def test_setting_nones_to_known_pairs_expect_fail():
lhs6328_spectrum1D = Spectrum1D(log_file_name=None)
wavecal = WavelengthCalibration(log_file_name=None)
lhs6328_spectrum1D.add_arc_spec(arc_spec)
wavecal.from_spectrum1D(lhs6328_spectrum1D)
# Find the peaks of the arc
wavecal.find_arc_lines(
save_fig=True,
fig_type="iframe+png",
filename=os.path.join(
HERE, "test_output", "test_wavecal_find_arc_lines"
),
display=False,
return_jsonstring=True,
)
wavecal.initialise_calibrator()
wavecal.set_known_pairs([None], [None])
def test_setting_known_pairs(mock_show):
lhs6328_spectrum1D = Spectrum1D(log_file_name=None)
wavecal = WavelengthCalibration(log_file_name=None)
lhs6328_spectrum1D.add_arc_spec(arc_spec)
wavecal.from_spectrum1D(lhs6328_spectrum1D)
# Find the peaks of the arc
wavecal.find_arc_lines(
save_fig=True,
fig_type="iframe+png",
filename=os.path.join(
HERE, "test_output", "test_wavecal_find_arc_lines"
),
display=True,
return_jsonstring=True,
)
wavecal.initialise_calibrator()
wavecal.set_known_pairs([123, 234], [456, 567])
assert len(wavecal.spectrum1D.calibrator.pix_known) == 2
assert len(wavecal.spectrum1D.calibrator.wave_known) == 2
def test_setting_a_known_pair():
lhs6328_spectrum1D = SpectrumOneD(log_file_name=None)
wavecal = WavelengthCalibration(log_file_name=None)
lhs6328_spectrum1D.add_arc_spec(arc_spec)
wavecal.from_spectrum1D(lhs6328_spectrum1D)
# Find the peaks of the arc
wavecal.find_arc_lines(
save_fig=True,
fig_type="iframe+png",
filename=os.path.join(
HERE, "test_output", "test_wavecal_find_arc_lines"
),
display=False,
return_jsonstring=True,
)
wavecal.initialise_calibrator()
wavecal.set_known_pairs(123, 456)
assert wavecal.spectrum1D.calibrator.pix_known == 123
assert wavecal.spectrum1D.calibrator.wave_known == 456
def test_overwritten_copy_of_spectrum1Ds_are_different():
lhs6328_spectrum1D = Spectrum1D(log_file_name=None)
wavecal_1 = WavelengthCalibration(log_file_name=None)
wavecal_1.from_spectrum1D(lhs6328_spectrum1D)
memory_1 = id(wavecal_1.spectrum1D)
wavecal_1.from_spectrum1D(copy.copy(lhs6328_spectrum1D), overwrite=True)
memory_2 = id(wavecal_1.spectrum1D)
assert memory_1 != memory_2
def test_quadratic_fit_chebyshev():
# Initialise the calibrator
wavecal = WavelengthCalibration(log_file_name=None)
wavecal.initialise_calibrator(peaks)
wavecal.set_calibrator_properties(num_pix=1000)
wavecal.set_hough_properties(
num_slopes=500,
range_tolerance=200.0,
xbins=100,
ybins=100,
min_wavelength=3000.0,
max_wavelength=8000.0,
)
wavecal.add_user_atlas(
elements=elements_quadratic, wavelengths=wavelengths_quadratic
)
wavecal.set_ransac_properties(sample_size=10, minimum_matches=20)
wavecal.do_hough_transform(brute_force=False)
# Run the wavelength calibration
(
best_p,
matched_peaks,
matched_atlas,
rms,
residual,
peak_utilisation,
atlas_utilisation,
) = wavecal.fit(
max_tries=2000,
fit_tolerance=5.0,
candidate_tolerance=2.0,
fit_deg=2,
fit_type="chebyshev",
)
def test_manual_refit_add_points():
# Initialise the calibrator
wavecal = WavelengthCalibration(log_file_name=None)
wavecal.initialise_calibrator(peaks)
wavecal.set_calibrator_properties(num_pix=1000)
wavecal.set_hough_properties(
num_slopes=1000,
range_tolerance=500.0,
xbins=200,
ybins=200,
min_wavelength=3000.0,
max_wavelength=8000.0,
)
wavecal.add_user_atlas(
elements=elements_linear, wavelengths=wavelengths_linear
)
wavecal.set_ransac_properties(minimum_matches=25)
wavecal.do_hough_transform(brute_force=False)
# Run the wavelength calibration
(
best_p,
atched_peaks,
matched_atlas,
rms,
residual,
peak_utilisation,
atlas_utilisation,
) = wavecal.fit(max_tries=500, fit_deg=1)
# Refine solution
(
best_p,
matched_peaks,
matched_atlas,
rms,
residual,
peak_utilisation,
atlas_utilisation,
) = wavecal.robust_refit(best_p, refine=False, robust_refit=True)
wavecal.add_pix_wave_pair(
2000.0, 3000.0 + 4 * 2000.0 + 1.0e-3 * 2000.0**2.0
)
(
best_p_manual,
matched_peaks,
matched_atlas,
rms,
residuals,
) = wavecal.manual_refit(matched_peaks, matched_atlas)
assert np.allclose(best_p_manual, best_p)
def test_wavecal():
lhs6328_spectrum1D = Spectrum1D(log_file_name=None)
wavecal = WavelengthCalibration(log_file_name=None)
# Science arc_spec
lhs6328_spectrum1D.add_arc_spec(arc_spec)
wavecal.from_spectrum1D(lhs6328_spectrum1D)
# Find the peaks of the arc
wavecal.find_arc_lines(
save_fig=True,
fig_type="iframe+png",
filename=os.path.join(
HERE, "test_output", "test_wavecal_find_arc_lines"
),
display=False,
return_jsonstring=True,
)
# Configure the wavelength calibrator
wavecal.initialise_calibrator()
wavecal.set_hough_properties(
num_slopes=1000,
xbins=200,
ybins=200,
min_wavelength=3500,
max_wavelength=8500,
)
wavecal.set_ransac_properties(filter_close=True)
wavecal.add_user_atlas(elements=element, wavelengths=atlas)
# Remove all lines between 3500 and 4000
wavecal.remove_atlas_lines_range(wavelength=3750, tolerance=250)
wavecal.do_hough_transform()
# Solve for the pixel-to-wavelength solution
wavecal.fit(max_tries=500, display=False)
# Getting the calibrator
wavecal.get_calibrator()
# Save a FITS file
wavecal.save_fits(
output="wavecal",
filename=os.path.join(HERE, "test_output", "test_wavecal"),
overwrite=True,
)
# Save a CSV file
wavecal.save_csv(
output="wavecal",
filename=os.path.join(HERE, "test_output", "test_wavecal"),
overwrite=True,
)
# Getting the calibrator
wavecal.get_spectrum1D()
wavecal.list_atlas()
wavecal.clear_atlas()
wavecal.list_atlas()
def test_linear_fit():
wavecal = WavelengthCalibration(log_file_name=None)
wavecal.initialise_calibrator(peaks)
wavecal.set_calibrator_properties(num_pix=1000)
wavecal.set_hough_properties(
num_slopes=1000,
range_tolerance=500.0,
xbins=200,
ybins=200,
min_wavelength=3000.0,
max_wavelength=8000.0,
)
wavecal.add_user_atlas(
elements=elements_linear, wavelengths=wavelengths_linear
)
wavecal.set_ransac_properties(minimum_matches=20)
wavecal.do_hough_transform(brute_force=False)
# Run the wavelength calibration
(
best_p,
matched_peaks,
matched_atlas,
rms,
residual,
peak_utilisation,
atlas_utilisation,
) = wavecal.fit(max_tries=500, fit_deg=1)
# Refine solution
(
best_p,
matched_peaks,
matched_atlas,
rms,
residual,
peak_utilisation,
atlas_utilisation,
) = wavecal.robust_refit(best_p, refine=False, robust_refit=True)
assert np.abs(best_p[1] - 5.0) / 5.0 < 0.001
assert np.abs(best_p[0] - 3000.0) / 3000.0 < 0.001
assert peak_utilisation > 0.8
assert atlas_utilisation > 0.0
def test_user_supplied_arc_lines(mock_show):
wavecal = WavelengthCalibration(log_file_name=None)
# Find the peaks of the arc
wavecal.add_arc_lines(arc_lines)
# Configure the wavelength calibrator
wavecal.initialise_calibrator()
wavecal.set_hough_properties(
num_slopes=200,
xbins=40,
ybins=40,
min_wavelength=3500,
max_wavelength=8500,
)
wavecal.set_ransac_properties(filter_close=True)
wavecal.add_user_atlas(elements=element, wavelengths=atlas)
wavecal.do_hough_transform()
# Solve for the pixel-to-wavelength solution
wavecal.fit(max_tries=500, display=True)
# Save a FITS file
wavecal.save_fits(
output="wavecal",
filename=os.path.join(
HERE, "test_output", "test_wavecal_user_supplied_arc_spec"
),
overwrite=True,
)
wavecal.remove_arc_lines()
7642.02,
7740.31,
7802.65,
7887.40,
7967.34,
8057.258,
]
element = ["Xe"] * len(atlas)
arc_spec = np.loadtxt(
os.path.join(HERE, "test_data", "test_full_run_science_0_arc_spec.csv"),
delimiter=",",
skiprows=1,
)
wavecal = WavelengthCalibration(log_file_name=None)
wavecal.add_arc_spec(arc_spec)
# Find the peaks of the arc
wavecal.find_arc_lines()
arc_lines = wavecal.spectrum1D.peaks
np.random.seed(0)
def test_wavecal():
lhs6328_spectrum1D = Spectrum1D(log_file_name=None)
wavecal = WavelengthCalibration(log_file_name=None)
