Merge pull request #21 from ayalab1/BARR_updates

Barr updates

Author: lkaraba

BARRs/BARR_PSTH.m

@@ -225,9 +225,9 @@ function BARR_PSTH(plotSave,useState)
                 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],1/1000);
+                    [PSTH_ripples, PSTH_t] = manualPSTH(spikes, ripples.timestamps(:,1),[-1,1],1/100); %was 1/1000
                     if runTags
-                        warning('NOT ADJUSTED TO NEW DIMENSIONS');
+                        %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)];
@@ -248,9 +248,9 @@ function BARR_PSTH(plotSave,useState)
                 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);
+                [PSTH_bar, PSTH_t] = manualPSTH(spikes, HSEuse.timestamps(:,1),[-1 1],1/100); %was 1/1000
                 if runTags
-                    warning('NOT ADJUSTED TO NEW DIMENSIONS');
+                    %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)];
@@ -414,7 +414,7 @@ function BARR_PSTH(plotSave,useState)
 shuffled_r = cumsum([shuffled_iri]); %raly had cumsum([0; shuffled_iri]);
 
 [ccg_ripple_barrage_shuf,t_ripple_barrage_shuf] = CCG(cat(1,shuffled_r,t_barrages{1}),cat(1,t_ripple_id{1},2*t_barrage_id{1}),'binSize',binsize,'duration',duration,'norm','rate');
-        figure(5);plot(t_ripple_barrage_shuf,ccg_ripple_barrage_shuf(:,2,1),'r');hold on;title('ccg barr-SWR'); yline(0,'k--');xlim([-3 3]);
+        figure(5);plot(t_ripple_barrage_shuf,ccg_ripple_barrage_shuf(:,2,1),'r');hold on;title('ccg barr-SWR shuffle'); yline(0,'k--');xlim([-3 3]);
         saveas(gcf,[plotSave 'CCG_shuff.png']);
         % Old jitter start
 %     for it = 1:10000

BARRs/detectBARR.m

@@ -53,12 +53,14 @@
 %               Default: 0
 % pareDur:      Minimum duration of BARRs kept, in seconds. This should
 %               generally be kept at or below 0.2. Default: 0.2
-% zeroRip:      Logical option to zero firing during SWRs. This is 
-%               typically used for sessions containing stimulation (ie 
-%               ripple generation). This seems to be a better option than 
-%               remRip.Default: false
-% remRip:       Logical option to remove BARRs which overlap with ripples.
+% zeroRip:      Logical option to remove BARRs which overlap with ripples.
+%               This seems to be a better option than remRip. 
 %               Default: false
+% remRip:       Logical option to zero firing during SWRs. This is 
+%               typically used for sessions containing stimulation (ie 
+%               ripple generation). Default: false
+% newSpks:      Logical option to regenerate spike groups if the regions or
+%               cell types have been adjusted. Default: false
 %
 %%%%%%%%%%%%%%%
 %%% OUTPUTS %%%
@@ -101,6 +103,7 @@
 addParameter(p, 'pareDur', 0.2, @isnumeric);
 addParameter(p, 'zeroRip', true, @islogical);
 addParameter(p, 'remRip', false, @islogical);
+addParameter(p, 'newSpks', false, @islogical);
 
 parse(p, varargin{:});
 
@@ -118,6 +121,7 @@
 pareDur = p.Results.pareDur;
 zeroRip = p.Results.zeroRip;
 remRip = p.Results.remRip;
+newSpks = p.Results.newSpks;
 
 %% Check if BARRs have already been detected
 basename = basenameFromBasepath(basepath);
@@ -135,7 +139,7 @@
     mkdir([basepath filesep 'Barrage_Files']);
 end
 
-pullSpikes('basepath', basepath, 'savePath', [basepath filesep 'Barrage_Files'], 'force', true); %Get region/cell type spike files
+pullSpikes('basepath', basepath, 'savePath', [basepath filesep 'Barrage_Files'], 'force', newSpks); %Get region/cell type spike files
 
 if ~exist(strcat(basepath,filesep,'Barrage_Files',filesep,basename,'.CA2pyr.cellinfo.mat'))
     disp('No CA2 pyramidal cells detected, exiting');
@@ -174,6 +178,12 @@
                 'recordMetrics',true,'remRip',remRip);
 
 HSE = pareBARRs(basepath, HSE, spikes, savePath, unMin, spkNum, pareDur, spkHz, zeroRip, unMax);
+%add unitsForDetection parameters
+HSE.detectorinfo.Hz = Hz;
+HSE.detectorinfo.ft = ft;
+HSE.detectorinfo.numEvt = numEvt;
+HSE.detectorinfo.savePath = savePath;
+save([savePath 'HSE.mat'], 'HSE');
 
 %% Save NeuroScope2 file
 BARR_N2(basepath);

BARRs/pareBARRs.m

@@ -136,5 +136,14 @@
 HSE.fin = HSE.keep(HSE.NREM(HSE.nonRip)); 
 disp(['Final num: ' num2str(length(HSE.fin))]);
 disp(['Num removed: ' num2str(length(HSE.NREM) - length(HSE.fin))]);
+
+%%add parameters
+HSE.detectorinfo.numCell = numCell;
+HSE.detectorinfo.numSpk = numSpk;
+HSE.detectorinfo.pareDur = pareDur;
+HSE.detectorinfo.singleHz = singleHz;
+HSE.detectorinfo.stim = stim;
+HSE.detectorinfo.maxCell = maxCell;
+
 save([savePath 'HSE.mat'], 'HSE');
 end

BARRs/pullSpikes.m

@@ -16,7 +16,7 @@ function pullSpikes(varargin)
 addParameter(p,'savePath',pwd,@ischar);
 addParameter(p,'force',false,@islogical);
 
-parse(p,varargin{:})
+parse(p, varargin{:});
 
 basepath = p.Results.basepath;
 savePath = p.Results.savePath;
@@ -27,8 +27,8 @@ function pullSpikes(varargin)
 basename = basenameFromBasepath(basepath);
 
 %% Remove old runs if necessary
+getFiles = dir();
 if force
-    getFiles = dir();
     fun_existsPyr = @(x) (contains(x, 'pyr.cellinfo.mat'));
     fun_existsInt = @(x) (contains(x, 'int.cellinfo.mat'));
     toDelete = zeros(size(getFiles,1),1);
@@ -53,6 +53,7 @@ function pullSpikes(varargin)
     fun_existsInt = @(x) (contains(x, 'int.cellinfo.mat'));
     for j = 1:size(getFiles,1)
         if fun_existsPyr(getFiles(j).name)||fun_existsInt(getFiles(j).name)
+            cd(original);
             disp('Region spike structures detected, returning');
             return
         end