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Bug: All JWST downloads are failing #360

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merged 4 commits into from
Dec 17, 2024
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Merged

Bug: All JWST downloads are failing #360

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6ac9aa5
Include calibration level 2 for JWST results
troyraen Dec 12, 2024
fc2bb99
Bugfix: Match query 'obsid' to product 'parent_obsid'
troyraen Dec 16, 2024
bf4d320
Ignore warning about all-NaN slices
troyraen Dec 17, 2024
0842e86
Update runtime
troyraen Dec 17, 2024
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11 changes: 8 additions & 3 deletions spectroscopy/code_src/mast_functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@ def JWST_get_spec_helper(sample_table, search_radius_arcsec, datadir, verbose,
query_results = Observations.query_criteria(
coordinates=search_coords, radius=search_radius_arcsec * u.arcsec,
dataproduct_type=["spectrum"], obs_collection=["JWST"], intentType="science",
calib_level=[3, 4], instrument_name=['NIRSPEC/MSA', 'NIRSPEC/SLIT'],
calib_level=[2, 3, 4], instrument_name=['NIRSPEC/MSA', 'NIRSPEC/SLIT'],
dataRights=['PUBLIC'])
print("Number of search results: {}".format(len(query_results)))

Expand All @@ -118,7 +118,7 @@ def JWST_get_spec_helper(sample_table, search_radius_arcsec, datadir, verbose,
# Filter
data_products_list_filter = Observations.filter_products(
data_products_list, productType=["SCIENCE"], extension="fits",
calib_level=[3, 4], # only fully reduced or contributed
calib_level=[2, 3, 4], # only calibrated data
productSubGroupDescription=["X1D"], # only 1D spectra
dataRights=['PUBLIC']) # only public data
print("Number of files to download: {}".format(len(data_products_list_filter)))
Expand All @@ -140,8 +140,10 @@ def JWST_get_spec_helper(sample_table, search_radius_arcsec, datadir, verbose,
tab = Table(names=keys + ["productFilename"], dtype=[str,
str, str, int, float, int, int, int, float]+[str])
for jj in range(len(data_products_list_filter)):
# Match query 'obsid' to product 'parent_obsid' (not 'obsID') because products may
# belong to a different group than the observation.
idx_cross = np.where(query_results["obsid"] ==
data_products_list_filter["obsID"][jj])[0]
data_products_list_filter["parent_obsid"][jj])[0]
tmp = query_results[idx_cross][keys]
tab.add_row(list(tmp[0]) + [data_products_list_filter["productFilename"][jj]])

Expand Down Expand Up @@ -240,6 +242,9 @@ def JWST_group_spectra(df, verbose, quickplot):
fluxes_int = np.asarray(
[np.interp(wave_grid, tab_sel.iloc[idx]["wave"], tab_sel.iloc[idx]["flux"]) for idx in idx_good])
fluxes_units = [tab_sel.iloc[idx]["flux"].unit for idx in idx_good]

# Sometimes fluxes are all NaN. We'll leave these in and ignore the RuntimeWarning.
warnings.filterwarnings("ignore", message='All-NaN slice encountered', category=RuntimeWarning)
fluxes_stack = np.nanmedian(fluxes_int, axis=0)
if verbose:
print("Units of fluxes for each spectrum: {}".format(
Expand Down
2 changes: 1 addition & 1 deletion spectroscopy/spectra_generator.md
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Expand Up @@ -81,7 +81,7 @@ The ones with an asterisk (*) are the challenging ones.
• ...
## Runtime

As of 2024 August, this notebook takes about 3 minutes to run to completion on Fornax using
As of 2024 December, this notebook takes about 17 minutes to run to completion on Fornax using
Server Type: 'Standard - 8GB RAM/4 CPU' and Environment: 'Default Astrophysics' (image).

## Authors:
Expand Down