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main_nodule_segmentation.m
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main_nodule_segmentation.m
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%% main function
clc;
clear;
%% toolbox
addpath(genpath([pwd '/toolbox']))
%% module path values
util_path=[pwd '/util'];
input_path=[pwd '/io'];
interpolation_path=[pwd '/interpolation'];
segmentation_path=[pwd '/lung_segmentation'];
nodule_segmentation_path=[pwd '/nodule_segmentation'];
candidates_path=[pwd '/nodule_candidate_detection'];
feature_extraction_path=[pwd '/feature_extraction'];
evaluation_path=[pwd '/evaluation'];
%% module addpath
addpath(genpath(util_path));
addpath(genpath(input_path));
addpath(genpath(interpolation_path));
addpath(genpath(segmentation_path));
addpath(genpath(nodule_segmentation_path));
addpath(genpath(candidates_path));
addpath(genpath(feature_extraction_path));
addpath(genpath(evaluation_path));
%% set global values
global path_nodule;
global path_data;
path_nodule = [pwd '/output_data']; %pwd : returns the current directory
path_data = [pwd '/DATA/LIDC-IRDI']; %dcm files directory
%% set values
iso_px_size=[]; % a standard unit ('mm-unit')
%% directory paths
ct_img_path=[path_nodule '/CT_Images/'];
img_path=[path_nodule '/interpolation_nodule_images/'];
seg_img_path=[path_nodule '/lung_segmentation_images/'];
candidates_img_path=[path_nodule '/nodule_candidate_detection_images/'];
feature_path=[path_nodule '/features/'];
evaluation_detection_result_path=[path_nodule '/evalation_result/'];
nodule_segmentation_path=[path_nodule '/nodule_segmentation/'];
nodule_segmentation_eval_path=[path_nodule '/nodule_segmentation_evaluation/'];
%% make directory
if ~isdir(ct_img_path); mkdir(ct_img_path); end
if ~isdir(img_path); mkdir(img_path); end
if ~isdir(seg_img_path); mkdir(seg_img_path); end
if ~isdir(candidates_img_path); mkdir(candidates_img_path); end
if ~isdir(feature_path); mkdir(feature_path); end
if ~isdir(evaluation_detection_result_path); mkdir(evaluation_detection_result_path); end
if ~isdir(nodule_segmentation_path); mkdir(nodule_segmentation_path); end;
if ~isdir(nodule_segmentation_eval_path); mkdir(nodule_segmentation_eval_path); end
%% saved data load or not
load_input = true;
load_interpoltaion = true;
load_segmentation = true;
load_nodule_segmentation = false;
load_nodule_segmentation_eval = false;
load_nodule_candidate_detection = true;
load_nodule_feature_extraction = true;
load_evaluation_detection = 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
nodule_segmentation_evaluation = [];
%% main process
for idx = 1:numel(pid_list)
fclose('all'); % to avoid too many files open
pid = pid_list{idx};
tic % tic starts a stopwatch timer
fprintf('%d %s\n', idx, pid);
%% input part
filename_input = [ct_img_path pid '_input.mat'];
if(fn_check_load_data(filename_input, load_input))
dicom_path = dicom_path_list{idx};
[lung_img_3d, nodule_img_3d, dicom_tags, thick, pixelsize, nodule_info] = fn_dicom_read(dicom_path,pid);
save(filename_input, 'lung_img_3d', 'nodule_img_3d' ,'dicom_tags', 'thick' ,'pixelsize', 'nodule_info');
else
load(filename_input);
end
fprintf('dicom images loaded ... \t\t\t %6.2f sec\n', toc);
%% minimum resoultion
min_resolution=max([thick pixelsize(1) pixelsize(2)]);
%% nodule segmentation part
% type
% type=1; % sphere ring model and general deformable model adaptation
% type=2; % cube ring model and general deformable model adaptation
% type=3; % sphere ring model and SMSM adaptation
% type=4; % cube ring model and SMSM adaptation
% type=5; % triangle mesh sphere model and proposed adaptation
type = 1;
if size(nodule_info,1) == 0
continue
end
filename_nodule_segmentation = [ nodule_segmentation_path pid '_' num2str(iso_px_size,'%3.1f') '_' num2str(type,'%3.1f') '_nodule_segmentation.mat'];
if(fn_check_load_data(filename_nodule_segmentation, load_nodule_segmentation))
%[s_list,v_list]=fn_nodule_segmentation(nodule_img_3d,lung_img_3d,nodule_info,thick,pixelsize,type);
s_list=[];
v_list = fn_nodule_segmentation_multitreshold(lung_img_3d,nodule_info,thick, pixelsize,iso_px_size);
save(filename_nodule_segmentation, 's_list','v_list','type');
else
load(filename_nodule_segmentation);
end
fprintf('nodule segmentaion completed ... \t\t\t %6.2f sec\n', toc);
%% evaluation part
% nodule segmentation evaluation
filename_nodule_segmentation_eval = [ nodule_segmentation_eval_path pid '_' num2str(iso_px_size,'%3.1f') '_' num2str(type,'%3.1f') '_nodule_segmentation_eval.mat'];
if(fn_check_load_data(filename_nodule_segmentation_eval, load_nodule_segmentation_eval))
[ ravd,voe,assd,v_r_list,lung_ext_list ] = fn_nodule_segmentation_eval(nodule_img_3d,lung_img_3d,nodule_info,thick,pixelsize,iso_px_size,[],v_list);
nodule_segmentation = [nodule_info(:,{'pid','sid','nid'}), table(ravd,voe,assd)]
if(numel(nodule_info)>0)
pt = [];
for sid = unique(nodule_info.sid)'
ravd = mean(nodule_segmentation(cell2mat(nodule_segmentation.sid(:)) == sid{1},:).ravd);
voe = mean(nodule_segmentation(cell2mat(nodule_segmentation.sid(:)) == sid{1},:).voe);
assd = mean(nodule_segmentation(cell2mat(nodule_segmentation.sid(:)) == sid{1},:).assd);
session = table;
session.pid = {pid};
session.sid = sid;
session.ravd = ravd;
session.voe = voe;
session.assd = assd;
pt = [pt; session];
end
pt = [pt; {pt.pid(1), {'a'}, mean(pt.ravd), mean(pt.voe), mean(pt.assd)}];
pt
nodule_segmentation_evaluation = [nodule_segmentation_evaluation; pt];
end
save(filename_nodule_segmentation_eval, 'nodule_segmentation','ravd','voe','assd','v_r_list','lung_ext_list','type');
else
load(filename_nodule_segmentation_eval);
end
fprintf('nodule evaluation completed ... \t\t\t %6.2f sec\n', toc);
end
% Overall Evaluation
nodule_segmentation_summary = [];
for sid = unique(nodule_segmentation_evaluation.sid)'
ravd = mean(nodule_segmentation_evaluation(cell2mat(nodule_segmentation_evaluation.sid(:)) == sid{1},:).ravd);
voe = mean(nodule_segmentation_evaluation(cell2mat(nodule_segmentation_evaluation.sid(:)) == sid{1},:).voe);
assd = mean(nodule_segmentation_evaluation(cell2mat(nodule_segmentation_evaluation.sid(:)) == sid{1},:).assd);
session = table;
session.sid = sid;
session.ravd = ravd;
session.voe = voe;
session.assd = assd;
nodule_segmentation_summary = [nodule_segmentation_summary; session];
end
nodule_segmentation_summary