How to fix issue with error using surf: Z must be a matrix, not a scalar or vector

Question

Rebeca Hannah Oliveira 2023-11-20

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评论： Rebeca Hannah Oliveira 2023-11-20

How can I fix the code to avoid the error: error using surf: Z must be a matrix, not a scalar or vector

I tried converting it to matrix format using cell2mat, but then I can't refer to the correct position of terms to plot on the surface. Is there an alternative way?

numODEs =3;

numParams=3;

% Parameters

parameters = rand(1, numParams); % Initialize parameters with random values

% Initial conditions

initial_conditions = rand(1, numODEs);

% Time span for simulation

tspan = [0 10];

% Set variation range based on a percentage of original parameters

min_variation_factor = 0.1;

max_variation_factor = 10;

variation_range = linspace(min_variation_factor, max_variation_factor, 5);

% Store results

balance_results = cell(numParams, numParams);

% Explore parameter balance for all combinations

for i = 1:numParams

for j = 1:numParams

% Perturb parameters based on variation_range

perturbed_params = parameters;

perturbed_params(i) = perturbed_params(i) * variation_range(1);

perturbed_params(j) = perturbed_params(j) * variation_range(2);

% Solve ODE system with perturbed parameters using ode15s

[~, Y_perturbed] = ode15s(@ode_system, tspan, initial_conditions, [], perturbed_params);

% Check if the solution compensates for variations

balance_results{i, j} = max(Y_perturbed, [], 1); % Adjust based on your specific measure

end

balance_results{1, 3}(:, 1)

ans = 0.8496

% Visualize parameter balance

figure;

for k = 1:numODEs

subplot(ceil(sqrt(numODEs)), ceil(sqrt(numODEs)), k);

colormap(parula(numParams^2));

for i = 1:numParams

for j = 1:numParams

surf(variation_range(1), variation_range(2), balance_results{i, j}(:, k)', 'FaceColor', 'interp', 'EdgeColor', 'none');

hold on;

end

xlabel('Variation in Parameter 1');

ylabel('Variation in Parameter 2');

zlabel(['Max Output for ODE ', num2str(k)]);

title(['Balance Exploration for ODE ', num2str(k)]);

view(-45, 30); % Adjust the view for better visibility

hold off;

end

Error using surf
Z must be a matrix, not a scalar or vector.

function dydt = ode_system(t, y, parameters)

% ODE system representing binding reactions (modify based on your specific system)

dydt = zeros(size(y));

% Parameters

k1 = parameters(1);

k2 = parameters(2);

k3 = parameters(3);

dydt(1) = -k1 * y(1) * y(2); % Example binding reaction

dydt(2) = k1 * y(1) * y(2) - k2 * y(2); % Example binding and unbinding reaction

dydt(3) = k2 * y(2) - k3 * y(3); % Example unbinding reaction

% Define the ODEs (modify based on your specific system)

% Example: dydt(1) = -parameters(1) * y(1) * y(2);

% Modify the code based on the structure of your ODE system

end

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Dyuman Joshi 2023-11-20

How do you plan to plot a surface where the data you have is scalar? You can't even plot a line with a single point.

What are you trying to do? What is the objective here?

Rebeca Hannah Oliveira 2023-11-20

编辑：Rebeca Hannah Oliveira 2023-11-20

在 MATLAB Online 中打开

Thank you! My goal is to get something like in the code below (which was specific for three ODEs and 3 parameters), but generalized to any number n of ODEs and parameters p. I want to generate n figures, each with p subplots that are surface plots showing what happens to the output of the ODEs when two parameters are varied within a range.

% function explore_parameter_balance_binding_reactions()

% Number of ODEs and parameters

numODEs = 3;

numParams = 3;

% Parameters

parameters = rand(1, numParams); % Initialize parameters with random values

% Initial conditions

initial_conditions = rand(1, numODEs);

% Time span for simulation

tspan = [0 10];

% Set variation range based on a percentage of original parameters

min_variation_factor = 0.1;

max_variation_factor = 10;

variation_range = linspace(min_variation_factor, max_variation_factor, 5);

% Store results

balance_results_1_2 = zeros(length(variation_range), length(variation_range), numODEs);

balance_results_1_3 = zeros(length(variation_range), length(variation_range), numODEs);

balance_results_2_3 = zeros(length(variation_range), length(variation_range), numODEs);

% Explore parameter balance for all combinations

for i = 1:length(variation_range)

for j = 1:length(variation_range)

% Perturb parameters based on variation_range

parameters_perturbed_1_2 = parameters .* [variation_range(i), variation_range(j), 1];

parameters_perturbed_1_3 = parameters .* [variation_range(i), 1, variation_range(j)];

parameters_perturbed_2_3 = parameters .* [1, variation_range(i), variation_range(j)];

% Solve ODE system with perturbed parameters using ode15s

[~, Y_perturbed_1_2] = ode15s(@ode_system, tspan, initial_conditions, [], parameters_perturbed_1_2);

[~, Y_perturbed_1_3] = ode15s(@ode_system, tspan, initial_conditions, [], parameters_perturbed_1_3);

[~, Y_perturbed_2_3] = ode15s(@ode_system, tspan, initial_conditions, [], parameters_perturbed_2_3);

% Check if the solution compensates for variations

balance_results_1_2(i, j, :) = max(Y_perturbed_1_2, [], 1); % Adjust based on your specific measure

balance_results_1_3(i, j, :) = max(Y_perturbed_1_3, [], 1);

balance_results_2_3(i, j, :) = max(Y_perturbed_2_3, [], 1);

end

% Visualize parameter balance for parameters 1 and 2

figure;

for k = 1:numODEs

subplot(ceil(sqrt(numODEs)), ceil(sqrt(numODEs)), k);

surf(variation_range, variation_range, squeeze(balance_results_1_2(:, :, k))');

xlabel('Variation in Parameter 1');

ylabel('Variation in Parameter 2');

zlabel(['Max Output for ODE ', num2str(k)]);

title(['Balance Exploration for ODE ', num2str(k), ' (Params 1 and 2)']);

end

sgtitle('Parameter Balance Exploration for Binding Reactions (Params 1 and 2)');

% Visualize parameter balance for parameters 1 and 3

figure;

for k = 1:numODEs

subplot(ceil(sqrt(numODEs)), ceil(sqrt(numODEs)), k);

surf(variation_range, variation_range, squeeze(balance_results_1_3(:, :, k))');

xlabel('Variation in Parameter 1');

ylabel('Variation in Parameter 3');

zlabel(['Max Output for ODE ', num2str(k)]);

title(['Balance Exploration for ODE ', num2str(k), ' (Params 1 and 3)']);

end

sgtitle('Parameter Balance Exploration for Binding Reactions (Params 1 and 3)');

% Visualize parameter balance for parameters 2 and 3

figure;

for k = 1:numODEs

subplot(ceil(sqrt(numODEs)), ceil(sqrt(numODEs)), k);

surf(variation_range, variation_range, squeeze(balance_results_2_3(:, :, k))');

xlabel('Variation in Parameter 2');

ylabel('Variation in Parameter 3');

zlabel(['Max Output for ODE ', num2str(k)]);

title(['Balance Exploration for ODE ', num2str(k), ' (Params 2 and 3)']);

end

sgtitle('Parameter Balance Exploration for Binding Reactions (Params 2 and 3)');

% end

function dydt = ode_system(t, y, parameters)

% ODE system representing binding reactions (modify based on your specific system)

dydt = zeros(size(y));

% Parameters

k1 = parameters(1);

k2 = parameters(2);

k3 = parameters(3);

% Define the ODEs (modify based on your specific system)

dydt(1) = -k1 * y(1) * y(2); % Example binding reaction

dydt(2) = k1 * y(1) * y(2) - k2 * y(2); % Example binding and unbinding reaction

dydt(3) = k2 * y(2) - k3 * y(3); % Example unbinding reaction

end

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Answer 1

Pratyush 2023-11-20

1
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2049412-how-to-fix-issue-with-error-using-surf-z-must-be-a-matrix-not-a-scalar-or-vector#answer_1356407

在 MATLAB Online 中打开

Hi Rebecca,

I understand that you are getting an error using the "surf" function in your script.

You could use "meshgrid" function to resolve the error. To fix this, you need to create a meshgrid of "variation_range(1)" and "variation_range(2)" to use as the X and Y inputs for the "surf" function. Then you can use the "meshgrid" function to create the grid and then plot the surfaces accordingly. Here's how you can modify your code:

% Visualize parameter balance
figure;
for k = 1:numODEs
    subplot(ceil(sqrt(numODEs)), ceil(sqrt(numODEs)), k);
    colormap(parula(numParams^2));
    [X, Y] = meshgrid(variation_range, variation_range);
    for i = 1:numParams
        for j = 1:numParams
            Z = balance_results{i, j}(:, k)';
            surf(X, Y, reshape(Z, size(X)), 'FaceColor', 'interp', 'EdgeColor', 'none');
            hold on;
        end
    end
    xlabel('Variation in Parameter 1');
    ylabel('Variation in Parameter 2');
    zlabel(['Max Output for ODE ', num2str(k)]);
    title(['Balance Exploration for ODE ', num2str(k)]);
    view(-45, 30); % Adjust the view for better visibility
    hold off;
end

I hope this should resolve the error.

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Dyuman Joshi 2023-11-20

在 MATLAB Online 中打开

There's an error when I try to run the code with your suggestion -

numODEs =3;

numParams=3;

% Parameters

parameters = rand(1, numParams); % Initialize parameters with random values

% Initial conditions

initial_conditions = rand(1, numODEs);

% Time span for simulation

tspan = [0 10];

% Set variation range based on a percentage of original parameters

min_variation_factor = 0.1;

max_variation_factor = 10;

variation_range = linspace(min_variation_factor, max_variation_factor, 5);

% Store results

balance_results = cell(numParams, numParams);

% Explore parameter balance for all combinations

for i = 1:numParams

for j = 1:numParams

% Perturb parameters based on variation_range

perturbed_params = parameters;

perturbed_params(i) = perturbed_params(i) * variation_range(1);

perturbed_params(j) = perturbed_params(j) * variation_range(2);

% Solve ODE system with perturbed parameters using ode15s

[~, Y_perturbed] = ode15s(@ode_system, tspan, initial_conditions, [], perturbed_params);

% Check if the solution compensates for variations

balance_results{i, j} = max(Y_perturbed, [], 1); % Adjust based on your specific measure

end

balance_results{1, 3}(:, 1)

ans = 0.3748

% Visualize parameter balance

figure;

for k = 1:numODEs

subplot(ceil(sqrt(numODEs)), ceil(sqrt(numODEs)), k);

colormap(parula(numParams^2));

[X, Y] = meshgrid(variation_range, variation_range);

for i = 1:numParams

for j = 1:numParams

Z = balance_results{i, j}(:, k)';

surf(X, Y, reshape(Z, size(X)), 'FaceColor', 'interp', 'EdgeColor', 'none');

hold on;

end

xlabel('Variation in Parameter 1');

ylabel('Variation in Parameter 2');

zlabel(['Max Output for ODE ', num2str(k)]);

title(['Balance Exploration for ODE ', num2str(k)]);

view(-45, 30); % Adjust the view for better visibility

hold off;

end

Error using reshape
Number of elements must not change. Use [] as one of the size inputs to automatically calculate the appropriate size for that dimension.

function dydt = ode_system(t, y, parameters)

% ODE system representing binding reactions (modify based on your specific system)

dydt = zeros(size(y));

% Parameters

k1 = parameters(1);

k2 = parameters(2);

k3 = parameters(3);

dydt(1) = -k1 * y(1) * y(2); % Example binding reaction

dydt(2) = k1 * y(1) * y(2) - k2 * y(2); % Example binding and unbinding reaction

dydt(3) = k2 * y(2) - k3 * y(3); % Example unbinding reaction

% Define the ODEs (modify based on your specific system)

% Example: dydt(1) = -parameters(1) * y(1) * y(2);

% Modify the code based on the structure of your ODE system

end

Rebeca Hannah Oliveira 2023-11-20

Pratyush, thank you. It is returning an error with reshape, though. Can you help again?

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How to fix issue with error using surf: Z must be a matrix, not a scalar or vector

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