def test__regrid_spect(self, data__interp_spect):
"""
Checks to make:
- Ensure new_wavl comes out correctly in output
- Ensure no interp'd points above/below input points
"""
wavl, data, new_wavl = data__interp_spect
gs = GHOSTSpect([])
new_data = gs._regrid_spect(data, wavl, new_wavl, waveunits='angstrom')
assert new_data.shape == new_wavl.shape, "Data was not successfully " \
"reshaped to the new " \
"wavelength scale " \
"(expected {}, " \
"have {})".format(
new_wavl.shape, new_data.shape,
)
max_wavl_spacing = np.max(wavl[1:] - wavl[:-1])
assert np.sum(new_data[np.logical_or(
new_wavl < np.min(wavl) - max_wavl_spacing,
new_wavl > np.max(wavl) + max_wavl_spacing,
)]) < 1e-6, "Non-zero interpolated data points " \
"have been identified outside the " \
"range of the original wavelength " \
"scale"
def test__compute_barycentric_correction_values(
self, ra, dec, dt, known_corr,
data__compute_barycentric_correction):
"""
Checks to make:
- Correct units of return based on input arguments
- Some regression test values
"""
ad, tmpsubdir = data__compute_barycentric_correction
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad.phu.set('RA', ra)
ad.phu.set('DEC', dec)
# Assume a 10 min exposure
exp_time_min = 10.
dt_obs = datetime.datetime.strptime(dt, '%Y-%m-%d %H:%M:%S')
dt_start = dt_obs - datetime.timedelta(minutes=exp_time_min)
ad.phu.set('DATE-OBS', dt_start.date().strftime('%Y-%m-%d'))
ad.phu.set('UTSTART', dt_start.time().strftime('%H:%M:%S.00'))
ad[0].hdr.set('EXPTIME', exp_time_min * 60.)
gs = GHOSTSpect([])
corr_fact = gs._compute_barycentric_correction(ad, )[0]
assert abs(corr_fact - known_corr) < 1e-6, \
"_compute_barycentric_correction " \
"returned an incorrect value " \
"(expected {}, returned {})".format(
known_corr, corr_fact,
)
def test_responseCorrect(self, tmpdir):
"""
Checks to make:
- Ensure skip option functions correctly
More complete testing to be made in 'all-up' reduction
"""
tmpsubdir = tmpdir.mkdir('ghost_responsecorr')
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad = self.generate_minimum_file()
gs = GHOSTSpect([])
# Test the skip functionality
ad_out = gs.responseCorrect([
ad,
], skip=True)[0]
assert ad_out.phu.get(
gs.timestamp_keys['responseCorrect']
) is None, "responseCorrect appears to have acted on a file " \
"when skip=True"
# Teardown - remove calibrations and output file
for _ in glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, '*.fits')):
os.remove(_)
try:
shutil.rmtree(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'calibrations'))
except OSError:
pass
def test_standardizeStructure(self, tmpdir):
"""
Checks to make:
- This is a no-op primitive - ensure no change is made
"""
tmpsubdir = tmpdir.mkdir('ghost_standstruct')
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad = self.generate_minimum_file()
ad_orig = copy.deepcopy(ad)
gs = GHOSTSpect([])
ad_out = gs.standardizeStructure([
ad,
])[0]
assert np.all([
ad_orig.info() == ad_out.info(),
ad_orig.phu == ad_out.phu,
ad_orig[0].hdr == ad_out[0].hdr,
len(ad_orig) == len(ad_out),
]), "standardizeStructure is no longer a no-op primitive"
# Teardown - remove calibrations and output file
for _ in glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, '*.fits')):
os.remove(_)
try:
shutil.rmtree(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'calibrations'))
except OSError:
pass
def test__interp_spect_invalid_type(self, data__interp_spect):
wavl, data, new_wavl = data__interp_spect
gs = GHOSTSpect([])
with pytest.raises(NotImplementedError):
new_data = gs._interp_spect(data,
wavl,
new_wavl,
interp='no-such-method')
def test_darkCorrect_rebin(self, xbin, ybin, tmpdir):
"""
Checks to make:
- Ensure re-binning of darks is correctly triggered (i.e. deliberately
pass science and dark data w/ different binning, ensure no failure)
- Error mode check: see for error if length of dark list != length of
science list
- Check for DARKIM in output header
- Check before & after data shape
"""
tmpsubdir = tmpdir.mkdir('ghost_darkcorrect')
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad = self.generate_minimum_file()
dark = self.generate_minimum_file()
dark.filename = 'dark.fits'
# 'Re-bin' the data file
ad[0].data = np.ones((
int(1024 / ybin),
int(1024 / xbin),
),
dtype=np.float64)
ad[0].hdr.set('CCDSUM', '{} {}'.format(
xbin,
ybin,
))
gs = GHOSTSpect([])
input_shape = ad[0].data.shape
ad_out = gs.darkCorrect([
ad,
], dark=[
dark,
])[0]
assert ad_out[0].data.shape == input_shape, "darkCorrect has mangled " \
"the shape of the input " \
"data"
# Teardown - remove calibrations and output file
for _ in glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, '*.fits')):
os.remove(_)
try:
shutil.rmtree(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'calibrations'))
except OSError:
pass
def test__compute_barycentric_correction_returnwavl(
self, return_wavl, units, data__compute_barycentric_correction):
"""
Check the return units of _compute_barycentric_correction
"""
# ad should be correctly populated from previous test
ad, tmpsubdir = data__compute_barycentric_correction
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
gs = GHOSTSpect([])
corr_fact = gs._compute_barycentric_correction(
ad, return_wavl=return_wavl)[0]
assert corr_fact.unit == units, \
"_compute_barycentric_correction returned incorrect units " \
"(expected {}, got {})".format(units, corr_fact.unit, )
def test_clipSigmaBPM(self, tmpdir):
"""
Checks to make:
- Send it dummy file with known number of pixels outside range,
make sure that many pixels are flagged out
"""
tmpsubdir = tmpdir.mkdir('ghost_clipsigma')
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad = self.generate_minimum_file()
ad[0].DQ = np.zeros(ad[0].data.shape, dtype=np.int)
# Insert some very large data points into the otherwise all-1s data
xs = list(range(0, 1024))
ys = list(range(0, 1024))
np.random.shuffle(xs)
np.random.shuffle(ys)
xs = xs[:10]
ys = ys[:10]
for i in range(10):
ad[0].data[ys[i], xs[i]] = 1000.
gs = GHOSTSpect([])
ad_out = gs.clipSigmaBPM([
ad,
], bpm_value=1)[0]
assert np.all([ad_out[0].mask[ys[i], xs[i]] == 1
for i in range(10)]), "clipSigmaBPM failed to mask " \
"out all injected outliers"
assert ad_out.phu.get(
gs.timestamp_keys['clipSigmaBPM']), "clipSigmaBPM did not " \
"timestamp-mark the " \
"output file"
# Teardown - remove calibrations and output file
for _ in glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, '*.fits')):
os.remove(_)
try:
shutil.rmtree(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'calibrations'))
except OSError:
pass
def test__get_polyfit_filename_errors(self, data__get_polyfit_filename):
"""
Check passing an invalid calib. type throws an error
"""
ad, tmpsubdir = data__get_polyfit_filename
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad.phu.set('SMPNAME', 'HI_ONLY')
ad.phu.set('CAMERA', 'RED')
ad.phu.set('UTSTART',
datetime.datetime.now().time().strftime('%H:%M:%S'))
ad.phu.set('DATE-OBS',
datetime.datetime.now().date().strftime('%Y-%m-%d'))
gs = GHOSTSpect([])
polyfit_file = gs._get_polyfit_filename(ad, 'not-a-cal-type')
assert polyfit_file is None, "_get_polyfit_filename didn't return " \
"None when asked for a bogus " \
"model type"
def test__interp_spect(self, interp, data__interp_spect):
"""
Checks to make:
- New wavelength array appears in output
- Any point in output can be interpolated from surrounding points in
input
- Verify allowed values for kwarg 'interp'
"""
wavl, data, new_wavl = data__interp_spect
gs = GHOSTSpect([])
new_data = gs._interp_spect(data, wavl, new_wavl, interp='linear')
assert new_data.shape == new_wavl.shape, "Data was not successfully " \
"reshaped to the new " \
"wavelength scale " \
"(expected {}, " \
"have {})".format(
new_wavl.shape, new_data.shape,
)
def test__get_polyfit_filename(self, arm, res, caltype,
data__get_polyfit_filename):
"""
Checks to make:
- Provide a set of input (arm, res, ) arguments, see if a/ name is
returned
"""
ad, tmpsubdir = data__get_polyfit_filename
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad.phu.set('SMPNAME', res)
ad.phu.set('CAMERA', arm)
ad.phu.set('UTSTART',
datetime.datetime.now().time().strftime('%H:%M:%S'))
ad.phu.set('DATE-OBS',
datetime.datetime.now().date().strftime('%Y-%m-%d'))
gs = GHOSTSpect([])
polyfit_file = gs._get_polyfit_filename(ad, caltype)
assert polyfit_file is not None, "Could not find polyfit file"
def test_applyFlatBPM(self, data_applyFlatBPM):
"""
Checks to make:
- Check for addition of flat BPM
- Make sure the flat BPM has been added correctly (find a second method
of combining and checking)
- Check before & after data shape
"""
ad, flat_ad, tmpsubdir = data_applyFlatBPM
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
# Check the AttributeError is no flat is provided
gs = GHOSTSpect([
ad,
])
with pytest.raises(AttributeError):
ad_output = gs.applyFlatBPM([ad, ]), "applyFlatBPM failed to " \
"raise AttributeError when " \
"not passed a flat or flat " \
"stream"
ad_output = gs.applyFlatBPM([
ad,
], flat=flat_ad)
# Check that flat BPM is correctly carried over to (blank) ad BPM
assert np.allclose(ad_output[0].mask,
flat_ad[0].mask), "applyFlatBPM failed to " \
"correctly apply a flat BPM " \
"to a data file with a blank " \
"BPM"
# Double the BPM on the data (i.e. make all the values 2), and ensure
# that the re-applied values come out as 3
ad[0].mask *= 2
ad_output = gs.applyFlatBPM([
ad,
], flat=flat_ad)
assert np.allclose(ad_output[0].mask,
flat_ad[0].mask * 3), "applyFlatBPM failed to " \
"correctly apply a flat BPM " \
"to a data file with a non-" \
"zero BPM"
# Ensure the correct behaviour when the data file has no BPM
ad[0].mask = None # Is this the right way to do this? del doesn't work
ad_output = gs.applyFlatBPM([
ad,
], flat=flat_ad)
assert np.allclose(ad_output[0].mask,
flat_ad[0].mask), "applyFlatBPM failed to " \
"correctly apply a flat BPM " \
"to a data file with no inital " \
"BPM"
# Check that the file has been marked as processed
assert ad.phu.get(
gs.timestamp_keys['applyFlatBPM']), "clipSigmaBPM did not " \
"timestamp-mark the " \
"output file"
def test_interpolateAndCombine(self, tmpdir):
"""
Checks to make:
- Error on invalid scale option
- Correct functioning of 'skip' parameter
Fuller testing needs to be done 'all-up' in a reduction sequence.
"""
tmpsubdir = tmpdir.mkdir('ghost_inc')
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad = self.generate_minimum_file()
gs = GHOSTSpect([])
# Make sure the correct error is thrown on an invalid scale
with pytest.raises(ValueError):
gs.interpolateAndCombine([
ad,
], scale='not-a-scale')
# Test the skip functionality
ad_out = gs.interpolateAndCombine([
ad,
], skip=True)[0]
assert ad_out.phu.get(
gs.timestamp_keys['interpolateAndCombine']
) is None, "interpolateAndCombine appears to have acted on a file " \
"when skip=True"
# Teardown - remove calibrations and output file
for _ in glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, '*.fits')):
os.remove(_)
try:
shutil.rmtree(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'calibrations'))
except OSError:
pass
def test_darkCorrect(self, tmpdir):
tmpsubdir = tmpdir.mkdir('ghost_darkcorr')
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad = self.generate_minimum_file()
dark = self.generate_minimum_file()
dark.filename = 'dark.fits'
gs = GHOSTSpect([])
ad_out = gs.darkCorrect([
ad,
], dark=[
dark,
])
# import pdb; pdb.set_trace()
assert ad_out[0].phu.get('DARKIM') == dark.filename, \
"darkCorrect failed to record the name of the dark " \
"file used in the output header (expected {}, got {})".format(
dark.filename, ad_out[0].phu.get('DARKIM'),
)
assert ad_out[0].phu.get(
gs.timestamp_keys['darkCorrect']), "darkCorrect did not " \
"timestamp-mark the " \
"output file"
# Teardown - remove calibrations and output file
for _ in glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, '*.fits')):
os.remove(_)
try:
shutil.rmtree(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'calibrations'))
except OSError:
pass
def test_barycentricCorrect(self, data_barycentricCorrect):
"""
Checks to make:
- Make random checks that a non-1.0 correction factor works properly
- Check before & after data shape
Testing of the helper _compute_barycentric_correction is done
separately.
"""
ad, orig_wavl, tmpsubdir = data_barycentricCorrect
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
orig_ad = copy.deepcopy(ad)
gs = GHOSTSpect([
ad,
])
corr_fact = random.uniform(0.5, 1.5)
ad_out = gs.barycentricCorrect([
ad,
], correction_factor=corr_fact)[0]
assert np.allclose(ad_out[0].WAVL / corr_fact,
orig_wavl), "barycentricCorrect appears not to " \
"have made a valid correction " \
"(tried to correct by {}, " \
"apparent correction {})".format(
corr_fact, np.average(ad_out[0].WAVL / orig_wavl)
)
assert orig_ad[0].WAVL.shape == ad_out[0].WAVL.shape, \
"barycentricCorrect has mangled the shape of the output " \
"WAVL extension"
assert ad_out.phu.get(
gs.timestamp_keys['barycentricCorrect']), "clipSigmaBPM did not " \
"timestamp-mark the " \
"output file"
def test_darkCorrect_errors(self, tmpdir):
tmpsubdir = tmpdir.mkdir('ghost_dcerrors')
os.chdir(os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
ad = self.generate_minimum_file()
dark = self.generate_minimum_file()
dark.filename = 'dark.fits'
gs = GHOSTSpect([])
# Passing in data inputs with different binnings
with pytest.raises(IOError):
ad2 = copy.deepcopy(ad)
ad2[0].hdr.set('CCDSUM', '2 2')
gs.darkCorrect([
ad,
ad2,
], dark=[
dark,
dark,
])
# Mismatched list lengths
with pytest.raises(Exception):
gs.darkCorrect([
ad,
ad2,
ad,
], dark=[
dark,
dark,
])
# Teardown - remove calibrations and output file
for _ in glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, '*.fits')):
os.remove(_)
try:
shutil.rmtree(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'calibrations'))
except OSError:
pass