ENH: codes for nodule characterization

Author: taznux

main_dicom_to_blocks.m

@@ -0,0 +1,228 @@
+%% main function
+clc;
+clear;
+
+%% 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')
+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];
+
+
+%% directory paths
+nrrd_img_path=[path_nodule '/nodule_radiomics/'];
+
+%% make directory
+if ~isdir(nrrd_img_path); mkdir(nrrd_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
+
+is_pass = 0;
+
+%% main process
+%for idx = randperm(numel(pid_list))
+for idx = 1:numel(pid_list)
+    pid = pid_list{idx};
+
+     if strfind(pid, '0405') > 0
+       is_pass = 0;
+     else
+       is_pass = 1;
+     end
+
+    if is_pass > 0 || sum(strfind(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);
+
+    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);
+
+
+    %% nrrd
+    if ~isdir([nrrd_img_path '/' pid]); mkdir([nrrd_img_path '/' pid]); end
+    writetable([nodule_info(:,[1:3 5:6 end 10:12 15:17]) nodule_info.Characteristics], [nrrd_img_path pid '/' pid '.csv'])
+
+    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';
+
+    fn_nrrdwrite([nrrd_img_path '/' pid '/' pid  '_CT.nrrd'], int16(lung_img_3d(:,:,end:-1:1)), meta);
+
+    meta.type = 'uint8';
+    fn_nrrdwrite([nrrd_img_path '/' pid '/' pid '_CT_all-label.nrrd'], uint8(nodule_img_3d(:,:,end:-1:1)>0), meta);
+%     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([nrrd_img_path '/' pid '/' pid '_CT_Phy' str_sid '-label.nrrd'], sid_nodule_image_3d(:,:,end:-1:1), meta)
+%         end
+%     end
+
+    %% nrrd 1mm
+    [interpol_lung_img_3d,interpol_nodule_img_3d]=fn_interpol3d(lung_img_3d,nodule_img_3d,thick,pixelsize,iso_px_size);
+
+    meta.type = 'int16';
+    meta.spacedirections = [reshape(dicom_tags{1}.ImageOrientationPatient,3,2),[0;0;1]];
+    fn_nrrdwrite([nrrd_img_path '/' pid '/' pid  '_CT-1mm.nrrd'], int16(interpol_lung_img_3d(:,:,end:-1:1)), meta);
+    meta.type = 'uint8';
+    fn_nrrdwrite([nrrd_img_path '/' pid '/' pid '_CT_all-1mm-label.nrrd'], uint8(interpol_nodule_img_3d(:,:,end:-1:1)>0), meta);
+
+
+
+    fprintf('dicom images and annotations converted ... \t\t\t %6.2f sec\n', toc);
+
+
+    %% blocks
+    lung_img_3d = interpol_lung_img_3d;
+    nodule_img_3d = interpol_nodule_img_3d;
+    meta_lung_img_3d = meta;
+    sz_img_3d = size(lung_img_3d);
+
+    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;
+
+    meta.type = 'float';
+    meta.encoding = 'gzip';
+    meta.endian = 'little';
+
+    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,5));
+        o_centroid = round(table2array(nodule_info(nid,8)));
+        if sum(isnan(o_centroid)) > 0; continue; end
+
+        % nodules
+        for oid = 1:size(l_offset,1)
+            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 > 1000
+                break
+            end
+        end
+    end
+
+    fprintf('block images saved ... \t\t\t %6.2f sec\n', toc);
+
+
+    fclose all;
+  end
+
+
+% module rmpath
+% rmpath('./io');
+% rmpath('./interpolation');
+% rmpath('./segmentation');
+% rmpath('./nodule_candidate_detection');