function [Xm, P, b, pcaDat] = aam_pca(AAM, indices, filenames,FractionPCs, meanshape, in_context_flag, lda_shape_flag)%function [Xm, P, b, pcaDat] = aam_pca(AAM, indices, filenames,FractionPCs, meanshape, in_context_flag, lda_shape_flag)%% Dr. A. I. Hanna (2006)if nargin<4    FractionPCs=0.95;end%v = 0.95;v = FractionPCs;% if(nargin < 1) error('No data defined for PCA'); endelements = get(AAM, 'elements');activeElements = get(AAM, 'activeElements');indx = 1;pmt = get(AAM, 'PointModelTemplate');templatename = get(pmt, 'name');templatename = templatename(1:length(templatename)-9);modelDirec=get(AAM,'modelDirec');X = [];for e =1:length(elements)    name = get(elements{e}, 'imagefilename');    %name = filenames{e};    name = name(1:length(name)-4);    fprintf('loading %s\n', name);    aligned_filename = fullfile(modelDirec,[name,'_aligned.mat']);    if exist(aligned_filename)        pts = load(aligned_filename);        pts = pts.pts;        pts = reshape(pts, 2, length(pts)/2);        if in_context_flag            ind = setdiff(1:size(pts,2), indices);            pts(:, ind) = meanshape(:, ind);        else            pts = pts(:, indices);        end        X(:, indx) = pts(:);        indx = indx+1;    endendif isempty(X)    uiwait(msgbox('There are not point models to process. Exiting.','No Point Models','modal'));    Xm = [];    P = [];    b = [];    pcaDat = [];    return;else    [Xm, P, b, pcaDat] = principle_component_analysis(X, v);endreturn;