.gitarchive

+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true)$
+ref-names: $Format:%D$

.gitattributes

+.gitarchive  export-subst
 tests/keplerian-orbits-1-0-2.h5 filter=lfs diff=lfs merge=lfs -text
 tests/esa-orbits-1-0-2.h5 filter=lfs diff=lfs merge=lfs -text
 tests/keplerian-orbits-2-0.h5 filter=lfs diff=lfs merge=lfs -text

.gitlab-ci.yml

@@ -4,19 +4,64 @@ image: python:3.8
 
 stages:
   - test
-  - generate
+  - document
+  - build
+  - deploy
 
 before_script:
   - pip install -r requirements.txt
-  - pip install .
+
+variables:
+  GIT_LFS_SKIP_SMUDGE: 1
+
+cache:
+  paths:
+    - public
 
 pylint:
   script:
     - pylint lisainstrument
 
 pytest:
+  variables:
+    GIT_LFS_SKIP_SMUDGE: 0
   script:
+    - pip install .
     - python -m pytest -v --junitxml=report.xml
   artifacts:
     reports:
       junit: report.xml
+
+dist:
+  stage: build
+  script:
+    - python -m build
+  rules:
+    - if: '$CI_COMMIT_TAG =~ /^v\d+(?:\.\d+){0,2}$/'
+  artifacts:
+    paths:
+      - dist
+
+tag-latest:
+  stage: deploy
+  image: datamachines/git-lfs
+  before_script:
+    - git config http.sslverify false
+    - git config user.email "${GITLAB_USER_EMAIL}"
+    - git config user.name "${GITLAB_USER_NAME}"
+    - git remote set-url origin https://gitlab-ci:${GITLAB_CI_TOKEN}@${CI_SERVER_HOST}/${CI_PROJECT_PATH}.git
+  script:
+    - git tag --force latest
+    - git push --force origin latest
+  rules:
+    - if: '$CI_COMMIT_TAG =~ /^v\d+(?:\.\d+){0,2}$/'
+
+pypi:
+  stage: deploy
+  script:
+    - twine check dist/*
+    - twine upload dist/*
+  dependencies:
+    - dist
+  rules:
+    - if: '$CI_COMMIT_TAG =~ /^v\d+(?:\.\d+){0,2}$/'

MANIFEST.in

+prune docs
+prune tests
+exclude .*
+exclude requirements.txt
+exclude zenodo.py

lisainstrument/__init__.py

@@ -2,9 +2,16 @@
 # -*- coding: utf-8 -*-
 """LISA Instrument module."""
 
-from .meta import __version__
-from .meta import __author__
-from .meta import __email__
+import importlib_metadata
 
 from .instrument import Instrument
 from .hexagon import Hexagon
+
+
+try:
+    metadata = importlib_metadata.metadata('lisainstrument').json
+    __version__ = importlib_metadata.version('lisainstrument')
+    __author__ = metadata['author']
+    __email__ = metadata['author_email']
+except importlib_metadata.PackageNotFoundError:
+    pass

lisainstrument/instrument.py

@@ -12,6 +12,7 @@ import re
 import logging
 import numpy as np
 import matplotlib.pyplot as plt
+import importlib_metadata
 
 from h5py import File
 from scipy.signal import lfilter, kaiserord, firwin
@@ -25,7 +26,6 @@ from lisaconstants import c
 from .containers import ForEachSC
 from .containers import ForEachMOSA
 
-from . import meta
 from . import dsp
 from . import noises
 
@@ -91,7 +91,8 @@ class Instrument:
                  sync_asds=0.42,
                  # Tilt-to-length (TTL)
                  ttl_coeffs='default',
-                 sc_jitter_asds=(5E-9, 5E-9, 5E-9), mosa_jitter_asds=(2E-9, 1e-9), mosa_angles='default',
+                 sc_jitter_asds=(5E-9, 5E-9, 5E-9), sc_jitter_fknees=(8E-4, 8E-4, 8E-4),
+                 mosa_jitter_asds=(2E-9, 1e-9), mosa_jitter_fknees=(8E-4, 8E-4), mosa_angles='default',
                  dws_asds=7E-8/335,
                  # Pseudo-ranging
                  ranging_biases=0, ranging_asds=3E-9, prn_ambiguity=None,
@@ -159,12 +160,17 @@ class Instrument:
             oms_fknees: dictionary of cutoff frequencies for OMS noise
             ttl_coeffs: tuple (local_phi, distant_phi, local_eta, distant_eta) of dictionaries of
                 tilt-to-length coefficients on each MOSA [m/rad], 'default' for a default set of
-                coefficients, or 'random' to randomly generate a set of coefficients in a uniform
-                distribution [-2.3, 2.3] mm/rad
+                coefficients, or 'random' to draw a set of coefficients from uniform distributions
+                (LISA-UKOB-INST-ML-0001-i2 LISA TTL STOP Model, summary table, 2.4 mm/rad and
+                2.2mm/rad for distant and local coefficients, respectively)
             sc_jitter_asds: tuple of dictionaries of angular jitter amplitude spectral densities
                 for spacecraft, ordered as (yaw, pitch, roll) [rad/sqrt(Hz)]
+            sc_jitter_fknees: tuple of dictionaries of cutoff frequencies for spacecraft angular jitter,
+                ordered as (yaw, pitch, roll) [Hz]
             mosa_jitter_asds: tuple of dictionaries of angular jitter amplitude spectral densities
                 for MOSA, ordered as (yaw, pitch) [rad/sqrt(Hz)]
+            mosa_jitter_fknees: tuple of dictionaries of cutoff frequencies for MOSA angular jitter,
+                ordered as (yaw, pitch) [Hz]
             mosa_angles: dictionary of oriented MOSA opening angles [deg], or 'default'
             dws_asds: dictionary of amplitude spectral densities for DWS measurement noise [rad/sqrt(Hz)]
             ranging_biases: dictionary of ranging noise bias [s]
@@ -176,7 +182,7 @@ class Instrument:
         # pylint: disable=too-many-arguments,too-many-statements,too-many-locals,too-many-branches
         logger.info("Initializing instrumental simulation")
         self.git_url = 'https://gitlab.in2p3.fr/lisa-simulation/instrument'
-        self.version = meta.__version__
+        self.version = importlib_metadata.version('lisainstrument')
         self.simulated = False
 
         # Check orbit dataset
@@ -236,6 +242,11 @@ class Instrument:
             np.arange(self.physics_size + self.initial_telemetry_physics_size, dtype=np.float64) * self.physics_dt
         self.physics_et_withinitial = self.physics_t_withinitial - self.t0
 
+        # Orbits, gravitational waves, glitches
+        self.init_orbits(orbits, orbit_dataset)
+        self.init_gws(gws)
+        self.init_glitches(glitches)
+
         # Instrument topology
         self.central_freq = float(central_freq)
         self.init_lock(lock)
@@ -337,29 +348,28 @@ class Instrument:
 
         # Tilt-to-length
         if ttl_coeffs == 'default':
-            # Default values drawn from uniform distribution [-2.3, 2.3] mm/rad
-            # for local and distant coeffs using `np.random.uniform()`
+            # Default values drawn from distributions set in 'random'
             self.ttl_coeffs_local_phis = ForEachMOSA({
-                '12': -3.79868389e-04, '23': 1.27445665e-03, '31': -8.19115231e-04,
-                '13': -5.03792762e-05, '32': 8.24348407e-04, '21': 1.80772079e-03,
+                '12': 2.005835e-03, '23': 2.105403e-04, '31': -1.815399e-03,
+                '13': -2.865050e-04, '32': -1.986657e-03, '21': 9.368319e-04,
             })
             self.ttl_coeffs_distant_phis = ForEachMOSA({
-                '12': -1.24812926e-03, '23': 7.49010812e-04, '31': -6.50959027e-05,
-                '13': -1.33360362e-03, '32': 6.12997141e-04, '21': -2.53955346e-04,
+                '12': 1.623910e-03, '23': 1.522873e-04, '31': -1.842871e-03,
+                '13': -2.091585e-03, '32': 1.300866e-03, '21': -8.445374e-04,
             })
             self.ttl_coeffs_local_etas = ForEachMOSA({
-                '12': -6.26115149e-04, '23': -2.13028857e-04, '31': 6.62915985e-04,
-                '13': 5.46940002e-04, '32': -9.50450080e-04, '21': 2.72098575e-04,
+                '12': -1.670389e-03, '23': 1.460681e-03, '31': -1.039064e-03,
+                '13': 1.640473e-04, '32': 1.205353e-03, '21': -9.205764e-04,
             })
             self.ttl_coeffs_distant_etas = ForEachMOSA({
-                '12': 1.87659513e-03, '23': -1.26813952e-03, '31': 8.64052482e-04,
-                '13': -4.54433476e-04, '32': -1.46396776e-03, '21': -2.06925864e-04,
+                '12': -1.076470e-03, '23': 5.228848e-04, '31': -5.662766e-05,
+                '13': 1.960050e-03, '32': 9.021890e-04, '21': 1.908239e-03,
             })
         elif ttl_coeffs == 'random':
-            self.ttl_coeffs_local_phis = ForEachMOSA(lambda _: np.random.uniform(-2.3E-3, 2.3E-3))
-            self.ttl_coeffs_distant_phis = ForEachMOSA(lambda _: np.random.uniform(-2.3E-3, 2.3E-3))
-            self.ttl_coeffs_local_etas = ForEachMOSA(lambda _: np.random.uniform(-2.3E-3, 2.3E-3))
-            self.ttl_coeffs_distant_etas = ForEachMOSA(lambda _: np.random.uniform(-2.3E-3, 2.3E-3))
+            self.ttl_coeffs_local_phis = ForEachMOSA(lambda _: np.random.uniform(-2.2E-3, 2.2E-3))
+            self.ttl_coeffs_distant_phis = ForEachMOSA(lambda _: np.random.uniform(-2.4E-3, 2.4E-3))
+            self.ttl_coeffs_local_etas = ForEachMOSA(lambda _: np.random.uniform(-2.2E-3, 2.2E-3))
+            self.ttl_coeffs_distant_etas = ForEachMOSA(lambda _: np.random.uniform(-2.4E-3, 2.4E-3))
         else:
             self.ttl_coeffs_local_phis = ForEachMOSA(ttl_coeffs[0])
             self.ttl_coeffs_distant_phis = ForEachMOSA(ttl_coeffs[1])
@@ -368,8 +378,13 @@ class Instrument:
         self.sc_jitter_phi_asds = ForEachSC(sc_jitter_asds[0])
         self.sc_jitter_eta_asds = ForEachSC(sc_jitter_asds[1])
         self.sc_jitter_theta_asds = ForEachSC(sc_jitter_asds[2])
+        self.sc_jitter_phi_fknees = ForEachSC(sc_jitter_fknees[0])
+        self.sc_jitter_eta_fknees = ForEachSC(sc_jitter_fknees[1])
+        self.sc_jitter_theta_fknees = ForEachSC(sc_jitter_fknees[2])
         self.mosa_jitter_phi_asds = ForEachMOSA(mosa_jitter_asds[0])
         self.mosa_jitter_eta_asds = ForEachMOSA(mosa_jitter_asds[1])
+        self.mosa_jitter_phi_fknees = ForEachMOSA(mosa_jitter_fknees[0])
+        self.mosa_jitter_eta_fknees = ForEachMOSA(mosa_jitter_fknees[1])
         self.dws_asds = ForEachMOSA(dws_asds)
 
         # MOSA opening angles
@@ -382,11 +397,6 @@ class Instrument:
         else:
             self.mosa_angles = ForEachMOSA(mosa_angles)
 
-        # Orbits, gravitational waves, glitches
-        self.init_orbits(orbits, orbit_dataset)
-        self.init_gws(gws)
-        self.init_glitches(glitches)
-
         # Interpolation and antialiasing filter
         self.init_interpolation(interpolation)
         self.init_aafilter(aafilter)
@@ -534,7 +544,7 @@ class Instrument:
                 # Switch between various fplan file standards
                 if version in SpecifierSet('== 1.1.*', True):
                     logger.debug("Interpolating locking beatnote frequencies with piecewise linear functions")
-                    times = self.t0 + np.arange(fplanf.attrs['size']) * fplanf.attrs['dt']
+                    times = self.orbit_t0 + np.arange(fplanf.attrs['size']) * fplanf.attrs['dt']
                     interpolate = lambda x: InterpolatedUnivariateSpline(times, x, k=1, ext='raise')(self.physics_t)
                     lock_beatnotes = {}
                     # Go through all MOSAs and pick locking beatnotes
@@ -571,6 +581,7 @@ class Instrument:
         if orbits == 'static':
             logger.info("Using default set of static proper pseudo-ranges")
             self.orbit_file = None
+            self.orbit_t0 = self.t0
             self.pprs = ForEachMOSA({
                 # Default PPRs based on first samples of Keplerian orbits (v2.0.dev)
                 '12': 8.33242295, '23': 8.30282196, '31': 8.33242298,
@@ -599,6 +610,7 @@ class Instrument:
         else:
             logger.info("Using user-provided proper pseudo-ranges and derivatives")
             self.orbit_file = None
+            self.orbit_t0 = self.t0
             self.pprs = ForEachMOSA(orbits)
             self.d_pprs = self.pprs.transformed(lambda _, x:
                 0 if np.isscalar(x) else np.gradient(x, self.physics_dt)
@@ -641,6 +653,13 @@ class Instrument:
             raise ValueError(f"invalid orbit dataset '{self.orbit_dataset}'")
 
         try:
+            logger.debug("Reading orbit's t0")
+            if self.orbit_dataset == 'tcb/ltt':
+                self.orbit_t0 = orbitf['tcb']['t'][0]
+            elif self.orbit_dataset == 'tps/ppr':
+                self.orbit_t0 = orbitf['tps']['tau'][0]
+            else:
+                raise ValueError(f"invalid orbit dataset '{self.orbit_dataset}'")
             logger.debug("Interpolating proper pseudo-ranges")
             self.pprs = ForEachMOSA(lambda mosa: pprs(mosa)(self.physics_t))
             logger.debug("Interpolating proper pseudo-range derivatives")
@@ -663,6 +682,8 @@ class Instrument:
         # Interpolate necessary orbital quantities,
         # show a helpful error message if orbit file is too short
         try:
+            logger.debug("Reading orbit's t0")
+            self.orbit_t0 = orbitf.attrs['t0']
             logger.debug("Interpolating proper pseudo-ranges")
             dataset = orbitf['tcb/ltt'] if self.orbit_dataset == 'tcb/ltt' else orbitf['tps/ppr']
             self.pprs = ForEachMOSA(lambda mosa: interpolate(dataset[:, link_index[mosa]], self.physics_t))
@@ -1513,22 +1534,27 @@ class Instrument:
         logger.info("Generating spacecraft angular jitters")
 
         self.sc_jitter_phis = ForEachSC(lambda sc:
-            noises.jitter(self.physics_fs, self.physics_size, self.sc_jitter_phi_asds[sc])
+            noises.jitter(self.physics_fs, self.physics_size,
+                self.sc_jitter_phi_asds[sc], self.sc_jitter_phi_fknees[sc])
         )
         self.sc_jitter_etas = ForEachSC(lambda sc:
-            noises.jitter(self.physics_fs, self.physics_size, self.sc_jitter_eta_asds[sc])
+            noises.jitter(self.physics_fs, self.physics_size,
+                self.sc_jitter_eta_asds[sc], self.sc_jitter_eta_fknees[sc])
         )
         self.sc_jitter_thetas = ForEachSC(lambda sc:
-            noises.jitter(self.physics_fs, self.physics_size, self.sc_jitter_theta_asds[sc])
+            noises.jitter(self.physics_fs, self.physics_size,
+                self.sc_jitter_theta_asds[sc], self.sc_jitter_theta_fknees[sc])
         )
 
         logger.info("Generating MOSA angular jitters")
 
         self.mosa_jitter_phis = ForEachMOSA(lambda mosa:
-            noises.jitter(self.physics_fs, self.physics_size, self.mosa_jitter_phi_asds[mosa])
+            noises.jitter(self.physics_fs, self.physics_size,
+                self.mosa_jitter_phi_asds[mosa], self.mosa_jitter_phi_fknees[mosa])
         )
         self.mosa_jitter_etas = ForEachMOSA(lambda mosa:
-            noises.jitter(self.physics_fs, self.physics_size, self.mosa_jitter_eta_asds[mosa])
+            noises.jitter(self.physics_fs, self.physics_size,
+                self.mosa_jitter_eta_asds[mosa], self.mosa_jitter_eta_fknees[mosa])
         )
 
         logger.info("Computing MOSA total angular jitters")
@@ -1783,7 +1809,7 @@ class Instrument:
             'sc_jitter_phi_asds', 'sc_jitter_eta_asds',
             'sc_jitter_theta_asds', 'mosa_jitter_phi_asds',
             'dws_asds', 'mosa_angles',
-            'orbit_file', 'orbit_dataset',
+            'orbit_file', 'orbit_dataset', 'orbit_t0',
             'gw_file', 'gw_group',
             'glitch_file',
             'interpolation_order',

lisainstrument/meta.py

-#! /usr/bin/env python3
-# -*- coding: utf-8 -*-
-# pylint: disable=missing-module-docstring
-
-__version__ = '1.2.dev'
-__author__ = 'Jean-Baptiste Bayle'
-__email__ = 'j2b.bayle@gmail.com'

lisainstrument/noises.py

@@ -266,7 +266,7 @@ def oms(fs, size, asd, fknee):
     Multiplying by (2π f / c)^2 to express it as fractional frequency deviations,
 
         S_oms(f) [ffd] = (2π asd / c)^2 [ f^2 + (fknee^4 / f^2) ]
-                      = (2π asd / c)^2 f^2 + (2π asd fknee^2 / c)^2 f^(-2).
+                       = (2π asd / c)^2 f^2 + (2π asd fknee^2 / c)^2 f^(-2).
 
     Note that the level of this noise depends on the interferometer and the type of beatnote.
 
@@ -283,22 +283,26 @@ def oms(fs, size, asd, fknee):
     return violet(fs, size, 2 * pi * asd / c) \
         + red(fs, size, 2 * pi * asd * fknee**2 / c)
 
-def jitter(fs, size, asd):
+def jitter(fs, size, asd, fknee):
     """Generate jitter for one angular degree of freedom.
 
     The power spectral density in angle is given by
 
-        S_jitter(f) [rad] = asd^2,
+        S_jitter(f) [rad] = asd^2 [ 1 + (fknee / f)^4 ],
 
     which is converted to angular velocity by mutliplying by (2π f)^2,
 
-        S_jitter(f) [rad/s] = (2π asd)^2 f^2.
+        S_jitter(f) [rad/s] = (2π asd)^2 [ f^2 + (fknee^4 / f^2) ]
+                            = (2π asd)^2 f^2 + (2π asd fknee^2)^2 f^(-2).
 
     Args:
         asd: amplitude spectral density [rad/sqrt(Hz)]
+        fknee: cutoff frequency [Hz]
     """
-    logger.debug("Generating jitter (fs=%s Hz, size=%s, asd=%s rad/sqrt(Hz))", fs, size, asd)
-    return violet(fs, size, 2 * pi * asd)
+    logger.debug("Generating jitter (fs=%s Hz, size=%s, asd=%s rad/sqrt(Hz), fknee=%s Hz)",
+        fs, size, asd, fknee)
+    return violet(fs, size, 2 * pi * asd) \
+        + red(fs, size, 2 * pi * asd * fknee**2)
 
 def dws(fs, size, asd):
     """Generate DWS measurement noise.

requirements.txt

@@ -13,6 +13,7 @@ bleach==5.0.0
 certifi==2021.10.8
 cffi==1.15.0
 charset-normalizer==2.0.12
+commonmark==0.9.1
 cycler==0.11.0
 debugpy==1.6.0
 decorator==5.1.1
@@ -23,7 +24,7 @@ entrypoints==0.4
 executing==0.8.3
 fastjsonschema==2.15.3
 fonttools==4.31.2
-h5py==3.6.0
+h5py==3.7.0
 healpy==1.15.2
 idna==3.3
 imagesize==1.3.0
@@ -33,12 +34,14 @@ ipykernel==6.11.0
 ipython==8.2.0
 ipython-genutils==0.2.0
 isort==5.10.1
+jaraco.classes==3.2.3
 jedi==0.18.1
 Jinja2==3.1.1
 jsonschema==4.6.0
 jupyter-client==7.2.1
 jupyter-core==4.9.2
 jupyterlab-pygments==0.2.2
+keyring==23.9.3
 kiwisolver==1.4.1
 lazy-object-proxy==1.7.1
 lisaconstants==1.3
@@ -50,6 +53,7 @@ mccabe==0.7.0
 mdit-py-plugins==0.3.0
 mdurl==0.1.0
 mistune==0.8.4
+more-itertools==9.0.0
 mypy==0.961
 mypy-extensions==0.4.3
 myst-parser==0.17.0
@@ -58,13 +62,14 @@ nbconvert==6.5.0
 nbformat==5.4.0
 nest-asyncio==1.5.4
 notebook==6.4.12
-numpy==1.22.3
+numpy==1.23.4
 packaging==21.3
 pandocfilters==1.5.0
 parso==0.8.3
 pexpect==4.8.0
 pickleshare==0.7.5
 Pillow==9.0.1
+pkginfo==1.8.3
 platformdirs==2.5.1
 pluggy==1.0.0
 prometheus-client==0.14.1
@@ -84,9 +89,14 @@ python-dateutil==2.8.2
 pytz==2022.1
 PyYAML==6.0
 pyzmq==22.3.0
+readme-renderer==37.2
 requests==2.27.1
+requests-toolbelt==0.10.0
+rfc3986==2.0.0
+rich==12.6.0
 scipy==1.8.0
 Send2Trash==1.8.0
+setuptools-scm==7.0.5
 six==1.16.0
 snowballstemmer==2.2.0
 soupsieve==2.3.2.post1
@@ -105,6 +115,7 @@ tomli==2.0.1
 tomlkit==0.11.0
 tornado==6.1
 traitlets==5.2.2.post1
+twine==4.0.1
 typing_extensions==4.1.1
 urllib3==1.26.9
 wcwidth==0.2.5

setup.py

@@ -2,26 +2,23 @@
 # -*- coding: utf-8 -*-
 # pylint: disable=line-too-long,missing-module-docstring,exec-used
 
-from typing import Dict
 import setuptools
 
 
 with open("README.md", 'r', encoding='utf-8') as fh:
     long_description = fh.read()
 
-META: Dict[str, str] = {}
-with open("lisainstrument/meta.py", 'r', encoding='utf-8') as file:
-    exec(file.read(), META)
 
 setuptools.setup(
     name='lisainstrument',
-    version=META['__version__'],
-    author=META['__author__'],
-    author_email=META['__email__'],
+    use_scm_version=True,
+    author='Jean-Baptiste Bayle',
+    author_email='j2b.bayle@gmail.com',
     description='LISA Instrument simulates instrumental noises, propagates laser beams, generates measurements and the on-board processing to deliver simulated telemetry data.',
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://gitlab.in2p3.fr/lisa-simulation/instrument",
+    license='BSD-3-Clause',
     packages=setuptools.find_packages(),
     install_requires=[
         'h5py',
@@ -30,7 +27,9 @@ setuptools.setup(
         'matplotlib',
         'lisaconstants',
         'packaging',
+        'importlib_metadata',
     ],
+    setup_requires=['setuptools_scm'],
     tests_require=['pytest'],
     python_requires='>=3.7',
 )