def test_run(master_dir):
# Masters
spectrograph = load_spectrograph('shane_kast_blue')
mstilt, edges = load_kast_blue_masters(mstilt=True, edges=True)
# Instantiate
#spectrograph.detector[0]['saturation'] = 60000.
#spectrograph.detector[0]['nonlinear'] = 0.9
par = pypeitpar.WaveTiltsPar()
wavepar = pypeitpar.WavelengthSolutionPar()
slits = edges.get_slits()
buildwaveTilts = wavetilts.BuildWaveTilts(mstilt, slits, spectrograph, par, wavepar, det=1)
# Run
waveTilts = buildwaveTilts.run(doqa=False)
assert isinstance(waveTilts.fit2tiltimg(slits.slit_img()), np.ndarray)
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_wavelengthsolution():
pypeitpar.WavelengthSolutionPar()
def initialise(arccen, slit=0, par=None, wv_calib_all=None):
"""Initialise the 'Identify' window for real-time wavelength calibration
.. todo::
* Implement multislit functionality
Parameters
----------
arccen : ndarray
Arc spectrum
slit : int, optional
The slit to be used for wavelength calibration
par : :obj:`int`, optional
The slit to be used for wavelength calibration
wv_calib_all : :obj:`dict`, None, optional
If a best-fitting solution exists, and you wish to load it, provide the wv_calib dictionary.
Returns
-------
class
Returns an instance of the Identify class, which contains the results of the fit
"""
# Double check that a WavelengthSolutionPar was input
par = pypeitpar.WavelengthSolutionPar() if par is None else par
# If a wavelength calibration has been performed already, load it:
wv_calib = wv_calib_all[str(slit)]
# Extract the lines that are detected in arccen
thisarc = arccen[:, slit]
tdetns, _, _, icut, _ = wvutils.arc_lines_from_spec(
thisarc,
sigdetect=par['sigdetect'],
nonlinear_counts=par['nonlinear_counts'])
detns = tdetns[icut]
# Load line lists
if 'ThAr' in par['lamps']:
line_lists_all = waveio.load_line_lists(par['lamps'])
line_lists = line_lists_all[np.where(
line_lists_all['ion'] != 'UNKNWN')]
else:
line_lists = waveio.load_line_lists(par['lamps'])
# Create a Line2D instance for the arc spectrum
spec = Line2D(np.arange(thisarc.size),
thisarc,
linewidth=1,
linestyle='solid',
color='k',
drawstyle='steps',
animated=True)
# Add the main figure axis
fig, ax = plt.subplots(figsize=(16, 9), facecolor="white")
plt.subplots_adjust(bottom=0.05, top=0.85, left=0.05, right=0.65)
ax.add_line(spec)
ax.set_ylim((0.0, 1.1 * spec.get_ydata().max()))
# Add two residual fitting axes
axfit = fig.add_axes([0.7, .5, .28, 0.35])
axres = fig.add_axes([0.7, .1, .28, 0.35])
# Residuals
lflag_color = ['grey', 'blue', 'yellow', 'red']
residcmap = LinearSegmentedColormap.from_list("my_list",
lflag_color,
N=len(lflag_color))
resres = axres.scatter(detns,
np.zeros(detns.size),
marker='x',
c=np.zeros(detns.size),
cmap=residcmap,
norm=Normalize(vmin=0.0, vmax=3.0))
axres.axhspan(-0.1, 0.1, alpha=0.5,
color='grey') # Residuals of 0.1 pixels
axres.axhline(0.0, color='r', linestyle='-') # Zero level
axres.set_xlim((0, thisarc.size - 1))
axres.set_ylim((-0.3, 0.3))
axres.set_xlabel('Pixel')
axres.set_ylabel('Residuals (Pix)')
# pixel vs wavelength
respts = axfit.scatter(detns,
np.zeros(detns.size),
marker='x',
c=np.zeros(detns.size),
cmap=residcmap,
norm=Normalize(vmin=0.0, vmax=3.0))
resfit = Line2D(np.arange(thisarc.size),
np.zeros(thisarc.size),
linewidth=1,
linestyle='-',
color='r')
axfit.add_line(resfit)
axfit.set_xlim((0, thisarc.size - 1))
axfit.set_ylim(
(-0.3, 0.3)) # This will get updated as lines are identified
axfit.set_xlabel('Pixel')
axfit.set_ylabel('Wavelength')
# Add an information GUI axis
axinfo = fig.add_axes([0.15, .92, .7, 0.07])
axinfo.get_xaxis().set_visible(False)
axinfo.get_yaxis().set_visible(False)
axinfo.text(0.5,
0.5,
"Press '?' to list the available options",
transform=axinfo.transAxes,
horizontalalignment='center',
verticalalignment='center')
axinfo.set_xlim((0, 1))
axinfo.set_ylim((0, 1))
specres = dict(pixels=respts, model=resfit, resid=resres)
axes = dict(main=ax, fit=axfit, resid=axres, info=axinfo)
# Initialise the identify window and display to screen
fig.canvas.set_window_title('PypeIt - Identify')
ident = Identify(fig.canvas,
axes,
spec,
specres,
detns,
line_lists,
par,
lflag_color,
slit=slit,
wv_calib=wv_calib)
plt.show()
# Now return the results
return ident