def test_total_quality_array_size():
"""
Test that total quality array defaults to the proper size
"""
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.fitsA')
cal_in.read_calfits(testfile)
# Create filler total quality array
cal_in.total_quality_array = np.zeros(
cal_in._total_quality_array.expected_shape(cal_in))
proper_shape = (cal_in.Nspws, cal_in.Nfreqs, cal_in.Ntimes, cal_in.Njones)
nt.assert_equal(cal_in.total_quality_array.shape, proper_shape)
del (cal_in)
# also test delay-type calibrations
cal_in = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.HH.uvc.fits')
message = testfile + ' appears to be an old calfits format'
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
cal_in.total_quality_array = np.zeros(
cal_in._total_quality_array.expected_shape(cal_in))
proper_shape = (cal_in.Nspws, 1, cal_in.Ntimes, cal_in.Njones)
nt.assert_equal(cal_in.total_quality_array.shape, proper_shape)
del (cal_in)
def test_input_flag_array():
"""
Test when data file has input flag array.
Currently we do not have a testfile, so we will artifically create one
and check for internal consistency.
"""
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.fitsA')
write_file = os.path.join(DATA_PATH, 'test/outtest_input_flags.fits')
message = testfile + ' appears to be an old calfits format which'
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
cal_in.input_flag_array = np.zeros(cal_in._input_flag_array.expected_shape(cal_in), dtype=bool)
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
# Repeat for delay version
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.HH.uvc.fits')
message = [testfile + ' appears to be an old calfits format which',
testfile + ' appears to be an old calfits format for delay files']
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message,
nwarnings=2)
cal_in.input_flag_array = np.zeros(cal_in._input_flag_array.expected_shape(cal_in), dtype=bool)
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
del(cal_in)
del(cal_out)
def test_jones():
"""
Test when data file has more than one element in Jones matrix.
Currently we do not have a testfile, so we will artifically create one
and check for internal consistency.
"""
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.fitsA')
write_file = os.path.join(DATA_PATH, 'test/outtest_jones.fits')
message = testfile + ' appears to be an old calfits format which'
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
# Create filler jones info
cal_in.jones_array = np.array([-5, -6, -7, -8])
cal_in.Njones = 4
cal_in.flag_array = np.zeros(cal_in._flag_array.expected_shape(cal_in),
dtype=bool)
cal_in.gain_array = np.ones(cal_in._gain_array.expected_shape(cal_in),
dtype=np.complex64)
cal_in.quality_array = np.zeros(
cal_in._quality_array.expected_shape(cal_in))
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
# Repeat for delay version
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.HH.uvc.fits')
message = [
testfile + ' appears to be an old calfits format which',
testfile + ' appears to be an old calfits format for delay files'
]
uvtest.checkWarnings(cal_in.read_calfits, [testfile],
message=message,
nwarnings=2)
# Create filler jones info
cal_in.jones_array = np.array([-5, -6, -7, -8])
cal_in.Njones = 4
cal_in.flag_array = np.zeros(cal_in._flag_array.expected_shape(cal_in),
dtype=bool)
cal_in.delay_array = np.ones(cal_in._delay_array.expected_shape(cal_in),
dtype=np.float64)
cal_in.quality_array = np.zeros(
cal_in._quality_array.expected_shape(cal_in))
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
del (cal_in)
del (cal_out)
def test_write_time_precision():
"""
Test that times are being written to appropriate precision (see issue 311).
"""
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.fitsA')
write_file = os.path.join(DATA_PATH, 'test/outtest_omnical.fits')
message = testfile + ' appears to be an old calfits format which'
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
# overwrite time array to break old code
dt = cal_in.integration_time / (24. * 60. * 60.)
cal_in.time_array = dt * np.arange(cal_in.Ntimes)
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
def test_readwriteread_total_quality_array():
"""
Test when data file has a total quality array.
Currently we have no such file, so we will artificially create one and
check for internal consistency.
"""
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.fitsA')
write_file = os.path.join(DATA_PATH,
'test/outtest_total_quality_array.fits')
message = testfile + ' appears to be an old calfits format which'
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
# Create filler total quality array
cal_in.total_quality_array = np.zeros(
cal_in._total_quality_array.expected_shape(cal_in))
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
del (cal_in)
del (cal_out)
# also test delay-type calibrations
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.HH.uvc.fits')
write_file = os.path.join(DATA_PATH,
'test/outtest_total_quality_array_delays.fits')
message = [
testfile + ' appears to be an old calfits format which',
testfile + ' appears to be an old calfits format for delay files'
]
uvtest.checkWarnings(cal_in.read_calfits, [testfile],
message=message,
nwarnings=2)
cal_in.total_quality_array = np.zeros(
cal_in._total_quality_array.expected_shape(cal_in))
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
del (cal_in)
del (cal_out)
def test_readwriteread_delays():
"""
Read-Write-Read test with a fits calibration files containing delays.
Read in uvfits file, write out new uvfits file, read back in and check for
object equality
"""
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.HH.uvc.fits')
write_file = os.path.join(DATA_PATH, 'test/outtest_firstcal.fits')
message = testfile + ' appears to be an old calfits format'
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
del (cal_in)
del (cal_out)
def test_readwriteread():
"""
Omnical fits loopback test.
Read in uvfits file, write out new uvfits file, read back in and check for
object equality.
"""
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.fitsA')
write_file = os.path.join(DATA_PATH, 'test/outtest_omnical.fits')
message = testfile + ' appears to be an old calfits format which'
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
# test without freq_range parameter
cal_in.freq_range = None
cal_in.write_calfits(write_file, clobber=True)
cal_out.read_calfits(write_file)
nt.assert_equal(cal_in, cal_out)
def test_extra_keywords():
cal_in = UVCal()
cal_out = UVCal()
calfits_file = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.fitsA')
testfile = os.path.join(DATA_PATH, 'test/outtest_omnical.fits')
message = calfits_file + ' appears to be an old calfits format which'
uvtest.checkWarnings(cal_in.read_calfits, [calfits_file], message=message)
# check for warnings & errors with extra_keywords that are dicts, lists or arrays
cal_in.extra_keywords['testdict'] = {'testkey': 23}
uvtest.checkWarnings(cal_in.check, message=['testdict in extra_keywords is a '
'list, array or dict'])
nt.assert_raises(TypeError, cal_in.write_calfits, testfile, run_check=False)
cal_in.extra_keywords.pop('testdict')
cal_in.extra_keywords['testlist'] = [12, 14, 90]
uvtest.checkWarnings(cal_in.check, message=['testlist in extra_keywords is a '
'list, array or dict'])
nt.assert_raises(TypeError, cal_in.write_calfits, testfile, run_check=False)
cal_in.extra_keywords.pop('testlist')
cal_in.extra_keywords['testarr'] = np.array([12, 14, 90])
uvtest.checkWarnings(cal_in.check, message=['testarr in extra_keywords is a '
'list, array or dict'])
nt.assert_raises(TypeError, cal_in.write_calfits, testfile, run_check=False)
cal_in.extra_keywords.pop('testarr')
# check for warnings with extra_keywords keys that are too long
cal_in.extra_keywords['test_long_key'] = True
uvtest.checkWarnings(cal_in.check, message=['key test_long_key in extra_keywords '
'is longer than 8 characters'])
uvtest.checkWarnings(cal_in.write_calfits, [testfile], {'run_check': False,
'clobber': True},
message=['key test_long_key in extra_keywords is longer than 8 characters'])
cal_in.extra_keywords.pop('test_long_key')
# check handling of boolean keywords
cal_in.extra_keywords['bool'] = True
cal_in.extra_keywords['bool2'] = False
cal_in.write_calfits(testfile, clobber=True)
cal_out.read_calfits(testfile)
nt.assert_equal(cal_in, cal_out)
cal_in.extra_keywords.pop('bool')
cal_in.extra_keywords.pop('bool2')
# check handling of int-like keywords
cal_in.extra_keywords['int1'] = np.int(5)
cal_in.extra_keywords['int2'] = 7
cal_in.write_calfits(testfile, clobber=True)
cal_out.read_calfits(testfile)
nt.assert_equal(cal_in, cal_out)
cal_in.extra_keywords.pop('int1')
cal_in.extra_keywords.pop('int2')
# check handling of float-like keywords
cal_in.extra_keywords['float1'] = np.int64(5.3)
cal_in.extra_keywords['float2'] = 6.9
cal_in.write_calfits(testfile, clobber=True)
cal_out.read_calfits(testfile)
nt.assert_equal(cal_in, cal_out)
cal_in.extra_keywords.pop('float1')
cal_in.extra_keywords.pop('float2')
# check handling of complex-like keywords
cal_in.extra_keywords['complex1'] = np.complex64(5.3 + 1.2j)
cal_in.extra_keywords['complex2'] = 6.9 + 4.6j
cal_in.write_calfits(testfile, clobber=True)
cal_out.read_calfits(testfile)
nt.assert_equal(cal_in, cal_out)
cal_in.extra_keywords.pop('complex1')
cal_in.extra_keywords.pop('complex2')
# check handling of comment keywords
cal_in.extra_keywords['comment'] = ('this is a very long comment that will '
'be broken into several lines\nif '
'everything works properly.')
cal_in.write_calfits(testfile, clobber=True)
cal_out.read_calfits(testfile)
nt.assert_equal(cal_in, cal_out)
def test_errors():
"""
Test for various errors.
"""
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.HH.uvc.fits')
write_file = os.path.join(DATA_PATH, 'test/outtest_firstcal.fits')
message = testfile + ' appears to be an old calfits format'
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
cal_in.set_unknown_cal_type()
nt.assert_raises(ValueError,
cal_in.write_calfits,
write_file,
run_check=False,
clobber=True)
# change values for various axes in flag and total quality hdus to not match primary hdu
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
# Create filler jones info
cal_in.jones_array = np.array([-5, -6, -7, -8])
cal_in.Njones = 4
cal_in.flag_array = np.zeros(cal_in._flag_array.expected_shape(cal_in),
dtype=bool)
cal_in.delay_array = np.ones(cal_in._delay_array.expected_shape(cal_in),
dtype=np.float64)
cal_in.quality_array = np.zeros(
cal_in._quality_array.expected_shape(cal_in))
# add total_quality_array so that can be tested as well
cal_in.total_quality_array = np.zeros(
cal_in._total_quality_array.expected_shape(cal_in))
header_vals_to_double = [{
'flag': 'CDELT2'
}, {
'flag': 'CDELT3'
}, {
'flag': 'CRVAL5'
}, {
'totqual': 'CDELT1'
}, {
'totqual': 'CDELT2'
}, {
'totqual': 'CRVAL4'
}]
for i, hdr_dict in enumerate(header_vals_to_double):
cal_in.write_calfits(write_file, clobber=True)
unit = hdr_dict.keys()[0]
keyword = hdr_dict[unit]
F = fits.open(write_file)
data = F[0].data
primary_hdr = F[0].header
hdunames = uvutils.fits_indexhdus(F)
ant_hdu = F[hdunames['ANTENNAS']]
flag_hdu = F[hdunames['FLAGS']]
flag_hdr = flag_hdu.header
totqualhdu = F[hdunames['TOTQLTY']]
totqualhdr = totqualhdu.header
if unit == 'flag':
flag_hdr[keyword] *= 2
elif unit == 'totqual':
totqualhdr[keyword] *= 2
prihdu = fits.PrimaryHDU(data=data, header=primary_hdr)
hdulist = fits.HDUList([prihdu, ant_hdu])
flag_hdu = fits.ImageHDU(data=flag_hdu.data, header=flag_hdr)
hdulist.append(flag_hdu)
totqualhdu = fits.ImageHDU(data=totqualhdu.data, header=totqualhdr)
hdulist.append(totqualhdu)
if float(astropy.__version__[0:3]) < 1.3:
hdulist.writeto(write_file, clobber=True)
else:
hdulist.writeto(write_file, overwrite=True)
nt.assert_raises(ValueError,
cal_out.read_calfits,
write_file,
strict_fits=True)
# repeat for gain type file
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.fitsA')
write_file = os.path.join(DATA_PATH, 'test/outtest_omnical.fits')
cal_in.read_calfits(testfile)
# Create filler jones info
cal_in.jones_array = np.array([-5, -6, -7, -8])
cal_in.Njones = 4
cal_in.flag_array = np.zeros(cal_in._flag_array.expected_shape(cal_in),
dtype=bool)
cal_in.gain_array = np.ones(cal_in._gain_array.expected_shape(cal_in),
dtype=np.complex64)
cal_in.quality_array = np.zeros(
cal_in._quality_array.expected_shape(cal_in))
# add total_quality_array so that can be tested as well
cal_in.total_quality_array = np.zeros(
cal_in._total_quality_array.expected_shape(cal_in))
header_vals_to_double = [{
'totqual': 'CDELT1'
}, {
'totqual': 'CDELT2'
}, {
'totqual': 'CDELT3'
}, {
'totqual': 'CRVAL4'
}]
for i, hdr_dict in enumerate(header_vals_to_double):
cal_in.write_calfits(write_file, clobber=True)
unit = hdr_dict.keys()[0]
keyword = hdr_dict[unit]
F = fits.open(write_file)
data = F[0].data
primary_hdr = F[0].header
hdunames = uvutils.fits_indexhdus(F)
ant_hdu = F[hdunames['ANTENNAS']]
totqualhdu = F[hdunames['TOTQLTY']]
totqualhdr = totqualhdu.header
if unit == 'totqual':
totqualhdr[keyword] *= 2
prihdu = fits.PrimaryHDU(data=data, header=primary_hdr)
hdulist = fits.HDUList([prihdu, ant_hdu])
totqualhdu = fits.ImageHDU(data=totqualhdu.data, header=totqualhdr)
hdulist.append(totqualhdu)
if float(astropy.__version__[0:3]) < 1.3:
hdulist.writeto(write_file, clobber=True)
else:
hdulist.writeto(write_file, overwrite=True)
nt.assert_raises(ValueError,
cal_out.read_calfits,
write_file,
strict_fits=True)
def test_read_oldcalfits():
"""
Test for proper behavior with old calfits files.
"""
# start with gain type files
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.fitsA')
write_file = os.path.join(DATA_PATH, 'test/outtest_omnical.fits')
cal_in.read_calfits(testfile)
# add total_quality_array so that can be tested as well
cal_in.total_quality_array = np.zeros(
cal_in._total_quality_array.expected_shape(cal_in))
# now read in the file and remove various CRPIX and CRVAL keywords to
# emulate old calfits files
header_vals_to_remove = [{
'primary': 'CRVAL5'
}, {
'primary': 'CRPIX4'
}, {
'totqual': 'CRVAL4'
}]
messages = [write_file, 'This file', write_file]
messages = [m + ' appears to be an old calfits format' for m in messages]
for i, hdr_dict in enumerate(header_vals_to_remove):
cal_in.write_calfits(write_file, clobber=True)
unit = hdr_dict.keys()[0]
keyword = hdr_dict[unit]
F = fits.open(write_file)
data = F[0].data
primary_hdr = F[0].header
hdunames = uvutils.fits_indexhdus(F)
ant_hdu = F[hdunames['ANTENNAS']]
totqualhdu = F[hdunames['TOTQLTY']]
totqualhdr = totqualhdu.header
if unit == 'primary':
primary_hdr.pop(keyword)
elif unit == 'totqual':
totqualhdr.pop(keyword)
prihdu = fits.PrimaryHDU(data=data, header=primary_hdr)
hdulist = fits.HDUList([prihdu, ant_hdu])
totqualhdu = fits.ImageHDU(data=totqualhdu.data, header=totqualhdr)
hdulist.append(totqualhdu)
if float(astropy.__version__[0:3]) < 1.3:
hdulist.writeto(write_file, clobber=True)
else:
hdulist.writeto(write_file, overwrite=True)
uvtest.checkWarnings(cal_out.read_calfits, [write_file],
message=messages[i])
nt.assert_equal(cal_in, cal_out)
nt.assert_raises(KeyError,
cal_out.read_calfits,
write_file,
strict_fits=True)
# now with delay type files
cal_in = UVCal()
cal_out = UVCal()
testfile = os.path.join(DATA_PATH, 'zen.2457698.40355.xx.HH.uvc.fits')
write_file = os.path.join(DATA_PATH, 'test/outtest_firstcal.fits')
message = testfile + ' appears to be an old calfits format'
uvtest.checkWarnings(cal_in.read_calfits, [testfile], message=message)
# add total_quality_array so that can be tested as well
cal_in.total_quality_array = np.zeros(
cal_in._total_quality_array.expected_shape(cal_in))
# now read in the file and remove various CRPIX and CRVAL keywords to
# emulate old calfits files
header_vals_to_remove = [{
'primary': 'CRVAL5'
}, {
'flag': 'CRVAL5'
}, {
'flag': 'CRPIX4'
}, {
'totqual': 'CRVAL4'
}]
messages = [write_file, 'This file', 'This file', write_file]
messages = [m + ' appears to be an old calfits format' for m in messages]
for i, hdr_dict in enumerate(header_vals_to_remove):
cal_in.write_calfits(write_file, clobber=True)
unit = hdr_dict.keys()[0]
keyword = hdr_dict[unit]
F = fits.open(write_file)
data = F[0].data
primary_hdr = F[0].header
hdunames = uvutils.fits_indexhdus(F)
ant_hdu = F[hdunames['ANTENNAS']]
flag_hdu = F[hdunames['FLAGS']]
flag_hdr = flag_hdu.header
totqualhdu = F[hdunames['TOTQLTY']]
totqualhdr = totqualhdu.header
if unit == 'primary':
primary_hdr.pop(keyword)
elif unit == 'flag':
flag_hdr.pop(keyword)
elif unit == 'totqual':
totqualhdr.pop(keyword)
prihdu = fits.PrimaryHDU(data=data, header=primary_hdr)
hdulist = fits.HDUList([prihdu, ant_hdu])
flag_hdu = fits.ImageHDU(data=flag_hdu.data, header=flag_hdr)
hdulist.append(flag_hdu)
totqualhdu = fits.ImageHDU(data=totqualhdu.data, header=totqualhdr)
hdulist.append(totqualhdu)
if float(astropy.__version__[0:3]) < 1.3:
hdulist.writeto(write_file, clobber=True)
else:
hdulist.writeto(write_file, overwrite=True)
uvtest.checkWarnings(cal_out.read_calfits, [write_file],
message=messages[i])
nt.assert_equal(cal_in, cal_out)
nt.assert_raises(KeyError,
cal_out.read_calfits,
write_file,
strict_fits=True)