76a0f6f9
 Laila Saadatifard
first commit to i...
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tic;
clc;
clear;
disp('***************** NEW RUN *********************');
total = tic;
% ******* Initialize voting parameters **************************************
rmax = 9; %maximum radius of the cell
phi_deg = 25.1; %half the angular range of the voting area
phi = phi_deg * pi / 180;
iter = 5; %number of voting iterations
t0 = 1.2; %threshold color
sigma = [4, 4, 2];
final_t = 75;
% ******** Testing parameters ******************************************
p = [50, 20, 50] ;
ps = [100, 100, 50] - 1;
volfile = 'img\nissl-rat.vol';
fid = fopen(volfile); % open the file that include the image
S = fread(fid, 3, 'int32');
X = S(1);
Y = S(2);
Z = S(3);
% load the VOL data into a 2D matrix
I = fread(fid,[X Y*Z], 'uint8');
fclose(fid);
%change this to a 3D matrix
I = reshape(I, [X, Y, Z]);
%invert the intensity
I = 255 - I;
%perform a gaussian blur
I_blur = gauss_blur3d(I, sigma);
% compute the gradient
[Igrad_x, Igrad_y, Igrad_z] = gradient(I_blur);
%%crop out a small subregion of I
Isub_x = Igrad_x(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3));
Isub_y = Igrad_y(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3));
Isub_z = Igrad_z(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3));
%calculate the gradient magnitude
Imag = sqrt(Isub_x .^ 2 + Isub_y .^ 2 + Isub_z .^2);
%set a threshold for the gradient magnitude
It = Imag > t0;
subplot(3, 3, 1),
imshow( squeeze( I(:, :, ceil(size(I, 3)/2)) ) ./ 255 );
%colormap(gray);
subplot(3, 3, 2),
imshow( squeeze( I(:, ceil(size(I, 2)/2), :) ) ./ 255 );
subplot(3, 3, 3),
imshow( squeeze( I(ceil(size(I, 1)/2), :, :) ) ./ 255 );
subplot(3, 3, 4),
imagesc( squeeze( Imag(:, :, ceil(size(Imag, 3)/2)) ) );
subplot(3, 3, 5),
imagesc( squeeze( Imag(:, ceil(size(Imag, 2)/2), :) ) );
subplot(3, 3, 6),
imagesc( squeeze( Imag(ceil(size(Imag, 1)/2), :, :) ) );
subplot(3, 3, 7),
imagesc( squeeze( It(:, :, ceil(size(It, 3)/2)) ) );
subplot(3, 3, 8),
imagesc( squeeze( It(:, ceil(size(It, 2)/2), :) ) );
subplot(3, 3, 9),
imagesc( squeeze( It(ceil(size(It, 1)/2), :, :) ) );
%
% thresholding
It_x = size(It,1);
It_y = size(It,2);
It_z = size(It,3);
%
It(1:rmax, :, :) = 0;
It(It_x - rmax:It_x, :,:) = 0;
S(:, 1:rmax, :) = 0;
S(:, It_y - rmax:It_y,:) = 0;
S(:, :, 1:rmax) = 0;
S(:,:, It_z - rmax:It_z) = 0;
%
[Itx,Ity,Itz] = ind2sub(size(It),find(It));
nV = nnz(It);
% create a meshgrid describing coordinates relative to the voter position
range = -rmax:rmax;
[mx, my, mz] = meshgrid(range, range, range);
m_mag = sqrt(mx.^2 + my.^2 + mz.^2);
%create a mask for the voting area
M_dist = mx.^2 + my.^2 + mz.^2 < rmax^2;
pxPerRow = size(I_blur,1);
pxPerCol = size(I_blur,2);
validPoints = zeros(nV,1);
g_v_prime = zeros(nV, ceil(rmax^2*phi/3));
%%
disp('done.');
%% vote
for itr = 1 : iter
Ivote = zeros(size(Iblur));
for v = 1: nV
% coordinates of the current voter
vx = Itx(v);
vy = Ity(v);
vz = Itz(v);
vgrad = [Isub_x(vx,vy,vz), Isub_y(vx,vy,vz), Isub_z(vx,vy,vz)];
%determine the gradient magnitude at the current voter location
vmag = Imag(vx,vy,vz);
ang_diff = zeros(2*rmax+1, 2*rmax+1, 2*rmax+1);
for i = 1 : 2*rmax+1
for j = 1 : 2*rmax+1
for k = 1 : 2*rmax+1
a = [mx(i,j,k), my(i,j,k), mz(i,j,k)];
c = dot(vgrad, a);
ang_diff(i,j,k) = acos(c/(m_mag(i,j,k)* vmag ));
end
end
end
M_diff = min(2*pi - ang_diff,ang_diff)<phi;
%compute the final mask
M = (M_dist .* M_diff);
% get the coordinates of each pixel in the final mask
[vx_prime,vy_prime,vz_prime] = ind2sub(size(M),find(M));
%transform the local coordinates of the pixels in the voting region
%to the global coordinates of the image
npts = numel(vx_prime);
validPoints(v) = npts;
g_v_prime(v,1:npts) = vx + (vx_prime - (rmax + 1)) + (vy + (vy_prime - (rmax + 1))-1).*pxPerRow + (vz + (vz_prime - (rmax + 1))-1).*pxPerRow*pxPerCol;
for n=1: npts
%
Ivote( g_v_prime(v,n)) = Ivote( g_v_prime(v,n)) + vmag;
end
end
disp('voting done.');
%% update the voting direction
for v = 1: nV
% coordinates of the current voter
vx = sx(v);
vy = sy(v);
vz = sz(v);
%get the local value of the voting image
local_Ivote = Ivote(g_v_prime(v,1:validPoints(v)));
%find the index of the maximum value
[~, local_max_idx] = max(local_Ivote);
%convert this into a global subscript
gz = ceil(g_v_prime(v,local_max_idx)/(pxPerRow*pxPerCol)) ;
gy = ceil((g_v_prime(v,local_max_idx)-(gz - 1)*pxPerRow*pxPerCol)/pxPerRow);
gx = g_v_prime(v,local_max_idx)- pxPerRow*((gy - 1) + (gz - 1) * pxPerCol);
%compute the vector from the voter position to this position
new_vx = gx - vx;
new_vy = gy - vy;
new_vz = gz - vz;
Igrad_x(vx,vy,vz) = new_vx;
Igrad_y(vx,vy,vz) = new_vy;
Igrad_z(vx,vy,vz) = new_vz;
end
end
cell_center = Ivote;
fido = fopen('out\outImg.vol', 'w+');
fwrite(fido, cell_center);
fclose(fido);
t1 = toc
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