Heatmap plotting incorrect, black lines on X and Y axis outside the figure itself

I implemented the minutia heat map presented in this paper (page 7): https://arxiv.org/pdf/1909.09901.pdf

For this, the following code is implemented: (X, Y, and A data is attached in a .dat file)

function HeatMapCreator()
    % Start plotting minutia 
    [X, Y, A] = GetMinData("TestData");
    
    % Count Minutiea
    n = length(X);

    % set Width and Hight
    W = 600; H = 750; K = 6;
    
    % Create the matixes
    MM = cell(K, 1);
    M = zeros(H,W);
    
    % Define the gussian paramater
    GP = 2*2^2;
    
    % Go through each pixel
    for k = 1:6
        for j = 1 : H
           for i = 1 : W
              Hijk = 0; 
              for t = 1 : n
                Xt = X(t);
                Yt = Y(t);
                At = A(t);

                %Calculate Cs
                ED = sqrt((i-Xt)^2+(j-Yt)^2);
                Cs = exp(-ED/GP);

                %Calculate Co
                DO = At - (2 * k * pi / K);
                if (DO < -pi) || (DO > pi)
                    DO = 2 * pi - DO;
                end                       
                Co = exp(-DO/GP);

                Hijk = Hijk + (Cs * Co);
              end

              M(j,i) = Hijk;
           end
        end
        MM{k} = M;
    end    
    
    % Show the 6 figures
    for k = 1:6
        figure(k)
        heatmap(MM{k},'Colormap',gray,'GridVisible','off');
    end
end

The following bugs does not make sense:

1- I am getting Black lines in the X and Y axis when plotting:

2- According to the paper, all 6 heatmaps should look different, as here:

But im my code, the matrixes are different from each other, but the heatmap is the same for all the 6 figues. I wonder weather the heat map function have anything to do regarding this error ?

All my figures looks like the first image.

Answer 1

[Adam Danz]

Problem 1: the black lines

Those black lines are merely 100s of tick labels (or, the equivalent of axis ticks in Heatmap) . Your data seems to be a matrix with size [750, 600] which means there are a few hundred ticks on each axis, all squished together. Notice the layers of ticks become thicker as ticks move from 1s to 10s to 100s. The problem can be recreated with this line of code:

heatmap(rand(750,600))

To remove the axis ticks,

h = heatmap(rand(600,750)); 
hs = struct(h); % See warning in command window
hs.XAxis.TickValues = []; 
hs.YAxis.TickValues = []; 

Alternatively, (better than the version above; added Dec 29, 2020)

h = heatmap(rand(600,750));
h.XDisplayData = [];
h.YDisplayData = [];

Or to show every 50 ticks (added Dec 29, 2020)

h = heatmap(rand(600,750));
h.YDisplayData = h.YDisplayData([1,50:50:end]);
h.YDisplayData = h.YDisplayData([1,50:50:end]);

However, I don't recommend using heatmap. Instead, I think imagesc() would be the better choice.

Problem 2: All plots look the same

It's tough to troubleshoot that one without seeing the data, your plots, or stepping through your code. If I were you, I'd follow these steps:

1. Run the code to produce 1 figure
2. Look into the data and find position within the matix where the values should indicate white areas of the plot. The function find() will come in handy.
3. Then find those location on the plot to confirm that they aren't white. If you use imagesc() note that the y-axis is reversed by default (as it is in Heatmap). If you'd like to flip it to normal: set(gca, 'YDir', 'Normal')
4. Then repeat the process for the 2nd plot and so on. If you find values that represent white, those areas should be white on your plot.

[Ahmed Madhun]

Thanks for your answer, i think the first problem is solved, and i am looking on the second one. But how do you mean imagesc() can be used in thiss case. (Step 3 of what you mentioned)

[Adam Danz]

Instead of plotting the values using heatmap, use imagesc.

I see that the same suggestion was made in this comment.