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 nose.tools as nt
import numpy as np
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 = pyuvdata.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.
nt.assert_true(np.allclose(ref_xyz, out_xyz, rtol=0, atol=1e-3))
# test error checking
nt.assert_raises(ValueError, pyuvdata.XYZ_from_LatLonAlt, ref_latlonalt[0],
ref_latlonalt[1], np.array([ref_latlonalt[2], ref_latlonalt[2]]))
nt.assert_raises(ValueError, pyuvdata.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 = pyuvdata.LatLonAlt_from_XYZ(ref_xyz)
# Got reference by forcing http://www.oc.nps.edu/oc2902w/coord/llhxyz.htm
# to give additional precision.
nt.assert_true(np.allclose(ref_latlonalt, out_latlonalt, rtol=0, atol=1e-3))
nt.assert_raises(ValueError, pyuvdata.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 = pyuvdata.LatLonAlt_from_XYZ(xyz_mult)
nt.assert_true(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(pyuvdata.LatLonAlt_from_XYZ, [xyz_mult.T],
message='The expected shape of ECEF xyz array',
category=PendingDeprecationWarning)
# 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(pyuvdata.LatLonAlt_from_XYZ, [xyz_3],
message='The xyz array in LatLonAlt_from_XYZ is',
category=PendingDeprecationWarning)
# check error if only 2 coordinates
nt.assert_raises(ValueError, pyuvdata.LatLonAlt_from_XYZ, xyz_mult[:, 0:2])
# test error checking
nt.assert_raises(ValueError, pyuvdata.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 = pyuvdata.XYZ_from_LatLonAlt(lats, lons, alts)
nt.assert_true(np.allclose(np.stack((x, y, z), axis=1), xyz, atol=1e-3))
enu = pyuvdata.ENU_from_ECEF(xyz, center_lat, center_lon, center_alt)
nt.assert_true(np.allclose(np.stack((east, north, up), axis=1), enu, atol=1e-3))
# check warning if array transposed
uvtest.checkWarnings(pyuvdata.ENU_from_ECEF, [xyz.T, center_lat, center_lon,
center_alt],
message='The expected shape of ECEF xyz array',
category=PendingDeprecationWarning)
# check warning if 3 x 3 array
uvtest.checkWarnings(pyuvdata.ENU_from_ECEF, [xyz[0:3], center_lat, center_lon,
center_alt],
message='The xyz array in ENU_from_ECEF is',
category=PendingDeprecationWarning)
# check error if only 2 coordinates
nt.assert_raises(ValueError, pyuvdata.ENU_from_ECEF, xyz[:, 0:2],
center_lat, center_lon, center_alt)
# check that a round trip gives the original value.
xyz_from_enu = pyuvdata.ECEF_from_ENU(enu, center_lat, center_lon, center_alt)
nt.assert_true(np.allclose(xyz, xyz_from_enu, atol=1e-3))
# check warning if array transposed
uvtest.checkWarnings(pyuvdata.ECEF_from_ENU, [enu.T, center_lat, center_lon,
center_alt],
message='The expected shape the ENU array',
category=PendingDeprecationWarning)
# check warning if 3 x 3 array
uvtest.checkWarnings(pyuvdata.ECEF_from_ENU, [enu[0:3], center_lat, center_lon,
center_alt],
message='The enu array in ECEF_from_ENU is',
category=PendingDeprecationWarning)
# check error if only 2 coordinates
nt.assert_raises(ValueError, pyuvdata.ENU_from_ECEF, enu[:, 0:2], center_lat,
center_lon, center_alt)
# check passing a single value
enu_single = pyuvdata.ENU_from_ECEF(xyz[0, :], center_lat, center_lon, center_alt)
nt.assert_true(np.allclose(np.array((east[0], north[0], up[0])), enu[0, :], atol=1e-3))
xyz_from_enu = pyuvdata.ECEF_from_ENU(enu_single, center_lat, center_lon, center_alt)
nt.assert_true(np.allclose(xyz[0, :], xyz_from_enu, atol=1e-3))
# error checking
nt.assert_raises(ValueError, pyuvdata.ENU_from_ECEF, xyz[:, 0:1], center_lat, center_lon, center_alt)
nt.assert_raises(ValueError, pyuvdata.ECEF_from_ENU, enu[:, 0:1], center_lat, center_lon, center_alt)
nt.assert_raises(ValueError, pyuvdata.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)
nt.assert_true(np.allclose(enu, enh))
# test other direction of ECEF rotation
rot_xyz = uvutils.rotECEF_from_ECEF(new_xyz, lon)
nt.assert_true(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,
representation='cartesian', 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,
representation='cartesian', 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
nt.assert_true(np.allclose(gcrs_uvw[0, 0], mwa_tools_calcuvw_u, atol=1e-3))
nt.assert_true(np.allclose(gcrs_uvw[0, 1], mwa_tools_calcuvw_v, atol=1e-3))
nt.assert_true(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))
nt.assert_true(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']
nt.assert_equal(pol_nums, uvutils.polstr2num(pol_str))
nt.assert_equal(pol_str, uvutils.polnum2str(pol_nums))
# Check individuals
nt.assert_equal(-6, uvutils.polstr2num('YY'))
nt.assert_equal('pV', uvutils.polnum2str(4))
# Check errors
nt.assert_raises(KeyError, uvutils.polstr2num, 'foo')
nt.assert_raises(ValueError, uvutils.polstr2num, 1)
nt.assert_raises(ValueError, uvutils.polnum2str, 7.3)
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']
nt.assert_equal(jnums, uvutils.jstr2num(jstr))
nt.assert_equal(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]
nt.assert_equal(jnums, uvutils.jstr2num(jstr))
# Check individuals
nt.assert_equal(-6, uvutils.jstr2num('jyy'))
nt.assert_equal('jxy', uvutils.jnum2str(-7))
# Check errors
nt.assert_raises(KeyError, uvutils.jstr2num, 'foo')
nt.assert_raises(ValueError, uvutils.jstr2num, 1)
nt.assert_raises(ValueError, uvutils.jnum2str, 7.3)
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]
nt.assert_equal(pol_nums, uvutils.conj_pol(cpol_nums))
nt.assert_equal(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']
nt.assert_equal(pol_str, uvutils.conj_pol(cpol_str))
nt.assert_equal(uvutils.conj_pol(pol_str), cpol_str)
nt.assert_equal([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']
nt.assert_equal(jstr, uvutils.conj_pol(cjstr))
nt.assert_equal(uvutils.conj_pol(jstr), uvutils.conj_pol(jstr))
# Test invalid pol
nt.assert_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')
