def create_twilight_inputs():
"""
Creates input data for tests using pre-processed twilight flat data and its
calibration files.
The raw files will be downloaded and saved inside the path stored in the
`$DRAGONS_TEST/raw_inputs` directory. Processed files will be stored inside
a new folder called "dragons_test_inputs". The sub-directory structure
should reflect the one returned by the `path_to_inputs` fixture.
"""
associated_calibrations = {
"S20190204S0006.fits": {
"bias": [
"S20190203S0110.fits", "S20190203S0109.fits",
"S20190203S0108.fits", "S20190203S0107.fits",
"S20190203S0106.fits"
],
"twilight": ["S20190204S0006.fits"],
},
"N20190103S0462.fits": {
"bias": [
"N20190102S0531.fits", "N20190102S0530.fits",
"N20190102S0529.fits", "N20190102S0528.fits",
"N20190102S0527.fits"
],
"twilight": ["N20190103S0462.fits", "N20190103S0463.fits"],
},
"N20190327S0056.fits": {
"bias": [
"N20190327S0098.fits", "N20190327S0099.fits",
"N20190327S0100.fits", "N20190327S0101.fits",
"N20190327S0102.fits"
],
"twilight": ["N20190327S0056.fits"],
},
"S20130602S0005.fits": {
"bias": [
"S20130601S0161.fits",
"S20130601S0160.fits",
"S20130601S0159.fits",
"S20130601S0158.fits",
"S20130601S0157.fits",
],
"twilight": ["S20130602S0005.fits"],
},
"N20190602S0306.fits": {
"bias": [
"N20190601S0648.fits",
"N20190601S0647.fits",
"N20190601S0646.fits",
"N20190601S0645.fits",
"N20190601S0644.fits",
],
"twilight": ["N20190602S0306.fits"],
}
}
root_path = os.path.join("./dragons_test_inputs/")
module_path = "geminidr/gmos/longslit/test_slit_illumination_correct/inputs"
path = os.path.join(root_path, module_path)
os.makedirs(path, exist_ok=True)
cwd = os.getcwd()
os.chdir(path)
print('Current working directory:\n {:s}'.format(os.getcwd()))
for filename, cals in associated_calibrations.items():
print('Download raw files')
bias_path = [download_from_archive(f) for f in cals['bias']]
twilight_path = [download_from_archive(f) for f in cals['twilight']]
twilight_ad = astrodata.open(twilight_path[0])
data_label = twilight_ad.data_label()
print('Reducing BIAS for {:s}'.format(data_label))
logutils.config(file_name='log_bias_{}.txt'.format(data_label))
bias_reduce = Reduce()
bias_reduce.files.extend(bias_path)
bias_reduce.runr()
bias_master = bias_reduce.output_filenames.pop()
del bias_reduce
print('Reducing twilight flat:')
logutils.config(file_name='log_twilight_{}.txt'.format(data_label))
with warnings.catch_warnings():
warnings.simplefilter("ignore")
p = GMOSLongslit([astrodata.open(f) for f in twilight_path])
p.prepare()
p.addDQ(static_bpm=None)
p.addVAR(read_noise=True)
p.overscanCorrect()
p.biasCorrect(bias=bias_master)
p.ADUToElectrons()
p.addVAR(poisson_noise=True)
p.stackFrames()
# Write non-mosaicked data
twilight = p.writeOutputs(suffix="_twilight", strip=True)[0]
# Write mosaicked data
p = GMOSLongslit([twilight])
p.makeSlitIllum()
p.writeOutputs()
os.chdir(cwd)
return
def create_inputs():
"""
Create inputs for `test_plot_spectra_for_qa_single_frame`.
The raw files will be downloaded and saved inside the path stored in the
`$DRAGONS_TEST/raw_inputs` directory. Processed files will be stored inside
a new folder called "dragons_test_inputs". The sub-directory structure
should reflect the one returned by the `path_to_inputs` fixture.
"""
import glob
import os
from geminidr.gmos.primitives_gmos_longslit import GMOSLongslit
from gempy.utils import logutils
from recipe_system.reduction.coreReduce import Reduce
from recipe_system.utils.reduce_utils import normalize_ucals
cwd = os.getcwd()
path = f"./dragons_test_inputs/geminidr/core/{__file__.split('.')[0]}/"
os.makedirs(path, exist_ok=True)
os.chdir(path)
os.makedirs("inputs/", exist_ok=True)
for raw_list, bias_list, quartz_list, arc_list in single_aperture_data:
if all([
os.path.exists(f"inputs/{s.split('.')[0]}_extracted.fits")
for s in raw_list
]):
print("Skipping already created input.")
continue
raw_paths = [download_from_archive(f) for f in raw_list]
bias_paths = [download_from_archive(f) for f in bias_list]
quartz_paths = [download_from_archive(f) for f in quartz_list]
arc_paths = [download_from_archive(f) for f in arc_list]
cals = []
raw_ads = [astrodata.open(p) for p in raw_paths]
data_label = raw_ads[0].data_label()
print('Current working directory:\n {:s}'.format(os.getcwd()))
if len(bias_paths):
logutils.config(file_name='log_bias_{}.txt'.format(data_label))
r = Reduce()
r.files.extend(bias_paths)
r.runr()
master_bias = r.output_filenames.pop()
cals.append(f"processed_bias:{master_bias}")
del r
else:
master_bias = None
if len(quartz_paths):
logutils.config(file_name='log_quartz_{}.txt'.format(data_label))
r = Reduce()
r.files.extend(quartz_paths)
r.ucals = normalize_ucals(r.files, cals)
r.runr()
master_quartz = r.output_filenames.pop()
cals.append(f"processed_flat:{master_quartz}")
del r
else:
master_quartz = None
logutils.config(file_name='log_arc_{}.txt'.format(data_label))
r = Reduce()
r.files.extend(arc_paths)
r.ucals = normalize_ucals(r.files, cals)
r.runr()
master_arc = r.output_filenames.pop()
logutils.config(file_name='log_{}.txt'.format(data_label))
p = GMOSLongslit(raw_ads)
p.prepare()
p.addDQ(static_bpm=None)
p.addVAR(read_noise=True)
p.overscanCorrect()
p.biasCorrect(do_bias=master_bias is not None, bias=master_bias)
p.ADUToElectrons()
p.addVAR(poisson_noise=True)
p.flatCorrect(do_flat=master_quartz is not None, flat=master_quartz)
p.QECorrect(arc=master_arc)
p.distortionCorrect(arc=master_arc)
p.findSourceApertures(max_apertures=3)
p.skyCorrectFromSlit()
p.traceApertures()
p.extract1DSpectra()
p.linearizeSpectra()
[os.remove(s) for s in glob.glob("*_arc.fits")]
[os.remove(s) for s in glob.glob("*_bias.fits")]
[os.remove(s) for s in glob.glob("*_flat.fits")]
[os.remove(s) for s in glob.glob("*_mosaic.fits")]
os.chdir("inputs/")
print("\n\n Writing processed files for tests into:\n"
" {:s}\n\n".format(os.getcwd()))
_ = p.writeOutputs()
os.chdir("../")
os.chdir(cwd)