finesse.py 26.7 KB
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# -*- coding: utf-8 -*-
"""
Created on Sun Jan 27 09:56:53 2013

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PyKat - Python interface and wrapper for FINESSE
Copyright (C) 2013 Daniel David Brown

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Contact at ddb@star.sr.bham.ac.uk

@author: Daniel Brown
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"""
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import sys
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import os
import subprocess
import tempfile
import numpy as np
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import datetime
import pickle
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import pykat
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import warnings
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import re
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from pykat.node_network import NodeNetwork
from pykat.detectors import Detector
from pykat.components import Component
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from pykat.commands import Command, xaxis
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from pykat.gui.gui import pyKatGUI

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import pykat.exceptions as pkex

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from PyQt4.QtCore import QCoreApplication
from PyQt4.QtGui import QApplication

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NO_GUI = False
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NO_BLOCK = "NO_BLOCK"

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class katRun(object):
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    def __init__(self):
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        self.runDateTime = datetime.datetime.now()
        self.x = None
        self.y = None
        self.xlabel = None
        self.ylabels = None
        self.katScript = None
        self.katVersion = None
        
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    def saveKatRun(self, filename):
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        with open(filename,'w') as outfile:
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            pickle.dump(self, outfile)
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    @staticmethod
    def loadKatRun(filename):
        with open(filename,'r') as infile:
            return pickle.load(infile)
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    def get(self, value): return self[value]
    
    def __getitem__(self, value):
        if value in self.ylabels:
            idx = self.ylabels.index(value)
            if len(self.y.shape) == 1:
                return self.y
            else:
                return self.y[:, idx]
        else:
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            raise  pkex.BasePyKatException("No output by the name {0} found", value)
      
class katRun2D(object):
    def __init__(self):
        self.runDateTime = datetime.datetime.now()
        self.x = None
        self.y = None
        self.z = None
        self.xlabel = None
        self.ylabel = None
        self.zlabels = None
        self.katScript = None
        self.katVersion = None
        
    def saveKatRun(self, filename):
        with open(filename,'w') as outfile:
            pickle.dump(self, outfile)
    
    @staticmethod
    def loadKatRun(filename):
        with open(filename,'r') as infile:
            return pickle.load(infile)
    
    def get(self, value): return self[value]
    
    def __getitem__(self, value):
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        idx = [i for i in range(len(self.zlabels)) if self.zlabels[i].split(" ")[0] == str(value)]
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        if len(idx) > 0:
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            return self.z[idx].squeeze()
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        else:
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            raise  pkex.BasePyKatException("No output by the name {0} found".format(str(value)))
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class Block:
    def __init__(self, name):
        self.__name = name
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        self.contents = [] # List of objects and strings of finesse code
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        self.enabled = True 
        
    @property
    def name(self): return self.__name
    
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class kat(object):                    
        
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    def __init__(self, kat_file=None, kat_code=None, katdir="", katname="", tempdir=None, tempname=None):
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        self.scene = None # scene object for GUI
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        self.verbose = True
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        self.__blocks = {} # dictionary of blocks that are used
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        self.__components = {}  # dictionary of optical components      
        self.__detectors = {}   # dictionary of detectors
        self.__commands = {}    # dictionary of commands
        self.__extra_lines = [] # an array of strings which are just normal finesse code to include when running
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        self.__gui = None
        self.nodes = NodeNetwork(self)  
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        self.__katdir = katdir
        self.__katname = katname
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        self.__tempdir = tempdir
        self.__tempname = tempname
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        self.pykatgui = None
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        # Various options for running finesse, typicaly the commands with just 1 input
        # and have no name attached to them.
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        self.__phase = None
        self.__maxtem = None
        self.__noxaxis = None
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        self.__time_code = None
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        if kat_code != None and kat_file != None:
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            raise BasePyKatException("Specify either a Kat file or some Kat code, not both.")
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        if kat_code != None:
            self.parseCommands(kat_code)
        
        if kat_file != None:
            self.loadKatFile(kat_file)
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        cls = type(self)
        self.__class__ = type(cls.__name__, (cls,), {})
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        #self.logo()
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    @property
    def maxtem(self): return self.__maxtem
    @maxtem.setter
    def maxtem(self,value): self.__maxtem = int(value)
    
    @property
    def phase(self): return self.__phase
    @phase.setter
    def phase(self,value): self.__phase = int(value)
    
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    @property
    def getPerformanceData(self): return self.__time_code
    @getPerformanceData.setter
    def getPerformanceData(self,value): self.__time_code = bool(value)
    
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    @property
    def noxaxis(self): return self.__noxaxis
    @noxaxis.setter
    def noxaxis(self,value): self.__noxaxis = bool(value)
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    def logo(self):
        print """                                              ..-
                          _                  '(
    PyKat                 \\`.|\\.__...-\"\"""-_." )
       ..+-----.._        /  ' `            .-'
   . '            `:      7/* _/._\\    \\   (
  (        '::;;+;;:      `-"' =" /,`"" `) /
  L.        \\`:::a:f            c_/     n_'
  ..`--...___`.  .    ,  
   `^-....____:   +."""
    
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    def loadKatFile(self, katfile):
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        commands=open(katfile).read()
        self.parseCommands(commands)
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    def parseKatCode(self, code):
        #commands = code.split("\n")
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        self.parseCommands(code)
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    def parseCommands(self, commands):
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        blockComment = False
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        self.__currentTag= NO_BLOCK
        
        if not (NO_BLOCK in self.__blocks):
            self.__blocks[NO_BLOCK] = Block(NO_BLOCK)
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        commands=self.remove_comments(commands)
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        after_process = [] # list of commands that should be processed after 
                           # objects have been set and created
        
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        for line in commands.split("\n"):
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            #for line in commands:
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            if len(line.strip()) >= 2:
                line = line.strip()
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                # Looking for block start or end
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                values = line.split(" ")
                if values[0] == "%%%":
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                    if values[1] == "FTblock":
                        newTag = values[2]
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                        if self.__currentTag != None and newTag != self.__currentTag: 
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                            warnings.warn("found block {0} before block {1} ended".format(newTag, self.__currentTag))    
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                        if newTag in self.__blocks:
                            raise pkex.BasePyKatException("Block `{0}` has already been read")
                            
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                        self.__blocks[newTag] = Block(newTag) # create new list to store all references to components in block
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                        self.__currentTag = newTag                            
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                    if values[1] == "FTend":
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                        self.__currentTag = NO_BLOCK
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                    continue
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                #warnings.warn("current tag {0}".format(self.__currentTag))    

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                # don't read comment lines
                if line[0] == "#" or line[0] == "%":
                    continue
                
                # check if block comment is being used
                if not blockComment and line[0:2] == "/*":
                    blockComment = True
                    continue
                elif blockComment and line[0:2] == "*/":
                    blockComment = False
                    continue
                
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                first = line.split(" ",1)[0]
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                obj = None
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                if(first == "m" or first == "m1" or first == "m2"):
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                    obj = pykat.components.mirror.parseFinesseText(line)
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                elif(first == "s"):
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                    obj = pykat.components.space.parseFinesseText(line)
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                elif(first == "l"):
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                    obj = pykat.components.laser.parseFinesseText(line)
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                elif(first[0:2] == "bs"):
                    obj = pykat.components.beamSplitter.parseFinesseText(line)
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                elif(first[0:2] == "gr"):
                    obj = pykat.components.grating.parseFinesseText(line)
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                elif(first[0:4] == "isol"):
                    obj = pykat.components.isolator.parseFinesseText(line)
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                elif(first[0:4] == "lens"):
                    obj = pykat.components.lens.parseFinesseText(line)
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                elif(first[0:3] == "mod"):
                    obj = pykat.components.modulator.parseFinesseText(line)
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                elif(first[0:2] == "pd"):
                    obj = pykat.detectors.photodiode.parseFinesseText(line)
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                elif(first == "xaxis" or first == "xaxis*"):
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                    obj = pykat.commands.xaxis.parseFinesseText(line)
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                elif(first == "x2axis" or first == "x2axis*"):
                    obj = pykat.commands.x2axis.parseFinesseText(line)
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                elif(first == "gauss" or first == "gauss*" or first == "gauss**"):
                    after_process.append(line)
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                else:
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                    if self.verbose:
                        print "Parsing `{0}` into pykat object not implemented yet, added as extra line.".format(line)
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                    obj = line
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                    # manually add the line to the block contents
                    self.__blocks[self.__currentTag].contents.append(line) 
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                if obj != None and not isinstance(obj, str):
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                    self.add(obj)
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        # now process all the varous gauss/attr etc. commands which require
        # components to exist first before they can be processed
        for line in after_process:
            first = line.split(" ",1)[0]
            
            if first == "gauss" or first == "gauss*" or first == "gauss**":
                pykat.commands.gauss.parseFinesseText(line)
            
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        self.__currentTag = NO_BLOCK 
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    def saveScript(self, filename=None):
        """
        Saves the current kat object to a Finesse input file
        """
        try:
            katScript = "".join(self.generateKatScript())       
            katfile = open(filename,'w')
            katfile.writelines(katScript)
            katfile.flush()
            katfile.close()

        except BasePyKatException as ex:
            print ex
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    def run(self, printout=0, printerr=0, save_output=False, save_kat=False,kat_name=None) :
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        """ 
        Runs the current simulation setup that has been built thus far.
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        It returns a katRun or katRun2D object which is populated with the various
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        data from the simulation run.
        """
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        try:        
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            if not hasattr(self, "xaxis") and self.noxaxis != None and self.noxaxis == False:
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                raise pkex.BasePyKatException("No xaxis was defined")
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            if len(self.__katdir) == 0:
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                # Get the environment variable for where Finesse is stored
                self.__finesse_dir = os.environ.get('FINESSE_DIR')
                
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                if self.__finesse_dir == None :
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                    raise MissingFinesseEnvVar()
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            else:
                self.__finesse_dir = self.__katdir
                
            if len(self.__katname) == 0:
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                katexe = "kat"
                
                if os.sys.platform == "win32":
                    katexe += ".exe"
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            else:
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                katexe = self.__katname
            
            kat_exec = os.path.join(self.__finesse_dir, katexe) 
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            # check if kat file exists and it is executable by user        
            if not (os.path.isfile(kat_exec) and os.access(kat_exec, os.X_OK)):
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                raise MissingFinesse()
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            print "--------------------------------------------------------------"
            start = datetime.datetime.now()
            print "Running kat - Started at " + str(start)
            
            if hasattr(self, "x2axis"):
                r = katRun2D()
            else:
                r = katRun()
                
            r.katScript = "".join(self.generateKatScript())   
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            # create a kat file which we will write the script into
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            if self.__tempname == None:
                katfile = tempfile.NamedTemporaryFile(suffix=".kat", dir=self.__tempdir)
            else:
                filepath =os.path.join(self.__tempdir, self.__tempname+".kat" )
                katfile = open( filepath, 'w' ) 
                
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            katfile.writelines(r.katScript)
            katfile.flush()
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            cmd=[kat_exec, '--perl1']
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            if self.__time_code:
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                cmd.append('--perf-timing')
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            cmd.append('--no-backspace')
            # set default format so that less repeated numbers are printed to the
            # output file, should speed up running and parsing of output files
            cmd.append('-format=%.15g')
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            cmd.append(katfile.name)
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            #if self.verbose:
                #print cmd
                
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            p=subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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            err = ""
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            print "Finesse binary output:"
            
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            for line in iter(p.stderr.readline, ""):
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                #err += line 
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                if len(line) > 0:
                    if line.rstrip().endswith('%'):
                        vals = line.split("-")
                        action = vals[0].strip()
                        prc = vals[1].strip()[:-1]
                        sys.stdout.write("\r{0} {1}%".format(action, prc))
                    elif line[0] == '*':
                        sys.stdout.write(line)
                        
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            [out,errpipe] = p.communicate()
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            # get the version number
            ix = out.find('build ') + 6
            ix2 = out.find(')',ix)
            r.katVersion = out[ix:ix2]
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            r.runDateTime = datetime.datetime.now()
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            if p.returncode != 0:
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                raise pkex.FinesseRunError(err, katfile.name)
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            if printout == 1: print out
            if printerr == 1: print err

            root = os.path.splitext(katfile.name)
            base = os.path.basename(root[0])            
            outfile = root[0] + ".out"
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            if save_output:        
                newoutfile = "{0}.out".format(base)
                
                cwd = os.path.os.getcwd()
                newoutfile = os.path.join(cwd,newoutfile)
                
                if os.path.isfile(newoutfile):
                    os.remove(newoutfile)
                    
                os.rename(outfile, newoutfile)
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                print "\nOutput data saved to '{0}'".format(newoutfile)
            
            if hasattr(self, "x2axis"):
                [r.x,r.y,r.z,hdr] = self.readOutFile(outfile)
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                r.xlabel = hdr[0]
                r.ylabel = hdr[1]
                r.zlabels = map(str.strip, hdr[2:])
            else:
                [r.x,r.y,hdr] = self.readOutFile(outfile)
            
                r.xlabel = hdr[0]
                r.ylabels = map(str.strip, hdr[1:])
                            
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            if save_kat:
                if kat_name == None:
                    kat_name = "pykat_output"                
                
                cwd = os.path.os.getcwd()
                newkatfile = os.path.join(cwd, kat_name + ".kat")
                
                if os.path.isfile(newkatfile):
                    os.remove(newkatfile)
                  
                os.rename(katfile.name, newkatfile)         
                
                print "Kat file saved to '{0}'".format(newkatfile)
                

            katfile.close()
            perfData = []
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            if self.__time_code:
                perffile = open(root[0] + ".perf",'r')
                
                for l in perffile.readlines():
                    vals = l.strip().split(' ')
                    perfData.append((vals[0], float(vals[1]), float(vals[2]), float(vals[3])))
                    
                return [r, perfData]
            else:
                return r
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        except pkex.FinesseRunError as fe:
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            print fe
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        finally:
            print ""
            print "Finished in " + str(datetime.datetime.now()-start)
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    def add(self, obj):
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        try:
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            obj.tag = self.__currentTag
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            self.__blocks[self.__currentTag].contents.append(obj)
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            if isinstance(obj, Component):
                
                if obj.name in self.__components :
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                    raise BasePyKatException("A component with name '{0}' has already been added".format([obj.name]))            
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                self.__components[obj.name] = obj
                self.__add_component(obj)
                
            elif isinstance(obj, Detector):
                
                if obj.name in self.__detectors :
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                        raise BasePyKatException("A detector '{0}' has already been added".format(obj.name))
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                self.__detectors[obj.name] = obj
                self.__add_detector(obj)
                
            elif isinstance(obj, Command):
                
                self.__commands[obj.__class__.__name__] = obj
                self.__add_command(obj)
                
            else :
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                raise BasePyKatException("Object {0} could not be added".format(obj))
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            obj._on_kat_add(self)
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        except pkex.BasePyKatException as ex:
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            print ex
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    def readOutFile(self, filename):
        
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        with open(filename,'r') as outfile:
            # read first to lines to get to header line
            outfile.readline()
            outfile.readline()
            
            hdr = outfile.readline().replace('%','').replace('\n','').split(',')
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        data = np.loadtxt(filename,comments='%',skiprows=4)
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        if hasattr(self, "x2axis"):
            # need to parse 2D outputs slightly different as they are effectively 2D matrices
            # written in linear form
            x = data[0::(1+self.x2axis.steps),0]
            y = data[0:(1+self.x2axis.steps),1]
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            # get rows and columns lined up so that we can reshape a single column of all x/y data
            # into a matrix
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            z = data[:,2:].transpose().reshape(data.shape[1]-2, 1+self.xaxis.steps, 1+self.x2axis.steps)
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            # once you do this the data for y and x axes need swapping
            z = z.swapaxes(1,2)
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            return [x, y, z, hdr]
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        else:
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            shape_len = len(data.shape)
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            if shape_len > 1:
                rows,cols = data.shape
                x = data[:,0]
                y = data[:,1:cols].squeeze()
            else:
                rows = 1
                cols = data.shape[0]
                
                x = data[0]
                y = data[1:cols].squeeze()
            
            return [x, y, hdr]
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    def generateKatScript(self) :
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        """ Generates the kat file which can then be run """
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        out = []    
        
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        for key in self.__blocks:
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            objs = self.__blocks[key].contents
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            out.append("%%% FTblock " + key + "\n")
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            for obj in objs:
                if isinstance(obj, str):
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                    out.append(obj + '\n')
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                elif isinstance(obj, Component) or isinstance(obj, Detector) or isinstance(obj, Command):
                    txt = obj.getFinesseText() 
                    
                    if txt != None:
                        if isinstance(txt,list):
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                            for t in txt:
                                out.append(t + "\n")
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                        else:
                            out.append(txt + "\n")
                            
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            out.append("%%% FTend " + key + "\n")
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        if self.noxaxis != None and self.noxaxis == True:
            out.append("noxaxis\n")
            
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        # now loop through all the nodes and get any gauss commands
        for key in self.nodes.getNodes():
            txt = self.nodes.getNodes()[key].getFinesseText()
            
            if txt != None:
                if isinstance(txt,list):
                    for t in txt: out.append(t+ "\n")
                else:
                    out.append(txt + "\n")
        
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        if self.phase != None: out.append("phase {0}\n".format(self.phase))
        if self.maxtem != None: out.append("maxtem {0}\n".format(self.maxtem))            
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        # ensure we don't do any plotting. That should be handled
        # by user themselves
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        out.append("gnuterm no\n")
        out.append("pyterm no\n")
        
        return out
        
    def openGUI(self):
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        if NO_GUI:
            print  "No PyQt4 module was installed so cannot open a GUI"
        else:
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            self.app = QCoreApplication.instance() 
            created = False
            
            if self.app == None:
                created = True
                self.app = QApplication([""])
                
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            if self.pykatgui == None:
                self.pykatgui = pyKatGUI(self)
                self.pykatgui.main()
            else:
                self.pykatgui.show()
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            if created: self.app.exec_()
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    def getComponents(self):
        return self.__components.values()
    
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    def hasComponent(self, name):
        return (name in self.__components)
    
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    def _newName(self, container, prefix):
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        n = 1
        name = "{0}{1}".format(prefix, n)
        
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        while name in container:
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            n += 1
            name = "{0}{1}".format(prefix,n)
        
        return name
    
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    def getNewComponentName(self,prefix):
        '''
        Returns a name for a component which hasn't already been added.
        Returns [prefix] + number, where number is greater than 1. e.g.
        if m1 exists getNewName('m') will return 'm2'
        '''
        return self._newName(self.__components, prefix)
    
    def getNewDetectorName(self,prefix):
        '''
        Returns a name for a component which hasn't already been added.
        Returns [prefix] + number, where number is greater than 1. e.g.
        if m1 exists getNewName('m') will return 'm2'
        '''
        return self._newName(self.__detectors, prefix)
        
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    def getNewNodeNames(self,prefix,N=1):
        '''
        Returns a list of names for N number of nodes which haven't already been added.
        Returns [prefix] + number, where number is greater than 1. e.g.
        if m1 exists getNewName('m') will return 'm2'
        '''
        rtn = []
        n = 1
        
        for M in range(1,N+1):
            name = "{0}{1}".format(prefix, n)
            
            while name in self.nodes.getNodes() or (name in rtn):
                n += 1
                name = "{0}{1}".format(prefix,n)
        
            rtn.append(name)
            
        return rtn
        
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    def __add_detector(self, det):

        if not isinstance(det, Detector):
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            raise exceptions.ValueError("Argument is not of type Detector")
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        name = det.name
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        fget = lambda self: self.__get_detector(name)
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        setattr(self.__class__, name, property(fget))
        setattr(self, '__det_' + name, det)                   

    def __get_detector(self, name):
        return getattr(self, '__det_' + name) 
        
        
    def __add_command(self, com):

        if not isinstance(com, Command):
            raise exceptions.ValueError("Argument is not of type Command")
        
        name = com.__class__.__name__
        fget = lambda self: self.__get_command(name)
        
        setattr(self.__class__, name, property(fget))
        setattr(self, '__com_' + name, com)                   

    def __get_command(self, name):
        return getattr(self, '__com_' + name)            
    
    def __add_component(self, comp):

        if not isinstance(comp, Component):
            raise exceptions.ValueError("Argument is not of type Component")
            
        fget = lambda self: self.__get_component(comp.name)
        
        setattr(self.__class__, comp.name, property(fget))
        setattr(self, '__comp_' + comp.name, comp)                   

    def __get_component(self, name):
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        return getattr(self, '__comp_' + name)        
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    def remove_comments(self, string):
        pattern = r"(\".*?\"|\'.*?\'|%{3}[^\r\n]*$)|(/\*.*?\*/|%[^\r\n]*$|#[^\r\n]*$|//[^\r\n]*$)"
        # first group captures quoted strings (double or single)
        # second group captures comments (//single-line or /* multi-line */)
        regex = re.compile(pattern, re.MULTILINE|re.DOTALL)
        def _replacer(match):
            # if the 2nd group (capturing comments) is not None,
            # it means we have captured a non-quoted (real) comment string.
            if match.group(2) is not None:
                return "" # so we will return empty to remove the comment
            else: # otherwise, we will return the 1st group
                return match.group(1) # captured quoted-string
        return regex.sub(_replacer, string)