From 647b7ef9da5e21cfac302bae222da01f6f977451 Mon Sep 17 00:00:00 2001
From: Jameson Graef Rollins <jrollins@finestructure.net>
Date: Wed, 8 Nov 2017 14:49:27 -0800
Subject: [PATCH] Add ability to load ifo data from YAML and MATLAB .mat files
This adds a Struct() class that mimics a MATLAB struct by storing values as
class attributes, but also includes methods for converting to/from dicts,
yaml, and mat_struct objects.
A convenience function load_ifo() is included to load an ifo definition
either from a .yaml or .mat file or from an included <ifo>.yaml.
An 'aLIGO.yaml' definition is included.
---
gwinc/__init__.py | 1 +
gwinc/ifo/__init__.py | 219 ++++++++++++++++++++++++++++++++
gwinc/ifo/aLIGO.yaml | 289 ++++++++++++++++++++++++++++++++++++++++++
3 files changed, 509 insertions(+)
create mode 100644 gwinc/ifo/aLIGO.yaml
diff --git a/gwinc/__init__.py b/gwinc/__init__.py
index 85a98ed..a825ae4 100644
--- a/gwinc/__init__.py
+++ b/gwinc/__init__.py
@@ -1,3 +1,4 @@
+from ifo import load_ifo
from util import precompIFO
from gwinc import noise_calc
from gwinc import gwinc
diff --git a/gwinc/ifo/__init__.py b/gwinc/ifo/__init__.py
index e69de29..0dec5e8 100644
--- a/gwinc/ifo/__init__.py
+++ b/gwinc/ifo/__init__.py
@@ -0,0 +1,219 @@
+import os
+import re
+import yaml
+import scipy
+import scipy.io
+import numpy as np
+from scipy.io.matlab.mio5_params import mat_struct
+
+
+# HACK: fix loading number in scientific notation
+#
+# https://stackoverflow.com/questions/30458977/yaml-loads-5e-6-as-string-and-not-a-number
+#
+# An apparent bug in python-yaml prevents it from regognizing
+# scientific notation as a float. The following is a modified version
+# of the parser that recognize scientific notation appropriately.
+#
+loader = yaml.SafeLoader
+loader.add_implicit_resolver(
+ u'tag:yaml.org,2002:float',
+ re.compile(u'''^(?:
+ [-+]?(?:[0-9][0-9_]*)\\.[0-9_]*(?:[eE][-+]?[0-9]+)?
+ |[-+]?(?:[0-9][0-9_]*)(?:[eE][-+]?[0-9]+)
+ |\\.[0-9_]+(?:[eE][-+][0-9]+)?
+ |[-+]?[0-9][0-9_]*(?::[0-5]?[0-9])+\\.[0-9_]*
+ |[-+]?\\.(?:inf|Inf|INF)
+ |\\.(?:nan|NaN|NAN))$''', re.X),
+ list(u'-+0123456789.'))
+
+
+class Struct(object):
+ """Matlab struct-like object
+
+ This is a simple implementation of a MATLAB struct-like object
+ that stores values as attributes of a simple class: and allows assigning to
+ attributes recursively, e.g.:
+
+ >>> s = Struct()
+ >>> s.a = 4
+ >>> s.b = Struct()
+ >>> s.b.c = 8
+
+ Various classmethods allow creating one of these objects from YAML
+ file, a nested dict, or a MATLAB struct object.
+
+ """
+
+ # FIXME: This would be a way to allow setting nested struct
+ # attributes, e.g.:
+ #
+ # >>> s = Struct()
+ # >>> s.a.b.c = 4
+ #
+ # Usage of __getattr__ like this is dangerous and creates
+ # non-intuitive behavior (i.e. an empty struct is returned with
+ # accessing attributes that don't exist). Is there a way to
+ # accomplish this without that adverse side affect?
+ #
+ # def __getattr__(self, name):
+ # if name not in self.__dict__:
+ # self.__dict__[name] = Struct()
+ # return self.__dict__[name]
+
+ ##########
+
+ def __contains__(self, item):
+ return item in self.__dict__
+
+ def to_dict(self):
+ """Return nested dictionary representation of Struct.
+
+ """
+ d = {}
+ for k,v in self.__dict__.iteritems():
+ if isinstance(v, Struct):
+ d[k] = v.to_dict()
+ else:
+ # handle lists of Structs
+ try:
+ d[k] = [i.to_dict() for i in v]
+ except (AttributeError, TypeError):
+ d[k] = v
+ return d
+
+ def to_yaml(self, path=None):
+ """Return YAML representation of Struct as nested dict.
+
+ Or write Struct to YAML file if file 'path' argument
+ specified.
+
+ """
+ y = yaml.dump(self.to_dict(), default_flow_style=False)
+ if path:
+ with open(path, 'w') as f:
+ f.write(y)
+ else:
+ return y
+
+ def __repr__(self):
+ return self.to_yaml().strip('\n')
+
+ def __str__(self):
+ return '<GWINC Struct: {}>'.format(self.__dict__.keys())
+
+ def __iter__(self):
+ return iter(self.__dict__)
+
+ def walk(self):
+ """Iterate over all leaves in the struct tree.
+
+ """
+ for k,v in self.__dict__.iteritems():
+ if type(v) is Struct:
+ for sk,sv in v.walk():
+ yield k+'.'+sk, sv
+ else:
+ try:
+ for i,vv in enumerate(v):
+ for sk,sv in vv.walk():
+ yield '{}[{}].{}'.format(k,i,sk), sv
+ except (AttributeError, TypeError):
+ yield k, v
+
+ @classmethod
+ def from_dict(cls, d):
+ """Create Struct from nested dict.
+
+ """
+ c = cls()
+ for k,v in d.iteritems():
+ if type(v) == dict:
+ c.__dict__[k] = Struct.from_dict(v)
+ else:
+ try:
+ c.__dict__[k] = map(Struct.from_dict, v)
+ except (AttributeError, TypeError):
+ c.__dict__[k] = v
+ return c
+
+ @classmethod
+ def from_matstruct(cls, s):
+ """Create Struct from scipy.io.matlab mat_struct object.
+
+ """
+ c = cls()
+ # FIXME: handle 'ifo' attribute at top level. should we
+ # ignore this?
+ try:
+ s = s['ifo']
+ except:
+ pass
+ for k,v in s.__dict__.iteritems():
+ if k in ['_fieldnames']:
+ # skip these fields
+ pass
+ # FIXME: manaually converting Stage list to individual
+ # named elements. what's the right thing to do here?
+ elif k == 'Stage':
+ for i,stage in enumerate(v):
+ name = 'Stage{}'.format(i+1)
+ struct = Struct.from_matstruct(stage)
+ c.__dict__[name] = struct
+ elif type(v) is mat_struct:
+ c.__dict__[k] = Struct.from_matstruct(v)
+ else:
+ # handle lists of Structs
+ try:
+ c.__dict__[k] = map(Struct.from_matstruct, v)
+ except:
+ c.__dict__[k] = v
+ return c
+
+
+ @classmethod
+ def from_file(cls, path):
+ """Load Struct from .yaml or GWINC .mat file.
+
+ File type will be determined by extension.
+
+ """
+ (root, ext) = os.path.splitext(path)
+ with open(path, 'r') as f:
+ if ext in ['.yaml', '.yml']:
+ d = yaml.load(f, Loader=loader)
+ return cls.from_dict(d)
+ elif ext == '.mat':
+ s = scipy.io.loadmat(f, squeeze_me=True, struct_as_record=False)
+ return cls.from_matstruct(s)
+ else:
+ raise IOError("Unknown file type: {}".format(ext))
+
+
+
+def load_ifo(name_or_path):
+ """Load IFO by name or from file.
+
+ IFO names will correspond to basename of included .yaml IFO
+ definition file.
+
+ When specifying path may be either .yaml or .mat.
+
+ """
+ if os.path.exists(name_or_path):
+ path = name_or_path
+ else:
+ path = os.path.join(os.path.dirname(__file__),
+ name_or_path+'.yaml')
+ s = Struct.from_file(path)
+ return s
+
+
+##################################################
+
+
+if __name__ == '__main__':
+ import sys
+ ifo = load_ifo(sys.argv[1])
+ # print(ifo.to_yaml())
+ print(ifo.to_dict())
diff --git a/gwinc/ifo/aLIGO.yaml b/gwinc/ifo/aLIGO.yaml
new file mode 100644
index 0000000..8a0b06d
--- /dev/null
+++ b/gwinc/ifo/aLIGO.yaml
@@ -0,0 +1,289 @@
+# GWINC aLIGO interferometer parameters
+#
+# parameters for quad pendulum suspension updated 3rd May 2006, NAR
+# References:
+# LIGO-T000012-00-D
+# * Differentiate between silica and sapphire substrate absorption
+# * Change ribbon suspension aspect ratio
+# * Change pendulum frequency
+# References:
+# 1. Electro-Optic Handbook, Waynant & Ediger (McGraw-Hill: 1993)
+# 2. LIGO/GEO data/experience
+# 3. Suspension reference design, LIGO-T000012-00
+# 4. Quartz Glass for Optics Data and Properties, Heraeus data sheet,
+# numbers for suprasil
+# 5. Y.S. Touloukian (ed), Thermophysical Properties of Matter
+# (IFI/Plenum,1970)
+# 6. Marvin J. Weber (ed) CRC Handbook of laser science and technology,
+# Vol 4, Pt 2
+# 7. R.S. Krishnan et al.,Thermal Expansion of Crystals, Pergamon Press
+# 8. P. Klocek, Handbook of infrared and optical materials, Marcel Decker,
+# 1991
+# 9. Rai Weiss, electronic log from 5/10/2006
+# 10. Wikipedia online encyclopedia, 2006
+# 11. D.K. Davies, The Generation and Dissipation of Static Charge on
+# dielectrics in a Vacuum, page 29
+# 12. Gretarsson & Harry, Gretarsson thesis
+# 13. Fejer
+# 14. Braginsky
+#
+#
+
+Constants:
+ # Temperature of the Vacuum
+ Temp: 290 # K
+
+Infrastructure:
+ Length: 3995 # m
+ ResidualGas:
+ pressure: 4.0e-7 # Pa
+ mass: 3.35e-27 # kg; Mass of H_2 (ref. 10)
+ polarizability: 7.8e-31 # m^3
+
+TCS:
+ s_cc: 7.024 # Watt^-2
+ s_cs: 7.321 # Watt^-2
+ s_ss: 7.631 # Watt^-2
+ # The hardest part to model is how efficient the TCS system is in
+ # compensating this loss. Thus as a simple Ansatz we define the
+ # TCS efficiency TCSeff as the reduction in effective power that produces
+ # a phase distortion. E.g. TCSeff=0.99 means that the compensated distortion
+ # of 1 Watt absorbed is eqivalent to the uncompensated distortion of 10mWatt.
+ # The above formula thus becomes:
+ # S= s_cc P_coat^2 + 2*s_cs*P_coat*P_subst + s_ss*P_subst^2 * (1-TCSeff)^2
+ #
+ # To avoid iterative calculation we define TCS.SCRloss = S as an input
+ # and calculate TCSeff as an output.
+ # TCS.SRCloss is incorporated as an additional loss in the SRC
+ SRCloss: 0.00
+
+Seismic:
+ Site: 'LHO' # LHO or LLO (only used for Newtonian noise)
+ KneeFrequency: 10 # Hz; freq where 'flat' noise rolls off
+ LowFrequencyLevel: 1e-9 # m/rtHz; seismic noise level below f_knee
+ Gamma: .8 # abruptness of change at f_knee
+ Rho: 1.8e3 # kg/m^3; density of the ground nearby
+ Beta: 0.5 # quiet times beta: 0.35-0.60
+ # noisy times beta: 0.15-1.4
+ Omicron: 1 # Feedforward cancellation factor
+
+Suspension:
+ # 0 for cylindrical suspension
+ #Type: 'Quad'
+ Type: 2
+ # 0: round, 1: ribbons
+ FiberType: 0
+ BreakStress: 750e6 # Pa; ref. K. Strain
+ Temp: 290
+ VHCoupling:
+ theta: 1e-3 # vertical-horizontal x-coupling
+
+ Silica:
+ Rho : 2200 # Kg/m^3;
+ C : 772 # J/Kg/K;
+ K : 1.38 # W/m/kg;
+ Alpha : 3.9e-7 # 1/K;
+ dlnEdT: 1.52e-4 # (1/K), dlnE/dT
+ Phi : 4.1e-10 # from G Harry e-mail to NAR 27April06 dimensionless units
+ Y : 72e9 # Pa; Youngs Modulus
+ Dissdepth: 1.5e-2 # from G Harry e-mail to NAR 27April06
+
+ C70Steel:
+ Rho: 7800
+ C: 486
+ K: 49
+ Alpha: 12e-6
+ dlnEdT: -2.5e-4
+ Phi: 2e-4
+ Y: 212e9 # measured by MB for one set of wires
+
+ MaragingSteel:
+ Rho: 7800
+ C: 460
+ K: 20
+ Alpha: 11e-6
+ dlnEdT: 0
+ Phi: 1e-4
+ Y: 187e9
+
+ # ref ---- http://design.caltech.edu/Research/MEMS/siliconprop.html
+ # all properties should be for T ~ 20 K
+ Silicon:
+ Rho: 2330 # Kg/m^3; density
+ C: 772 # J/kg/K heat capacity
+ K: 4980 # W/m/K thermal conductivity
+ Alpha: 1e-9 # 1/K thermal expansion coeff
+ # from Gysin, et. al. PRB (2004) E(T): E0 - B*T*exp(-T0/T)
+ # E0: 167.5e9 Pa T0: 317 K B: 15.8e6 Pa/K
+ dlnEdT: 2.5e-10 # (1/K) dlnE/dT T=20K
+ Phi: 2e-9 # Nawrodt (2010) loss angle 1/Q
+ Y: 150e9 # Pa Youngs Modulus
+ Dissdepth: 1.5e-3 # 10x smaller surface loss depth (Nawrodt (2010))
+
+ # Note stage numbering: mirror is at beginning of stack, not end
+ #
+ # last stage length adjusted for d: 10mm and and d_bend = 4mm
+ # (since 602mm is the CoM separation, and d_bend is accounted for
+ # in suspQuad, so including it here would double count)
+ Stage1:
+ Mass: 39.6 # kg; current numbers May 2006 NAR
+ Length: 0.59 # m
+ Dilution: .nan #
+ K: .nan # N/m; vertical spring constant
+ WireRadius: .nan # m
+ Blade: .nan # blade thickness
+ NWires: 4
+
+ Stage2:
+ Mass: 39.6
+ Length: 0.341
+ Dilution: 106
+ K: 5200
+ WireRadius: 310e-6
+ Blade: 4200e-6
+ NWires: 4
+
+ Stage3:
+ Mass: 21.8
+ Length: 0.277
+ Dilution: 80
+ K: 3900
+ WireRadius: 350e-6
+ Blade: 4600e-6
+ NWires: 4
+
+ Stage4:
+ Mass: 22.1
+ Length: 0.416
+ Dilution: 87
+ K: 3400
+ WireRadius: 520e-6
+ Blade: 4300e-6
+ NWires: 2
+
+ Ribbon:
+ Thickness: 115e-6 # m
+ Width: 1150e-6 # m
+
+ Fiber:
+ Radius: 205e-6 # m
+ Blade: 4300e-6
+
+## Optic Material -------------------------------------------------------
+Materials:
+ MassRadius: 0.17 # m;
+ MassThickness: 0.200 # m; Peter F 8/11/2005
+
+ ## Dielectric coating material parameters----------------------------------
+ Coating:
+ ## high index material: tantala
+ Yhighn: 140e9
+ Sigmahighn: 0.23
+ CVhighn: 2.1e6 # Crooks et al, Fejer et al
+ Alphahighn: 3.6e-6 # 3.6e-6 Fejer et al, 5e-6 from Braginsky
+ Betahighn: 1.4e-5 # dn/dT, value Gretarrson (G070161)
+ ThermalDiffusivityhighn: 33 # Fejer et al
+ Phihighn: 2.3e-4
+ Indexhighn: 2.06539
+
+ ## low index material: silica
+ Ylown: 72e9
+ Sigmalown: 0.17
+ CVlown: 1.6412e6 # Crooks et al, Fejer et al
+ Alphalown: 5.1e-7 # Fejer et al
+ Betalown: 8e-6 # dn/dT, (ref. 14)
+ ThermalDiffusivitylown: 1.38 # Fejer et al
+ Philown: 4.0e-5
+ Indexlown: 1.45
+
+ ## Substrate Material parameters--------------------------------------------
+ Substrate:
+ c2 : 7.6e-12 # Coeff of freq depend. term for bulk mechanical loss, 7.15e-12 for Sup2
+ MechanicalLossExponent: 0.77 # Exponent for freq dependence of silica loss, 0.822 for Sup2
+ Alphas: 5.2e-12 # Surface loss limit (ref. 12)
+ MirrorY: 7.27e10 # N/m^2; Youngs modulus (ref. 4)
+ MirrorSigma: 0.167 # Kg/m^3; Poisson ratio (ref. 4)
+ MassDensity: 2.2e3 # Kg/m^3; (ref. 4)
+ MassAlpha: 3.9e-7 # 1/K; thermal expansion coeff. (ref. 4)
+ MassCM: 739 # J/Kg/K; specific heat (ref. 4)
+ MassKappa: 1.38 # J/m/s/K; thermal conductivity (ref. 4)
+ RefractiveIndex: 1.45 # mevans 25 Apr 2008
+
+## Laser-------------------------------------------------------------------
+Laser:
+ Wavelength: 1.064e-6 # m
+ Power: 125 # W
+
+## Optics------------------------------------------------------------------
+Optics:
+ Type: 'SignalRecycled'
+ PhotoDetectorEfficiency: 0.95 # photo-detector quantum efficiency
+ Loss: 37.5e-6 # average per mirror power loss
+ BSLoss: 0.5e-3 # power loss near beamsplitter
+ coupling: 1.0 # mismatch btwn arms & SRC modes; used to
+
+ #SubstrateAbsorption: 0.5e-4 # 1/m; bulk absorption coef (ref. 2)
+ SubstrateAbsorption: 0.3e-4 # 1/m; 0.3 ppm/cm for Hereaus
+ pcrit: 10 # W; tolerable heating power (factor 1 ATC)
+ Quadrature:
+ dc: 1.5707963 # pi/2 # demod/detection/homodyne phase
+
+ ITM:
+ BeamRadius: 0.055 # m, 1/e^2 power radius
+ Transmittance: 0.014
+ CoatingThicknessLown: 0.308
+ CoatingThicknessCap: 0.5
+ CoatingAbsorption: 0.5e-6
+ SubstrateAbsorption: 0.3e-4 # 1/m, 0.3 ppm/cm for Hereaus
+ ETM:
+ BeamRadius: 0.062 # m, 1/e^2 power radius
+ Transmittance: 5e-6
+ CoatingThicknessLown: 0.27
+ CoatingThicknessCap: 0.5
+ PRM:
+ Transmittance: 0.03
+ SRM:
+ Transmittance: 0.20
+ CavityLength: 55 # m, ITM to SRM distance
+ Tunephase: 0.0 # SEC tuning
+
+ Curvature: # ROC
+ ITM: 1970
+ ETM: 2192
+
+## Squeezer Parameters------------------------------------------------------
+# Define the squeezing you want:
+# None: ignore the squeezer settings
+# Freq Independent: nothing special (no filter cavties)
+# Freq Dependent = applies the specified filter cavites
+# Optimal = find the best squeeze angle, assuming no output filtering
+# OptimalOptimal = optimal squeeze angle, assuming optimal readout phase
+Squeezer:
+ Type: 'None'
+ AmplitudedB: 10 # SQZ amplitude [dB]
+ InjectionLoss: 0.05 # power loss to sqz
+ SQZAngle: 0 # SQZ phase [radians]
+
+ # Parameters for frequency dependent squeezing
+ FilterCavity:
+ fdetune: -14.5 # detuning [Hz]
+ L: 100 # cavity length
+ Ti: 0.12e-3 # input mirror trasmission [Power]
+ Te: 0 # end mirror trasmission
+ Lrt: 100e-6 # round-trip loss in the cavity
+ Rot: 0 # phase rotation after cavity
+
+## Variational Output Parameters--------------------------------------------
+# Define the output filter cavity chain
+# None = ignore the output filter settings
+# Chain = apply filter cavity chain
+# Optimal = find the best readout phase
+OutputFilter:
+ Type: 'None'
+ FilterCavity:
+ fdetune: -30 # detuning [Hz]
+ L: 4000 # cavity length
+ Ti: 10e-3 # input mirror trasmission [Power]
+ Te: 0 # end mirror trasmission
+ Lrt: 100e-6 # round-trip loss in the cavity
+ Rot: 0 # phase rotation after cavity
--
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