def test_step_by_step(master_dir):
# Masters
spectrograph = load_spectrograph('shane_kast_blue')
msarc, tslits_dict, mstrace = load_kast_blue_masters(aimg=True, tslits=True)
# Instantiate
master_key = 'A_1_01'
parset = spectrograph.default_pypeit_par()
par = parset['calibrations']['tilts']
wavepar = parset['calibrations']['wavelengths']
waveTilts = wavetilts.WaveTilts(msarc, tslits_dict, spectrograph, par, wavepar,
det=1, master_key=master_key,
master_dir=master_dir,reuse_masters=True)
# Extract arcs
arccen, maskslits = waveTilts.extract_arcs(waveTilts.slitcen, waveTilts.slitmask, msarc, waveTilts.inmask)
assert arccen.shape == (2048,1)
# Tilts in the slit
slit = 0
waveTilts.slitmask = pixels.tslits2mask(waveTilts.tslits_dict)
thismask = waveTilts.slitmask == slit
waveTilts.lines_spec, waveTilts.lines_spat = waveTilts.find_lines(arccen[:, slit], waveTilts.slitcen[:, slit], slit)
trcdict = waveTilts.trace_tilts(waveTilts.msarc, waveTilts.lines_spec, waveTilts.lines_spat, thismask, slit)
assert isinstance(trcdict, dict)
# 2D Fit
spat_order = waveTilts._parse_param(waveTilts.par, 'spat_order', slit)
spec_order = waveTilts._parse_param(waveTilts.par, 'spec_order', slit)
coeffs = waveTilts.fit_tilts(trcdict, thismask, waveTilts.slitcen[:, slit], spat_order, spec_order,slit, doqa=False)
tilts = tracewave.fit2tilts(waveTilts.slitmask_science.shape, coeffs, waveTilts.par['func2d'])
assert np.max(tilts) < 1.01
def test_run(master_dir):
# Masters
spectrograph = load_spectrograph('shane_kast_blue')
msarc, tslits_dict, mstrace = load_kast_blue_masters(aimg=True, tslits=True)
# Instantiate
master_key = 'A_1_01'
spectrograph.detector[0]['saturation'] = 60000.
spectrograph.detector[0]['nonlinear'] = 0.9
par = pypeitpar.WaveTiltsPar()
wavepar = pypeitpar.WavelengthSolutionPar()
waveTilts = wavetilts.WaveTilts(msarc, tslits_dict, spectrograph, par, wavepar,
det=1, master_key=master_key,
master_dir=master_dir, reuse_masters=True)
# Run
tilts_dict, mask = waveTilts.run(doqa=False)
assert isinstance(tilts_dict['tilts'], np.ndarray)
def test_wavetilts():
#
wvtilts = wavetilts.WaveTilts(**instant_dict)
# I/O
outfile = data_path('tst_wavetilts.fits')
wvtilts.to_file(outfile, overwrite=True)
_wvtilts = wavetilts.WaveTilts.from_file(outfile)
# Test
for key in instant_dict.keys():
if isinstance(instant_dict[key], np.ndarray):
assert np.array_equal(wvtilts[key],_wvtilts[key])
else:
assert wvtilts[key] == _wvtilts[key]
# Write again
wvtilts.to_file(outfile, overwrite=True)
os.remove(outfile)
def get_tilts(self):
"""
Load or generate the tilts image
Requirements:
msarc, tslits_dict, wv_calib
det, par, spectrograph
Returns:
dict, ndarray: :attr:`tilts_dict` dictionary with tilts information (2D)
and the updated slit mask array
"""
# Check for existing data
if not self._chk_objs(['msarc', 'msbpm', 'tslits_dict', 'wv_calib']):
msgs.error('dont have all the objects')
self.tilts_dict = None
self.wt_maskslits = np.zeros_like(self.maskslits, dtype=bool)
self.tslits_dict['maskslits'] += self.wt_maskslits
return self.tilts_dict
# Check internals
self._chk_set(['det', 'calib_ID', 'par'])
if 'arc' not in self.master_key_dict.keys():
msgs.error('Arc master key not set. First run get_arc.')
# Return existing data
if self._cached('tilts_dict', self.master_key_dict['arc']) \
and self._cached('wtmask', self.master_key_dict['arc']):
self.tilts_dict = self.calib_dict[
self.master_key_dict['arc']]['tilts_dict']
self.wt_maskslits = self.calib_dict[
self.master_key_dict['arc']]['wtmask']
self.tslits_dict['maskslits'] += self.wt_maskslits
return self.tilts_dict
# Instantiate
self.waveTilts = wavetilts.WaveTilts(
self.msarc,
self.tslits_dict,
self.spectrograph,
self.par['tilts'],
self.par['wavelengths'],
det=self.det,
master_key=self.master_key_dict['arc'],
master_dir=self.master_dir,
reuse_masters=self.reuse_masters,
qa_path=self.qa_path,
msbpm=self.msbpm)
# Master
self.tilts_dict = self.waveTilts.load()
if self.tilts_dict is None:
# TODO still need to deal with syntax for LRIS ghosts. Maybe we don't need it
self.tilts_dict, self.wt_maskslits \
= self.waveTilts.run(maskslits=self.tslits_dict['maskslits'], doqa=self.write_qa,
show=self.show)
if self.save_masters:
self.waveTilts.save()
else:
self.wt_maskslits = np.zeros_like(self.tslits_dict['maskslits'],
dtype=bool)
# Save & return
self._update_cache('arc', ('tilts_dict', 'wtmask'),
(self.tilts_dict, self.wt_maskslits))
self.tslits_dict['maskslits'] += self.wt_maskslits
return self.tilts_dict
# Get Tilts from scienceB image
aImage = arcimage.ArcImage(spectrograph,
file_list=args.sciBfiles,
par=par['calibrations']['arcframe'])
msarc = aImage.process(bias_subtract='overscan',
trim=False)
pixlocn = pixels.gen_pixloc(aImage.stack.shape)
bpm = spectrograph.bpm(shape=msarc.shape, det=1)
# Extract spectrum at the center
arccen, mask, _ = arc.get_censpec(tslits_dict['lcen'],
tslits_dict['rcen'],
pixlocn,
msarc,
1)
waveTilts = wavetilts.WaveTilts(msarc, spectrograph=spectrograph,
par=par['calibrations']['tilts'], det=1,
tslits_dict=tslits_dict, pixlocn=pixlocn)
nslits = tslits_dict['lcen'].shape[1]
maskslits = np.zeros(nslits, dtype=bool)
# QA is not working here
mstilts, wt_maskslits = waveTilts.run(maskslits=maskslits,
wv_calib=None,
doqa=False)
# Wavelength calibration from scienceB image
arcparam = {}
spectrograph.setup_arcparam(arcparam)
setup = 'NIRES'
waveCalib = wavecalib.WaveCalib(msarc,
spectrograph=spectrograph,
#par=par['calibrations']['wavelengths'],
def load_kast_blue_masters(get_spectrograph=False, aimg=False, tslits=False, tilts=False,
datasec=False, wvcalib=False):
"""
Load up the set of shane_kast_blue master frames
Args:
get_spectrograph:
aimg:
tslits:
tilts:
datasec:
wvcalib:
Returns:
"""
spectrograph = load_spectrograph('shane_kast_blue')
spectrograph.naxis = (2112,350) # Image shape with overscan
root_path = data_path('MF') if os.getenv('PYPEIT_DEV') is None \
else os.path.join(os.getenv('PYPEIT_DEV'), 'Cooked', 'MF')
master_dir = root_path+'_'+spectrograph.spectrograph
reuse_masters = True
# Load up the Masters
ret = []
if get_spectrograph:
ret.append(spectrograph)
master_key = 'A_1_01'
if aimg:
AImg = arcimage.ArcImage(spectrograph, master_key=master_key, master_dir=master_dir, reuse_masters=reuse_masters)
msarc, _ = AImg.load_master(AImg.ms_name)
ret.append(msarc)
if tslits:
traceSlits = traceslits.TraceSlits(None,spectrograph,None)
# TODO: Should this be json now?
tslits_dict, mstrace = traceSlits.load_master(os.path.join(master_dir,'MasterTrace_A_1_01.fits'))
# This is a bit of a hack, but I'm adding the mstrace to the dict since we need it in the flat field test
tslits_dict['mstrace'] = mstrace
ret.append(tslits_dict)
if tilts:
wvTilts = wavetilts.WaveTilts(None, None, spectrograph, None, None, master_key=master_key,
master_dir=master_dir, reuse_masters=reuse_masters)
tilts_dict, _ = wvTilts.master()
ret.append(tilts_dict)
if datasec:
datasec_img = spectrograph.get_datasec_img(data_path('b1.fits.gz'), 1)
ret.append(datasec_img)
if wvcalib:
Wavecalib = wavecalib.WaveCalib(None, None, spectrograph,
spectrograph.default_pypeit_par()['calibrations']['wavelengths'],
master_key=master_key,
master_dir=master_dir, reuse_masters=reuse_masters)
wv_calib, _ = Wavecalib.master()
ret.append(wv_calib)
# Return
return ret