import_xvg.m

Contents

Version

2.11

Contact

Please report problems/bugs to michael.holmboe@umu.se

Examples

function Data = import_xvg(filename,varargin)

% Check if .xvg is given in the filename
if regexp(filename,'.xvg') ~= false
    filename = filename;
else
    filename = strcat(filename,'.xvg');
end

% Open and read the .xvg file
inputfile = fopen(filename, 'r');
C = textscan(inputfile, '%s', 'Delimiter', '\n');
fclose(inputfile);

nRows = size(C{1,1},1);
nColumns=size(strsplit(char(C{1,1}(end-1,:))),2);

% Search a specific string and find all rows containing matches
xaxis = strfind(C{1}, '@    xaxis  label ');
xaxislabel_row = find(~cellfun('isempty', xaxis));
xaxislabel=C{1,1}(xaxislabel_row);
xaxislabel = regexprep(xaxislabel,'@    xaxis  label "','');
xaxislabel = regexprep(xaxislabel,'"','');

yaxis = strfind(C{1}, '@    yaxis  label ');
yaxislabel_row = find(~cellfun('isempty', yaxis));
yaxislabel=C{1,1}(yaxislabel_row);
yaxislabel = regexprep(yaxislabel,'@    yaxis  label "','');
yaxislabel = regexprep(yaxislabel,'"','');
yaxislabel=strrep(yaxislabel,'\S-','-^');
yaxislabel=strrep(yaxislabel,'-^','^-^');
yaxislabel=strrep(yaxislabel,'\S','^');
yaxislabel=strrep(yaxislabel,'\N','');

yaxis_all_legends=[];
for i=1:nColumns-1
    yaxis = strfind(C{1},strcat('@ s',num2str(i-1),' legend '));
    yaxis_legend_row = find(~cellfun('isempty', yaxis));
    yaxis_legend=C{1,1}(yaxis_legend_row);
    yaxis_legend=strrep(yaxis_legend,'-','_');
    yaxis_legend = regexprep(yaxis_legend,strcat('@ s',num2str(i-1),' legend '),'');
    yaxis_all_legends = [yaxis_all_legends strtrim(regexprep(yaxis_legend,'"',''))];
end

% Option 1 (the faster way of doing it...)
D=C;
nondatarows1 = strfind(C{1}, '#');
nondatarows1 = find(~cellfun('isempty',nondatarows1));
nondatarows2 = strfind(C{1}, '@');
nondatarows2 = find(~cellfun('isempty',nondatarows2));
nondatarows3 = strfind(C{1}, '&');
nondatarows3 = find(~cellfun('isempty',nondatarows3));
D{1,1}([nondatarows1;nondatarows2;nondatarows3])=[];

D = regexp(D{1,1}, '\s+', 'split');
D = vertcat(D{:});
Data = cellfun(@str2double,D);

% End option 1

% %% Option 2 (depreceated)
% tic
% frewind(inputfile);
% i=1; j=0; allRows=nRows;
% Data=cell(nRows,1);NewData=cell(nRows,nColumns);
% while i<allRows+1;
%     tline = fgetl(inputfile);
%     if length(findstr('#',tline)) > 0 || length(findstr('@',tline)) > 0;
%         allRows=allRows-1;
%         i=i-1;
%         j=j+1;
%     else
%         Data{i,1}=strtrim(tline);
%         NewData(i,:)=strsplit(Data{i,1});
%     end
%     i=i+1;
% end
% Data = cellfun(@str2double,NewData);
% Data=Data(1:allRows,:);
% toc
% %% End option 2

try
    for i=1:nColumns
        if i==1
            assignin('caller','x',Data(:,i));
        else
            assignin('caller',strcat('y',num2str(i-1)),Data(:,i));
            yaxis_all_legends(i-1)=strtrim(yaxis_all_legends(i-1));
            yaxis_all_legends(i-1)=strrep(yaxis_all_legends(i-1),' ','_');
            yaxis_all_legends(i-1)=strrep(yaxis_all_legends(i-1),'.','');
            yaxis_all_legends(i-1)=strrep(yaxis_all_legends(i-1),'{}','');
            yaxis_all_legends(i-1)=strrep(yaxis_all_legends(i-1),'\','');
            yaxis_all_legends(i-1)=strrep(yaxis_all_legends(i-1),'/','');
            yaxis_all_legends(i-1)=strrep(yaxis_all_legends(i-1),'=','_');
            yaxis_all_legends(i-1)=strrep(yaxis_all_legends(i-1),',','_');
            yaxis_all_legends(i-1)=strrep(yaxis_all_legends(i-1),'(','_');
            yaxis_all_legends(i-1)=strrep(yaxis_all_legends(i-1),')','_');
            assignin('caller',char(yaxis_all_legends(i-1)),Data(:,i));
        end
    end
catch
    disp('Could not read the column labels, but you')
    disp('still have your data in the variable Data!')
end

% If we quickly want to plot the data, add a second argument when calling the function
if nargin>1
    plot(Data(:,1),Data(:,2:end),'LineWidth',2)
    set(gcf,'color','w');%,'units','normalized','position',[0,0,.4,.6]);
%     set(gca, 'FontName', 'Arial','FontSize',22,'TickDir','out','Ytick',min(Data(:,2:end)):ceil(max(Data(:,2:end))/10)*10/5:ceil(max(Data(:,2:end))/10)*10)
    set(gca,'LineWidth',2,'FontName', 'Arial','FontSize',22,'TickDir','out')%,'Xtick',floor(Data(1,1)/10)*10:ceil(Data(end,1)/10)*10/5:ceil(Data(end,1)/10)*10)
    xlabel(xaxislabel,'FontSize',24);
    ylabel(yaxislabel,'FontSize',24);
    xlim('auto')
    legend(yaxis_all_legends)
end

assignin('caller','Data',Data);
assignin('caller','xaxislabel',xaxislabel);
assignin('caller','yaxislabel',yaxislabel);
assignin('caller','yaxis_all_legends',yaxis_all_legends);

Published with MATLAB® R2022a