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Some updates to specutils.analysis functions #937

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Jan 30, 2024
Merged

Some updates to specutils.analysis functions #937

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714fdc9
Updated template_redshift to return final redshifted spectrum and _ch…
chloe-mt-cheng Mar 22, 2022
34ad35d
Update tests, only sum template where observed is not NaN
rosteen Jan 30, 2024
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12 changes: 8 additions & 4 deletions specutils/analysis/template_comparison.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,11 @@ def _normalize_for_template_matching(observed_spectrum, template_spectrum, stdde
"""
if stddev is None:
stddev = observed_spectrum.uncertainty.represent_as(StdDevUncertainty).quantity
num = np.sum((observed_spectrum.flux*template_spectrum.flux) / (stddev**2))
denom = np.sum((template_spectrum.flux / stddev)**2)
num = np.nansum((observed_spectrum.flux*template_spectrum.flux) / (stddev**2))
# We need to limit this sum to where observed_spectrum is not NaN as well.
template_filtered = ((template_spectrum.flux / stddev)**2)
template_filtered = template_filtered[np.where(~np.isnan(observed_spectrum.flux))]
denom = np.nansum(template_filtered)

return num/denom

Expand Down Expand Up @@ -107,7 +110,7 @@ def _chi_square_for_templates(observed_spectrum, template_spectrum, resample_met

# Get chi square
result = (num/denom)**2
chi2 = np.sum(result.value)
chi2 = np.nansum(result.value)

# Create normalized template spectrum, which will be returned with
# corresponding chi2
Expand Down Expand Up @@ -262,5 +265,6 @@ def template_redshift(observed_spectrum, template_spectrum, redshift):
if not np.isnan(chi2) and (chi2_min is None or chi2 < chi2_min):
chi2_min = chi2
final_redshift = rs
final_spectrum = redshifted_spectrum

return redshifted_spectrum, final_redshift, normalized_spectral_template, chi2_min, chi2_list
return final_spectrum, final_redshift, normalized_spectral_template, chi2_min, chi2_list
8 changes: 4 additions & 4 deletions specutils/tests/test_template_comparison.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def test_template_match_no_overlap():

# Get result from template_match
tm_result = template_comparison.template_match(spec, spec1)
assert np.isnan(tm_result[3])
assert tm_result[3] == 0.0

# Create new spectrum for comparison
spec_result = Spectrum1D(spectral_axis=spec_axis,
Expand Down Expand Up @@ -65,15 +65,15 @@ def test_template_match_minimal_overlap():

# Get result from template_match
tm_result = template_comparison.template_match(spec, spec1)
assert np.isnan(tm_result[3])
assert tm_result[3] == 0.0

# Create new spectrum for comparison
spec_result = Spectrum1D(spectral_axis=spec_axis,
flux=spec1.flux * template_comparison._normalize_for_template_matching(spec, spec1))
try:
assert quantity_allclose(tm_result[0].flux, spec_result.flux, atol=0.01*u.Jy)
except AssertionError:
pytest.xfail('TODO: investigate why the all elements in tm_result[1] are NaN even with overlap')
pytest.xfail('TODO: investigate why all elements in tm_result[0] are NaN even with overlap')


def test_template_match_spectrum():
Expand Down Expand Up @@ -332,7 +332,7 @@ def test_template_redshift_with_multiple_template_spectra_in_match():
# TODO: Determine cause of and fix failing assert
# np.testing.assert_almost_equal(tm_result[1], redshift)

np.testing.assert_almost_equal(tm_result[3], 6803.922741644725)
np.testing.assert_almost_equal(tm_result[3], 1172.135458895792)

# When a spectrum collection is matched with a redshift
# grid, a list-of-lists is returned with the trial chi2
Expand Down
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