fix major bug in parsechans where random trial extraction occured wit…

…hin a forloop causing different trials to be chosen every breath.

add new script probe_xcorrlab to analyze the time of max correlations between electrodes

spectral analysis/parse_xchan.m

@@ -41,6 +41,30 @@
 [pathname] = uipickfiles('refilter', '\.mat$', 'type', {'*.mat', 'MAT-files'},...
     'prompt', 'Select all .mat files from MEA channels', 'output', 'cell');
 
+
+tdt_allevents(:,1) = (events(:,1)*srate);
+tdt_allevents(:,2) = events(:,2);
+for odor = eventcodes;  
+    sel_events = find(tdt_allevents(:,2) == odor);
+    if max(sel_events,[],1) == size(events,1); % don't pick last trial (this leads to overflow errors)
+        sel_events = sel_events(1:(length(sel_events)-1)); %cut out last event because the experiment is often ended before a sufficient number of breaths are recorded after this event
+    end
+    for a = eventcodes;
+        b = find(tdt_allevents(:,2) == a);
+        c(a) = length(b);
+        clear b;
+    end
+    min_trials = min(c); %this is the lowest number of trials of an event type, set all trial num to this and exclude trials occuring aferwards
+    if length(sel_events)>min_trials % if this event type has as ton of trials
+        xx = randperm(length(sel_events)); % use randomly picked trials
+        sel_events_short = sel_events(xx(:,1:min_trials));
+    else
+        sel_events_short = sel_events(1:min_trials);
+    end
+    sel_events_all(:,odor) = sort(sel_events_short); %resort event indices back into chronological order
+    clear sel_events sel_events_short a c
+end
+
 for odor = eventcodes;
     disp('odor'); disp(odor);
     for n = 1:length(pathname); %n to number of selected channels 
@@ -49,7 +73,7 @@
         end
         load(pathname{n}); % name of imported data must be "wave"
         for x = 1:length(brthindx) %x to num of breaths
-            wave_segs(:,:,x,n) = parsechans(wave,events,breaths,srate,odor,brthindx(x),winsize,eventcodes);
+            wave_segs(:,:,x,n) = parsechans(wave,events,breaths,srate,sel_events_all(:,odor),winsize,brthindx(x));
             [S, t, f] = pmtm_cust(squeeze(wave_segs(:,:,x,n)),srate,maxfreq);
             spec(:,:,:,x) = S; clear S; %spec = (time, freq, trial, breath)
             %disp('breath'); disp(x);

spectral analysis/parsechans.m

@@ -1,4 +1,4 @@
-function [wave_segs] = parsechans(wave,events,breaths,srate,odor,brth_num,winsize,eventcodes)
+function [wave_segs] = parsechans(wave,events,breaths,srate,event_indices,winsize,brth_num)
 
 %INPUTS:
 % -- "events" matrix containing vectors with event time(in sec) 1st dim,
@@ -12,33 +12,33 @@
 %   eventcode - code of events to extract
 
 win_time = (winsize/2)*srate; %time (samples) to window forward (or beackward) from a breath
-win_offset = 0*srate; %time (seconds) to forward offset window in time
+win_offset = 0*srate; %time (samples) to forward offset window in time
 seek_time = 1000; %num samples to seek forward and backwards from event to find corresponding breath
 
 tdt_allevents(:,1) = (events(:,1)*srate);
 tdt_allevents(:,2) = events(:,2);
 tdt_breaths = round(breaths*srate);
-sel_events = find(tdt_allevents(:,2) == odor);
+% sel_events = find(tdt_allevents(:,2) == odor);
+% 
+% if max(sel_events,[],1) == size(events,1); % don't pick last trial (this leads to overflow errors)
+%     sel_events = sel_events(1:(length(sel_events)-1)); %cut out last event because the experiment is often ended before a sufficient number of breaths are recorded after this event
+% end
+% for a = eventcodes;
+%     b = find(tdt_allevents(:,2) == a);
+%     c(a) = length(b);
+%     clear b;
+% end
+% min_trials = min(c); %this is the lowest number of trials of an event type, set all trial num to this and exclude trials occuring aferwards
+% if length(sel_events)>min_trials % if this event type has as ton of trials
+%     xx = randperm(length(sel_events)); % use randomly picked trials
+%     sel_events_short = sel_events(xx(:,1:min_trials));
+% else
+%     sel_events_short = sel_events(1:min_trials);
+% end
+% sel_events_short = sort(sel_events_short); %resort event indices back into chronological order
 
-if max(sel_events,[],1) == size(events,1); % don't pick last trial (this leads to overflow errors)
-    sel_events = sel_events(1:(length(sel_events)-1)); %cut out last event because the experiment is often ended before a sufficient number of breaths are recorded after this event
-end
-for a = eventcodes;
-    b = find(tdt_allevents(:,2) == a);
-    c(a) = length(b);
-    clear b;
-end
-min_trials = min(c); %this is the lowest number of trials of an event type, set all trial num to this and exclude trials occuring aferwards
-if length(sel_events)>min_trials % if this event type has as ton of trials
-    xx = randperm(length(sel_events)); % use randomly picked trials
-    sel_events_short = sel_events(xx(:,1:min_trials));
-else
-    sel_events_short = sel_events(1:min_trials);
-end
-sel_events_short = sort(sel_events_short); %resort events back into chronological order
-
-for i=1:min_trials; %arbitrary number of trials
-    a = find((tdt_allevents(sel_events_short(i),1)-seek_time) <= tdt_breaths & tdt_breaths <= (tdt_allevents(sel_events_short(i),1)+seek_time));
+for i=1:length(event_indices); %number of trials
+    a = find((tdt_allevents(event_indices(i),1)-seek_time) <= tdt_breaths & tdt_breaths <= (tdt_allevents(event_indices(i),1)+seek_time));
     if length(a) ~= 1 %sometimes the search for breaths matching events returns two breaths.  This happens during abnormally quick respiration.  Eliminate the second one
         a = a(1);
     end

xcorrelation/corrmap_comparechans.m

@@ -3,7 +3,7 @@
 % chan1 = 14;
 % chan2 = 19;
 
-%data = wave_segs; %[corr, corr, tirals, breaths]
+%data = wave_segs; %[corr, corr, trials, breaths]
 tdt_map = [8,16,24,32;...
     7,15,23,31;...
     6,14,22,30;...
@@ -15,8 +15,11 @@
 
 rows = 8;
 cols = 4;
+basebreaths = 1:11;
+odorbreaths = 13:15;
+postbreaths = 16:30;
 
-spec_max = max(max(mean(mean(corr_breath,4),3)));
+spec_max = max(max(mean(mean(corr_breath(:,:,:,basebreaths),4),3)));
 %spec_max = .3;
 spec_min = min(min(mean(mean(corr_breath,4),3)));
 
@@ -26,7 +29,7 @@
         indx = tdt_map(x,y);
         chan1map = squeeze(mean(mean(corr_breath(indx,:,:,:),4),3));
         subplot(rows,cols,(x*cols)-cols+y,'align');
-        imagesc_mea(chan1map,spec_min,spec_max);
+        imagesc_mea(chan1map,0,spec_max);
     end
 end
 %subplot(2,1,1);imagesc_mea(chan1map);colorbar;

xcorrelation/probe_xcorrlag.m

@@ -0,0 +1,30 @@
+% input data is "corrtime_breath" output from xcorr_alltoall
+
+tdt_map = [8,16,24,32;...
+    7,15,23,31;...
+    6,14,22,30;...
+    5,13,21,29;...
+    4,12,20,28;...
+    3,11,19,27;...
+    2,10,18,26;...
+    1,9,17,25];
+rows = size(tdt_map,1);
+cols = size(tdt_map,2);
+
+basebreaths = 1:11;
+odorbreaths = 13:15;
+postbreaths = 16:30;
+
+avelag_odor = mean(mean(corrtime_breath(:,:,:,odorbreaths),4),3);
+avelag_base = mean(mean(corrtime_breath(:,:,:,basebreaths),4),3);
+
+for x=1:rows
+    for y=1:cols
+        indx = tdt_map(x,y);
+        plotlag_base(x,y) = mean(avelag_base(:,indx),1);
+        plotlag_odor(x,y) = mean(avelag_odor(:,indx),1);
+    end
+end
+
+lagdiff = plotlag_odor-plotlag_base;
+imagesc(lagdiff);colorbar;