Revision 4f75faeded2cb284dedbc856a8b2ae56075ea158 authored by Collin Capano on 20 June 2020, 18:27:09 UTC, committed by GitHub on 20 June 2020, 18:27:09 UTC
* use different acl for every chain in epsie * create base burn in class, move common functions to there; rename MCMCBurnInTests EnsembleMCMC, first stab at creating MCMC tests for independent chains * more changes to burn in module * simplify the attributes in the burn in classes * add write method to burn in classes * add write_data method to base_hdf * remove write_burn_in method from mcmc io; use the write method in burn in module instead * make use of new burn in functions in sampler/base_mcmc * have emcee and emcee pt use ensemble burn in tests * add compute_acf function to epsie * start separating ensemble and mcmc io methods * stop saving thin settings to file; just return on the fly * make read/write samples stand alone functions, and update emcee * rename write functions; update emcee * move multi temper read/write functions to stand alone and update emcee_pt * pass kwargs from emcee(_pt) io functions * simplify get_slice method * add function to base_mcmc to calculate the number of samples in a chain * use nsamples_in_chain function to calculate effective number of samples * add read_raw_samples function that can handle differing number of samples from different chains * add forgotten import * use write/read functions from base_multitemper in epsie io * use stand alone functions for computing ensemble acf/acls * separate out ensemble-specific attributes in sampler module; update emcee and emcee_pt * add acl and effective_nsample methods to epsie * simplify writing acls and burn in * fix various bugs and typos * use a single function for writing both acl and raw_acls * add some more logging info to burn in * reduce identical blocks of code in burn in module * fix self -> fp in read_raw_samples * reduce code duplication in base io and simplify read raw samples function * fix missed rename * reduce code redundacy in sampler/base_multitemper * whitespace * fix bugs and typos in burn_in module * fix code climate issues * use map in compute_acl * more code climate fixes * remove unused variable; try to silence pylint * fix issues reading epsie samples * only load samples from burned in chains by default * add act property to mcmc files * fix act logging message * fix effective number of samples calculation in epsie * remap walkers option to chains for reading samples * fix thinning update * fix acceptance ratio and temperature data thinning in epsie * allow for different fields to have differing number of temperatures when loading * don't try to figure out how many samples will be loaded ahead of time * store acts in file instead of acls * write burn in status to file before computing acls * drop write_acts function * fix issue with getting specific chains * fix typo * code climate issues * fix plot_acl
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test_resample.py
# Copyright (C) 2012 Alex Nitz, Josh Willis
#
# 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, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# =============================================================================
#
# Preamble
#
# =============================================================================
#
"""
These are the unittests for the pycbc.filter.matchedfilter module
"""
import sys
import unittest
from pycbc.types import *
from pycbc.filter import *
from pycbc.scheme import *
from utils import parse_args_all_schemes, simple_exit
from numpy.random import uniform
import scipy.signal
from pycbc.filter.resample import lfilter
_scheme, _context = parse_args_all_schemes("Resampling")
class TestUtils(unittest.TestCase):
def setUp(self,*args):
self.scheme = _scheme
self.context = _context
self.delta_t = 1.0 / 4096
self.target_delta_t = 1.0 / 1024
self.a = TimeSeries([1,2,3,4], delta_t=self.delta_t, dtype=float32)
self.b = TimeSeries([1,2,3,4], delta_t=self.delta_t, dtype=float64)
self.c = TimeSeries([1,2,3,4], delta_t=self.delta_t, dtype=complex64)
self.d = Array([1,2,3,4], dtype=float32)
if _scheme == 'cpu':
def test_resample_float32(self):
ra = resample_to_delta_t(self.a, self.target_delta_t)
self.assertAlmostEqual(ra[0], 0.00696246)
ra = resample_to_delta_t(self.a, self.delta_t)
self.assertAlmostEqual(ra[0], 1)
def test_resample_float64(self):
rb = resample_to_delta_t(self.b, self.target_delta_t)
self.assertAlmostEqual(rb[0], 0.00696246)
rb = resample_to_delta_t(self.b, self.delta_t)
self.assertAlmostEqual(rb[0], 1)
def test_resample_errors(self):
self.assertRaises(TypeError, resample_to_delta_t, self.c, self.target_delta_t)
self.assertRaises(TypeError, resample_to_delta_t, self.d, self.target_delta_t)
if self.scheme != 'cpu':
with self.context:
self.assertRaises(TypeError, resample_to_delta_t, self.a, self.target_delta_t)
def test_lfilter(self):
"Check our hand written lfilter"
c = uniform(-10, 10, size=1024)
ts = uniform(-1, 1, size=4323)
ref = scipy.signal.lfilter(c, 1.0, ts)
test = lfilter(c, ts)
# These only agree where there is no fft wraparound
# so excluded corrupted region from test
ref = ref[len(c):]
test = test[len(c):]
maxreldiff = ((ref - test) / ref).max()
self.assertTrue(maxreldiff < 1e-7)
suite = unittest.TestSuite()
suite.addTest(unittest.TestLoader().loadTestsFromTestCase(TestUtils))
if __name__ == '__main__':
results = unittest.TextTestRunner(verbosity=2).run(suite)
simple_exit(results)
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