finesse.py 46.3 KB
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# -*- coding: utf-8 -*-
"""
Created on Sun Jan 27 09:56:53 2013

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
"""
import sys
import os
import subprocess
import tempfile
import numpy as np
import datetime
import pickle
import pykat
import warnings
import re

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import itertools
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import ctypes
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import ctypes.util
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import collections
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from collections import namedtuple, OrderedDict
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from pykat.node_network import NodeNetwork
from pykat.detectors import Detector
from pykat.components import Component
from pykat.commands import Command, xaxis
from pykat.gui.gui import pyKatGUI
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from pykat.SIfloat import *
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from pykat.param import Param, AttrParam
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import pykat.exceptions as pkex

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

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from multiprocessing import Process, Manager

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NO_GUI = False
NO_BLOCK = "NO_BLOCK"
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pykat_web = "www.gwoptics.org/pykat"

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# containers used in the trace routine
space_trace = namedtuple("space_trace", ['gouyx','gouyy'])
node_trace = namedtuple("node_trace", ['qx','qy'])
cav_trace = namedtuple("cav_trace", ['isStable','gx','gy','qx','qy','finesse','loss','length','FSR','FWHM','pole'])
         
lkat_location = ctypes.util.find_library("kat")
                                     
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def f__lkat_process(callback, cmd, kwargs):
    """
    """
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    if lkat_location == None:
        raise RuntimeError("Could not find shared library 'libkat', please install to a system location or copy to the same directory as this script")
        
    lkat = ctypes.PyDLL(lkat_location)
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    try:
        lkat._pykat_preInit() # must always be called, sets up
                        # exception handling and such no simulation
                        # specifc code here

        # reads in the kat.ini and setups up other parts
        lkat._pykat_init()
        lkat._pykat_setup(cmd)
    
        callback(lkat, **kwargs)
    
    except Exception as ex: 
        print "Exception caught in python: ", ex.message
    finally:
        # This should always be called no matter what
        lkat._pykat_finish(0)
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def f__lkat_trace_callback(lkat, trace_info):
    """
    lkat callback for computing the beam traces through a setup.
    Returns a dictionary of nodes, spaces and cavities and the
    various outputs of the tracing algorithm.
    """
    import pylibkat

    # first we need to get a handle on the internals of Finesse
    inter = pylibkat.interferometer.in_dll(lkat, "inter")

    lkat._pykat_step()

    for n in range(0, inter.num_nodes):
        node = inter.node_list[n]

        node_info = node_trace(
                                qx = complex(node.qx.re, node.qx.im),
                                qy = complex(node.qy.re, node.qy.im)
                                )

        trace_info[node.name] = node_info

    for c in range(0, inter.num_cavities):
        cav = inter.cavity_list[c]

        cav_info = cav_trace(
                            isStable = (cav.stable == 1),
                            gx = cav.stability_x,
                            gy = cav.stability_y,
                            qx = complex(cav.qx.re, cav.qx.im),
                            qy = complex(cav.qy.re, cav.qy.im),
                            finesse = cav.finesse,
                            FSR = cav.FSR,
                            FWHM = cav.FWHM,
                            loss = cav.loss,
                            length = cav.length,
                            pole = cav.pole
                            )

        trace_info[cav.name] = cav_info

    for s in range(0, inter.num_spaces):
        space = inter.space_list[s]

        trace_info[space.name] = space_trace(gouyx = space.gouy_x,
                                             gouyy = space.gouy_y)
                     
                                             
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class katRun(object):
    def __init__(self):
        self.runDateTime = datetime.datetime.now()
        self.x = None
        self.y = None
        self.xlabel = None
        self.ylabels = 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.ylabels)) if self.ylabels[i].split()[0] == str(value)]
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        if len(idx) > 0:
            out = self.y[:, idx]
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            if out.size == 1:
                return float(out)
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            else:
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                return out.squeeze()
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        else:
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            raise  pkex.BasePyKatException("No output by the name '{0}' found in the output".format(str(value)))
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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:
            return self.z[idx].squeeze()
        else:
            raise  pkex.BasePyKatException("No output by the name {0} found".format(str(value)))
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class Signals(object):
    class fsig(object):
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        def __init__(self, param, name, amplitude, phase):
            self._params = []
            self.__target = param
            self.__name = name
            self.__amplitude = Param("amp", self, SIfloat(amplitude))
            self.__phase = Param("phase", self, SIfloat(phase))
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            self.__removed = False
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            # unfortunatenly the target names for fsig are not the same as the
            # various parameter names of the components, e.g. mirror xbeta is x 
            # for fsig. So we need to check here what type of component we are targetting
            # and then based on the parameter specfied get the name
            if not param.canFsig:
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                raise  pkex.BasePyKatException("Cannot fsig parameter {1} on component {0}".format(str(param._owner().name), param.name))
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        def _register_param(self, param):
            self._params.append(param)
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        @property
        def removed(self): return self.__removed
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        def remove(self):
            if self.__removed:
                raise pkex.BasePyKatException("Signal {0} has already been marked as removed".format(self.name))
            else:
                self._kat.remove(self)
        
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        @property
        def name(self): return self.__name

        @property
        def amplitude(self): return self.__amplitude
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        @amplitude.setter
        def amplitude(self,value): self.__amplitude.value = SIfloat(value)

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        @property
        def phase(self): return self.__phase
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        @phase.setter
        def phase(self,value): self.__phase.value = SIfloat(value)
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        @property
        def target(self): return self.__target.fsig_name

        @property
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        def owner(self): return self.__target._owner().name
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        def getFinesseText(self):
            rtn = []
    
            for p in self._params:
                rtn.extend(p.getFinesseText())
        
            return rtn
    
    @property
    def name(self):
        # if we don't have any signals yet then use a dummy name
        # however we need to always tune a real fsig command
        # so need to get the name of at least one of them
        # as if you tune one you tune them all
        if len(self.targets) == 0:
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            return "fsignal"
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        else:
            return self.targets[0].name
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    @property
    def removed(self): return False # we can never remove the Signal object altogethr just the
                                    # individual fsig targets
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    def remove(self):
        for t in self.targets:
            self._kat.remove(self)
            
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    @property
    def f(self): return self.__f
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    @f.setter
    def f(self,value): self.__f.value = SIfloat(value)
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    def __init__(self):

        self.targets = []
        self._params = []
        
        self.__f = Param("f", self, 1)
    
    def _register_param(self, param):
        self._params.append(param)
        
    def apply(self, target, amplitude, phase, name=None):
        
        if target == None:
            raise  pkex.BasePyKatException("No target was specified for signal to be applied")
        
        if name == None:
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            name = "sig_" + target._owner().name + "_" + target.name
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        self.targets.append(Signals.fsig(target, name, amplitude, phase))
        
    def getFinesseText(self):
        rtn = []
        
        for t in self.targets:
            rtn.extend(t.getFinesseText())
            rtn.append("fsig {name} {comp} {target} {frequency} {phase} {amplitude}".format(name = t.name, comp=t.owner, target=t.target, frequency=str(self.f), phase=str(t.phase), amplitude=str(t.amplitude)))
        
        for p in self._params:
            rtn.extend(p.getFinesseText())
        
        return rtn
        
        
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class Block:
    def __init__(self, name):
        self.__name = name
        self.contents = [] # List of objects and strings of finesse code
        self.enabled = True 
        
    @property
    def name(self): return self.__name
    
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Constant = namedtuple('Constant', 'name, value, usedBy')
    
class kat(object):  
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    def __init__(self, kat_file=None, kat_code=None, katdir="", katname="", tempdir=None, tempname=None):
        
        self.scene = None # scene object for GUI
        self.verbose = True
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        self.__blocks = OrderedDict() # 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.__gui = None
        self.nodes = NodeNetwork(self)  
        self.__katdir = katdir
        self.__katname = katname
        self.__tempdir = tempdir
        self.__tempname = tempname
        self.pykatgui = None
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        self.__signals = Signals()
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        self.constants = {}
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        self.vacuum = []
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        # initialise default block
        self.__currentTag= NO_BLOCK
        self.__blocks[NO_BLOCK] = Block(NO_BLOCK)
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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.retrace = None
        self.deriv_h = None
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        self.scale = None
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        self.__phase = None
        self.__maxtem = None
        self.__noxaxis = None
        self.__time_code = None
        
        if kat_code != None and kat_file != None:
            raise pkex.BasePyKatException("Specify either a Kat file or some Kat code, not both.")
        
        if kat_code != None:
            self.parseCommands(kat_code)
        
        if kat_file != None:
            self.loadKatFile(kat_file)
        
        cls = type(self)
        self.__class__ = type(cls.__name__, (cls,), {})
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    @property
    def signals(self): return self.__signals

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    @property
    def maxtem(self): return self.__maxtem
    @maxtem.setter
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    def maxtem(self,value):
        if value == "off":
            self.__maxtem = -1
        else:
            self.__maxtem = int(value)
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    @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 components(self):
        return self.__components.copy()
    
    @property
    def detectors(self):
        return self.__detectors.copy()
        
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    @property
    def noxaxis(self): return self.__noxaxis
    @noxaxis.setter
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    def noxaxis(self,value): self.__noxaxis = bool(value) 
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    @staticmethod
    def logo():
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        print """                                              ..-
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    PyKat {0:7}         _                  '(
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                          \\`.|\\.__...-\"\"""-_." )
       ..+-----.._        /  ' `            .-'
   . '            `:      7/* _/._\\    \\   (
  (        '::;;+;;:      `-"' =" /,`"" `) /
  L.        \\`:::a:f            c_/     n_'
  ..`--...___`.  .    ,  
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   `^-....____:   +.      {1}""".format(pykat.__version__, pykat_web)
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    def loadKatFile(self, katfile):
        commands=open(katfile).read()
        self.parseCommands(commands)
    
    def parseKatCode(self, code):
        #commands = code.split("\n")
        self.parseCommands(code)
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    def processConstants(self, commands):
        """
        Before fully parsing a bunch of commands firstly any constants or variables
        to be recorded and replaced.
        """
        constants = self.constants
        
        for line in commands:
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            values = line.split()
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            if len(values)>0 and values[0] == 'const':
                
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                if len(values) >= 3:
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                    if values[1] in constants:
                        raise pkex.BasePyKatException('const command with the name "{0}" already used'.format(values[1]))
                    else:
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                        constants[str(values[1])] = Constant(values[1], values[2], [])
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                else:
                    raise pkex.BasePyKatException('const command "{0}" was not the correct format'.format(line))
        
        commands_new = []
        
        for line in commands:
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            values = line.split()
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            if len(values) > 0 and values[0] != 'const':
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                # check if we have a var/constant in this line
                if line.find('$') >= 0:
                    for key in constants.keys():
                        if line.find('$'+key) > -1:
                            constants[key].usedBy.append(line)
                            line = line.replace('$'+key, str(constants[key].value))
                        
                        
                commands_new.append(line)
    
        self.constants = constants
        
        return commands_new
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    def parseCommands(self, commands):
        blockComment = False
        
        commands=self.remove_comments(commands)
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        commands=self.processConstants(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:
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            #for line in commands:
            if len(line.strip()) >= 2:
                line = line.strip()

                # Looking for block start or end
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                values = line.split()
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                if values[0] == "%%%":
                    if values[1] == "FTblock":
                        newTag = values[2]
                        
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                        if self.__currentTag != None and self.__currentTag != NO_BLOCK: 
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                            warnings.warn("found block {0} before block {1} ended".format(newTag, self.__currentTag))    
                            
                        if newTag in self.__blocks:
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                            raise pkex.BasePyKatException("Block `{0}` has already been read".format(newTag))
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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":
                        self.__currentTag = NO_BLOCK
                        
                    continue
                #warnings.warn("current tag {0}".format(self.__currentTag))    

                # 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
                
                first = line.split(" ",1)[0]
                obj = None
                if(first == "m" or first == "m1" or first == "m2"):
                    obj = pykat.components.mirror.parseFinesseText(line)
                elif(first == "s"):
                    obj = pykat.components.space.parseFinesseText(line)
                elif(first == "l"):
                    obj = pykat.components.laser.parseFinesseText(line)
                elif(first[0:2] == "bs"):
                    obj = pykat.components.beamSplitter.parseFinesseText(line)
                elif(first[0:2] == "gr"):
                    obj = pykat.components.grating.parseFinesseText(line)
                elif(first[0:4] == "isol"):
                    obj = pykat.components.isolator.parseFinesseText(line)
                elif(first[0:4] == "lens"):
                    obj = pykat.components.lens.parseFinesseText(line)
                elif(first[0:3] == "mod"):
                    obj = pykat.components.modulator.parseFinesseText(line)
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                elif(first[0:2] == "ad"):
                    obj = pykat.detectors.ad.parseFinesseText(line)
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                elif(first[0:2] == "pd" and first != "pdtype"):
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                    obj = pykat.detectors.pd.parseFinesseText(line)
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                elif(first == "qshot"):
                    obj = pykat.detectors.qshot.parseFinesseText(line)
                elif(first == "qnoised"):
                    obj = pykat.detectors.qnoised.parseFinesseText(line)
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                elif(first == "xaxis" or first == "xaxis*"):
                    obj = pykat.commands.xaxis.parseFinesseText(line)
                elif(first == "x2axis" or first == "x2axis*"):
                    obj = pykat.commands.x2axis.parseFinesseText(line)
                elif(first == "gauss" or first == "gauss*" or first == "gauss**"):
                    after_process.append(line)
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                elif(first == "scale"):
                    after_process.append(line)
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                elif(first == "pdtype"):
                    after_process.append(line)
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                elif(first == "attr"):
                    after_process.append(line)
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                elif(first == "noxaxis"):
                    self.noxaxis = True
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                elif(first == "phase"):
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                    v = line.split()
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                    if len(v) != 2:
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                        raise pkex.BasePyKatException("phase command `{0}` is incorrect.".format(line))
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                    else:
                        self.phase = int(v[1])
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                elif(first == "maxtem"):
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                    v = line.split()
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                    if len(v) != 2:
                        raise pkex.BasePyKatException("maxtem command `{0}` is incorrect.".format(line))
                    else:
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			if v[1] == "off":
				self.maxtem = -1
			else:
	                        self.maxtem = int(v[1])
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                elif(first == "retrace"):
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                    v = line.split()
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                    if len(v) > 2:
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                        raise pkex.BasePyKatException("Retrace command `{0}` is incorrect.".format(line))
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                    elif len(v) == 2:
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                        self.retrace = v[1]                        
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                elif(first == "deriv_h"):
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                    v = line.split()
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                    if len(v) != 2:
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                        raise pkex.BasePyKatException("deriv_h command `{0}` is incorrect.".format(line))
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                    else:
                        self.deriv_h = float(v[1])
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                elif(first == "gnuterm" or first == "pyterm"):
                    if self.verbose:
                        print "Ignoring Gnuplot/Python terminal command '{0}'".format(line)
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                else:
                    if self.verbose:
                        print "Parsing `{0}` into pykat object not implemented yet, added as extra line.".format(line)
                    obj = line
                    # manually add the line to the block contents
                    self.__blocks[self.__currentTag].contents.append(line) 
                
                if obj != None and not isinstance(obj, str):
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                    if self.hasNamedObject(obj.name):
                        getattr(self, obj.name).remove()
                        print "Removed existing object '{0}' of type {1} to add new object".format(obj.name, obj.__class__)
                        
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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:
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            first = line.split(" ",1)[0]            
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            if first == "gauss" or first == "gauss*" or first == "gauss**":
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                pykat.commands.gauss.parseFinesseText(line, self)
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            elif (first == "scale"):
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                v = line.split()
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                if len(v) == 3:
                    component_name = v[2]
                    if component_name in self.__detectors :
                        self.__detectors[component_name].scale = SIfloat(v[1])
                    else:
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                        raise pkex.BasePyKatException("scale command `{0}` refers to non-existing output".format(component_name))
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                elif len(values) == 2:
                    self.scale = SIfloat(v[1])
                else:
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                    raise pkex.BasePyKatException("scale command `{0}` is incorrect.".format(line))
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            elif (first == "pdtype"):
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                v = line.split()
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                if len(v) == 3:
                    component_name = v[1]
                    if component_name in self.__detectors :
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                        self.__detectors[component_name].pdtype = v[2]
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                    else:
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                        raise pkex.BasePyKatException("pdtype command `{0}` refers to non-existing detector".format(component_name))
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                else:
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                    raise pkex.BasePyKatException("pdtype command `{0}` is incorrect.".format(line))
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            elif(first == "attr"):
                v = line.split()
                                
                if len(v) < 4:
                    raise pkex.BasePyKatException("attr command `{0}` is incorrect.".format(line))
                else:
                    # get the component/detector in question
                    if v[1] in self.__components:
                        comp = self.__components[v[1]]
                    elif v[1] in self.__detectors:
                        comp = self.__detectors[v[1]]
                    else:
                        raise pkex.BasePyKatException("Could not find the component '{0}' for attr command in line '{1}'".format(v[1], line))
                
                    if len(v[2:]) % 2 == 1:
                        raise pkex.BasePyKatException("Attr command '{0}' must specify both parameter and value pairs".format(line))
                                                
                    # convert split list to key value pairs
                    kv = dict(itertools.izip_longest(*[iter(v[2:])] * 2, fillvalue=None))

                    comp.parseAttributes(kv)
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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 pkex.BasePyKatException as ex:
            print ex
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    def getProcess(self, callback, **kwargs):
        """
        """
        
        cmd = "\n".join(self.generateKatScript())
        
        return Process(target=f__lkat_process, args=(callback, cmd, kwargs))
           
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    def run(self, printout=0, printerr=0, save_output=False, save_kat=False,kat_name=None) :
        """ 
        Runs the current simulation setup that has been built thus far.
        It returns a katRun or katRun2D object which is populated with the various
        data from the simulation run.
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        printoutput=1 prints the Finesse banner
        printerr shows the Finesse progress (set kat.verbose=1 to see warnings and errors)
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        """
        start = datetime.datetime.now()
        
        try:        
            if not hasattr(self, "xaxis") and self.noxaxis != None and self.noxaxis == False:
                raise pkex.BasePyKatException("No xaxis was defined")
            
            if len(self.__katdir) == 0:
                # Get the environment variable for where Finesse is stored
                self.__finesse_dir = os.environ.get('FINESSE_DIR')
                
                if self.__finesse_dir == None :
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                    raise pkex.MissingFinesseEnvVar()
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            else:
                self.__finesse_dir = self.__katdir
                
            if len(self.__katname) == 0:
                katexe = "kat"
                
                if os.sys.platform == "win32":
                    katexe += ".exe"
            else:
                katexe = self.__katname
            
            kat_exec = os.path.join(self.__finesse_dir, katexe) 
            
            # 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 pkex.MissingFinesse()
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            if self.verbose: print "--------------------------------------------------------------"
            if self.verbose: print "Running kat - Started at " + str(start)
            
            if hasattr(self, "x2axis"):
                r = katRun2D()
            else:
                r = katRun()
                
            r.katScript = "".join(self.generateKatScript())   
            
            # create a kat file which we will write the script into
            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' ) 
                
            katfile.writelines(r.katScript)
            katfile.flush()
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            if printout == 1:
                cmd=[kat_exec]
            else:
                cmd=[kat_exec, '--perl1']
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            if self.__time_code:
                cmd.append('--perf-timing')

            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')

            cmd.append(katfile.name)
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            p=subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
            err = ""
            
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            #if self.verbose: print "Finesse output:"
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            for line in iter(p.stderr.readline, ""):
                
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                if len(line) > 0:
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                    if line.rstrip().endswith('s'):
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                        vals = line.split("-")
                        action = vals[0].strip()
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                        prc = vals[1].strip()[:]
                        
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                        if printerr == 1:
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                            sys.stdout.write("\r{0} {1}".format(action, prc))
                    elif line.rstrip().endswith('%'):
                        vals = line.split("-")
                        action = vals[0].strip()
                        prc = vals[1].strip()[:]
                        
                        if printerr == 1:
                            sys.stdout.write("\r{0} {1}".format(action, prc))
                            
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                    elif line[0:3] == '** ':
                        if self.verbose: sys.stdout.write(line)
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                    else:
                        err += line
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            [out,errpipe] = p.communicate()
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            if printout == 1: 
                print out
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            else:
                if printerr == 1: print ""
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            # get the version number
            ix = out.find('build ') + 6
            ix2 = out.find(')',ix)
            r.katVersion = out[ix:ix2]
            
            r.runDateTime = datetime.datetime.now()
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            # If Finesse returned an error, just print that and exit!
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            if p.returncode != 0:
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                print err
                sys.exit(1) 
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            root = os.path.splitext(katfile.name)
            base = os.path.basename(root[0])            
            outfile = root[0] + ".out"
            
            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)

                if self.verbose: print "\nOutput data saved to '{0}'".format(newoutfile)
            
            if hasattr(self, "x2axis"):
                [r.x,r.y,r.z,hdr] = self.readOutFile(outfile)
                
                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:])
                            
            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)         
                
                if self.verbose: print "Kat file saved to '{0}'".format(newkatfile)
                

            katfile.close()
            perfData = []
            
            if self.__time_code:
                perffile = open(root[0] + ".perf",'r')
                
                for l in perffile.readlines():
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                    vals = l.strip().split()
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                    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
        finally:
            if self.verbose: print ""
            if self.verbose: print "Finished in " + str(datetime.datetime.now()-start)
            
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    def remove(self, obj):
        if not (obj.name in self.__components or obj.name in self.__detectors or obj.name in self.__commands):
            raise pkex.BasePyKatException("{0} is not currently in the simulation".format(obj.name))
        
        if obj.removed:
            raise pkex.BasePyKatException("{0} has already been removed".format(obj.name))        
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        nodes = None
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        # store nodes that this componet is attached to as a reference for gui
        if isinstance(obj, Component):
            nodes = self.nodes.getComponentNodes(obj)

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        if isinstance(obj, Component):    
            del self.__components[obj.name]
            self.__del_component(obj)
            self.nodes.removeComponent(obj)
        elif isinstance(obj, Command):    
            del self.__commands[obj.name]
            self.__del_command(obj)
        elif isinstance(obj, Detector):    
            del self.__detectors[obj.name]
            self.__del_detector(obj)
        
        for b in self.__blocks:
            if obj in self.__blocks[b].contents:
                self.__blocks[b].contents.remove(obj)
        
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        if self.pykatgui != None:
            self.pykatgui._onComponentRemoved(obj, nodes)
    
        del nodes
        
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        import gc
        print gc.get_referrers(obj)
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    def hasNamedObject(self, name):
        return name in self.__components or name in self.__detectors or name in self.__commands
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    def add(self, obj):
        try:
            obj.tag = self.__currentTag
            self.__blocks[self.__currentTag].contents.append(obj)
            
            if isinstance(obj, Component):
                
                if obj.name in self.__components :
                    raise pkex.BasePyKatException("A component with name '{0}' has already been added".format([obj.name]))            
                            
                self.__components[obj.name] = obj
                self.__add_component(obj)
                
            elif isinstance(obj, Detector):
                
                if obj.name in self.__detectors :
                        raise pkex.BasePyKatException("A detector '{0}' has already been added".format(obj.name))
                        
                self.__detectors[obj.name] = obj
                self.__add_detector(obj)
                
            elif isinstance(obj, Command):
                
                self.__commands[obj.__class__.__name__] = obj
                self.__add_command(obj)
                
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            else:
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                raise pkex.BasePyKatException("Object {0} could not be added".format(obj))
                
            obj._on_kat_add(self)
            
        except pkex.BasePyKatException as ex:
            print ex

    def readOutFile(self, filename):
        
        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)

        # convert 1D arrays into 2D ones for simpler selection
        if len(data.shape) == 1:
            data = np.array([data])
                            
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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]
            # get rows and columns lined up so that we can reshape a single column of all x/y data
            # into a matrix
            z = data[:,2:].transpose().reshape(data.shape[1]-2, 1+self.xaxis.steps, 1+self.x2axis.steps)
            # once you do this the data for y and x axes need swapping
            z = z.swapaxes(1,2)
            return [x, y, z, hdr]
        else:
            shape_len = len(data.shape)
            
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            rows,cols = data.shape
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            x = data[:,0]
            y = data[:,1:cols]
        
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            return [x, y, hdr]
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    def removeLine(self, fragment) :
        for key in self.__blocks:
            objs = self.__blocks[key].contents
            for obj in objs:
                if isinstance(obj, str):
                    if fragment in obj:
                        print "  ** removing line '{0}'".format(obj)
                        objs.remove(obj)
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    def generateKatScript(self) :
        """ Generates the kat file which can then be run """
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        def writeBlock():
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            for obj in objs:
                if isinstance(obj, str):
                    out.append(obj + '\n')
                    
                elif isinstance(obj, Component) or isinstance(obj, Detector) or isinstance(obj, Command):
                    txt = obj.getFinesseText() 
                    
                    if txt != None: