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Deal with warnings #361

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merged 4 commits into from
Dec 9, 2024
Merged

Deal with warnings #361

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00ac891
Comment code that raises RuntimeWarning
troyraen Dec 5, 2024
4b70220
Suppress NoResultsWarning from astroquery.mast
troyraen Dec 5, 2024
1a110ee
Ignore 'divide by zero' warning in error calculations
troyraen Dec 6, 2024
e6253e0
Supress mast output with kwarg instead of stdout redirect
troyraen Dec 8, 2024
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5 changes: 4 additions & 1 deletion spectroscopy/code_src/keck_functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,10 @@ def KeckDEIMOS_get_spec(sample_table, search_radius_arcsec):
# Prepare arrays
wave = spec["LAMBDA"][0] * u.angstrom
flux_cgs = spec["FLUX"][0] * 1e-17 * u.erg/u.second/u.centimeter**2/u.angstrom
error_cgs = np.sqrt(1 / spec["IVAR"][0]) * 1e-17 * u.erg/u.second/u.centimeter**2/u.angstrom
# Inverse variances may be zero, resulting in infinite error.
# We'll leave these in and ignore the "divide by zero" warning.
with np.errstate(divide='ignore'):
error_cgs = np.sqrt(1 / spec["IVAR"][0]) * flux_cgs.unit
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This maybe a good example for a docs of good practices, e.g. deal with expected Warnings that are due to the nature of the functionality (e.g. either this or the occasional no result warning coming from astroquery when we loop through a list of coordinates where we expect to have no matches!); and any warnings the end user should/can do nothing about.


# Create MultiIndex object
dfsingle = pd.DataFrame(dict(wave=[wave],
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32 changes: 17 additions & 15 deletions spectroscopy/code_src/mast_functions.py
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
import io
import os
import shutil
from contextlib import redirect_stdout
import warnings

import astropy.constants as const
import astropy.units as u
import astroquery.exceptions
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
Expand Down Expand Up @@ -96,6 +96,11 @@ def JWST_get_spec_helper(sample_table, search_radius_arcsec, datadir, verbose,

# Query results
search_coords = stab["coord"]
# If no results are found, this will raise a warning. We explicitly handle the no-results
# case below, so let's suppress the warning to avoid confusing notebook users.
warnings.filterwarnings("ignore", message='Query returned no results.',
category=astroquery.exceptions.NoResultsWarning,
module="astroquery.mast.discovery_portal")
query_results = Observations.query_criteria(
coordinates=search_coords, radius=search_radius_arcsec * u.arcsec,
dataproduct_type=["spectrum"], obs_collection=["JWST"], intentType="science",
Expand All @@ -122,13 +127,9 @@ def JWST_get_spec_helper(sample_table, search_radius_arcsec, datadir, verbose,
print("Nothing to download for source {}.".format(stab["label"]))
continue

# Download (suppress output)
trap = io.StringIO()
with redirect_stdout(trap):
download_results = Observations.download_products(
data_products_list_filter, download_dir=this_data_dir)
if verbose:
print(trap.getvalue())
# Download
download_results = Observations.download_products(
data_products_list_filter, download_dir=this_data_dir, verbose=False)

# Create table
# NOTE: `download_results` has NOT the same order as `data_products_list_filter`.
Expand Down Expand Up @@ -311,6 +312,11 @@ def HST_get_spec(sample_table, search_radius_arcsec, datadir, verbose,

# Query results
search_coords = stab["coord"]
# If no results are found, this will raise a warning. We explicitly handle the no-results
# case below, so let's suppress the warning to avoid confusing notebook users.
warnings.filterwarnings("ignore", message='Query returned no results.',
category=astroquery.exceptions.NoResultsWarning,
module="astroquery.mast.discovery_portal")
query_results = Observations.query_criteria(
coordinates=search_coords, radius=search_radius_arcsec * u.arcsec,
dataproduct_type=["spectrum"], obs_collection=["HST"], intentType="science",
Expand All @@ -336,12 +342,8 @@ def HST_get_spec(sample_table, search_radius_arcsec, datadir, verbose,
continue

# Download
trap = io.StringIO()
with redirect_stdout(trap):
download_results = Observations.download_products(
data_products_list_filter, download_dir=this_data_dir)
if verbose:
print(trap.getvalue())
download_results = Observations.download_products(
data_products_list_filter, download_dir=this_data_dir, verbose=False)

# Create table
# NOTE: `download_results` has NOT the same order as `data_products_list_filter`.
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5 changes: 4 additions & 1 deletion spectroscopy/code_src/sdss_functions.py
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Expand Up @@ -47,7 +47,10 @@ def SDSS_get_spec(sample_table, search_radius_arcsec, data_release):
# only one entry because we only search for one xid at a time. Could change that?
wave = 10**sp[0]["COADD"].data.loglam * u.angstrom
flux = sp[0]["COADD"].data.flux*1e-17 * u.erg/u.second/u.centimeter**2/u.angstrom
err = np.sqrt(1/sp[0]["COADD"].data.ivar)*1e-17 * flux.unit
# Inverse variances may be zero, resulting in infinite error.
# We'll leave these in and ignore the "divide by zero" warning.
with np.errstate(divide='ignore'):
err = np.sqrt(1/sp[0]["COADD"].data.ivar)*1e-17 * flux.unit

# Add to df_spec.
dfsingle = pd.DataFrame(dict(wave=[wave], flux=[flux], err=[err],
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1 change: 1 addition & 0 deletions spectroscopy/spectra_generator.md
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Original file line number Diff line number Diff line change
Expand Up @@ -109,6 +109,7 @@ This cell will install them if needed:
```{code-cell} ipython3
# Uncomment the next line to install dependencies if needed.
# !pip install -r requirements_spectra_generator.txt
# !pip install --upgrade --pre astroquery # >=0.4.8.dev9474 needed for mast_functions
```

```{code-cell} ipython3
Expand Down