https://github.com/RadioAstronomySoftwareGroup/pyuvdata
Tip revision: 8390aaceafd4868ecbd14a4cb6294ca18be7af00 authored by Bryna Hazelton on 12 February 2020, 23:55:06 UTC
remove extra mwa_beam.py file that got added in the rebase
remove extra mwa_beam.py file that got added in the rebase
Tip revision: 8390aac
test_miriad.py
# -*- mode: python; coding: utf-8 -*-
# Copyright (c) 2018 Radio Astronomy Software Group
# Licensed under the 2-clause BSD License
"""Tests for Miriad object.
Note that because of the way that file handling is done in the C++ API, a miriad
file is not closed until the destructor function (tp_dealloc) is called. Due to
implementation details of CPython, it is sometimes not enough to `del` the
object--a manual garbage collection may be required. When adding new tests,
proper cleanup consists of: (1) deleting any Miriad objects or UVData objects,
(2) performing garbage collection (with `gc.collect()`), and (3) removing the
directory corresponding to the miriad file. Each test should do this, to avoid
open file handles interfering with other tests. The exception to this is if a
test uses the `uv_in_paper` or `uv_in_uvfits` fixture, as these handle cleanup
on their own.
"""
from __future__ import absolute_import, division, print_function
import os
import gc
import shutil
import copy
import numpy as np
import pytest
from astropy.time import Time, TimeDelta
from astropy import constants as const
from pyuvdata import UVData
from ..miriad import Miriad
import pyuvdata.utils as uvutils
import pyuvdata.tests as uvtest
from pyuvdata.data import DATA_PATH
from pyuvdata.uvdata import aipy_extracts
# always ignore the Altitude not present warning
# This does NOT break uvutils.checkWarnings tests for this warning
pytestmark = pytest.mark.filterwarnings("ignore:Altitude is not present in Miriad")
@pytest.fixture
def uv_in_paper():
uv_in = UVData()
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
uv_in.read(testfile)
uv_in.write_miriad(write_file, clobber=True)
uv_out = UVData()
yield uv_in, uv_out, write_file
# cleanup
del uv_in, uv_out
gc.collect()
if os.path.exists(write_file):
shutil.rmtree(write_file)
@pytest.fixture
def uv_in_uvfits():
uv_in = UVData()
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uvfits")
uv_in.read(testfile)
uv_out = UVData()
yield uv_in, uv_out, write_file
# cleanup
del uv_in, uv_out
gc.collect()
if os.path.exists(write_file):
os.remove(write_file)
@pytest.mark.filterwarnings("ignore:Telescope ATCA is not")
def test_ReadWriteReadATCA():
uv_in = UVData()
uv_out = UVData()
atca_file = os.path.join(DATA_PATH, "atca_miriad")
testfile = os.path.join(DATA_PATH, "test/outtest_atca_miriad.uv")
uvtest.checkWarnings(
uv_in.read,
[atca_file],
nwarnings=4,
category=[UserWarning, UserWarning, UserWarning, UserWarning],
message=[
"Altitude is not present in Miriad file, and "
"telescope ATCA is not in known_telescopes. ",
"Altitude is not present",
"Telescope location is set at sealevel at the file lat/lon "
"coordinates. Antenna positions are present, but the mean antenna "
"position does not give a telescope_location on the surface of the "
"earth. Antenna positions do not appear to be on the surface of the "
"earth and will be treated as relative.",
"Telescope ATCA is not in known_telescopes.",
],
)
uv_in.write_miriad(testfile, clobber=True)
uv_out.read(testfile)
assert uv_in == uv_out
# cleanup
del uv_in, uv_out
gc.collect()
shutil.rmtree(testfile)
@pytest.mark.filterwarnings("ignore:Telescope EVLA is not")
def test_ReadNRAOWriteMiriadReadMiriad():
"""Test reading in a CASA tutorial uvfits file, writing and reading as miriad"""
uvfits_uv = UVData()
miriad_uv = UVData()
testfile = os.path.join(DATA_PATH, "day2_TDEM0003_10s_norx_1src_1spw.uvfits")
writefile = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
uvfits_uv.read_uvfits(testfile)
uvfits_uv.write_miriad(writefile, clobber=True)
miriad_uv.read(writefile)
assert uvfits_uv == miriad_uv
# cleanup
del uvfits_uv, miriad_uv
gc.collect()
shutil.rmtree(writefile)
def test_ReadMiriadWriteUVFits(uv_in_uvfits):
"""
Miriad to uvfits loopback test.
Read in Miriad files, write out as uvfits, read back in and check for
object equality.
"""
miriad_uv, uvfits_uv, testfile = uv_in_uvfits
miriad_uv.write_uvfits(testfile, spoof_nonessential=True, force_phase=True)
uvfits_uv.read_uvfits(testfile)
assert miriad_uv == uvfits_uv
def test_miriad_read_warning_lat_lon_corrected():
miriad_uv = UVData()
miriad_file = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
# check warning when correct_lat_lon is set to False
uvtest.checkWarnings(
miriad_uv.read,
[miriad_file],
{"correct_lat_lon": False},
nwarnings=1,
message=[
"Altitude is not present in Miriad file, "
"using known location altitude value for "
"PAPER and lat/lon from file."
],
)
# cleanup
del miriad_uv
gc.collect()
@pytest.mark.parametrize(
"err_type,write_kwargs,err_msg",
[
(
ValueError,
{"spoof_nonessential": True},
"The data are in drift mode. Set force_phase",
),
(ValueError, {"force_phase": True}, "Required attribute"),
],
)
def test_ReadMiriadWriteUVFits_phasing_errors(
uv_in_uvfits, err_type, write_kwargs, err_msg
):
miriad_uv, uvfits_uv, testfile = uv_in_uvfits
# check error if phase_type is wrong and force_phase not set
with pytest.raises(err_type) as cm:
miriad_uv.write_uvfits(testfile, **write_kwargs)
assert str(cm.value).startswith(err_msg)
@pytest.mark.parametrize(
"err_type,read_kwargs,err_msg",
[
(
ValueError,
{"phase_type": "phased"},
'phase_type is "phased" but the RA values are varying',
),
(ValueError, {"phase_type": "foo"}, "The phase_type was not recognized."),
],
)
def test_ReadMiriad_phasing_errors(err_type, read_kwargs, err_msg):
miriad_uv = UVData()
miriad_file = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
# check that setting the phase_type to something wrong errors
with pytest.raises(err_type) as cm:
miriad_uv.read(miriad_file, **read_kwargs)
assert str(cm.value).startswith(err_msg)
# cleanup
del miriad_uv
gc.collect()
def test_read_miriad_write_uvfits_phasing_error(uv_in_uvfits):
miriad_uv, uvfits_uv, testfile = uv_in_uvfits
miriad_uv.set_unknown_phase_type()
with pytest.raises(ValueError) as cm:
miriad_uv.write_uvfits(testfile, spoof_nonessential=True)
assert str(cm.value).startswith("The phasing type of the data is unknown")
def test_wronglatlon():
"""
Check for appropriate warnings with incorrect lat/lon values or missing telescope
To test this, we needed files without altitudes and with wrong lat, lon or telescope values.
These test files were made commenting out the line in miriad.py that adds altitude
to the file and running the following code:
import os
import numpy as np
from pyuvdata import UVData
from pyuvdata.data import DATA_PATH
uv_in = UVData()
uv_out = UVData()
miriad_file = os.path.join(DATA_PATH, 'zen.2456865.60537.xy.uvcRREAA')
latfile = os.path.join(DATA_PATH, 'zen.2456865.60537_wronglat.xy.uvcRREAA')
lonfile = os.path.join(DATA_PATH, 'zen.2456865.60537_wronglon.xy.uvcRREAA')
latlonfile = os.path.join(DATA_PATH, 'zen.2456865.60537_wronglatlon.xy.uvcRREAA')
telescopefile = os.path.join(DATA_PATH, 'zen.2456865.60537_wrongtelecope.xy.uvcRREAA')
uv_in.read(miriad_file)
uv_in.select(times=uv_in.time_array[0])
uv_in.select(freq_chans=[0])
lat, lon, alt = uv_in.telescope_location_lat_lon_alt
lat_wrong = lat + 10 * np.pi / 180.
uv_in.telescope_location_lat_lon_alt = (lat_wrong, lon, alt)
uv_in.write_miriad(latfile, clobber=True)
uv_out.read(latfile)
lon_wrong = lon + 10 * np.pi / 180.
uv_in.telescope_location_lat_lon_alt = (lat, lon_wrong, alt)
uv_in.write_miriad(lonfile, clobber=True)
uv_out.read(lonfile)
uv_in.telescope_location_lat_lon_alt = (lat_wrong, lon_wrong, alt)
uv_in.write_miriad(latlonfile)
uv_out.read(latlonfile)
uv_in.telescope_location_lat_lon_alt = (lat, lon, alt)
uv_in.telescope_name = 'foo'
uv_in.write_miriad(telescopefile, clobber=True)
uv_out.read(telescopefile, run_check=False)
"""
uv_in = UVData()
latfile = os.path.join(DATA_PATH, "zen.2456865.60537_wronglat.xy.uvcRREAA")
lonfile = os.path.join(DATA_PATH, "zen.2456865.60537_wronglon.xy.uvcRREAA")
latlonfile = os.path.join(DATA_PATH, 'zen.2456865.60537_wronglatlon.xy.uvcRREAA')
telescopefile = os.path.join(
DATA_PATH, "zen.2456865.60537_wrongtelecope.xy.uvcRREAA"
)
uvtest.checkWarnings(
uv_in.read,
[latfile],
nwarnings=2,
message=[
"Altitude is not present in file and latitude value does not match",
"drift RA, Dec is off from lst, latitude by more than 1.0 deg"],
)
uvtest.checkWarnings(
uv_in.read,
[lonfile],
nwarnings=2,
message=[
"Altitude is not present in file and longitude value does not match",
"drift RA, Dec is off from lst, latitude by more than 1.0 deg"],
)
uvtest.checkWarnings(
uv_in.read,
func_args=[latlonfile],
func_kwargs={"correct_lat_lon": False},
nwarnings=1,
message=[
"Altitude is not present in file and latitude and longitude "
"values do not match",
],
)
uvtest.checkWarnings(
uv_in.read,
[telescopefile],
{"run_check": False},
nwarnings=4,
message=[
"Altitude is not present in Miriad file, and telescope",
"Altitude is not present in Miriad file, and telescope",
"Telescope location is not set, but antenna positions are "
"present. Mean antenna latitude and longitude values match file "
"values, so telescope_position will be set using the mean of the "
"antenna altitudes",
"Telescope foo is not in known_telescopes.",
],
)
# cleanup
del uv_in
gc.collect()
def test_miriad_location_handling():
uv_in = UVData()
uv_out = UVData()
miriad_file = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
testfile = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
aipy_uv = aipy_extracts.UV(miriad_file)
if os.path.exists(testfile):
shutil.rmtree(testfile)
# Test for using antenna positions to get telescope position
uv_in.read(miriad_file)
# extract antenna positions and rotate them for miriad
nants = aipy_uv["nants"]
rel_ecef_antpos = np.zeros((nants, 3), dtype=uv_in.antenna_positions.dtype)
for ai, num in enumerate(uv_in.antenna_numbers):
rel_ecef_antpos[num, :] = uv_in.antenna_positions[ai, :]
# find zeros so antpos can be zeroed there too
antpos_length = np.sqrt(np.sum(np.abs(rel_ecef_antpos) ** 2, axis=1))
ecef_antpos = rel_ecef_antpos + uv_in.telescope_location
longitude = uv_in.telescope_location_lat_lon_alt[1]
antpos = uvutils.rotECEF_from_ECEF(ecef_antpos, longitude)
# zero out bad locations (these are checked on read)
antpos[np.where(antpos_length == 0), :] = [0, 0, 0]
antpos = antpos.T.flatten() / const.c.to("m/ns").value
# make new file
aipy_uv2 = aipy_extracts.UV(testfile, status="new")
# initialize headers from old file
# change telescope name (so the position isn't set from known_telescopes)
# and use absolute antenna positions
aipy_uv2.init_from_uv(aipy_uv, override={"telescop": "foo", "antpos": antpos})
# copy data from old file
aipy_uv2.pipe(aipy_uv)
# close file properly
del aipy_uv2
gc.collect()
uvtest.checkWarnings(
uv_out.read,
[testfile],
nwarnings=4,
message=[
"Altitude is not present in Miriad file, and "
"telescope foo is not in known_telescopes. "
"Telescope location will be set using antenna positions.",
"Altitude is not present ",
"Telescope location is not set, but antenna "
"positions are present. Mean antenna latitude "
"and longitude values match file values, so "
"telescope_position will be set using the mean "
"of the antenna altitudes",
"Telescope foo is not in known_telescopes.",
],
)
# Test for handling when antenna positions have a different mean latitude than the file latitude
# make new file
if os.path.exists(testfile):
shutil.rmtree(testfile)
aipy_uv = aipy_extracts.UV(miriad_file)
aipy_uv2 = aipy_extracts.UV(testfile, status="new")
# initialize headers from old file
# change telescope name (so the position isn't set from known_telescopes)
# and use absolute antenna positions, change file latitude
new_lat = aipy_uv["latitud"] * 1.5
aipy_uv2.init_from_uv(
aipy_uv, override={"telescop": "foo", "antpos": antpos, "latitud": new_lat}
)
# copy data from old file
aipy_uv2.pipe(aipy_uv)
# close file properly
del aipy_uv2
gc.collect()
uvtest.checkWarnings(
uv_out.read,
[testfile],
nwarnings=5,
message=[
"Altitude is not present in Miriad file, and "
"telescope foo is not in known_telescopes. "
"Telescope location will be set using antenna positions.",
"Altitude is not present in Miriad file, and "
"telescope foo is not in known_telescopes. "
"Telescope location will be set using antenna positions.",
"Telescope location is set at sealevel at the "
"file lat/lon coordinates. Antenna positions "
"are present, but the mean antenna latitude "
"value does not match",
"drift RA, Dec is off from lst, latitude by more than 1.0 deg",
"Telescope foo is not in known_telescopes.",
],
)
# Test for handling when antenna positions have a different mean longitude than the file longitude
# this is harder because of the rotation that's done on the antenna positions
# make new file
if os.path.exists(testfile):
shutil.rmtree(testfile)
aipy_uv = aipy_extracts.UV(miriad_file)
aipy_uv2 = aipy_extracts.UV(testfile, status="new")
# initialize headers from old file
# change telescope name (so the position isn't set from known_telescopes)
# and use absolute antenna positions, change file longitude
new_lon = aipy_uv["longitu"] + np.pi
aipy_uv2.init_from_uv(
aipy_uv, override={"telescop": "foo", "antpos": antpos, "longitu": new_lon}
)
# copy data from old file
aipy_uv2.pipe(aipy_uv)
# close file properly
del aipy_uv2
gc.collect()
uvtest.checkWarnings(
uv_out.read,
[testfile],
nwarnings=5,
message=[
"Altitude is not present in Miriad file, and "
"telescope foo is not in known_telescopes. "
"Telescope location will be set using antenna positions.",
"Altitude is not present in Miriad file, and "
"telescope foo is not in known_telescopes. "
"Telescope location will be set using antenna positions.",
"Telescope location is set at sealevel at the "
"file lat/lon coordinates. Antenna positions "
"are present, but the mean antenna longitude "
"value does not match",
"drift RA, Dec is off from lst, latitude by more than 1.0 deg",
"Telescope foo is not in known_telescopes.",
],
)
# Test for handling when antenna positions have a different mean longitude &
# latitude than the file longitude
# make new file
if os.path.exists(testfile):
shutil.rmtree(testfile)
aipy_uv = aipy_extracts.UV(miriad_file)
aipy_uv2 = aipy_extracts.UV(testfile, status="new")
# initialize headers from old file
# change telescope name (so the position isn't set from known_telescopes)
# and use absolute antenna positions, change file latitude and longitude
aipy_uv2.init_from_uv(
aipy_uv,
override={
"telescop": "foo",
"antpos": antpos,
"latitud": new_lat,
"longitu": new_lon,
},
)
# copy data from old file
aipy_uv2.pipe(aipy_uv)
# close file properly
del aipy_uv2
gc.collect()
uvtest.checkWarnings(
uv_out.read,
[testfile],
nwarnings=5,
message=[
"Altitude is not present in Miriad file, and "
"telescope foo is not in known_telescopes. "
"Telescope location will be set using antenna positions.",
"Altitude is not present in Miriad file, and "
"telescope foo is not in known_telescopes. "
"Telescope location will be set using antenna positions.",
"Telescope location is set at sealevel at the "
"file lat/lon coordinates. Antenna positions "
"are present, but the mean antenna latitude and "
"longitude values do not match",
"drift RA, Dec is off from lst, latitude by more than 1.0 deg",
"Telescope foo is not in known_telescopes.",
],
)
# Test for handling when antenna positions are far enough apart to make the
# mean position inside the earth
good_antpos = np.where(antpos_length > 0)[0]
rot_ants = good_antpos[: len(good_antpos) // 2]
rot_antpos = uvutils.rotECEF_from_ECEF(ecef_antpos[rot_ants, :], longitude + np.pi)
modified_antpos = uvutils.rotECEF_from_ECEF(ecef_antpos, longitude)
modified_antpos[rot_ants, :] = rot_antpos
# zero out bad locations (these are checked on read)
modified_antpos[np.where(antpos_length == 0), :] = [0, 0, 0]
modified_antpos = modified_antpos.T.flatten() / const.c.to("m/ns").value
# make new file
if os.path.exists(testfile):
shutil.rmtree(testfile)
aipy_uv = aipy_extracts.UV(miriad_file)
aipy_uv2 = aipy_extracts.UV(testfile, status="new")
# initialize headers from old file
# change telescope name (so the position isn't set from known_telescopes)
# and use modified absolute antenna positions
aipy_uv2.init_from_uv(
aipy_uv, override={"telescop": "foo", "antpos": modified_antpos}
)
# copy data from old file
aipy_uv2.pipe(aipy_uv)
# close file properly
del aipy_uv2
gc.collect()
uvtest.checkWarnings(
uv_out.read,
[testfile],
nwarnings=4,
message=[
"Altitude is not present in Miriad file, and "
"telescope foo is not in known_telescopes. "
"Telescope location will be set using antenna positions.",
"Altitude is not present ",
"Telescope location is set at sealevel at the "
"file lat/lon coordinates. Antenna positions "
"are present, but the mean antenna position "
"does not give a telescope_location on the "
"surface of the earth.",
"Telescope foo is not in known_telescopes.",
],
)
# cleanup
del aipy_uv, uv_in, uv_out
gc.collect()
shutil.rmtree(testfile)
def test_singletimeselect_drift():
"""
Check behavior with writing & reading after selecting a single time from a drift file.
"""
uv_in = UVData()
uv_out = UVData()
miriad_file = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
testfile = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
uv_in.read(miriad_file)
uv_in.select(times=uv_in.time_array[0])
uv_in.write_miriad(testfile, clobber=True)
uv_out.read(testfile)
assert uv_in == uv_out
# check that setting the phase_type works
uv_out.read(testfile, phase_type="drift")
assert uv_in == uv_out
# check again with more than one time but only 1 unflagged time
uv_in.read(miriad_file)
time_gt0_array = np.where(uv_in.time_array > uv_in.time_array[0])[0]
uv_in.flag_array[time_gt0_array, :, :, :] = True
# get unflagged blts
blt_good = np.where(~np.all(uv_in.flag_array, axis=(1, 2, 3)))
assert np.isclose(np.mean(np.diff(uv_in.time_array[blt_good])), 0.0)
uv_in.write_miriad(testfile, clobber=True)
uv_out.read(testfile)
assert uv_in == uv_out
# check that setting the phase_type works
uv_out.read(testfile, phase_type="drift")
assert uv_in == uv_out
# cleanup
del uv_in, uv_out
gc.collect()
shutil.rmtree(testfile)
def test_poltoind():
miriad_uv = UVData()
miriad_file = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
miriad_uv.read(miriad_file)
pol_arr = miriad_uv.polarization_array
miriad = miriad_uv._convert_to_filetype("miriad")
miriad.polarization_array = None
with pytest.raises(ValueError) as cm:
miriad._pol_to_ind(pol_arr[0])
assert str(cm.value).startswith(
"Can't index polarization -7 because polarization_array is not set"
)
miriad.polarization_array = [pol_arr[0], pol_arr[0]]
with pytest.raises(ValueError) as cm:
miriad._pol_to_ind(pol_arr[0])
assert str(cm.value).startswith("multiple matches for pol=-7 in polarization_array")
# cleanup
del miriad_uv
gc.collect()
def test_miriad_extra_keywords():
uv_in = UVData()
uv_out = UVData()
miriad_file = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
testfile = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
uv_in.read(miriad_file)
# check for warnings & errors with extra_keywords that are dicts, lists or arrays
uv_in.extra_keywords["testdict"] = {"testkey": 23}
uvtest.checkWarnings(
uv_in.check, message=["testdict in extra_keywords is a " "list, array or dict"]
)
with pytest.raises(TypeError) as cm:
uv_in.write_miriad(testfile, clobber=True, run_check=False)
assert str(cm.value).startswith("Extra keyword testdict is of <class 'dict'>")
uv_in.extra_keywords.pop("testdict")
uv_in.extra_keywords["testlist"] = [12, 14, 90]
uvtest.checkWarnings(
uv_in.check, message=["testlist in extra_keywords is a " "list, array or dict"]
)
with pytest.raises(TypeError) as cm:
uv_in.write_miriad(testfile, clobber=True, run_check=False)
assert str(cm.value).startswith("Extra keyword testlist is of <class 'list'>")
uv_in.extra_keywords.pop("testlist")
uv_in.extra_keywords["testarr"] = np.array([12, 14, 90])
uvtest.checkWarnings(
uv_in.check, message=["testarr in extra_keywords is a " "list, array or dict"]
)
with pytest.raises(TypeError) as cm:
uv_in.write_miriad(testfile, clobber=True, run_check=False)
assert str(cm.value).startswith(
"Extra keyword testarr is of <class 'numpy.ndarray'>"
)
uv_in.extra_keywords.pop("testarr")
# check for warnings with extra_keywords keys that are too long
uv_in.extra_keywords["test_long_key"] = True
uvtest.checkWarnings(
uv_in.check,
message=["key test_long_key in extra_keywords " "is longer than 8 characters"],
)
uvtest.checkWarnings(
uv_in.write_miriad,
[testfile],
{"clobber": True, "run_check": False},
message=["key test_long_key in extra_keywords is longer than 8 characters"],
)
uv_in.extra_keywords.pop("test_long_key")
# check handling of boolean keywords
uv_in.extra_keywords["bool"] = True
uv_in.extra_keywords["bool2"] = False
uv_in.write_miriad(testfile, clobber=True)
uv_out.read(testfile)
assert uv_in == uv_out
uv_in.extra_keywords.pop("bool")
uv_in.extra_keywords.pop("bool2")
# check handling of int-like keywords
uv_in.extra_keywords["int1"] = np.int(5)
uv_in.extra_keywords["int2"] = 7
uv_in.write_miriad(testfile, clobber=True)
uv_out.read(testfile)
assert uv_in == uv_out
uv_in.extra_keywords.pop("int1")
uv_in.extra_keywords.pop("int2")
# check handling of float-like keywords
uv_in.extra_keywords["float1"] = np.int64(5.3)
uv_in.extra_keywords["float2"] = 6.9
uv_in.write_miriad(testfile, clobber=True)
uv_out.read(testfile)
assert uv_in == uv_out
uv_in.extra_keywords.pop("float1")
uv_in.extra_keywords.pop("float2")
# check handling of very long strings
long_string = "this is a very long string " * 1000
uv_in.extra_keywords["longstr"] = long_string
uv_in.write_miriad(testfile, clobber=True)
uv_out.read(testfile)
assert uv_in == uv_out
uv_in.extra_keywords.pop("longstr")
# check handling of complex-like keywords
# currently they are NOT supported
uv_in.extra_keywords["complex1"] = np.complex64(5.3 + 1.2j)
with pytest.raises(TypeError) as cm:
uv_in.write_miriad(testfile, clobber=True, run_check=False)
assert str(cm.value).startswith(
"Extra keyword complex1 is of <class 'numpy.complex64'>"
)
uv_in.extra_keywords.pop("complex1")
uv_in.extra_keywords["complex2"] = 6.9 + 4.6j
with pytest.raises(TypeError) as cm:
uv_in.write_miriad(testfile, clobber=True, run_check=False)
assert str(cm.value).startswith(
"Extra keyword complex2 is of <class 'complex'>"
)
# cleanup
del uv_in, uv_out
gc.collect()
shutil.rmtree(testfile)
def test_roundtrip_optional_params():
uv_in = UVData()
uv_out = UVData()
miriad_file = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
testfile = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
uv_in.read(miriad_file)
uv_in.x_orientation = "east"
uv_in.reorder_blts()
uv_in.write_miriad(testfile, clobber=True)
uv_out.read(testfile)
assert uv_in == uv_out
# test with bda as well (single entry in tuple)
uv_in.reorder_blts(order="bda")
uv_in.write_miriad(testfile, clobber=True)
uv_out.read(testfile)
assert uv_in == uv_out
# cleanup
del uv_in, uv_out
gc.collect()
shutil.rmtree(testfile)
def test_breakReadMiriad():
"""Test Miriad file checking."""
uv_in = UVData()
uv_out = UVData()
with pytest.raises(IOError) as cm:
uv_in.read("foo", file_type="miriad")
assert str(cm.value).startswith("foo not found")
miriad_file = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
testfile = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
uv_in.read(miriad_file)
uv_in.Nblts += 10
uv_in.write_miriad(testfile, clobber=True, run_check=False)
uvtest.checkWarnings(
uv_out.read,
[testfile],
{"run_check": False},
message=["Nblts does not match the number of unique blts in the data"],
)
uv_in.read(miriad_file)
uv_in.Nbls += 10
uv_in.write_miriad(testfile, clobber=True, run_check=False)
uvtest.checkWarnings(
uv_out.read,
[testfile],
{"run_check": False},
message=["Nbls does not match the number of unique baselines in the data"],
)
uv_in.read(miriad_file)
uv_in.Ntimes += 10
uv_in.write_miriad(testfile, clobber=True, run_check=False)
uvtest.checkWarnings(
uv_out.read,
[testfile],
{"run_check": False},
message=["Ntimes does not match the number of unique times in the data"],
)
# cleanup
del uv_in, uv_out
gc.collect()
shutil.rmtree(testfile)
def test_readWriteReadMiriad(uv_in_paper):
"""
PAPER file Miriad loopback test.
Read in Miriad PAPER file, write out as new Miriad file, read back in and
check for object equality.
"""
uv_in, uv_out, write_file = uv_in_paper
uv_out.read(write_file)
assert uv_in == uv_out
# check that we can read & write phased data
uv_in2 = copy.deepcopy(uv_in)
uv_in2.phase_to_time(Time(np.mean(uv_in2.time_array), format="jd"))
uv_in2.write_miriad(write_file, clobber=True)
uv_out.read(write_file)
assert uv_in2 == uv_out
del uv_in2
# check that trying to overwrite without clobber raises an error
with pytest.raises(OSError) as cm:
uv_in.write_miriad(write_file, clobber=False)
assert str(cm.value).startswith("File exists: skipping")
# check that if x_orientation is set, it's read back out properly
uv_in.x_orientation = "east"
uv_in.write_miriad(write_file, clobber=True)
uv_out.read(write_file)
assert uv_in == uv_out
def test_miriad_antenna_diameters(uv_in_paper):
# check that if antenna_diameters is set, it's read back out properly
uv_in, uv_out, write_file = uv_in_paper
uv_in.antenna_diameters = np.zeros((uv_in.Nants_telescope,), dtype=np.float) + 14.0
uv_in.write_miriad(write_file, clobber=True)
uv_out.read(write_file)
assert uv_in == uv_out
# check that antenna diameters get written if not exactly float
uv_in.antenna_diameters = (
np.zeros((uv_in.Nants_telescope,), dtype=np.float32) + 14.0
)
uv_in.write_miriad(write_file, clobber=True)
uv_out.read(write_file)
assert uv_in == uv_out
def test_miriad_write_miriad_unkonwn_phase_error(uv_in_paper):
uv_in, uv_out, write_file = uv_in_paper
# check that trying to write a file with unknown phasing raises an error
uv_in.set_unknown_phase_type()
with pytest.raises(ValueError) as cm:
uv_in.write_miriad(write_file, clobber=True)
assert str(cm.value).startswith("The phasing type of the data is unknown")
def test_miriad_write_read_diameters(uv_in_paper):
uv_in, uv_out, write_file = uv_in_paper
# check for backwards compatibility with old keyword 'diameter' for antenna diameters
testfile_diameters = os.path.join(DATA_PATH, "zen.2457698.40355.xx.HH.uvcA")
uv_in.read(testfile_diameters)
uv_in.write_miriad(write_file, clobber=True)
uv_out.read(write_file)
assert uv_in == uv_out
def test_miriad_and_aipy_reads(uv_in_paper):
uv_in, uv_out, write_file = uv_in_paper
# check that variables 'ischan' and 'nschan' were written to new file
# need to use aipy, since pyuvdata is not currently capturing these variables
uv_in.read(write_file)
uv_aipy = aipy_extracts.UV(
write_file
)
nfreqs = uv_in.Nfreqs
nschan = uv_aipy["nschan"]
ischan = uv_aipy["ischan"]
assert nschan == nfreqs
assert ischan == 1
# cleanup
del uv_aipy
gc.collect()
def test_miriad_telescope_locations():
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
# test load_telescope_coords w/ blank Miriad
uv_in = Miriad()
uv = aipy_extracts.UV(testfile)
uv_in._load_telescope_coords(uv)
assert uv_in.telescope_location_lat_lon_alt is not None
# test load_antpos w/ blank Miriad
uv_in = Miriad()
uv = aipy_extracts.UV(testfile)
uv_in._load_antpos(uv)
assert uv_in.antenna_positions is not None
# cleanup
del uv, uv_in
gc.collect()
def test_miriad_integration_time_precision():
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
# test that changing precision of integraiton_time is okay
# tolerance of integration_time (1e-3) is larger than floating point type conversions
uv_in = UVData()
uv_in.read(testfile)
uv_in.integration_time = uv_in.integration_time.astype(np.float32)
uv_in.write_miriad(write_file, clobber=True)
new_uv = UVData()
new_uv.read(write_file)
assert uv_in == new_uv
# cleanup
del new_uv, uv_in
gc.collect()
shutil.rmtree(write_file)
@pytest.mark.parametrize(
"select_kwargs",
[
{"bls": [(0, 0), (0, 1), (4, 2)]},
{"bls": [(0, 0), (2, 4)], "antenna_nums": [0, 2, 4]},
{"bls": (2, 4, "xy")},
{"bls": [(4, 2, "yx")]},
{"polarizations": [-7], "bls": [(4, 4)]},
{"bls": [(4, 4, "xy")]},
],
)
def test_readWriteReadMiriad_partial_bls(select_kwargs):
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
# check partial read selections
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
uv_in = UVData()
# test only specified bls were read, and that flipped antpair is loaded too
uv_in.read(write_file, **select_kwargs)
antpairs = uv_in.get_antpairs()
# indexing here is to ignore polarization if present, maybe there is a better way
bls = select_kwargs["bls"]
if isinstance(bls, tuple):
bls = [bls]
assert np.all(
[bl[:2] in antpairs or bl[:2][::-1] in antpairs for bl in bls]
)
exp_uv = full.select(inplace=False, **select_kwargs)
assert uv_in == exp_uv
# cleanup
del uv_in, full
gc.collect()
shutil.rmtree(write_file)
def test_readWriteReadMiriad_partial_antenna_nums():
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
# check partial read selections
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
uv_in = UVData()
# test all bls w/ 0 are loaded
uv_in.read(write_file, antenna_nums=[0])
diff = set(full.get_antpairs()) - set(uv_in.get_antpairs())
assert 0 not in np.unique(diff)
exp_uv = full.select(antenna_nums=[0], inplace=False)
assert np.max(exp_uv.ant_1_array) == 0
assert np.max(exp_uv.ant_2_array) == 0
assert uv_in == exp_uv
# cleanup
del uv_in, exp_uv, full
gc.collect()
shutil.rmtree(write_file)
@pytest.mark.parametrize(
"select_kwargs",
[
{"time_range": [2456865.607, 2456865.609]},
{"time_range": [2456865.607, 2456865.609], "antenna_nums": [0]},
{"time_range": [2456865.607, 2456865.609], "polarizations": [-7]},
],
)
def test_readWriteReadMiriad_partial_times(select_kwargs):
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
# check partial read selections
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
# test time loading
uv_in = UVData()
uv_in.read(write_file, **select_kwargs)
full_times = np.unique(
full.time_array[
(full.time_array > select_kwargs["time_range"][0])
& (full.time_array < select_kwargs["time_range"][1])
]
)
assert np.isclose(np.unique(uv_in.time_array), full_times).all()
# The exact time are calculated above, pop out the time range to compare time range with
# selecting on exact times
select_kwargs.pop("time_range", None)
exp_uv = full.select(times=full_times, inplace=False, **select_kwargs)
assert uv_in == exp_uv
# cleanup
del uv_in, full, exp_uv
gc.collect()
shutil.rmtree(write_file)
@pytest.mark.parametrize("pols", [["xy"], [-7]])
def test_readWriteReadMiriad_partial_pols(pols):
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
# check partial read selections
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
# test polarization loading
uv_in = UVData()
uv_in.read(write_file, polarizations=pols)
assert full.polarization_array == uv_in.polarization_array
exp_uv = full.select(polarizations=pols, inplace=False)
assert uv_in == exp_uv
# cleanup
del uv_in, full
gc.collect()
shutil.rmtree(write_file)
def test_readWriteReadMiriad_partial_ant_str():
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
# check partial read selections
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
uv_in = UVData()
# test ant_str
del uv_in
uv_in = UVData()
uv_in.read(write_file, ant_str="auto")
assert np.array([blp[0] == blp[1] for blp in uv_in.get_antpairs()]).all()
exp_uv = full.select(ant_str="auto", inplace=False)
assert uv_in == exp_uv
del uv_in
gc.collect()
shutil.rmtree(write_file)
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
uv_in = UVData()
uv_in.read(write_file, ant_str="cross")
assert np.array([blp[0] != blp[1] for blp in uv_in.get_antpairs()]).all()
exp_uv = full.select(ant_str="cross", inplace=False)
assert uv_in == exp_uv
del uv_in
gc.collect()
shutil.rmtree(write_file)
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
uv_in = UVData()
uv_in.read(write_file, ant_str="all")
assert uv_in == full
# cleanup
del uv_in, full, exp_uv
gc.collect()
shutil.rmtree(write_file)
@pytest.mark.parametrize(
"err_type,select_kwargs,err_msg",
[
(
AssertionError,
{"ant_str": "auto", "antenna_nums": [0, 1]},
"ant_str must be None if antenna_nums or bls is not None",
),
(ValueError, {"bls": "foo"}, "bls must be a list of tuples of antenna numbers"),
(
ValueError,
{"bls": [[0, 1]]},
"bls must be a list of tuples of antenna numbers",
),
(
ValueError,
{"bls": [("foo", "bar")]},
"bls must be a list of tuples of antenna numbers",
),
(
ValueError,
{"bls": [("foo",)]},
"bls tuples must be all length-2 or all length-3",
),
(
ValueError,
{"bls": [(1, 2), (2, 3, "xx")]},
"bls tuples must be all length-2 or all length-3",
),
(
ValueError,
{"bls": [(2, 4, 0)]},
"The third element in each bl must be a polarization string",
),
(
ValueError,
{"bls": [(2, 4, "xy")], "polarizations": ["xy"]},
"Cannot provide length-3 tuples and also specify polarizations.",
),
(
AssertionError,
{"antenna_nums": np.array([(0, 10)])},
"antenna_nums must be fed as a list of antenna number integers",
),
(
AssertionError,
{"polarizations": "xx"},
"pols must be a list of polarization strings or ints",
),
(
ValueError,
{"polarizations": ["yy"]},
"No data is present, probably as a result of select on read",
),
(
AssertionError,
{"time_range": "foo"},
"time_range must be a len-2 list of Julian Date floats",
),
(
AssertionError,
{"time_range": [1, 2, 3]},
"time_range must be a len-2 list of Julian Date floats",
),
(
AssertionError,
{"time_range": ["foo", "bar"]},
"time_range must be a len-2 list of Julian Date floats",
),
(
ValueError,
{"time_range": [10.1, 10.2]},
"No data is present, probably as a result of select on read",
),
(AssertionError, {"ant_str": 0}, "ant_str must be fed as a string"),
],
)
def test_readWriteReadMiriad_partial_errors(err_type, select_kwargs, err_msg):
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
# check partial read selections
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
uv_in = UVData()
with pytest.raises(err_type) as cm:
uv_in.read(write_file, **select_kwargs)
assert str(cm.value).startswith(err_msg)
del uv_in, full
gc.collect()
if os.path.exists(write_file):
shutil.rmtree(write_file)
def test_readWriteReadMiriad_partial_error_special_cases():
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
# check partial read selections
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
uv_in = UVData()
with pytest.raises(ValueError) as cm:
uv_in.read(write_file, polarizations=[1.0])
assert str(cm.value).startswith(
"Polarization 1.0 cannot be converted to a polarization number"
)
# cleanup
del uv_in, full
gc.collect()
shutil.rmtree(write_file)
def test_readWriteReadMiriad_partial_with_warnings():
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
# check partial read selections
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
uv_in = UVData()
# check handling for generic read selections unsupported by read_miriad
unique_times = np.unique(full.time_array)
times_to_keep = unique_times[
((unique_times > 2456865.607) & (unique_times < 2456865.609))
]
uvtest.checkWarnings(
uv_in.read,
[write_file],
{"times": times_to_keep},
message=["Warning: a select on read keyword is set"],
)
exp_uv = full.select(times=times_to_keep, inplace=False)
assert uv_in == exp_uv
del uv_in
gc.collect()
shutil.rmtree(write_file)
full = UVData()
full.read(testfile)
full.write_miriad(write_file, clobber=True)
uv_in = UVData()
# check handling for generic read selections unsupported by read_miriad
blts_select = np.where(full.time_array == unique_times[0])[0]
ants_keep = [0, 2, 4]
uvtest.checkWarnings(
uv_in.read,
[write_file],
{"blt_inds": blts_select, "antenna_nums": ants_keep},
nwarnings=1,
message=["Warning: blt_inds is set along with select on read"],
)
exp_uv = full.select(blt_inds=blts_select, antenna_nums=ants_keep, inplace=False)
assert uv_in != exp_uv
# cleanup
del uv_in, full
gc.collect()
shutil.rmtree(write_file)
def test_readWriteReadMiriad_partial_metadata_only():
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
write_file2 = os.path.join(DATA_PATH, "test/outtest_miriad2.uv")
# try metadata only read
uv_in = UVData()
uv_in.read(testfile, read_data=False)
assert uv_in.time_array is None
assert uv_in.data_array is None
assert uv_in.integration_time is None
metadata = [
"antenna_positions",
"antenna_names",
"antenna_positions",
"channel_width",
"history",
"vis_units",
"telescope_location",
]
for m in metadata:
assert getattr(uv_in, m) is not None
# metadata only multiple file read-in
del uv_in
uv_in = UVData()
uv_in.read(testfile)
new_uv = uv_in.select(freq_chans=np.arange(5), inplace=False)
new_uv.write_miriad(write_file, clobber=True)
new_uv = uv_in.select(freq_chans=np.arange(5) + 5, inplace=False)
new_uv.write_miriad(write_file2, clobber=True)
uv_in.read(testfile)
uv_in.select(freq_chans=np.arange(10))
uv_in2 = UVData()
uv_in2.read(np.array([write_file, write_file2]))
assert uv_in.history != uv_in2.history
uv_in2.history = uv_in.history
assert uv_in == uv_in2
# cleanup
del uv_in, new_uv, uv_in2
gc.collect()
shutil.rmtree(write_file)
shutil.rmtree(write_file2)
@uvtest.skipIf_no_casa
def test_readMSWriteMiriad_CASAHistory():
"""
read in .ms file.
Write to a miriad file, read back in and check for history parameter
"""
ms_uv = UVData()
miriad_uv = UVData()
ms_file = os.path.join(DATA_PATH, "day2_TDEM0003_10s_norx_1src_1spw.ms")
testfile = os.path.join(DATA_PATH, "test/outtest_miriad")
uvtest.checkWarnings(
ms_uv.read, [ms_file], message="Telescope EVLA is not", nwarnings=0
)
ms_uv.write_miriad(testfile, clobber=True)
uvtest.checkWarnings(miriad_uv.read, [testfile], message="Telescope EVLA is not")
assert miriad_uv == ms_uv
# cleanup
del ms_uv, miriad_uv
gc.collect()
shutil.rmtree(testfile)
def test_rwrMiriad_antpos_issues():
"""
test warnings and errors associated with antenna position issues in Miriad files
Read in Miriad PAPER file, mess with various antpos issues and write out as
a new Miriad file, read back in and check for appropriate behavior.
"""
uv_in = UVData()
uv_out = UVData()
testfile = os.path.join(DATA_PATH, "zen.2456865.60537.xy.uvcRREAA")
write_file = os.path.join(DATA_PATH, "test/outtest_miriad.uv")
uv_in.read(testfile)
uv_in.antenna_positions = None
uv_in.write_miriad(write_file, clobber=True, run_check=False)
uvtest.checkWarnings(
uv_out.read,
func_args=[write_file],
func_kwargs={"run_check": False},
nwarnings=2,
message=[
"Antenna positions are not present in the file.",
"Antenna positions are not present in the file.",
],
category=[UserWarning, UserWarning],
)
assert uv_in == uv_out
uv_in.read(testfile)
ants_with_data = list(set(uv_in.ant_1_array).union(uv_in.ant_2_array))
ant_ind = np.where(uv_in.antenna_numbers == ants_with_data[0])[0]
uv_in.antenna_positions[ant_ind, :] = [0, 0, 0]
uv_in.write_miriad(write_file, clobber=True, no_antnums=True)
uvtest.checkWarnings(uv_out.read, [write_file], message=["antenna number"])
assert uv_in == uv_out
uv_in.read(testfile)
uv_in.antenna_positions = None
ants_with_data = sorted(list(set(uv_in.ant_1_array).union(uv_in.ant_2_array)))
new_nums = []
new_names = []
for a in ants_with_data:
new_nums.append(a)
ind = np.where(uv_in.antenna_numbers == a)[0][0]
new_names.append(uv_in.antenna_names[ind])
uv_in.antenna_numbers = np.array(new_nums)
uv_in.antenna_names = new_names
uv_in.Nants_telescope = len(uv_in.antenna_numbers)
uv_in.write_miriad(write_file, clobber=True, no_antnums=True, run_check=False)
uvtest.checkWarnings(
uv_out.read,
func_args=[write_file],
func_kwargs={"run_check": False},
nwarnings=2,
message=[
"Antenna positions are not present in the file.",
"Antenna positions are not present in the file.",
],
category=[UserWarning, UserWarning],
)
assert uv_in == uv_out
# cleanup
del uv_in, uv_out
gc.collect()
shutil.rmtree(write_file)
@pytest.mark.filterwarnings("ignore:Telescope EVLA is not")
def test_multi_files():
"""
Reading multiple files at once.
"""
uv_full = UVData()
uvfits_file = os.path.join(DATA_PATH, "day2_TDEM0003_10s_norx_1src_1spw.uvfits")
testfile1 = os.path.join(DATA_PATH, "test/uv1")
testfile2 = os.path.join(DATA_PATH, "test/uv2")
uv_full.read_uvfits(uvfits_file)
# rename telescope to avoid name warning
uv_full.unphase_to_drift()
uv_full.conjugate_bls("ant1<ant2")
uv1 = copy.deepcopy(uv_full)
uv2 = copy.deepcopy(uv_full)
uv1.select(freq_chans=np.arange(0, 32))
uv2.select(freq_chans=np.arange(32, 64))
uv1.write_miriad(testfile1, clobber=True)
uv2.write_miriad(testfile2, clobber=True)
del uv1
uv1 = UVData()
uvtest.checkWarnings(
uv1.read,
func_args=[[testfile1, testfile2]],
func_kwargs={"file_type": "miriad"},
message=["Telescope EVLA is not"],
category=2 * [UserWarning],
nwarnings=2
)
# Check history is correct, before replacing and doing a full object check
assert uvutils._check_histories(
uv_full.history + " Downselected to "
"specific frequencies using pyuvdata. "
"Combined data along frequency axis using"
" pyuvdata.",
uv1.history,
)
uv1.history = uv_full.history
assert uv1 == uv_full
# again, setting axis
del uv1
uv1 = UVData()
uv1.read([testfile1, testfile2], axis="freq")
# Check history is correct, before replacing and doing a full object check
assert uvutils._check_histories(
uv_full.history + " Downselected to "
"specific frequencies using pyuvdata. "
"Combined data along frequency axis using"
" pyuvdata.",
uv1.history,
)
uv1.history = uv_full.history
assert uv1 == uv_full
# cleanup
del uv1, uv2, uv_full
gc.collect()
shutil.rmtree(testfile1)
shutil.rmtree(testfile2)
def test_antpos_units():
"""
Read uvfits, write miriad. Check written antpos are in ns.
"""
uv = UVData()
uvfits_file = os.path.join(DATA_PATH, "day2_TDEM0003_10s_norx_1src_1spw.uvfits")
testfile = os.path.join(DATA_PATH, "test/uv_antpos_units")
uvtest.checkWarnings(uv.read_uvfits, [uvfits_file], message="Telescope EVLA is not")
uv.write_miriad(testfile, clobber=True)
auv = aipy_extracts.UV(testfile)
aantpos = auv["antpos"].reshape(3, -1).T * const.c.to("m/ns").value
aantpos = aantpos[uv.antenna_numbers, :]
aantpos = (
uvutils.ECEF_from_rotECEF(aantpos, uv.telescope_location_lat_lon_alt[1])
- uv.telescope_location
)
assert np.allclose(aantpos, uv.antenna_positions)
# cleanup
del uv, auv
gc.collect()
shutil.rmtree(testfile)
def test_readMiriadwriteMiriad_check_time_format():
"""
test time_array is converted properly from Miriad format
"""
# test read-in
fname = os.path.join(DATA_PATH, "zen.2457698.40355.xx.HH.uvcA")
uvd = UVData()
uvd.read(fname)
uvd_t = uvd.time_array.min()
uvd_l = uvd.lst_array.min()
uv = aipy_extracts.UV(fname)
uv_t = uv["time"] + uv["inttime"] / (24 * 3600.0) / 2
lat, lon, alt = uvd.telescope_location_lat_lon_alt
t1 = Time(uv["time"], format="jd", location=(lon, lat))
dt = TimeDelta(uv["inttime"] / 2, format="sec")
t2 = t1 + dt
lsts = uvutils.get_lst_for_time(np.array([t1.jd, t2.jd]), lat, lon, alt)
delta_lst = lsts[1] - lsts[0]
uv_l = uv["lst"] + delta_lst
# assert starting time array and lst array are shifted by half integration
assert np.isclose(uvd_t, uv_t)
# avoid errors if IERS table is too old (if the iers url is down)
tolerance = 1e-8
assert np.allclose(uvd_l, uv_l, atol=tolerance)
# test write-out
fout = os.path.join(DATA_PATH, "ex_miriad")
uvd.write_miriad(fout, clobber=True)
# assert equal to original miriad time
uv2 = aipy_extracts.UV(fout)
assert np.isclose(uv["time"], uv2["time"])
assert np.isclose(uv["lst"], uv2["lst"], atol=tolerance)
# cleanup
del uv, uv2, uvd
gc.collect()
if os.path.exists(fout):
shutil.rmtree(fout)
def test_file_with_bad_extra_words():
"""Test file with bad extra words is iterated and popped correctly."""
fname = os.path.join(DATA_PATH, "test_miriad_changing_extra.uv")
uv = UVData()
warn_message = [
"Altitude is not present in Miriad file, "
"using known location values for PAPER.",
"Mean of empty slice.",
"invalid value encountered in double_scalars",
"npols=4 but found 1 pols in data file",
"Mean of empty slice.",
"invalid value encountered in double_scalars",
"antenna number 0 has visibilities associated with it, "
"but it has a position of (0,0,0)",
"antenna number 26 has visibilities associated with it, "
"but it has a position of (0,0,0)",
]
warn_category = (
[UserWarning]
+ [RuntimeWarning] * 2
+ [UserWarning]
+ [RuntimeWarning] * 2
+ [UserWarning] * 2
)
# This is an old PAPER file, run_check must be set to false
# The antenna positions is (0, 0, 0) vector
uv = uvtest.checkWarnings(
uv.read_miriad,
func_args=[fname],
func_kwargs={"run_check": False},
category=warn_category,
nwarnings=len(warn_message),
message=warn_message,
)
# cleanup
del uv
gc.collect()
