segmentation / ivote3

Commit c81508738f93816ed43adc8422c0ff05ab81147b

Authored by Laila Saadatifard
1 parent e4c75a97

fix the matlab ivote3 code to works on the synthetic image.

Showing 2 changed files with 38 additions and 265 deletions   Show diff stats
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@@ -6,11 +6,11 @@ total = tic; @@ -6,11 +6,11 @@ total = tic;
6 6
7 % ******* Initialize voting parameters ************************************** 7 % ******* Initialize voting parameters **************************************
8 rmax = 7; %maximum radius of the cell 8 rmax = 7; %maximum radius of the cell
9 -ang_deg = 15.1; %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 = 3; %number of voting iterations 11 +iter = 5; %number of voting iterations
12 t0 = 1.2; %threshold color 12 t0 = 1.2; %threshold color
13 -sigma = [4, 4, 2]; 13 +sigma = [1, 1, 1];
14 % t = 0.1; 14 % t = 0.1;
15 d_ang= ang / (iter); 15 d_ang= ang / (iter);
16 16
@@ -18,8 +18,7 @@ d_ang= ang / (iter); @@ -18,8 +18,7 @@ d_ang= ang / (iter);
18 % p = [100, 50, 100]; 18 % p = [100, 50, 100];
19 % ps = [200, 200, 100]; 19 % ps = [200, 200, 100];
20 ps = [100, 50, 40]; 20 ps = [100, 50, 40];
21 -r = 7;  
22 -I = syn_Img(r , ps); 21 +I = syn_Img(rmax , ps);
23 % volfile = 'img\nissl-rat.vol'; 22 % volfile = 'img\nissl-rat.vol';
24 % fid = fopen(volfile); % open the file that include the image 23 % fid = fopen(volfile); % open the file that include the image
25 % S = fread(fid, 3, 'int32'); 24 % S = fread(fid, 3, 'int32');
@@ -205,8 +204,6 @@ for itr = 1 : iter @@ -205,8 +204,6 @@ for itr = 1 : iter
205 t_v1 = toc; 204 t_v1 = toc;
206 disp(['voting done. time =',num2str(t_v1)]); 205 disp(['voting done. time =',num2str(t_v1)]);
207 206
208 - figure, imagesc(squeeze(Ivote(:, :, ceil(size(Ivote, 3)/2),:))); colormap(gray);  
209 -  
210 % update the voting direction 207 % update the voting direction
211 tic; 208 tic;
212 for v = 1: nV 209 for v = 1: nV
@@ -222,15 +219,12 @@ for itr = 1 : iter @@ -222,15 +219,12 @@ for itr = 1 : iter
222 [~, local_max_idx] = max(local_Ivote); 219 [~, local_max_idx] = max(local_Ivote);
223 220
224 %convert this into a global subscript 221 %convert this into a global subscript
225 - [gx, gy, gz] = ind2sub(size(Ivote), g_v_prime(v,local_max_idx)); 222 + [g_px, g_py, g_pz] = ind2sub(size(Ivote), g_v_prime(v,local_max_idx));
226 223
227 %compute the vector from the voter position to this position 224 %compute the vector from the voter position to this position
228 - dx = gx - vx;  
229 - dy = gy - vy;  
230 - dz = gz - vz;  
231 - Igrad_x(vx, vy, vz) = dx;  
232 - Igrad_y(vx, vy, vz) = dy;  
233 - Igrad_z(vx, vy, vz) = dz; 225 + Igrad_x(vx, vy, vz) = g_px - vx;
  226 + Igrad_y(vx, vy, vz) = g_py - vy;
  227 + Igrad_z(vx, vy, vz) = g_pz - vz;
234 228
235 end 229 end
236 230
@@ -241,7 +235,7 @@ for itr = 1 : iter @@ -241,7 +235,7 @@ for itr = 1 : iter
241 235
242 236
243 %% 237 %%
244 -t = 10; 238 +t = 2500;
245 out = Ivote; 239 out = Ivote;
246 out(out<t) = 0; 240 out(out<t) = 0;
247 % out(out>=t) = 255; 241 % out(out>=t) = 255;
@@ -250,10 +244,10 @@ out = imregionalmax(out); @@ -250,10 +244,10 @@ out = imregionalmax(out);
250 out1(:,:,:,1) = mat2gray(Iblur); 244 out1(:,:,:,1) = mat2gray(Iblur);
251 out1(:,:,:,2) = mat2gray(out); 245 out1(:,:,:,2) = mat2gray(out);
252 out1(:,:,:,3) = mat2gray(Iblur); 246 out1(:,:,:,3) = mat2gray(Iblur);
  247 +% out = out1;
253 248
254 249
255 -  
256 -figure(2); 250 +figure(4);
257 251
258 subplot(2, 3, 1), 252 subplot(2, 3, 1),
259 imagesc(squeeze(Iblur(:, :, ceil(size(Iblur, 3)/2)))); 253 imagesc(squeeze(Iblur(:, :, ceil(size(Iblur, 3)/2))));
@@ -282,19 +276,30 @@ colormap(gray); @@ -282,19 +276,30 @@ colormap(gray);
282 % % figure, imagesc(squeeze(Iblur( ceil(size(Iblur, 1)/2), :, :))); colormap(gray); 276 % % figure, imagesc(squeeze(Iblur( ceil(size(Iblur, 1)/2), :, :))); colormap(gray);
283 % figure, imagesc(squeeze(Ivote( ceil(size(Ivote, 1)/2), :, :))); colormap(gray); 277 % figure, imagesc(squeeze(Ivote( ceil(size(Ivote, 1)/2), :, :))); colormap(gray);
284 % 278 %
285 -fid0 = fopen('iblur.vol', 'w');  
286 -fwrite(fid0, Iblur);  
287 -fclose(fid0);  
288 -  
289 -fid1 = fopen('ivote1.vol', 'w');  
290 -fwrite(fid1, Ivote1);  
291 -fclose(fid1);  
292 -  
293 -fid2 = fopen('ivote2.vol', 'w');  
294 -fwrite(fid2, Ivote2);  
295 -fclose(fid2);  
296 -  
297 -fid3 = fopen('ivote3.vol', 'w');  
298 -fwrite(fid3, Ivote3);  
299 -fclose(fid3);  
300 - 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);
Matlab_3D/old-matlab.m deleted
View file @e4c75a9
1 -clc;  
2 -clear;  
3 -disp('***************** NEW RUN *********************');  
4 -total = tic;  
5 -  
6 -  
7 -% ******* Initialize voting parameters **************************************  
8 -rmax = 9; %maximum radius of the cell  
9 -ang_deg = 15.1; %half the angular range of the voting area  
10 -ang = ang_deg * pi / 180;  
11 -iter = 1; %number of voting iterations  
12 -t0 = 1.2; %threshold color  
13 -sigma = [4, 4, 2];  
14 -% t = 10;  
15 -d_ang= ang / (iter);  
16 -  
17 -% ******** Testing parameters ******************************************  
18 -p = [100, 50, 100] ;  
19 -ps = [50, 50, 25] - 1;  
20 -% p = [100, 100, 100] ;  
21 -% ps = [300, 300, 150] - 1;  
22 -  
23 -volfile = 'img\nissl-rat.vol';  
24 -fid = fopen(volfile); % open the file that include the image  
25 -S = fread(fid, 3, 'int32');  
26 -X = S(1);  
27 -Y = S(2);  
28 -Z = S(3);  
29 -  
30 -% load the VOL data into a 2D matrix  
31 -I = fread(fid,[X Y*Z], 'uint8');  
32 -fclose(fid);  
33 -  
34 -%change this to a 3D matrix  
35 -I = single(reshape(I, [X, Y, Z]));  
36 -  
37 -% invert the intensity  
38 -I = 255 - I;  
39 -  
40 -%perform a gaussian blur  
41 -I_blur = gauss_blur3d(I, sigma);  
42 -  
43 -% compute the gradient  
44 -[Igrad_x, Igrad_y, Igrad_z] = gradient(I_blur);  
45 -  
46 -%%crop out a small subregion of I  
47 -Isub_x = Igrad_x(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3));  
48 -Isub_y = Igrad_y(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3));  
49 -Isub_z = Igrad_z(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3));  
50 -  
51 -%calculate the gradient magnitude  
52 -Imag = sqrt(Isub_x .^ 2 + Isub_y .^ 2 + Isub_z .^2);  
53 -I_theta = acos(Isub_z./Imag);  
54 -I_phi = atan(Isub_y./Isub_x);  
55 -  
56 -  
57 -%set a threshold for the gradient magnitude  
58 -It = Imag > t0;  
59 -  
60 -%  
61 -% thresholding  
62 -It_x = size(It,1);  
63 -It_y = size(It,2);  
64 -It_z = size(It,3);  
65 -%  
66 -It(1:rmax, :, :) = 0;  
67 -It(It_x - rmax:It_x, :,:) = 0;  
68 -It(:, 1:rmax, :) = 0;  
69 -It(:, It_y - rmax:It_y,:) = 0;  
70 -It(:, :, 1:rmax) = 0;  
71 -It(:,:, It_z - rmax:It_z) = 0;  
72 -  
73 -%  
74 -[Itx,Ity,Itz] = (ind2sub(size(It),find(It)));  
75 -Itx = single(Itx);  
76 -Ity = single(Ity);  
77 -Itz = single(Itz);  
78 -nV = nnz(It);  
79 -  
80 -  
81 -% create a meshgrid describing coordinates relative to the voter position  
82 -range = single(-rmax):single(rmax);  
83 -[mx, my, mz] = (meshgrid(range, range, range));  
84 -m_mag = sqrt(mx.^2 + my.^2 + mz.^2);  
85 -  
86 -% create a mask for the voting area  
87 -M_dist = mx.^2 + my.^2 + mz.^2 < rmax^2;  
88 -M_theta = acos(mz./m_mag);  
89 -M_phi = atan(my./mx);  
90 -M_phi (my ==0 & mx ==0) = 0;  
91 -pxPerRow = single(size(It,1));  
92 -pxPerCol = single(size(It,2));  
93 -validPoints = single(zeros(nV,1));  
94 -  
95 -% g_v_prime = zeros(nV, ceil(rmax^2*ang/3));  
96 -g_v_prime = single(zeros(nV, (rmax^3)));  
97 -  
98 -  
99 -  
100 -disp('first part done.');  
101 -%% vote  
102 -tic;  
103 - for itr = 1 : iter  
104 -  
105 - Ivote = single(zeros(size(It)));  
106 - for v = 1: 1  
107 -  
108 -%  
109 - % coordinates of the current voter  
110 - vx = Itx(v);  
111 - vy = Ity(v);  
112 - vz = Itz(v);  
113 -%  
114 - vtheta= I_theta(vx,vy,vz);  
115 - vphi = I_phi(vx,vy,vz);  
116 - vmag = Imag(vx,vy,vz);  
117 -% ang_diff = single(zeros([2*rmax+1 2*rmax+1 2*rmax+1]));  
118 -% for i=1: 2*rmax +1  
119 -% for j=1: 2*rmax+1  
120 -% for k = 1:2*rmax+1  
121 -% ang_diff(i,j,k) = acos(dot([Isub_x(vx,vy,vz) Isub_y(vx,vy,vz) Isub_z(vx,vy,vz)], [mx(i,j,k) my(i,j,k) mz(i,j,k)])/(vmag*norm([mx(i,j,k) my(i,j,k) mz(i,j,k)])));  
122 -% end  
123 -% end  
124 -% end  
125 - ang_diff = acos(((sin(M_theta).*sin(vtheta)).*cos(vphi - M_phi)) + cos(M_theta).*cos(vtheta));  
126 - M_diff = min(2*pi - ang_diff,ang_diff)<ang;  
127 -% M_diff = abs(ang_diff)<ang;  
128 - %compute the final mask  
129 - M = single(M_dist .* M_diff);  
130 -%  
131 - % get the coordinates of each pixel in the final mask  
132 - [vx_prime,vy_prime,vz_prime] = ind2sub(size(M),find(M));  
133 -  
134 - %transform the local coordinates of the pixels in the voting region  
135 - %to the global coordinates of the image  
136 -  
137 - npts = numel(vx_prime);  
138 - validPoints(v) = npts;  
139 -  
140 - g_v_prime(v,1:npts) = vx + (single(vx_prime) - single(rmax + 1)) + (vy + (single(vy_prime) - single(rmax + 1))-1).*single(pxPerRow) + (vz + (single(vz_prime) - single(rmax + 1))-1).*single(pxPerRow)*single(pxPerCol);  
141 -  
142 - for n=1: npts  
143 - %  
144 - Ivote( g_v_prime(v,n)) = Ivote( single(g_v_prime(v,n))) + vmag;  
145 - end  
146 -  
147 - end  
148 -  
149 -  
150 - t_v1 = toc;  
151 - disp(['voting done. time =',num2str(t_v1)]);  
152 -  
153 -  
154 - % update the voting direction  
155 - tic;  
156 - for v = 1: nV  
157 - % coordinates of the current voter  
158 - vx = single(Itx(v));  
159 - vy = single(Ity(v));  
160 - vz = single(Itz(v));  
161 -  
162 - %get the local value of the voting image  
163 - local_Ivote = Ivote(g_v_prime(v,1:validPoints(v)));  
164 -  
165 - %find the index of the maximum value  
166 - [~, local_max_idx] = max(local_Ivote);  
167 -  
168 - %convert this into a global subscript  
169 - gz = ceil(g_v_prime(v,local_max_idx)/(pxPerRow*pxPerCol)) ;  
170 - gy = ceil((g_v_prime(v,local_max_idx)-(gz - 1)*pxPerRow*pxPerCol)/pxPerRow);  
171 - gx = g_v_prime(v,local_max_idx)- pxPerRow*((gy - 1) + (gz - 1) * pxPerCol);  
172 -  
173 - %compute the vector from the voter position to this position  
174 - up_vx = gx - vx;  
175 - up_vy = gy - vy;  
176 - up_vz = gz - vz;  
177 - I_theta(vx,vy,vz) = acos(up_vz/sqrt(up_vx^2 + up_vy^2 + up_vz^2));  
178 - I_phi(vx,vy,vz) = atan(up_vy/up_vx);  
179 - end  
180 -  
181 - tdir1 = toc;  
182 - display (['updating dir done. time = ', num2str(tdir1)]);  
183 - ang = ang - d_ang;  
184 - end  
185 -  
186 -  
187 -%%  
188 -out1(:,:,:,1) = mat2gray( I(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3)));  
189 -out1(:,:,:,2) = mat2gray(Ivote);  
190 -out1(:,:,:,3) = mat2gray(I(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3)));  
191 -  
192 -subplot(3, 3, 1),  
193 -imagesc( squeeze( out1(:, :, ceil(size(out1, 3)/2),:) ) );  
194 -  
195 -subplot(3, 3, 2),  
196 -imagesc( squeeze( out1(:, ceil(size(out1, 2)/2), :,:) ) );  
197 -  
198 -subplot(3, 3, 3),  
199 -imagesc( squeeze( out1(ceil(size(out1, 1)/2), :, :,:) ) );  
200 -  
201 -t = 10;  
202 -cell_center = Ivote;  
203 -cell_center(cell_center<t) =0;  
204 -cell_center(cell_center>=t) = 255;  
205 -% cell_center = imregionalmax(cell_center);  
206 -  
207 -out2(:,:,:,1) = mat2gray( I(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3)));  
208 -out2(:,:,:,2) = mat2gray(cell_center);  
209 -out2(:,:,:,3) = mat2gray(I(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3)));  
210 -  
211 -  
212 -subplot(3, 3, 4),  
213 -imagesc( squeeze( out2(:, :, ceil(size(out2, 3)/2),:) ) );  
214 -  
215 -subplot(3, 3, 5),  
216 -imagesc( squeeze( out2(:, ceil(size(out2, 2)/2), :,:) ) );  
217 -  
218 -subplot(3, 3, 6),  
219 -imagesc( squeeze( out2(ceil(size(out2, 1)/2), :, :,:) ) );  
220 -  
221 -colormap(gray);  
222 -subplot(3, 3, 7),  
223 -imagesc( squeeze( Imag(:, :, ceil(size(Imag, 3)/2),:) ) );  
224 -  
225 -subplot(3, 3, 8),  
226 -imagesc( squeeze( Imag(:, ceil(size(Imag, 2)/2), :,:) ) );  
227 -  
228 -subplot(3, 3, 9),  
229 -imagesc( squeeze( Imag(ceil(size(Imag, 1)/2), :, :,:) ) );  
230 -  
231 -  
232 -