added substantial body back end vPrime

setups/vestibular chair/vPrime/cfg/pb_createdir.m

+function handles = pb_createdir(handles)
+% PB_CREATEDIR()
+%
+% PB_CREATEDIR()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+   % Creates directory and sets parameters for data storage
+   cfg = handles.cfg;
+   
+   path = [cfg.dname filesep 'trial'];
+   if ~exist(path,'dir'); mkdir(path); end
+   
+   cd(path);
+   
+   fname = [cfg.expInitials '-' cfg.subjectid '-' cfg.datestring '-' cfg.recording '-0001.vc' ]; 
+   
+   while exist(fname,'file')
+      % Check for existing recordings
+      quest    = 'Recording already exists. Indicate how to proceed?'; 
+      answer   = questdlg(quest,'Choices','Overwrite', 'Increment','Stop','Stop');
+      switch answer
+         case 'Overwrite'
+            break;
+         case 'Increment'
+            cfg.recording = num2str(str2double(cfg.recording)+1,'%04d');
+            set(handles.editRec,'string',cfg.recording);   
+         case 'Stop'
+            error('Run stopped.');
+      end
+      fname = [cfg.expInitials '-' cfg.subjectid '-' cfg.datestring '-' cfg.recording '-0001.vc' ];
+   end
+   handles.cfg = cfg;
+   handles     = pb_gethandles(handles);
+end
+
+
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/cfg/pb_datapath.m

+function path = pb_datapath(path)
+% PB_DATAPATH()
+%
+% PB_DATAPATH()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+   if nargin == 0; path = []; end
+   if isempty(path) || ~exist(path)
+      username = char(java.lang.System.getProperty('user.name'));
+      if ismac                                                             % MAC       (personal   //    NO VC, NO TDT)
+         path = ['/Users/' username '/Documents/Data/Experiment'];
+         %path = '/Users/jjheckman/Documents/Data/PhD/Experiment/VC';
+      elseif isunix && ~ismac                                            	% LINUX     (public     //    VC, NO TDT)
+         path = ['/home/' username '/Documents/Data'];
+      elseif ispc                                                        	% WINDOWS   (public     //    VC, TDT)
+         path = ['C:\Users\' username '\Documents\Data'];
+      end  
+   end
+end
+ 
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/cfg/pb_getblock.m

+function handles = pb_getblock(handles)
+% PB_GETBLOCK()
+%
+% PB_GETBLOCK()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+   cfg            = handles.cfg;
+   
+   
+   [block, cfg]   = pb_vReadExp(cfg);
+   
+   block          = pb_vPrimeZ(block,cfg);
+   
+   handles.block  = block;
+   handles.cfg    = cfg;
+end
+ 
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/cfg/pb_getcfgdefaults.m

+function handles = pb_getcfgdefaults(handles)
+% PB_GETCFGDEFAULTS()
+%
+% PB_GETCFGDEFAULTS()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+   %% Default parameters
+   cfg.fpath		= pb_datapath; % default data folder
+   cfg.date			= date;
+
+   cd(cfg.fpath); % default data folder
+   d					= dir;
+   d					= d([d.isdir]);
+   d					= d(3:end);
+   cfg.expinitials		= {d.name};
+
+   formatOut	= 'yy-mm-dd';
+   d			= datestr(now,formatOut);
+   cfg.date	= d;
+   cfg.datestring = d;
+   cfg.trialnumber = 1;
+   cfg.blocknumber = 1;
+
+   %% TDT and PLC defaults
+   cfg = pb_tdtglobals(cfg);		% TDT defaults
+   
+   %% TDT and PLC defaults
+   cfg.nleds				= 256; % maximum number of LED configurations on PLC
+
+   cfg.calfile				= which('vPrime.net');
+   if isempty(cfg.calfile)
+      cfg.calfile			= which('defaultvPrime.net');
+   end
+
+   %% Convert experimental trial
+
+   cfg						= pb_vLSCpositions(cfg); % lookup structure
+
+   %% Data filter coefficients
+   % Do we use this?
+   % cfg.Fcutoff             = 80;       % Cutoff Frequency  (Hz)
+   % cfg.Order				= 50;
+   % 
+   % cfg.lpFilt = designfilt('lowpassfir', 'FilterOrder', cfg.Order, 'CutoffFrequency', ...
+   %                     cfg.Fcutoff, 'SampleRate', cfg.RZ6Fs, 'Window', 'hamming');
+               % check RZ6Fs
+   %% Led colours
+   cfg.ledcolours = {'g','r'}; % green and red
+   
+
+   %% handles
+   handles.cfg		= cfg;
+end
+ 
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/cfg/pb_gethandles.m

+function handles = pb_gethandles(handles)
+% PB_GETHANDLES()
+%
+% PB_GETHANDLES()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+   cfg					= handles.cfg;
+   
+   expIdx				= get(handles.popExperimenter,'Value');
+   expInitials			= get(handles.popExperimenter,'String');
+   cfg.expInitials	= expInitials{expIdx};
+   
+   cfg.subjectid		= get(handles.editPart,'String');
+   cfg.recording		= get(handles.editRec,'String');
+   cfg.fname			= [cfg.expInitials '-' sprintf('%04u',str2double(cfg.subjectid)) '-' cfg.datestring '-' sprintf('%04u',str2double(cfg.recording)) '.vc']; % file name
+   cfg.dname			= [cfg.fpath filesep cfg.expInitials filesep 'Recordings' filesep cfg.expInitials '-' sprintf('%04u',str2double(cfg.subjectid)) '-' cfg.datestring]; % directory name
+   cfg.expdir			= [cfg.fpath filesep cfg.expInitials filesep 'EXP' filesep]; % exp directory name
+   cfg.snddir			= [cfg.fpath filesep cfg.expInitials filesep 'SND' filesep]; % wav directory name
+
+   % get exp and cfg files
+   str					= [cfg.expdir filesep '*.exp'];
+   d					= dir(str); % default exp folder
+   cfg.expfiles		= {d.name};
+   if isempty(cfg.expfiles)
+
+   end
+   %set(handles.popupmenu_exp,'String',cfg.expfiles)
+   %expfileIdx			= get(handles.popupmenu_exp,'Value');
+   %cfg.expfname		= cfg.expfiles{expfileIdx};
+   cfg.expfname		= get(handles.editLoad,'String');
+
+%   d                 = dir([cfg.expdir filesep '*.cfg']);
+%  cfg.cfgfiles		= {d.name};
+%    set(handles.popupmenu_cfg,'String',cfg.cfgfiles);
+%    cfgfileIdx			= get(handles.popupmenu_cfg,'Value');
+%    cfg.cfgfname		= cfg.cfgfiles{cfgfileIdx};
+   handles.cfg			= cfg;
+end
+ 
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/cfg/pb_sethandles.m

+function pb_sethandles(handles)
+% PB_SETHANDLES()
+%
+% PB_SETHANDLES()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+   set(handles.popExperimenter,'String',handles.cfg.expinitials);
+   %set(handles.edit_date,'String',handles.cfg.date);
+end
+ 
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/cfg/pb_setupShow.m

+function pb_setupShow(handles)
+% PB_SETUPSHOW()
+%
+% PB_SETUPSHOW()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+axes(handles.signals); 
+cla; hold on; 
+axis([0 120 -50 50]);
+box off
+
+axes(handles.hTrace); 
+cla; hold on; 
+axis([0 2.5 0 300]);
+box off
+
+axes(handles.eTrace); 
+cla; hold on; 
+axis([0 2.5 0 300]);
+box off
+end
+ 
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/cfg/pb_vLSCpositions.m

+function cfg = pb_vLSCpositions(cfg,varargin)
+% PB_VLOOKUP()
+%
+% PB_VLOOKUP()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+
+   if nargin<1
+      cfg = [];
+   end
+
+   %% Optional arguments
+   dspFlag       = pb_keyval('display',varargin,false);
+   if dspFlag; close all; end
+   
+   %% File
+   fname		= which('vPrime Measurement.xlsx');
+   N			= xlsread(fname,'Values');
+   channel	= N(:,1);
+
+   %% Transform to Cartesian
+   % To be checked
+   % actual spherical azimuth, elevation
+   az			= -N(:,4)+90;
+   el			= N(:,5);
+   az			= pa_deg2rad(az);
+   el			= pa_deg2rad(el);
+   R			= 1;
+   [X,Y,Z]		= sph2cart(az,el,R);
+   [X,Y,Z]		= pitch(X,Y,Z,90);
+
+   % desired double-polar azimuth and elevation
+   daz			= N(:,2);
+   del			= N(:,3);
+   % [dX,dY,dZ]	= azel2cart(daz,del,R);
+
+   %% Transform to double-polar coordinate system
+   % actual double-polar azimuth, elevation
+   [X,Y,Z]		= yaw(X,Y,Z,-90);
+   [aazel]		= xyz2azel(X,Y,Z);
+   aaz			= aazel(:,1);
+   ael			= aazel(:,2);
+
+   sel			= daz>90;
+   aaz(sel)	= 90+(90-aaz(sel));
+
+   sel			= daz<-90;
+   aaz(sel)	= -90+(-90-aaz(sel));
+
+   sel			= del>90;
+   ael(sel)	= 90+(90-ael(sel));
+
+   cfg.lookup	= [aaz ael channel];
+end
+ 
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/cfg/pb_vLookup.m

+function cfg = pb_vLookup(cfg,varargin)
+% PB_VLOOKUP()
+%
+% PB_VLOOKUP()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+
+   if nargin<1
+      cfg = [];
+   end
+
+  	%% LED connections
+   % [Azimuth (deg) Elevation (deg) LED #]
+   % azimuths and elevations were measured by Sebastian Ausili in June 2015
+   cfg					= pb_vLSCpositions(cfg);
+   cfg.nstimchan		= 2^5; % number of PLC and MUX channels
+   cfg.nspeakers		= 17; % actual number of speakers
+   cfg.stimchan		= (1:cfg.nstimchan)-1;
+
+   %% Add missing channels
+   n					= size(cfg.lookup,1);
+   cfg.lookup			= [cfg.lookup; NaN(cfg.nstimchan-n,3)]; % add missing channel data as NaNs
+   sel					= ismember(cfg.stimchan,cfg.lookup(:,3)); % lookup existing channels
+   cfg.missingchan		= cfg.stimchan(~sel); % get missing channels
+   sel					= isnan(cfg.lookup(:,3)); % search for missing channels in lookup-table
+   cfg.lookup(sel,3)	= cfg.missingchan; % put missing channel numbers in lookup-table
+   cfg.lookup			= sortrows(cfg.lookup,[3 1 2]); % sort lookup-table by channel number
+
+   %% Speakers
+
+   cfg.nMUX          = 2; % 2 multiplexers
+   cfg.nMUXbit			= 16; % 16 bits per MUX
+   cfg.MUXind			= 1:cfg.nMUX;
+   cfg.MUXbit			= 1:cfg.nMUXbit;
+
+   LookUp(:,1)			= cfg.stimchan; % Stimulus channel 0-31
+   idx					= LookUp(:,1)+1;
+   LookUp(:,2)			= ceil(idx/(2^4));% MUX number
+   idx					= mod(idx,2^4);
+   idx(idx==0)			= 2^4;
+   LookUp(:,3)			= idx; % TDT bit
+
+   %% Combine
+   % [PLC-Chan# RP2# MUX# BIT# AZ EL]
+   cfg.lookup		= [cfg.lookup(:,3) LookUp(:,2:3) cfg.lookup(:,1)  cfg.lookup(:,2)];
+   cfg.lookuplabel = {'Channel' 'MUX' 'Bit' 'Azimuth' 'Elevation'};
+   % cfg.lookuplabel = {'Channel' 'RP2' 'MUX' 'Bit' 'Azimuth' 'Elevation'};
+
+
+   %% Interpolant
+   x		= cfg.lookup(:,4);
+   y		= cfg.lookup(:,5);
+   z		= cfg.lookup(:,1);
+   sel		= ~isnan(x);
+   x		= x(sel);
+   y		= y(sel);
+   z		= z(sel);
+   cfg.interpolant		= scatteredInterpolant(x,y,z,'nearest');
+   
+end
+ 
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+%                                                           %
+%       Part of Programmeer Beer Toolbox (PBToolbox)        %
+%       Written by: Jesse J. Heckman (2018)                 %
+%                                                           %
+% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
+

setups/vestibular chair/vPrime/cfg/pb_vPrimeZ.m

+function block = pb_vPrimeZ(block,cfg)
+% PB_VPRIMEZ()
+%
+% PB_VPRIMEZ()  ...
+%
+% See also ...
+
+% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
+
+   cfg;
+   for iBlck = 1:cfg.Blocks
+      ntrls = length(block(iBlck).trial);
+      for iTrl = 1:ntrls
+         nstms = length(block(iBlck).trial(iTrl).stim);
+         for iStm = 1:nstms
+            X = block(iBlck).trial(iTrl).stim(iStm); 
+            if ~isempty(X)
+               
+               ZI = cfg.interpolant(block(iBlck).trial(iTrl).stim(iStm).azimuth,block(iBlck).trial(iTrl).stim(iStm).elevation);
+               block(iBlck).trial(iTrl).stim(iStm).Z           = ZI;
+               block(iBlck).trial(iTrl).stim(iStm).azimuth   	= cfg.lookup(ZI+1,4);
+               block(iBlck).trial(iTrl).stim(iStm).elevation	= cfg.lookup(ZI+1,5);
+            end
+         end
+      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(h,block,iBlock)
+function [Dat,profile,dur] = pb_vSignalVC(handles,block,iBlock)
 % PB_VSIGNALVC()
 %
 % PB_VSIGNALVC()  ...
@@ -30,24 +30,30 @@ function [Dat,profile,dur] = pb_vSignalVC(h,block,iBlock)
    dur        = max([signal(1).duration signal(2).duration])+5;         % add 5 extra seconds for delay of the system
 
    %% FEEDBACK GUI
-   updateBlock(h,iBlock,signal);
+   updateBlock(handles,iBlock,signal);
    
-   axes(h.signals); cla; hold on; 
-   h.signals.YLim = [-50 50];
+   handles = pb_gethandles(handles);
+   
+   cb = handles.cfg.blocknumber;
+   dur = max([handles.block(cb).signal.ver.duration handles.block(cb).signal.hor.duration]);
+   
+   axes(handles.signals); cla; hold on; 
+   handles.signals.YLim = [-50 50];
+   handles.signals.XLim = [0 dur];
 
    plot(Dat.v.t,Dat.v.x,'k');
    plot(Dat.h.t,Dat.h.x,'b');
 end
 
-function updateBlock(h, iBlock, signal)
+function updateBlock(handles, iBlock, signal)
    % Updates the block information to the GUI
    
    bn = pb_sentenceCase(num2str(iBlock,'%03d'));                           % count block
-   set(h.Bn,'string',bn);
+   set(handles.Bn,'string',bn);
    
    vs = ['V = ' pb_sentenceCase(signal(1).type) ...                        % VC stim
          ', H = ' pb_sentenceCase(signal(2).type)];
-   set(h.Vs,'string',vs);
+   set(handles.Vs,'string',vs);
 end
  
 % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 

setups/vestibular chair/vPrime/core/experiment/pb_vInitialize.m

-function cnt = pb_vInitialize(h, initialize)
+function handles = pb_vInitialize(handles, initialize)
 % PB_VREADYEXP(h,initialize)
 %
 % PB_VREADYEXP() interacts with GUI during check in/out experiment. 
@@ -9,20 +9,15 @@ function cnt = pb_vInitialize(h, initialize)
 
    if initialize; initialize = 'off'; else; initialize = 'on'; end
 
-   set(h.buttonClose,   'Enable', initialize)                % avoid closing GUI during executing run function     
-   set(h.buttonRun,     'Enable', initialize)
-   set(h.buttonLoad,    'Enable', initialize)
+   set(handles.buttonClose,   'Enable', initialize)                % avoid closing GUI during executing run function     
+   set(handles.buttonRun,     'Enable', initialize)
+   set(handles.buttonLoad,    'Enable', initialize)
    
    if strcmp(initialize,'off')
-      % Ready feedback plots
-      axes(h.signals); cla;   
-      axes(h.eTrace); cla; h.eTrace.YLim = [0 300]; h.eTrace.XLim = [0 2.5]; 
-      axes(h.hTrace); cla; h.hTrace.YLim = [0 300]; h.hTrace.XLim = [0 2.5];
+      % test
    else
       disp([newline newline 'Experiment finished!']);
    end
-   
-   if nargout == 1; cnt = 0; end
 end
  
 % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 

setups/vestibular chair/vPrime/core/experiment/pb_vReadExp.m

-function [block,cfg] = pb_vReadExp(expfile)
+function [block,cfg] = pb_vReadExp(cfg)
 % PB_VREADEXP(expfile)
 %
 % PB_VREADEXP() reads experimental data from expfile and loads BLOCK and
@@ -10,13 +10,12 @@ function [block,cfg] = pb_vReadExp(expfile)
 
    %% INITIALIZE
    
+   expfile = cfg.expfname;
    if ~pb_fexist(expfile); return; end
    fid = fopen(expfile,'r');
    
    %% HEADER
    
-   cfg         = struct; 
-   
    cfg.comment = checkcomment(fid);
    cfg         = hread(fid,cfg);
    n           = cfg.Blocks;
@@ -117,7 +116,47 @@ function [block,cfg] = pb_vReadExp(expfile)
             block(bn).trial(tn).stim(sn).ondelay		= par(2);
       end
       
+   
+   end
+   cfg		= pb_vLookup(cfg);
+   
+   %% EXTRA:  Azimuth Elevation
+   for iBlck = 1:cfg.Blocks
+      ntrials = length(block(iBlck).trial);
+      for iTrl = 1:ntrials % for every trial
+         s			= block(iBlck).trial(iTrl).stim;
+         block(iBlck).trial(iTrl).nstim = numel(s); % number of stimuli per trial
+         for stmIdx	= 1:block(iBlck).trial(iTrl).nstim % for every stimulus in a trial
+            X			= block(iBlck).trial(iTrl).stim(stmIdx).X;
+            Y			= block(iBlck).trial(iTrl).stim(stmIdx).Y;
+            mod			= block(iBlck).trial(iTrl).stim(stmIdx).modality;
+            if ~isempty(X) % for every stimulus that has an X and Y parameter, determine azimuth and elevation
+               if cfg.Lab==1 % Hoop lab
+                  if strcmpi(mod,'sky')
+                     [Az,El] = hoopsky2azel(X,Y);
+                  else
+                     [Az,El]	= hoopXY2azel(X,Y);
+                  end
+               elseif ismember(cfg.Lab,[2 3]) % Sphere lab
+                  channel = cfg.interpolant(X,Y);
+                  Az		= cfg.lookup(channel+1,5);
+                  El		= cfg.lookup(channel+1,6);
+               elseif ismember(cfg.Lab,4) % SphereMinor lab
+                  channel = cfg.interpolant(X,Y);
+                  Az		= cfg.lookup(channel+1,4);
+                  El		= cfg.lookup(channel+1,5);
+               elseif ismember(cfg.Lab,5) % vPrime lab
+                  channel = cfg.interpolant(X,Y);
+                  Az		= cfg.lookup(channel+1,4);
+                  El		= cfg.lookup(channel+1,5);
+               end