Overlapping images in Matlab

Question

I am trying to overlap a set of images in Matlab. The images are of the same object at different times. In my code:

for k=1:20

% code executed with output 'image'

image_rotate = imrotate(image,-90); %put dataset in correct orientation

data.(['val' num2str(k)]) = image_rotate; % save the dataset. Access first iteration data.val1, ... data.val20 (all with same size 223x375 dataset, which in binary with the object '1' and background '0')

end

% what I have been using to plot the dataset

figure, imshow(data.val51),axis image, impixelinfo, colormap(jet)

I would like to overlap the figures (perhaps in a separate loop) with 'data.val51', 'data.val52', ... to show the object growing with time, with each image assigned a different colour with the background removed (white). Any help with implementing this would be appreciated.

Further guidance on how to find the distance using the image between the front of each time-step will very appreciated. Thanks.

Answer 1

I tried to build masks manually.
There are 9 masks: first mask applies first color, second applies second color...
Each mask has 1 where pixels belongs to section and zero where not.

See the following code sample that "grows":

close all

I = imread('CaNtG.jpg');
R0 = I(:, :, 1); %Red plane of I
G0 = I(:, :, 2); %Green plane of I
B0 = I(:, :, 3); %Blue plane of I


%Build masks with ones for each stage.
%Since I build the mask manaully, they are not perfect cut.
matHVS = rgb2hsv(double(I)/255);
H = round(matHVS(:, :, 1)*100);
%figure;imagesc(uint8(H));impixelinfo
Z = logical(zeros(size(H)));
M1 = Z;M1((H >= 99)) = 1;M1(:, 535:end) = 0;
M2 = Z;M2((H >= 8) & (H <= 11)) = 1;M2(:,1:330) = 0;M2(:, 615:end) = 0;
M3 = Z;M3((H >= 12) & (H <= 25)) = 1;M3(:,1:330) = 0;M3(:, 615:end) = 0;
M4 = Z;M4((H >= 26) & (H <= 37)) = 1;M4(:,1:529) = 0;M4(:, 755:end) = 0;
M5 = Z;M5((H >= 38) & (H <= 54)) = 1;M5(:,1:593) = 0;M5(:, 818:end) = 0;
M6 = Z;M6((H <= 1)) = 1;M6(:, 1:656) = 0;M6(:, 853:end) = 0;
M7 = Z;M7((H >= 55) & (H <= 70)) = 1;M7(:,1:816) = 0;M7(:, 1099:end) = 0;
M8 = Z;M8((H >= 71) & (H <= 90)) = 1;M8(:,1:893) = 0;M8(:, 1140:end) = 0;
M9 = Z;M9((H >= 91)) = 1;M9(:,1:1045) = 0;

%Create cell array of 9 masks.
MM = {M1, M2, M3, M4, M5, M6, M7, M8, M9};

J = uint8(ones(size(I))*255); %J starts with all pixels white.

R1 = J(:, :, 1); %Red plane of J
G1 = J(:, :, 2); %Green plane of J
B1 = J(:, :, 3); %Blue plane of J

figure;imshow(J);

for i = 1:9
    M = MM{i}; %M aplies mask of current stage.
    R1(M) = R0(M);
    G1(M) = G0(M);
    B1(M) = B0(M);
    J = cat(3, R1, G1, B1);
    imshow(J);
    pause(1);
    %imwrite(J, ['J', num2str(i), '.jpg']);
end

Since I built the masks semi-manually, the result is not perfect.
Please notice: this is just an example.
I didn't make the effort to make it accurate.

Result:

---

Improving results, by filling gaps and holes in masks:

Updated code is an expansion of the previous code.
The following code improves the mask creation:

close all

I = imread('CaNtG.jpg');
R0 = I(:, :, 1); %Red plane of I
G0 = I(:, :, 2); %Green plane of I
B0 = I(:, :, 3); %Blue plane of I


%Build masks with ones for each stage.
%Since I build the mask manaully, they are not perfect cut.
matHVS = rgb2hsv(double(I)/255);
H = round(matHVS(:, :, 1)*100);
%figure;imagesc(uint8(H));impixelinfo
Z = logical(zeros(size(H)));
M1 = Z;M1((H >= 99)) = 1;M1(:, 535:end) = 0; %Red
M2 = Z;M2((H >= 8) & (H <= 11)) = 1;M2(:,1:330) = 0;M2(:, 615:end) = 0;   %Brown
M3 = Z;M3((H >= 12) & (H <= 25)) = 1;M3(:,1:330) = 0;M3(:, 615:end) = 0;  %Yellow
M4 = Z;M4((H >= 26) & (H <= 37)) = 1;M4(:,1:529) = 0;M4(:, 755:end) = 0;  %Green
M5 = Z;M5((H >= 45) & (H <= 54)) = 1;M5(:,1:593) = 0;M5(:, 818:end) = 0;  %Cyan
M6 = Z;M6((H <= 44)) = 1;M6(:, 1:656) = 0;M6(:, 853:end) = 0;             %Gray
M7 = Z;M7((H >= 55) & (H <= 65)) = 1;M7(:,1:816) = 0;M7(:, 1099:end) = 0; %Blue
M8 = Z;M8((H >= 66) & (H <= 89)) = 1;M8(:,1:893) = 0;M8(:, 1140:end) = 0; %Magenta
M9 = Z;M9((H >= 90)) = 1;M9(:,1:1045) = 0;                                %Dark red

%Create cell array of 9 masks.
MM = {M1, M2, M3, M4, M5, M6, M7, M8, M9};


%Filling gaps between each two sequnital masks:
%---------------------------------------
%For each mask row, find last "1" of first section, first "1" in next section.
%Fill "1"s from up to the center from both sides.
%                     |    |
%                     V    V
%M0:         111111111100000000000
%M1:         000000000000001111111
%Gap:                  <-->         
%Fill M0:    111111111111000000000
%Fill M1:    000000000000111111111
for i = 1:length(MM)-1
    M0 = MM{i};    %Mask of section i
    M1 = MM{i+1};  %Mask of section i+1

    %Fill gaps - fill each mask row separatelly
    for y = 1:size(M0, 1)
        x0 = find(M0(y, :) == 1, 1, 'last'); %Last non-zero index in row of M0
        x1 = find(M1(y, :) == 1, 1, 'first'); %First non-zero index in row of M1
        gap_size = x1 - x0 - 1;
        if (gap_size > 0)
            gap0 = round(gap_size/2);
            gap1 = gap_size - gap0;
            if (gap0 > 0), M0(y, x0+1:x0+gap0) = 1; end %Fill first half gaps in M0
            if (gap1 > 0), M1(y, x1-gap1:x1-1) = 1; end %Fill second half gaps in M1
        end
    end

    MM{i} = M0;     %Update cell array MM with "filled" M0.
    MM{i+1} = M1;   %Update cell array MM with "filled" M1.
end
%---------------------------------------

%Find left white section, and fill "1"s in W:
%---------------------------------------
W = Z;
M1 = MM{1};
for y = 1:size(M0, 1)    
    x = find(M1(y, :) == 1, 1); %Find fisrt non-zero element in row of M0.
    W(y, 1:x) = 1;
end
%figure;imshow(W);
%---------------------------------------

%Fill holes inside the masks
%---------------------------------------
%A "hole" is a "0" that the value left to it is "1"
%Fill hols with "1"s 
%                     |    |
%                     V    V
%M0:         11111111110000011111
%Hole:                 <--->
%Fill hole:  11111111111111111111
for i = 1:length(MM)
    M0 = MM{i};    %Mask of section i

    %Fill holds - fill each mask row separatelly
    for y = 1:size(M0, 1)
        x0 = find(M0(y, :) == 1, 1, 'last'); %Last non-zero index in row of M0
        M0(y, 1:x0) = 1; %Fill all mask pixels to the left of the "1" with value "1".
    end

    M0(W == 1) = 0;  %Erase W pixels from the first mask.

    W(M0 == 1) = 1;  %Add all "1"s in mask M0 to W (W keeps unuion of all left sections up to section i).

    MM{i} = M0;     %Update cell array MM with "filled" M0.
end




J = uint8(ones(size(I))*255); %J starts with all pixels white.

R1 = J(:, :, 1); %Red plane of J
G1 = J(:, :, 2); %Green plane of J
B1 = J(:, :, 3); %Blue plane of J

figure;imshow(J);

for i = 1:length(MM)
    M = MM{i}; %M aplies mask of current stage.
    R1(M) = R0(M);
    G1(M) = G0(M);
    B1(M) = B0(M);
    J = cat(3, R1, G1, B1);
    imshow(J);
    pause(1);
    %imwrite(J, ['J', num2str(i), '.jpg']);
end

Result:

---

Produce a similar image from a set of 7 images:
The images are downloaded from: https://www.dropbox.com/s/nxixlk5jw2glu0i/Images%20%282%29.zip?dl=0
I didn't fill the holes this time.
I filled the sections with arbitrary solid colors:

num_parts = 7;

MM = cell(1, num_parts);

%Cell array of 7 colors to fill
colors = {[0,0,255], [0,255,0], [255,0,0], [128, 128, 128], [0,255,255], [255,0,255], [255,255,0]};

%Load masks from files 1 (2).tif to 7 (2).tif.
%Change mask format, and dimensions to match size and dimensions of I.
for i = 1:num_parts
    fname = [num2str(i), ' (2).tif']; %File name: 1 (2).tif to 7 (2).tif.
    M = imread(fname); %Load image.

    M = M(:, :, 1); %Keep the red color plane.

    [y0, x0] = find(M ~= 255, 1);
    [y1, x1] = find(M ~= 255, 1, 'last');

    M = M(y0:y1, x0:x1); %Crop the area that is not 255 (remove white background).

    M = logical(M); %Convert to logical mask of zeros and ones.

    MM{i} = M;
end

%Remove ovelap beetween masks (iterate from last mask backward):
for i = length(MM):-1:2
    MM{i}(MM{i-1}) = 0;
end


K = uint8(ones(size(M,1), size(M,2), 3)*255); %K starts with all pixels white.

R = K(:, :, 1); %Red plane of K
G = K(:, :, 2); %Green plane of K
B = K(:, :, 3); %Blue plane of K

figure;imshow(K);

for i = 1:length(MM)
    M = MM{i}; %M aplies mask of current stage.
    R(M) = colors{i}(1);
    G(M) = colors{i}(2);
    B(M) = colors{i}(3);
    K = uint8(cat(3, R, G, B));
    imshow(K);
    pause(1);
    %imwrite(K, ['K', num2str(i), '.jpg']);
end

Final result: