def test_run_pypeit():
# Just get a few files
testrawdir = data_path('')
outdir = data_path('REDUX_OUT_TEST')
# For previously failed tests
if os.path.isdir(outdir):
shutil.rmtree(outdir)
# Run the setup
sargs = Setup.parse_args([
'-r', testrawdir + 'b', '-s', 'shane_kast_blue', '-c all', '-o',
'--output_path', outdir
])
Setup.main(sargs)
# Change to the configuration directory and set the pypeit file
configdir = os.path.join(outdir, 'shane_kast_blue_A')
pyp_file = os.path.join(configdir, 'shane_kast_blue_A.pypeit')
assert os.path.isfile(pyp_file), 'PypeIt file not written.'
# Try to run with -m and -o
pargs = RunPypeIt.parse_args([pyp_file, '-o', '-m', '-r', configdir])
RunPypeIt.main(pargs)
# TODO: Add some code that will try to open the QA HTML and check that it
# has the correct PNGs in it.
# #########################################################
# Test!!
# Files exist
spec1d_file = os.path.join(
configdir, 'Science',
'spec1d_b27-J1217p3905_KASTb_20150520T045733.560.fits')
assert os.path.isfile(spec1d_file), 'spec1d file missing'
# spec1d
specObjs = specobjs.SpecObjs.from_fitsfile(spec1d_file)
# Check RMS
assert specObjs[
0].WAVE_RMS < 0.02 # difference must be less than 0.02 pixels
# Flexure
assert abs(-0.03 - specObjs[0].FLEX_SHIFT_TOTAL
) < 0.1 # difference must be less than 0.1 pixels
# Helio
assert abs(specObjs[0].VEL_CORR - 0.9999261685542624) < 1.0E-10
# Now re-use those master files
pargs = RunPypeIt.parse_args([pyp_file, '-o', '-r', configdir])
RunPypeIt.main(pargs)
# Clean-up
shutil.rmtree(outdir)
def test_read_combid():
# ------------------------------------------------------------------
# In case of failed tests
setup_dir = data_path('setup_files')
if os.path.isdir(setup_dir):
shutil.rmtree(setup_dir)
config_dir = data_path('shane_kast_blue_A')
if os.path.isdir(config_dir):
shutil.rmtree(config_dir)
# ------------------------------------------------------------------
# Generate the pypeit file with the comb_id
droot = data_path('b')
pargs = Setup.parse_args([
'-r', droot, '-s', 'shane_kast_blue', '-c=all', '-b',
'--extension=fits.gz', '--output_path={:s}'.format(data_path(''))
])
Setup.main(pargs)
shutil.rmtree(setup_dir)
pypeit_file = os.path.join(config_dir, 'shane_kast_blue_A.pypeit')
cfg_lines, data_files, frametype, usrdata, setups, _ = parse_pypeit_file(
pypeit_file)
# Get the spectrograph
spectrograph = None
for l in cfg_lines:
if 'spectrograph' in l:
spectrograph = load_spectrograph(l.split(' ')[-1])
break
assert spectrograph is not None, 'Did not appropriately read spectrograph'
# Set the metadata
pmd = PypeItMetaData(spectrograph,
spectrograph.default_pypeit_par(),
files=data_files,
usrdata=usrdata,
strict=False)
indx = pmd['filename'] == 'b27.fits.gz'
assert pmd['comb_id'][indx] == [1], 'Incorrect combination group ID'
assert pmd['comb_id'][np.where(~indx)
[0]][0] == -1, 'Incorrect combination group ID'
shutil.rmtree(config_dir)
def test_setup_keck_lris_red_mark4():
droot = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA/keck_lris_red_mark4/long_400_8500_d560')
droot += '/'
pargs = Setup.parse_args(['-r', droot, '-s', 'keck_lris_red_mark4'])
Setup.main(pargs)
cwd = os.getcwd()
setup_dir = os.path.join(cwd, 'setup_files')
assert os.path.isdir(setup_dir), 'No setup_files directory created'
files = glob.glob(os.path.join(setup_dir, 'keck_lris_red_mark4*'))
ext = [f.split('.')[-1] for f in files]
expected = expected_file_extensions()
assert np.all([e in ext for e in expected]), \
'Did not find all setup file extensions: {0}'.format(expected)
# Clean-up
shutil.rmtree(setup_dir)
def test_setup_gemini_gnirs():
droot = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA/gemini_gnirs/32_SB_SXD/')
droot += '/cN'
pargs = Setup.parse_args(['-r', droot, '-s', 'gemini_gnirs'])
Setup.main(pargs)
cwd = os.getcwd()
setup_dir = os.path.join(cwd, 'setup_files')
assert os.path.isdir(setup_dir), 'No setup_files directory created'
files = glob.glob(os.path.join(setup_dir, 'gemini_gnirs*'))
ext = [f.split('.')[-1] for f in files]
expected = expected_file_extensions()
assert np.all([e in ext for e in expected]), \
'Did not find all setup file extensions: {0}'.format(expected)
# Clean-up
shutil.rmtree(setup_dir)
def test_setup_not_alfosc():
droot = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA/not_alfosc/grism4')
droot += '/ALD'
pargs = Setup.parse_args(['-r', droot, '-s', 'not_alfosc'])
Setup.main(pargs)
cwd = os.getcwd()
setup_dir = os.path.join(cwd, 'setup_files')
assert os.path.isdir(setup_dir), 'No setup_files directory created'
files = glob.glob(os.path.join(setup_dir, 'not_alfosc*'))
ext = [f.split('.')[-1] for f in files]
expected = expected_file_extensions()
assert np.all([e in ext for e in expected]), \
'Did not find all setup file extensions: {0}'.format(expected)
# Build a PypeIt file
pargs = Setup.parse_args(['-r', droot, '-s', 'not_alfosc', '-c', 'A', '-d', data_path('')])
Setup.main(pargs)
pypeit_file = data_path('not_alfosc_A/not_alfosc_A.pypeit')
# TODO: Why is this using pypeit.PypeIt and not pypeitsetup.PypeItSetup?
pypeIt = pypeit.PypeIt(pypeit_file, calib_only=True)
# Clean-up
shutil.rmtree(setup_dir)
shutil.rmtree(data_path('not_alfosc_A'))
def test_run_setup():
""" Test the setup script
"""
# Remove .setup if needed
sfiles = glob.glob('*.setups')
for sfile in sfiles:
os.remove(sfile)
#
droot = data_path('b')
pargs = Setup.parse_args(['-r', droot, '-s', 'shane_kast_blue', '-c=all',
'--extension=fits.gz', '--output_path={:s}'.format(data_path(''))])
Setup.main(pargs)
#setup_file = glob.glob(data_path('setup_files/shane_kast_blue*.setups'))[0]
## Load
#with open(setup_file, 'r') as infile:
# setup_dict = yaml.load(infile)
## Test
#assert '01' in setup_dict['A'].keys()
#assert setup_dict['A']['--']['disperser']['name'] == '600/4310'
# Failures
pargs2 = Setup.parse_args(['-r', droot, '-s', 'shane_kast_blu', '-c=all',
'--extension=fits.gz', '--output_path={:s}'.format(data_path(''))])
with pytest.raises(ValueError):
Setup.main(pargs2)
# Cleanup
shutil.rmtree(data_path('setup_files'))
def test_setup_vlt_fors2():
droot = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA/vlt_fors2/300I/')
droot += '/FORS2'
pargs = Setup.parse_args(['-r', droot, '-s', 'vlt_fors2'])
Setup.main(pargs)
cwd = os.getcwd()
setup_dir = os.path.join(cwd, 'setup_files')
assert os.path.isdir(setup_dir), 'No setup_files directory created'
files = glob.glob(os.path.join(setup_dir, 'vlt_fors2*'))
ext = [f.split('.')[-1] for f in files]
expected = expected_file_extensions()
assert np.all([e in ext for e in expected]), \
'Did not find all setup file extensions: {0}'.format(expected)
# Clean-up
shutil.rmtree(setup_dir)
# Now chk calib
pargs = ChkForCalibs.parse_args([droot, '-s', 'vlt_fors2'])
answers, ps = ChkForCalibs.main(pargs)
assert answers['pass'][0], 'A must pass!'
def test_run_pypeit_calib_only():
# Get the directories
rawdir = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA',
'shane_kast_blue', '600_4310_d55')
assert os.path.isdir(rawdir), 'Incorrect raw directory'
master_key = 'A_1_DET01'
# File list
all_files = {
'arcs': ['b1.fits.gz'],
'flats': ['b11.fits.gz', 'b12.fits.gz', 'b13.fits.gz'],
'bias': ['b21.fits.gz', 'b22.fits.gz', 'b23.fits.gz'],
}
all_masters = [
f'MasterArc_{master_key}.fits', f'MasterTiltimg_{master_key}.fits',
f'MasterBias_{master_key}.fits', f'MasterTilts_{master_key}.fits',
f'MasterEdges_{master_key}.fits.gz', f'MasterFlat_{master_key}.fits',
f'MasterWaveCalib_{master_key}.fits'
]
# Just get a few files
for ss, sub_files, masters in zip(range(3), [[
'arcs', 'flats', 'bias'
], ['arcs', 'bias'], ['flats', 'bias']], [
all_masters,
[f'MasterArc_{master_key}.fits', f'MasterTiltimg_{master_key}.fits'],
[f'MasterEdges_{master_key}.fits.gz']
]):
# Grab the subset
files = []
for sub_file in sub_files:
files += all_files[sub_file]
#
testrawdir = os.path.join(rawdir, 'TEST')
if os.path.isdir(testrawdir):
shutil.rmtree(testrawdir)
os.makedirs(testrawdir)
for f in files:
shutil.copy(os.path.join(rawdir, f), os.path.join(testrawdir, f))
outdir = os.path.join(os.getenv('PYPEIT_DEV'), 'REDUX_OUT_TEST')
# For previously failed tests
if os.path.isdir(outdir):
shutil.rmtree(outdir)
# Run the setup
sargs = Setup.parse_args([
'-r', testrawdir, '-s', 'shane_kast_blue', '-c all', '-o',
'--output_path', outdir
])
Setup.main(sargs)
# Change to the configuration directory and set the pypeit file
configdir = os.path.join(outdir, 'shane_kast_blue_A')
pyp_file = os.path.join(configdir, 'shane_kast_blue_A.pypeit')
assert os.path.isfile(pyp_file), 'PypeIt file not written.'
# Perform the calib-only reduction
pargs = RunPypeIt.parse_args([pyp_file, '-c', '-r', configdir])
RunPypeIt.main(pargs)
# Test!
for master_file in masters:
assert os.path.isfile(
os.path.join(configdir, 'Masters',
master_file)), 'Master File {:s} missing!'.format(
master_file)
# Now test parse_calib_id
if ss == 0:
pargs2 = ParseCalibID.parse_args([pyp_file])
calib_dict = ParseCalibID.main(pargs2)
assert isinstance(calib_dict, dict)
assert len(calib_dict) > 0
assert calib_dict['1'][master_key]['arc']['raw_files'][
0] == 'b1.fits.gz'
# Clean-up
shutil.rmtree(outdir)
shutil.rmtree(testrawdir)