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Copy pathAnPSD_units_ca_muas.m
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AnPSD_units_ca_muas.m
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% A part of the old AnPSD script adapted to perform coherence and phase
% analyses for MUA vs population spiking rate of a different brain area.
% MUAsAll refers to the population rate of area 1
% PR refers to the population rate of area 2
%% LOAD PRE-PROCESSED DATA
if ~exist('dataStruct','var')
load(dataFile);
end
%% INITILIASE PARAMETERS
params
lists
overwrite = true; % Overwrites existig data. Otherwise if false, keeps the old data.
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 (applies only when running on NSG Portal)
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
%% DETERMINE SERIES TO COMPARE
series2compare
%% PERFORM COHERENCE ANALSYSES
animal = dataStruct.seriesData.(fnsData{1}).db(1).animal;
if ~isempty(dbEntries_c) && dbEntries_c(1) == inf % Here you can chose to execute only certain db entries
dbEntries_cLocal = 1:numel(series_c);
else
dbEntries_cLocal = dbEntries_c;
end
for dbCount = dbEntries_cLocal % Loop through db entries (area 1)
% Load the contents of dbStruct
seriesName1 = series_c{dbCount};
[dbStruct, ~, ~, entryName, ~, ~, shankIDs,...
~, period, ~, ~, srData, optCoh, ~, FOI,...
MUAsAll, spk, muas, ~, ~, muaMetadata] = get_dbStruct(dataStruct, find(endsWith(fnsData,seriesName1)));
optCoh.maxFreq = maxFreq_ca;
optCoh.winfactor = winfactor;
optCoh.freqfactor = freqfactor;
optCoh.monotoneFreq = true;
% Indices for truncating data and the population rate for the first series
if ~sum(MUAsAll)
continue
end
[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
[inds1, MUAsAll] = determineInds(period, srData, MUAsAll);
spk = spk(:,inds1);
for sca = 1:numel(series_ca{dbCount}) % Loop through comparison areas (area 2)
sca_name = series_ca{dbCount}{sca};
phaseCohDB.phaseFOI = [];
phaseCohDB.cohFOI = [];
phaseCohDB.coh_confFOI = [];
% Test if the analysis data already exists
if ~overwrite && isfield(dataStruct, 'seriesData_ca_muas')
dataString = [animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name)];
if isfield(dataStruct.seriesData_ca_muas, dataString)
continue
end
end
dbStruct2 = dataStruct.seriesData.([animal '_s' num2str(sca_name)]);
if iscell(dbStruct.dbSeries.period)
assert(iscell(dbStruct2.dbSeries.period))
for iPeriod = 1:numel(dbStruct.dbSeries.period)
assert(dbStruct.dbSeries.period{iPeriod}(1) == dbStruct2.dbSeries.period{iPeriod}(1));
assert(dbStruct.dbSeries.period{iPeriod}(2) == dbStruct2.dbSeries.period{iPeriod}(2));
end
else
assert(dbStruct.dbSeries.period(1) == dbStruct2.dbSeries.period(1));
assert(dbStruct.dbSeries.period(2) == dbStruct2.dbSeries.period(2));
end
PR = sum(dbStruct2.popData.MUAsAll,1); % PR for the second series
if excludeRunning && isfield(dataStruct, 'runningSpeedData') && ~isempty(dataStruct.runningSpeedData.(runningSpeedDataEntry).maxQuietPeriod)
period = combinePeriods(dbStruct2.dbSeries.period, dataStruct.runningSpeedData.(runningSpeedDataEntry).maxQuietPeriod, srData);
else
period = dbStruct2.dbSeries.period;
end
[inds2, PR] = determineInds(period, srData, PR);
if isempty(spk) || isempty(PR)
continue
elseif size(spk,2) > numel(PR)
PR = [PR zeros(1, size(spk,2) - numel(PR))]; %#ok<*AGROW>
elseif size(spk,2) < numel(PR)
PR = PR(1:size(spk,2));
end
dbStruct_ca = dataStruct.seriesData_ca.([animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name)]);
if ~isempty(muas)
parfor u = 1:numel(muas) % Loop through muas
%for u = 1:numel(muas)
unit = muas(u);
fprintf('Started processing unit %i\n',unit);
unitData = [];
unitData_ca = [];
spkOI = full(spk(u,:));
if isempty(spkOI)
continue
end
if ~isempty(dbStruct_ca)
for sh = 1:numel(shankIDs)
units = dbStruct_ca.shankData.(['shank' num2str(sh)]).units;
if ismember(unit, units)
unitData_ca = dbStruct_ca.shankData.(['shank' num2str(sh)]).phaseCoh{unit == units};
break
end
end
end
if isempty(unitData_ca)
for sh = 1:numel(shankIDs)
shankStruct = get_shankStruct(dbStruct, sh);
if isempty(shankStruct)
continue
else
units = shankStruct.units;
if isfield(shankStruct, 'phaseCoh') && ismember(unit, units)
unitData = shankStruct.phaseCoh{unit == units};
break
end
end
end
if isempty(unitData)
[unitData.mfr, unitData.mfr_1sthalf, unitData.mfr_2ndhalf] = rateCalc(full(spkOI), srData);
[unitData.psd_halves_freq, unitData.psd_halves, freqPSD, unitData.psd, unitData.psd_conf] = psdCalc(full(spkOI), srData, optCoh);
else
freqPSD = unitData.freq;
end
% Sumarry data
unitData_ca.unit = unit;
[unitData_ca.freq, unitData_ca.coh, unitData_ca.phase, unitData_ca.coh_conf, unitData_ca.phase_confU,...
unitData_ca.phase_confL, unitData_ca.coh_halves_freq, unitData_ca.coh_halves, unitData_ca.coh_conf_halves,...
unitData_ca.phase_halves, unitData_ca.phase_conf_halves] = phaseCohCalc(PR, spkOI, srData, optCoh);
% 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_ca.rateadjust_kappa, unitData_ca.rateadjust_kappa_halves] = kappaCalc(unitData.mfr, unitData.mfr_1sthalf,...
unitData.mfr_2ndhalf, unitData.psd, unitData.psd_halves, unitData_ca.coh, unitData_ca.coh_halves);
[~, ~, unitData_ca.freq, ~, ~, unitData_ca.coh, unitData_ca.phase, unitData_ca.coh_conf, unitData_ca.phase_confU,...
unitData_ca.phase_confL, unitData_ca.coh_halves_freq, unitData_ca.coh_halves, unitData_ca.coh_conf_halves,...
unitData_ca.phase_halves, unitData_ca.phase_conf_halves, unitData_ca.rateadjust_kappa, unitData_ca.rateadjust_kappa_halves...
] = correctFreq(unitData.psd_halves_freq, unitData.psd_halves, freqPSD, unitData.psd, unitData.psd_conf,...
unitData_ca.freq, unitData_ca.coh, unitData_ca.phase, unitData_ca.coh_conf, unitData_ca.phase_confU,...
unitData_ca.phase_confL, unitData_ca.coh_halves_freq, unitData_ca.coh_halves, unitData_ca.coh_conf_halves,...
unitData_ca.phase_halves, unitData_ca.phase_conf_halves, unitData_ca.rateadjust_kappa, unitData_ca.rateadjust_kappa_halves);
% Spike-trigerred population rate (stPR)
window = 1e2;
unitData_ca.stPR = stprCalc(spkOI, PR, window);
unitData_ca.stPR_halves = stprHalfCalc(spkOI, PR, window);
% Extract phase and coherence for every FOI
[unitData_ca.phaseFOI, unitData_ca.cohFOI, unitData_ca.coh_confFOI, unitData_ca.actualFOI, unitData_ca.fInds] = phaseCohFOI(FOI,...
unitData_ca.freq, unitData_ca.phase, unitData_ca.coh, unitData_ca.coh_conf, unitData_ca.rateadjust_kappa);
end
% Save unit summary data
saveParfor([entryName '_' unitNamer(u) '_phaseCoh.mat'], unitData_ca);
fprintf('Finished processing unit %i\n',unit);
end % loop over muas
end
% Save shank summary data
fileList = dir([entryName '_*_phaseCoh.mat']);
if ~isempty(fileList)
phaseCoh = struct([]);
for i = 1:size(fileList,1)
qPhaseCoh = load(fileList(i).name);
phaseCoh{end+1} = qPhaseCoh.q; %#ok<*SAGROW>
phaseCohDB.phaseFOI = [phaseCohDB.phaseFOI; phaseCoh{i}.phaseFOI];
phaseCohDB.cohFOI = [phaseCohDB.cohFOI; phaseCoh{i}.cohFOI];
phaseCohDB.coh_confFOI = [phaseCohDB.coh_confFOI; phaseCoh{i}.coh_confFOI];
end
dataString = ['dataStruct.seriesData_ca_muas.' animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name) '.phaseCoh = phaseCoh;'];
eval(dataString);
dataString = ['dataStruct.seriesData_ca_muas.' animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name) '.units = muas;'];
eval(dataString);
dataString = ['dataStruct.seriesData_ca_muas.' animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name) '.muaMetadata = muaMetadata;'];
eval(dataString);
dataString = ['dataStruct.seriesData_ca_muas.' animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name) '.popData.phaseCoh = phaseCohDB;'];
eval(dataString);
delete([entryName '_*.mat']);
else
dataString = ['dataStruct.seriesData_ca_muas.' animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name) '.phaseCoh = [];'];
eval(dataString);
dataString = ['dataStruct.seriesData_ca_muas.' animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name) '.units = [];'];
eval(dataString);
dataString = ['dataStruct.seriesData_ca_muas.' animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name) '.unitMetadata = [];'];
eval(dataString);
dataString = ['dataStruct.seriesData_ca_muas.' animal '_s' num2str(series_c{dbCount}) '__' animal '_s' num2str(sca_name) '.popData.phaseCoh = [];'];
eval(dataString);
end
if intermediateSaving
save(dataFile,'dataStruct','-v7.3'); %#ok<*UNRCH>
end
fprintf('Finished comparing against series %i\n',sca);
end % loop over compared against areas
fprintf('Finished processing db entry %i\n',dbCount);
end % loop over db entries
% Save data if it hasn't been already saved
if ~intermediateSaving
save(dataFile,'dataStruct','-v7.3');
end
clearvars -except dataFile dbEntries dbEntries_c dbEntries_ca dataStruct
function popData_ca = comparePops(PR, spkDB, FOI, srData, opt)
if numel(spkDB) > numel(PR)
PR = [PR zeros(1, numel(spkDB) - numel(PR))];
elseif numel(spkDB) < numel(PR)
spkDB = [spkDB zeros(1, numel(PR) - numel(spkDB))];
end
[popData_ca.mfr, popData_ca.mfr_1sthalf, popData_ca.mfr_2ndhalf, popData_ca.lfr1, popData_ca.lfr5] = rateCalc(spkDB, srData);
[popData_ca.psd_halves_freq, popData_ca.psd_halves, freqPSD, popData_ca.psd, popData_ca.psd_conf,...
popData_ca.psd_numelSignal, popData_ca.beta_halves, popData_ca.beta] = psdCalc(spkDB, srData, opt);
[popData_ca.freq, popData_ca.coh, popData_ca.phase, popData_ca.coh_conf, popData_ca.phase_confU,...
popData_ca.phase_confL, popData_ca.coh_halves_freq, popData_ca.coh_halves, popData_ca.coh_conf_halves,...
popData_ca.phase_halves, popData_ca.phase_conf_halves] = phaseCohCalc(PR, spkDB, srData, opt);
% Compute the rate adjustment factors for coherence report, per Aoi et al.
% we adjust as if the neuron's rate is 1 spk/s
[popData_ca.rateadjust_kappa, popData_ca.rateadjust_kappa_halves] = kappaCalc(popData_ca.mfr, popData_ca.mfr_1sthalf,...
popData_ca.mfr_2ndhalf, popData_ca.psd, popData_ca.psd_halves, popData_ca.coh, popData_ca.coh_halves);
[popData_ca.psd_halves_freq, popData_ca.psd_halves, popData_ca.freq, popData_ca.psd, popData_ca.psd_conf,...
popData_ca.coh, popData_ca.phase, popData_ca.coh_conf, popData_ca.phase_confU, popData_ca.phase_confL,...
popData_ca.coh_halves_freq, popData_ca.coh_halves, popData_ca.coh_conf_halves, popData_ca.phase_halves,...
popData_ca.phase_conf_halves, popData_ca.rateadjust_kappa, popData_ca.rateadjust_kappa_halves] = correctFreq(...
popData_ca.psd_halves_freq, popData_ca.psd_halves, freqPSD, popData_ca.psd, popData_ca.psd_conf,...
popData_ca.freq, popData_ca.coh, popData_ca.phase, popData_ca.coh_conf, popData_ca.phase_confU,...
popData_ca.phase_confL, popData_ca.coh_halves_freq, popData_ca.coh_halves, popData_ca.coh_conf_halves,...
popData_ca.phase_halves, popData_ca.phase_conf_halves, popData_ca.rateadjust_kappa, popData_ca.rateadjust_kappa_halves);
% Spike-trigerred population rate (stPR)
window = 1e2;
popData_ca.stPR = stprCalc(spkDB, PR, window);
popData_ca.stPR_halves = stprHalfCalc(spkDB, PR, window);
% Extract phase and coherence for every FOI
[popData_ca.phaseFOI, popData_ca.cohFOI, popData_ca.coh_confFOI, popData_ca.actualFOI, popData_ca.fInds] = phaseCohFOI(FOI,...
popData_ca.freq, popData_ca.phase, popData_ca.coh, popData_ca.coh_conf, popData_ca.rateadjust_kappa);
end