test_utils.py
# -*- mode: python; coding: utf-8 -*
# Copyright (c) 2018 Radio Astronomy Software Group
# Licensed under the 2-clause BSD License
"""Tests for common utility functions.
"""
from __future__ import absolute_import, division, print_function
import os
import pytest
import numpy as np
import six
from astropy import units
from astropy.time import Time
from astropy.coordinates import SkyCoord, Angle
from astropy.io import fits
import pyuvdata
from pyuvdata.data import DATA_PATH
import pyuvdata.utils as uvutils
import pyuvdata.tests as uvtest
import pyuvdata.version as uvversion
ref_latlonalt = (-26.7 * np.pi / 180.0, 116.7 * np.pi / 180.0, 377.8)
ref_xyz = (-2562123.42683, 5094215.40141, -2848728.58869)
def test_XYZ_from_LatLonAlt():
"""Test conversion from lat/lon/alt to ECEF xyz with reference values."""
out_xyz = uvutils.XYZ_from_LatLonAlt(ref_latlonalt[0], ref_latlonalt[1],
ref_latlonalt[2])
# Got reference by forcing http://www.oc.nps.edu/oc2902w/coord/llhxyz.htm
# to give additional precision.
assert np.allclose(ref_xyz, out_xyz, rtol=0, atol=1e-3)
# test error checking
pytest.raises(ValueError, uvutils.XYZ_from_LatLonAlt, ref_latlonalt[0],
ref_latlonalt[1], np.array([ref_latlonalt[2], ref_latlonalt[2]]))
pytest.raises(ValueError, uvutils.XYZ_from_LatLonAlt, ref_latlonalt[0],
np.array([ref_latlonalt[1], ref_latlonalt[1]]), ref_latlonalt[2])
def test_LatLonAlt_from_XYZ():
"""Test conversion from ECEF xyz to lat/lon/alt with reference values."""
out_latlonalt = uvutils.LatLonAlt_from_XYZ(ref_xyz)
# Got reference by forcing http://www.oc.nps.edu/oc2902w/coord/llhxyz.htm
# to give additional precision.
assert np.allclose(ref_latlonalt, out_latlonalt, rtol=0, atol=1e-3)
pytest.raises(ValueError, uvutils.LatLonAlt_from_XYZ, ref_latlonalt)
# test passing multiple values
xyz_mult = np.stack((np.array(ref_xyz), np.array(ref_xyz)))
lat_vec, lon_vec, alt_vec = uvutils.LatLonAlt_from_XYZ(xyz_mult)
assert np.allclose(ref_latlonalt, (lat_vec[1], lon_vec[1], alt_vec[1]), rtol=0, atol=1e-3)
# check warning if array transposed
uvtest.checkWarnings(uvutils.LatLonAlt_from_XYZ, [xyz_mult.T],
message='The expected shape of ECEF xyz array',
category=DeprecationWarning)
# check warning if 3 x 3 array
xyz_3 = np.stack((np.array(ref_xyz), np.array(ref_xyz), np.array(ref_xyz)))
uvtest.checkWarnings(uvutils.LatLonAlt_from_XYZ, [xyz_3],
message='The xyz array in LatLonAlt_from_XYZ is',
category=DeprecationWarning)
# check error if only 2 coordinates
pytest.raises(ValueError, uvutils.LatLonAlt_from_XYZ, xyz_mult[:, 0:2])
# test error checking
pytest.raises(ValueError, uvutils.LatLonAlt_from_XYZ, ref_xyz[0:1])
def test_ENU_tofrom_ECEF():
center_lat = -30.7215261207 * np.pi / 180.0
center_lon = 21.4283038269 * np.pi / 180.0
center_alt = 1051.7
lats = np.array([-30.72218216, -30.72138101, -30.7212785, -30.7210011,
-30.72159853, -30.72206199, -30.72174614, -30.72188775,
-30.72183915, -30.72100138]) * np.pi / 180.0
lons = np.array([21.42728211, 21.42811727, 21.42814544, 21.42795736,
21.42686739, 21.42918772, 21.42785662, 21.4286408,
21.42750933, 21.42896567]) * np.pi / 180.0
alts = np.array([1052.25, 1051.35, 1051.2, 1051., 1051.45, 1052.04, 1051.68,
1051.87, 1051.77, 1051.06])
# used pymap3d, which implements matlab code, as a reference.
x = [5109327.46674067, 5109339.76407785, 5109344.06370947,
5109365.11297147, 5109372.115673, 5109266.94314734,
5109329.89620962, 5109295.13656657, 5109337.21810468,
5109329.85680612]
y = [2005130.57953031, 2005221.35184577, 2005225.93775268,
2005214.8436201, 2005105.42364036, 2005302.93158317,
2005190.65566222, 2005257.71335575, 2005157.78980089,
2005304.7729239]
z = [-3239991.24516348, -3239914.4185286, -3239904.57048431,
-3239878.02656316, -3239935.20415493, -3239979.68381865,
-3239949.39266985, -3239962.98805772, -3239958.30386264,
-3239878.08403833]
east = [-97.87631659, -17.87126443, -15.17316938, -33.19049252, -137.60520964,
84.67346748, -42.84049408, 32.28083937, -76.1094745, 63.40285935]
north = [-72.7437482, 16.09066646, 27.45724573, 58.21544651, -8.02964511,
-59.41961437, -24.39698388, -40.09891961, -34.70965816, 58.18410876]
up = [0.54883333, -0.35004539, -0.50007736, -0.70035299, -0.25148791, 0.33916067,
-0.02019057, 0.16979185, 0.06945155, -0.64058124]
xyz = uvutils.XYZ_from_LatLonAlt(lats, lons, alts)
assert np.allclose(np.stack((x, y, z), axis=1), xyz, atol=1e-3)
enu = uvutils.ENU_from_ECEF(xyz, center_lat, center_lon, center_alt)
assert np.allclose(np.stack((east, north, up), axis=1), enu, atol=1e-3)
# check warning if array transposed
uvtest.checkWarnings(uvutils.ENU_from_ECEF, [xyz.T, center_lat, center_lon,
center_alt],
message='The expected shape of ECEF xyz array',
category=DeprecationWarning)
# check warning if 3 x 3 array
uvtest.checkWarnings(uvutils.ENU_from_ECEF, [xyz[0:3], center_lat, center_lon,
center_alt],
message='The xyz array in ENU_from_ECEF is',
category=DeprecationWarning)
# check error if only 2 coordinates
pytest.raises(ValueError, uvutils.ENU_from_ECEF, xyz[:, 0:2],
center_lat, center_lon, center_alt)
# check that a round trip gives the original value.
xyz_from_enu = uvutils.ECEF_from_ENU(enu, center_lat, center_lon, center_alt)
assert np.allclose(xyz, xyz_from_enu, atol=1e-3)
# check warning if array transposed
uvtest.checkWarnings(uvutils.ECEF_from_ENU, [enu.T, center_lat, center_lon,
center_alt],
message='The expected shape the ENU array',
category=DeprecationWarning)
# check warning if 3 x 3 array
uvtest.checkWarnings(uvutils.ECEF_from_ENU, [enu[0:3], center_lat, center_lon,
center_alt],
message='The enu array in ECEF_from_ENU is',
category=DeprecationWarning)
# check error if only 2 coordinates
pytest.raises(ValueError, uvutils.ENU_from_ECEF, enu[:, 0:2], center_lat,
center_lon, center_alt)
# check passing a single value
enu_single = uvutils.ENU_from_ECEF(xyz[0, :], center_lat, center_lon, center_alt)
assert np.allclose(np.array((east[0], north[0], up[0])), enu[0, :], atol=1e-3)
xyz_from_enu = uvutils.ECEF_from_ENU(enu_single, center_lat, center_lon, center_alt)
assert np.allclose(xyz[0, :], xyz_from_enu, atol=1e-3)
# error checking
pytest.raises(ValueError, uvutils.ENU_from_ECEF, xyz[:, 0:1], center_lat, center_lon, center_alt)
pytest.raises(ValueError, uvutils.ECEF_from_ENU, enu[:, 0:1], center_lat, center_lon, center_alt)
pytest.raises(ValueError, uvutils.ENU_from_ECEF, xyz / 2., center_lat, center_lon, center_alt)
def test_mwa_ecef_conversion():
'''
Test based on comparing the antenna locations in a Cotter uvfits file to
the antenna locations in MWA_tools.
'''
test_data_file = os.path.join(DATA_PATH, 'mwa128_ant_layouts.npz')
f = np.load(test_data_file)
# From the STABXYZ table in a cotter-generated uvfits file, obsid = 1066666832
xyz = f['stabxyz']
# From the East/North/Height columns in a cotter-generated metafits file, obsid = 1066666832
enh = f['ENH']
# From a text file antenna_locations.txt in MWA_Tools/scripts
txt_topo = f['txt_topo']
# From the unphased uvw coordinates of obsid 1066666832, positions relative to antenna 0
# these aren't used in the current test, but are interesting and might help with phasing diagnosis in the future
uvw_topo = f['uvw_topo']
# Sky coordinates are flipped for uvw derived values
uvw_topo = -uvw_topo
uvw_topo += txt_topo[0]
# transpose these arrays to get them into the right shape
txt_topo = txt_topo.T
uvw_topo = uvw_topo.T
# ARRAYX, ARRAYY, ARRAYZ in ECEF frame from Cotter file
arrcent = f['arrcent']
lat, lon, alt = uvutils.LatLonAlt_from_XYZ(arrcent)
# The STABXYZ coordinates are defined with X through the local meridian,
# so rotate back to the prime meridian
new_xyz = uvutils.ECEF_from_rotECEF(xyz.T, lon)
# add in array center to get real ECEF
ecef_xyz = new_xyz + arrcent
enu = uvutils.ENU_from_ECEF(ecef_xyz, lat, lon, alt)
assert np.allclose(enu, enh)
# test other direction of ECEF rotation
rot_xyz = uvutils.rotECEF_from_ECEF(new_xyz, lon)
assert np.allclose(rot_xyz.T, xyz)
def test_phasing_funcs():
# these tests are based on a notebook where I tested against the mwa_tools phasing code
ra_hrs = 12.1
dec_degs = -42.3
mjd = 55780.1
array_center_xyz = np.array([-2559454.08, 5095372.14, -2849057.18])
lat_lon_alt = uvutils.LatLonAlt_from_XYZ(array_center_xyz)
obs_time = Time(mjd, format='mjd', location=(lat_lon_alt[1], lat_lon_alt[0]))
icrs_coord = SkyCoord(ra=Angle(ra_hrs, unit='hr'), dec=Angle(dec_degs, unit='deg'),
obstime=obs_time)
gcrs_coord = icrs_coord.transform_to('gcrs')
# in east/north/up frame (relative to array center) in meters: (Nants, 3)
ants_enu = np.array([-101.94, 0156.41, 0001.24])
ant_xyz_abs = uvutils.ECEF_from_ENU(ants_enu, lat_lon_alt[0], lat_lon_alt[1], lat_lon_alt[2])
ant_xyz_rel_itrs = ant_xyz_abs - array_center_xyz
ant_xyz_rel_rot = uvutils.rotECEF_from_ECEF(ant_xyz_rel_itrs, lat_lon_alt[1])
array_center_coord = SkyCoord(x=array_center_xyz[0] * units.m,
y=array_center_xyz[1] * units.m,
z=array_center_xyz[2] * units.m,
frame='itrs',
obstime=obs_time)
itrs_coord = SkyCoord(x=ant_xyz_abs[0] * units.m,
y=ant_xyz_abs[1] * units.m,
z=ant_xyz_abs[2] * units.m,
frame='itrs',
obstime=obs_time)
gcrs_array_center = array_center_coord.transform_to('gcrs')
gcrs_from_itrs_coord = itrs_coord.transform_to('gcrs')
gcrs_rel = (gcrs_from_itrs_coord.cartesian - gcrs_array_center.cartesian).get_xyz().T
gcrs_uvw = uvutils.phase_uvw(gcrs_coord.ra.rad, gcrs_coord.dec.rad,
gcrs_rel.value)
mwa_tools_calcuvw_u = -97.122828
mwa_tools_calcuvw_v = 50.388281
mwa_tools_calcuvw_w = -151.27976
assert np.allclose(gcrs_uvw[0, 0], mwa_tools_calcuvw_u, atol=1e-3)
assert np.allclose(gcrs_uvw[0, 1], mwa_tools_calcuvw_v, atol=1e-3)
assert np.allclose(gcrs_uvw[0, 2], mwa_tools_calcuvw_w, atol=1e-3)
# also test unphasing
temp2 = uvutils.unphase_uvw(gcrs_coord.ra.rad, gcrs_coord.dec.rad,
np.squeeze(gcrs_uvw))
assert np.allclose(gcrs_rel.value, temp2)
def test_pol_funcs():
""" Test utility functions to convert between polarization strings and numbers """
pol_nums = [-8, -7, -6, -5, -4, -3, -2, -1, 1, 2, 3, 4]
pol_str = ['yx', 'xy', 'yy', 'xx', 'lr', 'rl', 'll', 'rr', 'pI', 'pQ', 'pU', 'pV']
assert pol_nums == uvutils.polstr2num(pol_str)
assert pol_str == uvutils.polnum2str(pol_nums)
# Check individuals
assert -6 == uvutils.polstr2num('YY')
assert 'pV' == uvutils.polnum2str(4)
# Check errors
pytest.raises(KeyError, uvutils.polstr2num, 'foo')
pytest.raises(ValueError, uvutils.polstr2num, 1)
pytest.raises(ValueError, uvutils.polnum2str, 7.3)
# Check parse
assert uvutils.parse_polstr("xX") == 'xx'
assert uvutils.parse_polstr("XX") == 'xx'
assert uvutils.parse_polstr('i') == 'pI'
def test_pol_funcs_x_orientation():
""" Test utility functions to convert between polarization strings and numbers with x_orientation """
pol_nums = [-8, -7, -6, -5, -4, -3, -2, -1, 1, 2, 3, 4]
x_orient1 = 'e'
pol_str = ['ne', 'en', 'nn', 'ee', 'lr', 'rl', 'll', 'rr', 'pI', 'pQ', 'pU', 'pV']
assert pol_nums == uvutils.polstr2num(pol_str, x_orientation=x_orient1)
assert pol_str == uvutils.polnum2str(pol_nums, x_orientation=x_orient1)
# Check individuals
assert -6 == uvutils.polstr2num('NN', x_orientation=x_orient1)
assert 'pV' == uvutils.polnum2str(4)
# Check errors
pytest.raises(KeyError, uvutils.polstr2num, 'foo', x_orientation=x_orient1)
pytest.raises(ValueError, uvutils.polstr2num, 1, x_orientation=x_orient1)
pytest.raises(ValueError, uvutils.polnum2str, 7.3, x_orientation=x_orient1)
# Check parse
assert uvutils.parse_polstr("eE", x_orientation=x_orient1) == 'ee'
assert uvutils.parse_polstr("xx", x_orientation=x_orient1) == 'ee'
assert uvutils.parse_polstr("NN", x_orientation=x_orient1) == 'nn'
assert uvutils.parse_polstr("yy", x_orientation=x_orient1) == 'nn'
assert uvutils.parse_polstr('i', x_orientation=x_orient1) == 'pI'
x_orient2 = 'n'
pol_str = ['en', 'ne', 'ee', 'nn', 'lr', 'rl', 'll', 'rr', 'pI', 'pQ', 'pU', 'pV']
assert pol_nums == uvutils.polstr2num(pol_str, x_orientation=x_orient2)
assert pol_str == uvutils.polnum2str(pol_nums, x_orientation=x_orient2)
# Check individuals
assert -6 == uvutils.polstr2num('EE', x_orientation=x_orient2)
assert 'pV' == uvutils.polnum2str(4)
# Check errors
pytest.raises(KeyError, uvutils.polstr2num, 'foo', x_orientation=x_orient2)
pytest.raises(ValueError, uvutils.polstr2num, 1, x_orientation=x_orient2)
pytest.raises(ValueError, uvutils.polnum2str, 7.3, x_orientation=x_orient2)
# Check parse
assert uvutils.parse_polstr("nN", x_orientation=x_orient2) == 'nn'
assert uvutils.parse_polstr("xx", x_orientation=x_orient2) == 'nn'
assert uvutils.parse_polstr("EE", x_orientation=x_orient2) == 'ee'
assert uvutils.parse_polstr("yy", x_orientation=x_orient2) == 'ee'
assert uvutils.parse_polstr('i', x_orientation=x_orient2) == 'pI'
# check warnings for non-recognized x_orientation
assert uvtest.checkWarnings(uvutils.polstr2num, ['xx'], {'x_orientation': 'foo'},
message='x_orientation not recognized') == -5
assert uvtest.checkWarnings(uvutils.polnum2str, [-6], {'x_orientation': 'foo'},
message='x_orientation not recognized') == 'yy'
def test_jones_num_funcs():
""" Test utility functions to convert between jones polarization strings and numbers """
jnums = [-8, -7, -6, -5, -4, -3, -2, -1]
jstr = ['Jyx', 'Jxy', 'Jyy', 'Jxx', 'Jlr', 'Jrl', 'Jll', 'Jrr']
assert jnums == uvutils.jstr2num(jstr)
assert jstr, uvutils.jnum2str(jnums)
# Check shorthands
jstr = ['yx', 'xy', 'yy', 'y', 'xx', 'x', 'lr', 'rl', 'll', 'l', 'rr', 'r']
jnums = [-8, -7, -6, -6, -5, -5, -4, -3, -2, -2, -1, -1]
assert jnums == uvutils.jstr2num(jstr)
# Check individuals
assert -6 == uvutils.jstr2num('jyy')
assert 'Jxy' == uvutils.jnum2str(-7)
# Check errors
pytest.raises(KeyError, uvutils.jstr2num, 'foo')
pytest.raises(ValueError, uvutils.jstr2num, 1)
pytest.raises(ValueError, uvutils.jnum2str, 7.3)
# check parse method
assert uvutils.parse_jpolstr('x') == 'Jxx'
assert uvutils.parse_jpolstr('xy') == 'Jxy'
assert uvutils.parse_jpolstr('XY') == 'Jxy'
def test_jones_num_funcs_x_orientation():
""" Test utility functions to convert between jones polarization strings and numbers with x_orientation"""
jnums = [-8, -7, -6, -5, -4, -3, -2, -1]
x_orient1 = 'east'
jstr = ['Jne', 'Jen', 'Jnn', 'Jee', 'Jlr', 'Jrl', 'Jll', 'Jrr']
assert jnums == uvutils.jstr2num(jstr, x_orientation=x_orient1)
assert jstr == uvutils.jnum2str(jnums, x_orientation=x_orient1)
# Check shorthands
jstr = ['ne', 'en', 'nn', 'n', 'ee', 'e', 'lr', 'rl', 'll', 'l', 'rr', 'r']
jnums = [-8, -7, -6, -6, -5, -5, -4, -3, -2, -2, -1, -1]
assert jnums == uvutils.jstr2num(jstr, x_orientation=x_orient1)
# Check individuals
assert -6 == uvutils.jstr2num('jnn', x_orientation=x_orient1)
assert 'Jen' == uvutils.jnum2str(-7, x_orientation=x_orient1)
# Check errors
pytest.raises(KeyError, uvutils.jstr2num, 'foo', x_orientation=x_orient1)
pytest.raises(ValueError, uvutils.jstr2num, 1, x_orientation=x_orient1)
pytest.raises(ValueError, uvutils.jnum2str, 7.3, x_orientation=x_orient1)
# check parse method
assert uvutils.parse_jpolstr('e', x_orientation=x_orient1) == 'Jee'
assert uvutils.parse_jpolstr('x', x_orientation=x_orient1) == 'Jee'
assert uvutils.parse_jpolstr('y', x_orientation=x_orient1) == 'Jnn'
assert uvutils.parse_jpolstr('en', x_orientation=x_orient1) == 'Jen'
assert uvutils.parse_jpolstr('NE', x_orientation=x_orient1) == 'Jne'
jnums = [-8, -7, -6, -5, -4, -3, -2, -1]
x_orient2 = 'north'
jstr = ['Jen', 'Jne', 'Jee', 'Jnn', 'Jlr', 'Jrl', 'Jll', 'Jrr']
assert jnums == uvutils.jstr2num(jstr, x_orientation=x_orient2)
assert jstr == uvutils.jnum2str(jnums, x_orientation=x_orient2)
# Check shorthands
jstr = ['en', 'ne', 'ee', 'e', 'nn', 'n', 'lr', 'rl', 'll', 'l', 'rr', 'r']
jnums = [-8, -7, -6, -6, -5, -5, -4, -3, -2, -2, -1, -1]
assert jnums == uvutils.jstr2num(jstr, x_orientation=x_orient2)
# Check individuals
assert -6 == uvutils.jstr2num('jee', x_orientation=x_orient2)
assert 'Jne' == uvutils.jnum2str(-7, x_orientation=x_orient2)
# Check errors
pytest.raises(KeyError, uvutils.jstr2num, 'foo', x_orientation=x_orient2)
pytest.raises(ValueError, uvutils.jstr2num, 1, x_orientation=x_orient2)
pytest.raises(ValueError, uvutils.jnum2str, 7.3, x_orientation=x_orient2)
# check parse method
assert uvutils.parse_jpolstr('e', x_orientation=x_orient2) == 'Jee'
assert uvutils.parse_jpolstr('x', x_orientation=x_orient2) == 'Jnn'
assert uvutils.parse_jpolstr('y', x_orientation=x_orient2) == 'Jee'
assert uvutils.parse_jpolstr('en', x_orientation=x_orient2) == 'Jen'
assert uvutils.parse_jpolstr('NE', x_orientation=x_orient2) == 'Jne'
# check warnings for non-recognized x_orientation
assert uvtest.checkWarnings(uvutils.jstr2num, ['x'], {'x_orientation': 'foo'},
message='x_orientation not recognized') == -5
assert uvtest.checkWarnings(uvutils.jnum2str, [-6], {'x_orientation': 'foo'},
message='x_orientation not recognized') == 'Jyy'
def test_conj_pol():
""" Test function to conjugate pols """
pol_nums = [-8, -7, -6, -5, -4, -3, -2, -1, 1, 2, 3, 4]
cpol_nums = [-7, -8, -6, -5, -3, -4, -2, -1, 1, 2, 3, 4]
assert pol_nums == uvutils.conj_pol(cpol_nums)
assert uvutils.conj_pol(pol_nums) == cpol_nums
pol_str = ['yx', 'xy', 'yy', 'xx', 'lr', 'rl', 'll', 'rr', 'pI', 'pQ', 'pU', 'pV']
cpol_str = ['xy', 'yx', 'yy', 'xx', 'rl', 'lr', 'll', 'rr', 'pI', 'pQ', 'pU', 'pV']
assert pol_str == uvutils.conj_pol(cpol_str)
assert uvutils.conj_pol(pol_str) == cpol_str
assert [pol_str, pol_nums] == uvutils.conj_pol([cpol_str, cpol_nums])
jstr = ['Jyx', 'Jxy', 'Jyy', 'Jxx', 'Jlr', 'Jrl', 'Jll', 'Jrr']
cjstr = ['Jxy', 'Jyx', 'Jyy', 'Jxx', 'Jrl', 'Jlr', 'Jll', 'Jrr']
conj_cjstr = uvtest.checkWarnings(uvutils.conj_pol, [cjstr], nwarnings=8,
category=DeprecationWarning,
message='conj_pol should not be called with jones')
assert jstr == conj_cjstr
# Test invalid pol
pytest.raises(ValueError, uvutils.conj_pol, 2.3)
def test_deprecated_funcs():
uvtest.checkWarnings(uvutils.get_iterable, [5], category=DeprecationWarning,
message='The get_iterable function is deprecated')
testfile = os.path.join(DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
with fits.open(testfile, memmap=True) as hdu_list:
uvtest.checkWarnings(uvutils.fits_indexhdus, [hdu_list],
category=DeprecationWarning,
message='The fits_indexhdus function is deprecated')
vis_hdu = hdu_list[0]
uvtest.checkWarnings(uvutils.fits_gethduaxis, [vis_hdu, 5],
category=DeprecationWarning,
message='The fits_gethduaxis function is deprecated')
uvtest.checkWarnings(uvutils.check_history_version, ['some random history',
uvversion.version],
category=DeprecationWarning,
message='The check_history_version function is deprecated')
uvtest.checkWarnings(uvutils.check_histories, ['some random history',
'some random history'],
category=DeprecationWarning,
message='The check_histories function is deprecated')
uvtest.checkWarnings(uvutils.combine_histories, ['some random history',
uvversion.version],
category=DeprecationWarning,
message='The combine_histories function is deprecated')
def test_redundancy_finder():
"""
Check that get_baseline_redundancies and get_antenna_redundancies return consistent
redundant groups for a test file with the HERA19 layout.
"""
uvd = pyuvdata.UVData()
uvd.read_uvfits(os.path.join(DATA_PATH, 'fewant_randsrc_airybeam_Nsrc100_10MHz.uvfits'))
uvd.select(times=uvd.time_array[0])
uvd.unphase_to_drift() # uvw_array is now equivalent to baseline positions
uvtest.checkWarnings(uvd.conjugate_bls, func_kwargs={'convention': 'u>0', 'use_enu': True},
message=['The default for the `center`'],
nwarnings=1, category=DeprecationWarning)
tol = 0.05 # meters
bl_positions = uvd.uvw_array
pytest.raises(ValueError, uvutils.get_baseline_redundancies,
uvd.baseline_array, bl_positions[0:2, 0:1])
baseline_groups, vec_bin_centers, lens = uvutils.get_baseline_redundancies(
uvd.baseline_array, bl_positions, tol=tol)
baseline_groups, vec_bin_centers, lens = uvutils.get_baseline_redundancies(
uvd.baseline_array, bl_positions, tol=tol)
for gi, gp in enumerate(baseline_groups):
for bl in gp:
bl_ind = np.where(uvd.baseline_array == bl)
bl_vec = bl_positions[bl_ind]
assert np.allclose(np.sqrt(np.dot(bl_vec, vec_bin_centers[gi])),
lens[gi], atol=tol)
# Shift the baselines around in a circle. Check that the same baselines are
# recovered to the corresponding tolerance increase.
# This moves one baseline at a time by a fixed displacement and checks that
# the redundant groups are the same.
hightol = 0.25 # meters. Less than the smallest baseline in the file.
Nbls = uvd.Nbls
Nshifts = 5
shift_angs = np.linspace(0, 2 * np.pi, Nshifts)
base_shifts = np.stack(((hightol - tol) * np.cos(shift_angs),
(hightol - tol) * np.sin(shift_angs),
np.zeros(Nshifts))).T
for sh in base_shifts:
for bi in range(Nbls):
# Shift one baseline at a time.
bl_positions_new = uvd.uvw_array
bl_positions_new[bi] += sh
baseline_groups_new, vec_bin_centers, lens = uvutils.get_baseline_redundancies(
uvd.baseline_array, bl_positions_new, tol=hightol)
for gi, gp in enumerate(baseline_groups_new):
for bl in gp:
bl_ind = np.where(uvd.baseline_array == bl)
bl_vec = bl_positions[bl_ind]
assert np.allclose(np.sqrt(np.abs(np.dot(bl_vec, vec_bin_centers[gi]))),
lens[gi], atol=hightol)
# Compare baseline groups:
a = [tuple(el) for el in baseline_groups]
b = [tuple(el) for el in baseline_groups_new]
assert set(a) == set(b)
tol = 0.05
antpos, antnums = uvtest.checkWarnings(uvd.get_ENU_antpos,
message=['The default for the `center`'],
category=DeprecationWarning,
nwarnings=1)
baseline_groups_ants, vec_bin_centers, lens = uvutils.get_antenna_redundancies(
antnums, antpos, tol=tol, include_autos=False)
# Under these conditions, should see 19 redundant groups in the file.
assert len(baseline_groups_ants) == 19
# Check with conjugated baseline redundancies returned
u16_0 = bl_positions[16, 0]
# Ensure at least one baseline has u==0 and v!=0 (for coverage of this case)
bl_positions[16, 0] = 0
baseline_groups, vec_bin_centers, lens, conjugates = uvutils.get_baseline_redundancies(
uvd.baseline_array, bl_positions, tol=tol, with_conjugates=True)
# restore baseline (16,0) and repeat to get correct groups
bl_positions[16, 0] = u16_0
baseline_groups, vec_bin_centers, lens, conjugates = uvutils.get_baseline_redundancies(
uvd.baseline_array, bl_positions, tol=tol, with_conjugates=True)
# Should get the same groups as with the antenna method:
baseline_groups_flipped = []
for bgp in baseline_groups:
bgp_new = []
for bl in bgp:
ai, aj = uvutils.baseline_to_antnums(bl, uvd.Nants_telescope)
if bl in conjugates:
bgp_new.append(uvutils.antnums_to_baseline(aj, ai, uvd.Nants_telescope))
else:
bgp_new.append(uvutils.antnums_to_baseline(ai, aj, uvd.Nants_telescope))
bgp_new.sort()
baseline_groups_flipped.append(bgp_new)
baseline_groups = [sorted(bgp) for bgp in baseline_groups]
assert np.all(sorted(baseline_groups_ants) == sorted(baseline_groups_flipped))
for gi, gp in enumerate(baseline_groups):
for bl in gp:
bl_ind = np.where(uvd.baseline_array == bl)
bl_vec = bl_positions[bl_ind]
if bl in conjugates:
bl_vec *= (-1)
assert np.isclose(np.sqrt(np.dot(bl_vec, vec_bin_centers[gi])),
lens[gi], atol=tol)
def test_redundancy_conjugates():
# Check that the correct baselines are flipped when returning redundancies with conjugates.
Nants = 10
tol = 0.5
ant1_arr = np.tile(np.arange(Nants), Nants)
ant2_arr = np.repeat(np.arange(Nants), Nants)
Nbls = ant1_arr.size
bl_inds = uvutils.antnums_to_baseline(ant1_arr, ant2_arr, Nants)
maxbl = 100.
bl_vecs = np.random.uniform(-maxbl, maxbl, (Nbls, 3))
bl_vecs[0, 0] = 0
bl_vecs[1, 0:2] = 0
expected_conjugates = []
for i, (u, v, w) in enumerate(bl_vecs):
if (u < 0) or (v < 0 and u == 0) or (w < 0 and u == v == 0):
expected_conjugates.append(bl_inds[i])
bl_gps, vecs, lens, conjugates = uvutils.get_baseline_redundancies(
bl_inds, bl_vecs, tol=tol, with_conjugates=True)
assert sorted(conjugates) == sorted(expected_conjugates)
def test_redundancy_finder_fully_redundant_array():
"""Test the redundancy finder only returns one baseline group for fully redundant array."""
uvd = pyuvdata.UVData()
uvd.read_uvfits(os.path.join(DATA_PATH, 'test_redundant_array.uvfits'))
uvd.select(times=uvd.time_array[0])
tol = 1 # meters
bl_positions = uvd.uvw_array
baseline_groups, vec_bin_centers, lens, conjugates = uvutils.get_baseline_redundancies(
uvd.baseline_array, bl_positions, tol=tol, with_conjugates=True)
# Only 1 set of redundant baselines
assert len(baseline_groups) == 1
# Should return the input baselines
assert baseline_groups[0].sort() == np.unique(uvd.baseline_array).sort()
def test_reraise_context():
with pytest.raises(ValueError) as cm:
try:
uvutils.LatLonAlt_from_XYZ(ref_xyz[0:1])
except ValueError:
uvutils._reraise_context('Add some info')
assert 'Add some info: xyz values should be ECEF x, y, z coordinates in meters' in str(cm.value)
with pytest.raises(ValueError) as cm:
try:
uvutils.LatLonAlt_from_XYZ(ref_xyz[0:1])
except ValueError:
uvutils._reraise_context('Add some info %s', 'and then more')
assert 'Add some info and then more: xyz values should be ECEF x, y, z coordinates in meters' in str(cm.value)
with pytest.raises(EnvironmentError) as cm:
try:
raise EnvironmentError(1, 'some bad problem')
except EnvironmentError:
uvutils._reraise_context('Add some info')
assert 'Add some info: some bad problem' in str(cm.value)
def test_str_to_bytes():
test_str = 'HERA'
test_bytes = uvutils._str_to_bytes(test_str)
assert type(test_bytes) == six.binary_type
assert test_bytes == b'\x48\x45\x52\x41'
return
def test_bytes_to_str():
test_bytes = b'\x48\x45\x52\x41'
test_str = uvutils._bytes_to_str(test_bytes)
assert type(test_str) == str
assert test_str == 'HERA'
return
def test_reorder_conj_pols_non_list():
pytest.raises(ValueError, uvutils.reorder_conj_pols, 4)
def test_reorder_conj_pols_strings():
pols = ['xx', 'xy', 'yx']
corder = uvutils.reorder_conj_pols(pols)
assert np.array_equal(corder, [0, 2, 1])
def test_reorder_conj_pols_ints():
pols = [-5, -7, -8] # 'xx', 'xy', 'yx'
corder = uvutils.reorder_conj_pols(pols)
assert np.array_equal(corder, [0, 2, 1])
def test_reorder_conj_pols_missing_conj():
pols = ['xx', 'xy'] # Missing 'yx'
pytest.raises(ValueError, uvutils.reorder_conj_pols, pols)
def test_collapse_mean_no_return_no_weights():
# Fake data
data = np.zeros((50, 25))
for i in range(data.shape[1]):
data[:, i] = i * np.ones_like(data[:, i])
out = uvutils.collapse(data, 'mean', axis=0)
out1 = uvutils.mean_collapse(data, axis=0)
# Actual values are tested in test_mean_no_weights
assert np.array_equal(out, out1)
def test_collapse_mean_returned_no_weights():
# Fake data
data = np.zeros((50, 25))
for i in range(data.shape[1]):
data[:, i] = i * np.ones_like(data[:, i])
out, wo = uvutils.collapse(data, 'mean', axis=0, return_weights=True)
out1, wo1 = uvutils.mean_collapse(data, axis=0, return_weights=True)
# Actual values are tested in test_mean_no_weights
assert np.array_equal(out, out1)
assert np.array_equal(wo, wo1)
def test_collapse_mean_returned_with_weights():
# Fake data
data = np.zeros((50, 25))
for i in range(data.shape[1]):
data[:, i] = i * np.ones_like(data[:, i]) + 1
w = 1. / data
out, wo = uvutils.collapse(data, 'mean', weights=w, axis=0, return_weights=True)
out1, wo1 = uvutils.mean_collapse(data, weights=w, axis=0, return_weights=True)
# Actual values are tested in test_mean_weights
assert np.array_equal(out, out1)
assert np.array_equal(wo, wo1)
def test_collapse_absmean_no_return_no_weights():
# Fake data
data = np.zeros((50, 25))
for i in range(data.shape[1]):
data[:, i] = (-1)**i * np.ones_like(data[:, i])
out = uvutils.collapse(data, 'absmean', axis=0)
out1 = uvutils.absmean_collapse(data, axis=0)
# Actual values are tested in test_absmean_no_weights
assert np.array_equal(out, out1)
def test_collapse_quadmean_no_return_no_weights():
# Fake data
data = np.zeros((50, 25))
for i in range(data.shape[1]):
data[:, i] = i * np.ones_like(data[:, i])
out = uvutils.collapse(data, 'quadmean', axis=0)
out1 = uvutils.quadmean_collapse(data, axis=0)
# Actual values are tested in test_absmean_no_weights
assert np.array_equal(out, out1)
def test_collapse_or_no_return_no_weights():
# Fake data
data = np.zeros((50, 25), np.bool)
data[0, 8] = True
o = uvutils.collapse(data, 'or', axis=0)
o1 = uvutils.or_collapse(data, axis=0)
assert np.array_equal(o, o1)
def test_collapse_and_no_return_no_weights():
# Fake data
data = np.zeros((50, 25), np.bool)
data[0, :] = True
o = uvutils.collapse(data, 'and', axis=0)
o1 = uvutils.and_collapse(data, axis=0)
assert np.array_equal(o, o1)
def test_collapse_error():
pytest.raises(ValueError, uvutils.collapse, np.ones((2, 3)), 'fooboo')
def test_mean_no_weights():
# Fake data
data = np.zeros((50, 25))
for i in range(data.shape[1]):
data[:, i] = i * np.ones_like(data[:, i])
out, wo = uvutils.mean_collapse(data, axis=0, return_weights=True)
assert np.array_equal(out, np.arange(data.shape[1]))
assert np.array_equal(wo, data.shape[0] * np.ones(data.shape[1]))
out, wo = uvutils.mean_collapse(data, axis=1, return_weights=True)
assert np.all(out == np.mean(np.arange(data.shape[1])))
assert len(out) == data.shape[0]
assert np.array_equal(wo, data.shape[1] * np.ones(data.shape[0]))
out, wo = uvutils.mean_collapse(data, return_weights=True)
assert out == np.mean(np.arange(data.shape[1]))
assert wo == data.size
out = uvutils.mean_collapse(data)
assert out == np.mean(np.arange(data.shape[1]))
def test_mean_weights():
# Fake data
data = np.zeros((50, 25))
for i in range(data.shape[1]):
data[:, i] = i * np.ones_like(data[:, i]) + 1
w = 1. / data
out, wo = uvutils.mean_collapse(data, weights=w, axis=0, return_weights=True)
assert np.allclose(out * wo, data.shape[0])
assert np.allclose(wo, float(data.shape[0]) / (np.arange(data.shape[1]) + 1))
out, wo = uvutils.mean_collapse(data, weights=w, axis=1, return_weights=True)
assert np.allclose(out * wo, data.shape[1])
assert np.allclose(wo, np.sum(1. / (np.arange(data.shape[1]) + 1)))
# Zero weights
w = np.ones_like(w)
w[0, :] = 0
w[:, 0] = 0
out, wo = uvutils.mean_collapse(data, weights=w, axis=0, return_weights=True)
ans = np.arange(data.shape[1]).astype(np.float) + 1
ans[0] = np.inf
assert np.array_equal(out, ans)
ans = (data.shape[0] - 1) * np.ones(data.shape[1])
ans[0] = 0
assert np.all(wo == ans)
out, wo = uvutils.mean_collapse(data, weights=w, axis=1, return_weights=True)
ans = np.mean(np.arange(data.shape[1])[1:] + 1) * np.ones(data.shape[0])
ans[0] = np.inf
assert np.all(out == ans)
ans = (data.shape[1] - 1) * np.ones(data.shape[0])
ans[0] = 0
assert np.all(wo == ans)
def test_mean_infs():
# Fake data
data = np.zeros((50, 25))
for i in range(data.shape[1]):
data[:, i] = i * np.ones_like(data[:, i])
data[:, 0] = np.inf
data[0, :] = np.inf
out, wo = uvutils.mean_collapse(data, axis=0, return_weights=True)
ans = np.arange(data.shape[1]).astype(np.float)
ans[0] = np.inf
assert np.array_equal(out, ans)
ans = (data.shape[0] - 1) * np.ones(data.shape[1])
ans[0] = 0
assert np.all(wo == ans)
out, wo = uvutils.mean_collapse(data, axis=1, return_weights=True)
ans = np.mean(np.arange(data.shape[1])[1:]) * np.ones(data.shape[0])
ans[0] = np.inf
assert np.all(out == ans)
ans = (data.shape[1] - 1) * np.ones(data.shape[0])
ans[0] = 0
assert np.all(wo == ans)
def test_absmean():
# Fake data
data1 = np.zeros((50, 25))
for i in range(data1.shape[1]):
data1[:, i] = (-1)**i * np.ones_like(data1[:, i])
data2 = np.ones_like(data1)
out1 = uvutils.absmean_collapse(data1)
out2 = uvutils.absmean_collapse(data2)
assert out1 == out2
def test_quadmean():
# Fake data
data = np.zeros((50, 25))
for i in range(data.shape[1]):
data[:, i] = i * np.ones_like(data[:, i])
o1, w1 = uvutils.quadmean_collapse(data, return_weights=True)
o2, w2 = uvutils.mean_collapse(np.abs(data)**2, return_weights=True)
o3 = uvutils.quadmean_collapse(data) # without return_weights
o2 = np.sqrt(o2)
assert o1 == o2
assert w1 == w2
assert o1 == o3
def test_or_collapse():
# Fake data
data = np.zeros((50, 25), np.bool)
data[0, 8] = True
o = uvutils.or_collapse(data, axis=0)
ans = np.zeros(25, np.bool)
ans[8] = True
assert np.array_equal(o, ans)
o = uvutils.or_collapse(data, axis=1)
ans = np.zeros(50, np.bool)
ans[0] = True
assert np.array_equal(o, ans)
o = uvutils.or_collapse(data)
assert o
def test_or_collapse_weights():
# Fake data
data = np.zeros((50, 25), np.bool)
data[0, 8] = True
w = np.ones_like(data, np.float)
o, wo = uvutils.or_collapse(data, axis=0, weights=w, return_weights=True)
ans = np.zeros(25, np.bool)
ans[8] = True
assert np.array_equal(o, ans)
assert np.array_equal(wo, np.ones_like(o, dtype=np.float))
w[0, 8] = 0.3
o = uvtest.checkWarnings(uvutils.or_collapse, [data], {'axis': 0, 'weights': w},
nwarnings=1, message='Currently weights are')
assert np.array_equal(o, ans)
def test_or_collapse_errors():
data = np.zeros(5)
pytest.raises(ValueError, uvutils.or_collapse, data)
def test_and_collapse():
# Fake data
data = np.zeros((50, 25), np.bool)
data[0, :] = True
o = uvutils.and_collapse(data, axis=0)
ans = np.zeros(25, np.bool)
assert np.array_equal(o, ans)
o = uvutils.and_collapse(data, axis=1)
ans = np.zeros(50, np.bool)
ans[0] = True
assert np.array_equal(o, ans)
o = uvutils.and_collapse(data)
assert not o
def test_and_collapse_weights():
# Fake data
data = np.zeros((50, 25), np.bool)
data[0, :] = True
w = np.ones_like(data, np.float)
o, wo = uvutils.and_collapse(data, axis=0, weights=w, return_weights=True)
ans = np.zeros(25, np.bool)
assert np.array_equal(o, ans)
assert np.array_equal(wo, np.ones_like(o, dtype=np.float))
w[0, 8] = 0.3
o = uvtest.checkWarnings(uvutils.and_collapse, [data], {'axis': 0, 'weights': w},
nwarnings=1, message='Currently weights are')
assert np.array_equal(o, ans)
def test_and_collapse_errors():
data = np.zeros(5)
pytest.raises(ValueError, uvutils.and_collapse, data)
