def test_median(self):
""" test Analyzer computing mediansignal within mask """
# settings dictionary for this test
settings = {'maskFile': maskFile,
'analysisChoice': 'Median',
'maskIsWeighted': False}
# create instance of Analyzer class
analyzer = Analyzer(settings)
# loop over series and test
seriesData = nib.load(seriesFile)
results = []
for volIdx in range(seriesData.shape[3]):
# extract the 3d array for this vol
thisVol = seriesData.get_data()[:, :, :, volIdx]
result = analyzer.runAnalysis(thisVol, volIdx)
results.append(result['median'])
# make np arrays of results and what results are expected to be
results = np.array(results)
expectedResults = np.array([1017.00, 1020.5, 1026.00])
# use np testing method to assert with customized precision
np.testing.assert_almost_equal(results, expectedResults, decimal=2)
def test_customAnalysis(self):
""" test Analyzer computing customAnalysis within mask """
# settings dictionary for this test
settings = {'maskFile': maskFile,
'numTimepts': 3,
'analysisChoice': join(paths['testDataDir'], 'test_customAnalysisScript.py'),
'maskIsWeighted': False}
# create instance of Analyzer class
analyzer = Analyzer(settings)
# loop over series and test
seriesData = nib.load(seriesFile)
results = []
for volIdx in range(seriesData.shape[3]):
# extract the 3d array for this vol
thisVol = seriesData.get_data()[:, :, :, volIdx]
result = analyzer.runAnalysis(thisVol, volIdx)
results.append(result['customResult'])
# make np arrays of results and what results are expected to be
results = np.array(results)
expectedResults = np.array([1029.15, 1032.78, 1034.14])
# use np testing method to assert with customized precision
np.testing.assert_almost_equal(results, expectedResults, decimal=2)
def test_median(self):
""" test Analyzer computing mediansignal within mask """
# settings dictionary for this test
settings = {
'maskFile': maskFile,
'analysisChoice': 'Median',
'maskIsWeighted': False
}
# create instance of Analyzer class
analyzer = Analyzer(settings)
# loop over series and test
seriesData = nib.load(seriesFile)
results = []
for volIdx in range(seriesData.shape[3]):
# extract the 3d array for this vol
thisVol = seriesData.get_data()[:, :, :, volIdx]
result = analyzer.runAnalysis(thisVol, volIdx)
results.append(result['median'])
# make np arrays of results and what results are expected to be
results = np.array(results)
expectedResults = np.array([1017.00, 1020.5, 1026.00])
# use np testing method to assert with customized precision
np.testing.assert_almost_equal(results, expectedResults, decimal=2)
def test_customAnalysis(self):
""" test Analyzer computing customAnalysis within mask """
# settings dictionary for this test
settings = {
'maskFile':
maskFile,
'numTimepts':
3,
'analysisChoice':
join(paths['testDataDir'], 'test_customAnalysisScript.py'),
'maskIsWeighted':
False
}
# create instance of Analyzer class
analyzer = Analyzer(settings)
# loop over series and test
seriesData = nib.load(seriesFile)
results = []
for volIdx in range(seriesData.shape[3]):
# extract the 3d array for this vol
thisVol = seriesData.get_data()[:, :, :, volIdx]
result = analyzer.runAnalysis(thisVol, volIdx)
results.append(result['customResult'])
# make np arrays of results and what results are expected to be
results = np.array(results)
expectedResults = np.array([1029.15, 1032.78, 1034.14])
# use np testing method to assert with customized precision
np.testing.assert_almost_equal(results, expectedResults, decimal=2)
def launchPyneal(headless=False, customSettingsFile=None):
"""Main Pyneal Loop.
This function will launch setup GUI, retrieve settings, initialize all
threads, and start processing incoming scans
"""
### Read Settings ------------------------------------
# Read the settings file, and launch the setup GUI to give the user
# a chance to update the settings. Hitting 'submit' within the GUI
# will update the setupConfig file with the new settings
if customSettingsFile:
print('Loading custom settings file: {}'.format(customSettingsFile))
settingsFile = customSettingsFile
else:
settingsFile = join(pynealDir, 'src/GUIs/pynealSetup/setupConfig.yaml')
if not headless:
# Launch GUI to let user update the settings file
setupGUI.launchPynealSetupGUI(settingsFile)
elif headless:
print('Running headless...')
print('Using settings in {}'.format(settingsFile))
assert os.path.exists(
settingsFile
), 'Running headless, but settings file does not exist: {}'.format(
settingsFile)
# Read the new settings file, store as dict
with open(settingsFile, 'r') as ymlFile:
settings = yaml.load(ymlFile)
### Create the output directory, put in settings dict
outputDir = createOutputDir(settings['outputPath'])
settings['seriesOutputDir'] = outputDir
### Set Up Logging ------------------------------------
# The createLogger function will do a lot of the formatting set up
# behind the scenes. You can write to this log by calling the
# logger var and specifying the level, e.g.: logger.debug('msg')
# Other modules can write to this same log by calling
# the command: logger = logging.getLogger('PynealLog')
logFname = join(outputDir, 'pynealLog.log')
logger = createLogger(logFname)
print('Logs written to: {}'.format(logFname))
# write all settings to log
for k in settings:
logger.info('Setting: {}: {}'.format(k, settings[k]))
print('-' * 20)
### Launch Threads -------------------------------------
# Scan Receiver Thread, listens for incoming volume data, builds matrix
scanReceiver = ScanReceiver(settings)
scanReceiver.daemon = True
scanReceiver.start()
logger.debug('Starting Scan Receiver')
# Results Server Thread, listens for requests from end-user (e.g. task
# presentation), and sends back results
resultsServer = ResultsServer(settings)
resultsServer.daemon = True
resultsServer.start()
logger.debug('Starting Results Server')
### Create processing objects --------------------------
# Class to handle all preprocessing
preprocessor = Preprocessor(settings)
# Class to handle all analysis
analyzer = Analyzer(settings)
### Launch Real-time Scan Monitor GUI
if settings['launchDashboard']:
### launch the dashboard app as its own separate process. Once called,
# it will set up a zmq socket to listen for inter-process messages on
# the 'dashboardPort', and will host the dashboard website on the
# 'dashboardClientPort'
pythonExec = sys.executable # path to the local python executable
p = subprocess.Popen([
pythonExec,
join(pynealDir, 'src/GUIs/pynealDashboard/pynealDashboard.py'),
str(settings['dashboardPort']),
str(settings['dashboardClientPort'])
])
# Set up the socket to communicate with the dashboard server
dashboardContext = zmq.Context.instance()
dashboardSocket = dashboardContext.socket(zmq.REQ)
dashboardSocket.connect('tcp://127.0.0.1:{}'.format(
settings['dashboardPort']))
# make sure subprocess and dashboard ports get killed at close
atexit.register(cleanup, p, dashboardContext)
# Open dashboard in browser
# s = '127.0.0.1:{}'.format(settings['dashboardClientPort'])
# print(s)
# web.open('127.0.0.1:{}'.format(settings['dashboardClientPort']))
# send configuration settings to dashboard
configDict = {
'mask':
os.path.split(settings['maskFile'])[1],
'analysisChoice':
(settings['analysisChoice'] if settings['analysisChoice']
in ['Average', 'Median'] else 'Custom'),
'volDims':
str(nib.load(settings['maskFile']).shape),
'numTimepts':
settings['numTimepts'],
'outputPath':
outputDir
}
sendToDashboard(dashboardSocket,
topic='configSettings',
content=configDict)
### Wait For Scan To Start -----------------------------
while not scanReceiver.scanStarted:
time.sleep(.5)
logger.debug('Scan started')
### Set up remaining configuration settings after first volume arrives
while not scanReceiver.completedVols[0]:
time.sleep(.1)
preprocessor.set_affine(scanReceiver.get_affine())
### Process scan -------------------------------------
# Loop over all expected volumes
for volIdx in range(settings['numTimepts']):
### make sure this volume has arrived before continuing
while not scanReceiver.completedVols[volIdx]:
time.sleep(.1)
### start timer
startTime = time.time()
### Retrieve the raw volume
rawVol = scanReceiver.get_vol(volIdx)
### Preprocess the raw volume
preprocVol = preprocessor.runPreprocessing(rawVol, volIdx)
### Analyze this volume
result = analyzer.runAnalysis(preprocVol, volIdx)
# send result to the resultsServer
resultsServer.updateResults(volIdx, result)
### Calculate processing time for this volume
elapsedTime = time.time() - startTime
# update dashboard (if dashboard is launched)
if settings['launchDashboard']:
# completed volIdx
sendToDashboard(dashboardSocket, topic='volIdx', content=volIdx)
# timePerVol
timingParams = {
'volIdx': volIdx,
'processingTime': np.round(elapsedTime, decimals=3)
}
sendToDashboard(dashboardSocket,
topic='timePerVol',
content=timingParams)
### Save output files
resultsServer.saveResults()
scanReceiver.saveResults()
### Figure out how to clean everything up nicely at the end
resultsServer.killServer()
scanReceiver.killServer()
def launchPyneal(headless=False, customSettingsFile=None):
"""Main Pyneal Loop.
This function will launch setup GUI, retrieve settings, initialize all
threads, and start processing incoming scans
"""
### Read Settings ------------------------------------
# Read the settings file, and launch the setup GUI to give the user
# a chance to update the settings. Hitting 'submit' within the GUI
# will update the setupConfig file with the new settings
if customSettingsFile:
print('Loading custom settings file: {}'.format(customSettingsFile))
settingsFile = customSettingsFile
else:
settingsFile = join(pynealDir, 'src/GUIs/pynealSetup/setupConfig.yaml')
if not headless:
# Launch GUI to let user update the settings file
setupGUI.launchPynealSetupGUI(settingsFile)
elif headless:
print('Running headless...')
print('Using settings in {}'.format(settingsFile))
assert os.path.exists(settingsFile), 'Running headless, but settings file does not exist: {}'.format(settingsFile)
# Read the new settings file, store as dict
with open(settingsFile, 'r') as ymlFile:
settings = yaml.load(ymlFile)
### Create the output directory, put in settings dict
outputDir = createOutputDir(settings['outputPath'])
settings['seriesOutputDir'] = outputDir
### Set Up Logging ------------------------------------
# The createLogger function will do a lot of the formatting set up
# behind the scenes. You can write to this log by calling the
# logger var and specifying the level, e.g.: logger.debug('msg')
# Other modules can write to this same log by calling
# the command: logger = logging.getLogger('PynealLog')
logFname = join(outputDir, 'pynealLog.log')
logger = createLogger(logFname)
print('Logs written to: {}'.format(logFname))
# write all settings to log
for k in settings:
logger.info('Setting: {}: {}'.format(k, settings[k]))
print('-'*20)
### Launch Threads -------------------------------------
# Scan Receiver Thread, listens for incoming volume data, builds matrix
scanReceiver = ScanReceiver(settings)
scanReceiver.daemon = True
scanReceiver.start()
logger.debug('Starting Scan Receiver')
# Results Server Thread, listens for requests from end-user (e.g. task
# presentation), and sends back results
resultsServer = ResultsServer(settings)
resultsServer.daemon = True
resultsServer.start()
logger.debug('Starting Results Server')
### Create processing objects --------------------------
# Class to handle all preprocessing
preprocessor = Preprocessor(settings)
# Class to handle all analysis
analyzer = Analyzer(settings)
### Launch Real-time Scan Monitor GUI
if settings['launchDashboard']:
### launch the dashboard app as its own separate process. Once called,
# it will set up a zmq socket to listen for inter-process messages on
# the 'dashboardPort', and will host the dashboard website on the
# 'dashboardClientPort'
pythonExec = sys.executable # path to the local python executable
p = subprocess.Popen([
pythonExec,
join(pynealDir,
'src/GUIs/pynealDashboard/pynealDashboard.py'),
str(settings['dashboardPort']),
str(settings['dashboardClientPort'])
])
# Set up the socket to communicate with the dashboard server
dashboardContext = zmq.Context.instance()
dashboardSocket = dashboardContext.socket(zmq.REQ)
dashboardSocket.connect('tcp://127.0.0.1:{}'.format(settings['dashboardPort']))
# make sure subprocess and dashboard ports get killed at close
atexit.register(cleanup, p, dashboardContext)
# Open dashboard in browser
# s = '127.0.0.1:{}'.format(settings['dashboardClientPort'])
# print(s)
# web.open('127.0.0.1:{}'.format(settings['dashboardClientPort']))
# send configuration settings to dashboard
configDict = {'mask': os.path.split(settings['maskFile'])[1],
'analysisChoice': (settings['analysisChoice'] if settings['analysisChoice'] in ['Average', 'Median'] else 'Custom'),
'volDims': str(nib.load(settings['maskFile']).shape),
'numTimepts': settings['numTimepts'],
'outputPath': outputDir}
sendToDashboard(dashboardSocket,
topic='configSettings',
content=configDict)
### Wait For Scan To Start -----------------------------
while not scanReceiver.scanStarted:
time.sleep(.5)
logger.debug('Scan started')
### Set up remaining configuration settings after first volume arrives
while not scanReceiver.completedVols[0]:
time.sleep(.1)
preprocessor.set_affine(scanReceiver.get_affine())
### Process scan -------------------------------------
# Loop over all expected volumes
for volIdx in range(settings['numTimepts']):
### make sure this volume has arrived before continuing
while not scanReceiver.completedVols[volIdx]:
time.sleep(.1)
### start timer
startTime = time.time()
### Retrieve the raw volume
rawVol = scanReceiver.get_vol(volIdx)
### Preprocess the raw volume
preprocVol = preprocessor.runPreprocessing(rawVol, volIdx)
### Analyze this volume
result = analyzer.runAnalysis(preprocVol, volIdx)
# send result to the resultsServer
resultsServer.updateResults(volIdx, result)
### Calculate processing time for this volume
elapsedTime = time.time() - startTime
# update dashboard (if dashboard is launched)
if settings['launchDashboard']:
# completed volIdx
sendToDashboard(dashboardSocket, topic='volIdx', content=volIdx)
# timePerVol
timingParams = {'volIdx': volIdx,
'processingTime': np.round(elapsedTime, decimals=3)}
sendToDashboard(dashboardSocket, topic='timePerVol',
content=timingParams)
### Save output files
resultsServer.saveResults()
scanReceiver.saveResults()
### Figure out how to clean everything up nicely at the end
resultsServer.killServer()
scanReceiver.killServer()