Singlecp dev

.gitignore

@@ -1 +1,9 @@
 *.DS_Store
+modularTasks/tasks/AdrianTests/trials_post_expt/*
+modularTasks/tasks/AdrianTests/trials_pre_expt/training_3.csv
+modularTasks/tasks/AdrianTests/trials_pre_expt/training_4.csv
+modularTasks/tasks/AdrianTests/trials_pre_expt/training_5.csv
+modularTasks/tasks/AdrianTests/trials_pre_expt/training_6.csv
+modularTasks/tasks/AdrianTests/trials_pre_expt/training_7.csv
+modularTasks/tasks/AdrianTests/trials_pre_expt/training_8.csv
+*.png

configuration/dots_PsychophysicsMacMini_MachineConfig.xml

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+<?xml version="1.0" encoding="utf-8"?>
+<dotsMachineConfig>
+   <defaults>
+      <clockFunction>@mglGetSecs</clockFunction>
+      <dOutClassName>['dotsDOut1208FS']</dOutClassName>
+      <dataPath>['/Users/joshuagold/Users/Adrian']</dataPath>
+      <imagesPath>[true ]</imagesPath>
+      <soundsPath>['~']</soundsPath>
+      <tasksPath>['~']</tasksPath>
+   </defaults>
+   <dotsTheMessenger>
+      <ackTimeout>[        1.0000000000]</ackTimeout>
+      <defaultClientIP>['127.0.0.1']</defaultClientIP>
+      <defaultClientPort>[    49200.0000000000]</defaultClientPort>
+      <defaultServerIP>['127.0.0.1']</defaultServerIP>
+      <defaultServerPort>[    49201.0000000000]</defaultServerPort>
+      <receiveTimeout>[        0.0000000000]</receiveTimeout>
+      <sendRetries>[       10.0000000000]</sendRetries>
+      <socketClassName>['dotsSocketPnet']</socketClassName>
+   </dotsTheMessenger>
+   <dotsTheScreen>
+      <backgroundColor>[        0.0000000000,        0.0000000000,        0.0000000000]</backgroundColor>
+      <bitDepth>[]</bitDepth>
+      <displayIndex>[        2.0000000000]</displayIndex>
+      <distance>[        70.0000000000]</distance>
+      <foregroundColor>[        1.0000000000,        1.0000000000,        1.0000000000]</foregroundColor>
+      <height>[        33.6550000000]</height>
+      <multisample>[        1.0000000000]</multisample>
+      <width>[        59.69000000000]</width>
+   </dotsTheScreen>
+</dotsMachineConfig>

modularTasks/tasks/AdrianTests/Lab_Matlab_Control_Adrian_Fork.json

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+[
+    {
+		"name": "Lab_Matlab_Control_Adrian_Fork",
+		"type": "git",
+        "update": "never",
+		"url": "https://github.com/aernesto/Lab_Matlab_Control.git",
+		"pathPlacement": "append"
+    },
+    {
+		"name": "Lab_Matlab_Utilities",
+		"flavor": "5d8a529991e7d1db7bd9560078e886ca3f9a818d",
+        "type": "git",
+        "pathPlacement": "append",
+		"url": "https://github.com/TheGoldLab/Lab_Matlab_Utilities.git"
+    },
+    {
+		"name": "mgl",
+		"type": "git",
+		"flavor": "85153d66e0935b0c78a5447494e212c0e8592afe",
+		"url": "https://github.com/justingardner/mgl.git",
+		"pathPlacement": "append"
+    },
+    {  
+		"name": "mQUESTPlus",
+		"pathPlacement": "append",
+        "flavor": "bd3673db5d3e47699bdb1820dcfe068262d8b609",
+		"type": "git",
+		"url": "https://github.com/brainardlab/mQUESTPlus.git"
+    }
+]

modularTasks/tasks/AdrianTests/payrate.m

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+function payrate(timestamp)
+% compute extra pay for subject
+% ARGS:
+%   timestamp -  string like '2019_11_06_12_43'
+
+%   max_rate  -  integer. maximum rate a subject can get. E.g. 10 $/hour
+max_rate=10;
+
+%   th_perf   -   percent correct above which max pay rate is reached.
+%   Between 0 and 1
+th_perf=0.75;
+
+pre= 'completed4AFCtrials_task100_date_';
+post='.csv';
+filename = which([pre, timestamp, post]);
+t1=readtable(filename);
+coh1 = t1(t1.coherence==100,:);
+refdim = size(coh1);
+dims=size(coh1(coh1.dirCorrect & coh1.cpCorrect, :));
+perf = dims(1) / refdim(1);
+%th_perf = .75;
+payrate = min(perf/th_perf, 1);  % dollars per hour
+disp(['additional payrate:  ', num2str( ceil(payrate * max_rate)), '$/hour'])
+end

modularTasks/tasks/AdrianTests/singlecp.m

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+function singlecp(subject_code, probCP)
+% function to launch single CP Reversing Dots task
+%
+% ARGS:
+%   subject_code     --  string that identifies subject uniquely, e.g. 'S4'
+%   first_block_of_day --  true or false
+%   probCP           --  numeric value
+%   dump_folder      --  e.g '/Users/joshuagold/Documents/MATLAB/projects/Lab_M
+%                        atlab_Control_Adrian_Fork/modularTasks/tasks/AdrianTests/'
+%   quest_task_topsDataLog -- full path to topsDataLog containing the Quest
+%                             task (can be '' if no prior Quest task is 
+%                             required)
+
+%-------------------------- DEFAULT ARGS
+dump_folder = '/Users/joshuagold/Documents/MATLAB/projects/Lab_Matlab_Control_Adrian_Fork/modularTasks/tasks/AdrianTests/trials_post_expt/';
+
+
+first_block_of_day = true;  % if true, Quest block is added
+
+% the following variable should hold the full path to a topsDataLog.mat
+% file where a valid Quest block was run. This is when one wants to skip
+% the Quest block presently, and thus use the threshold estimated from a
+% prior Quest block.
+% An example path would be:
+% '/Users/joshuagold/Users/Adrian/oneCP/raw/2019_12_13_13_37/2019_12_13_13_37_topsDataLog.mat'
+% It is okay to leave the following variable as an empty string if 
+% first_block_of_day is set to true above.
+quest_task_topsDataLog = '';    
+
+
+%-------------------------- DOTS STIMULUS PROPERTIES
+ddots.Density = 150;
+ddots.Speed = 5;
+ddots.PixelSize = 6;
+ddots.Diameter = 8;
+ddots.CoherenceSTD = 10;
+
+    function newStruct = setDotsParams(dots, someStruct)
+        someStruct.density = dots.Density;
+        someStruct.speed = dots.Speed;
+        someStruct.diameter = dots.Diameter;
+        someStruct.pixelSize = dots.PixelSize;
+        someStruct.coherenceSTD = dots.CoherenceSTD;
+        newStruct = someStruct;
+    end
+
+
+%-------------------------- CREATE TOPNODE
+topNode = topsTreeNodeTopNode('oneCP');
+
+    function ts = extract_timestamp(tn)
+        % returns the timestamp as a string 'YYYY_MM_DD_HH_mm' associated 
+        % with the topsTreeNodeTopNode object tn
+        ts = regexprep(tn.filename, ...
+            '[^[0-9]{4}_[0-9]{2}_[0-9]{2}_[0-9]{2}_[0-9]{2}]', '');
+        ts = ts(1:16);
+    end
+timestamp = extract_timestamp(topNode);
+
+
+%-------------------------- TURN DIARY ON (LOG CONSOLE OUTPUT TO FILE)
+diary([dump_folder, 'session_console_',timestamp,'.log'])
+
+
+%-------------------------- SET TOPNODE UP
+topNode.addHelpers('screenEnsemble',  ...
+    'displayIndex',      2, ...
+    'remoteDrawing',     false, ...
+    'topNode',           topNode);
+%topNode.addReadable('dotsReadableHIDKeyboard');
+topNode.addReadable('dotsReadableHIDGamepad');
+% -1 means wait for keypress -- see topsTreeNode.pauseBeforeTask
+pauseBeforeTask = -1; 
+
+    function add_block(topnode, taskID, task_name, trials_file, ...
+            stop_cond, block_description)
+        % add a task to the topnode object
+        t = topsTreeNodeTaskReversingDots4AFC(task_name);
+        t.taskID = taskID;
+        t.independentVariables=trials_file;
+%        t.trialIterationMethod='sequential';
+        t.randomizeWhenRepeating = false;
+        t.pauseBeforeTask = pauseBeforeTask;
+        t.stopCondition = stop_cond;
+
+        % must be numeric
+        t.subject = str2double(regexprep(subject_code,'[^0-9]',''));
+        t.date = str2double(regexprep(timestamp,'_',''));  % must be numeric
+        t.probCP = probCP;
+
+        t.message.message.Instructions.text = {...
+            block_description ...
+        };
+
+        % DOTS PROPERTIES
+        oldDots = t.drawable.stimulusEnsemble.dots;
+        t.drawable.stimulusEnsemble.dots = setDotsParams(ddots, oldDots);
+
+        topnode.addChild(t);
+    end
+
+    function add_training_block(tid, name, condstop)
+        add_block(topNode, tid, name, [name,'.csv'], condstop, ...
+            {'training block',num2str(tid)})
+    end
+
+
+%-------------------------- ADD TRAINING BLOCKS TO TOPNODE
+num_training_blocks=2;
+
+stop_conditions = {...
+    7, 'button' ...
+    };
+
+for jj = 1:num_training_blocks
+    if jj == 2
+        if probCP < .5
+            add_training_block(jj, 'training_2_lowprob', stop_conditions{jj})
+        else
+            add_training_block(jj, 'training_2_highprob', stop_conditions{jj})
+        end
+    else
+        add_training_block(jj, ['training_',num2str(jj)], stop_conditions{jj})
+    end
+end
+
+
+
+%-------------------------- ADD OPTIONAL QUEST BLOCK TO TOPNODE
+% only put Quest block if this is the first block of the day
+if first_block_of_day
+    questTask = topsTreeNodeTaskRTDots('Quest');
+    questTask.taskID = 99;
+    questTask.trialIterations = 60;
+    questTask.timing.dotsDuration = 0.4;
+    questTask.timing.showFeedback = 0;
+    questTask.pauseBeforeTask = pauseBeforeTask;
+    questTask.message.message.Instructions.text = {{'Quest block', ...
+        'There are no switches'}};
+    % DOTS PROPERTIES
+    oldieDots = questTask.drawable.stimulusEnsemble.dots;
+    questTask.drawable.stimulusEnsemble.dots = ...
+        setDotsParams(ddots, oldieDots);
+    topNode.addChild(questTask);
+
+else
+    % extract timestamp from full path
+    ts = regexprep(quest_task_topsDataLog, ...
+        '[^[0-9]{4}_[0-9]{2}_[0-9]{2}_[0-9]{2}_[0-9]{2}]', '');
+    ts = ts(1:16);
+
+
+    % get questTask from first topsDataLog of the day
+    % right now, stops at first Quest block found
+    [oldTopNode, ~] = topsTreeNodeTopNode.loadRawData('oneCP', ts);
+
+
+    for tt = 1:length(oldTopNode.children)
+        task_child = oldTopNode.children{tt};
+        if strcmp(task_child.name,'Quest')
+            questTask = task_child;
+            break
+        end
+    end
+end
+
+
+
+%-------------------------- ADD TASK BLOCKS (4 by default)
+
+
+ttt = topsTreeNodeTaskReversingDots4AFC('TASK');
+ttt.timing.showFeedback = 0;
+ttt.taskID = 100;
+
+if probCP < 0.5
+    task_file = 'Block1.csv';
+    ttt.message.message.Instructions.text = {...
+    {'REAL TASK', 'RARE SWITCHES'} ...
+    };
+else
+    task_file = 'Block0.csv';
+    ttt.message.message.Instructions.text = {...
+    {'REAL TASK', 'FREQUENT SWITCHES'} ...
+    };
+end
+
+ttt.independentVariables=task_file;
+% ttt.trialIterationMethod='sequential';
+ttt.randomizeWhenRepeating = false;
+ttt.pauseBeforeTask = pauseBeforeTask;
+ttt.stopCondition = 'button';
+
+% subject, date and probCP must be numeric
+ttt.subject = str2double(regexprep(subject_code,'[^0-9]',''));
+ttt.date = str2double(regexprep(timestamp,'_',''));  
+ttt.probCP = probCP;
+
+% set theshold coherence obtained from Quest
+if ~first_block_of_day
+    threshold = questTask.getQuestThreshold();
+    if (threshold <= 0) || (100 <= threshold)
+        error(['invalid threshold of', num2str(threshold)])
+    else
+        ttt.questThreshold = threshold; 
+    end
+else
+    % if threshold hasn't been estimated yet, pass the Quest task instead
+    ttt.questThreshold = questTask;
+end
+
+% DOTS PROPERTIES
+oldieDots = ttt.drawable.stimulusEnsemble.dots;
+ttt.drawable.stimulusEnsemble.dots = ...
+    setDotsParams(ddots, oldieDots);
+
+topNode.addChild(ttt);
+
+
+%-------------------------- RUN TOPNODE
+
+topNode.run();
+
+
+%-------------------------- DUMP FIRA INFO (ONE FILE PER BLOCK)
+
+    function dumpFIRA(topnode, child)
+        task = topnode.children{child};
+        csvfile = ...
+            [dump_folder, 'completed4AFCtrials_task', ...
+            num2str(task.taskID), '_date_', ...
+            timestamp,'.csv'];
+        task.saveTrials(csvfile, 'all');
+    end
+
+num_children = length(topNode.children);
+
+for c = 1:num_children
+    if numel(topNode.children{c}.trialData)
+        dumpFIRA(topNode, c)
+    end
+end
+
+%-------------------------- TURN OFF DIARY
+disp(['file with timestamp ', timestamp, ' produced'])
+diary off
+end

modularTasks/tasks/AdrianTests/test_battery.txt

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+High level description
+======================
+run 3 training + Quest + 1 task (low probCP)
+run 3 training + noQuest + 1 task (low probCP)
+run 3 training + noQuest + 1 task (low probCP)
+
+Aggregate all FIRA data for this subject into single .csv
+
+Perform basic analysis