usability fixes; cleanup

@spikesort/removeDoublets.m

@@ -33,7 +33,7 @@ function removeDoublets(s)
     end
 end
 
-if s.pref.ssDebug
+if s.verbosity
     cprintf('green','\n[INFO]')
     cprintf('text', [' B2A doublet resolution.' oval(length(B2A)) ' spikes swapped'])
 
@@ -65,7 +65,7 @@ function removeDoublets(s)
 B = sort(unique([B(:); A2B_cand(:)]));
 A = setdiff(A,A2B_cand);
 
-if s.pref.ssDebug
+if s.verbosity
     cprintf('green','\n[INFO]')
     cprintf('text', [' B2A doublet resolution.' oval(length(A2B_cand)) ' spikes swapped'])
 end

README.md

@@ -57,7 +57,7 @@ brew install tag
 
 This implementation of t-SNE is the the fastest I know of, and gets faster the more cores you throw at it. Follow the installation instructions [here](https://github.com/DmitryUlyanov/Multicore-TSNE#install). macOS users, [see this](https://github.com/DmitryUlyanov/Multicore-TSNE/issues/1#issuecomment-262938483) for installation troubleshooting. 
 
-You then need to tell MATLAB where `Multicore-TSNE is installed`. To do this, 
+You then need to tell MATLAB where `Multicore-TSNE` is installed. To do this, 
 
 1. first determine where it is installed (`pip show MulticoreTSNE`)
 2. Copy and paste this code to your MATLAB `startup.m` (use `edit startup.m`)
@@ -79,6 +79,8 @@ setenv('PATH', path1);
 
 ## Architecture
 
+![](images/arch.png)
+
 `spikesort` is built around a plugin architecture for the three most important things it does: 
 
 * Data handling

build_number

@@ -1 +1 @@
-     247
+     248

docs/README.md

@@ -15,7 +15,6 @@ deltat = 1e-4; % what is the time step of the data?
 
 %% ~~~~~~~~~~~~~~~~~  GENERAL  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-ssDebug = false; 			% should spikesort run in debug mode?
 useFastBandPass = true; 	% use a fast, FFT-based bandPass? 
 
 %% ~~~~~~~~~~~~~~~~~  DISPLAY  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~