def create_quartz_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 = {
"N20200715S0059.fits": {
"quartz": ["N20200715S0059.fits"],
},
"S20130601S0121.fits": {
"quartz": ["S20130601S0121.fits"],
},
"S20190204S0081.fits": {
"quartz": ["S20190204S0081.fits"],
},
}
root_path = os.path.join("./dragons_test_inputs/")
module_path = "geminidr/gmos/longslit/test_slit_illum_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')
quartz_path = [download_from_archive(f) for f in cals['quartz']]
quartz_ad = astrodata.open(quartz_path[0])
data_label = quartz_ad.data_label()
print('Reducing quartz lamp:')
logutils.config(file_name='log_quartz_{}.txt'.format(data_label))
with warnings.catch_warnings():
warnings.simplefilter("ignore")
p = GMOSLongslit([astrodata.open(f) for f in quartz_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
p.writeOutputs(suffix="_quartz", strip=True)
os.chdir(cwd)
def test_resample_linearize_trim_and_stack(input_ad_list, caplog):
p = GMOSLongslit(input_ad_list)
ads = p.resampleToCommonFrame(dw=0.15, trim_data=True)
assert len(ads) == len(test_datasets)
assert len({ad[0].shape[0] for ad in ads}) == 1
_check_params(caplog.records, 'w1=508.198 w2=978.802 dw=0.150 npix=3139')
adout = p.stackFrames()
assert len(adout) == 1
assert len(adout[0]) == 1
assert adout[0][0].shape[0] == 3139
def test_correlation_and_w1_w2(adinputs, caplog):
add_fake_offset(adinputs, offset=10)
p = GMOSLongslit(adinputs)
adout = p.adjustWCSToReference()
assert adout[1].phu['SLITOFF'] == -10
assert adout[2].phu['SLITOFF'] == -20
p.resampleToCommonFrame(dw=0.15, w1=700, w2=850)
_check_params(caplog.records, 'w1=700.000 w2=850.000 dw=0.150 npix=1001')
adstack = p.stackFrames()
assert adstack[0][0].shape == (512, 1001)
def test_correlation_non_linearize(adinputs, caplog):
add_fake_offset(adinputs, offset=10)
p = GMOSLongslit(adinputs)
adout = p.adjustWCSToReference()
assert adout[1].phu['SLITOFF'] == -10
assert adout[2].phu['SLITOFF'] == -20
p.resampleToCommonFrame(force_linear=False)
_check_params(caplog.records, 'w1=508.198 w2=1088.323 dw=0.151 npix=3841')
caplog.clear()
adout = p.resampleToCommonFrame(dw=0.15)
assert 'ALIGN' in adout[0].phu
_check_params(caplog.records, 'w1=508.198 w2=1088.232 dw=0.150 npix=3868')
adstack = p.stackFrames()
assert adstack[0][0].shape == (512, 3868)
def test_correlation_and_trim(adinputs, caplog):
add_fake_offset(adinputs, offset=10)
p = GMOSLongslit(adinputs)
adout = p.adjustWCSToReference()
assert adout[1].phu['SLITOFF'] == -10
assert adout[2].phu['SLITOFF'] == -20
p.resampleToCommonFrame(dw=0.15, trim_data=True)
_check_params(caplog.records, 'w1=508.198 w2=978.802 dw=0.150 npix=3139')
ad = p.stackFrames()[0]
assert ad[0].shape == (512, 3139)
caplog.clear()
ad = p.findSourceApertures(max_apertures=1)[0]
assert len(ad[0].APERTURE) == 1
np.testing.assert_allclose(ad[0].APERTURE['c0'], 260.8, atol=0.25)
ad = p.extract1DSpectra()[0]
assert ad[0].shape == (3139, )
def test_correlation(adinputs, caplog):
add_fake_offset(adinputs, offset=10)
p = GMOSLongslit(adinputs)
adout = p.adjustWCSToReference()
assert adout[1].phu['SLITOFF'] == -10
assert adout[2].phu['SLITOFF'] == -20
p.resampleToCommonFrame(dw=0.15)
_check_params(caplog.records, 'w1=508.198 w2=1088.323 dw=0.150 npix=3869')
ad = p.stackFrames()[0]
assert ad[0].shape == (512, 3869)
caplog.clear()
ad = p.findSourceApertures(max_apertures=1)[0]
assert len(ad[0].APERTURE) == 1
#assert caplog.records[3].message == 'Found sources at rows: 260.8'
np.testing.assert_allclose(ad[0].APERTURE['c0'], 260.8, atol=0.25)
ad = p.extract1DSpectra()[0]
assert ad[0].shape == (3869, )
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