kilotrodeRig/alignToALF.m at master · cortex-lab/kilotrodeRig · GitHub

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%% script to align a dataset in ALF format

mn = 'Robbins';
td = '2017-06-13';
en = 1;
[tags, hasEphys] = getEphysTags(mn, td);
masterAlign = tags{1};

rootE = dat.expPath(mn, td, 1, 'main', 'master');
root = fileparts(rootE);

alignDir = fullfile(root, 'alignments');

%% eye alignment

eyeFolder = fileparts(dat.expFilePath(mn, td, en, 'eyetracking', 'master'));

load(fullfile(eyeFolder, 'eye_timeStamps.mat'))

alignFile = dir(fullfile(alignDir, sprintf('correct_timeline*ephys_%s.npy', masterAlign)));
b = readNPY(fullfile(alignDir, alignFile.name));

tAligned = applyCorrection(tVid, b); % will be a column after this
nFr = numel(tVid);

writeNPY([[0:nFr-1]' tVid(:)], fullfile(eyeFolder, 'eye.timestamps_Timeline.npy'));
writeNPY([[0:nFr-1]' tAligned(:)], fullfile(eyeFolder, 'eye.timestamps.npy'));

%% for timeline

alignFile = dir(fullfile(alignDir, sprintf('correct_timeline*ephys_%s.npy', masterAlign)));
b = readNPY(fullfile(alignDir, alignFile.name));

tlFile = dat.expFilePath(mn, td, en, 'Timeline', 'master');
load(tlFile);

kilotrodeTimelineToAFF(Timeline, b, fileparts(tlFile))

%% for electrophysiology

for t = 1:length(tags)
    ksd = getKSdir(mn, td, tags{t});
    spikeStruct = loadParamsPy(fullfile(ksd, 'params.py'));
    ss = readNPY(fullfile(ksd, 'spike_times.npy'));
    st = double(ss)/spikeStruct.sample_rate;

    if t>1

        alignFN = sprintf('correct_ephys_%s_to_ephys_%s.npy', tags{t}, masterAlign);
        b = readNPY(fullfile(alignDir, alignFN));

        st = applyCorrection(st, b);

    end

    writeNPY(st, fullfile(ksd, 'spikes.times.npy'));

    cluFile = fullfile(ksd, 'spike_clusters.npy');
    if exist(cluFile, 'file')
        copyfile(fullfile(ksd, 'spike_clusters.npy'), fullfile(ksd, 'spikes.clusters.npy'));
    else
        copyfile(fullfile(ksd, 'spike_templates.npy'), fullfile(ksd, 'spikes.clusters.npy'));
    end
end