Problem with "Reshape"
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Hi! This might be a hard question to explain, but will do my best.
We constantly get this error message:
Error using reshape
To RESHAPE the number of elements must not change.
Error in DREAM_initialize
Error in DREAM
Error in runDREAM_4 (line 1231)
[chain,output,fx] = DREAM(Func_name,DREAMPar,Par_info,Meas_info,options);
The script "Dream" calibrates parameters for another function. We have tried to transpose our data so it should fit, but this does not help.
Our code look like this:
if example == 20, % Fit the van Genuchten solution of the contaminant transport equation to measured data (Derived from Example 4)
% Problem specific parameter settings
DREAMPar.d = 3; % Dimension of the problem
DREAMPar.N = 10; % Number of Markov chains
DREAMPar.T = 500; % Number of generations
DREAMPar.lik = 11; % Gaussian likelihood with measurement integrated out (see file
% Calc_density.m and Table 2, p. 29 of DREAM manual for reference)
options.modout = 'yes'; % Return model (function) simulations of samples Yes or No)?
% Define modelName
Func_name = 'WaterqualityStr4_fit';
% Give the parameter ranges (minimum and maximum values). [v DD tp]
Par_info.min = [10 0 0 1 0 0 1];
Par_info.max = [60 2e5 5e5 1e7 2e5 5e5 1e7];
Par_info.initial = 'latin'
Par_info.boundhandling = 'reflect'; % Explicit boundary handling
% Load the experimental data
load dataAssignment_04.mat;
fieldnames(dataChassieu);
global file
file = dataChassieu;
% Define constant input parameters
global Extra
%Extra.Q=[(dataChassieu(1).flow)';(dataChassieu(2).flow)';(dataChassieu(3).flow)';(dataChassieu(4).flow)';(dataChassieu(5).flow)';(dataChassieu(6).flow)';(dataChassieu(7).flow)';(dataChassieu(8).flow)';(dataChassieu(9).flow)'];
Extra.Q=(dataChassieu(1).flow)'
%Extra.q=q;
Extra.t=(dataChassieu(1).time)';
Extra.distPuls_1=2e5; % distPuls_1
Extra.injMass_1=5e5; % injMass_1
Extra.D_1=1e7; % D_1
Extra.distPuls_2=2e5;% distPuls_2
Extra.injMass_2=5e5; % injMass_1
Extra.D_2=1e7; % D_1
% Define the measured concentrations
%Meas_info.Y=[(dataChassieu(1).TSS)';(dataChassieu(2).TSS)';(dataChassieu(3).TSS)';(dataChassieu(4).TSS)';(dataChassieu(5).TSS)';(dataChassieu(6).TSS)';(dataChassieu(7).TSS)';(dataChassieu(8).TSS)';(dataChassieu(9).TSS)'];
Meas_info.Y=dataChassieu(1).TSS';
%Extra.flow = dataChassieu(1).flow;
% Run the DREAM algorithm
[chain,output,fx] = DREAM(Func_name,DREAMPar,Par_info,Meas_info,options);
% Post-processing
addpath('PostProcessing')
DREAM_postproc
% Modify labels Note these lines would be better placed in the file postprocMCMC.m
% but are included here to make things easier for the students.
figure(10) % select figure 10
xlabel('time [s]','fontsize',14,'fontweight','bold','fontname','bold','fontname','times');
ylabel('concentration [mg/L]','fontsize',14,'fontweight','bold','fontname','bold','fontname','times');
legend('95% confidence bounds (total uncertainity)','analytical solution (parameter uncertainty)','experimental data');
close(11); %close graph on residual autocorrelation (not needed for course)
close(12); %close graph on QQ posterior vs normal distribution (not needed for the course)
end
% Create a single matrix with values sampled by chains
ParSet = GenParSet(chain);
The function, "WaterqualityStr4_fit" looks like this:
function cvG = WaterqualityStr4_fit(Par,file,Extra)
global file
global Extra
%All par values have been changed from Pars to Par
% parameters to be fitted - based on the results from Morris we the most
% important parameters where 1. TSS_back, 2. injMass_2 and 3. D_2
TSS_back=Par(1); %TSS_back - background concentration
distPuls_1=Par(2);
injMass_1=Par(3);
D_1=Par(4);
distPuls_2=Par(5);
injMass_2=Par(6);% injMass_2
D_2=Par(7);% D_2
% Other function parameters passed through the Extra global variable
global Extra
Extra.dt=1;
Extra.flow = file(1).flow;
% distPuls_1=Extra.distPuls_1; % distPuls_1
% injMass_1=Extra.injMass_1; % injMass_1
% D_1=Extra.D_1; % D_1
% distPuls_2=Extra.distPuls_2;% distPuls_2
%
%%inserted from WaterqualityStr4
%%define additional data and information
%Q=Extra.flow; % measured flow [m3/s]
t=(1:length(Extra.Q))*Extra.dt*60; % time vector [min]->[s]
num_pulses=(length(Par)-1)/3; % the number of injections in the sewer system, it is a predefined number.
%%define function parameters
TSS_back=Par(1); % [g/m3] baseline TSS concentration
% inizialize parameter vectors
distPuls =nan(num_pulses,1); % [m] distance from TSS point of injection
injMass=nan(num_pulses,1); % [g] TSS mass injected
dispCoef=nan(num_pulses,1); % [m2/s] dispersion coefficient
for i=1:num_pulses
distPuls(i)=Par(1+i);
injMass(i)=Par(1+num_pulses+i);
dispCoef(i)=Par(1+2*num_pulses+i);
end
%%Hydraulic variables (used for transport)
% calculate water level based on Q-h relationship
h=0.0146883323.*((Extra.Q*1e3).^0.4678812104) ; % [m] wather depth, regression for Chassieu (calculated using Q in l/s)
D=1.6; % [m] diameter fo the pipeline
theta=acos(1-2*mean(h)./D); % [radians] angle of wet area (average)
A=(D^2)/4*(theta-sin(2*theta)/2); % [m2] wet area
u=nanmean(Extra.Q/A); % [m/s] mean velocity
%%calculate TSS transport (based on diffusion-advection equation in one dimensional flows
TSSconc=zeros(num_pulses,length(Extra.Q)); % a TSS profile for each injection
for i=1:num_pulses
for j=1:length(t)
TSSconc(i,j)=injMass(i)/(4*A*pi()*dispCoef(i)*t(j))^.5 * ...
exp(-(distPuls(i)-u*t(j))^2/(4*dispCoef(i)*t(j)));
end
end
%%overlap TSS curves and add background concentrations
cvG=sum(TSSconc,1)+TSS_back;
end
Sorry for the long post! I hope somebody is able to help us out! Can anybody figure out what we are doing wrong?
Kind Regards Ida
6 commentaires
Rik
le 27 Nov 2017
The fact it has over 1200 lines makes me shiver straight away though!
@Adam, I have one script that is about 1750 lines (including comments and white space), and another that is even almost 4000 lines (including comments and white space). Long files aren't a problem, keeping your functions reasonably short is the goal. Although I must admit that last one is on the edge of not being manageable anymore. (the first has 23 functions inside 1 file, the later 33)
A huge file can also be an artifact of copying older versions of a function when updating. A function name of runDREAM_4 makes me suspect this might be the case.
(and yes, I know there's an important difference between script, function, and file, but I like to use script and file interchangeably)
Adam
le 27 Nov 2017
Modifié(e) : Adam
le 27 Nov 2017
Well, yes, now that scripts can have sub-functions, which they couldn't until recently, it is possible to have a > 1000 line script file that isn't a complete mess!
If it is just 1200+ lines of pure script though without sub-functions that really is unpleasant!
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