From 5eeb87af846de52167eaaf3741b355bf24ba2620 Mon Sep 17 00:00:00 2001
From: "Steven.le-cam" <steven.le-cam@univ-lorraine.fr>
Date: Sun, 10 Sep 2023 12:37:43 +0200
Subject: [PATCH] add class labels as VBDS method output
---
VBDS.m | 6 +++++-
main.m | 25 +++++++++++--------------
2 files changed, 16 insertions(+), 15 deletions(-)
diff --git a/VBDS.m b/VBDS.m
index c1354e6..c3ddcfb 100644
--- a/VBDS.m
+++ b/VBDS.m
@@ -1,4 +1,4 @@
-function [paramVBDS,Spike,w]=VBDS(xb,Fs,paramVBDS,display,verbose)
+function [paramVBDS,Spike,w,Z]=VBDS(xb,Fs,paramVBDS,display,verbose)
% Pipeline for spike detection, feature extraction and spike/LFP
% classification/separation
% input:
@@ -11,6 +11,7 @@ function [paramVBDS,Spike,w]=VBDS(xb,Fs,paramVBDS,display,verbose)
% paramVDBS: updated method parameters
% Spike: matrix of estimated spike waveforms
% w: despiked LFP
+% Z: spike labels
%%
%Band pass filtering to highlight the spikes and thresholding
@@ -44,6 +45,7 @@ for t=1:10
KGMM(t)=mixture.K;
end
+
paramVBDS.K=ceil(mean(KGMM));
end
@@ -53,5 +55,7 @@ end
% Classif and despiking
%
[paramVBDS,Spike,w]=LFPSpikeDemixing(xbr,xb,Fs,ideltasr,gB,wfeat,paramVBDS,indsupp,verbose);
+[~,Z]=max(paramVBDS.param.piapost,[],2);
+Z(paramVBDS.param.r==1)=0;
end
\ No newline at end of file
diff --git a/main.m b/main.m
index 34f63d8..d91e334 100644
--- a/main.m
+++ b/main.m
@@ -30,17 +30,17 @@ verbose=true; % verbose mode
% process
%%% SIMULATED DATA Le Cam et. al.
-% DATA_PATH='./';
-% DATA_NAME='example.mat';
-% load([DATA_PATH DATA_NAME],'xb','Fs');
+DATA_PATH='./';
+DATA_NAME='example.mat';
+load([DATA_PATH DATA_NAME],'xb','Fs');
%%%
%%% SIMULATED DATA CAMUNAS (EXAMPLE 4)
-paramVBDS.coef=4.5; % better parameters for these simulated data
-paramVBDS.nbfeat=12;
-load('simulation_4.mat');
-xb=data;
-Fs=24000;
+% paramVBDS.coef=4.5; % better parameters for these simulated data
+% paramVBDS.nbfeat=12;
+% load('simulation_4.mat');
+% xb=data;
+% Fs=24000;
%%%
[l,c]=size(xb);
@@ -77,7 +77,7 @@ end
%%%%%%%%%%%%%%%%%%%%%
%% VBDS
-[paramVBDS,Spike,w]=VBDS(xb,Fs,paramVBDS,display,verbose);
+[paramVBDS,Spike,w,Z]=VBDS(xb,Fs,paramVBDS,display,verbose);
%%%%%%%%%%%%%%%%%%%%%
@@ -87,7 +87,6 @@ end
if display
-[~,classif]=max(paramVBDS.param.piapost');
K=paramVBDS.K;
ns=paramVBDS.ds*Fs/1000;
@@ -102,16 +101,14 @@ rootK2=ceil(K/rootK);
for k=1:K
subplot(rootK,rootK2,k);
- piapostk=paramVBDS.param.piapost(:,k).*(1-paramVBDS.param.r);
- Ik=find(piapostk>0.5);
- plot((-ns/2+1:ns/2)/Fs*1000,Spike(Ik,:)');
+ plot((-ns/2+1:ns/2)/Fs*1000,Spike(Z==k,:)');
hold on,
plot((-ns/2+1:ns/2)/Fs*1000,paramVBDS.S0(k,:),'r--','Linewidth',2);
plot((-ns/2+1:ns/2)/Fs*1000,paramVBDS.S0(k,:)+2.2*sqrt(paramVBDS.varskt(k)),'k--','Linewidth',1.5);
plot((-ns/2+1:ns/2)/Fs*1000,paramVBDS.S0(k,:)-2.2*sqrt(paramVBDS.varskt(k)),'k--','Linewidth',1.5);
ylim(1.05*[miny maxy]) %ylim(1.1*[-maxy maxy]);
xlim([-1 1]);
- title(['#' num2str(length(Ik))],'FontSize',16)
+ title(['#' num2str(sum(Z==k))],'FontSize',16)
xlabel('Time (ms)','FontSize',16)
ylabel('Voltage','FontSize',16)
end
--
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