Merge branch 'split-up-gw-likelihood' into 'master'

Split up gw likelihood

Closes #602

See merge request !1027

.gitlab-ci.yml

@@ -45,11 +45,15 @@ containers:
   script:
     - python -m pip install .
     - python -c "import bilby"
+    - python -c "import bilby.bilby_mcmc"
     - python -c "import bilby.core"
     - python -c "import bilby.core.prior"
     - python -c "import bilby.core.sampler"
+    - python -c "import bilby.core.utils"
     - python -c "import bilby.gw"
     - python -c "import bilby.gw.detector"
+    - python -c "import bilby.gw.eos"
+    - python -c "import bilby.gw.likelihood"
     - python -c "import bilby.gw.sampler"
     - python -c "import bilby.hyper"
     - python -c "import cli_bilby"

bilby/gw/likelihood/__init__.py

+from .base import GravitationalWaveTransient
+from .basic import BasicGravitationalWaveTransient
+from .roq import BilbyROQParamsRangeError, ROQGravitationalWaveTransient
+from .multiband import MBGravitationalWaveTransient
+
+from ..source import lal_binary_black_hole
+from ..waveform_generator import WaveformGenerator
+
+
+def get_binary_black_hole_likelihood(interferometers):
+    """ A wrapper to quickly set up a likelihood for BBH parameter estimation
+
+    Parameters
+    ==========
+    interferometers: {bilby.gw.detector.InterferometerList, list}
+        A list of `bilby.detector.Interferometer` instances, typically the
+        output of either `bilby.detector.get_interferometer_with_open_data`
+        or `bilby.detector.get_interferometer_with_fake_noise_and_injection`
+
+    Returns
+    =======
+    bilby.GravitationalWaveTransient: The likelihood to pass to `run_sampler`
+
+    """
+    waveform_generator = WaveformGenerator(
+        duration=interferometers.duration,
+        sampling_frequency=interferometers.sampling_frequency,
+        frequency_domain_source_model=lal_binary_black_hole,
+        waveform_arguments={'waveform_approximant': 'IMRPhenomPv2',
+                            'reference_frequency': 50})
+    return GravitationalWaveTransient(interferometers, waveform_generator)
+
+

bilby/gw/likelihood/basic.py

+import numpy as np
+
+from ...core.likelihood import Likelihood
+
+
+class BasicGravitationalWaveTransient(Likelihood):
+
+    def __init__(self, interferometers, waveform_generator):
+        """
+
+        A likelihood object, able to compute the likelihood of the data given
+        some model parameters
+
+        The simplest frequency-domain gravitational wave transient likelihood. Does
+        not include distance/phase marginalization.
+
+
+        Parameters
+        ==========
+        interferometers: list
+            A list of `bilby.gw.detector.Interferometer` instances - contains the
+            detector data and power spectral densities
+        waveform_generator: bilby.gw.waveform_generator.WaveformGenerator
+            An object which computes the frequency-domain strain of the signal,
+            given some set of parameters
+
+        """
+        super(BasicGravitationalWaveTransient, self).__init__(dict())
+        self.interferometers = interferometers
+        self.waveform_generator = waveform_generator
+
+    def __repr__(self):
+        return self.__class__.__name__ + '(interferometers={},\n\twaveform_generator={})' \
+            .format(self.interferometers, self.waveform_generator)
+
+    def noise_log_likelihood(self):
+        """ Calculates the real part of noise log-likelihood
+
+        Returns
+        =======
+        float: The real part of the noise log likelihood
+
+        """
+        log_l = 0
+        for interferometer in self.interferometers:
+            log_l -= 2. / self.waveform_generator.duration * np.sum(
+                abs(interferometer.frequency_domain_strain) ** 2 /
+                interferometer.power_spectral_density_array)
+        return log_l.real
+
+    def log_likelihood(self):
+        """ Calculates the real part of log-likelihood value
+
+        Returns
+        =======
+        float: The real part of the log likelihood
+
+        """
+        log_l = 0
+        waveform_polarizations = \
+            self.waveform_generator.frequency_domain_strain(
+                self.parameters.copy())
+        if waveform_polarizations is None:
+            return np.nan_to_num(-np.inf)
+        for interferometer in self.interferometers:
+            log_l += self.log_likelihood_interferometer(
+                waveform_polarizations, interferometer)
+        return log_l.real
+
+    def log_likelihood_interferometer(self, waveform_polarizations,
+                                      interferometer):
+        """
+
+        Parameters
+        ==========
+        waveform_polarizations: dict
+            Dictionary containing the desired waveform polarization modes and the related strain
+        interferometer: bilby.gw.detector.Interferometer
+            The Interferometer object we want to have the log-likelihood for
+
+        Returns
+        =======
+        float: The real part of the log-likelihood for this interferometer
+
+        """
+        signal_ifo = interferometer.get_detector_response(
+            waveform_polarizations, self.parameters)
+
+        log_l = - 2. / self.waveform_generator.duration * np.vdot(
+            interferometer.frequency_domain_strain - signal_ifo,
+            (interferometer.frequency_domain_strain - signal_ifo) /
+            interferometer.power_spectral_density_array)
+        return log_l.real

setup.py

@@ -12,7 +12,7 @@ if python_version < (3, 7):
 
 
 def write_version_file(version):
-    """ Writes a file with version information to be used at run time
+    """Writes a file with version information to be used at run time
 
     Parameters
     ----------
@@ -27,31 +27,32 @@ def write_version_file(version):
     """
     try:
         git_log = subprocess.check_output(
-            ['git', 'log', '-1', '--pretty=%h %ai']).decode('utf-8')
-        git_diff = (subprocess.check_output(['git', 'diff', '.']) +
-                    subprocess.check_output(
-                        ['git', 'diff', '--cached', '.'])).decode('utf-8')
-        if git_diff == '':
-            git_status = '(CLEAN) ' + git_log
+            ["git", "log", "-1", "--pretty=%h %ai"]
+        ).decode("utf-8")
+        git_diff = (
+            subprocess.check_output(["git", "diff", "."])
+            + subprocess.check_output(["git", "diff", "--cached", "."])
+        ).decode("utf-8")
+        if git_diff == "":
+            git_status = "(CLEAN) " + git_log
         else:
-            git_status = '(UNCLEAN) ' + git_log
+            git_status = "(UNCLEAN) " + git_log
     except Exception as e:
-        print("Unable to obtain git version information, exception: {}"
-              .format(e))
-        git_status = 'release'
+        print("Unable to obtain git version information, exception: {}".format(e))
+        git_status = "release"
 
-    version_file = '.version'
+    version_file = ".version"
     if os.path.isfile(version_file) is False:
-        with open('bilby/' + version_file, 'w+') as f:
-            f.write('{}: {}'.format(version, git_status))
+        with open("bilby/" + version_file, "w+") as f:
+            f.write("{}: {}".format(version, git_status))
 
     return version_file
 
 
 def get_long_description():
-    """ Finds the README and reads in the description """
+    """Finds the README and reads in the description"""
     here = os.path.abspath(os.path.dirname(__file__))
-    with open(os.path.join(here, 'README.rst')) as f:
+    with open(os.path.join(here, "README.rst")) as f:
         long_description = f.read()
     return long_description
 
@@ -73,32 +74,51 @@ VERSION = '1.1.4'
 version_file = write_version_file(VERSION)
 long_description = get_long_description()
 
-setup(name='bilby',
-      description='A user-friendly Bayesian inference library',
-      long_description=long_description,
-      long_description_content_type="text/x-rst",
-      url='https://git.ligo.org/lscsoft/bilby',
-      author='Greg Ashton, Moritz Huebner, Paul Lasky, Colm Talbot',
-      author_email='paul.lasky@monash.edu',
-      license="MIT",
-      version=VERSION,
-      packages=['bilby', 'bilby.core', 'bilby.core.prior', 'bilby.core.sampler',
-                'bilby.core.utils', 'bilby.gw', 'bilby.gw.detector',
-                'bilby.gw.sampler', 'bilby.hyper', 'bilby.gw.eos', 'bilby.bilby_mcmc',
-                'cli_bilby'],
-      package_dir={'bilby': 'bilby', 'cli_bilby': 'cli_bilby'},
-      package_data={'bilby.gw': ['prior_files/*'],
-                    'bilby.gw.detector': ['noise_curves/*.txt', 'detectors/*'],
-                    'bilby.gw.eos': ['eos_tables/*.dat'],
-                    'bilby': [version_file]},
-      python_requires='>=3.6',
-      install_requires=get_requirements(),
-      entry_points={'console_scripts':
-                    ['bilby_plot=cli_bilby.plot_multiple_posteriors:main',
-                     'bilby_result=cli_bilby.bilby_result:main']
-                    },
-      classifiers=[
-          "Programming Language :: Python :: 3.6",
-          "Programming Language :: Python :: 3.7",
-          "License :: OSI Approved :: MIT License",
-          "Operating System :: OS Independent"])
+setup(
+    name="bilby",
+    description="A user-friendly Bayesian inference library",
+    long_description=long_description,
+    long_description_content_type="text/x-rst",
+    url="https://git.ligo.org/lscsoft/bilby",
+    author="Greg Ashton, Moritz Huebner, Paul Lasky, Colm Talbot",
+    author_email="paul.lasky@monash.edu",
+    license="MIT",
+    version=VERSION,
+    packages=[
+        "bilby",
+        "bilby.bilby_mcmc",
+        "bilby.core",
+        "bilby.core.prior",
+        "bilby.core.sampler",
+        "bilby.core.utils",
+        "bilby.gw",
+        "bilby.gw.detector",
+        "bilby.gw.eos",
+        "bilby.gw.likelihood",
+        "bilby.gw.sampler",
+        "bilby.hyper",
+        "cli_bilby",
+    ],
+    package_dir={"bilby": "bilby", "cli_bilby": "cli_bilby"},
+    package_data={
+        "bilby.gw": ["prior_files/*"],
+        "bilby.gw.detector": ["noise_curves/*.txt", "detectors/*"],
+        "bilby.gw.eos": ["eos_tables/*.dat"],
+        "bilby": [version_file],
+    },
+    python_requires=">=3.7",
+    install_requires=get_requirements(),
+    entry_points={
+        "console_scripts": [
+            "bilby_plot=cli_bilby.plot_multiple_posteriors:main",
+            "bilby_result=cli_bilby.bilby_result:main",
+        ]
+    },
+    classifiers=[
+        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+)