organized vPrime structure

setups/vestibular chair/vPrime/core/experiment/trial/pb_vSetupTrial.m → setups/vestibular chair/vPrime/core/experiment/block/trial/pb_vSetupTrial.m

@@ -22,7 +22,6 @@ function [stim, cfg] = pb_vSetupTrial(stim,cfg)
       n		= nled*2; % LEDs need to be turned on and off
       s		= ledpattern(n);
 
-      %%
       cnt		= 0;
       for iLED = 1:nled
          % TDT RZ6
@@ -50,7 +49,7 @@ function [stim, cfg] = pb_vSetupTrial(stim,cfg)
             cnt = cnt+1;
             if ii==1
                s(cnt).set(led(iLED).Z,cfg.ledcolours{col},1);
-               s(cnt).intensity(cfg.ledcolours{col},led(iLED).intensity); % hoop: range 0-255, sphere range 1-50
+               s(cnt).intensity(cfg.ledcolours{col},led(iLED).intensity); % Vestibular range 0-100;
             else
                s(cnt).set(led(iLED).Z,cfg.ledcolours{col},0);
             end
@@ -89,10 +88,10 @@ function [stim, cfg] = pb_vSetupTrial(stim,cfg)
    cfg.maxSamples = maxSamples;
 
    %% Wait for?
-   % This needs some tweaking
    % search for latest event with longest offset
    % which should also include sampling period and sound although this does not have an
    % offevent
+   
    e				= [stim.offevent];
    d				= [stim.offdelay];
    mxevent			= max(e);

setups/vestibular chair/vPrime/core/experiment/block/pb_vSafety.m → setups/vestibular chair/vPrime/core/experiment/block/vc/pb_vSafety.m

@@ -9,8 +9,6 @@ function signal = pb_vSafety(signal)
 
 % PBToolbox (2018): JJH: j.heckman@donders.ru.nl
 
-   %% TODO: CONTROL SPEED OF EXPERIMENT (DIFF(SIGNAL))
-
    vAx = {'Vertical','Horizontal'};
 
    for iAx = 1:2
@@ -19,9 +17,9 @@ function signal = pb_vSafety(signal)
             warning(['Detected unsafe signal. ' vAx{iAx} ' duration too long!']);
             signal(iAx).duration = 300;
          end
-         if signal(iAx).amplitude > 40/iAx
+         if signal(iAx).amplitude > 100/iAx
             warning(['Detected unsafe signal. ' vAx{iAx} ' amplitude too large!']);
-            signal(iAx).amplitude = 40/iAx;
+            signal(iAx).amplitude = 100/iAx;
          end
         	if signal(iAx).frequency > .3
             warning(['Detected unsafe signal. ' vAx{iAx} ' frequency too high!']);

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

@@ -8,17 +8,23 @@ function [profile,dur] = pb_vSignalVC(handles)
 
 % PBToolbox (2018): JJH: j.heckman@donders.ru.nl
 
+   %% INITIALIZE 
+   %  Selects relevant handles
+   
    block       = handles.block;
    bnumber     = handles.cfg.blocknumber;
    
-   % Read & create signals
+   %% SIGNALS
+   %  Creates safe vestibular signals.
+   
+   %  Read & create signals
    signal      = pb_vBuildSignal(block(bnumber).signal);  
    signal      = pb_vSafety(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 signals
+   %  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;
@@ -27,7 +33,7 @@ function [profile,dur] = pb_vSignalVC(handles)
    sigData.h.t    = (0:1:length(sigData.h.x)-1)/10;      
    profile.h      = sigData.h.x;
    
-   % Check signal safety
+   %  Check signal safety
    [hSafe,~]      = pb_vCheckVelSignal(profile.h);
    [vSafe,mvel]   = pb_vCheckVelSignal(profile.v);
    
@@ -35,19 +41,21 @@ function [profile,dur] = pb_vSignalVC(handles)
       error(['Vestibular signals were not safe! (velocity exceeds ' num2str(mvel) ')']);
    end
    
-   % Feedback GUI
+   %% FEEDBACK GUI
+   %  interacts with GUI for feedback
+   
    updateBlock(handles, signal);
 
    handles  = pb_gethandles(handles);
    dur      = max([handles.block(bnumber).signal.ver.duration handles.block(bnumber).signal.hor.duration]);
    
-   % set axis
+   %  Set axis
    axes(handles.signals); 
    cla; hold on; 
    handles.signals.YLim    = [-50 50];
    handles.signals.XLim    = [0 dur];
    
-   % plot signals
+   %  Plot signals
    dv    = 10 * [0 diff(profile.v)];
    dh    = 10 * [0 diff(profile.h)];
    t     = sigData.v.t;

setups/vestibular chair/vPrime/core/experiment/data/pb_vCreateDat.m

-classdef pb_dataobj < handle
-% PB_VCREATEDAT()
-%
-% PB_VCREATEDAT()  ...
-%
-% See also ...
-
-% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
-
-
-
-    % LEDPATTERN
-    % Create a collection of stimulus patterns for the PA_LEDS
-    % class.
-    % s = ledpattern creates a single pattern
-    % s = ledpattern(n) creates a vector of n patterns
-    % s = ledpattern(m,n) creates a mxn matrix of patterns
-    %
-    % See also INTENSITY, SET, CLEAR, CLEAR_ALL, GET_LEDS, DELETE,
-    % DUMP.
-    properties (Access=protected)
-        intensity_red = uint16(50);
-        intensity_grn = uint16(50);
-        leds_red = zeros(128, 1);
-        leds_grn = zeros(128, 1);
-    end
-
-    methods
-        function obj = ledpattern(m,n)
-            % PA_LEDPATTERN constructor            
-            if nargin ~= 0 % Allow nargin == 0 syntax
-                if nargin < 2
-                    n = 1;
-                end
-                obj(m, n) = ledpattern; % Preallocate object array
-            end
-        end
-
-        function intensity(this, color, value)
-            % INTENSITY(color, value)
-            % Set the intensity of the red or green leds
-            % if color starts with 'r' the intensity of the red leds is set
-            % by manpulating the PWM output duty cycle. Otherwise the green
-            % intensity is set.
-            % The value should be in the range 1..50
-            if color(1) == 'r'
-                this.intensity_red = uint16(value);
-            else
-                this.intensity_grn  = uint16(value);
-            end
-        end
-
-        function delete(obj) %#ok<INUSD>
-            % DELETE - destructor
-        end
-
-        function set(this, lednr, color, value)
-            % SET(lednr, color, value)
-            % Turn the led with color on output lednr on or off, depending
-            % on the value paramater. 0 is off, otherwise on. If not specified,
-            % value is assumed to be 1
-            %
-            % Note that LEDNRs start at 0!
-            if nargin < 4
-                value = 1;
-            end
-            if color(1) == 'r'
-                this.leds_red(lednr+1) = (value ~= 0);
-            else
-                this.leds_grn(lednr+1) = (value ~= 0);
-            end
-        end
-
-        function clear(this, lednr, color)
-            % CLEAR(lednr, color)
-            % Shorthand for SET(lednr, color, 0);
-            this.set(lednr, color, 0);
-        end
-
-        function clear_all(this)
-            % CLEAR_ALL
-            % Turn all leds off. 
-						this.leds_red = zeros(128,1);
-            this.leds_grn = zeros(128,1);
-        end
-
-        function [r, g, ir, ig] = get_leds(this)
-            % [leds_red, leds_grn,intens_red, intens_grn] = GET_LEDS;
-            % Returns the value of the internal variables holding led 
-            % values and intensities.
-            if nargout > 0
-                r=this.leds_red;
-            end
-            if nargout > 1
-                g=this.leds_grn;
-            end
-            if nargout > 2
-                ir=this.intensity_red;
-            end
-            if nargout > 3
-                ig=this.intensity_grn;
-            end
-        end
-                
-        function dump(this)
-            % DUMP - show the content of the internal variables
-            this.intensity_red
-            this.intensity_grn
-            this.leds_red' %#ok<NOPRT>
-            this.leds_grn' %#ok<NOPRT>
-        end
-    end
-end
- 
-% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
-%                                                           %
-%       Part of Programmeer Beer Toolbox (PBToolbox)        %
-%       Written by: Jesse J. Heckman (2018)                 %
-%                                                           %
-% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
-

setups/vestibular chair/vPrime/core/experiment/block/pb_vStoreBlockDat.m → setups/vestibular chair/vPrime/core/experiment/data/pb_vStoreData.m

-function pb_vStoreBlockDat(cfg, Dat)
+function pb_vStoreData(cfg, Dat)
 % PB_VSTOREBLOCKDAT
 %
 % PB_VSTOREBLOCKDAT(cfg, Dat)  stores 'Dat' Data in files.
@@ -10,7 +10,6 @@ function pb_vStoreBlockDat(cfg, Dat)
    [~,fn] = pb_fext(cfg.fname);
    file = [cfg.dname filesep 'block_info_' fn '.mat'];
    save(file, 'Dat');
-   
 end
  
 % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 

setups/vestibular chair/vPrime/core/experiment/block/pb_vEndExp.m → setups/vestibular chair/vPrime/core/experiment/pb_vEndExp.m

@@ -7,79 +7,36 @@ function pb_vEndExp
 
 % PBToolbox (2018): JJH: j.heckman@donders.ru.nl
 
-   stim.X			= 0;
-   stim.Y			= 0;
+   stim.X            = 0;
+   stim.Y            = 0;
    stim.channel		= [];
-   stim.detect		= [];
-   stim.event		= [];
-   stim.intensity	= 60;
-   stim.modality	= 'sound';
-   stim.offdelay	= 0;
-   stim.offevent	= 0;
-   stim.ondelay	= 0;
-   stim.onevent	= 0;
-   stim.matfile	= 'rehandel.mat';
-   stim.azimuth	= 3.5084e-15;
-   stim.elevation	= -3.5084e-15;
-   stim.Z			= 10;
-   stim.ledhandle	= [];
+   stim.detect       = [];
+   stim.event        = [];
+   stim.intensity    = 60;
+   stim.modality     = 'sound';
+   stim.offdelay     = 0;
+   stim.offevent     = 0;
+   stim.ondelay      = 0;
+   stim.onevent      = 0;
+   stim.matfile      = 'rehandel.mat';
+   stim.azimuth      = 3.5084e-15;
+   stim.elevation    = -3.5084e-15;
+   stim.Z            = 10;
+   stim.ledhandle    = [];
    stim.parameters	= 99;
 
-%    fname		= fullfile('C:\DATA\SND',stim.matfile);
-%    if ~exist(fname)
-%       disp('You do not have Handel installed.');
-%       disp('1000 monkeys are doing your work for you, and are now writing Handel.');
-%       load handel;
-%       snd = resample(y,round(cfg.RZ6Fs),Fs); %#ok<NASGU>
-%       nsamples = numel(snd);
-%       dur = round( nsamples/cfg.RZ6Fs*1000);
-%       stim.duration = dur;
-%       save(fname,'snd');
-%    end
-
-%    disp('Hallelujah');
-%    warning('cannot load into RZ6 circuit as it cannot handle .mat files');
-   % stim = trialSetupMinor(cfg,stim);
-   % trialRunMinor(cfg,stim);
-
    %% Let's run some LEDs instead
-   import org.zeromq.ZMQ
-
-   n = 8;
-   s = ledpattern(n);
-   
-   seq1 = [0:2:9 fliplr(16:2:24)];
-   seq2 = [1:2:9 fliplr(17:2:24)];
 
-   ir=50;
-   ig=ir;
-   for i=1:n
-      if mod(i,2) == 0
-         s(i).set(seq1,'r');
-      else 
-         s(i).set(seq2,'g');
-      end
-       s(i).intensity('r', ir);
-       s(i).intensity('g', ig);
-   end
-
-   leds = ledcontroller_pi('dcn-led06','dcn-led07');
-
-   leds.write(s);
-   for i=1:n
-       leds.trigger;
-      pause(0.35);
-   end
+   pb_lightshow;
 
    %% Mop up
    % Turn off the lights
-   t=ledpattern;
+   
+   t = ledpattern;
    leds.write(t);
    leds.trigger;
    
-   delete(leds);
-   delete(s);
-   delete(t);
+   delete([leds,t]);
 end
  
 % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 

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

@@ -82,10 +82,7 @@ function [block,cfg] = pb_vReadExp(cfg)
             block(bn).trial(tn).stim(sn).modality		= 'LED';
 				block(bn).trial(tn).stim(sn).X            = par(1);
 				block(bn).trial(tn).stim(sn).Y            = par(2);
-
-				block(bn).trial(tn).stim(sn).intensity    = par(3);
-
-				block(bn).trial(tn).stim(sn).intensity    = par(3);  % hoop: range 0-255, sphere range 1-50
+				block(bn).trial(tn).stim(sn).intensity    = par(3);  % vestibular 0-100
 
 				block(bn).trial(tn).stim(sn).onevent		= par(4);
 				block(bn).trial(tn).stim(sn).ondelay		= par(5);

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

@@ -74,8 +74,8 @@ function pb_vRunExp(handles)
          pb_vTraces(handles);       
          
          %  save trial
-         handles        = pb_vStoreData(handles, profile);
-         handles.cfg    = pb_updatecount(handles.cfg,'trial','count');
+         handles              = pb_vStoreData(handles, profile);
+         handles.cfg          = pb_updatecount(handles.cfg,'trial','count');
          toc(trialTime);
       end
       
@@ -112,6 +112,8 @@ function pb_vRunExp(handles)
    pb_vEndExp;
    pb_vStoreBlockDat(handles.cfg, Dat);
    pb_vInitialize(handles, false);
+   
+   delete([ses, rc, str]);
    toc(expTime);
 end
 

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

-function Dat = pb_vRunVC(signal)
-% PB_VRUNVC()
-%
-% PB_VRUNVC()  ...
-%
-% See also ...
-
-% PBToolbox (2018): JJH: j.heckman@donders.ru.nl
-
-   %% CREATE SIGNALS
-   vSignal = pb_vCreateSignal(1, signal(1).duration, 10, .1, signal(1).type);
-   hSignal = pb_vCreateSignal(1, signal(2).duration, 10, .1, signal(2).type);
- 
-   Dat.v.x = vSignal.x .* signal(1).amplitude;
-   Dat.v.t = (0:1:length(Dat.v.x)-1)/10;
-   Dat.h.x = hSignal.x .* signal(2).amplitude;
-   Dat.h.t = (0:1:length(Dat.h.x)-1)/10;
-   
-   %% RUN CHAIR
-
-   profile.v = Dat.v.x;
-   profile.h = Dat.h.x;
-
-   %% excecute profile
-   
-   dur = max([signal(1).duration signal(2).duration]);
-   send_profile(profile); 
-   run_profile(dur);
-   %[sv,pv] = read_profile;
-
-   %% save data
-   Dat.signal = [1 1];
-   Dat.amplitude = [signal(1).amplitude signal(2).amplitude];
-   %Dat.sv = sv;
-   %Dat.pv = pv;
-
-end
-
-function send_profile(profile)
-   disp('writing profile to servo');
-   
-   %vs   = vs_servo;
-   %vs.write_profile(profile.v,profile.h);
-   %delete(vs);
-end
-
-function [sv,pv]=read_profile
-   %vs=vs_servo;
-   %[sv.vertical,sv.horizontal] = vs.read_profile_sv;
-   %[pv.vertical,pv.horizontal] = vs.read_profile_pv;
-   %delete(vs);
-end
-
-function run_profile(dur)
-   %vs=vs_servo;
-   %vs.enable;
-   %pause(1);
-   %vs.start;
-   %disp('started');
-   %pause(dur+5);
-   %vs.stop;
-   %disp('stopped');
-   %vs.disable;
-   %disp('done');
-   %delete(vs);
-end
- 
-% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
-%                                                           %
-%       Part of Programmeer Beer Toolbox (PBToolbox)        %
-%       Written by: Jesse J. Heckman (2018)                 %
-%                                                           %
-% % % % % % % % % % % % % % % % % % % % % % % % % % % % % % % 
-