finesse.py

# -*- 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
import math       
import itertools
import ctypes
import ctypes.util
import collections
from collections import namedtuple, OrderedDict

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
from pykat.SIfloat import *
from pykat.param import Param, AttrParam

import pykat.exceptions as pkex

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

from multiprocessing import Process, Manager

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

# 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")
                                     
def f__lkat_process(callback, cmd, kwargs):
    """
    """
    
    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)

    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)


def f__lkat_trace_callback(lkat, trace_info, getCavities, getNodes, getSpaces):
    """
    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()

    if getNodes:
        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

    if getCavities:
        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

    if getSpaces:
        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)
                     
                                             
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
        self.yaxis = None
        
    def plot(self):
        import pylab
        
        pylab.plot(self.x, self.y)
        pylab.legend(self.ylabels,0)
        pylab.xlabel(self.xlabel)
        pylab.show()
        
    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):
        idx = [i for i in range(len(self.ylabels)) if self.ylabels[i].split()[0] == str(value)]
        
        
        if len(idx) > 0:
            out = self.y[:, idx]
            
            if self.yaxis == "abs:deg":
                out = self.y[:, idx[0]] * np.exp(1j*math.pi*self.y[:, idx[1]]/180.0)
            elif self.yaxis == "re:im":
                out = self.y[:, idx[0]] + 1j*self.y[:, idx[1]]
            
            out.squeeze()
            
            if out.size == 1:
                return out[0]
            else:
                return out
        else:
            raise  pkex.BasePyKatException("No output by the name '{0}' found in the output".format(str(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].squeeze()
    
    def __getitem__(self, value):
        idx = [i for i in range(len(self.zlabels)) if self.zlabels[i].split()[0] == str(value)]
        
        if len(idx) > 0:
            return self.z[idx].squeeze()
        else:
            raise  pkex.BasePyKatException("No output by the name {0} found".format(str(value)))
    
        
class Signals(object):
    class fsig(object):
        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))
            self.__removed = False
            
            # 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:
                raise  pkex.BasePyKatException("Cannot fsig parameter {1} on component {0}".format(str(param._owner().name), param.name))
            
        def _register_param(self, param):
            self._params.append(param)
        
        @property
        def removed(self): return self.__removed
  
        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)
        
        @property
        def name(self): return self.__name

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


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

        @property
        def target(self): return self.__target.fsig_name

        @property
        def owner(self): return self.__target._owner().name
    
        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:
            return "fsignal"
        else:
            return self.targets[0].name
            
    @property
    def removed(self): return False # we can never remove the Signal object altogethr just the
                                    # individual fsig targets

    def remove(self):
        for t in self.targets:
            self._kat.remove(self)
            
    @property
    def f(self): return self.__f
    @f.setter
    def f(self,value): self.__f.value = SIfloat(value)
    
    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:
            name = "sig_" + target._owner().name + "_" + target.name
        
        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
        
        
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
    
Constant = namedtuple('Constant', 'name, value, usedBy')
    
class kat(object):  
        
    def __init__(self, kat_file=None, kat_code=None, katdir="", katname="", tempdir=None, tempname=None):

        cls = type(self)
        self.__class__ = type(cls.__name__, (cls,), {})
        
        self.scene = None # scene object for GUI
        self.verbose = True
        self.__blocks = OrderedDict() # dictionary of blocks that are used
        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
        self.__signals = Signals()
        self.constants = {}
        self.vacuum = []
        self.__prevrunfilename = None
        self.printmatrix = None
        
        # initialise default block
        self.__currentTag= NO_BLOCK
        self.__blocks[NO_BLOCK] = Block(NO_BLOCK)
        
        # Various options for running finesse, typicaly the commands with just 1 input
        # and have no name attached to them.
        self.retrace = None
        self.deriv_h = None
        self.scale = None
        self.__trace = None
        self.__phase = None
        self.__maxtem = None
        self.__noxaxis = False
        self.__time_code = None
        self.__yaxis = "abs" # default yaxis
        self.__lambda0 = 1064e-9
        
        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)

    @property
    def signals(self): return self.__signals

    yaxis_options = ["abs:deg","db:deg","re:im","abs","db","deg"]
    @property
    def yaxis(self): return self.__yaxis
    @yaxis.setter
    def yaxis(self, value):
        
        if not str(value) in self.yaxis_options:
            raise pkex.BasePyKatException("yaxis value '{0}' is not a value option. Valid options are: {1}".format(str(value), ",".join(self.yaxis_options) ))
            
        self.__yaxis = str(value)

    @property
    def trace(self): return self.__trace
    @trace.setter
    def trace(self, value):
        value = int(value)

        if value < 0 or value > 255:
            raise pkex.BasePyKatException('trace command only accepts values in the range 0-255.')
        else:
            self.__trace = value

    @property
    def lambda0(self): return self.__lambda0
    @lambda0.setter
    def lambda0(self, value):
        self.__lambda0 = SIfloat(value)
        
        for node in self.nodes.getNodes():
            if self.nodes[node].q != None:
                self.nodes[node].q.wavelength = self.__lambda0

    @property
    def maxtem(self): return self.__maxtem
    @maxtem.setter
    def maxtem(self,value):
        if value == "off":
            self.__maxtem = -1
        else:
            self.__maxtem = int(value)
    
    @property
    def phase(self): return self.__phase
    @phase.setter
    def phase(self,value): self.__phase = int(value)
        
    @property
    def getPerformanceData(self): return self.__time_code
    @getPerformanceData.setter
    def getPerformanceData(self,value): self.__time_code = bool(value)
    
    @property
    def components(self):
        return self.__components.copy()
    
    @property
    def detectors(self):
        return self.__detectors.copy()
        
    @property
    def noxaxis(self): return self.__noxaxis
    @noxaxis.setter
    def noxaxis(self,value): self.__noxaxis = bool(value) 

    @staticmethod
    def logo():
        print """                                              ..-
    PyKat {0:7}         _                  '(
                          \\`.|\\.__...-\"\"""-_." )
       ..+-----.._        /  ' `            .-'
   . '            `:      7/* _/._\\    \\   (
  (        '::;;+;;:      `-"' =" /,`"" `) /
  L.        \\`:::a:f            c_/     n_'
  ..`--...___`.  .    ,  
   `^-....____:   +.      {1}""".format(pykat.__version__, pykat_web)
    
    def loadKatFile(self, katfile):
        commands=open(katfile).read()
        self.parseCommands(commands)
    
    def parseKatCode(self, code):
        #commands = code.split("\n")
        self.parseCommands(code)

    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:
            values = line.split()
            
            if len(values)>0 and values[0] == 'const':
                
                if len(values) >= 3:
                    if values[1] in constants:
                        raise pkex.BasePyKatException('const command with the name "{0}" already used'.format(values[1]))
                    else:
                        constants[str(values[1])] = Constant(values[1], values[2], [])
                else:
                    raise pkex.BasePyKatException('const command "{0}" was not the correct format'.format(line))
        
        commands_new = []
        
        for line in commands:
            values = line.split()
            
            if len(values) > 0 and values[0] != 'const':
                # 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('$'+key+' ', str(constants[key].value)+ ' ')
                        elif line.endswith('$'+key):
                            constants[key].usedBy.append(line)
                            line = line.replace('$'+key, str(constants[key].value))
                        
                commands_new.append(line)
    
        self.constants = constants
        
        return commands_new
        
    def parseCommands(self, commands):
        blockComment = False
        
        commands=self.remove_comments(commands)
        
        commands=self.processConstants(commands)
        
        after_process = [] # list of commands that should be processed after 
                           # objects have been set and created
        
        for line in commands:
            #for line in commands:
            if len(line.strip()) >= 2:
                line = line.strip()

                # Looking for block start or end
                values = line.split()
                if values[0] == "%%%":
                    if values[1] == "FTblock":
                        newTag = values[2]
                        
                        if self.__currentTag != None and self.__currentTag != NO_BLOCK: 
                            warnings.warn("found block {0} before block {1} ended".format(newTag, self.__currentTag))    
                            
                        if newTag in self.__blocks:
                            raise pkex.BasePyKatException("Block `{0}` has already been read".format(newTag))
                            
                        self.__blocks[newTag] = Block(newTag) # create new list to store all references to components in block
                        self.__currentTag = newTag
                        
                    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 == "sq"):
                    obj = pykat.components.squeezer.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)
                elif(first[0:2] == "ad"):
                    obj = pykat.detectors.ad.parseFinesseText(line)
                elif(first[0:2] == "bp"):
                    obj = pykat.detectors.bp.parseFinesseText(line)
                elif(first[0:4] == "gouy"):
                    obj = pykat.detectors.gouy.parseFinesseText(line)
                elif(first[0:2] == "pd" and first != "pdtype"):
                    obj = pykat.detectors.pd.parseFinesseText(line)
                elif(first == "qshot" or first == "qshotS" or first == "qshotN"):
                    obj = pykat.detectors.qshot.parseFinesseText(line)
                elif(first == "qnoised" or first == "qnoisedS" or first == "qnoisedN"):
                    obj = pykat.detectors.qnoised.parseFinesseText(line)
                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)
                elif(first == "scale"):
                    after_process.append(line)
                elif(first == "pdtype"):
                    after_process.append(line)
                elif(first == "attr"):
                    after_process.append(line)
                elif(first == "noxaxis"):
                    self.noxaxis = True
                elif(first == "lambda"):
                    v = line.split()
                    self.lambda0 = SIfloat(v[-1])
                elif(first == "yaxis"):
                    v = line.split()
                    
                    self.yaxis = v[-1]
                elif(first == "phase"):
                    v = line.split()
                    if len(v) != 2:
                        raise pkex.BasePyKatException("phase command `{0}` is incorrect.".format(line))
                    else:
                        self.phase = int(v[1])
                elif(first == "maxtem"):
                    v = line.split()
                    if len(v) != 2:
                        raise pkex.BasePyKatException("maxtem command `{0}` is incorrect.".format(line))
                    else:
                        if v[1] == "off":
                        	self.maxtem = -1
                        else:
	                        self.maxtem = int(v[1])
                elif(first == "trace"):
                    v = line.split()
                    if len(v) > 2:
                        raise pkex.BasePyKatException("Trace command `{0}` is incorrect.".format(line))
                    elif len(v) == 2:
                        self.trace = v[1]
                elif(first == "retrace"):
                    v = line.split()
                    if len(v) > 2:
                        raise pkex.BasePyKatException("Retrace command `{0}` is incorrect.".format(line))
                    elif len(v) == 2:
                        self.retrace = v[1]                        
                elif(first == "deriv_h"):
                    v = line.split()
                    if len(v) != 2:
                        raise pkex.BasePyKatException("deriv_h command `{0}` is incorrect.".format(line))
                    else:
                        self.deriv_h = float(v[1])
                elif(first == "gnuterm" or first == "pyterm"):
                    if self.verbose:
                        print "Ignoring Gnuplot/Python terminal command '{0}'".format(line)
                #elif(first == "fsig"):
                #    after_process.append(line)
                elif(first == "noplot"):
                    obj = line
                    self.__blocks[self.__currentTag].contents.append(line) 
                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):
                    if self.hasNamedObject(obj.name):
                        getattr(self, obj.name).remove()
                        print "Removed existing object '{0}' of type {1} to add line '{2}'".format(obj.name, obj.__class__, line)
                        
                    self.add(obj)
                    
                    
        # 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, self)
            elif (first == "scale"):
                v = line.split()
                if len(v) == 3:
                    component_name = v[2]
                    if component_name in self.__detectors :
                        self.__detectors[component_name].scale = SIfloat(v[1])
                    else:
                        raise pkex.BasePyKatException("scale command `{0}` refers to non-existing output".format(component_name))
                elif len(values) == 2:
                    self.scale = SIfloat(v[1])
                else:
                    raise pkex.BasePyKatException("scale command `{0}` is incorrect.".format(line))
            elif (first == "pdtype"):
                v = line.split()
                if len(v) == 3:
                    component_name = v[1]
                    if component_name in self.__detectors :
                        self.__detectors[component_name].pdtype = v[2]
                    else:
                        raise pkex.BasePyKatException("pdtype command `{0}` refers to non-existing detector".format(component_name))
                else:
                    raise pkex.BasePyKatException("pdtype command `{0}` is incorrect.".format(line))
            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)
                    
            elif(first == "fsig"):
                
                v = line.split()
                
                if v[2] in self.__components:
                    comp = self.__components[v[1]]
                else:
                    raise pkex.BasePyKatException("Could not find the component '{0}' for attr command in line '{1}'".format(v[1], line))
                
                
                #kat.siganls.apply()
                
            else:
                raise pkex.BasePyKatException("Haven't handled parsing of '{0}'".format(line))
                    
        self.__currentTag = NO_BLOCK 
        
    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

            
    def getProcess(self, callback, **kwargs):
        """
        """
        
        cmd = "\n".join(self.generateKatScript())
        
        return Process(target=f__lkat_process, args=(callback, cmd, kwargs))
           
    def run(self, printout=0, printerr=0, plot=None, 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.
        printout=1 prints the Finesse banner
        printerr shows the Finesse progress (set kat.verbose=1 to see warnings and errors)
        """
        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 :
                    raise pkex.MissingFinesseEnvVar()
            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)):
                raise pkex.MissingFinesse()
                
            if self.verbose: print "--------------------------------------------------------------"
            if self.verbose: print "Running kat - Started at " + str(start)
            
            if hasattr(self, "x2axis") and self.noxaxis == False:
                r = katRun2D()
            else:
                r = katRun()
                
            r.yaxis = self.yaxis
            r.katScript = "".join(self.generateKatScript())   

            if (plot==None):
                # ensure we don't do any plotting. That should be handled
                # by user themselves
                r.katScript+=("gnuterm no\n")
                r.katScript+=("pyterm no\n")
            else:
                r.katScript+=(plot+"\n")
            
            # 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()

            if printout == 1 or plot != None:
                cmd=[kat_exec]
            else:
                cmd=[kat_exec, '--perl1']
            
            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)
                            
            p=subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
            err = ""
            
            #if self.verbose: print "Finesse output:"

            for line in iter(p.stderr.readline, ""):
                
                if len(line) > 0:
                    
                    if line.rstrip().endswith('s'):
                        vals = line.split("-")
                        action = vals[0].strip()
                        prc = vals[1].strip()[:]
                        
                        if printerr == 1:
                            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))
                            
                    elif line[0:3] == '** ':
                        if self.verbose: sys.stdout.write(line)
                    else:
                        err += line

            
            [out,errpipe] = p.communicate()
            
            if printout == 1: 
                print out
            else:
                if printerr == 1: print ""

            # get the version number
            ix = out.find('build ') + 6
            ix2 = out.find(')',ix)
            r.katVersion = out[ix:ix2]
            
            r.runDateTime = datetime.datetime.now()

            # If Finesse returned an error, just print that and exit!
            if p.returncode != 0:
                print err
                sys.exit(1) 
            
            self.__prevrunfilename = katfile.name
            
            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") and self.noxaxis == False:
                [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)
                
            if self.trace != None and self.trace > 0:
                #print "{0}".format(out)
                #if self.trace & 1:
                    #search = out.find(' --- highest order of TEM modes')
                    #if search > -1:
                        #print "Trace 1: {0}".format(out[search:])

                # for now, just try to print the trace block in full
                print out[out.find(' ---') :]

            katfile.close()
            perfData = []
            
            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
            
        except pkex.FinesseRunError as fe:
            print fe
        finally:
            if self.verbose: print ""
            if self.verbose: print "Finished in " + str(datetime.datetime.now()-start)
            
    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))        

        nodes = None
        
        # store nodes that this componet is attached to as a reference for gui
        if isinstance(obj, Component):
            nodes = self.nodes.getComponentNodes(obj)

        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)
        
        if self.pykatgui != None:
            self.pykatgui._onComponentRemoved(obj, nodes)
    
        del nodes
        
        #import gc
        #print gc.get_referrers(obj)
    
    def getMatrices(self):
        
        import scipy
        from scipy.sparse import coo_matrix
        
        prev = self.noxaxis
        
        self.noxaxis = True
        self.printmatrix = True
        print "".join(self.generateKatScript())
        self.verbose = True
        self.run(printout=1)
        self.printmatrix = None
        self.noxaxis = prev        
        
        if self.__prevrunfilename == None:
            return None
        else:
            
            Mcarrier = None
            Msignal = None
            
            if os.path.exists("klu_full_matrix_car.dat"):
                M = np.loadtxt("klu_full_matrix_car.dat")
                
                if M.size > 0:
                    row = M[:,0]-1
                    col = M[:,1]-1
                    data = M[:,2] + 1j * M[:,3]
                    N = row.max()+1
                    Mcarrier = coo_matrix((data,(row,col)), shape=(N,N))
                
        
            if os.path.exists("klu_full_matrix_sig.dat"):
                M = np.loadtxt("klu_full_matrix_sig.dat")
                
                if M.size > 0:
                    row = M[:,0]-1
                    col = M[:,1]-1
                    data = M[:,2] + 1j * M[:,3]
                    N = row.max()+1
                    Msignal = coo_matrix((data,(row,col)), shape=(N,N))
        
            return (Mcarrier, Msignal)

        
    def hasNamedObject(self, name):
        return name in self.__components or name in self.__detectors or name in self.__commands
        
    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)
                
            else:
                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(',')
        
        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])
                            
        if hasattr(self, "x2axis") and self.noxaxis == False:
            # 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)
            
            rows,cols = data.shape
            
            x = data[:,0]
            y = data[:,1:cols]
        
            return [x, y, hdr]

    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)

                    
    def generateKatScript(self) :
        """ Generates the kat file which can then be run """

        def writeBlock():
            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:
                        if isinstance(txt,list):
                            for t in txt:
                                out.append(t + "\n")
                        else:
                            out.append(txt + "\n")

        
        out = []    
        import datetime
        strtoday = datetime.datetime.now()
        out.append(strtoday.strftime("%% Generated by PyKat %d.%m.%Y %H:%M:%S\n") )

        # write the FTblocks
        for key in self.__blocks:
            objs = self.__blocks[key].contents

            if key != NO_BLOCK:
                if np.size(objs)>0:
                    out.append("\n")
                    out.append("%%% FTblock " + key + "\n")
                    writeBlock()
                    out.append("%%% FTend " + key + "\n")

        # write the NO_BLOCK blocks
        for key in self.__blocks:
            objs = self.__blocks[key].contents


            if key == NO_BLOCK:
                if np.size(objs)>0:
                    out.append("\n")
                    writeBlock()
                
        # 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")
        

        # now get any signal commands
        txt = self.signals.getFinesseText()
        
        if txt != None:
            if isinstance(txt,list):
                for t in txt: out.append(t+ "\n")
            else:
                out.append(txt + "\n")

        if self.vacuum != None:
            
            if isinstance(self.vacuum, collections.Container):
                objs = []
                
                if len(self.vacuum) > 0:
                    for a in self.vacuum:
                        if hasattr(a, 'name'):
                            objs.append(a.name)
                        else:
                            objs.append(str(a))

                    out.append("vacuum {0}\n".format(" ".join(objs)))
                                        
            elif isinstance(self.vacuum, str):
                out.append("vacuum {0}\n".format(self.vacuum))
            else:
                pkex.BasePyKatException("Couldn't understand vacuum input list")

        if self.scale != None and self.scale !='': out.append("scale {0}\n".format(self.scale))
        if self.phase != None: out.append("phase {0}\n".format(self.phase))
        if self.trace != None: out.append("trace {0}\n".format(self.trace))
        if self.maxtem != None:
                if self.maxtem == -1:
                        out.append("maxtem off\n")
                else:
                        out.append("maxtem {0}\n".format(self.maxtem))

        if self.noxaxis == True:
            out.append("noxaxis\n")
            
        if self.yaxis != None:
            out.append("yaxis {0}\n".format(self.yaxis))
         
        if self.printmatrix != None and self.printmatrix == True:
            out.append("printmatrix\n")
            
        if self.lambda0 != 1064e-9:
            out.append("lambda {0}\n".format(self.lambda0))
            
        # ensure we don't do any plotting. That should be handled
        # by user themselves
        #out.append("gnuterm no\n")
        #out.append("pyterm no\n")
        
        return out
        
    def openGUI(self):
        if NO_GUI:
            print  "No PyQt4 module was installed so cannot open a GUI"
        else:
            self.app = QCoreApplication.instance() 
            created = False
            
            if self.app == None:
                created = True
                self.app = QApplication([""])
                
            if self.pykatgui == None:
                self.pykatgui = pyKatGUI(self)
                self.pykatgui.main()
            else:
                self.pykatgui.show()
                
            if created: self.app.exec_()
    
    def getComponents(self):
        return self.__components.values()
    
    def hasComponent(self, name):
        return (name in self.__components)
    
    def _newName(self, container, prefix):
        n = 1
        name = "{0}{1}".format(prefix, n)
        
        while name in container:
            n += 1
            name = "{0}{1}".format(prefix,n)
        
        return name
    
    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)
        
    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<