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https://github.com/RaymondLab/Code
25 June 2024, 13:39:08 UTC
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  • alignCXandMaestro.m
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Tip revision: 8ed0bc61f74cbe8b9d07278a25fd9f49c0af3f2b authored by Kellen Vu on 03 November 2022, 01:23:38 UTC
Fixes a bug where eyeCalibration.mlapp was trying to get the sample rate from the wrong smr channel. I tested this in D243b, and it should work for other computers, but let me know if it doesn't.
Tip revision: 8ed0bc6
alignCXandMaestro.m
function [behaviorDat, shiftAmt, shiftConfidence] = alignCXandMaestro(behaviorDat, ephysData, plotOn)

    % Don't plot by default
    if ~exist('plotOn','var')
        plotOn = 0;
    end
    
    shiftConfidence = 0;
    shiftAmt = 0;
    
    eSamplerate = 50000;%ephysDat.samplerate;
    %ephysData = datchandata(ephysDat,'Ephys');
    timeEphys = 0:1/eSamplerate:(length(ephysData)-1)/eSamplerate;
    
    %% Allign Ephys Data
    spikesForAlignment = 100:120;
    
    timeofsimplespikes = datchandata(behaviorDat,'ss');    
    eventsSampleTime = timeofsimplespikes * eSamplerate;
    eventsSampleTime = eventsSampleTime(spikesForAlignment);
    eventsSampleTime = round(eventsSampleTime);
    eventsSampleTime = eventsSampleTime - eventsSampleTime(1);
    
    sumofthingsInitial = nan(length(ephysData),length(eventsSampleTime));
    ephysData = ephysData - mean(ephysData);
    for x = 1:length(ephysData)
        if max(eventsSampleTime + x) > length(ephysData)/2%min([150000, length(ephysData)])
            break
        end
        sumofthingsInitial(x,:) = sum(ephysData(eventsSampleTime + x));
    end
    
    sumofthings = sum(sumofthingsInitial,2);
    if ~sum(~isnan(sumofthings))
        return
    end
    
    %% Modify ephys
    maxMatchValue = max(abs(sumofthings));
    maxSumLoc = timeEphys(find(abs(sumofthings) == maxMatchValue));
    maxSumLoc = maxSumLoc(1);
    
    if maxMatchValue > 30
        shiftAmt = -(maxSumLoc - timeofsimplespikes(100));
        timeEphys = timeEphys + shiftAmt;
        shiftConfidence = maxMatchValue;
        
        if plotOn
            figure(9); clf
            plot(timeEphys, abs(sumofthings))
            %ylim([0 100])
            if ~isempty(maxSumLoc)
                vline(maxSumLoc + shiftAmt, ':r')
                %xlim([timeEphys(1) timeEphys(1)+1])
            end

            figure(10); clf
            plot(timeEphys, ephysData);
            vline(timeofsimplespikes(1:100), '--r')
            xlim([timeEphys(1) timeEphys(1)+1])
            
            figure(11); clf
            csLocs = zeros(length(ephysData),1);
            behaviorDat(9).data(behaviorDat(9).data < 0) = [];
            
            for k = 1:length(behaviorDat(9).data)
                csLocs(round(behaviorDat(9).data(k)*eSamplerate)) = 1;
            end
            [c,lags] = xcorr(ephysData,csLocs);
            plot(lags/50000, c);
            xCorrShiftVal = lags(find(c == max(c)))/eSamplerate;
            disp(xCorrShiftVal)
            disp(shiftAmt)
            shiftAmt = xCorrShiftVal;
        end
        

    else
        shiftAmt = 0;
        shiftConfidence = 0;
    end
    
    %% add shifted ephys channel to behavior structure
    behaviorDat(end+1) = dat(ephysData, 'Ephys', length(behaviorDat)+1, eSamplerate, timeEphys(1),timeEphys(end),'mV?');

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