number of channels and sampling frequency will be read from the chann…

…el map file if available and NOT already specified in ops

configFiles/StandardConfig_MOVEME.m

@@ -8,10 +8,10 @@
 ops.fproc               = 'C:\DATA\Spikes\Piroska\temp_wh.dat'; % residual from RAM of preprocessed data		
 ops.root                = 'C:\DATA\Spikes\Piroska'; % 'openEphys' only: where raw files are		
 
-ops.fs                  = 25000;        % sampling rate		
-ops.NchanTOT            = 32;           % total number of channels		
-ops.Nchan               = 32;           % number of active channels 		
-ops.Nfilt               = 32;           % number of filters to use (2-4 times more than Nchan, should be a multiple of 32)     		
+ops.fs                  = 25000;        % sampling rate		(omit if already in chanMap file)
+ops.NchanTOT            = 32;           % total number of channels (omit if already in chanMap file)
+ops.Nchan               = 32;           % number of active channels (omit if already in chanMap file)
+ops.Nfilt               = 64;           % number of clusters to use (2-4 times more than Nchan, should be a multiple of 32)     		
 ops.nNeighPC            = 12; % visualization only (Phy): number of channnels to mask the PCs, leave empty to skip (12)		
 ops.nNeigh              = 16; % visualization only (Phy): number of neighboring templates to retain projections of (16)		
 

configFiles/createChannelMapFile.m

@@ -8,8 +8,9 @@
 ycoords   = [1:Nchannels]';
 kcoords   = ones(Nchannels,1); % grouping of channels (i.e. tetrode groups)
 
+fs = 25000; % sampling frequency
 save('C:\DATA\Spikes\20150601_chan32_4_900s\chanMap.mat', ...
-    'chanMap','connected', 'xcoords', 'ycoords', 'kcoords', 'chanMap0ind')
+    'chanMap','connected', 'xcoords', 'ycoords', 'kcoords', 'chanMap0ind', 'fs')
 
 %%
 
@@ -24,8 +25,10 @@
 ycoords   = ycoords(:);
 kcoords   = ones(Nchannels,1); % grouping of channels (i.e. tetrode groups)
 
+fs = 25000; % sampling frequency
+
 save('C:\DATA\Spikes\Piroska\chanMap.mat', ...
-    'chanMap','connected', 'xcoords', 'ycoords', 'kcoords', 'chanMap0ind')
+    'chanMap','connected', 'xcoords', 'ycoords', 'kcoords', 'chanMap0ind', 'fs')
 %%
 
 % kcoords is used to forcefully restrict templates to channels in the same

eMouse/config_eMouse.m

@@ -12,10 +12,7 @@
 ops.chanMap             = fullfile(fpath, 'chanMap.mat'); % make this file using createChannelMapFile.m		
 % ops.chanMap = 1:ops.Nchan; % treated as linear probe if unavailable chanMap file		
 
-ops.fs                  = 25000;        % sampling rate		
-ops.NchanTOT            = 34;           % total number of channels		
-ops.Nchan               = 32;           % number of active channels 		
-ops.Nfilt               = 64;           % number of filters to use (2-4 times more than Nchan, should be a multiple of 32)     		
+ops.Nfilt               = 64;  % number of clusters to use (2-4 times more than Nchan, should be a multiple of 32)     		
 ops.nNeighPC            = 12; % visualization only (Phy): number of channnels to mask the PCs, leave empty to skip (12)		
 ops.nNeigh              = 16; % visualization only (Phy): number of neighboring templates to retain projections of (16)		
 

eMouse/make_eMouseChannelMap.m

@@ -41,4 +41,7 @@ function make_eMouseChannelMap(fpath)
 % no "adjacency graphs" like in KlustaKwik). 
 % Now we can save our channel map for the eMouse. 
 
-save(fullfile(fpath, 'chanMap.mat'), 'chanMap', 'connected', 'xcoords', 'ycoords', 'kcoords')
+% would be good to also save the sampling frequency here
+fs = 25000; 
+
+save(fullfile(fpath, 'chanMap.mat'), 'chanMap', 'connected', 'xcoords', 'ycoords', 'kcoords', 'fs')

fitTemplates.m

@@ -1,6 +1,5 @@
 function rez = fitTemplates(rez, DATA, uproj)
 
-rez.ops.nt0 	= getOr(rez.ops, {'nt0'}, 61);
 nt0             = rez.ops.nt0;
 rez.ops.nt0min  = ceil(20 * nt0/61);
 

preprocessData.m

@@ -1,7 +1,8 @@
 function [rez, DATA, uproj] = preprocessData(ops)
 tic;
 uproj = [];
-nt0 	= getOr(ops, {'nt0'}, 61);
+ops.nt0 	= getOr(ops, {'nt0'}, 61);
+
 
 if strcmp(ops.datatype , 'openEphys')
    ops = convertOpenEphysToRawBInary(ops);  % convert data, only for OpenEphys
@@ -19,12 +20,20 @@
             xc = zeros(numel(chanMapConn), 1);
             yc = [1:1:numel(chanMapConn)]';
         end
+        ops.Nchan    = sum(connected>1e-6);
+        ops.NchanTOT = numel(connected);
+        if exist('fs', 'var')
+            ops.fs       = fs;
+        end
     else
         chanMap = ops.chanMap;
         chanMapConn = ops.chanMap;
         xc = zeros(numel(chanMapConn), 1);
         yc = [1:1:numel(chanMapConn)]';
-        connected = true(numel(chanMap), 1);        
+        connected = true(numel(chanMap), 1);      
+
+        ops.Nchan    = numel(connected);
+        ops.NchanTOT = numel(connected);
     end
 else
     chanMap  = 1:ops.Nchan;
@@ -40,14 +49,14 @@
     kcoords = kcoords(connected);
 end
 NchanTOT = ops.NchanTOT;
-NT = ops.NT ;
+NT       = ops.NT ;
 
+rez.ops         = ops;
 rez.xc = xc;
 rez.yc = yc;
 rez.xcoords = xcoords;
 rez.ycoords = ycoords;
 rez.connected   = connected;
-rez.ops         = ops;
 rez.ops.chanMap = chanMap;
 rez.ops.kcoords = kcoords; 
 
@@ -66,7 +75,7 @@
 
 NTbuff      = NT + 4*ops.ntbuff;
 Nbatch      = ceil(d.bytes/2/NchanTOT /(NT-ops.ntbuff));
-Nbatch_buff = floor(4/5 * nint16s/ops.Nchan /(NT-ops.ntbuff)); % factor of 4/5 for storing PCs of spikes
+Nbatch_buff = floor(4/5 * nint16s/rez.ops.Nchan /(NT-ops.ntbuff)); % factor of 4/5 for storing PCs of spikes
 Nbatch_buff = min(Nbatch_buff, Nbatch);
 
 %% load data into patches, filter, compute covariance
@@ -79,7 +88,7 @@
 fprintf('Time %3.0fs. Loading raw data... \n', toc);
 fid = fopen(ops.fbinary, 'r');
 ibatch = 0;
-Nchan = ops.Nchan;
+Nchan = rez.ops.Nchan;
 if ops.GPU
     CC = gpuArray.zeros( Nchan,  Nchan, 'single');
 else
@@ -93,7 +102,7 @@
     end
 end
 if ~exist('DATA', 'var')
-    DATA = zeros(NT, ops.Nchan, Nbatch_buff, 'int16');
+    DATA = zeros(NT, rez.ops.Nchan, Nbatch_buff, 'int16');
 end
 
 isproc = zeros(Nbatch, 1);
@@ -183,7 +192,7 @@
 
 if strcmp(ops.initialize, 'fromData')
     i0 = 0;
-    ixt = round(linspace(1, size(ops.wPCA,1), nt0));
+    ixt = round(linspace(1, size(ops.wPCA,1), ops.nt0));
     wPCA = ops.wPCA(ixt, 1:3);
     uproj = zeros(1e6,  size(wPCA,2) * Nchan, 'single');
 end