clear vesitbular pathway

setups/vestibular chair/vPrime/core/experiment/block/pb_vBuildSignal.m

+function signal = pb_vBuildSignal(block)
+% PB_VBUILDSIGNAL
+%
+% PB_VBUILDSIGNAL(block) will create the vestibular signals for a given
+% experimental block.
+%
+% See also PB_VPRIME, PB_VSIGNALVC, PB_VSAFETY, PB_VCHECKVELSIGNAL
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+   % read signals
+   signal(1)   = block.ver;
+   signal(2)   = block.hor; 
+   
+   for iSig = 1:2
+      % correct for vestibular chair's inertia.
+      if strcmp(signal(iSig).type,'sine'); signal(iSig).type = 'predictsine'; end
+   end
+end
+ 
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/core/experiment/block/pb_vSignalVC.m

-function [Dat,profile,dur] = pb_vSignalVC(handles)
+function [profile,dur] = pb_vSignalVC(handles)
 % PB_VSIGNALVC
 %
 % PB_VSIGNALVC(handles) reads vestibular signal from handles, writes
@@ -11,57 +11,49 @@ function [Dat,profile,dur] = pb_vSignalVC(handles)
    block       = handles.block;
    bnumber     = handles.cfg.blocknumber;
    
-   %% READ SIGNAL PARAMETERS
-   signal(1)   = block(bnumber).signal.ver;
-   signal(2)   = block(bnumber).signal.hor;     
+   % Read & create signals
+   signal      = pb_vBuildSignal(block(bnumber).signal);  
    signal      = pb_vSafety(signal); 
    
-   for iSig = 1:2
-      if strcmp(signal(iSig).type,'sine'); signal(iSig).type = 'predictsine'; end
-   end
-
-   %% CREATE BASIC SIGNAL
    vSignal     = pb_vCreateSignal(1, signal(1).duration, 10, signal(1).frequency, signal(1).type);
    hSignal     = pb_vCreateSignal(1, signal(2).duration, 10, signal(2).frequency, signal(2).type);
 
-   %% FINALIZE SIGNAL
-   Dat.v.x     = vSignal.x .* signal(1).amplitude;    
-   Dat.v.t     = (0:1:length(Dat.v.x)-1)/10;
-   profile.v   = Dat.v.x;
-   
-   Dat.h.x     = hSignal.x .* signal(2).amplitude;    
-   Dat.h.t     = (0:1:length(Dat.h.x)-1)/10;      
-   profile.h   = Dat.h.x;
-   
-   Dat.v.amplitude   = signal(1).amplitude;
-   Dat.h.amplitude   = signal(2).amplitude;
+   % Finalize signals
+   sigData.v.x    = vSignal.x .* signal(1).amplitude;    
+   sigData.v.t    = (0:1:length(sigData.v.x)-1)/10;
+   profile.v      = sigData.v.x;
    
-   %% CHECK SAFETY FINAL SIGNAL
+   sigData.h.x    = hSignal.x .* signal(2).amplitude;    
+   sigData.h.t    = (0:1:length(sigData.h.x)-1)/10;      
+   profile.h      = sigData.h.x;
    
-   [hSafe,~]      = pb_vCheckVelSignal(Dat.h.x);
-   [vSafe,mvel]   = pb_vCheckVelSignal(Dat.v.x);
+   % Check signal safety
+   [hSafe,~]      = pb_vCheckVelSignal(profile.h);
+   [vSafe,mvel]   = pb_vCheckVelSignal(profile.v);
    
    if ~hSafe || ~vSafe
       error(['Vestibular signals were not safe! (velocity exceeds ' num2str(mvel) ')']);
    end
    
-   
-   %% FEEDBACK GUI
+   % Feedback GUI
    updateBlock(handles, signal);
-   
+
    handles  = pb_gethandles(handles);
    dur      = max([handles.block(bnumber).signal.ver.duration handles.block(bnumber).signal.hor.duration]);
    
+   % set axis
    axes(handles.signals); 
    cla; hold on; 
    handles.signals.YLim    = [-50 50];
    handles.signals.XLim    = [0 dur];
    
-   dv = 10 * [0 diff(Dat.v.x)];
-   dh = 10 * [0 diff(Dat.h.x)];
+   % plot signals
+   dv    = 10 * [0 diff(profile.v)];
+   dh    = 10 * [0 diff(profile.h)];
+   t     = sigData.v.t;
    
-   plot(Dat.v.t,dv,'k');
-   plot(Dat.h.t,dh,'b');
+   plot(t,dv,'k');
+   plot(t,dh,'b');
 end
 
 function updateBlock(handles, signal)

setups/vestibular chair/vPrime/core/experiment/trial/pb_vStoreData.m

@@ -14,7 +14,6 @@ function handles = pb_vStoreData(handles, data)
    [~,prefix]        = pb_fext(cfg.fname);
    fname             = [prefix '-' num2str(cfg.trialnumber(2),'%04d') '.vc'];
    
-   data = data;                        %% TO DO: <-- FIX: SELECT DATA FOR TRIAL ONLY
    beta  = setCFG(cfg);                %% TO DO: <-- FIX: SELECT CFGs FOR TRIAL ONLY
    
    save(fname,'data', 'beta', '-mat');

setups/vestibular chair/vPrime/core/pb_vRunExp.m

@@ -18,10 +18,10 @@ function pb_vRunExp(handles)
    
    %  set handles
    pb_setupShow(handles);
-   handles	= pb_gethandles(handles);
-   handles 	= pb_getblock(handles);
-   handles 	= pb_createdir(handles);
-   handles	= pb_vInitialize(handles, true);
+   handles     = pb_gethandles(handles);
+   handles     = pb_getblock(handles);
+   handles     = pb_createdir(handles);
+   handles     = pb_vInitialize(handles, true);
    
    %  set block information
    block       = handles.block;  
@@ -29,20 +29,19 @@ function pb_vRunExp(handles)
    Dat         = pb_dataobj(nblocks);
     
    %  initialize recordings
-   rc             = pb_runPupil; 
-   [ses,streams]  = pb_runLSL;
-   experimentTime = tic;
+   rc          = pb_runPupil; 
+   [ses,str]   = pb_runLSL;
+   expTime     = tic;
    
    %% START BLOCK 
    %  iterate experimental blocks 
    
    for iBlck = 1:nblocks
-      %  Runs blocks of trials with a vestibular condition
       
       %  set block information
-      nTrials              = length(block(iBlck).trial);
-      handles              = updateCount(handles,'trial','reset');
-      [sig,profile,dur]    = pb_vSignalVC(handles);
+      nTrials          	= length(block(iBlck).trial);
+      handles          	= updateCount(handles,'trial','reset');
+      [profile,dur]    	= pb_vSignalVC(handles);
       
       %  start recording
       pb_startLSL(ses);
@@ -51,8 +50,9 @@ function pb_vRunExp(handles)
       %  start vestibular chair
       if ~ismac && ~debug     
          pb_vCheckServo;
-         vs          = pb_sendServo(profile);
-         blockTime   = tic; 
+         
+         vs            	= pb_sendServo(profile);
+         blockTime    	= tic; 
          pb_startServo(vs);
          pause(6);                                                         % allow vestibular chair to get in sync with input signal
       end
@@ -61,19 +61,20 @@ function pb_vRunExp(handles)
       %  iterate over trials per block
       
       for iTrl = 1:nTrials
-         % Runs all trials within one block
          
-         % setup trial
+         %  setup trial
          updateTrial(handles);
          stim                 = handles.block(iBlck).trial(iTrl).stim;
          handles.cfg          = pb_vClearTrial(stim, handles.cfg); 
          [~, handles.cfg]     = pb_vSetupTrial(stim, handles.cfg);
          trialTime            = tic;
          
+         %  run trial
          pb_vRunTrial(handles.cfg.zBus, handles.cfg.trialdur);
          pb_vTraces(handles);       
          
-         handles        = pb_vStoreData(handles, sig);
+         %  save trial
+         handles        = pb_vStoreData(handles, profile);
          handles.cfg    = updateCount(handles.cfg,'trial','count');
          toc(trialTime);
       end
@@ -95,9 +96,9 @@ function pb_vRunExp(handles)
       pb_stopLSL(ses); 
       
       %  store data
-      Dat(iBlck).event_data    = streams(1).read;
-      Dat(iBlck).pupil_labs    = streams(2).read;
-      Dat(iBlck).optitrack     = streams(3).read;
+      Dat(iBlck).event_data    = str(1).read;
+      Dat(iBlck).pupil_labs    = str(2).read;
+      Dat(iBlck).optitrack     = str(3).read;
       Dat(iBlck).block_info    = handles.block(iBlck);
 
       %  update block information
@@ -111,7 +112,7 @@ function pb_vRunExp(handles)
    pb_vEndExp;
    pb_vStoreBlockDat(handles.cfg, Dat);
    pb_vInitialize(handles, false);
-   toc(experimentTime)
+   toc(expTime)
 end
 
 %-- GUI feedback functions --%