segmentation / ivote3

Commit 567f008c002550d5ef72e37ba9fc032c278e74c3

Authored by Laila Saadatifard
1 parent c8150873

fix the ivote_3d code in matlab for the nissl-rat input data

Showing 1 changed file with 30 additions and 119 deletions   Show diff stats
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@@ -5,45 +5,44 @@ total = tic; @@ -5,45 +5,44 @@ total = tic;
5 5
6 6
7 % ******* Initialize voting parameters ************************************** 7 % ******* Initialize voting parameters **************************************
8 -rmax = 7; %maximum radius of the cell 8 +rmax = 10; %maximum radius of the cell
9 ang_deg = 25.1; %half the angular range of the voting area 9 ang_deg = 25.1; %half the angular range of the voting area
10 ang = ang_deg * pi / 180; 10 ang = ang_deg * pi / 180;
11 -iter = 5; %number of voting iterations 11 +iter = 6; %number of voting iterations
12 t0 = 1.2; %threshold color 12 t0 = 1.2; %threshold color
13 -sigma = [1, 1, 1]; 13 +sigma = [4, 4, 2];
14 % t = 0.1; 14 % t = 0.1;
15 d_ang= ang / (iter); 15 d_ang= ang / (iter);
16 16
17 % ******** Testing parameters ****************************************** 17 % ******** Testing parameters ******************************************
18 -% p = [100, 50, 100];  
19 -% ps = [200, 200, 100];  
20 -ps = [100, 50, 40];  
21 -I = syn_Img(rmax , ps);  
22 -% volfile = 'img\nissl-rat.vol';  
23 -% fid = fopen(volfile); % open the file that include the image  
24 -% S = fread(fid, 3, 'int32');  
25 -% X = S(1);  
26 -% Y = S(2);  
27 -% Z = S(3);  
28 -%  
29 -% % load the VOL data into a 2D matrix  
30 -% I = fread(fid,[X Y*Z], 'uint8');  
31 -% fclose(fid);  
32 -%  
33 -% %change this to a 3D matrix  
34 -% I = (reshape(I, [X, Y, Z]));  
35 -%  
36 -% % invert the intensity  
37 -% I = 255 - I; 18 +p = [100, 50, 100];
  19 +ps = [100, 100, 50];
  20 +% ps = [100, 50, 40];
  21 +% I = syn_Img(rmax , ps);
  22 +volfile = 'nissl-rat.vol';
  23 +fid = fopen(volfile); % open the file that include the image
  24 +S = fread(fid, 3, 'int32');
  25 +X = S(1);
  26 +Y = S(2);
  27 +Z = S(3);
  28 +
  29 +% load the VOL data into a 2D matrix
  30 +I = fread(fid,[X Y*Z], 'uint8');
  31 +fclose(fid);
  32 +
  33 +%change this to a 3D matrix
  34 +I = (reshape(I, [X, Y, Z]));
  35 +
  36 +% invert the intensity
  37 +I = 255 - I;
38 38
39 %perform a gaussian blur 39 %perform a gaussian blur
40 Iblur = gauss_blur3d(I, sigma); 40 Iblur = gauss_blur3d(I, sigma);
41 41
42 -%%crop out a small subregion of I and Iblur  
43 -% Iblur = Iblur(p(1):p(1)+ps(1)-1, p(2):p(2)+ps(2)-1, p(3):p(3)+ps(3)-1);  
44 -% I = I(p(1):p(1)+ps(1)-1, p(2):p(2)+ps(2)-1, p(3):p(3)+ps(3)-1); 42 +%crop out a small subregion of I and Iblur
  43 +Iblur = Iblur(p(1):p(1)+ps(1)-1, p(2):p(2)+ps(2)-1, p(3):p(3)+ps(3)-1);
  44 +I = I(p(1):p(1)+ps(1)-1, p(2):p(2)+ps(2)-1, p(3):p(3)+ps(3)-1);
45 45
46 -%  
47 % compute the gradient 46 % compute the gradient
48 [Igrad_y, Igrad_x, Igrad_z] = gradient(Iblur); 47 [Igrad_y, Igrad_x, Igrad_z] = gradient(Iblur);
49 48
@@ -90,35 +89,6 @@ validPixels = (zeros(nV,1)); @@ -90,35 +89,6 @@ validPixels = (zeros(nV,1));
90 % indices reference the 3D image 89 % indices reference the 3D image
91 g_v_prime = (zeros(nV, (rmax^3))); 90 g_v_prime = (zeros(nV, (rmax^3)));
92 91
93 -%--------------Display current data-------------------------  
94 -% subplot(3, 3, 1),  
95 -% imagesc(squeeze(I(:, :, ceil(size(I, 3)/2))));  
96 -%  
97 -% subplot(3, 3, 2),  
98 -% imagesc(squeeze(I(:, ceil(size(I, 2)/2), :)));  
99 -%  
100 -% subplot(3, 3, 3),  
101 -% imagesc(squeeze(I( ceil(size(I, 1)/2), :, :)));  
102 -% %  
103 -% subplot(3, 3, 4),  
104 -% imagesc(squeeze(Iblur(:, :, ceil(size(Iblur, 3)/2))));  
105 -%  
106 -% subplot(3, 3, 5),  
107 -% imagesc(squeeze(Iblur(:, ceil(size(Iblur, 2)/2), :)));  
108 -%  
109 -% subplot(3, 3, 6),  
110 -% imagesc(squeeze(Iblur(ceil(size(Iblur, 1)/2), :, :)));  
111 -%  
112 -% subplot(3, 3, 7),  
113 -% imagesc(squeeze(Imag(:, :, ceil(size(Imag, 3)/2))));  
114 -%  
115 -% subplot(3, 3, 8),  
116 -% imagesc(squeeze(Imag(:, ceil(size(Imag, 2)/2), :)));  
117 -%  
118 -% subplot(3, 3, 9),  
119 -% imagesc(squeeze(Imag(ceil(size(Imag, 1)/2), :, :)));  
120 -%  
121 -% colormap(gray);  
122 92
123 %% vote 93 %% vote
124 tic; 94 tic;
@@ -235,71 +205,12 @@ for itr = 1 : iter @@ -235,71 +205,12 @@ for itr = 1 : iter
235 205
236 206
237 %% 207 %%
238 -t = 2500; 208 +t = 250;
239 out = Ivote; 209 out = Ivote;
240 out(out<t) = 0; 210 out(out<t) = 0;
241 -% out(out>=t) = 255;  
242 -out = imregionalmax(out);  
243 211
244 -out1(:,:,:,1) = mat2gray(Iblur);  
245 -out1(:,:,:,2) = mat2gray(out);  
246 -out1(:,:,:,3) = mat2gray(Iblur);  
247 -% out = out1; 212 +fid_out = fopen('D:\ivote3_files\out.vol', 'w');
  213 +fwrite(fid_out, out);
  214 +fclose(fid_out);
248 215
249 216
250 -figure(4);  
251 -  
252 -subplot(2, 3, 1),  
253 -imagesc(squeeze(Iblur(:, :, ceil(size(Iblur, 3)/2))));  
254 -  
255 -subplot(2, 3, 2),  
256 -imagesc(squeeze(Iblur(:, ceil(size(Iblur, 2)/2), :)));  
257 -  
258 -subplot(2, 3, 3),  
259 -imagesc(squeeze(Iblur( ceil(size(Iblur, 1)/2), :, :)));  
260 -  
261 -subplot(2, 3, 4),  
262 -imagesc( squeeze( out1(:, :, ceil(size(Ivote, 3)/2),:) ) );  
263 -  
264 -subplot(2, 3, 5),  
265 -imagesc(squeeze(out1(:, ceil(size(Ivote, 2)/2), :, :)));  
266 -  
267 -subplot(2, 3, 6),  
268 -imagesc(squeeze(out1( ceil(size(Ivote, 1)/2), :, :, :)));  
269 -  
270 -colormap(gray);  
271 -%%  
272 -% figure, imagesc(squeeze(Iblur(:, :, ceil(size(Iblur, 3)/2)))); colormap(gray);  
273 -% figure, imagesc(squeeze(Ivote(:, :, ceil(size(Ivote, 3)/2),:))); colormap(gray);  
274 -% figure, imagesc(squeeze(Iblur(:, ceil(size(Iblur, 2)/2), :))); colormap(gray);  
275 -% figure, imagesc(squeeze(I(:, ceil(size(Ivote, 2)/2), :))); colormap(gray);  
276 -% % figure, imagesc(squeeze(Iblur( ceil(size(Iblur, 1)/2), :, :))); colormap(gray);  
277 -% figure, imagesc(squeeze(Ivote( ceil(size(Ivote, 1)/2), :, :))); colormap(gray);  
278 -%  
279 -% fid0 = fopen('D:\ivote3_files\iblur.vol', 'w');  
280 -% fwrite(fid0, Iblur);  
281 -% fclose(fid0);  
282 -%  
283 -% fid1 = fopen('D:\ivote3_files\ivote1.vol', 'w');  
284 -% fwrite(fid1, Ivote1);  
285 -% fclose(fid1);  
286 -%  
287 -% fid2 = fopen('D:\ivote3_files\ivote2.vol', 'w');  
288 -% fwrite(fid2, Ivote2);  
289 -% fclose(fid2);  
290 -%  
291 -% fid3 = fopen('D:\ivote3_files\ivote3.vol', 'w');  
292 -% fwrite(fid3, Ivote3);  
293 -% fclose(fid3);  
294 -%  
295 -% fid4 = fopen('D:\ivote3_files\ivote4.vol', 'w');  
296 -% fwrite(fid4, Ivote4);  
297 -% fclose(fid4);  
298 -%  
299 -% fid5 = fopen('D:\ivote3_files\ivote5.vol', 'w');  
300 -% fwrite(fid5, Ivote5);  
301 -% fclose(fid5);  
302 -%  
303 -% fid10 = fopen('D:\ivote3_files\ivote10.vol', 'w');  
304 -% fwrite(fid10, Ivote);  
305 -% fclose(fid10);