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code/shape_exception_handling.m
0 → 100644
| 1 | +data_path = '..\data\MICCAI_BraTS_2019_Data_Training\HGG_seg_flair\BraTS19_CBICA_AVG_1_seg_flair.nii'; | ||
| 2 | +data = niftiread(data_path); | ||
| 3 | + | ||
| 4 | +cp_data = flipud(rot90(mat2gray(double(data(:,:,82))))); | ||
| 5 | + | ||
| 6 | +type = '.png'; | ||
| 7 | +filename = strcat('BraTS19_CBICA_AVG_1_seg_flair_8', type); % BraTS19_2013_2_1_seg_flair_c.png | ||
| 8 | +outpath = strcat('..\data\MICCAI_BraTS_2019_Data_Training\zero to valid\', filename); | ||
| 9 | +imwrite(cp_data, outpath); | ||
| 10 | + | ||
| 11 | + | ||
| 12 | +% st, end 10 | ||
| 13 | + | ||
| 14 | +%% (circle 0, ellipse 0) | ||
| 15 | +% BraTS19_CBICA_AOP_1_seg_flair_0 | ||
| 16 | +% BraTS19_CBICA_ASF_1_seg_flair_9 -> 8 | ||
| 17 | +% BraTS19_CBICA_ASR_1_seg_flair_8 | ||
| 18 | +% BraTS19_CBICA_ASR_1_seg_flair_9 | ||
| 19 | +% BraTS19_CBICA_AVG_1_seg_flair_9 -> 8 | ||
| 20 | +% | ||
| 21 | +% | ||
| 22 | +% | ||
| 23 | +% | ||
| 24 | +% | ||
| 25 | +% | ||
| 26 | +% | ||
| 27 | +% | ||
| 28 | +% | ||
| 29 | +% | ||
| 30 | +% | ||
| 31 | +% | ||
| ... | \ No newline at end of file | ... | \ No newline at end of file |
code/shape_exception_handling_all.m
0 → 100644
| 1 | +getname_path = '..\data\MICCAI_BraTS_2019_Data_Training\zero2\'; | ||
| 2 | +inputheader = '..\data\MICCAI_BraTS_2019_Data_Training\HGG_seg_flair\'; | ||
| 3 | +outfolder = '..\data\MICCAI_BraTS_2019_Data_Training\zero to valid2\'; | ||
| 4 | + | ||
| 5 | +files = dir(getname_path); | ||
| 6 | +id = {files.name}; | ||
| 7 | +% files + dir file | ||
| 8 | +flag = ~strcmp(id, '.') & ~strcmp(id, '..'); | ||
| 9 | +files = files(flag); | ||
| 10 | + | ||
| 11 | +% get filenames in getname_path folder | ||
| 12 | +for i = 1 : length(files) | ||
| 13 | + %id = split(files(i).name, '.nii'); | ||
| 14 | + fname = files(i).name; | ||
| 15 | + id = reverse(extractBetween(reverse(fname), 7, strlength(fname))); | ||
| 16 | + | ||
| 17 | + data_path = convertCharsToStrings(strcat(inputheader,'\', id, '.nii')); | ||
| 18 | + data = niftiread(data_path); | ||
| 19 | + | ||
| 20 | + fprintf('ID #%d = %s\n', i, data_path); | ||
| 21 | + | ||
| 22 | + idx = 1; | ||
| 23 | + frames = zeros(1,1); | ||
| 24 | + for j = 1 : z | ||
| 25 | + n_nonblack = numel(find(data(:,:,j) > 0)); | ||
| 26 | + if(n_nonblack > 70) | ||
| 27 | + frames(idx,1) = j; | ||
| 28 | + idx = idx + 1; | ||
| 29 | + end | ||
| 30 | + end | ||
| 31 | + | ||
| 32 | +% for j = z : -1 : 1 | ||
| 33 | +% n_nonblack = numel(find(data(:,:,j) > 0)); | ||
| 34 | +% if(n_nonblack > 50) | ||
| 35 | +% fprintf('%s: %d\n ','number: ', n_nonblack); | ||
| 36 | +% en = j; | ||
| 37 | +% break; | ||
| 38 | +% end | ||
| 39 | +% end | ||
| 40 | + | ||
| 41 | + | ||
| 42 | + c = 0; | ||
| 43 | + [nrow, ncol] = size(frames); | ||
| 44 | + step = round(nrow/11); | ||
| 45 | +% fprintf('%s: %d \n', 'nrow', nrow); | ||
| 46 | +% fprintf('%s: %d\n ','st: ', frames(1, 1)); | ||
| 47 | +% fprintf('%s: %d\n ','end: ', frames(nrow, 1)); | ||
| 48 | + %disp(frames); | ||
| 49 | + | ||
| 50 | + for k = 1 : step : step*10 | ||
| 51 | + %fprintf('%d ', k); | ||
| 52 | + fprintf('%d ', frames(k, 1)); | ||
| 53 | + type = '.png'; | ||
| 54 | + filename = strcat(id, '_', int2str(c), type); % BraTS19_2013_2_1_seg_flair_c.png | ||
| 55 | + outpath = convertCharsToStrings(strcat(outfolder, filename)); | ||
| 56 | + % typecase int16 to double, range[0, 1], rotate 90 and filp updown | ||
| 57 | + % range [0, 1] | ||
| 58 | + cp_data = flipud(rot90(mat2gray(double(data(:,:,frames(k, 1)))))); | ||
| 59 | +% M = max(cp_data(:)); | ||
| 60 | +% disp(M); | ||
| 61 | + imwrite(cp_data, outpath); | ||
| 62 | + | ||
| 63 | + c = c+ 1; | ||
| 64 | + end | ||
| 65 | + | ||
| 66 | + | ||
| 67 | +end | ||
| 68 | + |
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