Select Git revision
semi_coherent_search_using_MCMC.py
finesse.py 63.89 KiB
# -*- 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
"""
from __future__ import print_function
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
import re
import copy
from collections import namedtuple, OrderedDict
from pykat.node_network import NodeNetwork
from pykat.detectors import BaseDetector as Detector
from pykat.components import Component
from pykat.commands import Command, xaxis
from pykat.SIfloat import *
from pykat.param import Param, AttrParam
import pykat.exceptions as pkex
from pykat import USE_GUI, HAS_OPTIVIS, NoGUIException
if USE_GUI:
from pykat.gui.gui import pyKatGUI
from PyQt4.QtCore import QCoreApplication
from PyQt4.QtGui import QApplication
from multiprocessing import Process, Manager
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)]
out = None
if len(idx) > 0:
if len(idx) == 1:
if self.yaxis == "abs:deg":
out = self.y[:, idx[0]]
elif self.yaxis == "re:im":
out = self.y[:, idx[0]]
else:
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]]
if out == None:
out = self.y[:, idx]
if out.size == 1:
return out[0].squeeze()
else:
return out.squeeze()
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, signal):
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
self.__signal = signal
# 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):
self.__signal._kat.remove(self)
def _on_remove(self):
if self.__removed:
raise pkex.BasePyKatException("Signal {0} has already been marked as removed".format(self.name))
else:
self.__signal.targets.remove(self)
self.__remove = True
@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:
t.remove()
del self.targets[:]
@property
def f(self): return self.__f
@f.setter
def f(self,value): self.__f.value = SIfloat(value)
def __init__(self, kat):
self.targets = []
self._params = []
self.__f = Param("f", self, 1)
self._kat = kat
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, self))
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 if t.amplitude != None else "")))
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 __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.
return object.__new__(type(pykat.finesse.kat.__name__, (pykat.finesse.kat,), {}), *args, **kwargs)
def __init__(self, kat_file=None, kat_code=None, katdir="", katname="", tempdir=None, tempname=None):
self.scene = None # scene object for GUI
self.verbose = True
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)
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)
def __deepcopy__(self, memo):
"""
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.
"""
result = self.__class__.__new__(self.__class__)
memo[id(self)] = result
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])
return result
@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}\n""".format(pykat.__version__, pykat_web))
def loadKatFile(self, katfile, blocks=None):
commands=open(katfile).read()
self.parseCommands(commands, blocks=blocks)
def parseKatCode(self, code, blocks=None):
#commands = code.split("\n")
self.parseCommands(code, blocks=blocks)
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('$') >= 0:
for key in constants.keys():
# TODO: need to fix this for checking mulitple instances of const in a single line
chars = [' ', '+', '-', '*', '/', ')']
for c in chars:
none_found = False
while not none_found:
if line.find('$'+key+c) > -1:
constants[key].usedBy.append(line)
line = line.replace('$'+key+c, str(constants[key].value)+ c)
else:
none_found = True
if line.endswith('$'+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, blocks=None):
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:
try:
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
# only include listed blocks, if we have specfied them
if blocks != None and self.__currentTag not in blocks:
continue
# 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[0:2] == "hd"):
obj = pykat.detectors.hd.parseFinesseText(line)
elif(first.startswith("qhd")):
obj = pykat.detectors.qhd.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)
except:
print("--------------------------------------------------------")
print("Error parsing line: " + line)
print("--------------------------------------------------------")
raise
# 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()
accepted = ["psd","psd_hf","asd","asd_hf","meter", "ampere", "degs"]
if len(v) == 3:
component_name = v[2]
if v[1].lower() in accepted:
val = v[1]
else:
try:
val = SIfloat(v[1])
except ValueError as ex:
raise pkex.BasePyKatException("Line `{0}`:\nAccepted scale values are decimal numbers or %s." % (line,str(accepted)))
if component_name in self.__detectors :
self.__detectors[component_name].scale.append(val)
else:
raise pkex.BasePyKatException("scale command `{0}` refers to non-existing output".format(component_name))
elif len(v) == 2:
if v[1] == "meter" or v[1] == "ampere" or v[1] == "deg":
self.scale = v[1]
else:
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()
name = str(v[1])
if v[2] not in self.__components:
raise pkex.BasePyKatException("Could not find the component '{0}'. Line: '{1}'".format(v[2], line))
comp = self.__components[v[2]]
if comp._default_fsig() == None:
raise pkex.BasePyKatException("Component '{0}' cannot be fsig'd. Line: '{1}'".format(comp.name, line))
param = None
amp = None
if len(v) == 5:
param == None
freq = SIfloat(v[3])
phase = SIfloat(v[4])
elif len(v) == 6:
if v[3][0].isdigit():
freq = SIfloat(v[3])
phase = SIfloat(v[4])
amp = SIfloat(v[5])
else:
param = str(v[3])
freq = SIfloat(v[4])
phase = SIfloat(v[5])
elif len(v) == 7:
param = v[3]
freq = SIfloat(v[4])
phase = SIfloat(v[5])
amp = SIfloat(v[6])
else:
raise pkex.BasePyKatException("'{0}' isnot a valid fsig command".format(line))
self.signals.f = freq
self.signals.apply(comp._default_fsig(), amp, phase, name)
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, cmd_args=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)
plot (string) - Sets gnuterm for plotting
save_output (bool) - if true does not delete out file
save_kat (bool) - if true does not delete kat file
kat_name (string) - name of kat file if needed, will be randomly generated otherwise
cmd_args (list of strings) - command line flags to pass to FINESSE
"""
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')
if cmd_args != None:
cmd.extend(cmd_args)
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:
# remove any ANSI commands
ansi = re.compile(r'\x1b[^m]*m')
line = ansi.sub('', line)
# warnings and errors start with an asterisk
# so if verbose show them
if line.lstrip().startswith('*PROG*'):
line = line[8:-1]
vals = line.split("-",1)
action = vals[0].strip()
prc = vals[1].strip()[:]
if printerr == 1:
sys.stdout.write("\r{0} {1}".format(action, prc))
elif line.lstrip().startswith('*'):
if self.verbose: sys.stdout.write(line)
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))
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 isinstance(obj, pykat.finesse.Signals) and not (obj.name in self.__components or obj.name in self.__detectors or obj.name in self.__commands or obj in self.signals.targets):
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)
elif isinstance(obj, pykat.finesse.Signals):
obj.remove()
elif isinstance(obj, pykat.finesse.Signals.fsig):
obj._on_remove()
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].squeeze()
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).squeeze()
# 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].squeeze()
y = data[:,1:cols]
return [x, y, hdr]
def removeLine(self, fragment) :
"""
This will search all blocks and search for the string
fragment specified and remove it.
WARNING: This will only remove non-parsed commands, it will not
remove commands that have already been parsed
into a pykat object, such as mirrors and beamsplitters, use
kat.remove or kat.component.remove() to delete parsed objects.
"""
found = False
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)
found = True
if not found:
pkex.BasePyKatException("The command fragment '%s' is not an extra line added to this kat object. Please check that the item you are trying to remove has not been parsed as a pykat object." % fragment)
def addLine(self, line, block=NO_BLOCK) :
"""
This will forcefully add a line of FINESSE code to a particular block
if specfied. This command will not undergo any parsing so it will remain
as just a string. This of course can create possible conflicts with other
pykat object that create similar commands so becareful.
"""
self.__blocks[block].contents.append(line)
def printExtraLines(self):
"""
This prints all the Finesse commands that have not been parsed
into pykat objects. This should be used for reference only. To
add or remove extra lines use the addLine and removeLine methods.
"""
found = False
for key in self.__blocks:
objs = self.__blocks[key].contents
for obj in objs:
if isinstance(obj, str):
print(obj)
found = True
if not found:
print("No extra lines were found")
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 optivis(self):
if not HAS_OPTIVIS:
print("Optivis is not installed")
return None
import optivis.scene as scene
import optivis.bench.links as links
import optivis.view.canvas as canvas
scene = scene.Scene(title="Example 2", azimuth=180)
# Run through once to add components, ignoring spaces
for c in self.getComponents():
if isinstance(c, pykat.components.space): continue
print("Adding %s" % c.name)
optivis_op = getattr(c, "getOptivisComponent", None)
if callable(optivis_op):
scene.addComponent(c.getOptivisComponent())
# Run through again to add links
for c in self.getComponents():
if not isinstance(c, pykat.components.space):
continue
a = c.connectingComponents()
c1 = a[0].getOptivisComponent()
c2 = a[1].getOptivisComponent()
no = a[0].getOptivisNode("Output", c.nodes[0])
ni = a[1].getOptivisNode("Input", c.nodes[1])
if no is None or ni is None:
raise pkex.BasePyKatException("Optivis node is None")
print("Link %s (%s) -> %s (%s)" %(a[0].name, no.name, a[1].name, ni.name))
scene.addLink(links.Link(no, ni, c.L.value))
gui = canvas.Simple(scene=scene)
return gui
def openGUI(self):
if not USE_GUI:
raise NoGUIException
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
name = "{0}{1}".format(prefix,n)
rtn.append(name)
return rtn
def lkat_trace(self, getCavities=True, getNodes=True, getSpaces=True):
"""
Given the current state of the kat object a new FINESSE process is called and just
the beam tracing routine is run. The object that is returned contains all the information
from the beam tracing routine for each node and space components defined as well as cavity
commands.
"""
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")
trace_info = Manager().dict()
prev = self.maxtem
self.maxtem = 0
try:
p = self.getProcess(f__lkat_trace_callback, trace_info=trace_info,
getCavities=getCavities, getNodes=getNodes, getSpaces=getSpaces)
p.start()
p.join()
p.terminate()
# return a local copy of the trace information dictionary
return dict(trace_info)
finally:
self.maxtem = prev
def __add_detector(self, det):
if not isinstance(det, Detector):
raise exceptions.ValueError("Argument is not of type Detector")
name = det.name
fget = lambda self: self.__get_detector(name)
setattr(self.__class__, name, property(fget))
setattr(self, '__det_' + name, det)
def __del_detector(self, det):
if not isinstance(det, Detector):
raise pkex.BasePyKatException("Argument is not of type Detector")
name = det.name
delattr(self.__class__, name)
delattr(self, '__det_' + name)
def __get_detector(self, name):
return getattr(self, '__det_' + name)
def __add_command(self, com):
if not isinstance(com, Command):
raise pkex.BasePyKatException("Argument is not of type Command")
name = com.__class__.__name__
fget = lambda self: self.__get_command(name)
setattr(self.__class__, name, property(fget))
setattr(self, '__com_' + name, com)
def __del_command(self, com):
if not isinstance(com, Command):
raise exceptions.ValueError("Argument is not of type Command")
name = com.__class__.__name__
print(getattr(self.__class__, name))
delattr(self.__class__, name)
delattr(self, '__com_' + name)
def __get_command(self, name):
return getattr(self, '__com_' + name)
def __add_component(self, comp):
if not isinstance(comp, Component):
raise pkex.BasePyKatException("Argument is not of type Component")
fget = lambda self: self.__get_component(comp.name)
setattr(self.__class__, comp.name, property(fget))
setattr(self, '__comp_' + comp.name, comp)
def __del_component(self, comp):
if not isinstance(comp, Component):
raise pkex.BasePyKatException("Argument is not of type Component")
delattr(self.__class__, comp.name)
delattr(self, '__comp_' + comp.name)
def __get_component(self, name):
return getattr(self, '__comp_' + name)
def remove_comments(self, string):
"""
This takes a raw Finesse code string and removes any comments
It returns a list of lines however, not a multiline string.
Also removes any extrawhite space in command lines.
"""
pattern = r"(\".*?\"|\'.*?\'|%{3}[^\r\n]*$)|(/\*.*?\*/|%[^\r\n]*$|#[^\r\n]*$|//[^\r\n]*$)"
# first group captures quoted strings (double or single)
# second group captures comments (//single-line or /* multi-line */)
regex = re.compile(pattern, re.MULTILINE|re.DOTALL)
def _replacer(match):
# if the 2nd group (capturing comments) is not None,
# it means we have captured a non-quoted (real) comment string.
if match.group(2) is not None:
return "" # so we will return empty to remove the comment
else: # otherwise, we will return the 1st group
return match.group(1) # captured quoted-string
# remove any inline comments
string = regex.sub(_replacer, string)
commands = []
for line in string.split('\n'):
line = line.replace('\r','')
if len(line) > 0:
# remove any mutliple whitespace
line = " ".join(line.split())
# add to a list all the positions of any inline comment markers
i = [line.find('#'), line.find('\\')]
i = filter(lambda a: a != -1, i)
if len(i) == 0:
commands.append(line)
else:
line = line[0:min(i)]
if len(line):
commands.append(line)
return commands
# printing pykat logo on first input
kat.logo()