conda activate rtcloud
+ - bash ./scripts/run-projectInterface.sh --test -p sample --subjectRemote
+
+2. Connect a web browser to the main page
+ - http://localhost:8888/
+ - Enter 'test' for both the usnername and password since we are running it in unsecure test mode.
+
+3. Connect a web browser to the jsPsych feedback page
+ - http://localhost:8888/jspsych
+
+4. Click the 'Run' button on the main page and view the subject feedback shown on the jsPsych page
\ No newline at end of file
diff --git a/projects/sample/sample.py b/projects/sample/sample.py
index 275a4995..3cc8a9d7 100644
--- a/projects/sample/sample.py
+++ b/projects/sample/sample.py
@@ -36,6 +36,7 @@
# import important modules
import os
import sys
+import time
import argparse
import warnings
import numpy as np
@@ -91,6 +92,8 @@ def doRuns(cfg, dataInterface, subjInterface, webInterface):
OUTPUT:
None.
"""
+ subjInterface.setMessage("Preparing Run ...")
+ time.sleep(1)
# variables we'll use throughout
scanNum = cfg.scanNum[0]
@@ -296,7 +299,11 @@ def doRuns(cfg, dataInterface, subjInterface, webInterface):
# the presentation computer.
if verbose:
print("| send result to the presentation computer for provide subject feedback")
- subjInterface.setResult(runNum, int(this_TR), float(avg_niftiData))
+ # convert to value between 0 and 1
+ minAvg = 305
+ maxAvg = 315
+ feedback = (avg_niftiData - minAvg) / (maxAvg - minAvg)
+ subjInterface.setResult(runNum, int(this_TR), float(feedback), 1000)
# Finally we will use use webInterface.plotDataPoint() to send the result
# to the web browser to be plotted in the --Data Plots-- tab.
@@ -310,12 +317,22 @@ def doRuns(cfg, dataInterface, subjInterface, webInterface):
# save the activations value info into a vector that can be saved later
all_avg_activations[this_TR] = avg_niftiData
+ time.sleep(1)
# create the full path filename of where we want to save the activation values vector.
# we're going to save things as .txt and .mat files
output_textFilename = '/tmp/cloud_directory/tmp/avg_activations.txt'
output_matFilename = os.path.join('/tmp/cloud_directory/tmp/avg_activations.mat')
+ time.sleep(1)
+ subjInterface.setMessage("End Run")
+ responses = subjInterface.getAllResponses()
+ keypresses = [response.get('key_pressed') for response in responses]
+ stimDurations = [response.get('stimulus_duration') for response in responses]
+ if verbose:
+ print(f'Keypresses: {keypresses}')
+ print(f'Durations: {stimDurations}')
+
# use 'putFile' from the dataInterface to save the .txt file
# INPUT:
# [1] filename (full path!)
diff --git a/rtCommon/dataInterface.py b/rtCommon/dataInterface.py
index 3eca57d5..40e84494 100644
--- a/rtCommon/dataInterface.py
+++ b/rtCommon/dataInterface.py
@@ -13,7 +13,6 @@
import re
import time
import glob
-import chardet
import threading
import logging
from pathlib import Path
@@ -461,4 +460,5 @@ def downloadFilesFromCloud(dataInterface, srcFilePattern :str, outputDir :str, d
# 'downloadFolderFromCloud',
# 'downloadFilesFromCloud',
# ]
-# self.addLocalAttributes(localOnlyFunctions)
\ No newline at end of file
+# self.addLocalAttributes(localOnlyFunctions)
+
diff --git a/rtCommon/subjectInterface.py b/rtCommon/subjectInterface.py
index cafc4892..de3807f7 100644
--- a/rtCommon/subjectInterface.py
+++ b/rtCommon/subjectInterface.py
@@ -13,6 +13,7 @@
import time
from queue import Queue, Empty
from rtCommon.remoteable import RemoteableExtensible
+from rtCommon.errors import ValidationError
class SubjectInterface(RemoteableExtensible):
@@ -41,35 +42,67 @@ def __init__(self, subjectRemote=False):
if subjectRemote is True:
return
self.msgQueue = Queue()
+ self.message = ""
- def setResult(self, runId :int, trId :int, value: float) -> None:
+ # NOTE: The below function implementations will only be used when there is no
+ # external subjectInterface connected to the projectServer. Thus these
+ # implementations are just for testing or as a place holder when no external
+ # subjectInterface is used.
+
+ def setResult(self, runId :int, trId :int, value: float, onsetTimeDelayMs: int=0) -> None:
"""
- Whe setResult is called by the experiment script it queues the result for
+ When setResult is called by the experiment script it queues the result for
the presentation script to later read and use to provide subject feedback.
Args:
runId: experiment specific identifier of the run
trId: volume number of the dicom within a run
value: the classification result from processing the dicom image for this TR
+ onsetTimeDelayMs: time in milliseconds to wait before presenting the feedback stimulus
"""
print(f'SubjectInterface: setResult: run {runId}, tr {trId}, value {value}')
+ if onsetTimeDelayMs < 0:
+ raise ValidationError(f'onsetTimeDelayMs must be >= 0, {onsetTimeDelayMs}')
+
feedbackMsg = {
'runId': runId,
'trId': trId,
'value': value,
+ 'onsetTimeDelayMs': onsetTimeDelayMs,
'timestamp': time.time()
}
self.msgQueue.put(feedbackMsg)
- def dequeueResult(self, block :bool=False, timeout :int=None) -> float:
+ def setMessage(self, message: str) -> None:
"""
- Return the next result value send by the experiment script. Used by the
- presentation script.
+ Updates the message displayed to the subject
"""
- return self.msgQueue.get(block=block, timeout=timeout)
+ print(f'SubjectInterface: setMessage: {message}')
+ self.message = message
def getResponse(self, runId :int, trId :int):
"""
Retrieve the subject response, used by the classification script.
+ See *note* above - these local versions of the function are just
+ for testing or as a place holder when no external subjectInterface
+ is used.
"""
print(f'SubjectInterface: getResponse: run {runId}, tr {trId}')
- pass
+ return {}
+
+ def getAllResponses(self):
+ """
+ Retrieve all subject responses since the last time this call was made
+ """
+ print(f'SubjectInterface: getAllResponses')
+ return [{}]
+
+ def dequeueResult(self, block :bool=False, timeout :int=None) -> float:
+ """
+ Return the next result value sent by the experiment script. Used by the
+ presentation script.
+ See *note* above - these local versions of the function are just
+ for testing or as a place holder when no external version is used.
+ """
+ return self.msgQueue.get(block=block, timeout=timeout)
+
+
diff --git a/rtCommon/webServer.py b/rtCommon/webServer.py
index 347349a5..e696cb8c 100644
--- a/rtCommon/webServer.py
+++ b/rtCommon/webServer.py
@@ -20,7 +20,7 @@
from rtCommon.certsUtils import getCertPath, getKeyPath
from rtCommon.structDict import StructDict, recurseCreateStructDict
from rtCommon.webHttpHandlers import HttpHandler, LoginHandler, LogoutHandler, certsDir
-from rtCommon.webSocketHandlers import sendWebSocketMessage, BaseWebSocketHandler
+from rtCommon.webSocketHandlers import BaseWebSocketHandler
from rtCommon.webDisplayInterface import WebDisplayInterface
from rtCommon.projectServerRPC import ProjectRPCService
from rtCommon.dataInterface import uploadFilesFromList
@@ -62,10 +62,13 @@ def start(params, cfg, testMode=False):
params.confDir = os.path.join(Web.webDir, 'conf/')
if params.port:
Web.httpPort = params.port
+ if not os.path.exists(certsDir):
+ os.makedirs(certsDir)
src_root = os.path.join(Web.webDir, 'src')
css_root = os.path.join(Web.webDir, 'css')
img_root = os.path.join(Web.webDir, 'img')
build_root = os.path.join(Web.webDir, 'build')
+ jsPsych_root = os.path.join(Web.webDir, 'jsPsych')
cookieSecret = getCookieSecret(certsDir)
settings = {
"cookie_secret": cookieSecret,
@@ -101,6 +104,7 @@ def start(params, cfg, testMode=False):
Web.app = tornado.web.Application([
(r'/', HttpHandler, dict(htmlDir=Web.htmlDir, page='index.html')),
(r'/feedback', HttpHandler, dict(htmlDir=Web.htmlDir, page='biofeedback.html')), # shows image
+ (r'/jspsych', HttpHandler, dict(htmlDir=Web.htmlDir, page='jsPsychFeedback.html')),
(r'/login', LoginHandler, dict(htmlDir=Web.htmlDir, page='login.html', testMode=Web.testMode)),
(r'/logout', LogoutHandler),
(r'/wsUser', BaseWebSocketHandler, dict(name='wsUser', callback=Web.browserRequestHandler._wsBrowserCallback)),
@@ -109,6 +113,10 @@ def start(params, cfg, testMode=False):
(r'/css/(.*)', tornado.web.StaticFileHandler, {'path': css_root}),
(r'/img/(.*)', tornado.web.StaticFileHandler, {'path': img_root}),
(r'/build/(.*)', tornado.web.StaticFileHandler, {'path': build_root}),
+ (r'/jspsych/(.*)', tornado.web.StaticFileHandler, {'path': jsPsych_root}),
+ # /wsSubject gets added in projectServer.py when remoteSubject is True
+ # /wsData gets added in projectServer.py when remoteData is True
+ # (r'/wsSubject', BaseWebSocketHandler, dict(name='wsSubject', callback=defaultWebsocketCallback)),
], **settings)
Web.httpServer = tornado.httpserver.HTTPServer(Web.app, ssl_options=ssl_ctx)
Web.httpServer.listen(Web.httpPort)
@@ -124,15 +132,15 @@ def stop():
"""Stop the web server."""
Web.ioLoopInst.add_callback(Web.ioLoopInst.stop)
Web.app = None
-
+
# Possibly use raise exception to stop a thread
# def raise_exception(self): i.e. for stop()
- # thread_id = self.get_id()
- # res = ctypes.pythonapi.PyThreadState_SetAsyncExc(thread_id,
- # ctypes.py_object(SystemExit))
- # if res > 1:
- # ctypes.pythonapi.PyThreadState_SetAsyncExc(thread_id, 0)
- # print('Exception raise failure')
+ # thread_id = self.get_id()
+ # res = ctypes.pythonapi.PyThreadState_SetAsyncExc(thread_id,
+ # ctypes.py_object(SystemExit))
+ # if res > 1:
+ # ctypes.pythonapi.PyThreadState_SetAsyncExc(thread_id, 0)
+ # print('Exception raise failure')
@staticmethod
def close():
diff --git a/tests/test_subjectInterface.py b/tests/test_subjectInterface.py
index b1e048f4..91b816ca 100644
--- a/tests/test_subjectInterface.py
+++ b/tests/test_subjectInterface.py
@@ -1,6 +1,7 @@
import pytest
from tests.backgroundTestServers import BackgroundTestServers
from rtCommon.clientInterface import ClientInterface
+from rtCommon.errors import ValidationError
class TestSubjectInterface:
@@ -37,10 +38,20 @@ def runSubjectFeedbackTest(isRemote):
runId = 3
for trId in range(1, 10):
value = 20 + trId
- subjInterface.setResult(runId, trId, value)
+ onsetTimeDelayMs = trId + 4
+ subjInterface.setResult(runId, trId, value, onsetTimeDelayMs)
for i in range(1, 10):
feedbackMsg = subjInterface.dequeueResult(block=False, timeout=1)
assert feedbackMsg['runId'] == runId
assert feedbackMsg['trId'] == i
assert feedbackMsg['value'] == 20 + i
+ assert feedbackMsg['onsetTimeDelayMs'] == i + 4
+
+ subjInterface.setResult(1, 2, 3, 3.1)
+ feedbackMsg = subjInterface.dequeueResult(block=False, timeout=1)
+ assert feedbackMsg['onsetTimeDelayMs'] == 3.1
+
+ with pytest.raises((ValidationError, Exception)):
+ # Try setting a negative onsetTimeDelay
+ subjInterface.setResult(1, 2, 3, -1)
\ No newline at end of file
diff --git a/web/html/jsPsychFeedback.html b/web/html/jsPsychFeedback.html
new file mode 100644
index 00000000..e13583d6
--- /dev/null
+++ b/web/html/jsPsychFeedback.html
@@ -0,0 +1,182 @@
+
+
+
+
+
+ The experiment failed to load.
'; + loadfail = true; + DOM_target.innerHTML = message; + } + + core.getSafeModeStatus = function() { + return file_protocol; + } + + function TimelineNode(parameters, parent, relativeID) { + + // a unique ID for this node, relative to the parent + var relative_id; + + // store the parent for this node + var parent_node; + + // parameters for the trial if the node contains a trial + var trial_parameters; + + // parameters for nodes that contain timelines + var timeline_parameters; + + // stores trial information on a node that contains a timeline + // used for adding new trials + var node_trial_data; + + // track progress through the node + var progress = { + current_location: -1, // where on the timeline (which timelinenode) + current_variable_set: 0, // which set of variables to use from timeline_variables + current_repetition: 0, // how many times through the variable set on this run of the node + current_iteration: 0, // how many times this node has been revisited + done: false + } + + // reference to self + var self = this; + + // recursively get the next trial to run. + // if this node is a leaf (trial), then return the trial. + // otherwise, recursively find the next trial in the child timeline. + this.trial = function() { + if (typeof timeline_parameters == 'undefined') { + // returns a clone of the trial_parameters to + // protect functions. + return jsPsych.utils.deepCopy(trial_parameters); + } else { + if (progress.current_location >= timeline_parameters.timeline.length) { + return null; + } else { + return timeline_parameters.timeline[progress.current_location].trial(); + } + } + } + + this.markCurrentTrialComplete = function() { + if(typeof timeline_parameters == 'undefined'){ + progress.done = true; + } else { + timeline_parameters.timeline[progress.current_location].markCurrentTrialComplete(); + } + } + + this.nextRepetiton = function() { + this.setTimelineVariablesOrder(); + progress.current_location = -1; + progress.current_variable_set = 0; + progress.current_repetition++; + for (var i = 0; i < timeline_parameters.timeline.length; i++) { + timeline_parameters.timeline[i].reset(); + } + } + + // set the order for going through the timeline variables array + this.setTimelineVariablesOrder = function() { + + // check to make sure this node has variables + if(typeof timeline_parameters === 'undefined' || typeof timeline_parameters.timeline_variables === 'undefined'){ + return; + } + + var order = []; + for(var i=0; iThe minimum width is '+mw+'px. Your current width is '+w+'px.
'+ + 'The minimum height is '+mh+'px. Your current height is '+h+'px.
'; + core.getDisplayElement().innerHTML = msg; + } else { + clearInterval(interval); + core.getDisplayElement().innerHTML = ''; + checkExclusions(exclusions, success, fail); + } + }, 100); + return; // prevents checking other exclusions while this is being fixed + } + } + + // WEB AUDIO API + if(typeof exclusions.audio !== 'undefined' && exclusions.audio) { + if(window.hasOwnProperty('AudioContext') || window.hasOwnProperty('webkitAudioContext')){ + // clear + } else { + clear = false; + var msg = 'Your browser does not support the WebAudio API, which means that you will not '+ + 'be able to complete the experiment.
Browsers that support the WebAudio API include '+ + 'Chrome, Firefox, Safari, and Edge.
'; + core.getDisplayElement().innerHTML = msg; + fail(); + return; + } + } + + // GO? + if(clear){ success(); } + } + + function drawProgressBar(msg) { + document.querySelector('.jspsych-display-element').insertAdjacentHTML('afterbegin', + '