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Copy pathAnPSD_unitsLaminar_positive.m
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AnPSD_unitsLaminar_positive.m
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% A part of the old AnPSD script adapted to perform coherence and phase
% analyses for positive unit and positive population spiking rate data
% comparing cortical layers.
%% LOAD PRE-PROCESSED DATA
if ~exist('dataStruct','var')
load(dataFile);
end
%% INITILIASE PARAMETERS
params
lists
intermediateSaving = false; % Save everytime a db series is finished being analysed (bad idea since saving is a lengthy process)
%% ADJUST THE NUMBER OF PARALLEL PROCESSORS
p = gcp('nocreate'); % If no pool, do not create new one.
if isempty(p)
poolsize = 0;
else
poolsize = p.NumWorkers;
end
if poolsize == 20
delete(gcp('nocreate'))
parpool(24);
end
%% PERFORM COHERENCE ANALSYSES
fnsData = fieldnames(dataStruct.seriesData);
if ~isempty(dbEntries) && dbEntries(1) == inf % Here you can chose to execute only certain db entries
dbEntriesLocal = 1:numel(fnsData);
else
dbEntriesLocal = dbEntries;
end
for dbCount = dbEntriesLocal % Loop through db entries
% Load the contents of dbStruct
if ~isfield(dataStruct, 'seriesData_positive')
continue
end
dbCountPositive = find(ismember(fieldnames(dataStruct.seriesData_positive), fnsData{dbCount}));
if isempty(dbCountPositive)
continue
end
dbStruct0 = get_dbStruct(dataStruct, dbCount);
[dbStruct, repository, ~, entryName, ~, ~, shankIDs,...
~, period, ~, ~, srData, optCoh, exclRad, FOI,...
MUAsAll, spkDB, spkDB_units] = get_dbStruct(dataStruct, dbCountPositive, 'positive');
optCoh.maxFreq = maxFreq;
optCoh.winfactor = winfactor;
optCoh.freqfactor = freqfactor;
optCoh.monotoneFreq = true;
if numel(shankIDs) > 1 || isempty(MUAsAll) || ~sum(MUAsAll) || isempty(spkDB)
continue
end
[~, ~, area] = determineArea(seriesFromEntry(entryName));
if ~contains(area,'S1') && ~contains(area,'RSC') &&...
~contains(area,'V1') && ~contains(area,'V2') && ~contains(area,'VIS')
continue
end
if size(spkDB_units,2) > 1
spkDB_units = spkDB_units(:,2);
end
% Indices for truncating data
[seriesName, animal] = seriesFromEntry(entryName);
runningSpeedDataEntry = [animal '_s' seriesName(1:min([14 numel(seriesName)]))];
if excludeRunning && isfield(dataStruct, 'runningSpeedData') && ~isempty(dataStruct.runningSpeedData.(runningSpeedDataEntry).maxQuietPeriod)
period = combinePeriods(period, dataStruct.runningSpeedData.(runningSpeedDataEntry).maxQuietPeriod, srData);
end
[inds, spkDB] = determineInds(period, srData, spkDB);
% Load the contents of shankStruct
[~, ~, units0, unitMetadata0] = get_shankStruct(dbStruct0, 1);
[~, shank, units, unitMetadata, xcoords, ycoords, spk] = get_shankStruct(dbStruct, 1);
if isempty(units)
continue
end
muaMetadata = dbStruct0.popData.muaMetadata(ismember(dbStruct0.popData.spkDB_units, spkDB_units),:);
% Truncate shank data
if ~isempty(spk)
if size(spk,2) < size(MUAsAll,2)
spk = [full(spk) zeros(size(spk,1), size(MUAsAll,2)-size(spk,2))];
end
spk = spk(:,inds);
end
if strcmpi(repository, 'allensdk')
divCh = mean([min(dbStruct0.popData.muaMetadata(:,9)) max(dbStruct0.popData.muaMetadata(:,9))]);
MUAsAll1 = sum(spkDB(muaMetadata(:,9) <= divCh,:), 1);
MUAsAll2 = sum(spkDB(muaMetadata(:,9) > divCh,:), 1);
else
divCh = min(dbStruct.dbSeries.chOI) + round(numel(dbStruct.dbSeries.chOI)/2) - 1;
MUAsAll1 = sum(spkDB(muaMetadata(:,3) <= divCh,:), 1);
MUAsAll2 = sum(spkDB(muaMetadata(:,3) > divCh,:), 1);
end
parfor u = 1:numel(units) % Loop through units
%for u = 1:numel(units)
fprintf('Started processing unit %i\n',units(u));
unitData = struct();
unitData.unit = units(u);
if strcmpi(repository, 'allensdk')
unitCh = unitMetadata0(ismember(units0, unitData.unit),9);
else
unitCh = unitMetadata(u,3); %#ok<*PFBNS>
end
spkOI = full(spk(u,:));
if unitCh <= divCh
PR = full(MUAsAll2);
else
PR = full(MUAsAll1);
end
% Summary data
[unitData.mfr, unitData.mfr_1sthalf, unitData.mfr_2ndhalf, unitData.lfr1, unitData.lfr5] = rateCalc(spkOI, srData);
[unitData.psd_halves_freq, unitData.psd_halves, unitData.freq, unitData.psd, unitData.psd_conf,...
unitData.psd_numelSignal, unitData.beta_halves, unitData.beta] = psdCalc(spkOI, srData, optCoh);
freqPSD = unitData.freq;
if sum(PR)
[unitData.freq, unitData.coh, unitData.phase, unitData.coh_conf, unitData.phase_confU, unitData.phase_confL,...
unitData.coh_halves_freq, unitData.coh_halves, unitData.coh_conf_halves, unitData.phase_halves,...
unitData.phase_conf_halves] = phaseCohCalc(PR, spkOI, srData, optCoh);
[unitData.mfr_pop, unitData.mfr_1sthalf_pop, unitData.mfr_2ndhalf_pop, unitData.lfr1_pop,...
unitData.lfr5_pop] = rateCalc(PR, srData);
% Compute the rate adjustment factors for coherence report, per Aoi et al.
% we adjust as if the neuron's rate is 1 spk/s
[unitData.rateadjust_kappa, unitData.rateadjust_kappa_halves] = kappaCalc(unitData.mfr, unitData.mfr_1sthalf,...
unitData.mfr_2ndhalf, unitData.psd, unitData.psd_halves, unitData.coh, unitData.coh_halves);
[unitData.psd_halves_freq, unitData.psd_halves, unitData.freq, unitData.psd, unitData.psd_conf,...
unitData.coh, unitData.phase, unitData.coh_conf, unitData.phase_confU, unitData.phase_confL,...
unitData.coh_halves_freq, unitData.coh_halves, unitData.coh_conf_halves, unitData.phase_halves,...
unitData.phase_conf_halves, unitData.rateadjust_kappa, unitData.rateadjust_kappa_halves] = correctFreq(...
unitData.psd_halves_freq, unitData.psd_halves, freqPSD, unitData.psd, unitData.psd_conf,...
unitData.freq, unitData.coh, unitData.phase, unitData.coh_conf, unitData.phase_confU,...
unitData.phase_confL, unitData.coh_halves_freq, unitData.coh_halves, unitData.coh_conf_halves,...
unitData.phase_halves, unitData.phase_conf_halves, unitData.rateadjust_kappa, unitData.rateadjust_kappa_halves);
% stPR with the local (same shank/tetrode) population rate
window = 1e2;
unitData.stPRsh = stprCalc(spkOI, PR, window);
unitData.stPR = stprHalfCalc(spkOI, PR, window);
% Mean vs var using different bin sizes
[unitData.m, unitData.mv1, unitData.mv2, unitData.mean_var, unitData.mean_var_timeBin] = meanVarCalc(spkOI, srData);
% Extract phase and coherence for every FOI
[unitData.phaseFOI, unitData.cohFOI, unitData.coh_confFOI, unitData.actualFOI, unitData.fInds] = phaseCohFOI(FOI,...
unitData.freq, unitData.phase, unitData.coh, unitData.coh_conf, unitData.rateadjust_kappa);
else
unitData.phaseFOI = nan(size(FOI));
unitData.cohFOI = nan(size(FOI));
unitData.coh_confFOI = nan(size(FOI));
unitData.actualFOI = nan(size(FOI));
unitData.fInds = nan(size(FOI));
end
% Save unit summary data
saveParfor([entryName '_' unitNamer(u) '_phaseCoh.mat'], unitData);
fprintf('Finished processing unit %i\n',unitData.unit);
end % loop over units
% Save shank summary data
fileList = dir([entryName '_*_phaseCoh.mat']);
if ~isempty(fileList)
phaseCohDeep = struct([]);
phaseCohSuperficial = struct([]);
for i = 1:size(fileList,1)
qPhaseCoh = load(fileList(i).name);
if strcmpi(repository, 'allensdk')
unitInd = unitMetadata0(:,1) == qPhaseCoh.q.unit;
unitCh2 = unitMetadata0(unitInd,9);
else
unitInd = unitMetadata(:,1) == qPhaseCoh.q.unit;
unitCh2 = unitMetadata(unitInd,3);
end
if unitCh2 <= divCh
phaseCohDeep{end+1} = qPhaseCoh.q; %#ok<SAGROW>
else
phaseCohSuperficial{end+1} = qPhaseCoh.q; %#ok<SAGROW>
end
end
dataString = ['dataStruct.seriesDataLaminar_positive.' entryName '.shankData.' shankIDs{1} '.phaseCohDeep = phaseCohDeep;'];
eval(dataString);
dataString = ['dataStruct.seriesDataLaminar_positive.' entryName '.shankData.' shankIDs{1} '.phaseCohSuperficial = phaseCohSuperficial;'];
eval(dataString);
if intermediateSaving
save(dataFile,'dataStruct','-v7.3'); %#ok<*UNRCH>
end
delete([entryName '_*.mat']);
end
fprintf('Finished processing db entry %i\n',dbCount);
end % loop over db entries
%% SAVE DATA
if ~intermediateSaving
save(dataFile,'dataStruct','-v7.3');
end
clearvars -except dataFile dbEntries dbEntries_c dbEntries_ca dataStruct