prt_getKernelModel.m

function [Phi_all,ID,fid] = prt_getKernelModel (PRT,prt_dir,mid,flag)

% Function to load the kernels according to the samples considered in a
%given model. These kernels will be added if the machine is a single kernel
%technique.
%
% Inputs:
% -------
% PRT:            data structure
% prt_dir:        path for PRT.mat (string)
% mid :           index of model in the data structure/ PRT.mat
% flag:           1 to compute one model for each kernel, 0 otherwise (def)
%
% Output:
% --------
% Phi_all :  cell array with one kernel per cell or a single cell
%            with the samples considered in the
%            specified model, as defined by the class/regression selection.
% ID :       the ID matrix for the considered samples
% fid :      index of feature set in data structure / PRT.mat
%
%__________________________________________________________________________
% Copyright (C) 2011 Machine Learning & Neuroimaging Laboratory

% Written by J Schrouff
% $Id: prt_getKernelModel.m 855 2014-05-27 09:35:15Z schrouff $

% load data files and configure ID matrix
disp('Loading data files.....>>');

samp_idx = PRT.model(mid).input.samp_idx;   % which samples are in the model
Phi_all=[];

if nargin<4 || isempty(flag)
    flag = 0;
end

for i = 1:length(PRT.model(mid).input.fs)
    %Backwards compatibility with v0 and v1: transform kernel into cell if needed
    
    fid = prt_init_fs(PRT, PRT.model(mid).input.fs(i));
    load(fullfile(prt_dir, PRT.fs(fid).k_file));
    if ~iscell(Phi)
        Phi = {Phi};
    end
    
    
    %first case: combine feature sets
    if length(PRT.model(mid).input.fs)>1
        if i == 1
            ID = PRT.fs(fid).id_mat(samp_idx,:);
        end        
        
        for j = 1:length(Phi)
            Phi_all = [Phi_all, {Phi{j}(samp_idx,samp_idx)}]; % in case one feature set comprises multiple kernels already
        end
        
    else
        %If only one feature set, load kernel to see which case
        
        ID = PRT.fs(fid).id_mat(samp_idx,:);
        if length(Phi)==1
            Phi_all{1} = Phi{1}(samp_idx,samp_idx);
        else
            Phi_all=cell(1,length(Phi));
            for j=1:length(Phi)
                Phi_all{j}=Phi{j}(samp_idx,samp_idx);
            end
        end
        
    end
    %Check that if multiple kernels, MKL was selected,
    %otherwise kernels will be added when calling prt_machine
    if length(Phi_all)>1 &&...                                                  %Multiple kernels
            isempty(strfind(PRT.model(mid).input.machine.function,'MKL')) &&... %not simpleMKL
            isempty(strfind(PRT.model(mid).input.machine.function,'wip')) &&... %not wip
            ~flag                                                               %not independent models
        warning('prt_getKernelModel:AddKernels',...
            'Multiple kernels but machine cannot deal with them, adding the kernels');
        Phi_tmp = zeros(length(samp_idx));
        for j=1:length(Phi_all)
            try
                %add kernels
                tp = Phi_all{j};
                Phi_tmp=Phi_tmp + tp;
            catch
                error('prt_cv_model:KernelsWithDifferentDimensions', ...
                    'Kernels cannot be added since they have different dimensions')
            end
        end
        Phi_all = {Phi_tmp};
        clear Phi_tmp
    end
end
clear Phi