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aarbelleaarbelle
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UPDATE BRANCH
1 parent 3e1199c commit 715f838

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lines changed

‎MATLAB-scripts/convert_isbi_to_net.m

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -43,8 +43,8 @@
4343
mkdir(fullfile(net_path_base,'Seg'))
4444
mkdir(fullfile(net_path_base,'Raw'))
4545
%%
46-
fidT = fopen(fullfile(net_path_base,'train.csv'),'w');
47-
fidV = fopen(fullfile(net_path_base,'val.csv'),'w');
46+
% fidT = fopen(fullfile(net_path_base,'train.csv'),'w');
47+
% fidV = fopen(fullfile(net_path_base,'val.csv'),'w');
4848
lenT = floor(numel(T)/2);
4949
clear T2
5050
for i = 1:lenT
@@ -55,12 +55,15 @@
5555
if mod(numel(T),2)
5656
T2(end+1) = T(end);
5757
end
58+
m_I = 0
5859
for i = 1:numel(T)
5960
t = T2(i);
6061
im_path = sprintf(im_path_base,t);
6162
seg_path = sprintf(seg_path_base,t);
6263
S = imread(seg_path);
6364
I = imread(im_path);
65+
m_I = max(max(I(:)),m_I)
66+
continue
6467
s = size(S);
6568
RGB = zeros(s(1),s(2),3);
6669
RGB(:,:,1) = S==0;

‎MATLAB-scripts/convert_isbi_to_net_BiLSTM_one_seg.m

Lines changed: 127 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,127 @@
1+
% Convert ISBI to Net For LSTM
2+
sequence_length = 9;
3+
4+
% im_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/01/t%03d.tif';
5+
% test_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Challenge/DIC-C2DH-HeLa/01/t%03d.tif';
6+
% seg_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/01_GT/SEG/man_Seg%03d.tif';
7+
% net_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/01_GT/NET/';
8+
% T = [2,5,21,31,33,39,54];
9+
% im_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/02/t%03d.tif';
10+
% test_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Challenge/DIC-C2DH-HeLa/02/t%03d.tif';
11+
% seg_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/02_GT/SEG/man_Seg%03d.tif';
12+
% net_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/02_GT/NET/';
13+
% T = [6,7,14,27,34,38,42,61,67];
14+
15+
16+
17+
% %
18+
% im_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/01/t%03d.tif';
19+
% test_path_base = '/home/arbellea/ISBI-Challenge-Data/Challenge/Fluo-C2DL-MSC/01/t%03d.tif';
20+
% seg_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/01_GT/SEG/man_seg%03d.tif';
21+
% net_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/01_GT/NET/';
22+
% T = [5,7,11,19,24,25,29,33,34,35,45];
23+
24+
im_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/02/t%03d.tif';
25+
test_path_base = '/home/arbellea/ISBI-Challenge-Data/Challenge/Fluo-C2DL-MSC/02/t%03d.tif';
26+
seg_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/02_GT/SEG/man_seg%03d.tif';
27+
net_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/02_GT/NET/';
28+
29+
T = [0,3,5,6,7,8,9,10,11,12,13,14,15,16,18,19,20,22,24,25,26,27,28,30,34,35,36,38,40,41,42,43,47];
30+
31+
32+
%%
33+
mkdir(net_path_base)
34+
mkdir(fullfile(net_path_base,'Seg'))
35+
mkdir(fullfile(net_path_base,'Raw'))
36+
%%
37+
fidT = fopen(fullfile(net_path_base,'train_Bilstm.csv'),'w');
38+
fidV = fopen(fullfile(net_path_base,'val_Bilstm.csv'),'w');
39+
lenT = floor(numel(T)/2);
40+
clear T2
41+
for i = 1:lenT
42+
T2(2*i-1) = T(lenT+(i));
43+
T2(2*i) = T(lenT-(i-1));
44+
45+
end
46+
if mod(numel(T),2)
47+
T2(end+1) = T(end);
48+
end
49+
for i = 1:numel(T2)
50+
try
51+
t = T2(i);
52+
if t - (sequence_length-1)/2 <0
53+
continue
54+
end
55+
im_path = sprintf(im_path_base,t);
56+
seg_path = sprintf(seg_path_base,t);
57+
S = imread(seg_path);
58+
for tt = t-(sequence_length-1)/2:t+(sequence_length-1)/2
59+
im_path = sprintf(im_path_base,tt);
60+
I = imread(im_path);
61+
I = uint16(I);
62+
out_im_path = sprintf('./Raw/t%03d.png',tt);
63+
imwrite(I, fullfile(net_path_base,out_im_path))
64+
end
65+
s = size(S);
66+
RGB = zeros(s(1),s(2),3);
67+
RGB(:,:,1) = S==0;
68+
E = zeros(s);
69+
F = zeros(s);
70+
for l = unique(S(S>0))'
71+
BW = imerode(S==l,ones(3));
72+
E(S==l&(~BW)) = 1;
73+
F(BW) = 1;
74+
end
75+
RGB(:,:,2) = F;
76+
RGB(:,:,3) = E;
77+
L = RGB(:,:,2) + RGB(:,:,3)*2;
78+
79+
out_seg_path = sprintf('./Seg/t%03d.png',t);
80+
imwrite(uint8(L),fullfile(net_path_base,out_seg_path))
81+
out_row = '';
82+
for tt = t-(sequence_length-1)/2:t+(sequence_length-1)/2
83+
out_row = sprintf('%s./Raw/t%03d.png,',out_row,tt);
84+
85+
86+
87+
88+
end
89+
out_row = sprintf('%s./Seg/t%03d.png\n',out_row, t);
90+
if i/numel(T)<0.7
91+
fprintf(fidT,out_row);
92+
else
93+
94+
fprintf(fidV,out_row);
95+
end
96+
catch
97+
98+
end
99+
100+
end
101+
fclose(fidT);
102+
103+
fclose(fidV);
104+
%%
105+
t=0;
106+
fid = fopen(fullfile(net_path_base,'test_lstm.csv'),'w');
107+
mkdir(fullfile(net_path_base,'ALL'))
108+
while true
109+
im_path = sprintf(test_path_base,t);
110+
if ~exist(im_path,'file')
111+
fprintf('%s Does not exist.\n Done\n', im_path);
112+
break
113+
end
114+
out_im_path = sprintf('./ALL/t%03d.png',t);
115+
I = uint16(imread(im_path));
116+
imwrite(I, fullfile(net_path_base,out_im_path));
117+
fprintf(fid,'%s\n', out_im_path);
118+
t = t+1;
119+
end
120+
fclose(fid);
121+
122+
123+
124+
125+
126+
127+

‎MATLAB-scripts/convert_isbi_to_net_LSTM.m

Lines changed: 144 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,144 @@
1+
% Convert ISBI to Net For LSTM
2+
sequence_length = 5;
3+
4+
% im_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/01/t%03d.tif';
5+
% test_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Challenge/DIC-C2DH-HeLa/01/t%03d.tif';
6+
% seg_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/01_GT/SEG/man_Seg%03d.tif';
7+
% net_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/01_GT/NET/';
8+
% T = [2,5,21,31,33,39,54];
9+
% im_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/02/t%03d.tif';
10+
% test_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Challenge/DIC-C2DH-HeLa/02/t%03d.tif';
11+
% seg_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/02_GT/SEG/man_Seg%03d.tif';
12+
% net_path_base = '/Users/assafarbelle/Documents/ISBI-Data/Training/DIC-C2DH-HeLa/02_GT/NET/';
13+
% T = [6,7,14,27,34,38,42,61,67];
14+
15+
16+
im_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-N2DH-SIM+/01/t%03d.tif';
17+
test_path_base = '/home/arbellea/ISBI-Challenge-Data/Challenge/Fluo-N2DH-SIM+/01/t%03d.tif';
18+
seg_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-N2DH-SIM+/01_GT/SEG/man_seg%03d.tif';
19+
net_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-N2DH-SIM+/01_GT/NET/';
20+
T = 0:64;
21+
22+
23+
24+
%
25+
% im_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-N2DH-SIM+/02/t%03d.tif';
26+
% test_path_base = '/home/arbellea/ISBI-Challenge-Data/Challenge/Fluo-N2DH-SIM+/02/t%03d.tif';
27+
% seg_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-N2DH-SIM+/02_GT/SEG/man_seg%03d.tif';
28+
% net_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-N2DH-SIM+/02_GT/NET/';
29+
% T = 0:149;
30+
31+
% %
32+
% im_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/01/t%03d.tif';
33+
% test_path_base = '/home/arbellea/ISBI-Challenge-Data/Challenge/Fluo-C2DL-MSC/01/t%03d.tif';
34+
% seg_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/01_GT/SEG/man_seg%03d.tif';
35+
% net_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/01_GT/NET/';
36+
% T = [5,7,11,19,24,25,29,33,34,35,45];
37+
38+
% im_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/02/t%03d.tif';
39+
% test_path_base = '/home/arbellea/ISBI-Challenge-Data/Challenge/Fluo-C2DL-MSC/02/t%03d.tif';
40+
% seg_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/02_GT/SEG/man_seg%03d.tif';
41+
% net_path_base = '/home/arbellea/ISBI-Challenge-Data/Training/Fluo-C2DL-MSC/02_GT/NET/';
42+
% T = [0,3,5,6,7,8,9,10,11,12,];
43+
44+
45+
%%
46+
mkdir(net_path_base)
47+
mkdir(fullfile(net_path_base,'Seg'))
48+
mkdir(fullfile(net_path_base,'Raw'))
49+
%%
50+
fidT = fopen(fullfile(net_path_base,'train_lstm.csv'),'w');
51+
fidV = fopen(fullfile(net_path_base,'val_lstm.csv'),'w');
52+
lenT = floor((numel(T)-sequence_length)/2);
53+
clear T2
54+
for i = 1:lenT
55+
T2(2*i-1) = T(lenT+(i));
56+
T2(2*i) = T(lenT-(i-1));
57+
58+
end
59+
if mod(numel(T),2)
60+
T2(end+1) = T(end);
61+
end
62+
for i = 1:numel(T)
63+
t = T2(i);
64+
im_path = sprintf(im_path_base,t);
65+
seg_path = sprintf(seg_path_base,t);
66+
S = imread(seg_path);
67+
I = imread(im_path);
68+
s = size(S);
69+
RGB = zeros(s(1),s(2),3);
70+
RGB(:,:,1) = S==0;
71+
E = zeros(s);
72+
F = zeros(s);
73+
for l = unique(S(S>0))'
74+
BW = imerode(S==l,ones(3));
75+
E(S==l&(~BW)) = 1;
76+
F(BW) = 1;
77+
end
78+
RGB(:,:,2) = F;
79+
RGB(:,:,3) = E;
80+
L = RGB(:,:,2) + RGB(:,:,3)*2;
81+
out_row = '';
82+
for tt = 0:(sequence_length-1)
83+
out_row = sprintf('%s./Raw/t%03d.png,./Seg/t%03d.png',out_row,t+tt,t+tt);
84+
85+
if tt<(sequence_length-1)
86+
out_row = sprintf('%s,',out_row);
87+
else
88+
out_row = sprintf('%s\n',out_row);
89+
end
90+
end
91+
if i/numel(T)<0.7
92+
fprintf(fidT,out_row);
93+
else
94+
95+
fprintf(fidV,out_row);
96+
end
97+
%I = uint16(I);
98+
%imwrite(I, fullfile(net_path_base,out_im_path))
99+
%imwrite(uint8(L),fullfile(net_path_base,out_seg_path))
100+
end
101+
fclose(fidT);
102+
103+
fclose(fidV);
104+
%%
105+
t=0;
106+
fid = fopen(fullfile(net_path_base,'test_lstm.csv'),'w');
107+
mkdir(fullfile(net_path_base,'ALL'))
108+
while true
109+
im_path = sprintf(test_path_base,t);
110+
if ~exist(im_path,'file')
111+
fprintf('%s Does not exist.\n Done\n', im_path);
112+
break
113+
end
114+
out_im_path = sprintf('./ALL/t%03d.png',t);
115+
I = uint16(imread(im_path));
116+
imwrite(I, fullfile(net_path_base,out_im_path));
117+
fprintf(fid,'%s\n', out_im_path);
118+
t = t+1;
119+
end
120+
fclose(fid);
121+
122+
%%
123+
124+
t=0;
125+
fid = fopen(fullfile(net_path_base,'test_train_lstm.csv'),'w');
126+
mkdir(fullfile(net_path_base,'ALL_Train'))
127+
while true
128+
im_path = sprintf( im_path_base,t);
129+
if ~exist(im_path,'file')
130+
fprintf('%s Does not exist.\n Done\n', im_path);
131+
break
132+
end
133+
out_im_path = sprintf('./ALL_Train/t%03d.png',t);
134+
I = uint16(imread(im_path));
135+
imwrite(I, fullfile(net_path_base,out_im_path));
136+
fprintf(fid,'%s\n', out_im_path);
137+
t = t+1;
138+
end
139+
fclose(fid);
140+
141+
142+
143+
144+

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