def test_cosmics_on_mosaiced_data(path_to_inputs, caplog):
ad = astrodata.open(os.path.join(path_to_inputs, TESFILE1))
ext = ad[0]
# add some additional fake cosmics
size = 50
np.random.seed(42)
cr_x = np.random.randint(low=5, high=ext.shape[0] - 5, size=size)
cr_y = np.random.randint(low=5, high=ext.shape[1] - 5, size=size)
# Don't add cosmics in masked regions
mask = binary_dilation(ext.mask > 0, iterations=3)
sel = ~mask[cr_x, cr_y]
cr_x = cr_x[sel]
cr_y = cr_y[sel]
cr_brightnesses = np.random.uniform(low=1000, high=5000, size=len(cr_x))
ext.data[cr_x, cr_y] += cr_brightnesses
# Store mask of CR to help debugging
crmask = np.zeros(ext.shape, dtype=np.uint8)
crmask[cr_x, cr_y] = 1
ext.CRMASK = crmask
debug = os.getenv('DEBUG') is not None
p = GMOSSpect([ad])
adout = p.flagCosmicRays(y_order=3, bkgfit_niter=5, debug=debug)[0]
if debug:
p.writeOutputs()
mask = adout[0].mask
# check some pixels with real cosmics
for pix in [(496, 519), (138, 219), (420, 633), (297, 1871)]:
assert (mask[pix] & DQ.cosmic_ray) == DQ.cosmic_ray
# And check our fake cosmics.
assert np.all(mask[np.where(ext.CRMASK)] & DQ.cosmic_ray == DQ.cosmic_ray)
def create_inputs_recipe():
"""
Creates input data for tests using pre-processed standard star and its
calibration files.
The raw files will be downloaded and saved inside the path stored in the
`$DRAGONS_TEST/raw_inputs` directory. Processed files will be stored inside
a new folder called "dragons_test_inputs". The sub-directory structure
should reflect the one returned by the `path_to_inputs` fixture.
"""
fnames = ["S20190808S0048.fits"]
path = pathlib.Path('dragons_test_inputs')
path = path / "geminidr" / "gmos" / "spect" / "test_cosmics" / "inputs"
path.mkdir(exist_ok=True, parents=True)
os.chdir(path)
print('Current working directory:\n {!s}'.format(path.cwd()))
for fname in fnames:
sci_ad = astrodata.open(download_from_archive(fname))
data_label = sci_ad.data_label()
print('===== Reducing pre-processed data =====')
logutils.config(file_name=f'log_{data_label}.txt')
p = GMOSSpect([sci_ad])
p.prepare()
p.addDQ(static_bpm=None)
p.addVAR(read_noise=True)
p.overscanCorrect()
p.ADUToElectrons()
p.addVAR(poisson_noise=True)
p.writeOutputs()
p.mosaicDetectors()
p.writeOutputs()
def create_inputs_recipe():
"""
Creates input data for tests using pre-processed standard star and its
calibration files.
The raw files will be downloaded and saved inside the path stored in the
`$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.
"""
import os
from astrodata.testing import download_from_archive
from geminidr.gmos.tests.spect import CREATED_INPUTS_PATH_FOR_TESTS
from gempy.utils import logutils
from recipe_system.reduction.coreReduce import Reduce
module_name, _ = os.path.splitext(os.path.basename(__file__))
path = os.path.join(CREATED_INPUTS_PATH_FOR_TESTS, module_name)
os.makedirs(path, exist_ok=True)
os.chdir(path)
os.makedirs("inputs", exist_ok=True)
cwd = os.getcwd()
associated_arcs = {
"N20180109S0287.fits":
"N20180109S0315.fits", # GN-2017B-FT-20-13-001 B600 0.505um
"N20190302S0089.fits":
"N20190302S0274.fits", # GN-2019A-Q-203-7-001 B600 0.550um
"N20190313S0114.fits":
"N20190313S0132.fits", # GN-2019A-Q-325-13-001 B600 0.482um
"N20190427S0126.fits":
"N20190427S0267.fits", # GN-2019A-FT-206-7-004 R400 0.625um
"N20190910S0028.fits":
"N20190910S0279.fits", # GN-2019B-Q-313-5-001 B600 0.550um
"S20180919S0139.fits":
"S20180919S0141.fits", # GS-2018B-Q-209-13-003 B600 0.45um
"S20191005S0051.fits":
"S20191005S0147.fits", # GS-2019B-Q-132-35-001 R400 0.73um
}
for sci_fname, arc_fname in associated_arcs.items():
sci_path = download_from_archive(sci_fname)
arc_path = download_from_archive(arc_fname)
sci_ad = astrodata.open(sci_path)
data_label = sci_ad.data_label()
logutils.config(file_name='log_arc_{}.txt'.format(data_label))
arc_reduce = Reduce()
arc_reduce.files.extend([arc_path])
# arc_reduce.ucals = normalize_ucals(arc_reduce.files, calibration_files)
os.chdir("inputs/")
arc_reduce.runr()
arc_ad = arc_reduce.output_filenames.pop()
logutils.config(file_name='log_{}.txt'.format(data_label))
p = GMOSSpect([sci_ad])
p.prepare()
p.addDQ(static_bpm=None)
p.addVAR(read_noise=True)
p.overscanCorrect()
p.ADUToElectrons()
p.addVAR(poisson_noise=True)
p.distortionCorrect(arc=arc_ad)
p.writeOutputs()
os.chdir("../")
os.chdir(cwd)