add solo_spec_stats to redo statitistics without having to run whole …

…parsexchan script over again

xcorr_alltoall has major changes to pick max correlation ina  time window, and to also output the specific time of maximum xcorr in whole time segment

compare_sigs.m

@@ -15,7 +15,7 @@
 
 sum_sigs = squeeze(sum(sig_breaths_allodors(:,:,:,:),1)); %sig_breaths_allodors dimensions (breaths,sigtype,channel,event_type)
 
-% 
+%
 % for i=1:numodors
 %     for x=1:rows
 %         for y=1:cols
@@ -27,15 +27,28 @@
 %     hold on;
 % end
 
-for x=1:rows
-    for y=1:cols
-        indx = tdt_map(x,y);
-        subplot(rows,cols,(x*cols)-cols+y,'align');
-        plot(sum_sigs(indx,:));
+for f = 1:size(sig_breaths_allodors,3)
+    max_sig = max(max(sum_sigs));
+    figure
+    for x=1:rows
+        for y=1:cols
+            indx = tdt_map(x,y);
+            sig_image(x,y) = sum_sigs(indx,f);
+        end
     end
+    imagesc(sig_image, [0 max_sig]);colorbar;
 end
 
-% for h=1:numodors 
+% figure
+% for x=1:rows
+%     for y=1:cols
+%         indx = tdt_map(x,y);
+%         subplot(rows,cols,(x*cols)-cols+y,'align');
+%         plot(sum_sigs(indx,:));
+%     end
+% end
+
+% for h=1:numodors
 % subplot(numodors,1,h);imagesc(squeeze(sig_breaths_allodors(:,:,h)));
 % hold on;
 % end

spectral analysis/test_breathsig.m

@@ -4,23 +4,23 @@
 
 baseline = find(brthindx <= 0); %get all breaths before stimilus (stim triggered on breath 0, so event occurs on next breath)
 signal = find(brthindx >= 1); %get all breaths after stimilus
-alpha = .05;
+alpha = .01;
 
-%     base_mean = squeeze(mean(spec_norm(:,g_freqs,:,baseline),1));
-%     base_gmean = squeeze(mean(base_mean,1));
-%     all_mean = squeeze(mean(spec_norm(:,g_freqs,:,:),1));
-%     all_gmean = squeeze(mean(all_mean,1));
-%     for i=1:size(all_gmean,2) %for each breath
-%         [sig_breaths(i,n),sig_vals(i,n),cis(i,:,n)] = ttest2(all_gmean(:,i),base_gmean(:),alpha/size(all_gmean,2),'both'); %do two-tailed t-test
-%     end
-%     all_spec = all_gmean;
-
-base_max = squeeze(max(spec_norm(:,g_freqs,:,baseline),[],1));
-base_gmax = squeeze(max(base_max,[],1));
-all_max = squeeze(max(spec_norm(:,g_freqs,:,:),[],1));
-all_gmax = squeeze(max(all_max,[],1));
-for i=1:size(all_gmax,2) %for each breath
-    [sig_breaths(i),sig_vals(i),cis(i,:)] = ranksum(all_gmax(:,i),base_gmax(:),alpha/size(all_gmax,2)); %do two-tailed t-test, use bonferroni correction for n=all breaths
+base_mean = squeeze(mean(spec_norm(:,g_freqs,:,baseline),1));
+base_gmean = squeeze(mean(base_mean,1));
+all_mean = squeeze(mean(spec_norm(:,g_freqs,:,:),1));
+all_gmean = squeeze(mean(all_mean,1));
+for i=1:size(all_gmean,2) %for each breath
+    [sig_vals(i),sig_breaths(i),cis(i,:)] = ranksum(all_gmean(:,i),base_gmean(:),alpha);%/size(all_gmean,2),'both'); %do two-tailed t-test
 end
-all_spec = all_gmax;
+all_spec = all_gmean;
+
+% base_max = squeeze(max(spec_norm(:,g_freqs,:,baseline),[],1));
+% base_gmax = squeeze(max(base_max,[],1));
+% all_max = squeeze(max(spec_norm(:,g_freqs,:,:),[],1));
+% all_gmax = squeeze(max(all_max,[],1));
+% for i=1:size(all_gmax,2) %for each breath
+%     [sig_vals(i),sig_breaths(i),cis(i,:)] = ranksum(all_gmax(:,i),base_gmax(:),alpha);%/size(all_gmax,2)); %do ranksum test, use bonferroni correction for n=all breaths
+% end
+% all_spec = all_gmax;
 end

testing/solo_spec_stats.m

@@ -0,0 +1,21 @@
+% import "f" vector
+% sequentially load all "spec_norm" matrices for each odor presentation
+
+gamma = [50 100];
+g_freqs = find(f>gamma(1) & f<gamma(2));
+brthindx = [-10:1:20];
+
+% sequentially import all channels
+[pathname] = uipickfiles('refilter', '\.mat$', 'type', {'*.mat', 'MAT-files'},...
+    'prompt', 'Select all .mat files from MEA channels', 'output', 'cell');
+
+for odor = 1:length(pathname);
+    load(pathname{odor}); % filename must be "spec_norm"
+    for n=1:size(spec_norm,5);
+        [sig_breaths(:,n),sig_vals(:,n),cis(:,n),all_specmax(:,:,n)] = test_breathsig(spec_norm(:,:,:,:,n),brthindx,g_freqs);
+    end    
+    sig_breaths_allodors(:,:,odor) = sig_breaths;
+    sig_vals_allodors(:,:,odor) = sig_vals;
+end
+
+sumbreaths = squeeze(sum(sig_breaths_allodors,1));

xcorrelation/xcorr_alltoall.m

@@ -1,4 +1,4 @@
-function[corr_breath]= xcorr_alltoall(data,FirstChannel,LastChannel,sampFreq,filttype,filtorder)
+%function[corr_breath]= xcorr_alltoall(data,FirstChannel,LastChannel,sampFreq,filttype,filtorder)
 
 %function outputs the zerolag correlation per breath, (averaging along
 %events) in the matrix Corr_Per_Breath(32X32X11 matrix, last dimension is the number of breaths). It is for plotting correlations
@@ -8,6 +8,8 @@
 %SampFreq is the sampling frequency, in our case 3051.76
 %filttype= filttype for sinofilt.m specifies frequency band e.g. [40 100]
 %filtorder is order for SimoFilt.m, 200 typically works best for gamma
+
+corr_win = 30; %window in which to find max correlation, in samples
 data_filtered = filter_data(data,sampFreq,filttype,filtorder);
 
 t0=clock;
@@ -18,14 +20,18 @@
         finalcorr = xcorr(segs,'coeff');
         [qq,ww] = size(segs);
         m=1;
-        for x=1:((LastChannel-FirstChannel)+1)          % we are referencing every channels correlation into a separated third dimension
+        for x=1:((LastChannel-FirstChannel)+1)% we are referencing every channels correlation into a separated third dimension
             newmatrix(:,:,x) = finalcorr(:,(m):(m+(LastChannel-FirstChannel)));
             m=m+((LastChannel-FirstChannel)+1);
         end
-        corr_event(:,:,event)= newmatrix(qq,:,:);   %Check from here, supposed to get the zerolag correlation for all channels, per reference channel, per event
+        corr_event(:,:,event) = squeeze(max(newmatrix((qq-corr_win/2):(qq+corr_win/2),:,:),[],1));%get max correlation in window around time zero
+        [C max_index] = squeeze(max(newmatrix,[],1));
+        max_index = squeeze(max_index)-qq;
+        corrtime_event(:,:,event) = max_index;
         t2=etime(clock,t1);
         ['xcorr_alltoall will complete in t - ', num2str(t2*size(data,3)*size(data,2)-etime(t1,t0)), ' seconds.  Go get some coffee']
     end
     corr_breath(:,:,:,breath)=corr_event;
+    corrtime_breath(:,:,:,breath)=corrtime_event;
 end
-end
+%end