def test_slitdark_in_calservice(self, get_or_create_tmpdir, do_slit_dark):
"""
Check that:
- A bias slit calibrator exists in the local calibrations dir;
- It can be retrieved using a getProcessedSlitBias call.
"""
# Ensure the slit dark reduction has been done
_, _, _ = do_slit_dark
_, cal_service = get_or_create_tmpdir
# import pdb; pdb.set_trace()
assert len(glob.glob(os.path.join(
os.getcwd(), 'calibrations', 'processed_dark', '*dark*slit*.fits'
))) == 1, "Couldn't find the stored slit bias in the calibrations " \
"system OR found multiples\n " \
"(calibration ls: {})\n" \
"(caldb contents: {})".format(
glob.glob(os.path.join(os.getcwd(), 'calibrations',
'processed_dark', '*')),
[_ for _ in cal_service.list_files()],
)
# Do the master bias generation
reduce = Reduce()
reduce.drpkg = 'ghostdr'
# Use one of the 'dark slit' files to try and retrieve the slit bias
reduce.files = glob.glob(
os.path.join(os.getcwd(), 'flat95*MEF_2x2_slit.fits'))
reduce.mode = [
'test',
]
reduce.recipename = 'recipeRetrieveSlitDarkTest'
# reduce.mode = ['sq', ]
reduce.logfile = os.path.join(os.getcwd(),
'reduce_slitdark_retrieve.log')
reduce.logmode = 'quiet'
reduce.suffix = '_testSlitDarkRetrieve'
# FIXME cal_service will hopefully find the calibration itself later
# reduce.ucals = normalize_ucals(reduce.files, [
# 'processed_dark:{}'.format(
# glob.glob(os.path.join(
# 'calibrations',
# 'processed_dark',
# '*slit*dark*.fits'))[0]),
# ])
logutils.config(file_name=reduce.logfile, mode=reduce.logmode)
try:
reduce.runr()
except IOError as e:
assert 0, 'Calibration system could not locate the slit bias ' \
'frame ({})'.format(e.message)
finally:
# Teardown code
for _ in glob.glob(
os.path.join(os.getcwd(),
'*{}.fits'.format(reduce.suffix)), ):
os.remove(_)
def test_mode_not_found():
testfile = download_from_archive("N20160524S0119.fits")
red = Reduce()
red.files = [testfile]
red.mode = 'aa'
with pytest.raises(RecipeNotFound,
match="GMOS recipes do not define a 'aa' recipe"):
red.runr()
def do_overscan_subtract(self, get_or_create_tmpdir, request):
"""
Run overscan correction on the main data.
.. note::
Fixture.
"""
# Copy the raw data file into here
rawfilename = 'bias*{}*.fits'.format(request.param)
tmpsubdir, cal_service = get_or_create_tmpdir
# Make sure we're working inside the temp dir
# rawfiles = glob.glob(os.path.join(
# os.path.dirname(os.path.abspath(__file__)),
# 'testdata',
# rawfilename))
# shutil.copy(
# rawfiles[0],
# os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
rawfile = glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
rawfilename))[0]
# Do the overscan subtraction
reduce = Reduce()
reduce.drpkg = 'ghostdr'
reduce.files = [
rawfile,
]
reduce.mode = [
'test',
]
reduce.recipename = 'recipeBiasRemoveOverscan'
reduce.logfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'reduce_overscancorrect.log')
reduce.logmode = 'quiet'
reduce.suffix = '_testOverscanCorrect'
logutils.config(file_name=reduce.logfile, mode=reduce.logmode)
reduce.runr()
corrfilename = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'*' + reduce.suffix + '.fits')
corrfilename = glob.glob(corrfilename)[0]
corrfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
corrfilename)
# Return filenames of raw, subtracted files
yield rawfile, corrfile
# Execute teardown code
for _ in glob.glob(
os.path.join(os.getcwd(), '*{}.fits'.format(reduce.suffix))):
os.remove(_)
def test_slitbias_in_calservice(self, get_or_create_tmpdir):
"""
Check that:
- A bias slit calibrator exists in the local calibrations dir;
- It can be retrieved using a getProcessedSlitBias call.
"""
assert len(glob.glob(os.path.join(
os.getcwd(), 'calibrations', 'processed_bias', '*bias*slit*.fits'
))) == 1, "Couldn't find the stored slit bias in the calibrations " \
"system OR found multiples"
# Do the master bias generation
reduce = Reduce()
reduce.drpkg = 'ghostdr'
# Use one of the 'dark slit' files to try and retrieve the slit bias
reduce.files = [
os.path.join(os.getcwd(), 'dark95_1_MEF_2x2_slit.fits'),
]
reduce.mode = [
'test',
]
reduce.recipename = 'recipeRetrieveSlitBiasTest'
# reduce.mode = ['sq', ]
# reduce.recipename = 'makeProcessedBias'
reduce.logfile = os.path.join(os.getcwd(),
'reduce_slitbias_retrieve.log')
# FIXME cal_service will hopefully find the calibration itself later
reduce.ucals = normalize_ucals(reduce.files, [
'processed_bias:{}'.format(
glob.glob(
os.path.join('calibrations', 'processed_bias',
'*slit*bias*.fits'))[0]),
])
reduce.logmode = 'quiet'
reduce.suffix = '_testSlitBiasRetrieve'
logutils.config(file_name=reduce.logfile, mode=reduce.logmode)
try:
reduce.runr()
except IOError as e:
assert 0, 'Calibration system could not locate the slit bias ' \
'frame ({})'.format(e.message)
finally:
# Teardown code
for _ in glob.glob(
os.path.join(os.getcwd(),
'*{}.fits'.format(reduce.suffix)), ):
os.remove(_)
def processed_slit_illum(change_working_dir, path_to_inputs, request):
"""
Returns the processed slit illumination function that will be analysed.
Parameters
----------
change_working_dir : pytest.fixture
Fixture that changes the working directory (see :mod:`astrodata.testing`).
path_to_inputs : pytest.fixture
Fixture defined in :mod:`astrodata.testing` with the path to the
pre-processed input file.
request : pytest.fixture
PyTest built-in fixture containing information about parent test.
Returns
-------
AstroData
Input spectrum processed up to right before the `applyQECorrection`.
"""
twi_filename = request.param
twi_path = download_from_archive(twi_filename)
twi_ad = astrodata.open(twi_path)
print(twi_ad.tags)
master_bias = os.path.join(
path_to_inputs, associated_calibrations[twi_filename])
assert os.path.exists(master_bias)
calibration_files = ['processed_bias:{}'.format(master_bias)]
with change_working_dir():
print("Reducing SLITILLUM in folder:\n {}".format(os.getcwd()))
logutils.config(
file_name='log_flat_{}.txt'.format(twi_ad.data_label()))
reduce = Reduce()
reduce.files.extend([twi_path])
reduce.mode = 'sq'
reduce.recipename = 'makeProcessedSlitIllum'
reduce.ucals = normalize_ucals(reduce.files, calibration_files)
reduce.runr()
_processed_twi_filename = reduce.output_filenames.pop()
_processed_twi = astrodata.open(_processed_twi_filename)
return _processed_twi
def _reduce_flat(datalabel, flat_fname, master_bias):
with output_path():
logutils.config(file_name='log_flat_{}.txt'.format(datalabel))
calibration_files = ['processed_bias:{}'.format(master_bias)]
reduce = Reduce()
reduce.files.extend([flat_fname])
reduce.mode = 'ql'
reduce.ucals = normalize_ucals(reduce.files, calibration_files)
reduce.runr()
master_flat = reduce.output_filenames.pop()
master_flat_ad = astrodata.open(master_flat)
return master_flat_ad
def do_slit_bias(self, get_or_create_tmpdir):
"""
Reduce the bias slit test data.
.. note::
Fixture.
"""
rawfilename = 'bias*slit*.fits'
# Copy the raw data file into here
tmpsubdir, cal_service = get_or_create_tmpdir
# Find all the relevant files
rawfiles = glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, rawfilename))
# Do the master bias generation
reduce = Reduce()
reduce.drpkg = 'ghostdr'
reduce.files = rawfiles
reduce.mode = [
'test',
]
reduce.recipename = 'recipeSlitBiasTest'
reduce.logfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'reduce_slitbias.log')
reduce.logmode = 'quiet'
reduce.suffix = '_testSlitBias'
logutils.config(file_name=reduce.logfile, mode=reduce.logmode)
reduce.runr()
corrfilename = '*' + reduce.suffix + '.fits'
corrfilename = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
glob.glob(corrfilename)[0])
corrfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
corrfilename)
# Return filenames of raw, subtracted files
yield rawfiles, corrfile
# Execute teardown code
for _ in glob.glob(
os.path.join(
os.getcwd(),
# rawfilename,
corrfilename,
)):
os.remove(_)
def processed_flat(change_working_dir, path_to_inputs, request):
"""
Returns the processed flat that will be analysed.
Parameters
----------
change_working_dir : pytest.fixture
Fixture that changes the working directory (see :mod:`astrodata.testing`).
path_to_inputs : pytest.fixture
Fixture defined in :mod:`astrodata.testing` with the path to the
pre-processed input file.
request : pytest.fixture
PyTest built-in fixture containing information about parent test.
Returns
-------
AstroData
Input spectrum processed up to right before the `applyQECorrection`.
"""
np.random.seed(0)
flat_filename = request.param
flat_path = download_from_archive(flat_filename)
flat_raw = astrodata.open(flat_path)
master_bias = os.path.join(path_to_inputs,
associated_calibrations[flat_filename])
calibration_files = ['processed_bias:{}'.format(master_bias)]
with change_working_dir():
print("Reducing FLATs in folder:\n {}".format(os.getcwd()))
logutils.config(
file_name='log_flat_{}.txt'.format(flat_raw.data_label()))
reduce = Reduce()
reduce.files.extend([flat_path])
reduce.mode = 'ql'
reduce.ucals = normalize_ucals(reduce.files, calibration_files)
reduce.runr()
# Clean up duplicated files
shutil.rmtree('calibrations/')
_processed_flat_filename = reduce.output_filenames.pop()
_processed_flat = astrodata.open(_processed_flat_filename)
return _processed_flat
def _reduce_flat(data_label, flat_fnames, master_bias):
with change_working_dir():
print("Reducing FLATs in folder:\n {}".format(os.getcwd()))
logutils.config(file_name='log_flat_{}.txt'.format(data_label))
calibration_files = ['processed_bias:{}'.format(master_bias)]
reduce = Reduce()
reduce.files.extend(flat_fnames)
reduce.mode = 'ql'
reduce.ucals = normalize_ucals(calibration_files)
reduce.runr()
master_flat = reduce.output_filenames.pop()
master_flat_ad = astrodata.open(master_flat)
return master_flat_ad
def test_make_processed_flat(change_working_dir, flat_fnames, master_bias,
path_to_inputs):
"""
Regression test for GMOS
Parameters
----------
change_working_dir : fixture
Custom fixture defined astrodata.testing that changes temporarily the
working dir.
flat_fnames : list
Contains the flat names that will be reduced.
master_bias : str
Contains the name of the master flat.
path_to_inputs : fixture
Custom fixture that defines where the input data is stored.
"""
master_bias = os.path.join(path_to_inputs, master_bias)
calibration_files = ['processed_bias:{}'.format(master_bias)]
with change_working_dir():
logutils.config(
file_name=f"log_flat_{flat_fnames[0].split('.')[0]}.txt")
r = Reduce()
r.files = [download_from_archive(f) for f in flat_fnames]
r.mode = 'qa'
r.ucals = normalize_ucals(r.files, calibration_files)
r.runr()
# Delete files that won't be used
shutil.rmtree('calibrations/')
[os.remove(f) for f in glob.glob('*_forStack.fits')]
ad = astrodata.open(r.output_filenames[0])
for ext in ad:
data = np.ma.masked_array(ext.data, mask=ext.mask)
if not data.mask.all():
np.testing.assert_allclose(np.ma.median(data.ravel()),
1,
atol=0.071)
np.testing.assert_allclose(data[~data.mask], 1, atol=0.45)
def do_slit_arc(self, request, get_or_create_tmpdir):
"""
Reduce the test slit arc data.
.. note::
Fixture.
"""
# import pdb; pdb.set_trace()
# rawfilename = '{}*slit*.fits'.format(slit_type)
# Copy the raw data file into here
tmpsubdir, cal_service = get_or_create_tmpdir
slit_type, res = request.param
filenames = glob.glob('{}*{}*slit.fits'.format(slit_type, res))
# Do the master bias generation
reduce = Reduce()
reduce.drpkg = 'ghostdr'
reduce.mode = ['test', ]
reduce.recipename = 'recipeSlitArcTest' if slit_type == 'arc' \
else 'recipeSlitTest'
# Make sure refresh is used for all primitives
reduce.upars = ['refresh=True', ]
# FIXME cal_service will hopefully find the calibration itself later
calibs = {
'processed_bias': glob.glob(os.path.join(
'calibrations',
'processed_bias',
'*slit*bias*.fits'))[0],
'processed_dark': glob.glob(os.path.join(
'calibrations',
'processed_dark',
'*slit*dark*.fits'))[0],
'processed_slitflat': glob.glob(os.path.join(
'calibrations',
'processed_slitflat',
'*{}*slit*slitflat*.fits'.format(res, )))[0]
}
reduce.logfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'reduce_slit{}.log'.format(slit_type))
reduce.logmode = 'standard'
reduce.suffix = '_{}_testSlit'.format(slit_type)
logutils.config(file_name=reduce.logfile, mode=reduce.logmode)
corrfiles = []
for filename in filenames:
reduce.files = [filename, ]
reduce.ucals = normalize_ucals(reduce.files, [
'{}:{}'.format(k, v) for k, v in calibs.items()
])
reduce.runr()
# import pdb; pdb.set_trace()
corrfilename = '*' + reduce.suffix + '.fits'
corrfilename = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
glob.glob(corrfilename)[0])
corrfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
corrfilename)
corrfiles.append(corrfile)
# Return filenames of raw, subtracted files
yield filenames, corrfiles, calibs
# import pdb; pdb.set_trace()
# Execute teardown code
for _ in glob.glob(os.path.join(
os.getcwd(),
# rawfilename,
corrfilename,
)):
os.remove(_)
def do_master_flat(self, get_or_create_tmpdir, request):
"""
Run the recipeFlatCreateMaster recipe.
.. note::
Fixture.
"""
arm, res = request.param
rawfilename = 'flat*{}*{}*.fits'.format(res, arm)
# Copy the raw data file into here
tmpsubdir, cal_service = get_or_create_tmpdir
# Find all the relevant files
# rawfiles = glob.glob(os.path.join(os.path.dirname(
# os.path.abspath(__file__)),
# 'testdata',
# rawfilename))
# for f in rawfiles:
# shutil.copy(f, os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
rawfiles = glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, rawfilename))
# Do the master bias generation
reduce = Reduce()
reduce.drpkg = 'ghostdr'
reduce.files = rawfiles
reduce.mode = [
'test',
]
reduce.recipename = 'recipeFlatCreateMaster'
# reduce.mode = ['sq', ]
# reduce.recipename = 'makeProcessedBias'
reduce.logfile = os.path.join(
tmpsubdir.dirname, tmpsubdir.basename,
'reduce_masterflat_{}_{}.log'.format(res, arm))
reduce.logmode = 'quiet'
reduce.suffix = '_{}_{}_testMasterFlat'.format(res, arm)
logutils.config(file_name=reduce.logfile, mode=reduce.logmode)
# import pdb; pdb.set_trace()
calibs = {
'processed_bias':
glob.glob(
os.path.join('calibrations', 'processed_bias',
'bias*{}*.fits'.format(arm)))[0],
'processed_dark':
glob.glob(
os.path.join('calibrations', 'processed_dark',
'dark*{}*.fits'.format(arm)))[0],
'processed_slitflat':
glob.glob(
os.path.join('calibrations', 'processed_slitflat',
'flat*{}*slitflat*.fits'.format(res)))[0],
}
reduce.ucals = normalize_ucals(
reduce.files, ['{}:{}'.format(k, v) for k, v in calibs.items()])
reduce.runr()
if res == 'std' and arm == 'red':
pass
# import pdb;
# pdb.set_trace()
corrfilename = '*' + reduce.suffix + '.fits'
corrfilename = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
glob.glob(corrfilename)[0])
corrfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
corrfilename)
# Return filenames of raw, subtracted files
yield rawfiles, corrfile, calibs
# Execute teardown code
pass
def do_slit_dark(self, get_or_create_tmpdir):
"""
Reduce the test slit dark data.
.. note::
Fixture.
"""
rawfilename = 'dark*slit*.fits'
# Copy the raw data file into here
tmpsubdir, cal_service = get_or_create_tmpdir
# Find all the relevant files
rawfiles = glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, rawfilename))
# Do the master bias generation
reduce = Reduce()
reduce.drpkg = 'ghostdr'
reduce.files = rawfiles
reduce.mode = [
'test',
]
reduce.recipename = 'recipeSlitDarkTest'
# Make sure refresh is used for all primitives
reduce.upars = [
'refresh=True',
]
# FIXME cal_service will hopefully find the calibration itself later
calibs = {
'processed_bias':
glob.glob(
os.path.join('calibrations', 'processed_bias',
'*slit*bias*.fits'))[0],
}
reduce.ucals = normalize_ucals(
reduce.files, ['{}:{}'.format(k, v) for k, v in calibs.items()])
reduce.logfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
'reduce_slitdark.log')
reduce.logmode = 'standard'
reduce.suffix = '_testSlitDark'
logutils.config(file_name=reduce.logfile, mode=reduce.logmode)
reduce.runr()
corrfilename = '*' + reduce.suffix + '.fits'
corrfilename = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
glob.glob(corrfilename)[0])
corrfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
corrfilename)
# Return filenames of raw, subtracted files
yield rawfiles, corrfile, calibs
# import pdb; pdb.set_trace()
# Execute teardown code
for _ in glob.glob(
os.path.join(
os.getcwd(),
# rawfilename,
corrfilename,
)):
os.remove(_)
def do_master_bias(self, get_or_create_tmpdir, request):
"""
Perform bias subtraction on the main data.
.. note::
Fixture.
"""
rawfilename = 'bias*{}*.fits'.format(request.param)
# Copy the raw data file into here
tmpsubdir, cal_service = get_or_create_tmpdir
# Find all the relevant files
# rawfiles = glob.glob(os.path.join(os.path.dirname(
# os.path.abspath(__file__)),
# 'testdata',
# rawfilename))
# for f in rawfiles:
# shutil.copy(f, os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
rawfiles = glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, rawfilename))
# Do the master bias generation
reduce = Reduce()
reduce.drpkg = 'ghostdr'
reduce.files = rawfiles
reduce.mode = [
'test',
]
reduce.recipename = 'recipeBiasCreateMaster'
reduce.upars = [
'refresh=True',
]
# reduce.mode = ['sq', ]
# reduce.recipename = 'makeProcessedBias'
reduce.logfile = os.path.join(
tmpsubdir.dirname, tmpsubdir.basename,
'reduce_masterbias_{}.log'.format(request.param))
reduce.logmode = 'quiet'
reduce.suffix = '_{}_testMasterBias'.format(request.param)
logutils.config(file_name=reduce.logfile, mode=reduce.logmode)
reduce.runr()
# import pdb; pdb.set_trace()
corrfilename = '*' + reduce.suffix + '.fits'
corrfilename = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
glob.glob(corrfilename)[0])
corrfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
corrfilename)
# Find the overscan-corrected bias files
rawfiles = glob.glob(
os.path.join(
tmpsubdir.dirname,
tmpsubdir.basename,
rawfilename.split('.')[0] + '*_overscanCorrect*.fits',
))
# Return filenames of raw, subtracted files
yield rawfiles, corrfile
# Execute teardown code
pass
def do_bias_subtract(self, get_or_create_tmpdir, request):
"""
Perform basic bias subtraction on the dark frame.
.. note::
Fixture.
"""
rawfilename = 'dark*{}*.fits'.format(request.param)
# Copy the raw data file into here
tmpsubdir, cal_service = get_or_create_tmpdir
# Find all the relevant files
# rawfiles = glob.glob(os.path.join(os.path.dirname(
# os.path.abspath(__file__)),
# 'testdata',
# rawfilename))
# for f in rawfiles:
# shutil.copy(f, os.path.join(tmpsubdir.dirname, tmpsubdir.basename))
rawfiles = glob.glob(
os.path.join(tmpsubdir.dirname, tmpsubdir.basename, rawfilename))
# Do the master bias generation
reduce = Reduce()
reduce.drpkg = 'ghostdr'
reduce.files = rawfiles[0]
reduce.mode = [
'test',
]
reduce.recipename = 'recipeDarkBiasCorrect'
# reduce.mode = ['sq', ]
# reduce.recipename = 'makeProcessedBias'
reduce.logfile = os.path.join(
tmpsubdir.dirname, tmpsubdir.basename,
'reduce_biascorrect_{}.log'.format(request.param))
reduce.logmode = 'quiet'
reduce.suffix = '_{}_testBiasCorrect'.format(request.param)
logutils.config(file_name=reduce.logfile, mode=reduce.logmode)
# import pdb; pdb.set_trace()
calibs = {
'processed_bias':
glob.glob(
os.path.join('calibrations', 'processed_bias',
'bias*{}*.fits'.format(request.param)))[0],
}
reduce.ucals = normalize_ucals(
reduce.files, ['{}:{}'.format(k, v) for k, v in calibs.items()])
# import pdb;
# pdb.set_trace()
reduce.runr()
corrfilename = '*' + reduce.suffix + '.fits'
corrfilename = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
glob.glob(corrfilename)[0])
corrfile = os.path.join(tmpsubdir.dirname, tmpsubdir.basename,
corrfilename)
# Return filenames of raw, subtracted files
yield rawfiles, corrfile, calibs
# Execute teardown code
for _ in glob.glob(
os.path.join(os.getcwd(), '*{}.fits'.format(reduce.suffix))):
os.remove(_)