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Merged
lkaraba merged 1 commit into from
Apr 14, 2026
Merged

remove dependency on saved spikes files #27

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302 changes: 124 additions & 178 deletions BARRs/BARR_PSTH.m
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Original file line number Diff line number Diff line change
Expand Up @@ -154,40 +154,8 @@ function BARR_PSTH(plotSave,useState)


%% PSTH
tempUseReg = unique(cell_metrics.brainRegion);
regions = []; tuC = 1; y1 = 0; y2 = 0; y3=0;
for i = 1:length(tempUseReg)
if contains(convertCharsToStrings(tempUseReg{i}),"CA1")
if ~y1
regions{tuC} = "CA1";
tuC = tuC+1; y1 = 1;
end
elseif contains(convertCharsToStrings(tempUseReg{i}),"CA2")
if (~y2)
regions{tuC} = "CA2";
tuC = tuC+1; y2 = 1;
end
elseif contains(convertCharsToStrings(tempUseReg{i}),"CA3")
if (~y3)
regions{tuC} = "CA3";
tuC = tuC+1; y3 = 1;
end
else
regions{tuC} = convertCharsToStrings(tempUseReg{i});
tuC = tuC+1;
end
end

check = ["CA1" "CA2" "CA3" "CTX" "DG" "MEC" "LEC"];
regTot = 0;
for i = 1:length(check)
for j = 1:length(regions)
regCheck = regions{j};
if contains(regCheck,check(i))
regTot = regTot+1;
end
end
end
useReg = pullSpikes(basepath);
regTot = size(useReg,2);

if (~isfield(cell_metrics.tags,'Pb'))&&(~isfield(cell_metrics.tags,'Nb'))&&(~isfield(cell_metrics.tags,'Pr'))&&(~isfield(cell_metrics.tags,'Nr'))
runTags = 1;
Expand All @@ -210,168 +178,146 @@ function BARR_PSTH(plotSave,useState)
end

subNum = 1;
for i = 1:length(check)
for j=1:length(regions)
regCheck = regions{j};
if contains(regCheck, check(i))
br = convertStringsToChars(check(i));
if ~exist([basepath filesep 'Barrage_Files' filesep basename '.' br 'pyr.cellinfo.mat'])
spikes = importSpikes('brainRegion', check(i), 'cellType', "Pyramidal Cell");
save([basepath filesep 'Barrage_Files' filesep basename '.' br 'pyr.cellinfo.mat'], 'spikes');
for i=1:size(useReg,2)
br = useReg{i};
spikes = importSpikes('cellType', "Pyramidal Cell", 'brainRegion', br);
if ~isempty(spikes.times)
if plotRips
% PSTH_ripples = computePSTH(ripples,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_ripples,PSTH_t] = makePETH(spikes,ripples.timestamps(:,1),[-3 3]);
[PSTH_ripples, PSTH_t] = manualPSTH(spikes, ripples.timestamps(:,1),[-1,1],1/100); %was 1/1000
if runTags
%warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_ripples,1)
% if ((max(PSTH_ripples(k,91:111))-max(PSTH_ripples(k,1:71))) > 1.5*std(PSTH_ripples(k,:)))
% cell_metrics.tags.Pr = [cell_metrics.tags.Pr spikes.UID(k)];
% else
% cell_metrics.tags.Nr = [cell_metrics.tags.Nr spikes.UID(k)];
% end
% end
end
% [PSTH_ripples,PSTH_t] = makePETH(spikes,ripples.peaks,[-1 1]);
% index = getSort(PSTH_ripples);
index = 1:size(PSTH_ripples,1);
% PSTH_ripples = manualZscore(PSTH_ripples,spikes);
% PSTH_ripples = zscore(PSTH_ripples,1,2);
plotPSTH(PSTH_ripples, PSTH_t, index, regTot, subNum, strcat(br, '/ripples'),1);
PSTHmets.PSTH_ripples = PSTH_ripples;
PSTHmets.PSTH_ripT = PSTH_t;
PSTHmets.UID = spikes.UID;
end
% PSTH_bar = computePSTH(HSEnrem,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_bar,PSTH_t] = makePETH(spikes,HSEuse.timestamps(:,1),[-3 3]);
[PSTH_bar, PSTH_t] = manualPSTH(spikes, HSEuse.timestamps(:,1),[-1 1],1/100); %was 1/1000
if runTags
%warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_bar,1)
% if (mean(PSTH_bar(k,1001:2001))-mean(PSTH_bar(k,1:100))) > 0.3
% cell_metrics.tags.Pb = [cell_metrics.tags.Pb spikes.UID(k)];
% else
% cell_metrics.tags.Nb = [cell_metrics.tags.Nb spikes.UID(k)];
% end
% end
end
% PSTH_bar = manualZscore(PSTH_bar,spikes);
% PSTH_bar = zscore(PSTH_bar,1,2);
% [PSTH_bar,PSTH_t] = makePETH(spikes,HSEuse.peaks,[-1 1]);
plotPSTH(PSTH_bar, PSTH_t, index, regTot, subNum+(regTot*2), strcat(br, '/barrages'),1);
PSTHmets.PSTH_bar = PSTH_bar;
PSTHmets.PSTH_barT = PSTH_t;

if useState == "NREM"
if contains(plotSave, 'clean')
save(strcat(basepath, filesep, 'Barrage_Files', filesep, 'PSTHmet', filesep, basename, '.clean.', br, 'PSTHmets.mat'), 'PSTHmets');
else
load([basepath filesep 'Barrage_Files' filesep basename '.' br 'pyr.cellinfo.mat']);
save(strcat(basepath, filesep, 'Barrage_Files', filesep, 'PSTHmet', filesep, basename, '.', br, 'PSTHmets.mat'), 'PSTHmets');
end
if ~isempty(spikes.times)
if plotRips
% PSTH_ripples = computePSTH(ripples,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_ripples,PSTH_t] = makePETH(spikes,ripples.timestamps(:,1),[-3 3]);
[PSTH_ripples, PSTH_t] = manualPSTH(spikes, ripples.timestamps(:,1),[-1,1],1/100); %was 1/1000
if runTags
%warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_ripples,1)
% if ((max(PSTH_ripples(k,91:111))-max(PSTH_ripples(k,1:71))) > 1.5*std(PSTH_ripples(k,:)))
% cell_metrics.tags.Pr = [cell_metrics.tags.Pr spikes.UID(k)];
% else
% cell_metrics.tags.Nr = [cell_metrics.tags.Nr spikes.UID(k)];
% end
% end
end
% [PSTH_ripples,PSTH_t] = makePETH(spikes,ripples.peaks,[-1 1]);
% index = getSort(PSTH_ripples);
index = 1:size(PSTH_ripples,1);
% PSTH_ripples = manualZscore(PSTH_ripples,spikes);
% PSTH_ripples = zscore(PSTH_ripples,1,2);
plotPSTH(PSTH_ripples, PSTH_t, index, regTot, subNum, strcat(check(i), '/ripples'),1);
PSTHmets.PSTH_ripples = PSTH_ripples;
PSTHmets.PSTH_ripT = PSTH_t;
PSTHmets.UID = spikes.UID;
end
% PSTH_bar = computePSTH(HSEnrem,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_bar,PSTH_t] = makePETH(spikes,HSEuse.timestamps(:,1),[-3 3]);
[PSTH_bar, PSTH_t] = manualPSTH(spikes, HSEuse.timestamps(:,1),[-1 1],1/100); %was 1/1000
if runTags
%warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_bar,1)
% if (mean(PSTH_bar(k,1001:2001))-mean(PSTH_bar(k,1:100))) > 0.3
% cell_metrics.tags.Pb = [cell_metrics.tags.Pb spikes.UID(k)];
% else
% cell_metrics.tags.Nb = [cell_metrics.tags.Nb spikes.UID(k)];
% end
% end
end
% PSTH_bar = manualZscore(PSTH_bar,spikes);
% PSTH_bar = zscore(PSTH_bar,1,2);
% [PSTH_bar,PSTH_t] = makePETH(spikes,HSEuse.peaks,[-1 1]);
plotPSTH(PSTH_bar, PSTH_t, index, regTot, subNum+(regTot*2), strcat(check(i), '/barrages'),1);
PSTHmets.PSTH_bar = PSTH_bar;
PSTHmets.PSTH_barT = PSTH_t;

if useState == "NREM"
if contains(plotSave, 'clean')
save([basepath filesep 'Barrage_Files' filesep 'PSTHmet' filesep basename '.clean.' br 'PSTHmets.mat'], 'PSTHmets');
else
save([basepath filesep 'Barrage_Files' filesep 'PSTHmet' filesep basename '.' br 'PSTHmets.mat'], 'PSTHmets');
end
else
if contains(plotSave, 'clean')
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.clean.', br, 'PSTHmets.mat'), 'PSTHmets');
else
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.', br, 'PSTHmets.mat'), 'PSTHmets');
end
end

else
if contains(plotSave, 'clean')
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.clean.', br, 'PSTHmets.mat'), 'PSTHmets');
else
warning(['No pyramidal cells in ' br]);
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.', br, 'PSTHmets.mat'), 'PSTHmets');
end

subNum = subNum+1; % should max at 4
end

else
warning(['No pyramidal cells in ' br]);
end
subNum = subNum+1; % should max at 4
end
sgtitle('Pyramidal PSTH');
saveas(gcf,[plotSave 'PSTH.png']);

subNum = 1; intEmpt = 0;
for i = 1:length(check)
for j=1:length(regions)
regCheck = regions{j};
if contains(regCheck, check(i))
br = convertStringsToChars(check(i));
spikes = [];
if ~exist([basepath filesep 'Barrage_Files' filesep basename '.' br 'int.cellinfo.mat'])
spikes = importSpikes('brainRegion', check(i), 'cellType', ["Wide Interneuron"; "Narrow Interneuron"]);
save([basepath filesep 'Barrage_Files' filesep basename '.' br 'int.cellinfo.mat'], 'spikes');
for i=1:size(useReg,2)
br = useReg{i};
spikes = importSpikes('cellType', "Interneuron", 'brainRegion', br);
if ~isempty(spikes.times)
if plotRips
% PSTH_ripples = computePSTH(ripples,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_ripples,PSTH_t] = makePETH(spikes,ripples.timestamps(:,1),[-3 3]);
% [PSTH_ripples,PSTH_t] = makePETH(spikes,ripples.peaks,[-1 1]);
[PSTH_ripples, PSTH_t] = manualPSTH(spikes, ripples.timestamps(:,1),[-1 1],1/1000);
if runTags
warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_ripples,1)
% if (max(PSTH_ripples(k,91:111))-max(PSTH_ripples(k,1:71))) > 1.5*std(PSTH_ripples(k,:))
% cell_metrics.tags.Pr = [cell_metrics.tags.Pr spikes.UID(k)];
% else
% cell_metrics.tags.Nr = [cell_metrics.tags.Nr spikes.UID(k)];
% end
% end
end
% index = getSort(PSTH_ripples);
index = 1:size(PSTH_ripples,1);
% PSTH_ripples = manualZscore(PSTH_ripples,spikes);
% PSTH_ripples = zscore(PSTH_ripples,1,2);
plotPSTH(PSTH_ripples, PSTH_t, index, regTot, subNum, strcat(br, '/ripples'),2);
PSTHmetsINT.PSTH_ripples = PSTH_ripples;
PSTHmetsINT.ripT = PSTH_t;
PSTHmetsINT.UID = spikes.UID;
end
% PSTH_bar = computePSTH(HSEnrem,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_bar,PSTH_t] = makePETH(spikes,HSEuse.timestamps(:,1),[-3 3]);
[PSTH_bar, PSTH_t] = manualPSTH(spikes, HSEuse.timestamps(:,1),[-1 1],1/1000);
if runTags
warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_bar,1)
% if (mean(PSTH_bar(k,101:201))-mean(PSTH_bar(k,1:100))) > 0.3
% cell_metrics.tags.Pb = [cell_metrics.tags.Pb spikes.UID(k)];
% else
% cell_metrics.tags.Nb = [cell_metrics.tags.Nb spikes.UID(k)];
% end
% end
end
% [PSTH_bar,PSTH_t] = makePETH(spikes,HSEuse.peaks,[-1 1]);
% PSTH_bar = manualZscore(PSTH_bar,spikes);
% PSTH_bar = zscore(PSTH_bar, 1, 2);
plotPSTH(PSTH_bar, PSTH_t, index, regTot, subNum+(regTot*2), strcat(br, '/barrages'),2);
PSTHmetsINT.PSTH_bar = PSTH_bar;
PSTHmetsINT.barT = PSTH_t;

if useState == "NREM"
if contains(plotSave, 'clean')
save(strcat(basepath, filesep, 'Barrage_Files', filesep, 'PSTHmet', filesep, basename, '.clean.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
else
load([basepath filesep 'Barrage_Files' filesep basename '.' br 'int.cellinfo.mat']);
save(strcat(basepath, filesep, 'Barrage_Files', filesep, 'PSTHmet', filesep, basename, '.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
end
if ~isempty(spikes.times)
if plotRips
% PSTH_ripples = computePSTH(ripples,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_ripples,PSTH_t] = makePETH(spikes,ripples.timestamps(:,1),[-3 3]);
% [PSTH_ripples,PSTH_t] = makePETH(spikes,ripples.peaks,[-1 1]);
[PSTH_ripples, PSTH_t] = manualPSTH(spikes, ripples.timestamps(:,1),[-1 1],1/1000);
if runTags
warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_ripples,1)
% if (max(PSTH_ripples(k,91:111))-max(PSTH_ripples(k,1:71))) > 1.5*std(PSTH_ripples(k,:))
% cell_metrics.tags.Pr = [cell_metrics.tags.Pr spikes.UID(k)];
% else
% cell_metrics.tags.Nr = [cell_metrics.tags.Nr spikes.UID(k)];
% end
% end
end
% index = getSort(PSTH_ripples);
index = 1:size(PSTH_ripples,1);
% PSTH_ripples = manualZscore(PSTH_ripples,spikes);
% PSTH_ripples = zscore(PSTH_ripples,1,2);
plotPSTH(PSTH_ripples, PSTH_t, index, regTot, subNum, strcat(check(i), '/ripples'),2);
PSTHmetsINT.PSTH_ripples = PSTH_ripples;
PSTHmetsINT.ripT = PSTH_t;
PSTHmetsINT.UID = spikes.UID;
end
% PSTH_bar = computePSTH(HSEnrem,spikes,'duration',1,'plots', false,'alignment','peaks','zscorePlot',false);
% [PSTH_bar,PSTH_t] = makePETH(spikes,HSEuse.timestamps(:,1),[-3 3]);
[PSTH_bar, PSTH_t] = manualPSTH(spikes, HSEuse.timestamps(:,1),[-1 1],1/1000);
if runTags
warning('NOT ADJUSTED TO NEW DIMENSIONS');
% for k = 1:size(PSTH_bar,1)
% if (mean(PSTH_bar(k,101:201))-mean(PSTH_bar(k,1:100))) > 0.3
% cell_metrics.tags.Pb = [cell_metrics.tags.Pb spikes.UID(k)];
% else
% cell_metrics.tags.Nb = [cell_metrics.tags.Nb spikes.UID(k)];
% end
% end
end
% [PSTH_bar,PSTH_t] = makePETH(spikes,HSEuse.peaks,[-1 1]);
% PSTH_bar = manualZscore(PSTH_bar,spikes);
% PSTH_bar = zscore(PSTH_bar, 1, 2);
plotPSTH(PSTH_bar, PSTH_t, index, regTot, subNum+(regTot*2), strcat(check(i), '/barrages'),2);
PSTHmetsINT.PSTH_bar = PSTH_bar;
PSTHmetsINT.barT = PSTH_t;

if useState == "NREM"
if contains(plotSave, 'clean')
save([basepath filesep 'Barrage_Files' filesep 'PSTHmet' filesep basename '.clean.' br 'PSTHmetsINT.mat'], 'PSTHmetsINT');
else
save([basepath filesep 'Barrage_Files' filesep 'PSTHmet' filesep basename '.' br 'PSTHmetsINT.mat'], 'PSTHmetsINT');
end
else
if contains(plotSave, 'clean')
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.clean.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
else
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
end
end

else
if contains(plotSave, 'clean')
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.clean.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
else
warning(['No interneurons in ' br]);
intEmpt = intEmpt+1;
save(strcat(basepath, filesep, 'Barrage_Files', filesep, useState, filesep, basename, '.', br, 'PSTHmetsINT.mat'), 'PSTHmetsINT');
end
subNum = subNum+1; % should max at 4
end

else
warning(['No interneurons in ' br]);
intEmpt = intEmpt+1;
end
subNum = subNum+1; % should max at 4
end
if ~(intEmpt == length(regions))
if ~(intEmpt == size(useReg,2))
sgtitle('Interneuron PSTH');
saveas(gcf,[plotSave 'PSTHint.png']);
end
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