Add basic simulations and simulation classes

lvcnrpy/Sim.py

+# Copyright (C) 2016 Edward Fauchon-Jones
+#
+# 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 3 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, see <http://www.gnu.org/licenses/>.
+
+from h5py import File
+import numpy as np
+from scipy.interpolate import InterpolatedUnivariateSpline as IUS
+
+
+class Sim(File):
+    """Wrapper to load a single hdf5 NR file
+
+    Parameters
+    ----------
+    name: str
+        Path to the hdf5 NR file to load
+    """
+
+    def getAmpIUS(self, l, m):
+        """Load amp_lm mode from the hdf5 NR file as a spline
+
+        Parameters
+        ----------
+        l,m: int
+            load mode of degree l and order m. This corresponds to the hdf5
+            group `amp_l{l}_m{m}`.
+
+        Returns
+        -------
+        amp_lm: scipy.interpolate.InterpolatedUnivariateSpline
+            Return `amp_lm` as an spline using 5th degree interpolants
+        """
+        ampPath = 'amp_l{0:d}_m{1:d}'.format(l, m)
+        t = self['{0:s}/knots'.format(ampPath)]
+        amp = self['{0:s}/data'.format(ampPath)]
+        ampIUS = IUS(t, amp, k=5)
+
+        return ampIUS
+
+    def getPhaseIUS(self, l, m):
+        """Load phase_lm mode from the hdf5 NR file as a spline
+
+        Parameters
+        ----------
+        l,m: int
+            load mode of degree l and order m. This corresponds to the hdf5
+            group `phase_l{l}_m{m}`.
+
+        Returns
+        -------
+        phase_lm: scipy.interpolate.InterpolatedUnivariateSpline
+            Return `phase_lm` as an spline using 5th degree interpolants
+        """
+        phasePath = 'phase_l{0:d}_m{1:d}'.format(l, m)
+        t = self['{0:s}/knots'.format(phasePath)]
+        phase = self['{0:s}/data'.format(phasePath)]
+        phaseIUS = IUS(t, phase, k=5)
+
+        return phaseIUS
+
+    def att(self, att):
+        """Get value of attribute from hdf5 NR file
+
+        Convinience method to functional access attributes of the hdf5 NR file
+
+        Parameters
+        ----------
+        att: str
+            Name of the attribute to get the value of
+
+        Returns
+        -------
+        value: type(self.attrs[att])
+            Value of the attribute with name `att`. The type will match that of
+            the stored attribute.
+        """
+        try:
+            return self.attrs[att]
+        except:
+            return 0

lvcnrpy/Sims.py

+# Copyright (C) 2016 Edward Fauchon-Jones
+#
+# 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 3 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, see <http://www.gnu.org/licenses/>.
+
+from h5py import File
+import os
+import glob
+from .Sim import Sim
+from . import LVCNR_DATADIR
+from operator import concat
+
+
+class Sims:
+    """Collection of simulations from the LVC-NR Waveform Repository
+
+    Instancing this obejct without the option `paths` parameter will provide
+    access to all hdf5 NR files within the LVC-NR Waveform Repository.
+
+    Parameters
+    ----------
+    paths: list of str, optional
+        Optional list of paths to hdf5 NR files.
+    """
+
+    def __init__(self, paths=None):
+        if paths is None:
+            self.paths = self.getAllPaths()
+        elif all(isinstance(s, basestring) for s in paths):
+            self.paths = paths
+        else:
+            self.paths = []
+
+    def getAllPaths(self):
+        """Find all paths of hdf5 NR files in the LVC-NR Waveform Repository
+
+        Returns
+        -------
+        simualtions: list of str
+            All hdf5 NR file paths
+        """
+        # Find all valid (no `.` prefix) subdirectories of LVCNR_DATADIR
+        children = glob.glob('{0:s}/*/'.format(LVCNR_DATADIR))
+        descendants = [[[y[0], y[2]] for y in os.walk(x)] for x in children]
+        descendants = reduce(concat, descendants)
+
+        # Find all hdf5 files
+        paths = [[os.path.join(d[0], f) for f in d[1]] for d in descendants]
+        paths = reduce(concat, paths)
+        simPaths = [path for path in paths if path.endswith('.h5')]
+
+        # Remove RAW Cardiff data (temporary hack)
+        simPaths = [p for p in simPaths if 'Psi4ModeDecomp' not in p]
+
+        # Instance Sim object for each simulation
+        # sims = [Sim(simPath, 'r') for simPath in simPaths]
+
+        return simPaths  # sims
+
+    def __len__(self):
+        """List like length of contained simulations
+
+        Returns
+        -------
+        length: int
+            Length of `self.paths`
+        """
+        return len(self.paths)
+
+    def __getitem__(self, index):
+        """List like access to the contained simulations
+
+        Parameters
+        ----------
+        index: int
+            Index of simulation to return.
+
+        Returns
+        -------
+        simualtion: lvcnrpy.Sim.Sim
+            The requeted simulation object.
+        """
+        if isinstance(index, slice):
+            return Sims(self.paths[index])
+        else:
+            return Sim(self.paths[index], 'r')

lvcnrpy/__init__.py

+# Copyright (C) 2016 Edward Fauchon-Jones
+#
+# 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 3 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, see <http://www.gnu.org/licenses/>.
+
+import os
+
+LVCNR_DATADIR = '{0:s}'.format(os.environ['LVCNR_DATADIR'])

setup.py

+#!/usr/bin/env python
+#
+# Copyright (C) 2016 Edward Fauchon-Jones
+#
+# 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 3 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, see <http://www.gnu.org/licenses/>.
+
+from distutils.core import setup
+from setuptools import find_packages
+
+setup(name='lvcnrpy',
+      version='0.1.0',
+      description='Thin Python API to interact with the LVC NR catalogue',
+      author='Edward Fauchon-Jones',
+      author_email='edward.fauchon-jones@ligo.org',
+      packages=find_packages(),
+      url='https://git.ligo.org/edward.fauchon-jones/lvcnrpy',
+      download_url='https://git.ligo.org/edward.fauchon-jones/lvcnrpy',
+      install_requires=[
+        'h5py',
+        'numpy',
+        'scipy',
+        'matplotlib',
+        'pytest',
+        'colorama'],
+      scripts=['bin/lvcnrcheck'],
+      license='GPLv3')