finesse.py 92.9 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
"""
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from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals

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import sys
import os
import subprocess
import tempfile
import numpy as np
import datetime
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import time
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import pickle
import pykat
import warnings
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import re
import math       
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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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import re
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import copy
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try:
    # Python 2
    from itertools import izip_longest
except ImportError:
    # Python 3
    from itertools import zip_longest as izip_longest
"""
try:
    from future_builtins import zip_longest
except ImportError: # not 2.6+ or is 3.x
    try:
        from itertools import izip_longest as zip_longest # < 2.5 or 3.x
    except ImportError:
        print("boom")
        pass
"""
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from math import erfc, pi
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from collections import namedtuple, OrderedDict
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from pykat.node_network import NodeNetwork
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from pykat.detectors import BaseDetector as Detector
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from pykat.components import Component
from pykat.commands import Command, xaxis
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from pykat.SIfloat import *
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from pykat.param import Param, AttrParam
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import pykat.external.six as six

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import pykat.exceptions as pkex

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from pykat import USE_GUI, HAS_OPTIVIS, NoGUIException

    
if HAS_OPTIVIS:
    from optivis.bench.labels import Label as optivis_label
    from optivis.geometry import Coordinates as optivis_coord
    import PyQt4
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if USE_GUI:
    from pykat.gui.gui import pyKatGUI
    from PyQt4.QtCore import QCoreApplication
    from PyQt4.QtGui import QApplication
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from multiprocessing import Process, Manager

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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 is None:
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        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: 
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        print ("Exception caught in python: ", ex.message)
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    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, getCavities, getNodes, getSpaces):
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    """
    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()

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    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
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                                )

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            trace_info[cav.name] = cav_info
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    if getSpaces:
        for s in range(0, inter.num_spaces):
            space = inter.space_list[s]
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            trace_info[space.name] = space_trace(gouyx = space.gouy_x,
                                                 gouyy = space.gouy_y)
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class KatBatch(object):
    """
    
    """
    
    def __init__(self):
        from IPython.parallel import Client

        self._c = Client()
        self._lb = c.load_balanced_view()
        self.lb.block = False
        
        self._todo = []
    
    def _run(dir, commands, **kwargs):
        import pykat
        kat = pykat.finesse.kat()
        kat.verbose = False
        kat.parseCommands(commands)
        
        kw = dict()
        
        if "cmd_args" in kwargs:
            kw["cmd_args"] = kwargs["cmd_args"]
        
        return kat.run(printerr=1, **kw)
    
    def addKat(self, kat, **kwargs):
        import os
        cdir = os.getcwd()
        script = "\n".join(kat.generateKatScript())
        self.todo.append(self.lb.apply_async(self._run, script, **kwargs))
        return self.todo[-1]
    
    def wait(self):
        return self.lb.wait(self.todo)
        
    def results(self):
        return self.todo

                                  
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def GUILength(L):
    """
    Should scale the lengths in some way to handle km and mm for time being
    """
    return L # * ( 40 * erfc(L/400.0) + 0.01)
            
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class katRun(object):
    def __init__(self):
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        self.runtime = None
        self.StartDateTime = datetime.datetime.now()
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        self.x = None
        self.y = None
        self.xlabel = None
        self.ylabels = None
        self.katScript = None
        self.katVersion = None
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        self.yaxis = None
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    def info(self):
        
        kat = pykat.finesse.kat()
        kat.verbose = False
        kat.parseCommands(self.katScript)
        
        detectors = list(set([lbl.split()[0] for lbl in self.ylabels]))
        detectors.sort()
        
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        print("")
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        print("--- Output info ---")
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        print("")
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        print("Run date and time: %s" % self.StartDateTime)
        print("Detectors used: %s" % (", ".join(detectors)))
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        print("")

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        if kat.noxaxis:
            print("No xaxis used")
        else:
            print("One xaxis used: %s" % kat.xaxis.getFinesseText())
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        import numpy as np

        maxs = np.max(self.y, 0)
        mins = np.min(self.y, 0)
        
        maxlbl = max([len(lbl) for lbl in self.ylabels])    
        
        for i, lbl in enumerate(self.ylabels):
            a = "{0:" + str(maxlbl) + "} : min = {1:.15e} max = {2:.15e}"
            print(a.format(lbl, mins[i], maxs[i]))
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    def plot(self, detectors=None, filename=None, show=True,
                   yaxis=None, legend=True, loc=0, title=None, styles=None,
                   ylabel=None, y2label=None, xlabel=None, x2label=None):
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        """
        This will generate a plot for the output data of this particular pykat run.
        It will attempt to generate a plot that shows all the various traces and plots
        by default for quick viewing of the data. Similar to that which would be
        generated by running the Finesse file from the command line.
        
        There are some additional keyword options to customise the plot output slightly:
        
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            detectors:          a list of detectors that you want to plot
            filename:           providing a filename here will save the plot to a file.
                                The format is given by the extension provided.
            show:               True | False - whether to display the plot or not
            yaxis:              Set the Finesse yaxis command to base the plot on. By
                                default the original one will be used.
            legend:             True | False - whether to include a legend
            loc:                Location value for the legend, the usual matplotlib one.
            title:              Provide a title for the plot if required.
            styles:             A dictionary which keys being the detector names and the
                                value being a colour and linestyle of the sort 'k:'
            ylabel, xlabel:     Text for the first plot x and y labels
            y2label, x2label:   Text for the second plot x and y labels 
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        """
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        import matplotlib.pyplot as pyplot
        import pykat.plotting as plt

        kat = pykat.finesse.kat()
        kat.verbose = False
        kat.parseCommands(self.katScript)

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        if yaxis is not None:
            kat.yaxis = yaxis
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        if "log" in kat.yaxis:
            if kat.xaxis.scale == "log":
                plot_cmd = pyplot.loglog
            else:
                plot_cmd = pyplot.semilogy
        else:
            if kat.xaxis.scale == "log":
                plot_cmd = pyplot.semilogx
            else:
                plot_cmd = pyplot.plot

        dual_plot = False
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        _func1 = np.abs
        _func2 = None
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        plot_cmd1 = None
        plot_cmd2 = None
        
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        if "re:im" in kat.yaxis:
            _func1 = np.real
            _func2 = np.imag
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            plot_cmd1 = plot_cmd2 = plot_cmd
            
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            dual_plot = True
        elif "abs:deg" in kat.yaxis:
            _func1 = np.abs
            _func2 = lambda x: np.rad2deg(np.angle(x))
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            plot_cmd1 = plot_cmd
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            plot_cmd2 = pyplot.plot if kat.xaxis.scale == "lin" else pyplot.semilogx
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            dual_plot = True
        elif "db:deg" in kat.yaxis:
            _func1 = lambda x: 10*np.log10(x)
            _func2 = lambda x: np.rad2deg(np.angle(x))
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            plot_cmd1 = plot_cmd
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            plot_cmd2 = pyplot.plot if kat.xaxis.scale == "lin" else pyplot.semilogx
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            dual_plot = True
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        elif "abs" in kat.yaxis:
            _func1 = np.abs
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            plot_cmd1 = plot_cmd
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        elif "db" in kat.yaxis:
            _func1 = lambda x: 10*np.log10(x)
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            plot_cmd1 = plot_cmd
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        elif "deg" in kat.yaxis:
            _func1 = lambda x: np.rad2deg(np.angle(x))
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            plot_cmd1 = plot_cmd
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        if dual_plot:
            fig = plt.figure(width="full", height=1)
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        else:
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            fig = plt.figure(width="full")   
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        if detectors is None:
            detectors = [lbl.split()[0] for lbl in self.ylabels]
            
        detectors = list(set(detectors))
        detectors.sort()
        
        for det in detectors:
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            if not hasattr(kat, det) or (hasattr(kat, det) and not getattr(kat, det).noplot):
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                if dual_plot:
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                    ax = pyplot.subplot(2,1,1)
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                if styles is not None and det in styles:
                    l, = plot_cmd1(self.x, _func1(self[det]), styles[det], label=det)
                else:
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                    l, = plot_cmd1(self.x, _func1(self[det]), label=det)
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                if dual_plot: 
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                    pyplot.subplot(2,1,2)
                    plot_cmd2(self.x, _func2(self[det]), color=l.get_color(), ls=l.get_linestyle(), label=det)
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        if dual_plot:
            if ylabel is None:
                if "abs" in kat.yaxis: ylabel = "Absolute [au]"
                if "re" in kat.yaxis:  ylabel = "Real part [au]"
                
            if y2label is None:
                if "deg" in kat.yaxis: y2label = "Phase [deg]"
                if "im" in kat.yaxis:  y2label = "Imaginary part [au]"
        else:
            if ylabel is None:
                ylabel = "[au]"
        
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        if xlabel is None:
            xlabel = self.xlabel
            
        if x2label is None:
            x2label = self.xlabel
            
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        font_label_size = pyplot.rcParams["font.size"]-1
        
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        if dual_plot:
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            ax = pyplot.subplot(2,1,1)
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            pyplot.xlabel(xlabel, fontsize=font_label_size)
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            pyplot.xlim(self.x.min(), self.x.max())
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            pyplot.ylabel(ylabel, fontsize=font_label_size)
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            if title is not None:
                pyplot.title(title, fontsize=font_label_size)
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            pyplot.subplot(2,1,2)
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            pyplot.xlabel(x2label, fontsize=font_label_size)
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            pyplot.xlim(self.x.min(), self.x.max())
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            pyplot.ylabel(y2label, fontsize=font_label_size)
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        else:
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            pyplot.xlabel(xlabel, fontsize=font_label_size)
            pyplot.ylabel(ylabel)
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            pyplot.xlim(self.x.min(), self.x.max())
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            if title is not None:
                pyplot.title(title, fontsize=font_label_size)
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        pyplot.tight_layout()
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        if legend:
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            fig.axes[0].legend(loc=loc, fontsize=font_label_size)
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        if filename is not None:
            fig.savefig(filename)
            
        if show:
            pyplot.show(fig)
        
        return fig
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    def savekatRun(self, filename):
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        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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        out = None
        
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        if len(idx) > 0:
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            #out = self.y[:, idx]
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            if len(idx) == 1:
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                if "abs:deg" in self.yaxis:
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                    out = self.y[:, idx[0]]
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                elif "re:im" in self.yaxis:
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                    out = self.y[:, idx[0]]
            else: 
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                if "abs:deg" in self.yaxis:
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                    out = self.y[:, idx[0]] * np.exp(1j*math.pi*self.y[:, idx[1]]/180.0)
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                elif "re:im" in self.yaxis :
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                    out = self.y[:, idx[0]] + 1j*self.y[:, idx[1]]
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            if out is None:
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                out = self.y[:, idx]

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            if out.size == 1:
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                return out[0].squeeze()
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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):
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        self.runtime = None
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        self.startDateTime = datetime.datetime.now()
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        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)
    
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    def get(self, value): return self[value].squeeze()
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    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, signal):
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            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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            self.__signal = signal
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            # unfortunatenly the target names for fsig are not the same as the
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            # various parameter names of the components, e.g. mirror xbeta is x 
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            # 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):
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            self.__signal._kat.remove(self)
            
        def _on_remove(self):
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            if self.__removed:
                raise pkex.BasePyKatException("Signal {0} has already been marked as removed".format(self.name))
            else:
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                self.__signal.targets.remove(self)
                self.__remove = True
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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
    
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    @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 self._default_name
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        else:
            return self.targets[0].name
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    @property
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    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:
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            t.remove()
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        del self.targets[:]
        
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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, kat):
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        self._default_name = "fsignal"
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        self.targets = []
        self._params = []
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        self.__f = Param("f", self, 0)
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        self._kat = kat
        
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    def _register_param(self, param):
        self._params.append(param)
        
    def apply(self, target, amplitude, phase, name=None):
        
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        if target is None:
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            raise  pkex.BasePyKatException("No target was specified for signal to be applied")
        
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        if name is 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, self))
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    def getFinesseText(self):
        rtn = []
        
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        if len(self.targets) == 0 and (self.f != 0 and self.f is not None):
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            rtn.append("fsig {name} {frequency}"
                            .format(name = self.name,
                                    frequency=str(self.f)))
        else:
            for t in self.targets:
                rtn.extend(t.getFinesseText())
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                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 if t.amplitude != None else "")))
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        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')
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id___ = 0

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class kat(object):  
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    def __new__(cls, *args, **kwargs):
        # This may seem like an arbitrary step but here we are creating a
        # new class that is a base class of itself. This is because when
        # the kat object adds new components it also adds properties for
        # each of these. There properties are unique to each kat object,
        # but properties are part of the class definition. Thus if two
        # kat objects share the same class definition they also have the
        # same properties regardless of whether they have the actual
        # object added to it. So we create an instance specific class.
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        global id___
        id___ += 1
        cnew = type(pykat.finesse.kat.__name__ + str("_") + str(id___), (pykat.finesse.kat,), {})
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        return object.__new__(cnew)
    
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    def __init__(self, kat_file=None, kat_code=None, katdir="", katname="", tempdir=None, tempname=None):
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        self.scene = None # scene object for GUI
        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(self)
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        self.constants = {}
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        self.vacuum = []
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        self.__prevrunfilename = None
        self.printmatrix = None
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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.__trace = None
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        self.__phase = None
        self.__maxtem = None
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        self.__noxaxis = False
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        self.__time_code = None
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        self.__yaxis = "abs" # default yaxis
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        self.__lambda0 = 1064e-9
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        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)
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    def deepcopy(self):
        return copy.deepcopy(self)
    
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    def getAll(self, type):
        """
        Returns a collection of all objects of the type argument that are
        part of this kat object.
        
        Example:
            # returns all cav commands that are present in this kat object
            cavs = kat.getAll(pykat.commands.cavity)
        """
        items = []
        
        for a in (item for item in self.__class__.__dict__):
            b = getattr(self, a)
            
            if isinstance(b, type):
                items.append(b)

        return tuple(items)
        
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    def __deepcopy__(self, memo):
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        """
        When deep copying a kat object we need to take into account
        the instance specific properties. This is because when
        the kat object adds new components it also adds properties for
        each of these. There properties are unique to each kat object,
        but properties are part of the class definition. Thus if two
        kat objects share the same class definition they also have the
        same properties regardless of whether they have the actual
        object added to it. So we create an instance specific class.
        """
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        result = self.__class__.__new__(self.__class__.__base__)
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        memo[id(self)] = result
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        result.__dict__ = copy.deepcopy(self.__dict__, memo)

        # Find all properties in class we are copying
        # and deep copy these to the new class instance
        for x in self.__class__.__dict__.items():
            if isinstance(x[1], property):
                setattr(result.__class__, x[0], x[1])
    
        result.nodes._NodeNetwork__update_nodes_properties()
                
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        # Update any weakrefs
        for c in result.components:
            result.components[c]._Component__update_node_setters()
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        return result
    
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    @property
    def signals(self): return self.__signals

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    yaxis_options = ["abs:deg","db:deg","re:im","abs","db","deg"]
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    @property
    def yaxis(self): return self.__yaxis
    @yaxis.setter
    def yaxis(self, value):
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        values = value.split()
        
        if len(values) == 2:
            scale = values[0]
            mode = values[1]
        else:
            scale = "lin"
            mode = value
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        if not str(scale) in ["lin", "log"]:
            raise pkex.BasePyKatException("yaxis value '{0}' is not a valid option. Valid options are: lin or log".format(str(mode)))
                
        if not str(mode) in self.yaxis_options:
            raise pkex.BasePyKatException("yaxis value '{0}' is not a valid option. Valid options are: {1}".format(str(mode), ",".join(self.yaxis_options) ))
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        self.__yaxis = str(scale + " " + mode).strip()
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    @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

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    @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

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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
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    def timeCode(self): return self.__time_code
    @timeCode.setter
    def timeCode(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 commands(self):
        return self.__commands.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}\n""".format(pykat.__version__, pykat_web))
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    def loadKatFile(self, katfile, blocks=None):
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        commands=open(katfile).read()
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        self.parseCommands(commands, blocks=blocks)
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    def parseKatCode(self, code, blocks=None):
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        #commands = code.split("\n")
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        self.parseCommands(code, blocks=blocks)
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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.
        """
        
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        try:
            constants = self.constants
        
            for line in commands:
                values = line.split()
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                if len(values)>0 and values[0] == 'const':
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                    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], [])
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                    else:
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                        raise pkex.BasePyKatException('const command "{0}" was not the correct format'.format(line))
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            commands_new = []
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            for line in commands:
                values = line.split()
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                if len(values) > 0 and values[0] != 'const':
                    # check if we have a var/constant in this line
                    if line.find('$') >= 0:
                        for key in constants.keys():
                            # TODO: need to fix this for checking mulitple instances of const in a single line
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                            chars = [' ', '+', '-', '*', '/', ')']
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                            for c in chars:
                                none_found = False
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                                while not none_found:
                                    if line.find('$'+key+c) > -1:
                                        constants[key].usedBy.append(line)
                                        line = line.replace('$'+key+c, str(constants[key].value)+ c)
                                    else:
                                        none_found = True
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                            if line.endswith('$'+key):
                                constants[key].usedBy.append(line)
                                line = line.replace('$'+key, str(constants[key].value))
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                    commands_new.append(line)
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            self.constants = constants
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            return commands_new
            
        except pkex.BasePyKatException as ex:
            pkex.PrintError("Error processing constants:", ex)
            sys.exit(1)
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    def getBlocks(self):
        return self.__blocks.keys()
    
    def removeBlock(self, name, failOnBlockNotFound=True):
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        if name not in self.__blocks:
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            if failOnBlockNotFound:
                pkex.PrintError("Error removing block:", pkex.BasePyKatException('Block "{0}" was not found'.format(name)))
                sys.exit(1)
            else:
                return
                
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        for o in self.__blocks[name].contents:
            self.remove(o)
        
        del self.__blocks[name]
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    def __str__(self):
         return "".join(self.generateKatScript())
         
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    def parseCommands(self, commands, blocks=None, addToBlock=None):
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        try:
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            if addToBlock is not None and blocks is not None:
                raise pkex.BasePyKatException("When parsing commands you cannot set both blocks and addToBlock arguments")
            
            # Create a new block if one asked for isn't present
            if addToBlock is not None:
                if addToBlock not in self.__blocks:
                    self.__blocks[addToBlock] = Block(addToBlock)
                
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            blockComment = False
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            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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                if len(line.strip()) >= 2:
                    line = line.strip()

                    # Looking for block start or end
                    values = line.split()
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                    if addToBlock is None:
                        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))    
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                                if newTag in self.__blocks:
                                    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
                                self.__currentTag = newTag
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                            if values[1] == "FTend":
                                self.__currentTag = NO_BLOCK
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                            continue
                    else:
                        self.__currentTag = addToBlock
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                    # only include listed blocks, if we have specfied them
                    if blocks != None and self.__currentTag not in blocks:
                        continue
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                    # don't read comment lines
                    if line[0] == "#" or line[0] == "%":
                        continue
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                    # check if block comment is being used
                    if not blockComment and line[0:2] == "/*":
                        blockComment = True
                        continue
                    elif blockComment and line[0:2] == "*/":
                        blockComment = False
                        continue
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                    first = line.split(" ",1)[0]
                    obj = None
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                    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)
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                    elif(first[0:2] == "xd"):
                        obj = pykat.detectors.xd.parseFinesseText(line)
                    elif(first[0:2] == "tf"):
                        obj = pykat.commands.tf.parseFinesseText(line)
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                    elif(first[0:2] == "cp"):
                        obj = pykat.detectors.cp.parseFinesseText(line)
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                    elif(first[0:2] == "bp"):
                        obj = pykat.detectors.bp.parseFinesseText(line)
                    elif(first[0:4] == "gouy"):
                        obj = pykat.detectors.gouy.parseFinesseText(line)
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                    elif(first[0:4] == "beam"):
                        obj = pykat.detectors.beam.parseFinesseText(line)
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                    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*"):
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                        self.noxaxis = False
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                        obj = pykat.commands.xaxis.parseFinesseText(line)
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                    elif(first[0:2] == "hd"):
                        obj = pykat.detectors.hd.parseFinesseText(line)
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                    elif(first.startswith("qhd")):
                        obj = pykat.detectors.qhd.parseFinesseText(line)
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                    elif(first == "x2axis" or first == "x2axis*"):
                        obj = pykat.commands.x2axis.parseFinesseText(line)
                    elif(first == "gauss" or first == "gauss*" or first == "gauss**"):
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                        after_process.append((line, self.__currentTag))
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                    elif(first == "scale"):
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                        after_process.append((line, self.__currentTag))
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                    elif(first == "pdtype"):
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                        after_process.append((line, self.__currentTag))
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                    elif(first == "cav"):
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                        after_process.append((line, self.__currentTag))
                    elif(first == "func"):
                        after_process.append((line, self.__currentTag))
                    elif(first == "variable"):
                        after_process.append((line, self.__currentTag))
                    elif(first == "lock"):
                        after_process.append((line, self.__currentTag))
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                    elif(first == "attr"):
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                        after_process.append((line, self.__currentTag))
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                    elif(first == "noxaxis"):
                        self.noxaxis = True
                    elif(first == "lambda"):
                        v = line.split()
                        self.lambda0 = SIfloat(v[-1])
                    elif(first == "yaxis"):
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                        v = line.split(" ", 1)
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                        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":
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                                self.maxtem = -1
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                            else:
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                                self.maxtem = int(v[1])
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                    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))
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                        else:
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                            self.deriv_h = float(v[1])
                    elif(first == "gnuterm" or first == "pyterm"):
                        if self.verbose: