v3.2.3

1. Bugfix: incorrect "gather" function was called when Bigdata toolbox is installed in Matlab R2017.

2. Faster and more robust fft_clean operation (run if `fft_thresh` > 0)
  It can handle a limited GPU memory.
`nLoads_gpu` parameter is introduced, which is the ratio of the system memory (RAM) to GPU memory.
  If your GPU memory size is 12 GB and RAM is 96 GB, set nLoads_gpu = 8.
  Increase this value if GPU error occurs (default: 8), do not change the default value otherwise.
  `nSamples_gpu` is now deprecated, and automatically calculated from `nLoads_gpu` parameter.

change_log.txt

@@ -2,6 +2,19 @@
 J. James Jun
 
 --------------------------------------------------------------------
+[2019/1/3: v3.2.3]
+Bugfix: incorrect "gather" function was called for R2017b when Bigdata toolbox is installed.
+Faster and more robust fft_clean operation (run if `fft_thresh` > 0)
+  It can handle a limited GPU memory.
+`nLoads_gpu` parameter is introduced, which is the ratio of the system memory (RAM) to GPU memory.
+  If your GPU memory size is 12 GB and RAM is 96 GB, set nLoads_gpu = 8.
+  Increase this value if GPU error occurs (default: 8), do not change the default value otherwise.
+  `nSamples_gpu` is now deprecated, and automatically calculated from `nLoads_gpu` parameter.
+
+[2017/12/30: v3.2.2]
+Bugfix: PSTH histogram plot error is fixed and two PSTH plots are displayed
+  top and bottom when two units are selected.
+
 [2017/12/29: v3.2.1]
 Old multishank probe file format is supported (v1, jrclust.m). 
   'cviShank' which is a cell containing a list of sites is converted to 'shank' format

default.prm

@@ -16,15 +16,15 @@ fInverse_file = 0;          % Set to 1 to flip the polarity of the signal
 header_offset = 0;          % File header offset (set to 0 for files containing no header info (e.g. WHISPER format)
 
 % #Execution parameters
-version = 'v3.2.1';        % JRCLUST version. Updated on Dec 29, 2017
+version = 'v3.2.3';         % JRCLUST version. Updated on Jan 3, 2018
 fVerbose = 0;               % Verbose flag, set to 0 to suppress displaying extra information 
 fParfor = 1;                % Use Multiple CPU cores (if parallel processing toolbox is installed)
 fGpu = 1;                   % Use GPU if parallel processing toolbox is installed
 iGpu = 1;                   % Use specific GPU ID (run 'gpuDevice()' to retrieve the list of GPUs)
 MAX_BYTES_LOAD = [];        % Default memory loading block size (bytes)
 MAX_LOAD_SEC = [];          % Maximum loading duration (seconds). This overrides "MAX_BYTES_LOAD".
-MAX_LOG = 5;               % Maximum number of histories to track for 'manual' GUI
-nSamples_gpu = 250000;      % Number of samples to process in GPU at a time. Reduce this number if GPU crashes for high-channel arrays
+MAX_LOG = 5;                % Maximum number of histories to track for 'manual' GUI
+nLoads_gpu = 8;             % Ratio of RAM to GPU memory. If your GPU memory is 12 GB and RAM is 96 GB, set nLoads_gpu = 8. Increase this number if you get GPU memory error.
 vcFile_thresh = '';         % Name of .mat file taht stores the spike detection threshold in 'vnThresh_site' variable. Created by 'preview' GUI
 sec_per_load_preview = 1;   % Recording duration (sec) per continuous segment to preview
 nLoads_max_preview = 30;    % Number of time segments to load for preview

fft_clean.m

@@ -1,4 +1,6 @@
 function mr1 = fft_clean(mr, thresh, nbins)
+% mr must be single
+
 if nargin<2, thresh = 6; end
 if nargin<3, nbins = 20; end
 nSkip_med = 4;
@@ -8,22 +10,16 @@
 if thresh==0, thresh = []; end
 if isempty(thresh), mr1=mr; return ;end
 
-mr = single(mr);
+% mr = single(mr);
 vrMu = mean(mr, 1);
 mr1 = bsxfun(@minus, mr, vrMu);
 n = size(mr1,1);
-% pad if needed
 n_pow2 = 2^nextpow2(n);
-% try
-    if n < n_pow2
-        mr1 = fft(mr1, n_pow2);
-    else
-        mr1 = fft(mr1);
-    end
-% catch
-%     disp('fft_clean: GPU-based FFT failed. Trying CPU-based FFT. Reset GPU or restart Matlab.');
-%     mr1 = fft(gather(mr1), n_pow2); %GPU-based FFT failed
-% end
+if n < n_pow2
+    mr1 = fft(mr1, n_pow2);
+else
+    mr1 = fft(mr1);
+end
 n1 = floor(n_pow2/2);
 viFreq = (1:n1)';
 % vrFft1 = abs(mean(bsxfun(@times, mr1(1+viFreq,:), viFreq), 2));
@@ -64,12 +60,9 @@
 
 mr1(1+vi_noise,:) = 0;
 mr1(end-vi_noise+1,:) = 0;
-mr1 = real(ifft(mr1)); %slow
-if n < n_pow2
-    mr1 = mr1(1:n,:);
-end
-
-
+mr1 = real(ifft(mr1, n_pow2, 'symmetric')); %~30% faster than below
+% mr1 = real(ifft(mr1));
+if n < n_pow2, mr1 = mr1(1:n,:); end
 mr1 = bsxfun(@plus, mr1, vrMu); %add mean back
 
 if nargout==0 || fDebug