old-matlab.m
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clc;
clear;
disp('***************** NEW RUN *********************');
total = tic;
% ******* Initialize voting parameters **************************************
rmax = 9; %maximum radius of the cell
ang_deg = 15.1; %half the angular range of the voting area
ang = ang_deg * pi / 180;
iter = 1; %number of voting iterations
t0 = 1.2; %threshold color
sigma = [4, 4, 2];
% t = 10;
d_ang= ang / (iter);
% ******** Testing parameters ******************************************
p = [100, 50, 100] ;
ps = [50, 50, 25] - 1;
% p = [100, 100, 100] ;
% ps = [300, 300, 150] - 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 = single(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);
I_theta = acos(Isub_z./Imag);
I_phi = atan(Isub_y./Isub_x);
%set a threshold for the gradient magnitude
It = Imag > t0;
%
% 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;
It(:, 1:rmax, :) = 0;
It(:, It_y - rmax:It_y,:) = 0;
It(:, :, 1:rmax) = 0;
It(:,:, It_z - rmax:It_z) = 0;
%
[Itx,Ity,Itz] = (ind2sub(size(It),find(It)));
Itx = single(Itx);
Ity = single(Ity);
Itz = single(Itz);
nV = nnz(It);
% create a meshgrid describing coordinates relative to the voter position
range = single(-rmax):single(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;
M_theta = acos(mz./m_mag);
M_phi = atan(my./mx);
M_phi (my ==0 & mx ==0) = 0;
pxPerRow = single(size(It,1));
pxPerCol = single(size(It,2));
validPoints = single(zeros(nV,1));
% g_v_prime = zeros(nV, ceil(rmax^2*ang/3));
g_v_prime = single(zeros(nV, (rmax^3)));
disp('first part done.');
%% vote
tic;
for itr = 1 : iter
Ivote = single(zeros(size(It)));
for v = 1: 1
%
% coordinates of the current voter
vx = Itx(v);
vy = Ity(v);
vz = Itz(v);
%
vtheta= I_theta(vx,vy,vz);
vphi = I_phi(vx,vy,vz);
vmag = Imag(vx,vy,vz);
% ang_diff = single(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
% 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)])));
% end
% end
% end
ang_diff = acos(((sin(M_theta).*sin(vtheta)).*cos(vphi - M_phi)) + cos(M_theta).*cos(vtheta));
M_diff = min(2*pi - ang_diff,ang_diff)<ang;
% M_diff = abs(ang_diff)<ang;
%compute the final mask
M = single(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 + (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);
for n=1: npts
%
Ivote( g_v_prime(v,n)) = Ivote( single(g_v_prime(v,n))) + vmag;
end
end
t_v1 = toc;
disp(['voting done. time =',num2str(t_v1)]);
% update the voting direction
tic;
for v = 1: nV
% coordinates of the current voter
vx = single(Itx(v));
vy = single(Ity(v));
vz = single(Itz(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
up_vx = gx - vx;
up_vy = gy - vy;
up_vz = gz - vz;
I_theta(vx,vy,vz) = acos(up_vz/sqrt(up_vx^2 + up_vy^2 + up_vz^2));
I_phi(vx,vy,vz) = atan(up_vy/up_vx);
end
tdir1 = toc;
display (['updating dir done. time = ', num2str(tdir1)]);
ang = ang - d_ang;
end
%%
out1(:,:,:,1) = mat2gray( I(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3)));
out1(:,:,:,2) = mat2gray(Ivote);
out1(:,:,:,3) = mat2gray(I(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3)));
subplot(3, 3, 1),
imagesc( squeeze( out1(:, :, ceil(size(out1, 3)/2),:) ) );
subplot(3, 3, 2),
imagesc( squeeze( out1(:, ceil(size(out1, 2)/2), :,:) ) );
subplot(3, 3, 3),
imagesc( squeeze( out1(ceil(size(out1, 1)/2), :, :,:) ) );
t = 10;
cell_center = Ivote;
cell_center(cell_center<t) =0;
cell_center(cell_center>=t) = 255;
% cell_center = imregionalmax(cell_center);
out2(:,:,:,1) = mat2gray( I(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3)));
out2(:,:,:,2) = mat2gray(cell_center);
out2(:,:,:,3) = mat2gray(I(p(1):p(1)+ps(1), p(2):p(2)+ps(2), p(3):p(3)+ps(3)));
subplot(3, 3, 4),
imagesc( squeeze( out2(:, :, ceil(size(out2, 3)/2),:) ) );
subplot(3, 3, 5),
imagesc( squeeze( out2(:, ceil(size(out2, 2)/2), :,:) ) );
subplot(3, 3, 6),
imagesc( squeeze( out2(ceil(size(out2, 1)/2), :, :,:) ) );
colormap(gray);
subplot(3, 3, 7),
imagesc( squeeze( Imag(:, :, ceil(size(Imag, 3)/2),:) ) );
subplot(3, 3, 8),
imagesc( squeeze( Imag(:, ceil(size(Imag, 2)/2), :,:) ) );
subplot(3, 3, 9),
imagesc( squeeze( Imag(ceil(size(Imag, 1)/2), :, :,:) ) );