def test_ff_inv(rtdata, fitsdiff_default_kwargs):
"""Test flat field inversion"""
with dm.open(rtdata.get_data('nirspec/imaging/usf_assign_wcs.fits')) as data:
flatted = FlatFieldStep.call(data)
unflatted = FlatFieldStep.call(flatted, inverse=True)
assert np.allclose(data.data, unflatted.data), 'Inversion failed'
def test_ff_inv(rtdata, fitsdiff_default_kwargs):
"""Test flat field inversion"""
data = dm.open(rtdata.get_data('nirspec/ifu/nrs_ifu_nrs1_assign_wcs.fits'))
flatted = FlatFieldStep.call(data)
unflatted = FlatFieldStep.call(flatted, inverse=True)
assert np.allclose(data.data, unflatted.data), 'Inversion failed'
def test_ff_inv(rtdata, fitsdiff_default_kwargs):
"""Test flat field inversion"""
with dm.open(rtdata.get_data('nirspec/mos/usf_wavecorr.fits')) as data:
flatted = FlatFieldStep.call(data)
unflatted = FlatFieldStep.call(flatted, inverse=True)
bad_slits = []
for idx, slits in enumerate(zip(data.slits, unflatted.slits)):
data_slit, unflatted_slit = slits
if not np.allclose(data_slit.data, unflatted_slit.data):
bad_slits.append(idx)
assert not bad_slits, f'Inversion failed for slits {bad_slits}'
def test_flat_field_bots_interp_flat(rtdata, fitsdiff_default_kwargs):
"""Test the interpolated flat for a NRS BOTS exposure"""
data = rtdata.get_data(
'nirspec/tso/jw93056001001_short_nrs1_wavecorr.fits')
FlatFieldStep.call(data, save_interpolated_flat=True)
rtdata.output = 'jw93056001001_short_nrs1_wavecorr_interpolatedflat.fits'
rtdata.get_truth(
'truth/test_nirspec_brightobj_spec2/jw93056001001_short_nrs1_wavecorr_interpolatedflat.fits'
)
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_correction_pars(rtdata, fitsdiff_default_kwargs):
"""Test use of correction parameters"""
with dm.open(rtdata.get_data('nirspec/imaging/usf_assign_wcs.fits')) as data:
# First use of FlatFieldStep will store the correction.
# The next use will use that correction
step = FlatFieldStep()
flatted = step.run(data)
assert step.correction_pars['flat'] is not None
step.use_correction_pars = True
reflatted = step.run(data)
assert np.allclose(flatted.data, reflatted.data), 'Re-run with correction parameters failed'
def test_flatfield_step_interface(instrument, exptype):
"""Test that the basic inferface works for data requiring a FLAT reffile"""
shape = (20, 20)
data = datamodels.ImageModel(shape)
data.meta.instrument.name = instrument
data.meta.exposure.type = exptype
data.meta.subarray.xstart = 1
data.meta.subarray.ystart = 1
data.meta.subarray.xsize = shape[1]
data.meta.subarray.ysize = shape[0]
flat = datamodels.FlatModel(shape)
flat.meta.instrument.name = instrument
flat.meta.subarray.xstart = 1
flat.meta.subarray.ystart = 1
flat.meta.subarray.xsize = shape[1]
flat.meta.subarray.ysize = shape[0]
flat.data += 1
flat.data[0, 0] = np.nan
flat.err = np.random.random(shape) * 0.05
# override class attribute so only the `flat` type needs to be overriden
# in the step call. Otherwise CRDS calls will be made for the other 3
# types of flat reference file not used in this test.
FlatFieldStep.reference_file_types = ["flat"]
result = FlatFieldStep.call(data, override_flat=flat)
assert (result.data == data.data).all()
assert result.var_flat.shape == shape
assert result.meta.cal_step.flat_field == 'COMPLETE'
def test_nirspec_flatfield_step_interface(exptype):
"""Test that the interface works all NIRSpec types"""
shape = (20, 20)
data = datamodels.ImageModel(shape)
data.meta.observation.date = "2019-01-01"
data.meta.observation.time = "00:00:00"
data.meta.instrument.name = "NIRSPEC"
data.meta.instrument.detector = "NRS1"
data.meta.instrument.filter = "CLEAR"
data.meta.instrument.grating = "MIRROR"
data.meta.exposure.type = exptype
data.meta.subarray.xstart = 1
data.meta.subarray.ystart = 1
data.meta.subarray.xsize = shape[1]
data.meta.subarray.ysize = shape[0]
FlatFieldStep.call(data)
def test_flat_cases(cases, reffile):
'''Test to check flat field step for different files.'''
# get input data
with fits.open(cases) as hduraw:
in_data = hduraw['SCI'].data
in_err = hduraw['ERR'].data
in_dq = hduraw['DQ'].data[500, 500]
# call flat field step
outname = cases[:-5] + '_flat_field.fits'
if reffile is not "None":
print(reffile)
default = FlatFieldStep.call(cases,
override_flat=reffile,
output_file=outname)
else:
print(reffile)
default = FlatFieldStep.call(cases, output_file=outname)
# grab reference file
with fits.open(outname) as hduout:
hdr = hduout['PRIMARY'].header['R_FLAT']
print('header', hdr)
jwst = np.int(hdr.find('jwst'))
print('jwst', jwst)
if hdr[:4] == 'crds':
reffile = '/grp/crds/cache/references/jwst/' + hdr[jwst:]
else:
reffile = hdr
print(reffile)
# get output data -- check SCI, ERR, and DQ extensions
ref_data = fits.getdata(reffile, 1)
out_data = hduout['SCI'].data
out_err = hduout['ERR'].data
out_dq = hduout['DQ'].data[500, 500]
# SCI data should be SCI/REF, ERR data should be ERR/ref, DQout == DQin
assert np.array_equal(out_data, in_data / ref_data) == True
assert np.array_equal(out_err, in_err / ref_data) == True
assert in_dq == out_dq
def test_flat_field_step_user_supplied_flat(rtdata, fitsdiff_default_kwargs):
"""Test providing a user-supplied flat field to the FlatFieldStep"""
data = rtdata.get_data('nirspec/imaging/usf_assign_wcs.fits')
user_supplied_flat = rtdata.get_data('nirspec/imaging/usf_flat.fits')
data_flat_fielded = FlatFieldStep.call(data, user_supplied_flat=user_supplied_flat)
rtdata.output = 'flat_fielded_step_user_supplied.fits'
data_flat_fielded.write(rtdata.output)
rtdata.get_truth('truth/test_nirspec_image2/flat_fielded_step_user_supplied.fits')
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_flat_field_step_user_supplied_flat(rtdata, fitsdiff_default_kwargs):
"""Test providing a user-supplied flat field to the FlatFieldStep"""
data = rtdata.get_data('nirspec/ifu/nrs_ifu_nrs1_assign_wcs.fits')
user_supplied_flat = rtdata.get_data('nirspec/ifu/nrs_ifu_nrs1_interpolated_flat.fits')
data_flat_fielded = FlatFieldStep.call(data, user_supplied_flat=user_supplied_flat)
rtdata.output = 'flat_fielded_step_user_supplied.fits'
data_flat_fielded.write(rtdata.output)
rtdata.get_truth(TRUTH_PATH + '/' + 'flat_fielded_step_user_supplied.fits')
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_flat_field_step_user_supplied_flat(rtdata, fitsdiff_default_kwargs):
"""Test providing a user-supplied flat field to the FlatFieldStep"""
data = rtdata.get_data('nirspec/tso/nrs2_wavecorr.fits')
user_supplied_flat = rtdata.get_data('nirspec/tso/nrs2_interpolatedflat.fits')
data_flat_fielded = FlatFieldStep.call(data, user_supplied_flat=user_supplied_flat)
rtdata.output = 'flat_fielded_step_user_supplied.fits'
data_flat_fielded.write(rtdata.output)
rtdata.get_truth('truth/test_nirspec_brightobj_spec2/flat_fielded_step_user_supplied.fits')
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_fake_data():
'''Test flat field step with fake data.'''
# open ramp to get data shape and headers, fill it with fake data
with fits.open('nrca1_47Tuc_subpix_dither1_newpos_rate.fits') as hduraw:
nrows = 2048
ncols = 2048
new_data = np.zeros((nrows, ncols), dtype=np.float32)
new_data[:, :] = 50
hduraw['SCI'].data = new_data
hduraw['ERR'].data = new_data / 10.
hduraw['DQ'].data[500, 500] = 50
hduraw.writeto("fake_test.fits", overwrite=True)
# call flat field step
FlatFieldStep.call('fake_test.fits', output_file='fake_test_flat.fits')
# grab reference file
with fits.open('fake_test_flat.fits') as hduout:
hdr = hduout['PRIMARY'].header['R_FLAT']
print('header', hdr)
jwst = np.int(hdr.find('jwst'))
print('jwst', jwst)
if hdr[:4] == 'crds':
reffile = '/grp/crds/cache/references/jwst/' + hdr[jwst:]
else:
reffile = hdr
print(reffile)
# get output data -- check SCI, ERR, and DQ extensions
refdata = fits.getdata(reffile, 1)
scidata = hduout['SCI'].data
errdata = hduout['ERR'].data
dqdata = hduout['DQ'].data
# SCI data should be SCI/REF, ERR data should be ERR/ref, DQout == DQin
assert np.array_equal(scidata, hduraw['SCI'].data / refdata) == True
assert np.array_equal(errdata, hduraw['ERR'].data / refdata) == True
assert dqdata[500, 500] == hduraw['DQ'].data[500, 500]
def test_flat_field_step_user_supplied_flat(jail, rtdata_module,
fitsdiff_default_kwargs):
"""Test providing a user-supplied flat field to the FlatFieldStep"""
rtdata = rtdata_module
data = rtdata.get_data('nirspec/mos/usf_wavecorr.fits')
user_supplied_flat = rtdata.get_data('nirspec/mos/usf_flat.fits')
data_flat_fielded = FlatFieldStep.call(
data, user_supplied_flat=user_supplied_flat)
rtdata.output = 'flat_fielded_step_user_supplied.fits'
data_flat_fielded.write(rtdata.output)
rtdata.get_truth(
'truth/test_nirspec_mos_spec2/flat_fielded_step_user_supplied.fits')
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
