https://github.com/RadioAstronomySoftwareGroup/pyuvdata
Tip revision: 7e2f55193ae0a91039060ff4976ed3419bf7310c authored by Bryna Hazelton on 21 December 2021, 17:40:05 UTC
update the changelog for v2.2.5
update the changelog for v2.2.5
Tip revision: 7e2f551
test_mwa_corr_fits.py
# -*- mode: python; coding: utf-8 -*-
# Copyright (c) 2019 Radio Astronomy Software Group
# Licensed under the 2-clause BSD License
"""Tests for MWACorrFITS object."""
import pytest
import os
import h5py
import itertools
import numpy as np
from pyuvdata import UVData
from pyuvdata.data import DATA_PATH
import pyuvdata.tests as uvtest
from pyuvdata.uvdata.mwa_corr_fits import input_output_mapping
from astropy.io import fits
# set up MWA correlator file list
testdir = os.path.join(DATA_PATH, "mwa_corr_fits_testfiles/")
testfiles = [
"1131733552.metafits",
"1131733552_20151116182537_mini_gpubox01_00.fits",
"1131733552_20151116182637_mini_gpubox06_01.fits",
"1131733552_mini_01.mwaf",
"1131733552_mini_06.mwaf",
"1131733552_mod.metafits",
"1131733552_mini_cotter.uvfits",
"1131733552_metafits_ppds.fits",
"1061315448_20130823175130_mini_gpubox07_01.fits",
"1061315448.metafits",
"1061315448_20130823175130_mini_vv_07_01.uvh5",
"1320409688.metafits",
"1320409688_20211108122750_mini_ch137_000.fits",
]
filelist = [os.path.join(testdir, filei) for filei in testfiles]
@pytest.fixture(scope="module")
def flag_file_init(tmp_path_factory):
tmp_path = tmp_path_factory.mktemp("pyuvdata_corr_fits", numbered=True)
spoof_file1 = str(tmp_path / "spoof_01_00.fits")
spoof_file6 = str(tmp_path / "spoof_06_00.fits")
# spoof box files of the appropriate size
with fits.open(filelist[1]) as mini1:
mini1[1].data = np.repeat(mini1[1].data, 8, axis=0)
extra_dat = np.copy(mini1[1].data)
for app_ind in range(2):
mini1.append(fits.ImageHDU(extra_dat))
mini1[2].header["MILLITIM"] = 500
mini1[2].header["TIME"] = mini1[1].header["TIME"]
mini1[3].header["MILLITIM"] = 0
mini1[3].header["TIME"] = mini1[1].header["TIME"] + 1
mini1.writeto(spoof_file1)
with fits.open(filelist[2]) as mini6:
mini6[1].data = np.repeat(mini6[1].data, 8, axis=0)
extra_dat = np.copy(mini6[1].data)
for app_ind in range(2):
mini6.append(fits.ImageHDU(extra_dat))
mini6[2].header["MILLITIM"] = 500
mini6[2].header["TIME"] = mini6[1].header["TIME"]
mini6[3].header["MILLITIM"] = 0
mini6[3].header["TIME"] = mini6[1].header["TIME"] + 1
mini6.writeto(spoof_file6)
flag_testfiles = [spoof_file1, spoof_file6, filelist[0]]
yield flag_testfiles
def test_read_mwa_write_uvfits(tmp_path):
"""
MWA correlator fits to uvfits loopback test.
Read in MWA correlator files, write out as uvfits, read back in and check
for object equality.
"""
mwa_uv = UVData()
uvfits_uv = UVData()
messages = [
"some coarse channel files were not submitted",
]
with uvtest.check_warnings(UserWarning, messages):
mwa_uv.read_mwa_corr_fits(
filelist[0:2], correct_cable_len=True, phase_to_pointing_center=True
)
testfile = str(tmp_path / "outtest_MWAcorr.uvfits")
mwa_uv.write_uvfits(testfile, spoof_nonessential=True)
uvfits_uv.read_uvfits(testfile)
# make sure filenames are what we expect
assert set(mwa_uv.filename) == {
"1131733552.metafits",
"1131733552_20151116182537_mini_gpubox01_00.fits",
}
assert uvfits_uv.filename == ["outtest_MWAcorr.uvfits"]
mwa_uv.filename = uvfits_uv.filename
mwa_uv._filename.form = (1,)
assert mwa_uv == uvfits_uv
@pytest.mark.filterwarnings("ignore:antnums_to_baseline")
@pytest.mark.filterwarnings("ignore:Found antenna numbers > 256 in this data")
def test_read_mwax_write_uvfits(tmp_path):
"""
MWAX correlator fits to uvfits loopback test.
Read in MWAX correlator files, write out as uvfits, read back in and check
for object equality.
"""
# spoof testfile to contain 2 times and 2 freqs
spoof_file = str(tmp_path / "mwax_spoof_ch137_000.fits")
with fits.open(filelist[12]) as mini1:
mini1[0].header["NFINECHS"] = 2
mini1[1].data = np.repeat(mini1[1].data, 2, axis=1)
mini1[2].data = np.repeat(mini1[2].data, 2, axis=1)
extra_dat = np.copy(mini1[1].data)
extra_samps = np.copy(mini1[2].data)
# mini1.append(fits.HDUList([mini1[1], mini1[2]]))
mini1.append(fits.ImageHDU(extra_dat))
mini1.append(fits.ImageHDU(extra_samps))
mini1[3].header["TIME"] = 1636374472
mini1[4].header["TIME"] = 1636374472
mini1[3].header["MILLITIM"] = 0
mini1[4].header["MILLITIM"] = 0
mini1.writeto(spoof_file)
mwax_uv = UVData()
uvfits_uv = UVData()
messages = [
"some coarse channel files were not submitted",
]
with uvtest.check_warnings(UserWarning, messages):
mwax_uv.read_mwa_corr_fits(
[spoof_file, filelist[11]],
correct_cable_len=True,
phase_to_pointing_center=True,
)
testfile = str(tmp_path / "outtest_MWAXcorr.uvfits")
mwax_uv.write_uvfits(testfile, spoof_nonessential=True)
uvfits_uv.read_uvfits(testfile)
assert mwax_uv == uvfits_uv
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_mwax_metafits_keys(tmp_path):
"""Check that mwax keywords are removed from extra_keywords for legacy files"""
meta_spoof_file = str(tmp_path / "spoof_1131733552.metafits")
with fits.open(filelist[0]) as meta:
meta[0].header["DELAYMOD"] = None
meta.writeto(meta_spoof_file)
uv = UVData()
uv.read([meta_spoof_file, filelist[1]])
assert "DELAYMOD" not in uv.extra_keywords.keys()
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_select_on_read():
mwa_uv = UVData()
mwa_uv2 = UVData()
mwa_uv.read_mwa_corr_fits(filelist[0:2], correct_cable_len=True)
unique_times = np.unique(mwa_uv.time_array)
select_times = unique_times[
np.where(
(unique_times >= np.min(mwa_uv.time_array))
& (unique_times <= np.mean(mwa_uv.time_array))
)
]
mwa_uv.select(times=select_times)
with uvtest.check_warnings(
UserWarning,
[
'Warning: select on read keyword set, but file_type is "mwa_corr_fits"',
"some coarse channel files were not submitted",
],
):
mwa_uv2.read(
filelist[0:2],
correct_cable_len=True,
time_range=[np.min(mwa_uv.time_array), np.mean(mwa_uv.time_array)],
)
assert mwa_uv == mwa_uv2
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
def test_read_mwa_read_cotter():
"""
Pyuvdata and cotter equality test.
Read in MWA correlator files and the corresponding cotter file and check
for data array equality.
"""
mwa_uv = UVData()
cotter_uv = UVData()
# cotter data has cable correction and is unphased
mwa_uv.read(
filelist[0:2],
correct_cable_len=True,
remove_dig_gains=False,
remove_coarse_band=False,
remove_flagged_ants=False,
)
cotter_uv.read(filelist[6])
# cotter doesn't record the auto xy polarizations
# due to a possible bug in cotter, the auto yx polarizations are conjugated
# fix these before testing data_array
autos = np.isclose(mwa_uv.ant_1_array - mwa_uv.ant_2_array, 0.0)
cotter_uv.data_array[autos, :, :, 2] = cotter_uv.data_array[autos, :, :, 3]
cotter_uv.data_array[autos, :, :, 3] = np.conj(cotter_uv.data_array[autos, :, :, 3])
assert np.allclose(
mwa_uv.data_array[:, :, :, :],
cotter_uv.data_array[:, :, :, :],
atol=1e-4,
rtol=0,
)
assert mwa_uv.freq_array == cotter_uv.freq_array
def test_read_mwa_write_uvfits_meta_mod(tmp_path):
"""
MWA correlator fits to uvfits loopback test with a modified metafits file.
Read in MWA correlator files, write out as uvfits, read back in and check
for object equality.
"""
# The metafits file has been modified to contain some coarse channels < 129,
# and to have an uncorrected cable length.
mwa_uv = UVData()
uvfits_uv = UVData()
messages = [
"some coarse channel files were not submitted",
]
files = [filelist[1], filelist[5]]
with uvtest.check_warnings(UserWarning, messages):
mwa_uv.read(files, correct_cable_len=True, phase_to_pointing_center=True)
testfile = str(tmp_path / "outtest_MWAcorr.uvfits")
mwa_uv.write_uvfits(testfile, spoof_nonessential=True)
uvfits_uv.read_uvfits(testfile)
# make sure filenames are what we expect
assert set(mwa_uv.filename) == {
"1131733552_20151116182537_mini_gpubox01_00.fits",
"1131733552_mod.metafits",
}
assert uvfits_uv.filename == ["outtest_MWAcorr.uvfits"]
mwa_uv.filename = uvfits_uv.filename
mwa_uv._filename.form = (1,)
assert mwa_uv == uvfits_uv
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:Combined frequencies are separated by more than")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_read_mwa_multi():
"""Test reading in two sets of files."""
set1 = filelist[0:2]
set2 = [filelist[0], filelist[2]]
mwa_uv = UVData()
mwa_uv.read([set1, set2])
mwa_uv2 = UVData()
messages = [
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
"Combined frequencies are separated by more than their channel width",
]
with uvtest.check_warnings(UserWarning, messages):
mwa_uv2.read([set1, set2], file_type="mwa_corr_fits")
assert mwa_uv == mwa_uv2
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:Combined frequencies are separated by more than")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_read_mwa_multi_concat(tmp_path):
"""Test reading in two sets of files with fast concatenation."""
# modify file so that time arrays are matching
mod_mini_6 = str(tmp_path / "mini_gpubox06_01.fits")
with fits.open(filelist[2]) as mini6:
mini6[1].header["time"] = 1447698337
mini6.writeto(mod_mini_6)
set1 = filelist[0:2]
set2 = [filelist[0], mod_mini_6]
mwa_uv = UVData()
mwa_uv.read([set1, set2], axis="freq")
mwa_uv2 = UVData()
messages = [
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
"Combined frequencies are separated by more than their channel width",
]
with uvtest.check_warnings(UserWarning, messages):
mwa_uv2.read([set1, set2], axis="freq", file_type="mwa_corr_fits")
assert mwa_uv == mwa_uv2
os.remove(mod_mini_6)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
def test_read_mwa_flags():
"""Test handling of flag files."""
mwa_uv = UVData()
subfiles = [filelist[0], filelist[1], filelist[3], filelist[4]]
messages = [
"mwaf files submitted with use_aoflagger_flags=False",
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
]
with uvtest.check_warnings(UserWarning, messages):
mwa_uv.read(subfiles, use_aoflagger_flags=False)
del mwa_uv
mwa_uv = UVData()
with pytest.raises(ValueError) as cm:
mwa_uv.read(subfiles[0:2], use_aoflagger_flags=True)
assert str(cm.value).startswith("no flag files submitted")
del mwa_uv
def test_multiple_coarse():
"""
Test two coarse channel files.
Read in MWA correlator files with two different orderings of the files
and check for object equality.
"""
order1 = filelist[0:3]
order2 = [filelist[0], filelist[2], filelist[1]]
mwa_uv1 = UVData()
mwa_uv2 = UVData()
messages = [
"coarse channels are not contiguous for this observation",
"some coarse channel files were not submitted",
"cable length correction is now defaulted to True",
]
with uvtest.check_warnings(UserWarning, messages):
mwa_uv1.read(order1)
with uvtest.check_warnings(UserWarning, messages):
mwa_uv2.read(order2)
assert mwa_uv1 == mwa_uv2
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_ppds(tmp_path):
"""Test handling of ppds files"""
# turnaround test with just ppds file given
mwa_uv = UVData()
mwa_uv.read_mwa_corr_fits(
[filelist[1], filelist[7]], phase_to_pointing_center=True, flag_init=False
)
testfile = str(tmp_path / "outtest_MWAcorr.uvfits")
mwa_uv.write_uvfits(testfile, spoof_nonessential=True)
uvfits_uv = UVData()
uvfits_uv.read_uvfits(testfile)
# make sure filenames are what we expect
assert set(mwa_uv.filename) == {
"1131733552_20151116182537_mini_gpubox01_00.fits",
"1131733552_metafits_ppds.fits",
}
assert uvfits_uv.filename == ["outtest_MWAcorr.uvfits"]
mwa_uv.filename = uvfits_uv.filename
mwa_uv._filename.form = (1,)
assert mwa_uv == uvfits_uv
del mwa_uv
del uvfits_uv
# check that extra keywords are added when both ppds file and metafits file given
mwa_uv = UVData()
mwa_uv.read_mwa_corr_fits([filelist[0], filelist[1], filelist[7]])
assert "MWAVER" in mwa_uv.extra_keywords and "MWADATE" in mwa_uv.extra_keywords
def test_fine_channels(tmp_path):
"""
Break read_mwa_corr_fits by submitting files with different fine channels.
Test that error is raised if files with different numbers of fine channels
are submitted.
"""
mwa_uv = UVData()
bad_fine = str(tmp_path / "bad_gpubox06_01.fits")
with fits.open(filelist[2]) as mini6:
mini6[1].data = np.concatenate((mini6[1].data, mini6[1].data))
mini6.writeto(bad_fine)
with pytest.raises(ValueError) as cm:
mwa_uv.read([bad_fine, filelist[1]])
assert str(cm.value).startswith("files submitted have different numbers")
del mwa_uv
def test_fine_channels_mwax(tmp_path):
"""
Break read_mwa_corr_fits by submitting mwax files with different fine channels.
Test that error is raised if files with different numbers of fine channels
are submitted.
"""
mwax_uv = UVData()
bad_fine = str(tmp_path / "bad_ch137_000.fits.fits")
with fits.open(filelist[12]) as mini:
mini[1].data = np.repeat(mini[1].data, 2, axis=1)
mini[2].data = np.repeat(mini[2].data, 2, axis=1)
mini[0].header["NFINECHS"] = 2
mini.writeto(bad_fine)
with pytest.raises(ValueError) as cm:
mwax_uv.read([bad_fine, filelist[12]])
assert str(cm.value).startswith("files submitted have different numbers")
del mwax_uv
@pytest.mark.parametrize(
"files,err_msg",
[
([filelist[0]], "no data files submitted"),
([filelist[1]], "no metafits file submitted"),
(
[filelist[0], filelist[1], filelist[5]],
"multiple metafits files in filelist",
),
],
)
def test_break_read_mwacorrfits(files, err_msg):
"""Break read_mwa_corr_fits by submitting files incorrectly."""
mwa_uv = UVData()
with pytest.raises(ValueError) as cm:
mwa_uv.read(files)
assert str(cm.value).startswith(err_msg)
del mwa_uv
def test_file_extension(tmp_path):
"""
Break read_mwa_corr_fits by submitting file with the wrong extension.
Test that error is raised if a file with an extension that is not fits,
metafits, or mwaf is submitted.
"""
mwa_uv = UVData()
bad_ext = str(tmp_path / "1131733552.meta")
with fits.open(filelist[0]) as meta:
meta.writeto(bad_ext)
with pytest.raises(ValueError) as cm:
mwa_uv.read(bad_ext, file_type="mwa_corr_fits")
assert str(cm.value).startswith("only fits, metafits, and mwaf files supported")
del mwa_uv
def test_diff_obs(tmp_path):
"""
Break read_mwa_corr_fits by submitting files from different observations.
Test that error is raised if files from different observations are
submitted in the same file list.
"""
mwa_uv = UVData()
bad_obs = str(tmp_path / "bad2_gpubox06_01.fits")
with fits.open(filelist[2]) as mini6:
mini6[0].header["OBSID"] = "1131733555"
mini6.writeto(bad_obs)
with pytest.raises(ValueError) as cm:
mwa_uv.read([bad_obs, filelist[0], filelist[1]])
assert str(cm.value).startswith("files from different observations")
del mwa_uv
def test_misaligned_times(tmp_path):
"""
Break read_mwa_corr_fits by submitting files with misaligned times.
Test that error is raised if file start times are different by an amount
that is not an integer multiiple of the integration time.
"""
mwa_uv = UVData()
bad_obs = str(tmp_path / "bad3_gpubox06_01.fits")
with fits.open(filelist[2]) as mini6:
mini6[1].header["MILLITIM"] = 250
mini6.writeto(bad_obs)
with pytest.raises(ValueError) as cm:
mwa_uv.read([bad_obs, filelist[0], filelist[1]])
assert str(cm.value).startswith("coarse channel start times are misaligned")
del mwa_uv
@pytest.mark.filterwarnings(
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_flag_nsample_basic():
"""
Test that the flag(without flag_int) and nsample arrays correctly reflect data.
"""
uv = UVData()
uv.read_mwa_corr_fits(
filelist[0:3],
flag_init=False,
propagate_coarse_flags=False,
remove_flagged_ants=False,
)
# check that only bad antennas are flagged for all times, freqs, pols
bad_ants = [59, 114]
good_ants = np.delete(np.unique(uv.ant_1_array), bad_ants)
bad = uv.select(antenna_nums=np.unique(uv.ant_1_array)[bad_ants], inplace=False)
good = uv.select(antenna_nums=good_ants, inplace=False)
assert np.all(bad.flag_array)
good.flag_array = good.flag_array.reshape(
(good.Ntimes, good.Nbls, good.Nfreqs, good.Npols)
)
# good ants should be flagged except for the first time and second freq,
# and for the second time and first freq
assert np.all(good.flag_array[1:-1, :, :, :])
assert np.all(good.flag_array[0, :, 1, :] == 0)
assert np.all(good.flag_array[-1, :, 0, :] == 0)
assert np.all(good.flag_array[0, :, 0, :])
assert np.all(good.flag_array[-1, :, 1, :])
# check that nsample array is filled properly
uv.nsample_array = uv.nsample_array.reshape(
(uv.Ntimes, uv.Nbls, uv.Nfreqs, uv.Npols)
)
assert np.all(uv.nsample_array[1:-1, :, :, :] == 0.0)
assert np.all(uv.nsample_array[0, :, 1, :] == 1.0)
assert np.all(uv.nsample_array[-1, :, 0, :] == 1.0)
assert np.all(uv.nsample_array[0, :, 0, :] == 0.0)
assert np.all(uv.nsample_array[-1, :, 1, :] == 0.0)
@pytest.mark.filterwarnings(
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_flag_init(flag_file_init):
"""
Test that routine MWA flagging works as intended.
"""
uv = UVData()
uv.read(
flag_file_init,
flag_init=True,
start_flag=0,
end_flag=0,
propagate_coarse_flags=False,
)
freq_inds = [0, 1, 4, 6, 7, 8, 9, 12, 14, 15]
freq_inds_complement = [ind for ind in range(16) if ind not in freq_inds]
assert np.all(
uv.flag_array[:, :, freq_inds, :]
), "Not all of edge and center channels are flagged!"
assert not np.any(
np.all(uv.flag_array[:, :, freq_inds_complement, :], axis=(0, 1, -1))
), "Some non-edge/center channels are entirely flagged!"
@pytest.mark.filterwarnings(
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_flag_start_flag(flag_file_init):
uv = UVData()
uv.read(
flag_file_init,
flag_init=True,
start_flag=1.0,
end_flag=1.0,
edge_width=0,
flag_dc_offset=False,
propagate_coarse_flags=False,
)
reshape = [uv.Ntimes, uv.Nbls, uv.Nfreqs, uv.Npols]
time_inds = [0, 1, -1, -2]
assert np.all(
uv.flag_array.reshape(reshape)[time_inds, :, :, :]
), "Not all of start and end times are flagged."
# Check that it didn't just flag everything
# Should have unflagged data for time inds [2, -3]
assert not np.any(
np.all(uv.flag_array.reshape(reshape)[[2, -3], :, :, :], axis=(1, 2, 3))
), "All the data is flagged for some intermediate times!"
@pytest.mark.parametrize(
"err_type,read_kwargs,err_msg",
[
(
ValueError,
{"flag_init": True, "start_flag": 0, "end_flag": 0, "edge_width": 90e3},
"The edge_width must be an integer multiple of the channel_width",
),
(
ValueError,
{"flag_init": True, "start_flag": 1.2, "end_flag": 0},
"The start_flag must be an integer multiple of the integration_time",
),
(
ValueError,
{"flag_init": True, "start_flag": 0, "end_flag": 1.2},
"The end_flag must be an integer multiple of the integration_time",
),
],
)
@pytest.mark.filterwarnings(
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_flag_init_errors(flag_file_init, err_type, read_kwargs, err_msg):
uv = UVData()
# give noninteger multiple inputs
with pytest.raises(err_type) as cm:
uv.read(flag_file_init, **read_kwargs)
assert str(cm.value).startswith(err_msg)
def test_read_metadata_only(tmp_path):
"""Test reading an MWA corr fits file as metadata only."""
uvd = UVData()
messages = [
"some coarse channel files were not submitted",
]
with uvtest.check_warnings(UserWarning, messages):
uvd.read_mwa_corr_fits(
filelist[0:2],
correct_cable_len=True,
phase_to_pointing_center=True,
read_data=False,
)
assert uvd.metadata_only
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_data_array_precision():
uv = UVData()
uv2 = UVData()
# read in data array as single precision
uv.read(filelist[0:2], data_array_dtype=np.complex64)
# now read as double precision
uv2.read(filelist[0:2], data_array_dtype=np.complex128)
assert uv == uv2
assert uv.data_array.dtype.type is np.complex64
assert uv2.data_array.dtype.type is np.complex128
return
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_nsample_array_precision():
uv = UVData()
uv2 = UVData()
uv3 = UVData()
# read in nsample array at different precisions
uv.read(filelist[0:2], nsample_array_dtype=np.float32)
uv2.read(filelist[0:2], nsample_array_dtype=np.float64)
uv3.read(filelist[0:2], nsample_array_dtype=np.float16)
assert uv == uv2
assert uv == uv3
assert uv.nsample_array.dtype.type is np.float32
assert uv2.nsample_array.dtype.type is np.float64
assert uv3.nsample_array.dtype.type is np.float16
return
def test_invalid_precision_errors():
uv = UVData()
# raise errors by passing bogus precision values
with pytest.raises(ValueError, match="data_array_dtype must be np.complex64"):
uv.read_mwa_corr_fits(filelist[0:2], data_array_dtype=np.float64)
with pytest.raises(
ValueError, match="nsample_array_dtype must be one of: np.float64"
):
uv.read_mwa_corr_fits(filelist[0:2], nsample_array_dtype=np.complex128)
return
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_remove_dig_gains():
"""Test digital gain removal."""
uv1 = UVData()
uv1.read(filelist[0:2], data_array_dtype=np.complex64)
uv2 = UVData()
uv2.read(filelist[0:2], remove_dig_gains=False)
with fits.open(filelist[0]) as meta:
meta_tbl = meta[1].data
antenna_inds = meta_tbl["Antenna"][1::2]
dig_gains = meta_tbl["Gains"][1::2, :].astype(np.float64) / 64
reordered_inds = antenna_inds.argsort()
bad_ant_inds = [59, 114]
good_ants = np.delete(reordered_inds, bad_ant_inds)
ant_1_inds, ant_2_inds = np.transpose(
list(itertools.combinations_with_replacement(np.arange(uv2.Nants_data), 2))
)
ant_1_inds = np.tile(np.array(ant_1_inds), uv2.Ntimes).astype(np.int_)
ant_2_inds = np.tile(np.array(ant_2_inds), uv2.Ntimes).astype(np.int_)
dig_gains = dig_gains[good_ants, 23]
uv2.data_array = uv2.data_array / (
dig_gains[ant_1_inds, np.newaxis, np.newaxis, np.newaxis]
* dig_gains[ant_2_inds, np.newaxis, np.newaxis, np.newaxis]
)
uv2.history = uv1.history
# make sure correction doesn't change data_array type
assert uv1.data_array.dtype == np.complex64
assert "Divided out digital gains" in uv1.history
assert uv1 == uv2
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_remove_coarse_band(tmp_path):
"""Test coarse band removal."""
# generate a spoof file with 32 channels
cb_spoof = str(tmp_path / "cb_spoof_01_00.fits")
with fits.open(filelist[1]) as mini1:
mini1[1].data = np.repeat(mini1[1].data, 32, axis=0)
mini1.writeto(cb_spoof)
uv1 = UVData()
uv1.read([filelist[0], cb_spoof], data_array_dtype=np.complex64)
uv2 = UVData()
uv2.read([filelist[0], cb_spoof], remove_coarse_band=False)
with h5py.File(
DATA_PATH + "/mwa_config_data/MWA_rev_cb_10khz_doubles.h5", "r"
) as f:
cb = f["coarse_band"][:]
cb_array = cb.reshape(32, 4)
cb_array = np.average(cb_array, axis=1)
uv2.data_array /= cb_array[:, np.newaxis]
uv2.history = uv1.history
# make sure correction doesn't change data_array type
assert uv1.data_array.dtype == np.complex64
assert "Divided out pfb coarse channel bandpass" in uv1.history
assert uv1 == uv2
def test_aoflagger_flags():
"""Test using aoflagger flags"""
uv = UVData()
files = filelist[0:2]
files.append(filelist[3])
messages = [
"some coarse channel files were not submitted",
"coarse channel, start time, and end time flagging will default",
]
with uvtest.check_warnings(UserWarning, messages):
uv.read_mwa_corr_fits(
files, flag_init=False, remove_flagged_ants=False, correct_cable_len=False,
)
with fits.open(filelist[3]) as aoflags:
flags = aoflags[1].data.field("FLAGS")
flags = flags[:, np.newaxis, :, np.newaxis]
flags = np.repeat(flags, 4, axis=3)
assert np.all(uv.flag_array == flags)
@pytest.mark.filterwarnings(
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:coarse channel, start time, and end time flagging")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_aoflagger_flags_multiple(tmp_path):
"""Test aoflagger flags with multiple coarse bands"""
mod_mini_6 = str(tmp_path / "mini_gpubox06_01.fits")
with fits.open(filelist[2]) as mini6:
mini6[1].header["time"] = 1447698337
mini6.writeto(mod_mini_6)
files = filelist[0:2] + filelist[3:5]
files.append(mod_mini_6)
uv = UVData()
uv.read_mwa_corr_fits(files, flag_init=False, remove_flagged_ants=False)
with fits.open(filelist[3]) as aoflags:
flags1 = aoflags[1].data.field("FLAGS")
with fits.open(filelist[4]) as aoflags:
flags2 = aoflags[1].data.field("FLAGS")
flags = np.array([flags2[:, 0], flags1[:, 0]])
flags = np.transpose(flags)
flags = flags[:, np.newaxis, :, np.newaxis]
flags = np.repeat(flags, 4, axis=3)
assert np.all(uv.flag_array == flags)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:coarse channel, start time, and end time flagging")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_mismatch_flags():
"""Break by submitting flag and gpubox files from different coarse bands."""
uv = UVData()
files = filelist[0:2]
files.append(filelist[4])
with pytest.raises(ValueError) as cm:
uv.read(files)
assert str(cm.value).startswith("flag file coarse bands do not match")
@pytest.mark.filterwarnings(
"ignore:coarse channels are not contiguous for this observation"
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_propagate_coarse_flags():
"""
Test that the flag(without flag_int) and nsample arrays correctly reflect data.
"""
uv = UVData()
uv.read_mwa_corr_fits(filelist[0:3], flag_init=False, propagate_coarse_flags=True)
assert np.all(uv.flag_array)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_start_flag(tmp_path):
"""Test the default value of start_flag."""
uv1 = UVData()
uv1.read_mwa_corr_fits(
filelist[0:2],
flag_init=True,
start_flag="goodtime",
end_flag=0,
edge_width=0,
flag_dc_offset=False,
)
good_ants = np.delete(np.unique(uv1.ant_1_array), [59, 114])
uv1.select(antenna_nums=good_ants)
# start_time is after goodtime, so data for good antennas should be unflagged
assert np.all(~uv1.flag_array)
mod_mini = str(tmp_path / "starttime_gpubox01_00.fits")
with fits.open(filelist[1]) as mini:
mini[1].header["time"] = 1447698334
mini.writeto(mod_mini)
uv2 = UVData()
uv2.read_mwa_corr_fits(
[filelist[0], mod_mini],
flag_init=True,
start_flag="goodtime",
end_flag=0,
edge_width=0,
flag_dc_offset=False,
)
# start_time is before goodtime, so all data should be flagged
assert np.all(uv2.flag_array)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_start_flag_goodtime_ppds():
"""Test that error is thrown using 'goodtime' with only ppds file."""
uv = UVData()
with pytest.raises(ValueError) as cm:
uv.read([filelist[1], filelist[7]], flag_init=True, start_flag="goodtime")
assert str(cm.value).startswith("To use start_flag='goodtime',")
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_start_flag_bad_string():
"""Test that error is thrown if start_flag is given string other than 'goodtime'"""
uv = UVData()
with pytest.raises(ValueError) as cm:
uv.read(filelist[0:2], flag_init=True, start_flag="badstring")
assert str(cm.value).startswith("start_flag must be int or float or 'goodtime'")
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_start_flag_int_time(tmp_path):
"""Test goodtime returning a start_flag smaller than integration time."""
uv = UVData()
new_meta = str(tmp_path / "1131733552_goodtime.metafits")
with fits.open(filelist[0]) as meta:
meta[0].header["GOODTIME"] = 1447698337.25
meta.writeto(new_meta)
uv.read(
[new_meta, filelist[1]], flag_init=True, start_flag="goodtime",
)
# first integration time should be flagged
# data only has one integration time, so all data should be flagged
assert np.all(uv.flag_array)
def test_input_output_mapping():
"""Test the input_output_mapping function."""
mapping_dict = {}
# fmt: off
pfb_mapper = [
0, 16, 32, 48, 1, 17, 33, 49, 2, 18, 34, 50, 3, 19, 35, 51,
4, 20, 36, 52, 5, 21, 37, 53, 6, 22, 38, 54, 7, 23, 39, 55,
8, 24, 40, 56, 9, 25, 41, 57, 10, 26, 42, 58, 11, 27, 43, 59,
12, 28, 44, 60, 13, 29, 45, 61, 14, 30, 46, 62, 15, 31, 47, 63,
]
# fmt: on
for p in range(4):
for i in range(64):
mapping_dict[pfb_mapper[i] + p * 64] = p * 64 + i
# compare with output from function
function_output = input_output_mapping()
assert function_output == mapping_dict
return
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
def test_van_vleck_int():
"""Test van vleck correction integral implementation."""
uv1 = UVData()
uv1.read(
filelist[8:10],
flag_init=False,
data_array_dtype=np.complex64,
correct_van_vleck=True,
cheby_approx=False,
remove_coarse_band=False,
remove_dig_gains=False,
remove_flagged_ants=False,
correct_cable_len=False,
)
# read in file corrected using integrate.quad with 1e-10 precision
uv2 = UVData()
uv2.read(filelist[10])
assert np.allclose(uv1.data_array, uv2.data_array)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
def test_van_vleck_cheby():
"""Test van vleck correction chebyshev implementation."""
uv1 = UVData()
uv1.read(
filelist[8:10],
flag_init=False,
correct_van_vleck=True,
cheby_approx=True,
remove_coarse_band=False,
remove_dig_gains=False,
correct_cable_len=False,
)
# read in file corrected using integrate.quad with 1e-10 precision
uv2 = UVData()
uv2.read(filelist[10])
# select only good ants
good_ants = np.delete(np.unique(uv2.ant_1_array), 76)
uv2.select(antenna_nums=good_ants)
assert np.allclose(uv1.data_array, uv2.data_array)
def test_van_vleck_interp(tmp_path):
"""Test van vleck correction with sigmas out of cheby interpolation range."""
small_sigs = str(tmp_path / "small_sigs07_01.fits")
with fits.open(filelist[8]) as mini:
mini[1].data = np.full((1, 66048), 7744)
mini.writeto(small_sigs)
messages = [
"values are being corrected with the van vleck integral",
]
messages = messages * 10
messages.append("some coarse channel files were not submitted")
uv = UVData()
with uvtest.check_warnings(UserWarning, messages):
uv.read(
[small_sigs, filelist[9]],
flag_init=False,
correct_van_vleck=True,
cheby_approx=True,
remove_coarse_band=False,
remove_dig_gains=False,
correct_cable_len=False,
)
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_remove_flagged_ants(tmp_path):
"""Test remove_flagged_ants."""
uv1 = UVData()
uv1.read(
filelist[8:10], remove_flagged_ants=True,
)
uv2 = UVData()
uv2.read(
filelist[8:10], remove_flagged_ants=False,
)
good_ants = np.delete(np.unique(uv2.ant_1_array), 76)
uv2.select(antenna_nums=good_ants)
assert uv1 == uv2
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
@pytest.mark.filterwarnings("ignore:.*values are being corrected with the van vleck")
@pytest.mark.filterwarnings("ignore:cable length correction is now defaulted to True")
def test_small_sigs(tmp_path):
"""Test flag_small_auto_ants."""
small_sigs = str(tmp_path / "small_sigs07_02.fits")
with fits.open(filelist[8]) as mini:
mini[1].data[0, 0] = 1000
mini.writeto(small_sigs)
uv1 = UVData()
uv1.read(
[small_sigs, filelist[9]], correct_van_vleck=True, flag_small_auto_ants=True,
)
messages = [
"values are being corrected with the van vleck integral",
]
messages = messages * 8
messages.append("some coarse channel files were not submitted")
messages.append("cable length correction is now defaulted to True")
uv2 = UVData()
with uvtest.check_warnings(UserWarning, messages):
uv2.read(
[small_sigs, filelist[9]],
correct_van_vleck=True,
flag_small_auto_ants=False,
)
assert "flagged by the Van Vleck" in uv1.history
assert uv2.Nants_data - uv1.Nants_data == 1
@pytest.mark.filterwarnings("ignore:some coarse channel files were not submitted")
def test_deprecated_keywords():
"""Test warnings for deprecated keywords"""
uv = UVData()
messages = ["Use `use_aoflagger_flags`"]
messages.append("Use `flag_small_auto_ants`")
messages.append("some coarse channel files were not submitted")
messages.append("cable length correction is now defaulted to True")
with uvtest.check_warnings(
[DeprecationWarning, DeprecationWarning, UserWarning, UserWarning], messages,
):
uv.read(
filelist[0:2], use_cotter_flags=False, flag_small_sig_ants=True,
)