createXmlFile_v2.m

function createXmlFile_v2(savePath, numberNeurons, reps, initDelay, durationVector, powerVector, spiralVector, iterations, varName, flagRandom)

%{
Function to create a xml file to be uploaded to the prairie view
savePAth --> path where to save the .xml file
numberNeurons -> How many neurons to randomly activate
reps --> amount of stim per neuron
flagRandom --> adding randomness to the targets of stimulation
Random only happens within repetitions
power 0.4 is a 100 in the gui
%}

    if nargin < 6
        flagRandom = true;
    end
    
    if nargin<5
        varname = '';
    end

    %% Parameters of the GUI
    Iter = 1;
    IterDelay = 1000.00;
    UncagingLaser = "Monaco";
    UncagingLaserPower = power;
    InitialDelay = initDelay;
    InterPointDelay =  0.12;
    Duration = 40;
    SpiralRevolutions = 20; 
    Repetitions = 1;  
    AllPointsAtOnce = "False";
    
    %% Array of random holostims 
    holovector = nan(numberNeurons,reps);
    for rr = 1:reps
        if flagRandom
            holovector(:,rr) = randsample(numberNeurons,numberNeurons);
        else
            holovector(:,rr) = 1:numberNeurons;
        end
    end
    holovector = holovector(:);
    
    
    %% prepare file

    % print the first part of the text
    fileID = fopen(fullfile(savePath, [varName, 'holostim.xml']),'wt');
    fprintf(fileID,'<?xml version="1.0" encoding="utf-8"?>\n');
    fprintf(fileID,'<PVSavedMarkPointSeriesElements Iterations="%d" IterationDelay="%.2f">\n', Iter, IterDelay);
    
    % print for each point
    formatSpec1 = ['  <PVMarkPointElement Repetitions="%d" UncagingLaser="%s" UncagingLaserPower="%.1f"', ...
        ' TriggerFrequency="None" TriggerSelection="None" TriggerCount="1"', ...
        ' AsyncSyncFrequency="None" VoltageOutputCategoryName="None" VoltageRecCategoryName="None"', ...
        ' parameterSet="CurrentSettings">\n'];
    formatSpec2 = ['    <PVGalvoPointElement InitialDelay="%.2f"', ...
        ' InterPointDelay="%d" Duration="%d" SpiralRevolutions="%d" AllPointsAtOnce="%s"', ...
        ' Points="Point %d" Indices="%d" />\n'];
    
    for ind = 1:numberNeurons*reps
        %TODO change from pixelspace to motorspace
        content1 = [InitialDelay, InterPointDelay, Duration, SpiralRevolutions]; 
        content2 = [holovector(ind), holovector(ind)];
        fprintf(fileID, formatSpec1, Repetitions, UncagingLaser, UncagingLaserPower);
        fprintf(fileID, formatSpec2, content1, AllPointsAtOnce, content2);
        fprintf(fileID, '  </PVMarkPointElement>\n');
    end
    fprintf(fileID,'</PVSavedMarkPointSeriesElements>\n');
    fclose(fileID);
end