parameters.KVP = dicom_tags{1}.KVP;
parameters.XRayTubeCurrent = dicom_tags{1}.XRayTubeCurrent;
parameters.Exposure = dicom_tags{1}.Exposure;
try
parameters.ExposureTime = dicom_tags{1}.ExposureTime;
catch
parameters.ExposureTime = 0;
end
try
parameters.GeneratorPower = dicom_tags{1}.GeneratorPower;
catch
parameters.GeneratorPower = 0;
end
parameters.pixelsize = pixelsize';
parameters.thick = thick;
parameters.SliceThickness = dicom_tags{1}.SliceThickness;
try
parameters.SingleCollimationWidth = dicom_tags{1}.SingleCollimationWidth;
catch
parameters.SingleCollimationWidth = 0;
end
parameters.ConvolutionKernel = {dicom_tags{1}.ConvolutionKernel};
parameters.FilterType = {dicom_tags{1}.FilterType};
try
parameters.ContrastBolusAgent = {dicom_tags{1}.ContrastBolusAgent};
parameters.ContrastBolusRoute = {dicom_tags{1}.ContrastBolusRoute};
catch
parameters.ContrastBolusAgent = {''};
parameters.ContrastBolusRoute = {''};
end
try
parameters.StudyDescription = {dicom_tags{1}.StudyDescription};
catch
parameters.StudyDescription = {''};
end
try
parameters.SeriesDescription = {dicom_tags{1}.SeriesDescription};
catch
parameters.SeriesDescription = {''};
end
parameters.Manufacturer = {dicom_tags{1}.Manufacturer};
parameters.ManufacturerModelName = {dicom_tags{1}.ManufacturerModelName};
try
parameters.ProtocolName = {dicom_tags{1}.ProtocolName};
catch
parameters.ProtocolName = {''};
end
tic
if ~isdir([ct_img_path '/' pid]); mkdir([ct_img_path '/' pid]); end
fn_nrrdwrite([ct_img_path '/' pid '/' pid '_CT.nrrd'], int16(lung_img_3d(:,:,end:-1:1)), meta)
writetable([nodule_info(:,[1:3 5:6 end 10:12 15:17]) nodule_info.Characteristics], [ct_img_path pid '/' pid '.csv'])
meta.type = 'uint8';
for sid = 1:4
str_sid = num2str(sid);
sid_nodule_image_3d = uint8(bitand(uint8(nodule_img_3d),2^(sid-1))>0);
sid_nodules = strcmp(nodule_info.sid, str_sid);
if sum(sid_nodules) > 0
fn_nrrdwrite([ct_img_path '/' pid '/' pid '_CT_Phy' str_sid '-label.nrrd'], sid_nodule_image_3d(:,:,end:-1:1), meta)
end
end
fprintf('dicom images and annotations converted ... \t\t\t %6.2f sec\n', toc);
all_parameters = [all_parameters; parameters];
end
% module rmpath
% rmpath('./io');
% rmpath('./interpolation');
% rmpath('./segmentation');
% rmpath('./nodule_candidate_detection');