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add support for scientific notation in unit string #3200

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Sep 26, 2024
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add support for scientific notation in unit string #3200

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c1180b1
add support for scientific notation in unit string, update associated…
gibsongreen Sep 23, 2024
36b8381
update test to use scaled values
gibsongreen Sep 23, 2024
783db28
add changes.rst
gibsongreen Sep 23, 2024
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2 changes: 1 addition & 1 deletion CHANGES.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ New Features

- Added flux/surface brightness translation and surface brightness
unit conversion in Cubeviz and Specviz. [#2781, #2940, #3088, #3111, #3113, #3129,
#3139, #3149, #3155, #3178, #3185, #3187, #3190, #3156]
#3139, #3149, #3155, #3178, #3185, #3187, #3190, #3156, #3200]

- Plugin tray is now open by default. [#2892]

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8 changes: 6 additions & 2 deletions jdaviz/configs/cubeviz/plugins/parsers.py
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Expand Up @@ -178,7 +178,7 @@ def _get_celestial_wcs(wcs):
return wcs.celestial if hasattr(wcs, 'celestial') else None


def _return_spectrum_with_correct_units(flux, wcs, metadata, data_type,
def _return_spectrum_with_correct_units(flux, wcs, metadata, data_type=None,
target_wave_unit=None, hdulist=None,
uncertainty=None, mask=None, apply_pix2=False):
"""Upstream issue of WCS not using the correct units for data must be fixed here.
Expand All @@ -199,6 +199,10 @@ def _return_spectrum_with_correct_units(flux, wcs, metadata, data_type,
if uncertainty is not None:
uncertainty = uncertainty / (u.pix * u.pix)

# handle scale factors when they are included in the unit
if not np.isclose(flux.unit.scale, 1.0, rtol=1e-5):
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my only concern here is if there was a case that fell within the tolerance because of an actual scale in the unit, but I don't think that's a realistic real-case scenario and this is probably a better idea than checking ==1 anyways.

flux = flux.to(flux.unit / flux.unit.scale)

sc = Spectrum1D(flux=flux, wcs=wcs, uncertainty=uncertainty, mask=mask)

if target_wave_unit is None and hdulist is not None:
Expand Down Expand Up @@ -461,7 +465,7 @@ def _parse_spectrum1d_3d(app, file_obj, data_label=None,
if hasattr(file_obj, 'wcs'):
meta['_orig_spatial_wcs'] = _get_celestial_wcs(file_obj.wcs)

s1d = Spectrum1D(flux=flux, wcs=file_obj.wcs, meta=meta)
s1d = _return_spectrum_with_correct_units(flux, wcs=file_obj.wcs, metadata=meta)

# convert data loaded in flux units to a per-square-pixel surface
# brightness unit (e.g Jy to Jy/pix**2)
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4 changes: 2 additions & 2 deletions jdaviz/configs/cubeviz/plugins/spectral_extraction/tests/test_spectral_extraction.py
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Expand Up @@ -432,12 +432,12 @@ def test_cube_extraction_with_nan(cubeviz_helper, image_cube_hdu_obj):
cubeviz_helper.load_data(image_cube_hdu_obj, data_label="with_nan")
extract_plg = cubeviz_helper.plugins['Spectral Extraction']
sp = extract_plg.extract() # Default settings (sum)
assert_allclose(sp.flux.value, 96) # (10 x 10) - 4
assert_allclose(sp.flux.value, 9.6E-16) # (10 x 10) - 4

cubeviz_helper.load_regions(RectanglePixelRegion(PixCoord(1.5, 1.5), width=4, height=4))
extract_plg.aperture = 'Subset 1'
sp_subset = extract_plg.extract() # Default settings but on Subset
assert_allclose(sp_subset.flux.value, 12) # (4 x 4) - 4
assert_allclose(sp_subset.flux.value, 1.2E-16) # (4 x 4) - 4


def test_autoupdate_results(cubeviz_helper, spectrum1d_cube_largest):
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15 changes: 10 additions & 5 deletions jdaviz/configs/cubeviz/plugins/tests/test_parsers.py
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Expand Up @@ -45,10 +45,17 @@ def test_fits_image_hdu_with_microns(image_cube_hdu_obj_microns, cubeviz_helper)
label_mouseover = cubeviz_helper.app.session.application._tools['g-coords-info']
label_mouseover._viewer_mouse_event(flux_viewer,
{'event': 'mousemove', 'domain': {'x': 0, 'y': 0}})

# This secondarily tests a scale factor embedded in a unit at parse-time to make sure it
# is applied to the values, then it is removed from the actual display unit
flux_unit_str = "erg / (Angstrom s cm2 pix2)"
assert label_mouseover.as_text() == (f'Pixel x=00.0 y=00.0 Value +5.00000e+00 1e-17 {flux_unit_str}', # noqa
assert label_mouseover.as_text() == (f'Pixel x=00.0 y=00.0 Value +5.00000e-17 {flux_unit_str}', # noqa
'World 13h41m45.5759s +27d00m12.3044s (ICRS)',
'205.4398995981 27.0034178810 (deg)') # noqa

# verify that scale factor embedded in unit is removed
assert np.allclose(flux_cube.unit.scale, 1.0)

unc_viewer = cubeviz_helper.app.get_viewer('uncert-viewer')
label_mouseover._viewer_mouse_event(unc_viewer,
{'event': 'mousemove', 'domain': {'x': -1, 'y': 0}})
Expand Down Expand Up @@ -87,7 +94,6 @@ def test_fits_image_hdu_parse_from_file(tmpdir, image_cube_hdu_obj, cubeviz_help
assert cubeviz_helper.app.data_collection[0].label == "test_fits_image.fits[FLUX]"

# This tests the same data as test_fits_image_hdu_parse above.

cubeviz_helper.app.data_collection[0].meta['EXTNAME'] == 'FLUX'
cubeviz_helper.app.data_collection[1].meta['EXTNAME'] == 'MASK'
cubeviz_helper.app.data_collection[2].meta['EXTNAME'] == 'ERR'
Expand All @@ -99,7 +105,7 @@ def test_fits_image_hdu_parse_from_file(tmpdir, image_cube_hdu_obj, cubeviz_help
label_mouseover._viewer_mouse_event(flux_viewer,
{'event': 'mousemove', 'domain': {'x': 0, 'y': 0}})
flux_unit_str = "erg / (Angstrom s cm2 pix2)"
assert label_mouseover.as_text() == (f'Pixel x=00.0 y=00.0 Value +1.00000e+00 1e-17 {flux_unit_str}', # noqa
assert label_mouseover.as_text() == (f'Pixel x=00.0 y=00.0 Value +1.00000e-17 {flux_unit_str}', # noqa
'World 13h41m46.5994s +26d59m58.6136s (ICRS)',
'205.4441642302 26.9996148973 (deg)')

Expand Down Expand Up @@ -129,12 +135,11 @@ def test_spectrum3d_parse(image_cube_hdu_obj, cubeviz_helper):
label_mouseover._viewer_mouse_event(flux_viewer,
{'event': 'mousemove', 'domain': {'x': 0, 'y': 0}})
flux_unit_str = "erg / (Angstrom s cm2 pix2)"
assert label_mouseover.as_text() == (f'Pixel x=00.0 y=00.0 Value +1.00000e+00 1e-17 {flux_unit_str}', # noqa
assert label_mouseover.as_text() == (f'Pixel x=00.0 y=00.0 Value +1.00000e-17 {flux_unit_str}', # noqa
'World 13h41m46.5994s +26d59m58.6136s (ICRS)',
'205.4441642302 26.9996148973 (deg)')

# These viewers have no data.

unc_viewer = cubeviz_helper.app.get_viewer(cubeviz_helper._default_uncert_viewer_reference_name)
label_mouseover._viewer_mouse_event(unc_viewer,
{'event': 'mousemove', 'domain': {'x': -1, 'y': 0}})
Expand Down
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