From abc993520256aab7110cfd3c36392212624300e0 Mon Sep 17 00:00:00 2001
From: Jakob Voigts <jvoigts@mit.edu>
Date: Sun, 8 Oct 2017 16:31:00 -0400
Subject: [PATCH] small fixes and perfornamce updates

---
 sc_loadmuadata.m         | 17 ++++++++++++++++-
 sc_mua2features.m        | 18 +++++++++++++++++-
 sc_updateclusterimages.m |  8 ++++----
 simple_clust.m           |  2 +-
 4 files changed, 38 insertions(+), 7 deletions(-)

diff --git a/sc_loadmuadata.m b/sc_loadmuadata.m
index 2d144d3..6e62f37 100644
--- a/sc_loadmuadata.m
+++ b/sc_loadmuadata.m
@@ -9,10 +9,22 @@
 switch muafile_ext
     
     case 'spikes' % open ephys data format
-        [data, timestamps, info] = load_open_ephys_data(muafile);
+        [data, timestamps, info] = load_open_ephys_data_faster(muafile);
+        
+       % remove end of file? 
+       % cutoff_t=3.9100e+03;
+       % cutoff=min(find(timestamps>cutoff_t));
+       % data=data(1:cutoff,:,:);
+       % timestamps=timestamps(1:cutoff);
+        
         
         features.chnumstr = info.header.electrode;
+        
         features.sourcechannel= str2num(info.header.electrode(end-1:end));
+        if numel( features.sourcechannel)==0
+            features.sourcechannel= str2num(info.header.electrode(end));
+        end;
+        
         sourcechannel=features.sourcechannel; % just so we dont overwrite it in  'features=sc_mua2features(mua,s_opt);'
         
         
@@ -474,6 +486,9 @@
     
     features.waveformscale=0.0001;
     
+    mua.waveforms( find(abs(mua.waveforms) > 10000) ) =0;
+ mua.waveforms( isnan(mua.waveforms) ) =0;
+    
     % find appropriate scale for plotting waveforms
     features.waveformscale=0.1 ./ quantile(mua.waveforms(1:100:end)-mean(mua.waveforms(1:100:end)),.95);
     
diff --git a/sc_mua2features.m b/sc_mua2features.m
index 3b86fb7..ddfc39d 100644
--- a/sc_mua2features.m
+++ b/sc_mua2features.m
@@ -136,6 +136,22 @@
     
     if n==1; features.name{c}=['time']; end;
     
+    
+    %max peak
+    if 0
+        for d=1:mua.ncontacts %size(spike,1)
+            c=c+1;
+            %features.data(c,n)= nle(d,n);
+            
+            x=spike(trodeboundaries(d):trodeboundaries(d+1)-1);
+            
+            features.data(c,n)= -x(9);
+            
+            if n==1; features.name{c}=['peak ',num2str(d)]; end;
+            
+        end;
+    end;
+    
     %peak height
     for d=1:mua.ncontacts %size(spike,1)
         x=spike(trodeboundaries(d):trodeboundaries(d+1)-1);
@@ -144,7 +160,7 @@
         c=c+1;
         features.data(c,n)= neo(d);
         
-        if n==1; features.name{c}=['peak ',num2str(d)]; end;
+        if n==1; features.name{c}=['max ',num2str(d)]; end;
         
     end;
         
diff --git a/sc_updateclusterimages.m b/sc_updateclusterimages.m
index 83e3d44..bbdd2e3 100644
--- a/sc_updateclusterimages.m
+++ b/sc_updateclusterimages.m
@@ -45,10 +45,11 @@
         sfact = features.imagesize/x;
         features.waveforms_hi=zeros(size(mua.waveforms,1),round(x*sfact));
         
+        ii_intp=round(L_im);
         
         for i=1:size( mua.waveforms,1)
             
-            if mod(i,4000)==0
+            if mod(i,10000)==0
                 clf; hold on;
                 fill([-2 -2 5 5],[-2 2 2 -2],'k','FaceColor',[.95 .95 .95]);
                 
@@ -66,9 +67,8 @@
                 drawnow;
             end;
             
-            
-            
-            features.waveforms_hi(i,:) = interp1(1:x,mua.waveforms(i,:),L_im, 'linear'); % use 'linear' for speed or even 'nearest'
+            %features.waveforms_hi(i,:) = interp1(1:x,mua.waveforms(i,:),L_im, 'nearest'); % use 'linear' for speed or even 'nearest'
+            features.waveforms_hi(i,:) = mua.waveforms(i,ii_intp);
         end;
     end;
 end;
diff --git a/simple_clust.m b/simple_clust.m
index 1d70ef2..3796320 100644
--- a/simple_clust.m
+++ b/simple_clust.m
@@ -105,7 +105,7 @@
 % specify what features to compute:
 s_opt.features.pca=0;
 s_opt.features.wavelet=0;
-s_opt.features.nonlinear_energy=1;
+s_opt.features.nonlinear_energy=0;
 s_opt.features.max_derivative=1;
 
 %% init