def run(self):
'''
This function overloads the Thread class function,
and is called when you run start() to start a new thread.
'''
try:
#Get options and show some information about settings
adir = self.acossoDir
self.setupWorkingDir()
rscriptExe = self.dat.foqusSettings.rScriptPath
xdata = self.options["Input Data File"].value
ydata = self.options["Output Data File"].value
cv = self.options["CV"].value
order = self.options["Order"].value
modelFile = self.options["Model File"].value
driverFile = self.options["FOQUS Model (for UQ)"].value
if self.checkNumVars():
return
self.msgQueue.put("------------------------------------")
self.msgQueue.put("Starting ACOSSO\n")
self.msgQueue.put("Model File: " + str(modelFile))
self.msgQueue.put("Py File (UQ): " + str(driverFile))
self.msgQueue.put("RScript Path: " + str(rscriptExe))
self.msgQueue.put("Sub-directory: " + str(adir))
self.msgQueue.put("X data file: " + str(xdata))
self.msgQueue.put("Y data file: " + str(ydata))
self.msgQueue.put("Order: " + str(order))
self.msgQueue.put("CV: " + str(cv))
self.msgQueue.put("------------------------------------")
# Run the R script
if self.options["Use Flowsheet Data"].value == "Yes":
self.msgQueue.put("Exporting Data...")
if len(self.input) < 1:
self.msgQueue.put(
" Must select at least 2 input variables")
return
self.msgQueue.put(" Inputs: {0}".format(
json.dumps(self.input)))
self.dat.flowsheet.results.exportVarsCSV(
xdata,
inputs = self.input,
outputs = [],
flat = True)
if len(self.output) < 1:
self.msgQueue.put(
" Must select an output variable")
return
self.msgQueue.put(" Output: {0}".format(
json.dumps(self.output)))
self.dat.flowsheet.results.exportVarsCSV(
ydata,
inputs = [],
outputs = self.output,
flat = True)
self.msgQueue.put("Running ACOSSO...")
rscriptFile = os.path.basename(rscriptExe)
process = subprocess.Popen([
rscriptFile,
'acosso_fit.R',
os.path.abspath(xdata),
os.path.abspath(ydata),
modelFile,
str(order),
cv], #need to add categorical arg
executable=rscriptExe,
cwd=adir,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
line = process.stdout.readline()
while process.poll() == None or line != b'':
if line == b'': time.sleep(0.2)
if line != b'':
self.msgQueue.put(line.decode("utf-8").rstrip())
line = process.stdout.readline()
if self.stop.isSet():
self.msgQueue.put("**terminated by user**")
process.kill()
break
self.msgQueue.put(
"Process completed code: {0}".format(process.poll()))
line = process.stderr.readline()
while line != b'':
self.msgQueue.put(line.decode("utf-8").rstrip())
line = process.stderr.readline()
modelFile2 = os.path.join(adir, modelFile)
driverFile2 = os.path.join(adir, driverFile)
rfile = os.path.join(adir, 'acosso_pred.R')
acossoData = {
'outputNames': self.output, # assume univariate
'modelNames': [modelFile2],
'rscriptPath': rscriptExe,
'rfile': rfile}
SurrogateParser.writeAcossoDriver(acossoData, driverFile2)
self.msgQueue.put(
"Wrote Python driver file: {0}".format(driverFile2))
self.result = "Done, see Python driver file: {0}".format(driverFile2)
self.driverFile = driverFile2
self.writePlugin() # added by BN, 2/4/2016
except Exception:
self.ex = sys.exc_info()
logging.getLogger("foqus." + __name__).exception(
"Exception in ACOSSO Thread")
def run(self):
'''
This function overloads the Thread class function,
and is called when you run start() to start a new thread.
'''
alamoExe = self.dat.foqusSettings.alamo_path
try:
assert(os.path.isfile(alamoExe))
except AssertionError:
msg = "The ALAMO executable was not found. Check the ALAMO exec "\
"path in settings and that ALAMO is installed."
self.msgQueue.put(msg)
raise AssertionError(msg)
try:
#Setup dictionaries to convert between foqus and ALAMO
#variable names. Also setup a list of input and output
#variable names for ALAMO. I'm going to keep the dicts
#for now in case using the FOQUS variables names in ALAMO
#doesn't work out for some reason.
uq_file = self.options[
"FOQUS Model (for UQ)"].value
self.xList = self.input
self.zList = self.output
self.xi = {}
self.zi = {}
cn = self.graph.input.compoundNames(sort=True)
for v in self.xList:
self.xi[v] = cn.index(v)
cn = self.graph.output.compoundNames(sort=False)
for v in self.zList:
self.zi[v] = cn.index(v)
#Get options and show some information about settings
adaptive = self.options['SAMPLER'].value
alamoDir = self.alamoDir
alamoDirFull = os.path.abspath(alamoDir)
self.setupWorkingDir()
adpexe = os.path.join(alamoDirFull, 'foqusALAMOClient.py')
self.writeAlamoInputFile(adaptiveExe=adpexe)
if self.checkNumVars():
return
alamoInput = self.options["Input File"].value
alamoOutput = alamoInput.rsplit('.', 1)[0] + '.lst'
self.msgQueue.put("------------------------------------")
self.msgQueue.put("Starting ALAMO\n")
self.msgQueue.put("Exec File Path: " + alamoExe)
self.msgQueue.put("Sub-directory: " + alamoDir)
self.msgQueue.put("Input File Name: " + alamoInput)
self.msgQueue.put("Output File Name: " + alamoOutput)
self.msgQueue.put("SAMPLER: " + str(adaptive))
self.msgQueue.put("UQ Driver File: " + uq_file)
self.msgQueue.put("------------------------------------")
# If using adaptive sampleing open a network socket to listen
if adaptive:
listener = listen.foqusListener(self.dat)
listener.setInputs(self.input)
listener.setOutputs(self.output)
listener.failValue = self.options["PRESET"].value
address = listener.address
listener.start()
#Run Alamo
process = subprocess.Popen([
alamoExe,
alamoInput],
cwd=alamoDir,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
stdin = None,
creationflags=win32process.CREATE_NO_WINDOW)
line = process.stdout.readline()
while process.poll() == None or line != b'':
if line == b'': time.sleep(0.2)
if line != b'':
self.msgQueue.put(line.decode("utf-8").rstrip())
line = process.stdout.readline()
if self.stop.isSet():
self.msgQueue.put("**terminated by user**")
process.kill()
break
if adaptive:
# stop the listener
conn = Client(address)
conn.send(['quit'])
conn.close()
alamoOutput = os.path.join(alamoDir, alamoOutput)
if self.options['FUNFORM'].value != "Fortran":
self.msgQueue.put("MUST USE FORTRAN FORM to make UQ and flowsheet plugins")
self.msgQueue.put("Skipping plugin creation")
return
res = SurrogateParser.parseAlamo(alamoOutput)
self.result = res
#self.msgQueue.put(str(res))
self.writePlugin()
SurrogateParser.writeAlamoDriver(
self.result,
uq_file,
ii=self.ii,
oi=self.oi,
inputNames=self.xList2,
outputNames=self.zList2)
self.driverFile = uq_file
except Exception:
self.ex = sys.exc_info()
logging.getLogger("foqus." + __name__).error(
"Exception in ALAMO Thread",
exc_info=sys.exc_info())
def run(self):
'''
This function overloads the Thread class function,
and is called when you run start() to start a new thread.
'''
try:
#Get options and show some information about settings
adir = self.bssanovaDir
self.setupWorkingDir()
rscriptExe = self.dat.foqusSettings.rScriptPath
xdata = self.options["Input Data File"].value
ydata = self.options["Output Data File"].value
burnin = self.options["Burn In"].value
mcmcit = self.options["MCMC Iterations"].value
recint = self.options["Record Interval"].value
nterms = self.options["nterms"].value
order = self.options["order"].value
prior = self.options["priorprob"].value
modelFile = self.options["Model File"].value
driverFile = self.options["FOQUS Model (for UQ)"].value
bte = json.dumps([burnin, mcmcit, recint])
if self.checkNumVars():
return
self.msgQueue.put("------------------------------------")
self.msgQueue.put("Starting BSS-ANOVA\n")
self.msgQueue.put("Model File: " + str(modelFile))
self.msgQueue.put("Py File (UQ): " + str(driverFile))
self.msgQueue.put("RScript Path: " + str(rscriptExe))
self.msgQueue.put("Sub-directory: " + str(adir))
self.msgQueue.put("X data file: " + str(xdata))
self.msgQueue.put("Y data file: " + str(ydata))
self.msgQueue.put("Burn In: " + str(burnin))
self.msgQueue.put("MCMC Iterations: " + str(mcmcit))
self.msgQueue.put("Record Interval: " + str(recint))
self.msgQueue.put("N. Terms: " + str(nterms))
self.msgQueue.put("Order: " + str(order))
self.msgQueue.put("Prior Prob.: " + str(prior))
self.msgQueue.put("bte: " + str(bte))
self.msgQueue.put("------------------------------------")
# Run the R script
if self.options["Use Flowsheet Data"].value == "Yes":
self.msgQueue.put("Exporting Data...")
if len(self.input) < 1:
self.msgQueue.put(
" Must select at least 2 input variables")
return
self.msgQueue.put(" Inputs: {0}".format(
json.dumps(self.input)))
self.dat.flowsheet.results.exportVarsCVS(xdata,
inputs=self.input,
outputs=[],
flat=True)
if len(self.output) < 1:
self.msgQueue.put(" Must select an output variable")
return
self.msgQueue.put(" Output: {0}".format(
json.dumps(self.output)))
self.dat.flowsheet.results.exportVarsCVS(ydata,
inputs=[],
outputs=self.output,
flat=True)
self.msgQueue.put("Running BSS-ANOVA...")
rscriptFile = os.path.basename(rscriptExe)
process = subprocess.Popen([
rscriptFile, 'bssanova_fit.R',
os.path.abspath(xdata),
os.path.abspath(ydata), modelFile, bte, 'auto',
str(nterms),
str(order),
str(prior)
],
executable=rscriptExe,
cwd=adir,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
line = process.stdout.readline()
while process.poll() == None or line != '':
if line == '': time.sleep(0.2)
if line != '':
self.msgQueue.put(line.rstrip())
line = process.stdout.readline()
if self.stop.isSet():
self.msgQueue.put("**terminated by user**")
process.kill()
break
self.msgQueue.put("Process completed code: {0}".format(
process.poll()))
line = process.stderr.readline()
while line != '':
self.msgQueue.put(line.rstrip())
line = process.stderr.readline()
modelFile2 = os.path.join(adir, modelFile)
driverFile2 = os.path.join(adir, driverFile)
rfile = os.path.join(adir, 'bssanova_pred.R')
bssAnovaData = {
'outputNames': self.output, # assume univariate
'modelNames': [modelFile2],
'rscriptPath': rscriptExe,
'rfile': rfile
}
SurrogateParser.writeBssAnovaDriver(bssAnovaData, driverFile2)
self.msgQueue.put(
"Wrote Python driver file: {0}".format(driverFile2))
self.result = "Done, see Python driver file: {0}".format(
driverFile2)
self.driverFile = driverFile2
self.writePlugin() # added by BN, 2/4/2016
except Exception:
self.ex = sys.exc_info()
logging.getLogger("foqus." + __name__).exception(
"Exception in BSS-ANOVA Thread")