Merge pull request #128 from eslickj/master

Fixing 'tolist' and time step problems

foqus.py

@@ -271,7 +271,7 @@ def signal_handler(signal, frame):
                         help="Add an application type to TurbineLite DB")
     parser.add_argument("--terminateConsumer",
                         help = "Terminate the consumer with the given UUID")
-    parser.add_argument("--runUITestScript",
+    parser.add_argument("-s", "--runUITestScript",
                         help="Load and run a user interface test script")
     args = parser.parse_args()
     # before changing the directory get absolute path for file to load

foqus_lib/framework/graph/graph.py

@@ -843,7 +843,7 @@ def run(self):
                     for vkey in job[nkey]:
                         if type(job[nkey][vkey]).\
                             __module__ == numpy.__name__:
-                            job[nkey][vkey] = job[nkey][vkey].tolist()
+                            job[nkey][vkey] = job[nkey][vkey]
             if self.turbineSession is None:
                 self.solveListValTurbine(self.runList)
             else:

foqus_lib/framework/graph/node.py

@@ -411,7 +411,7 @@ def upadteSCDefaults(self, outfile=None):
         for name, item in sc["inputs"].iteritems():
             if name in self.gr.input[self.name]:
                 item['default'] = self.gr.input[self.name][name].value
-                item['default'] = item['default'].tolist()
+                item['default'] = item['default']
         with open(outfile, "wb") as f:
             json.dump(sc, f, indent=2)
 
@@ -583,9 +583,9 @@ def generateInputJSON(self):
             if var.set == "sinter":
                 try:
                     if self.altInput is not None:
-                        inputSetL2[vkey] = self.altInput[vkey].tolist()
+                        inputSetL2[vkey] = self.altInput[vkey]
                     else:
-                        inputSetL2[vkey] = var.value.tolist()
+                        inputSetL2[vkey] = var.value
                 except:
                     self.calcError = 23
                     raise NodeEx(

foqus_lib/framework/listen/listen.py

@@ -9,7 +9,7 @@ class foqusListener2(threading.Thread):
     '''
         This class uses a multiprocessing listener to allow
         FOQUS to be controlled over a socket connection.
-        The main purpose for this is ALAMO adaptive 
+        The main purpose for this is ALAMO adaptive
         sampling.
     '''
     def __init__(self, dat, host = 'localhost', port=56002):
@@ -20,22 +20,22 @@ def __init__(self, dat, host = 'localhost', port=56002):
         # Create a listener
         self.address = (host, port)
         self.listener = Listener(self.address)
-    
+
     def run(self):
         quitListening = False
         while True:
             #Wait for a connection to be made
             conn = self.listener.accept()
             while True:
                 msg = conn.recv()
-                if not (msg and isinstance(msg, list) and msg[0]): 
+                if not (msg and isinstance(msg, list) and msg[0]):
                     # ignore improperly formatted messages
                     continue
                 if msg[0] == "close":
                     # close the connection
                     conn.close()
                     break
-                elif msg[0] == "quit": 
+                elif msg[0] == "quit":
                     # close the connection and don't wait for another
                     quitListening = True
                     if self.gt:
@@ -57,11 +57,11 @@ def run(self):
                         logging.exception("Error running flowsheet")
                         conn.send([1])
                 elif msg[0] == "saveValues":
-                    self.gt.join(10) 
+                    self.gt.join(10)
                     if self.gt.isAlive():
                         # still waiting but continue so you have a
                         # chance to shutdown the listener if you want
-                        conn.send([1, "Still Running"]) 
+                        conn.send([1, "Still Running"])
                     else:
                         if self.gt.res:
                             self.dat.flowsheet.loadValues(self.gt.res)
@@ -76,7 +76,7 @@ class foqusListener(threading.Thread):
     '''
         This class uses a multiprocessing listener to allow
         FOQUS to be controlled over a socket connection.
-        The main purpose for this is ALAMO adaptive 
+        The main purpose for this is ALAMO adaptive
         sampling.
     '''
     def __init__(self, dat, host = 'localhost', port=56001):
@@ -94,34 +94,34 @@ def __init__(self, dat, host = 'localhost', port=56001):
         # Create a listener
         self.address = (host, port)
         self.listener = Listener(self.address)
-        
+
     def setInputs(self, l):
         self.inputNames = l
-        
+
     def setOutputs(self, l):
         self.outputNames = l
-    
+
     def run(self):
         '''
             Called by Thread when you run start() method
         '''
         quitListening = False
         # create an input dictionary structure to load values from
-        inpDict = self.dat.flowsheet.saveValues()['input'] 
+        inpDict = self.dat.flowsheet.saveValues()['input']
         # Enter loop waiting for requests from client
         while True:
             #Wait for a connection to be made
             conn = self.listener.accept()
             while True:
                 msg = conn.recv()
-                if not (msg and isinstance(msg, list) and msg[0]): 
+                if not (msg and isinstance(msg, list) and msg[0]):
                     # ignore improperly formatted messages
                     continue
                 if msg[0] == "close":
                     # close the connection
                     conn.close()
                     break
-                elif msg[0] == "quit": 
+                elif msg[0] == "quit":
                     # close the connection and don't wait for another
                     quitListening = True
                     conn.close()
@@ -145,14 +145,12 @@ def run(self):
                     varVals = msg[1]  #List of variable values
                     sampInput = copy.deepcopy(inpDict)
                     vals = self.dat.flowsheet.input.unflatten(
-                        self.inputNames, 
-                        varVals, 
+                        self.inputNames,
+                        varVals,
                         unScale=self.scaled)
                     for nkey in vals:
                         for vkey in vals[nkey]:
-                            ts = self.dat.flowsheet.input[nkey][vkey].ts
-                            sampInput[nkey][vkey][ts]=\
-                                vals[nkey][vkey].tolist()   
+                            sampInput[nkey][vkey] = vals[nkey][vkey]
                     self.samples.append(sampInput)
                     runIndex = len(self.samples) - 1
                     conn.send(['submitted', runIndex])
@@ -166,9 +164,9 @@ def run(self):
                     stat = []
                     for res in self.gt.res:
                         self.dat.flowsheet.results.addFromSavedValues(
-                            self.resStoreSet, 
+                            self.resStoreSet,
                             'res_{0}'.format(self.runid),
-                            None, 
+                            None,
                             res)
                         self.runid += 1
                         stat.append(res['graphError'])
@@ -177,9 +175,7 @@ def run(self):
                             vn = vn.split('.', 1)
                             nodeName = vn[0]
                             varName = vn[1]
-                            r += np.array(
-                                res['output'][nodeName][varName]\
-                                    ).flatten().tolist()
+                            r += res['output'][nodeName][varName]
                         if res['graphError'] != 0:
                             for i in range(len(r)):
                                 r[i] = self.failValue

foqus_lib/framework/sampleResults/results.py

@@ -106,13 +106,16 @@ def sd_col_list(sd, time=None):
         for n, d in sd[s[0]].iteritems():
             for v in d:
                 columns.append("{}.{}.{}".format(s[1], n, v))
-                dat.append(sd[s[0]][n][v])
+                el = sd[s[0]][n][v]
+                if s[1] == "setting":
+                    el = repr(el)
+                dat.append(el)
     #node error and turbine messages columns
     for s in [["nodeError", "node_err"], ["turbineMessages", "turb"]]:
         for n in sd[s[0]]:
             columns.append("{}.{}".format(s[1], n))
             dat.append(sd[s[0]][n])
-    # return the list of of columns and list of accosiated data.
+    # return the list of of columns and list of associated data.
     return (columns, dat)
 
 def incriment_name(name, exnames):
@@ -217,21 +220,19 @@ def loadDict(self, sd):
         except:
             logging.getLogger("foqus." + __name__).exception(
                 "Error loading stored results")
-        try:
-            for i in sd["__filters"]:
-                self.filters[i] = dataFilter().loadDict(sd["__filters"][i])
-        except:
-            pass
+        for i in sd.get("__filters", []):
+            self.filters[i] = dataFilter().loadDict(sd["__filters"][i])
         self.update_filter_indexes()
 
     def data_sets(self):
-        """
-        Return a set of data set labels
-        """
+        """Return a set of data set labels"""
         return set(self.loc[:,"set"])
 
-    def addFromSavedValues(self, set_name, result_name, time, sd):
-        self.add_result(sd, set_name=set_name, result_name=result_name, time=time)
+    def addFromSavedValues(self, setName, name, time=None, valDict=None):
+        """Temoprary function for compatablility
+        should move to add_result()
+        """
+        self.add_result(valDict, set_name=setName, result_name=name, time=time)
 
     def add_result(self, sd, set_name="default", result_name="res", time=None):
         """

foqus_lib/framework/surrogate/surrogate.py

@@ -297,7 +297,7 @@ def writePluginTop(
             lines.append(s12+'vdesc = "{0}",'.format(desc))
             lines.append(s12+'tags = [],')
             lines.append(s12+'dtype = float)')
-            inputvals.append(defVal.tolist())
+            inputvals.append(defVal)
         # input vector of default values (needed for ACOSSO, BSS-ANOVA & iREVEAL)
         lines.append(s8+"self.inputvals = {0}".format(json.dumps(inputvals)))
         # output variables

foqus_lib/framework/uq/Common.py

@@ -6,6 +6,7 @@
 import tempfile
 import time
 import platform
+import logging
 
 try:
     from PyQt5 import QtGui, QtCore, QtWidgets
@@ -37,16 +38,16 @@ def __init__(self, parent=None):
                 #self.doneButton.setEnabled(False)
                 #self.doneButton.clicked.connect(self.close)
                 #self.gridLayout.addWidget(self.doneButton)
-                
+
             def showError(self, error, out = None):
                 msgBox = QtWidgets.QMessageBox()
                 msgBox.setIcon(QtWidgets.QMessageBox.Critical)
                 msgBox.setText(error + '\nPlease consult the FOQUS UQ developers for assistance.')
                 if out is not None:
                     msgBox.setDetailedText(out)
                 msgBox.exec_()
-            
-            
+
+
     @staticmethod
     def getPsuadePath():  ### OBSOLETE in this release
         # Brenda's version of getPsuadePath(), superceded by LocalExecutionModule.getPsuadePath()
@@ -111,7 +112,7 @@ def showError(error, out = None, showDeveloperHelpMessage = True):
     # Pass a filename as a string to use as input file (e.g. "psuade ps.in")
     #   Requires a psuade formatted file
     # Pass a file handle to use it as a script (e.g.  "psuade < script")
-    def invokePsuade(arg1, arg2 = None, printOutputToScreen = False, textDialog = None, 
+    def invokePsuade(arg1, arg2 = None, printOutputToScreen = False, textDialog = None,
                                                                     dialogShowSignal = None,
                                                                     dialogCloseSignal = None,
                                                                     textInsertSignal = None,
@@ -120,7 +121,7 @@ def invokePsuade(arg1, arg2 = None, printOutputToScreen = False, textDialog = No
                                                                     plotOuuValuesSignal = None,
                                                                     ):
         from LocalExecutionModule import LocalExecutionModule
-        
+
         psuadePath = LocalExecutionModule.getPsuadePath()
         if psuadePath is None:
             return (None, None)
@@ -185,18 +186,18 @@ def runCommandInWindow(command,
                              stderr=subprocess.PIPE,
                              executable=executable,
                              shell=True)
-            
+
 
         logFile = open(logFile, 'w')
-        
-       
+
+
         if usePyside and QtWidgets.QApplication.instance() is not None:
             if textDialog is None:
-                Common.dialog = Common.textDialog()  
-                Common.dialog.show()      
+                Common.dialog = Common.textDialog()
+                Common.dialog.show()
             else:
-                Common.dialog = textDialog  
-                dialogShowSignal.emit()  
+                Common.dialog = textDialog
+                dialogShowSignal.emit()
 
         out = ''
         count = 0
@@ -295,10 +296,15 @@ def runCommandInWindow(command,
             print '\n\n'
 
         logFile.close()
-        
+
         # process error
         out2, error = p.communicate()
-        p.terminate()
+        try:
+            p.terminate()
+        except:
+            logging.getLogger("foqus." + __name__)\
+                .exception('Error terminating PSUADE process, this may be okay'
+                'but not sure so logged it (JCE)')
         if error:
             if showErrorSignal is None:
                 Common.showError(error, out)
@@ -337,5 +343,3 @@ def getUserRegressionOutputName(outName, userRegressionFile, data):
              index = outName.index('.')
              outName = outName[index + 1:]
         return outName
-
-