matlab coder report Size mismatch (size [0 x 0] ~= size [1 x 2])

Question

zhou caiwei 2022-8-15

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https://ww2.mathworks.cn/matlabcentral/answers/1779525-matlab-coder-report-size-mismatch-size-0-x-0-size-1-x-2

评论： Walter Roberson 2023-2-13

I tried to use matlab coder to convert my matlab file into C\C++ source file. In my *.m file,I defined a dynamic array:

...
coord_list = [];
I_list = [];
...
for i=1:n
    ....
    coordinate = yy;
    I = zz;
    coord_list = [coord_list;coordinate];
    I_list = [I_list;I]
end

The error occurs like:

??? Size mismatch (size [0 x 0] ~= size [1 x 2]).
The size to the left is the size of the left-hand side of the assignment.

How could I fix this bug? how should I modify my matlab code so that It meets the requirements of C\C++ style for matlab-coder?

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Chiluveru 2023-2-13

hi Raghu,

I am alsp facing same issue like the error below:

Size mismatch (size [1 x 0] ~= size [16 x 0]).

need your help for solving it

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Answer 1

Chunru 2022-8-15

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1779525-matlab-coder-report-size-mismatch-size-0-x-0-size-1-x-2#answer_1026580

在 MATLAB Online 中打开

...
coord_list = zeros(n, m1);   % m1 is the length of yy below
I_list = zeros(n, m2);       % m2 is the lenght of zz
...
for i=1:n
    ....
    coordinate = yy;
    I = zz;
    coord_list(i, :) = coordinate;
    I_list(i, :) = I;
end

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zhou caiwei 2022-8-16

在 MATLAB Online 中打开

here is the one of the results.

I noticed that the mex file（generated from Matlab coder） takes twice as long to execute as the m file, no matter the data size.

TVSTORM processing time: 15.7764 seconds
TVSTORM mex processing time: 29.826 seconds

here is the test function which could be excute directly:

%% This is to test the TVSTORM algorithm with 2D STORM image reconstruction
close all;
clear;
clc;
%% Set up the parameters
density = 20;            % emitter density (fluorophores per um^2)
pixelsize = 0.075;      % camera pixel size (um)
width = 30;             % image width (pixel)
height = 30;            % image height (pixel)
g_noise = 5;            % gaussian noise level (photons/pixel)
photons = 500;         % average photon number
sigma = 1.5;            % standard deviation of system PSF (pixel)
% measurement matrix for ADCG
div2 = 2;
A2 = STORM_2D_Gen_Meas_Mat(width, height, div2, sigma);
%% Generate simulated image
disp('Generating simulated image ...');
[im, emitterList] = STORM_2D_Simulation(density, pixelsize, ...
    width, height, g_noise, photons, sigma);
%% TVSTORM
ns = 0.9;
thresh = 150;
t1 = tic;
[clustCent3, I_list3] = TVSTORM_2D_mex(A2, im, height, width, sigma, div2, ns, thresh);
disp(['TVSTORM processing time: ', num2str(toc(t1)), ' seconds']);
ns = 0.9;
thresh = 150;
t1 = tic;
[clustCent3, I_list3] = TVSTORM_2D_mex_mex(A2, im, height, width, sigma, div2, ns, thresh);
disp(['TVSTORM mex processing time: ', num2str(toc(t1)), ' seconds']);

here is the main function to build:

function [clustCent, I_list] = TVSTORM_2D_mex(A, im, height, width, sigma,...
    div, ns, thresh)%#codegen
% PURPOSE:
% STORM 2D reconstruction using TVSTORM.
%---------------------------------------------------
% USAGE:
% [clustCent, I_list] = TVSTORM(A, im, height, width, sigma, div, ns, thresh)
%---------------------------------------------------
% INPUTS:
% A:                measurement matrix
% im:               acquired image
% height:           image height
% width:            image width
% sigma:            standard deviation of system PSF (pixel)
% div:              upsampling factor in x y-dimension
% ns:               parameter that controls the balance between
%                   data fidelity and sparsity
%                   typically 1.5 is used for Poisson noise
% thresh:           threshold for backward step
%---------------------------------------------------
% OUTPUTS:
% clustCent(:, 1):  x coordinates (pixel)
% clustCent(:, 2):  y coordinates (pixel)
% I_list:           intensity list
%---------------------------------------------------
%% Pre-processing for TVSTORM
im = double(im(:));
eps = ns * sqrt(sum(im));
[xxx, yyy] = meshgrid(0.5 + 1 / div / 2 : 1 / div : width + 0.5 - 1 / div / 2,...
    0.5 + 1 / div / 2 : 1 / div : height + 0.5 - 1 / div / 2);
%% Iterate
bg = min(im);
iter = 1;
max_iter = 40;
coder.varsize('coord_list',[200 2],[1 0]);
coder.varsize('I_list',[200 1],[1 0]);
coder.varsize('coord_list_before',[max_iter 2],[1 0]);
coder.varsize('I_list_before',[max_iter 1],[1 0]);
coord_list = zeros(0,2);
I_list = zeros(0,1);
coord_list_before = zeros(0,2);
I_list_before = zeros(0,1);
while iter < max_iter
    % calculate the residual
    im_gen = Gen_Im_From_2D_Coord(coord_list, I_list, height, width, sigma);
    res = im - im_gen;
    
    res_iter = norm(res);
    % terminate if residual small enough
    if res_iter <= eps
        break;
    end
    
    if sum(I_list < thresh) ~= 0
        if sum(I_list < thresh) == 1 && I_list(end) < thresh
            coord_list = coord_list_before;
            I_list = I_list_before;
            break;
        else
            while sum(I_list < thresh) ~= 0
                list = I_list > thresh;
                coord_list = coord_list(list, :);
                I_list = I_list(list, :);
                [coord_list, I_list, bg] = Coordinate_Descent_2D(...
                    coord_list, I_list, bg, im, height, width, sigma);
            end
            break;
        end
    end
    
    coord_list_before = coord_list;
    I_list_before = I_list;
    
    % find one atom
    coeff = A' * (res - bg);
    [~, idx] = max(coeff);
    coord_list = [coord_list; xxx(idx), yyy(idx)];
    I_list = [I_list; max(coeff(idx) / norm(A(:, idx)) ^ 2, 100)];
    % coordinate descent on the support
    [coord_list, I_list, bg] = Coordinate_Descent_2D(...
        coord_list, I_list, bg, im, height, width, sigma);
    iter = iter + 1;
end
clustCent = coord_list;

the related function files:

function [coord_list, I_list, bg] = Coordinate_Descent_2D(...
    coord_list, I_list, bg, im, height, width, sigma)%#codegen
% PURPOSE:
% Gradient descent on 2D coordinate and weight refinement.
%---------------------------------------------------
% USAGE:
% [coord_list, I_list, bg] = Coordinate_Descent_2D(...
%   coord_list, I_list, bg, height, width, sigma)
%---------------------------------------------------
% INPUTS:
% coord_list:   list of input coordinate
% I_list:       list of input intensity
% bg:           background photon
% im:           acquired image
% height:       image height
% width:        image width
% sigma:        standard deviation of system PSF (pixel)
%---------------------------------------------------
% OUTPUTS:
% coord_list:   list of output coordinate
% I_list:       list of output intensity
% bg:           background photon
%---------------------------------------------------
%%
iter = 1;
max_iter = 200;
[xx, yy] = meshgrid(1 : width, 1 : height);
xx_r = xx(:); yy_r = yy(:);
A = Gen_Meas_From_2D_Coord(coord_list, height, width, sigma);
coder.varsize('res_list',[1 max_iter],[0 1]);
res_list = zeros(1,0);
%%
while iter < max_iter
    mu = A * I_list + bg;
    res_list = [res_list, sum(mu - im .* log(mu + 1e-5))];
    %% background descent
    grad_bg = sum((mu - im) ./ (mu + 1e-5));
    % backtracking
    alpha = 0.5;
    epsilon = 1;
    if grad_bg > 0
        epsilon = min(epsilon, bg / grad_bg);
    end
    df = -1e-6 * norm(grad_bg) ^ 2;
    mu = A * I_list + bg;
    fc = sum(mu - im .* log(mu + 1e-5));
    bg_temp = bg - epsilon * grad_bg;
    mu_base = A * I_list;
    mu = mu_base + bg_temp;
    while sum(mu - im .* log(mu + 1e-5)) > fc + epsilon * df
        epsilon = epsilon * max(alpha, 0.1);
        alpha = alpha * 0.8;
        if epsilon < 1e-10
            epsilon = 0;
            break;
        end
        bg_temp = bg - epsilon * grad_bg;
        mu = mu_base + bg_temp;
    end
    bg = bg - epsilon * grad_bg;
    
    %%
    for i = 1 : size(coord_list, 1)
        %% intensity descent
        temp_xx = erf((xx + 0.5 - coord_list(i, 1)) / sqrt(2) / sigma) -...
            erf((xx - 0.5 - coord_list(i, 1)) / sqrt(2) / sigma);
        temp_yy = erf((yy + 0.5 - coord_list(i, 2)) / sqrt(2) / sigma) -...
            erf((yy - 0.5 - coord_list(i, 2)) / sqrt(2) / sigma);
        
        grad_I = sum((mu - im) ./ (mu + 1e-5) .* temp_xx(:) .* temp_yy(:));
        
        % backtracking
        alpha = 0.5;
        epsilon = 1000;
        if grad_I > 0
            epsilon = min(epsilon, I_list(i) / grad_I);
        end
        df = -1e-6 * norm(grad_I) ^ 2;
        mu = A * I_list + bg;
        fc = sum(mu - im .* log(mu + 1e-5));
        
        I = I_list(i) - epsilon * grad_I;
        mu_base = A(:, [1 : i - 1, i + 1 : end]) * I_list([1 : i - 1, i + 1 : end], :);
        mu = mu_base + A(:, i) * I + bg;
        
        while sum(mu - im .* log(mu + 1e-5)) > fc + epsilon * df
            epsilon = epsilon * max(alpha, 0.1);
            alpha = alpha * 0.8;
            if epsilon < 1e-10
                epsilon = 0;
                break;
            end
            I = I_list(i) - epsilon * grad_I;
            mu = mu_base + A(:, i) * I + bg;
        end
        I_list(i) = I_list(i) - epsilon * grad_I;
        %% x y coord descent
        mu = A * I_list + bg;
        
        d_mu_x = I_list(i) / (2 * sqrt(2 * pi) * sigma) *...
            (exp(-(xx - 0.5 - coord_list(i, 1)) .^ 2 / (2 * sigma ^ 2)) -...
            exp(-(xx + 0.5 - coord_list(i, 1)) .^ 2 / (2 * sigma ^ 2))) .* temp_yy;
        d_mu_y = I_list(i) / (2 * sqrt(2 * pi) * sigma) * temp_xx .*...
            (exp(-(yy - 0.5 - coord_list(i, 2)) .^ 2 / (2 * sigma ^ 2)) -...
            exp(-(yy + 0.5 - coord_list(i, 2)) .^ 2 / (2 * sigma ^ 2)));
        
        grad_xy = [sum((mu - im) ./ (mu + 1e-5) .* d_mu_x(:)),...
            sum((mu - im) ./ (mu + 1e-5) .* d_mu_y(:))];
        
        % backtracking
        alpha = 0.5;
        epsilon = 1e-1;
        df = -1e-6 * norm(grad_xy) ^ 2;
        mu = A * I_list + bg;
        fc = sum(mu - im .* log(mu + 1e-5));
        
        coord = coord_list(i, :) - epsilon * grad_xy;
        mu_base = A(:, [1 : i - 1, i + 1 : end]) * I_list([1 : i - 1, i + 1 : end], :);
        meas_col = 1 / 4 *...
            (erf((xx_r + 0.5 - coord(1)) / sqrt(2) / sigma) -...
            erf((xx_r - 0.5 - coord(1)) / sqrt(2) / sigma)) .*...
            (erf((yy_r + 0.5 - coord(2)) / sqrt(2) / sigma) -...
            erf((yy_r - 0.5 - coord(2)) / sqrt(2) / sigma));
        mu = mu_base + meas_col * I_list(i) + bg;
        
        while sum(mu - im .* log(mu + 1e-5)) > fc + epsilon * df
            epsilon = epsilon * max(alpha, 0.1);
            alpha = alpha * 0.8;
            if epsilon < 1e-10
                epsilon = 0;
                meas_col = A(:, i);
                break;
            end
            coord = coord_list(i, :) - epsilon * grad_xy;
            meas_col = 1 / 4 *...
                (erf((xx_r + 0.5 - coord(1)) / sqrt(2) / sigma) -...
                erf((xx_r - 0.5 - coord(1)) / sqrt(2) / sigma)) .*...
                (erf((yy_r + 0.5 - coord(2)) / sqrt(2) / sigma) -...
                erf((yy_r - 0.5 - coord(2)) / sqrt(2) / sigma));
            mu = mu_base + meas_col * I_list(i) + bg;
        end
        A(:, i) = meas_col;
        coord_list(i, :) = coord_list(i, :) - epsilon * grad_xy;
    end
    
    if iter > 1 && res_list(iter - 1) - res_list(iter) < 1e-2
        break;
    end
    iter = iter + 1;
end

..

function im = Gen_Im_From_2D_Coord(coord_list, I_list, height, width, sigma)
% PURPOSE:
% Generate image based on input emitter coordinate and intensity.
%---------------------------------------------------
% USAGE:
% im = Gen_Im_From_Coord(coord_list, I_list, height, width, sigma)
%---------------------------------------------------
% INPUTS:
% coord_list:   list of input coordinate
% I_list:       list of input intensity
% height:       image height
% width:        image width
% sigma:        standard deviation of system PSF (pixel)
%---------------------------------------------------
% OUTPUTS:
% im:           generated image
%---------------------------------------------------
[xx, yy] = meshgrid(1 : width, 1 : height);
xx_r = xx(:); yy_r = yy(:);
im = zeros(height * width, 1);
% iterate through all input coordinate
for i = 1 : size(coord_list, 1)
    % generate measurement on a given point
    im = im + I_list(i) / 4 *...
        (erf((xx_r + 0.5 - coord_list(i, 1)) / sqrt(2) / sigma) -...
        erf((xx_r - 0.5 - coord_list(i, 1)) / sqrt(2) / sigma)) .*...
        (erf((yy_r + 0.5 - coord_list(i, 2)) / sqrt(2) / sigma) -...
        erf((yy_r - 0.5 - coord_list(i, 2)) / sqrt(2) / sigma));
end

...

function A = Gen_Meas_From_2D_Coord(coord_list, height, width, sigma)
% PURPOSE:
% Generate measurement matrix based on input emitter coordinate.
%---------------------------------------------------
% USAGE:
% A = Gen_Meas_From_2D_Coord(coord_list, height, width, sigma)
%---------------------------------------------------
% INPUTS:
% coord_list:   list of input coordinate
% height:       image height
% width:        image width
% sigma:        standard deviation of system PSF (pixel)
%---------------------------------------------------
% OUTPUTS:
% A:            generated measurement matrix
%---------------------------------------------------
[xx, yy] = meshgrid(1 : width, 1 : height);
xx_r = xx(:); yy_r = yy(:);
A = zeros(height * width, size(coord_list, 1));
% iterate through all input coordinate
for i = 1 : size(coord_list, 1)
    % generate measurement on a given point
    A(:, i) = 1 / 4 *...
        (erf((xx_r + 0.5 - coord_list(i, 1)) / sqrt(2) / sigma) -...
        erf((xx_r - 0.5 - coord_list(i, 1)) / sqrt(2) / sigma)) .*...
        (erf((yy_r + 0.5 - coord_list(i, 2)) / sqrt(2) / sigma) -...
        erf((yy_r - 0.5 - coord_list(i, 2)) / sqrt(2) / sigma));
end

Bruno Luong 2022-8-17

编辑：Bruno Luong 2022-8-17

Your code is too long for me to look in detail. I notice that the code is not even optimized (growing array, call function in the loop, some common calculation is repeated, some constant quantity is computed inside the loop, etc...)

My recommendation is working on your matlab code before feed it to the coder.

zhou caiwei 2022-8-18

you are right, I think I should optimize my code.Is there any reference materials?

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Answer 2

Raghu Boggavarapu 2022-8-25

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https://ww2.mathworks.cn/matlabcentral/answers/1779525-matlab-coder-report-size-mismatch-size-0-x-0-size-1-x-2#answer_1033370

Hi,

MATLAB Coder supports growing an array only by concatenation, growing an array by index is not supported. Please see: https://in.mathworks.com/help/coder/ug/limitations-with-variable-size-support-for-code-generation.html

If you wish to assign varying sized arrays to same variable, you can use coder.varize .

Also if you would like to optimize the MEX runtime, you can try disabling IntegrityChecks and ResponsivenessChecks in the MEX coder config.

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Chiluveru 2023-2-13

need help to solve the above error

Walter Roberson 2023-2-13

You are assigning an empty array with 16 rows to a variable that was first assigned an empty array with one row.

When you use MATLAB Function Blocks in Simulink, then unless you use coder.varsize then the first assignment to a variable sets the limits on how large the variable is. This is different from regular MATLAB as regular MATLAB adjusts sizes as needed.

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matlab coder report Size mismatch (size [0 x 0] ~= size [1 x 2])

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matlab coder report Size mismatch (size [0 x 0] ~= size [1 x 2])

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