Added analyses collection file into trisurf package

Samo Penic

2017-01-14 d2f7b0c053e93b4d409d9661dbaff2eedcf391c1

 trisurf/trisurf.py

@@ -186,7 +186,6 @@
      self.path=path
      self.filename=filename
      self.fullname=os.path.join(path,filename)
      self.fileOK=self.read()
      return

   def exists(self):
@@ -196,7 +195,7 @@
      else:
         return False

   def mapcount(self):
   def lineCount(self):
      '''
      Internal method for determining the number of the lines in the most efficient way. Is it really the most efficient?
      '''
@@ -213,19 +212,26 @@
         f.close()
      return lines

   def tail(self,filename,n=2):
      with open(filename,'r') as myfile:
   def tail(self):
      with open(self.fullname,'r') as myfile:
         lines=myfile.readlines()
      return [lines[len(lines)-2].replace('\n',''),lines[len(lines)-1].replace('\n','')]

   def read(self):
   def checkFileValidity(self):
      try:
         lines=self.tail(self.fullname)
         lines=self.tail()
      except:
         return(False)
      if len(lines)<2:
         return(False)
      #print (line)
      return(True)

   def getSimulationDeltaTime(self):
      try:
         lines=self.tail()
      except:
         return 0
		
      fields=shlex.split(lines[0])
      epoch1=fields[0]
      n1=fields[1]
@@ -234,61 +240,59 @@
      epoch2=fields[0]
      n2=fields[1]
      try:
         self.dT=int(epoch2)-int(epoch1)
         self.last=n2
         #print(epoch1)
         #print(epoch2)
         #print(self.dT)
         #print(self.last)
         self.startDate=os.path.getmtime(os.path.join(self.path,'.lock'))
         dT=int(epoch2)-int(epoch1)
      except:
         return(False)
      return(True)
         return 0
      return dT

   def getLastIterationInStatistics(self):
      try:
         lines=self.tail()
      except:
         return 0
		
      fields=shlex.split(lines[0])
      epoch1=fields[0]
      n1=fields[1]
		
      fields=shlex.split(lines[1])
      epoch2=fields[0]
      return (fields[1])

   def getColumn(self,n=0):
      lines=self.readText().splitlines()
      col=[]
      name=lines[0].split()[n]
      for line in lines:
         col.append(line.split()[n])
      return col[2:],name

   def getTable(self):
      lines=self.readText().splitlines()
      keys=lines[0].split()
      table={}
      def num(s):
         try:
            return int(s)
         except ValueError:
            return float(s)
      for key in keys:
         table[key]=[]
      for line in lines:
         fields=line.split()
         for i in range(0,len(keys)):
            try:
               value=num(fields[i])
               table[keys[i]].append(value)
            except:
               pass
      return table	
		

   def readText(self):
      with open(self.fullname, 'r+') as fin:
         cont=fin.read()
      return cont

   def read_old(self):
      '''
      Method read() reads the statistics if it exists. It sets local variable dT storing the time differential between two intervals of simulation (outer loops). It also stores last simulation loop and the start of the run.
      '''
      if(self.exists()):
      #   epoch1=0
      #   epoch2=0
      #   n1=0
      #   n2=0
         nlines=self.mapcount()
         if nlines<2:
            return(False)
         try:
            with open(self.fullname, "r+") as fin:
               i=0;
               for line in fin:
                  if(i==1):
                     #print (line)
                     fields=shlex.split(line)
                     epoch1=fields[0]
                     n1=fields[1]
                  if(i==nlines-1):
                     fields=shlex.split(line)
                     epoch2=fields[0]
                     n2=fields[1]
                  i=i+1
         except:
            #print("Cannot read statistics file in "+self.fullname+"\n")
            return(False)
      else:
         #print("File "+self.fullname+" does not exists.\n")
         return(False)
      try:
         self.dT=(int(epoch2)-int(epoch1))/(int(n2)-int(n1))
      except:
         self.dT=0
      self.last=n2
      self.startDate=epoch1
      return(True)

   def __str__(self):
      '''
@@ -365,6 +369,13 @@
         return True
      else:
         return False


   def getStartTime(self):
      try:
         return os.path.getmtime(os.path.join(self.Dir.fullpath(),'.lock'))
      except:
         return -1

   def getStatus(self):
      pid=self.getPID()
@@ -469,8 +480,8 @@
      self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment"))
      pid=self.getPID()
      status=self.getStatus()
      if(self.Statistics.fileOK):
         ETA=str(datetime.timedelta(microseconds=(int(self.Tape.config['iterations'])-int(self.Statistics.last))*self.Statistics.dT)*1000000)
      if(self.Statistics.checkFileValidity()):
         ETA=str(datetime.timedelta(microseconds=(int(self.Tape.config['iterations'])-int(self.Statistics.getLastIterationInStatistics()))*self.Statistics.getSimulationDeltaTime())*1000000)
      if(status==TS_NONEXISTANT or status==TS_NOLOCK):
         statustxt="Not running"
         pid=""
@@ -485,8 +496,8 @@
      else:
         statustxt="Running"

      if(self.Statistics.fileOK):
         report=[time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(self.Statistics.startDate))),ETA, statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
      if(self.Statistics.checkFileValidity()):
         report=[time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(self.getStartTime()))),ETA, statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
      else:
         report=["N/A","N/A",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()]
      return report
@@ -505,12 +516,20 @@
      self.Comment.writefile(data,mode=mode)


   def getLastVTU(self):
   def getLastVTUold(self):
      vtuidx=self.getLastIteration()-int(self.Tape.getValue("inititer"))
      if vtuidx<0:
         return None
      else:
         return  'timestep_{:06d}.vtu'.format(vtuidx)

   def getLastVTU(self):
      flist=[]
      for file in os.listdir(self.Dir.fullpath()):
         if file.endswith(".vtu"):
            flist.append(file)
      flist.sort()		
      return(flist[-1])

   def __str__(self):
      if(self.getStatus()==0):
@@ -519,4 +538,5 @@
         str=" running."
      return(self.Dir.fullpath()+str)


   def __repr__(self):
      return("Instance of trisurf in "+self.Dir.fullpath())