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Make curve fitting faster

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Marek Dostal
Marek Dostal on 24 Nov 2018
Edited: Matt J on 21 Jun 2019
Hi,
I would like to make my curve fitting faster by using GPU. Is it possible? If yes how?
Thanks
  1 Comment
Matt J
Matt J on 25 Mar 2019
Marek's problem description copied here for reference:
I have MRI data of brain (each subject has approx. 0,5 mil voxels) with 10 different parameters and I want to in each voxel fit this 10 points by specific biexponencial curve (so I receive parametric maps of brain). I tried to optimize the script before I used parallel computing (1 brain ~4 hours) but I used only parfor (~1,25 hours) and because I am still beginner with Matlab I was curious if other users have experience with GPU and can help me make this faster than parfor.
Thanks
Marek

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Accepted Answer

Matt J
Matt J on 26 Nov 2018
Edited: Matt J on 21 Jun 2019
I want to in each voxel fit this 10 points by specific biexponencial curve (so I receive parametric maps of brain)
@Marek,
Do not fit one voxel at a time in a loop. Instead, write the model as an N-dimensional curve where N is the number of voxels and apply lsqcurvefit to this model. Do not let lsqcurvefit use its default finite difference derivative calculations. Instead, supply your own Jacobian*x operator using the JacobianMultiplyFcn option (EDIT: or provide a sparse block diagonal Jacobian matrix computation).
Your problem is a good example of what I was discussing with Joss: both the model function and the JacobianMultiplyFcn could be GPU-optimized if lsqcurvefit could work with gpuArray variables without constantly doing GPU/CPU transfers. However, I expect the fit will still be reasonably fast if you use appropriate Matlab vectorization techniques.
  16 Comments
sarah goldberg
sarah goldberg on 6 May 2019
Hi Matt,
I've been trying to generalize the ND Jacobian solution, with Jacobian not calculated/calculated/only Jacobian multiply calculated. The Jacobian multiply option is currently not working.
Here k is the number of 1D fits with n points and p parameters, N=n x k, P=p x k. Jacobian size is indeed (N x P) - I checked the output of lsqcurvefit.
I'm running into the following issue with the Jacobian multiply function (myJ): the size of the input vector Y is either (Nx1) or (Px1) or (Px2). How is this possible?
Code below. I am simply looking at
size(Y)
Thanks,
Sarah
clear all; close all; fclose all; clc;
s=rng('shuffle');
rng(828016308,'twister');
global history;
history=[];
% plot
doPlot=false; %true;
num_plot=4; % how many fits to plot
% fit params
alg='trust-region-reflective' ; % 'trust-region-reflective' or 'levenberg-marquardt'
displaySetting='off'; % 'iter', 'off', 'final', etc.
maxIter=1e5;
maxFunEvals=1e5;
tolfun=1e-6;
% options
opts = optimoptions('lsqcurvefit','MaxIter',maxIter,'MaxFunEvals',maxFunEvals,'OutputFcn', @myoutput,'display',displaySetting,'Algorithm',alg,'tolfun',tolfun);
optsJ = optimoptions('lsqcurvefit','MaxIter',maxIter,'MaxFunEvals',maxFunEvals,'OutputFcn', @myoutput,'display',displaySetting,'Algorithm',alg,'tolfun',tolfun,'Jacobian','on');
optsJm = optimoptions('lsqcurvefit','MaxIter',maxIter,'MaxFunEvals',maxFunEvals,'OutputFcn', @myoutput,'display',displaySetting,'Algorithm',alg,'tolfun',tolfun,'SpecifyObjectiveGradient',true,'JacobianMultiplyFcn',@(Jinfo,Y,flag,xdata)myJ(Jinfo,Y,flag));
% THE MODEL. generate function handles for evaluating f (f_func) and its partial derivatives (dfdp_func).
[f_func,dfdp_func,num_params]=sym_model_derivatives();
% general 2D model
num_g=2; % number of gaussians
npoints=[3,5]; % image size [r,c]=[y,x], ROI intentionally not symmetric for debugging
min_width=1; % so we don't have sigma==0
a0=30;
a_std=1;
mu_std=0.1;
sigma0=[2,1]; % be careful, do not make these too small!
sigma_std=0.1;
theta=0*(pi/180); % in radians
theta_std=10*(pi/180);
bg=10;
bg_std=5;
mu0=npoints/2; % place gaussians roughly at center
im=zeros(npoints);
% generate data: num_g images of size(im)
ims=zeros(num_g,size(im,1),size(im,2)); % image set size
mus=mu0'*ones(1,num_g) + mu_std*randn(2,num_g); % 1 per dimension
sigmas=sigma0'*ones(1,num_g) + sigma_std*randn(2,num_g); % 1 per dimension
as=a0 + a_std*randn(1,num_g); % 1 per gaussian
sigmas(sigmas<0.1)=min_width; % to avoid division by 0
thetas=theta+theta_std*randn(1,num_g);
bgs=bg+bg_std*randn(1,num_g);
[X,Y]=meshgrid(1:size(im,2),1:size(im,1)); % x-y coordinates - weird order so that data can be reshaped correctly
x_ind=X(:); % x, column vector
y_ind=Y(:); % y, column vector
for mm=1:num_g
% parameter order: %Amplitude % Row (y) % Col (x) % Theta -3* 3* % Sigma_row (y) % Sigma_col (x) % Background
c0s(mm,:)=[as(mm) mus(2,mm) mus(1,mm) thetas(mm) sigmas(2,mm) sigmas(1,mm) bgs(mm)];
ims(mm,:)=model_func(c0s(mm,:),x_ind,y_ind,f_func); % 1D vector per 2D plot
end
% guesses
guesses=zeros(num_g,num_params);
% parameter order: %Amplitude % Row % Col % Theta -3* 3* % Sigma_row % Sigma_col % Background
for mm=1:num_g
[maxval,~]=max(ims(mm,:));
tmp_im=reshape(ims(mm,:)',size(im,1),size(im,2));
[xpos,ypos]=find(tmp_im==maxval);
[~,half_x]=min(abs(tmp_im(ypos,:) - maxval/2));
[~,half_y]=min(abs(tmp_im(:,xpos) - maxval/2));
guesses(mm,:)=[maxval xpos ypos 0 (abs(half_x(1)-xpos)+min_width) (abs(half_y(1)-ypos)+min_width) 0]; % adding something small to avoid 0
end
%% N x 2D - setup
im_data=zeros(num_g,prod(size(im)));
xdata=kron(ones(1,num_g),x_ind)';
ydata=kron(ones(1,num_g),y_ind)';
guesses_ND=zeros(num_g,num_params);
% images
for mm=1:num_g
im_data(mm,:)=ims(mm,:);
end
% guesses
guesses_ND=guesses;
%% N x 2D
history=[];
results_ND=zeros(num_g,num_params);
fprintf(1,['\n']);
tic
f_ND = @(c,xdata)model_func_ND(c,xdata,ydata,f_func); % need to pass x_ind, y_ind to model_func
[results_ND,resnormN,residualN,exitflagN,outputN,lambdaN,jacobianN]=lsqcurvefit(f_ND,guesses_ND,xdata,im_data,[],[],opts); % each row is 1 object
toc
fprintf(1,['Nx2D\n']);
resnormN
historyN=history;
exitflagN
%% N x 2D + Jacobian
results_ND_J=zeros(num_g,num_params);
fprintf(1,['\n']);
tic
f_ND = @(c,xdata)model_func_ND_J(c,xdata,ydata,f_func,dfdp_func); % need to pass args x_ind, y_ind, etc. to model_func
[results_ND_J,resnormN_J,residualN_J,exitflagN_J,outputN_J,lambdaN_J,jacobianN_J]=lsqcurvefit(f_ND,guesses_ND,xdata,im_data,[],[],optsJ); % each row is 1 object
toc
fprintf(1,['Nx2D + Jacobian\n']);
resnormN_J
exitflagN_J
%% N x 2D + Jacobian multiply
history=[];
results_ND_J=zeros(num_g,num_params);
fprintf(1,['\n']);
tic
f_ND = @(c,xdata)model_func_ND_Jm(c,xdata,ydata,f_func,dfdp_func); % need to pass args x_ind, y_ind, etc. to model_func
[results_ND_Jm,resnormN_Jm,residualN_Jm,exitflagN_Jm,outputN_Jm,lambdaN_Jm,jacobianN_Jm]=lsqcurvefit(f_ND,guesses_ND,xdata,im_data,[],[],optsJm); % each row is 1 object
toc
fprintf(1,['Nx2D + Jacobian multiply\n']);
resnormN_Jm
historyNm=history;
exitflagN_Jm
return
%% ----- functions -------
% model:
% f = Amplitude*.*exp(- ( A*(x-Col).^2 + 2*B*(x-Col).*(y-Row) + C*(y-Row).^2 ) ) + Background
% A = cos(Theta)^2/(2*Sigma_col) + sin(Theta)^2/(2*Sigma_row)
% B = sin(2*Theta) * (1/Sigma_row^2 - 1/Sigma_col^2)/4;
% C = sin(Theta)^2/(2*Sigma_col) + cos(Theta)^2/(2*Sigma_row);
% parameter order: %Amplitude % Row % Col % Theta -3* 3* % Sigma_row % Sigma_col % Background
function [f_func,df,num_params]=sym_model_derivatives()
num_params=7;
p=sym('p',[1 num_params]);
syms f x y A B C tmp_df;
% model definition HERE
A=cos(p(4))^2/(2*p(6)^2) + sin(p(4))^2/(2*p(5)^2);
B=sin(2*p(4)) * (1/p(5)^2 - 1/p(6)^2)/4;
C=sin(p(4))^2/(2*p(6)^2) + cos(p(4))^2/(2*p(5)^2);
f = p(1)*exp(- ( A*(x-p(3))^2 + 2*B*(x-p(3))*(y-p(2)) + C*(y-p(2))^2 ) ) + p(7);
% end of model definition
vars=[p x y];
for ii=1:length(p)
tmp_df=diff(f,p(ii));
% convert dfdp to matlab function
df{ii}=matlabFunction(tmp_df,'vars',vars);
end
% convert f to matlab function
f_func=matlabFunction(f,'vars',vars);
end
% 2D model - used to generate data
function [f]=model_func(p,x,y,f_func)
p_list=num2cell(p); % to avoid p(1),p(2),...,p(n) argument passing
f=f_func(p_list{:},x,y);
end
% Nx2D model
function [f]=model_func_ND(c,x,y,f_func)
G_n=size(x,2); % number of data points
G_k=size(x,1); % number of fits
f = zeros(G_k, G_n);
for ff=1:G_k
xp=x(ff,:); % points for this fit (n)
yp=y(ff,:);
cp=c(ff,:); % params for this fit (m)
cp_list=num2cell(cp);
% f
f(ff,:)=f_func(cp_list{:},xp,yp);
end
end
% Nx2D + Jinfo model
function [f,Jinfo]=model_func_ND_info(c,x,y,f_func)
G_n=size(x,2); % number of data points
G_k=size(x,1); % number of fits
f = zeros(G_k, G_n);
for ff=1:G_k
xp=x(ff,:); % points for this fit (n)
yp=y(ff,:);
cp=c(ff,:); % params for this fit (m)
cp_list=num2cell(cp);
% f
f(ff,:)=f_func(cp_list{:},xp,yp);
end
G_p=numel(c)/G_k; % number of parameters per fit
Jinfo = spalloc(G_n*G_k, G_p*G_k, 0);
end
% Nx2D + Jacobian
function [f,J]=model_func_ND_J(c,x,y,f_func,dfdp_func)
G_n=size(x,2); % number of data points
G_k=size(x,1); % number of fits
G_p=numel(dfdp_func); % number of parameters per fit
f = zeros(G_k, G_n);
J = spalloc(G_n*G_k, G_p*G_k, G_n*G_k*G_p);
% calculate fit values and partial derivatives for each fit
for ff=1:G_k
xp=x(ff,:); % points for this fit (n)
yp=y(ff,:);
cp=c(ff,:); % params for this fit (m)
cp_list=num2cell(cp);
% f
f(ff,:)=f_func(cp_list{:},xp,yp);
% J
for pp=1:length(dfdp_func)
df=dfdp_func{pp}; % function handle of this partial derivative
J(ff:G_k:end , (pp-1)*G_k + ff) = df(cp_list{:},xp,yp);
% full(J)
end
%size(J)
end
end
% Nx2D + Jacobian multiply
function [f,Jinfo] = model_func_ND_Jm(c,xdata,ydata,f_func,dfdp_func)
global G_df_func G_P G_n G_k G_xd G_yd; % needed for jacobian multiply function
G_n=size(xdata,2); % number of data points
G_k=size(xdata,1); % number of fits
f = zeros(G_k, G_n);
for ff=1:G_k
xp=xdata(ff,:); % points for this fit (n)
yp=ydata(ff,:);
cp=c(ff,:); % params for this fit (m)
cp_list=num2cell(cp);
% f
f(ff,:)=f_func(cp_list{:},xp,yp);
end
% update globals
G_P=c; % parameters
G_p=numel(dfdp_func);% number of parameters per fit
G_xd=xdata; % indices
G_yd=ydata;
G_df_func=dfdp_func; % partial derivative function handles
% Jinfo sparse matrix for preconditioning, required even when jacobian
% multiply is used. size should equal the size of the jacobian.
Jinfo = spalloc(G_n*G_k, G_p*G_k, G_n*G_k*G_p); % all zeros
end
% compute Jacobian multiply functions.
% note: Jacobian C is sparse. the only nonzero elements are
% derivatives of points xi belonging to fit j
% with respect to their own fitting parameters. there positions within the
% jacobian can be viewed by looking at the jacobian generated in model_func_ND_J
% using the command full(J).
function w = myJ(Jinfo,Y,flag)
size(Y) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
global G_df_func G_P G_n G_k G_xd G_yd;
P=G_P;
n=G_n;
k=G_k;
xd=G_xd;
yd=G_yd;
df_func=G_df_func;
if flag > 0
w = Jpositive(Y, df_func,P,n,k,xd,yd);
elseif flag < 0
w = Jnegative(Y, df_func,P,n,k,xd,yd);
else
w1= Jpositive(Y, df_func,P,n,k,xd,yd);
w = Jnegative(w1,df_func,P,n,k,xd,yd);
end
function a = Jpositive(q,df_func,P,n,k,xd,yd)
% Calculate C*q (dimensions NxP, Px1 => Nx1)
a = zeros(n*k,1);
for ff=1:k % loop over fits, calculate n sums for each fit
xp=xd(ff,:); % points for this fit (n)
yp=yd(ff,:);
p=P(ff,:); % params for this fit (m)
qp=q(ff:k:end); % values of q for this fit (m)
sump=zeros(1,n);
for pp=1:numel(df_func)
df=df_func{pp}; % 1 of m function handles
p_list=num2cell(p);
dfp=df(p_list{:},xp,yp); % n partial derivatives (may have 1 value if derivative is a const)
sump=sump+qp(pp)*dfp; % add n terms for each of m params
end
a(ff:k:end)=sump'; % n terms
end
end
function a = Jnegative(q,df_func,P,n,k,xd,yd)
% Calculate C'*q (dimensions PxN, Nx1 => Px1)
a = zeros(prod(size(P)),1); % Px1
for ff=1:k % loop over fits, calculate 3 sums for 3 fit parameters
xp=xd(ff,:); % points for this fit (n)
yp=yd(ff,:);
p=P(ff,:); % params for this fit (m)
qp=q(ff:k:end); % part of input vector q that contributes for this fit (n)
for pp=1:numel(df_func)
df=df_func{pp}; % 1 of m function handles
p_list=num2cell(p);
dfp=df(p_list{:},xp,yp); % n partial derivatives
a(ff+(pp-1)*k)=sum(qp'.*dfp);
end
end
end
end
% append history if state=='iter', useful for checking convergence
function stop = myoutput(x,optimvalues,state)
global history;
stop = false;
if isequal(state,'iter')
history = [history; x];
end
end

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More Answers (1)

Joss Knight
Joss Knight on 24 Nov 2018
Edited: Joss Knight on 24 Nov 2018
It does rather depend on what you're doing. The functions polyfit and interp1 work with gpuArray inputs.
  8 Comments
Matt J
Matt J on 27 Nov 2018
Thanks, Joss.

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