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test_uvdata.py
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test_uvdata.py
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# -*- coding: utf-8 -*-
"""Tests for uvdata object.
"""
from __future__ import absolute_import, division, print_function
import nose.tools as nt
import os
import numpy as np
import copy
import six
from astropy.time import Time
from astropy.coordinates import Angle
from pyuvdata import UVData
import pyuvdata.utils as uvutils
import pyuvdata.tests as uvtest
from pyuvdata.data import DATA_PATH
if six.PY2:
nt.assert_count_equal = nt.assert_items_equal
class TestUVDataInit(object):
def setUp(self):
"""Setup for basic parameter, property and iterator tests."""
self.required_parameters = ['_data_array', '_nsample_array',
'_flag_array', '_Ntimes', '_Nbls',
'_Nblts', '_Nfreqs', '_Npols', '_Nspws',
'_uvw_array', '_time_array', '_ant_1_array',
'_ant_2_array', '_lst_array',
'_baseline_array', '_freq_array',
'_polarization_array', '_spw_array',
'_integration_time', '_channel_width',
'_object_name', '_telescope_name',
'_instrument', '_telescope_location',
'_history', '_vis_units', '_Nants_data',
'_Nants_telescope', '_antenna_names',
'_antenna_numbers', '_phase_type']
self.required_properties = ['data_array', 'nsample_array',
'flag_array', 'Ntimes', 'Nbls',
'Nblts', 'Nfreqs', 'Npols', 'Nspws',
'uvw_array', 'time_array', 'ant_1_array',
'ant_2_array', 'lst_array',
'baseline_array', 'freq_array',
'polarization_array', 'spw_array',
'integration_time', 'channel_width',
'object_name', 'telescope_name',
'instrument', 'telescope_location',
'history', 'vis_units', 'Nants_data',
'Nants_telescope', 'antenna_names',
'antenna_numbers', 'phase_type']
self.extra_parameters = ['_extra_keywords', '_antenna_positions',
'_x_orientation', '_antenna_diameters',
'_gst0', '_rdate', '_earth_omega', '_dut1',
'_timesys', '_uvplane_reference_time',
'_phase_center_ra', '_phase_center_dec',
'_phase_center_epoch', '_phase_center_frame']
self.extra_properties = ['extra_keywords', 'antenna_positions',
'x_orientation', 'antenna_diameters', 'gst0',
'rdate', 'earth_omega', 'dut1', 'timesys',
'uvplane_reference_time',
'phase_center_ra', 'phase_center_dec',
'phase_center_epoch', 'phase_center_frame']
self.other_properties = ['telescope_location_lat_lon_alt',
'telescope_location_lat_lon_alt_degrees',
'phase_center_ra_degrees', 'phase_center_dec_degrees',
'pyuvdata_version_str']
self.uv_object = UVData()
def teardown(self):
"""Test teardown: delete object."""
del(self.uv_object)
def test_order_pols(self):
test_uv1 = UVData()
testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(test_uv1.read_uvfits, [testfile],
message='Telescope EVLA is not')
test_uv1.order_pols(order='AIPS')
# check that we have aips ordering
aips_pols = np.array([-1, -2, -3, -4]).astype(int)
nt.assert_true(np.all(test_uv1.polarization_array == aips_pols))
test_uv2 = copy.deepcopy(test_uv1)
test_uv2.order_pols(order='CASA')
casa_pols = np.array([-1, -3, -4, -2]).astype(int)
nt.assert_true(np.all(test_uv2.polarization_array == casa_pols))
order = np.array([0, 2, 3, 1])
nt.assert_true(np.all(test_uv2.data_array == test_uv1.data_array[:, :, :, order]))
nt.assert_true(np.all(test_uv2.flag_array == test_uv1.flag_array[:, :, :, order]))
# check that we have casa ordering
test_uv2.order_pols(order='AIPS')
# check that we have aips ordering again
nt.assert_equal(test_uv1, test_uv2)
uvtest.checkWarnings(test_uv2.order_pols, ['unknown'], message='Invalid order supplied')
del(test_uv1)
del(test_uv2)
def test_parameter_iter(self):
"Test expected parameters."
all = []
for prop in self.uv_object:
all.append(prop)
for a in self.required_parameters + self.extra_parameters:
nt.assert_true(a in all, msg='expected attribute ' + a
+ ' not returned in object iterator')
def test_required_parameter_iter(self):
"Test expected required parameters."
required = []
for prop in self.uv_object.required():
required.append(prop)
for a in self.required_parameters:
nt.assert_true(a in required, msg='expected attribute ' + a
+ ' not returned in required iterator')
def test_extra_parameter_iter(self):
"Test expected optional parameters."
extra = []
for prop in self.uv_object.extra():
extra.append(prop)
for a in self.extra_parameters:
nt.assert_true(a in extra, msg='expected attribute ' + a
+ ' not returned in extra iterator')
def test_unexpected_parameters(self):
"Test for extra parameters."
expected_parameters = self.required_parameters + self.extra_parameters
attributes = [i for i in self.uv_object.__dict__.keys() if i[0] == '_']
for a in attributes:
nt.assert_true(a in expected_parameters,
msg='unexpected parameter ' + a + ' found in UVData')
def test_unexpected_attributes(self):
"Test for extra attributes."
expected_attributes = self.required_properties + \
self.extra_properties + self.other_properties
attributes = [i for i in self.uv_object.__dict__.keys() if i[0] != '_']
for a in attributes:
nt.assert_true(a in expected_attributes,
msg='unexpected attribute ' + a + ' found in UVData')
def test_properties(self):
"Test that properties can be get and set properly."
prop_dict = dict(list(zip(self.required_properties + self.extra_properties,
self.required_parameters + self.extra_parameters)))
for k, v in prop_dict.items():
rand_num = np.random.rand()
setattr(self.uv_object, k, rand_num)
this_param = getattr(self.uv_object, v)
try:
nt.assert_equal(rand_num, this_param.value)
except(AssertionError):
print('setting {prop_name} to a random number failed'.format(prop_name=k))
raise(AssertionError)
class TestUVDataBasicMethods(object):
def setUp(self):
"""Setup for tests of basic methods."""
self.uv_object = UVData()
self.testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(self.uv_object.read_uvfits, [self.testfile],
message='Telescope EVLA is not')
self.uv_object2 = copy.deepcopy(self.uv_object)
def teardown(self):
"""Test teardown: delete objects."""
del(self.uv_object)
del(self.uv_object2)
def test_equality(self):
"""Basic equality test."""
nt.assert_equal(self.uv_object, self.uv_object)
def test_check(self):
"""Test simple check function."""
nt.assert_true(self.uv_object.check())
# Check variety of special cases
self.uv_object.Nants_data += 1
nt.assert_raises(ValueError, self.uv_object.check)
self.uv_object.Nants_data -= 1
self.uv_object.Nbls += 1
nt.assert_raises(ValueError, self.uv_object.check)
self.uv_object.Nbls -= 1
self.uv_object.Ntimes += 1
nt.assert_raises(ValueError, self.uv_object.check)
self.uv_object.Ntimes -= 1
# Check case where all data is autocorrelations
# Currently only test files that have autos are fhd files
testdir = os.path.join(DATA_PATH, 'fhd_vis_data/')
file_list = [testdir + '1061316296_flags.sav',
testdir + '1061316296_vis_XX.sav',
testdir + '1061316296_params.sav',
testdir + '1061316296_settings.txt']
if not uvtest.scipy_warnings:
self.uv_object.read_fhd(file_list)
else:
# numpy 1.14 introduced a new deprecation warning
n_scipy_warnings, scipy_warn_list, scipy_category_list = uvtest.get_scipy_warnings(n_scipy_warnings=550)
uvtest.checkWarnings(self.uv_object.read_fhd, [file_list],
message=scipy_warn_list, category=scipy_category_list,
nwarnings=n_scipy_warnings)
self.uv_object.select(blt_inds=np.where(self.uv_object.ant_1_array
== self.uv_object.ant_2_array)[0])
nt.assert_true(self.uv_object.check())
# test auto and cross corr uvw_array
uvd = UVData()
uvd.read_miriad(os.path.join(DATA_PATH, "zen.2457698.40355.xx.HH.uvcA"))
autos = np.isclose(uvd.ant_1_array - uvd.ant_2_array, 0.0)
auto_inds = np.where(autos)[0]
cross_inds = np.where(~autos)[0]
# make auto have non-zero uvw coords, assert ValueError
uvd.uvw_array[auto_inds[0], 0] = 0.1
nt.assert_raises(ValueError, uvd.check)
# make cross have |uvw| zero, assert ValueError
uvd.read_miriad(os.path.join(DATA_PATH, "zen.2457698.40355.xx.HH.uvcA"))
uvd.uvw_array[cross_inds[0]][:] = 0.0
nt.assert_raises(ValueError, uvd.check)
def test_nants_data_telescope(self):
self.uv_object.Nants_data = self.uv_object.Nants_telescope - 1
nt.assert_true(self.uv_object.check)
self.uv_object.Nants_data = self.uv_object.Nants_telescope + 1
nt.assert_raises(ValueError, self.uv_object.check)
def test_converttofiletype(self):
fhd_obj = self.uv_object._convert_to_filetype('fhd')
self.uv_object._convert_from_filetype(fhd_obj)
nt.assert_equal(self.uv_object, self.uv_object2)
nt.assert_raises(
ValueError, self.uv_object._convert_to_filetype, 'foo')
class TestBaselineAntnumMethods(object):
"""Setup for tests on antnum, baseline conversion."""
def setup(self):
self.uv_object = UVData()
self.uv_object.Nants_telescope = 128
self.uv_object2 = UVData()
self.uv_object2.Nants_telescope = 2049
def teardown(self):
"""Test teardown: delete objects."""
del(self.uv_object)
del(self.uv_object2)
def test_baseline_to_antnums(self):
"""Test baseline to antnum conversion for 256 & larger conventions."""
nt.assert_equal(self.uv_object.baseline_to_antnums(67585), (0, 0))
nt.assert_raises(
Exception, self.uv_object2.baseline_to_antnums, 67585)
ant_pairs = [(10, 20), (280, 310)]
for pair in ant_pairs:
if np.max(np.array(pair)) < 255:
bl = self.uv_object.antnums_to_baseline(
pair[0], pair[1], attempt256=True)
ant_pair_out = self.uv_object.baseline_to_antnums(bl)
nt.assert_equal(pair, ant_pair_out)
bl = self.uv_object.antnums_to_baseline(
pair[0], pair[1], attempt256=False)
ant_pair_out = self.uv_object.baseline_to_antnums(bl)
nt.assert_equal(pair, ant_pair_out)
def test_antnums_to_baselines(self):
"""Test antums to baseline conversion for 256 & larger conventions."""
nt.assert_equal(self.uv_object.antnums_to_baseline(0, 0), 67585)
nt.assert_equal(self.uv_object.antnums_to_baseline(257, 256), 594177)
nt.assert_equal(self.uv_object.baseline_to_antnums(594177), (257, 256))
# Check attempt256
nt.assert_equal(self.uv_object.antnums_to_baseline(
0, 0, attempt256=True), 257)
nt.assert_equal(self.uv_object.antnums_to_baseline(257, 256), 594177)
uvtest.checkWarnings(self.uv_object.antnums_to_baseline, [257, 256],
{'attempt256': True}, message='found > 256 antennas')
nt.assert_raises(
Exception, self.uv_object2.antnums_to_baseline, 0, 0)
# check a len-1 array returns as an array
ant1 = np.array([1])
ant2 = np.array([2])
nt.assert_true(isinstance(self.uv_object.antnums_to_baseline(ant1, ant2), np.ndarray))
def test_known_telescopes():
"""Test known_telescopes method returns expected results."""
uv_object = UVData()
known_telescopes = ['PAPER', 'HERA', 'MWA']
nt.assert_equal(known_telescopes.sort(),
uv_object.known_telescopes().sort())
def test_HERA_diameters():
miriad_file = os.path.join(DATA_PATH, 'zen.2456865.60537.xy.uvcRREAA')
uv_in = UVData()
uvtest.checkWarnings(uv_in.read_miriad, [miriad_file],
known_warning='miriad')
uv_in.telescope_name = 'HERA'
uvtest.checkWarnings(uv_in.set_telescope_params, message='antenna_diameters '
'is not set. Using known values for HERA.')
nt.assert_equal(uv_in.telescope_name, 'HERA')
nt.assert_true(uv_in.antenna_diameters is not None)
uv_in.check()
def test_phase_unphaseHERA():
"""
Read in drift data, phase to an RA/DEC, unphase and check for object equality.
"""
testfile = os.path.join(DATA_PATH, 'hera_testfile')
UV_raw = UVData()
# Note the RA/DEC values in the raw file were calculated from the lat/long
# in the file, which don't agree with our known_telescopes.
# So for this test we use the lat/lon in the file.
uvtest.checkWarnings(UV_raw.read_miriad, [testfile], {'correct_lat_lon': False},
message='Altitude is not present in file and latitude and '
'longitude values do not match')
UV_phase = UVData()
uvtest.checkWarnings(UV_phase.read_miriad, [testfile], {'correct_lat_lon': False},
message='Altitude is not present in file and '
'latitude and longitude values do not match')
UV_phase.phase(0., 0., epoch="J2000")
UV_phase.unphase_to_drift()
# check that phase + unphase gets back to raw
nt.assert_equal(UV_raw, UV_phase)
# check that phase + unphase work using gcrs
UV_phase.phase(Angle('5d').rad, Angle('30d').rad, phase_frame='gcrs')
UV_phase.unphase_to_drift()
nt.assert_equal(UV_raw, UV_phase)
# check that phase + unphase work using a different epoch
UV_phase.phase(Angle('180d').rad, Angle('90d'), epoch=Time('2010-01-01T00:00:00', format='isot', scale='utc'))
UV_phase.unphase_to_drift()
nt.assert_equal(UV_raw, UV_phase)
# check that phase + unphase work with one baseline
UV_raw_small = UV_raw.select(blt_inds=[0], inplace=False)
UV_phase_small = copy.deepcopy(UV_raw_small)
UV_phase_small.phase(Angle('23h').rad, Angle('15d').rad)
UV_phase_small.unphase_to_drift()
nt.assert_equal(UV_raw_small, UV_phase_small)
# check that they match if you phase & unphase using antenna locations
# first replace the uvws with the right values
antenna_enu = uvutils.ENU_from_ECEF((UV_raw.antenna_positions + UV_raw.telescope_location),
*UV_raw.telescope_location_lat_lon_alt)
uvw_calc = np.zeros_like(UV_raw.uvw_array)
unique_times, unique_inds = np.unique(UV_raw.time_array, return_index=True)
for ind, jd in enumerate(unique_times):
inds = np.where(UV_raw.time_array == jd)[0]
for bl_ind in inds:
ant1_index = np.where(UV_raw.antenna_numbers == UV_raw.ant_1_array[bl_ind])[0][0]
ant2_index = np.where(UV_raw.antenna_numbers == UV_raw.ant_2_array[bl_ind])[0][0]
uvw_calc[bl_ind, :] = antenna_enu[ant2_index, :] - antenna_enu[ant1_index, :]
UV_raw_new = copy.deepcopy(UV_raw)
UV_raw_new.uvw_array = uvw_calc
UV_phase.phase(0., 0., epoch="J2000", use_ant_pos=True)
UV_phase2 = copy.deepcopy(UV_raw_new)
UV_phase2.phase(0., 0., epoch="J2000")
# The uvw's only agree to ~1mm. should they be better?
nt.assert_true(np.allclose(UV_phase2.uvw_array, UV_phase.uvw_array, atol=1e-3))
# the data array are just multiplied by the w's for phasing, so a difference
# at the 1e-3 level makes the data array different at that level too.
# -> change the tolerance on data_array for this test
UV_phase2._data_array.tols = (0, 1e-3)
nt.assert_equal(UV_phase2, UV_phase)
# check that phase + unphase gets back to raw using antpos
UV_phase.unphase_to_drift(use_ant_pos=True)
nt.assert_equal(UV_raw_new, UV_phase)
# check that phasing to zenith with one timestamp has small changes
# (it won't be identical because of precession/nutation changing the coordinate axes)
# use gcrs rather than icrs to reduce differences (don't include abberation)
UV_raw_small = UV_raw.select(times=UV_raw.time_array[0], inplace=False)
UV_phase_simple_small = copy.deepcopy(UV_raw_small)
UV_phase_simple_small.phase_to_time(time=Time(UV_raw.time_array[0], format='jd'),
phase_frame='gcrs')
# it's unclear to me how close this should be...
nt.assert_true(np.allclose(UV_phase_simple_small.uvw_array, UV_raw_small.uvw_array, atol=1e-2))
# check error if not passing a Time object to phase_to_time
nt.assert_raises(TypeError, UV_raw.phase_to_time, UV_raw.time_array[0])
# check errors when trying to unphase drift or unknown data
nt.assert_raises(ValueError, UV_raw.unphase_to_drift)
UV_raw.set_unknown_phase_type()
nt.assert_raises(ValueError, UV_raw.unphase_to_drift)
UV_raw.set_drift()
# check errors when trying to phase phased or unknown data
UV_phase.phase(0., 0., epoch="J2000")
nt.assert_raises(ValueError, UV_phase.phase, 0., 0., epoch="J2000")
nt.assert_raises(ValueError, UV_phase.phase_to_time,
UV_phase.time_array[0])
UV_phase.set_unknown_phase_type()
nt.assert_raises(ValueError, UV_phase.phase, 0., 0., epoch="J2000")
nt.assert_raises(ValueError, UV_phase.phase_to_time,
UV_phase.time_array[0])
# check errors when trying to phase to an unsupported frame
UV_phase = copy.deepcopy(UV_raw)
nt.assert_raises(ValueError, UV_phase.phase, 0., 0., epoch="J2000", phase_frame='cirs')
del(UV_phase)
del(UV_raw)
def test_phasing():
""" Use MWA files phased to 2 different places to test phasing. """
file1 = os.path.join(DATA_PATH, '1133866760.uvfits')
file2 = os.path.join(DATA_PATH, '1133866760_rephase.uvfits')
uvd1 = UVData()
uvd2 = UVData()
uvd1.read_uvfits(file1)
uvd2.read_uvfits(file2)
uvd1_drift = copy.deepcopy(uvd1)
uvd1_drift.unphase_to_drift(phase_frame='gcrs')
uvd1_drift_antpos = copy.deepcopy(uvd1)
uvd1_drift_antpos.unphase_to_drift(phase_frame='gcrs', use_ant_pos=True)
uvd2_drift = copy.deepcopy(uvd2)
uvd2_drift.unphase_to_drift(phase_frame='gcrs')
uvd2_drift_antpos = copy.deepcopy(uvd2)
uvd2_drift_antpos.unphase_to_drift(phase_frame='gcrs', use_ant_pos=True)
# the tolerances here are empirical -- based on what was seen in the external
# phasing test. See the phasing memo in docs/references for details
nt.assert_true(np.allclose(uvd1_drift.uvw_array, uvd2_drift.uvw_array, atol=2e-2))
nt.assert_true(np.allclose(uvd1_drift_antpos.uvw_array, uvd2_drift_antpos.uvw_array))
uvd2_rephase = copy.deepcopy(uvd2_drift)
uvd2_rephase.phase(uvd1.phase_center_ra,
uvd1.phase_center_dec,
uvd1.phase_center_epoch,
phase_frame='gcrs')
uvd2_rephase_antpos = copy.deepcopy(uvd2_drift_antpos)
uvd2_rephase_antpos.phase(uvd1.phase_center_ra,
uvd1.phase_center_dec,
uvd1.phase_center_epoch,
phase_frame='gcrs',
use_ant_pos=True)
# the tolerances here are empirical -- based on what was seen in the external
# phasing test. See the phasing memo in docs/references for details
nt.assert_true(np.allclose(uvd1.uvw_array, uvd2_rephase.uvw_array, atol=2e-2))
nt.assert_true(np.allclose(uvd1.uvw_array, uvd2_rephase_antpos.uvw_array, atol=5e-3))
# rephase the drift objects to the original pointing and verify that they match
uvd1_drift.phase(uvd1.phase_center_ra, uvd1.phase_center_dec,
uvd1.phase_center_epoch, phase_frame='gcrs')
uvd1_drift_antpos.phase(uvd1.phase_center_ra, uvd1.phase_center_dec,
uvd1.phase_center_epoch, phase_frame='gcrs',
use_ant_pos=True)
# the tolerances here are empirical -- caused by one unphase/phase cycle.
# the antpos-based phasing differences are based on what was seen in the external
# phasing test. See the phasing memo in docs/references for details
nt.assert_true(np.allclose(uvd1.uvw_array, uvd1_drift.uvw_array, atol=1e-4))
nt.assert_true(np.allclose(uvd1.uvw_array, uvd1_drift_antpos.uvw_array, atol=5e-3))
uvd2_drift.phase(uvd2.phase_center_ra, uvd2.phase_center_dec,
uvd2.phase_center_epoch, phase_frame='gcrs')
uvd2_drift_antpos.phase(uvd2.phase_center_ra, uvd2.phase_center_dec,
uvd2.phase_center_epoch, phase_frame='gcrs',
use_ant_pos=True)
# the tolerances here are empirical -- caused by one unphase/phase cycle.
# the antpos-based phasing differences are based on what was seen in the external
# phasing test. See the phasing memo in docs/references for details
nt.assert_true(np.allclose(uvd2.uvw_array, uvd2_drift.uvw_array, atol=1e-4))
nt.assert_true(np.allclose(uvd2.uvw_array, uvd2_drift_antpos.uvw_array, atol=2e-2))
def test_set_phase_unknown():
uv_object = UVData()
testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(uv_object.read_uvfits, [
testfile], message='Telescope EVLA is not')
uv_object.set_unknown_phase_type()
nt.assert_equal(uv_object.phase_type, 'unknown')
nt.assert_false(uv_object._phase_center_epoch.required)
nt.assert_false(uv_object._phase_center_ra.required)
nt.assert_false(uv_object._phase_center_dec.required)
nt.assert_true(uv_object.check())
def test_select_blts():
uv_object = UVData()
testfile = os.path.join(DATA_PATH, 'zen.2456865.60537.xy.uvcRREAA')
uvtest.checkWarnings(uv_object.read_miriad, [testfile],
known_warning='miriad')
old_history = uv_object.history
blt_inds = np.array([172, 182, 132, 227, 144, 44, 16, 104, 385, 134, 326, 140, 116,
218, 178, 391, 111, 276, 274, 308, 38, 64, 317, 76, 239, 246,
34, 39, 83, 184, 208, 60, 374, 295, 118, 337, 261, 21, 375,
396, 355, 187, 95, 122, 186, 113, 260, 264, 156, 13, 228, 291,
302, 72, 137, 216, 299, 341, 207, 256, 223, 250, 268, 147, 73,
32, 142, 383, 221, 203, 258, 286, 324, 265, 170, 236, 8, 275,
304, 117, 29, 167, 15, 388, 171, 82, 322, 248, 160, 85, 66,
46, 272, 328, 323, 152, 200, 119, 359, 23, 363, 56, 219, 257,
11, 307, 336, 289, 136, 98, 37, 163, 158, 80, 125, 40, 298,
75, 320, 74, 57, 346, 121, 129, 332, 238, 93, 18, 330, 339,
381, 234, 176, 22, 379, 199, 266, 100, 90, 292, 205, 58, 222,
350, 109, 273, 191, 368, 88, 101, 65, 155, 2, 296, 306, 398,
369, 378, 254, 67, 249, 102, 348, 392, 20, 28, 169, 262, 269,
287, 86, 300, 143, 177, 42, 290, 284, 123, 189, 175, 97, 340,
242, 342, 331, 282, 235, 344, 63, 115, 78, 30, 226, 157, 133,
71, 35, 212, 333])
selected_data = uv_object.data_array[np.sort(blt_inds), :, :, :]
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(blt_inds=blt_inds)
nt.assert_equal(len(blt_inds), uv_object2.Nblts)
# verify that histories are different
nt.assert_false(uvutils._check_histories(old_history, uv_object2.history))
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific baseline-times using pyuvdata.',
uv_object2.history))
nt.assert_true(np.all(selected_data == uv_object2.data_array))
# check that it also works with higher dimension array
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(blt_inds=blt_inds[np.newaxis, :])
nt.assert_equal(len(blt_inds), uv_object2.Nblts)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific baseline-times using pyuvdata.',
uv_object2.history))
nt.assert_true(np.all(selected_data == uv_object2.data_array))
# check for errors associated with out of bounds indices
nt.assert_raises(ValueError, uv_object.select, blt_inds=np.arange(-10, -5))
nt.assert_raises(ValueError, uv_object.select, blt_inds=np.arange(
uv_object.Nblts + 1, uv_object.Nblts + 10))
def test_select_antennas():
uv_object = UVData()
testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(uv_object.read_uvfits, [testfile],
message='Telescope EVLA is not')
old_history = uv_object.history
unique_ants = np.unique(
uv_object.ant_1_array.tolist() + uv_object.ant_2_array.tolist())
ants_to_keep = np.array([0, 19, 11, 24, 3, 23, 1, 20, 21])
blts_select = [(a1 in ants_to_keep) & (a2 in ants_to_keep) for (a1, a2) in
zip(uv_object.ant_1_array, uv_object.ant_2_array)]
Nblts_selected = np.sum(blts_select)
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(antenna_nums=ants_to_keep)
nt.assert_equal(len(ants_to_keep), uv_object2.Nants_data)
nt.assert_equal(Nblts_selected, uv_object2.Nblts)
for ant in ants_to_keep:
nt.assert_true(
ant in uv_object2.ant_1_array or ant in uv_object2.ant_2_array)
for ant in np.unique(uv_object2.ant_1_array.tolist() + uv_object2.ant_2_array.tolist()):
nt.assert_true(ant in ants_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific antennas using pyuvdata.',
uv_object2.history))
# check that it also works with higher dimension array
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(antenna_nums=ants_to_keep[np.newaxis, :])
nt.assert_equal(len(ants_to_keep), uv_object2.Nants_data)
nt.assert_equal(Nblts_selected, uv_object2.Nblts)
for ant in ants_to_keep:
nt.assert_true(
ant in uv_object2.ant_1_array or ant in uv_object2.ant_2_array)
for ant in np.unique(uv_object2.ant_1_array.tolist() + uv_object2.ant_2_array.tolist()):
nt.assert_true(ant in ants_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific antennas using pyuvdata.',
uv_object2.history))
# now test using antenna_names to specify antennas to keep
uv_object3 = copy.deepcopy(uv_object)
ants_to_keep = np.array(sorted(list(ants_to_keep)))
ant_names = []
for a in ants_to_keep:
ind = np.where(uv_object3.antenna_numbers == a)[0][0]
ant_names.append(uv_object3.antenna_names[ind])
uv_object3.select(antenna_names=ant_names)
nt.assert_equal(uv_object2, uv_object3)
# check that it also works with higher dimension array
uv_object3 = copy.deepcopy(uv_object)
ants_to_keep = np.array(sorted(list(ants_to_keep)))
ant_names = []
for a in ants_to_keep:
ind = np.where(uv_object3.antenna_numbers == a)[0][0]
ant_names.append(uv_object3.antenna_names[ind])
uv_object3.select(antenna_names=[ant_names])
nt.assert_equal(uv_object2, uv_object3)
# check for errors associated with antennas not included in data, bad names or providing numbers and names
nt.assert_raises(ValueError, uv_object.select,
antenna_nums=np.max(unique_ants) + np.arange(1, 3))
nt.assert_raises(ValueError, uv_object.select, antenna_names='test1')
nt.assert_raises(ValueError, uv_object.select,
antenna_nums=ants_to_keep, antenna_names=ant_names)
def sort_bl(p):
"""Sort a tuple that starts with a pair of antennas, and may have stuff after."""
if p[1] >= p[0]:
return p
return (p[1], p[0]) + p[2:]
def test_select_bls():
uv_object = UVData()
testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(uv_object.read_uvfits, [testfile],
message='Telescope EVLA is not')
old_history = uv_object.history
first_ants = [6, 2, 7, 2, 21, 27, 8]
second_ants = [0, 20, 8, 1, 2, 3, 22]
new_unique_ants = np.unique(first_ants + second_ants)
ant_pairs_to_keep = list(zip(first_ants, second_ants))
sorted_pairs_to_keep = [sort_bl(p) for p in ant_pairs_to_keep]
sorted_pairs_object = [sort_bl(p) for p in zip(
uv_object.ant_1_array, uv_object.ant_2_array)]
blts_select = [sort_bl((a1, a2)) in sorted_pairs_to_keep for (a1, a2) in
zip(uv_object.ant_1_array, uv_object.ant_2_array)]
Nblts_selected = np.sum(blts_select)
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(bls=ant_pairs_to_keep)
sorted_pairs_object2 = [sort_bl(p) for p in zip(
uv_object2.ant_1_array, uv_object2.ant_2_array)]
nt.assert_equal(len(new_unique_ants), uv_object2.Nants_data)
nt.assert_equal(Nblts_selected, uv_object2.Nblts)
for ant in new_unique_ants:
nt.assert_true(
ant in uv_object2.ant_1_array or ant in uv_object2.ant_2_array)
for ant in np.unique(uv_object2.ant_1_array.tolist() + uv_object2.ant_2_array.tolist()):
nt.assert_true(ant in new_unique_ants)
for pair in sorted_pairs_to_keep:
nt.assert_true(pair in sorted_pairs_object2)
for pair in sorted_pairs_object2:
nt.assert_true(pair in sorted_pairs_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific baselines using pyuvdata.',
uv_object2.history))
# check select with polarizations
first_ants = [6, 2, 7, 2, 21, 27, 8]
second_ants = [0, 20, 8, 1, 2, 3, 22]
pols = ['RR', 'RR', 'RR', 'RR', 'RR', 'RR', 'RR']
new_unique_ants = np.unique(first_ants + second_ants)
bls_to_keep = list(zip(first_ants, second_ants, pols))
sorted_bls_to_keep = [sort_bl(p) for p in bls_to_keep]
sorted_pairs_object = [sort_bl(p) for p in zip(
uv_object.ant_1_array, uv_object.ant_2_array)]
blts_select = [sort_bl((a1, a2, 'RR')) in sorted_bls_to_keep for (a1, a2) in
zip(uv_object.ant_1_array, uv_object.ant_2_array)]
Nblts_selected = np.sum(blts_select)
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(bls=bls_to_keep)
sorted_pairs_object2 = [sort_bl(p) + ('RR',) for p in zip(
uv_object2.ant_1_array, uv_object2.ant_2_array)]
nt.assert_equal(len(new_unique_ants), uv_object2.Nants_data)
nt.assert_equal(Nblts_selected, uv_object2.Nblts)
for ant in new_unique_ants:
nt.assert_true(
ant in uv_object2.ant_1_array or ant in uv_object2.ant_2_array)
for ant in np.unique(uv_object2.ant_1_array.tolist() + uv_object2.ant_2_array.tolist()):
nt.assert_true(ant in new_unique_ants)
for bl in sorted_bls_to_keep:
nt.assert_true(bl in sorted_pairs_object2)
for bl in sorted_pairs_object2:
nt.assert_true(bl in sorted_bls_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific baselines, polarizations using pyuvdata.',
uv_object2.history))
# check that you can use numpy integers with out errors:
first_ants = list(map(np.int32, [6, 2, 7, 2, 21, 27, 8]))
second_ants = list(map(np.int32, [0, 20, 8, 1, 2, 3, 22]))
ant_pairs_to_keep = list(zip(first_ants, second_ants))
uv_object2 = uv_object.select(bls=ant_pairs_to_keep, inplace=False)
sorted_pairs_object2 = [sort_bl(p) for p in zip(
uv_object2.ant_1_array, uv_object2.ant_2_array)]
nt.assert_equal(len(new_unique_ants), uv_object2.Nants_data)
nt.assert_equal(Nblts_selected, uv_object2.Nblts)
for ant in new_unique_ants:
nt.assert_true(
ant in uv_object2.ant_1_array or ant in uv_object2.ant_2_array)
for ant in np.unique(uv_object2.ant_1_array.tolist() + uv_object2.ant_2_array.tolist()):
nt.assert_true(ant in new_unique_ants)
for pair in sorted_pairs_to_keep:
nt.assert_true(pair in sorted_pairs_object2)
for pair in sorted_pairs_object2:
nt.assert_true(pair in sorted_pairs_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific baselines using pyuvdata.',
uv_object2.history))
# check that you can specify a single pair without errors
uv_object2.select(bls=(0, 6))
sorted_pairs_object2 = [sort_bl(p) for p in zip(
uv_object2.ant_1_array, uv_object2.ant_2_array)]
nt.assert_equal(list(set(sorted_pairs_object2)), [(0, 6)])
# check for errors associated with antenna pairs not included in data and bad inputs
nt.assert_raises(ValueError, uv_object.select,
bls=list(zip(first_ants, second_ants)) + [0, 6])
nt.assert_raises(ValueError, uv_object.select,
bls=[(uv_object.antenna_names[0], uv_object.antenna_names[1])])
nt.assert_raises(ValueError, uv_object.select, bls=(5, 1))
nt.assert_raises(ValueError, uv_object.select, bls=(0, 5))
nt.assert_raises(ValueError, uv_object.select, bls=(27, 27))
nt.assert_raises(ValueError, uv_object.select, bls=(6, 0, 'RR'), polarizations='RR')
nt.assert_raises(ValueError, uv_object.select, bls=(6, 0, 8))
def test_select_times():
uv_object = UVData()
testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(uv_object.read_uvfits, [testfile],
message='Telescope EVLA is not')
old_history = uv_object.history
unique_times = np.unique(uv_object.time_array)
times_to_keep = unique_times[[0, 3, 5, 6, 7, 10, 14]]
Nblts_selected = np.sum([t in times_to_keep for t in uv_object.time_array])
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(times=times_to_keep)
nt.assert_equal(len(times_to_keep), uv_object2.Ntimes)
nt.assert_equal(Nblts_selected, uv_object2.Nblts)
for t in times_to_keep:
nt.assert_true(t in uv_object2.time_array)
for t in np.unique(uv_object2.time_array):
nt.assert_true(t in times_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific times using pyuvdata.',
uv_object2.history))
# check that it also works with higher dimension array
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(times=times_to_keep[np.newaxis, :])
nt.assert_equal(len(times_to_keep), uv_object2.Ntimes)
nt.assert_equal(Nblts_selected, uv_object2.Nblts)
for t in times_to_keep:
nt.assert_true(t in uv_object2.time_array)
for t in np.unique(uv_object2.time_array):
nt.assert_true(t in times_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific times using pyuvdata.',
uv_object2.history))
# check for errors associated with times not included in data
nt.assert_raises(ValueError, uv_object.select, times=[
np.min(unique_times) - uv_object.integration_time])
def test_select_frequencies():
uv_object = UVData()
testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(uv_object.read_uvfits, [testfile],
message='Telescope EVLA is not')
old_history = uv_object.history
freqs_to_keep = uv_object.freq_array[0, np.arange(12, 22)]
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(frequencies=freqs_to_keep)
nt.assert_equal(len(freqs_to_keep), uv_object2.Nfreqs)
for f in freqs_to_keep:
nt.assert_true(f in uv_object2.freq_array)
for f in np.unique(uv_object2.freq_array):
nt.assert_true(f in freqs_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific frequencies using pyuvdata.',
uv_object2.history))
# check that it also works with higher dimension array
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(frequencies=freqs_to_keep[np.newaxis, :])
nt.assert_equal(len(freqs_to_keep), uv_object2.Nfreqs)
for f in freqs_to_keep:
nt.assert_true(f in uv_object2.freq_array)
for f in np.unique(uv_object2.freq_array):
nt.assert_true(f in freqs_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific frequencies using pyuvdata.',
uv_object2.history))
# check that selecting one frequency works
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(frequencies=freqs_to_keep[0])
nt.assert_equal(1, uv_object2.Nfreqs)
nt.assert_true(freqs_to_keep[0] in uv_object2.freq_array)
for f in uv_object2.freq_array:
nt.assert_true(f in [freqs_to_keep[0]])
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific frequencies using pyuvdata.',
uv_object2.history))
# check for errors associated with frequencies not included in data
nt.assert_raises(ValueError, uv_object.select, frequencies=[
np.max(uv_object.freq_array) + uv_object.channel_width])
# check for warnings and errors associated with unevenly spaced or non-contiguous frequencies
uv_object2 = copy.deepcopy(uv_object)
uvtest.checkWarnings(uv_object2.select, [], {'frequencies': uv_object2.freq_array[0, [0, 5, 6]]},
message='Selected frequencies are not evenly spaced')
write_file_uvfits = os.path.join(DATA_PATH, 'test/select_test.uvfits')
write_file_miriad = os.path.join(DATA_PATH, 'test/select_test.uv')
nt.assert_raises(ValueError, uv_object2.write_uvfits, write_file_uvfits)
nt.assert_raises(ValueError, uv_object2.write_miriad, write_file_miriad)
uv_object2 = copy.deepcopy(uv_object)
uvtest.checkWarnings(uv_object2.select, [], {'frequencies': uv_object2.freq_array[0, [0, 2, 4]]},
message='Selected frequencies are not contiguous')
nt.assert_raises(ValueError, uv_object2.write_uvfits, write_file_uvfits)
nt.assert_raises(ValueError, uv_object2.write_miriad, write_file_miriad)
def test_select_freq_chans():
uv_object = UVData()
testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(uv_object.read_uvfits, [testfile],
message='Telescope EVLA is not')
old_history = uv_object.history
chans_to_keep = np.arange(12, 22)
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(freq_chans=chans_to_keep)
nt.assert_equal(len(chans_to_keep), uv_object2.Nfreqs)
for chan in chans_to_keep:
nt.assert_true(uv_object.freq_array[0, chan] in uv_object2.freq_array)
for f in np.unique(uv_object2.freq_array):
nt.assert_true(f in uv_object.freq_array[0, chans_to_keep])
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific frequencies using pyuvdata.',
uv_object2.history))
# check that it also works with higher dimension array
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(freq_chans=chans_to_keep[np.newaxis, :])
nt.assert_equal(len(chans_to_keep), uv_object2.Nfreqs)
for chan in chans_to_keep:
nt.assert_true(uv_object.freq_array[0, chan] in uv_object2.freq_array)
for f in np.unique(uv_object2.freq_array):
nt.assert_true(f in uv_object.freq_array[0, chans_to_keep])
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific frequencies using pyuvdata.',
uv_object2.history))
# Test selecting both channels and frequencies
freqs_to_keep = uv_object.freq_array[0, np.arange(
20, 30)] # Overlaps with chans
all_chans_to_keep = np.arange(12, 30)
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(frequencies=freqs_to_keep, freq_chans=chans_to_keep)
nt.assert_equal(len(all_chans_to_keep), uv_object2.Nfreqs)
for chan in all_chans_to_keep:
nt.assert_true(uv_object.freq_array[0, chan] in uv_object2.freq_array)
for f in np.unique(uv_object2.freq_array):
nt.assert_true(f in uv_object.freq_array[0, all_chans_to_keep])
def test_select_polarizations():
uv_object = UVData()
testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(uv_object.read_uvfits, [testfile],
message='Telescope EVLA is not')
old_history = uv_object.history
pols_to_keep = [-1, -2]
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(polarizations=pols_to_keep)
nt.assert_equal(len(pols_to_keep), uv_object2.Npols)
for p in pols_to_keep:
nt.assert_true(p in uv_object2.polarization_array)
for p in np.unique(uv_object2.polarization_array):
nt.assert_true(p in pols_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific polarizations using pyuvdata.',
uv_object2.history))
# check that it also works with higher dimension array
uv_object2 = copy.deepcopy(uv_object)
uv_object2.select(polarizations=[pols_to_keep])
nt.assert_equal(len(pols_to_keep), uv_object2.Npols)
for p in pols_to_keep:
nt.assert_true(p in uv_object2.polarization_array)
for p in np.unique(uv_object2.polarization_array):
nt.assert_true(p in pols_to_keep)
nt.assert_true(uvutils._check_histories(old_history + ' Downselected to '
'specific polarizations using pyuvdata.',
uv_object2.history))
# check for errors associated with polarizations not included in data
nt.assert_raises(ValueError, uv_object2.select, polarizations=[-3, -4])
# check for warnings and errors associated with unevenly spaced polarizations
uvtest.checkWarnings(uv_object.select, [], {'polarizations': uv_object.polarization_array[[0, 1, 3]]},
message='Selected polarization values are not evenly spaced')
write_file_uvfits = os.path.join(DATA_PATH, 'test/select_test.uvfits')
nt.assert_raises(ValueError, uv_object.write_uvfits, write_file_uvfits)
def test_select():
# now test selecting along all axes at once
uv_object = UVData()
testfile = os.path.join(
DATA_PATH, 'day2_TDEM0003_10s_norx_1src_1spw.uvfits')
uvtest.checkWarnings(uv_object.read_uvfits, [testfile],
message='Telescope EVLA is not')
old_history = uv_object.history
blt_inds = np.array([1057, 461, 1090, 354, 528, 654, 882, 775, 369, 906, 748,
875, 296, 773, 554, 395, 1003, 476, 762, 976, 1285, 874,
717, 383, 1281, 924, 264, 1163, 297, 857, 1258, 1000, 180,
1303, 1139, 393, 42, 135, 789, 713, 527, 1218, 576, 100,
1311, 4, 653, 724, 591, 889, 36, 1033, 113, 479, 322,
118, 898, 1263, 477, 96, 935, 238, 195, 531, 124, 198,
992, 1131, 305, 154, 961, 6, 1175, 76, 663, 82, 637,
288, 1152, 845, 1290, 379, 1225, 1240, 733, 1172, 937, 1325,