
!echo $RTCLOUD_PATH


import warnings; warnings.simplefilter('ignore')

#---- Import the necessary python modules
import os
import sys
import threading
import argparse

#---- Load important brainiak modules
import brainiak.utils.fmrisim_real_time_generator as sim

#---- Load important rtcloud modules
# add the path to the rtcloud repo to PYTHONPATH to access rtCommon functions
path_to_rtcloud = os.getenv('RTCLOUD_PATH')
if path_to_rtcloud == None:
    print("Please set RTCLOUD_PATH, see instructions")
    raise ValueError
sys.path.append(path_to_rtcloud)

from rtCommon.projectServer import ProjectServer
from rtCommon.structDict import StructDict

#---- Declare and append important paths 
# declare the path to this jupyter notebook
path_to_notebook = os.getcwd()  # check and change notebook path as needed

# declare the scripts that will be wrapped by the projectInterface and 
#   accessed through the webServer
scriptToRun = os.path.join(path_to_notebook, 'sample.py')
initScript = os.path.join(path_to_notebook, 'initialize.py')
finalizeScript = os.path.join(path_to_notebook, 'finalize.py')

#---- Declare the total number of TRs (timepoints) you want to generate, and how many should be training
num_TRs = 200
num_training = 100


#---- Set up the config and parameters for this rtcloud tutorial

# NOTE: you can also change these parameters in the Settings tab on the web server
config = StructDict({
    'title' : 'rtCloud Tutorial', # study name
    'sessionId' : '20200101T120000', # session ID on the scanner
    'subjectName' : '001_synthetic', # subject ID on the scanner
    'datestr' : '20200101', # session date
    
    'isSynthetic' : True, # are we using synthetic data?
    'numSynthetic' : num_TRs, # total number of synthetic TRs
    'numTrainingTRs' : num_training, # number of TRs used for training the classifier
    'imgDir' : '/tmp/notebook-simdata', # location of synthetic TRs
    
    'subjectNum' : 101, # subject number
    'subjectDay' : 1, # study day (relevant if multi-day study)
    'sessionNum' : 1, # session number
    'runNum' : [1], # list of scanning runs that were done during the session
    'scanNum' : [14], # list of corresponding scan numbers for the runs

    # Plotting settings
    'plotTitle' : 'Realtime Plot', # plot title
    'plotXLabel' : 'TR #', # plot x-axis label
    'plotYLabel' : 'Classifier Prediction', # plot y-axis label
    'plotXRangeLow' : num_training, # plot x-axis minimum limit
    'plotXRangeHigh' : num_TRs, # plot x-axis maximum limit
    'plotYRangeLow' : -1, # plot y-axis minimum limit
    'plotYRangeHigh' : 1, # plot y-axis maximum limit
    'plotAutoRangeX' : False, # do we want the x-axis limit to automatically fit the range?
    'plotAutoRangeY' : True, # do we want the x-axis limit to automatically fit the range?

    # important variables about the dicom files
    'dicomNamePattern' : "rt_{TR:03d}.dcm", # naming pattern for the dicom files
    'minExpectedDicomSize' : 200000, # expected size for the dicom data
})

args = argparse.Namespace()
args.projectName = 'sample'
args.projectDir = path_to_notebook
args.mainScript = scriptToRun
args.initScript = initScript
args.finalizeScript = finalizeScript
args.dataRemote = False
args.subjectRemote = False
args.test = True
args.config = config
args.port = 8889


#---- Start the project server
def runProjectServer(args):
    projectServer = ProjectServer(args)
    projectServer.start()


try:
    project_thread = threading.Thread(name='projectServer', 
                                      target=runProjectServer,
                                      args=(args,))
    project_thread.setDaemon(True)
    project_thread.start()
except RuntimeError as err:
    # ignore event loop already running error
    if str(err) != 'This event loop is already running':
        raise


#---- Set up the parameters for the synthetic data generator

sim_settings = sim.default_settings
sim_settings['save_dicom'] = True
sim_settings['save_realtime'] = True
sim_settings['numTRs'] = num_TRs
sim_settings['different_ROIs'] = True
sim_settings['scale_percentage'] = 1

outdir = '/tmp/notebook-simdata'
if not os.path.exists(outdir):
    os.makedirs(outdir)

#---- Run sim.generate_data(outdir, sim_settings) as a thread

syndata_thread = threading.Thread(name='syndata', 
                                  target=sim.generate_data, 
                                  args=(outdir, sim_settings))
syndata_thread.setDaemon(True)
syndata_thread.start()


%%html
<iframe src="http://localhost:8889" width="800" height="600"></iframe>

Implementing a Real-Time fMRI Cloud-Based Framework¶

Overview¶

Annotated Bibliography¶

Table of Contents¶

Before Running This Notebook ¶

Import Necessary Modules and Declare Important Variables ¶

Step 1: Start the ProjectInterface Web Server ¶

Step 2: Start the Synthetic Data Generator ¶

Step 3: Open the Web Server on the localhost ¶

Summary ¶