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Fix mixed unit spectral region extraction #1187

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merged 6 commits into from
Oct 15, 2024
Merged

Fix mixed unit spectral region extraction #1187

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f70b33a
Fix extraction when only one of region/spectrum are in a reversed spe…
rosteen Oct 15, 2024
991bb32
Changelog
rosteen Oct 15, 2024
7375600
Add test
rosteen Oct 15, 2024
6231a8b
Get rid of more pointless random calls
rosteen Oct 15, 2024
d3f4a1d
Update specutils/tests/test_region_extract.py
rosteen Oct 15, 2024
358a6ce
Better test improvement
rosteen Oct 15, 2024
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3 changes: 3 additions & 0 deletions CHANGES.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@ Bug Fixes
- Fixed ``Spectrum1D.with_flux_unit()`` not converting uncertainty along
with flux unit. [#1181]

- Fixed extracting a spectral region when one of spectrum/region is in wavelength
and the other is in frequency units. [#1187]

Other Changes and Additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^

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6 changes: 5 additions & 1 deletion specutils/manipulation/extract_spectral_region.py
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Expand Up @@ -103,7 +103,11 @@ def _subregion_to_edge_pixels(subregion, spectrum):

right_index = _edge_value_to_pixel(right_reg_in_spec_unit, spectrum, order, "right")

return left_index, right_index
# If the spectrum is in wavelength and region is in Hz (for example), these still might be reversed
if left_index < right_index:
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return left_index, right_index
else:
return right_index, left_index


def extract_region(spectrum, region, return_single_spectrum=False):
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37 changes: 18 additions & 19 deletions specutils/tests/test_region_extract.py
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Expand Up @@ -18,10 +18,9 @@


def test_region_simple(simulated_spectra):
np.random.seed(42)

spectrum = simulated_spectra.s1_um_mJy_e1
uncertainty = StdDevUncertainty(0.1*np.random.random(len(spectrum.flux))*u.mJy)
uncertainty = StdDevUncertainty(np.full(spectrum.flux.shape, 0.1) * u.mJy)
spectrum.uncertainty = uncertainty

region = SpectralRegion(0.6*u.um, 0.8*u.um)
Expand Down Expand Up @@ -112,10 +111,8 @@ def test_pixel_spectralaxis_extraction():


def test_slab_simple(simulated_spectra):
np.random.seed(42)

spectrum = simulated_spectra.s1_um_mJy_e1
uncertainty = StdDevUncertainty(0.1*np.random.random(len(spectrum.flux))*u.mJy)
uncertainty = StdDevUncertainty(np.full(spectrum.flux.shape, 0.1) * u.mJy)
spectrum.uncertainty = uncertainty

sub_spectrum = spectral_slab(spectrum, 0.6*u.um, 0.8*u.um)
Expand Down Expand Up @@ -148,6 +145,16 @@ def test_region_ghz(simulated_spectra):
assert_quantity_allclose(sub_spectrum.flux, sub_spectrum_flux_expected)


def test_region_ghz_spectrum_wave(simulated_spectra):
spectrum = simulated_spectra.s1_um_mJy_e1
region = SpectralRegion(499654.09666667*u.GHz, 374740.5725*u.GHz)

sub_spectrum = extract_region(spectrum, region)

sub_spectrum_flux_expected = FLUX_ARRAY * u.mJy
assert_quantity_allclose(sub_spectrum.flux, sub_spectrum_flux_expected)


def test_region_simple_check_ends(simulated_spectra):
np.random.seed(42)

Expand All @@ -168,13 +175,11 @@ def test_region_simple_check_ends(simulated_spectra):
assert sub_spectrum.spectral_axis.value[-1] == 25


def test_region_empty(simulated_spectra):
np.random.seed(42)

def test_region_empty():
empty_spectrum = Spectrum1D(spectral_axis=[]*u.um, flux=[]*u.Jy)

# Region past upper range of spectrum
spectrum = Spectrum1D(spectral_axis=np.linspace(1, 25, 25)*u.um, flux=np.random.random(25)*u.Jy)
spectrum = Spectrum1D(spectral_axis=np.linspace(1, 25, 25)*u.um, flux=np.ones(25)*u.Jy)
region = SpectralRegion(28*u.um, 30*u.um)
sub_spectrum = extract_region(spectrum, region)

Expand All @@ -185,7 +190,7 @@ def test_region_empty(simulated_spectra):
assert sub_spectrum.flux.unit == empty_spectrum.flux.unit

# Region below lower range of spectrum
spectrum = Spectrum1D(spectral_axis=np.linspace(1, 25, 25)*u.um, flux=np.random.random(25)*u.Jy)
spectrum = Spectrum1D(spectral_axis=np.linspace(1, 25, 25)*u.um, flux=np.ones(25)*u.Jy)
region = SpectralRegion(0.1*u.um, 0.3*u.um)
sub_spectrum = extract_region(spectrum, region)

Expand All @@ -212,10 +217,8 @@ def test_region_empty(simulated_spectra):


def test_region_descending(simulated_spectra):
np.random.seed(42)

spectrum = simulated_spectra.s1_um_mJy_e1
uncertainty = StdDevUncertainty(0.1*np.random.random(len(spectrum.flux))*u.mJy)
uncertainty = StdDevUncertainty(np.full(spectrum.flux.shape, 0.1) * u.mJy)
spectrum.uncertainty = uncertainty

region = SpectralRegion(0.8*u.um, 0.6*u.um)
Expand Down Expand Up @@ -244,10 +247,8 @@ def test_descending_spectral_axis(simulated_spectra):


def test_region_two_sub(simulated_spectra):
np.random.seed(42)

spectrum = simulated_spectra.s1_um_mJy_e1
uncertainty = StdDevUncertainty(0.1*np.random.random(len(spectrum.flux))*u.mJy)
uncertainty = StdDevUncertainty(np.full(spectrum.flux.shape, 0.1) * u.mJy)
spectrum.uncertainty = uncertainty

region = SpectralRegion([(0.6*u.um, 0.8*u.um), (0.86*u.um, 0.89*u.um)])
Expand Down Expand Up @@ -284,10 +285,8 @@ def test_region_two_sub(simulated_spectra):


def test_bounding_region(simulated_spectra):
np.random.seed(42)

spectrum = simulated_spectra.s1_um_mJy_e1
uncertainty = StdDevUncertainty(0.1*np.random.random(len(spectrum.flux))*u.mJy)
uncertainty = StdDevUncertainty(np.full(spectrum.flux.shape, 0.1) * u.mJy)
spectrum.uncertainty = uncertainty

region = SpectralRegion([(0.6*u.um, 0.8*u.um), (0.86*u.um, 0.89*u.um)])
Expand Down
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