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.parser([
'-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.parser([
'-r', droot, '-s', 'shane_kast_blu', '-c=all', '--extension=fits.gz',
'--output_path={:s}'.format(data_path(''))
])
with pytest.raises(ValueError):
setup.main(pargs2)
def test_trace_edges():
# Define the output directories (HARDCODED!!)
setupdir = os.path.join(os.getcwd(), 'setup_files')
outdir = os.path.join(os.getcwd(), 'shane_kast_blue_A')
# Remove them if they already exist
if os.path.isdir(setupdir):
shutil.rmtree(setupdir)
if os.path.isdir(outdir):
shutil.rmtree(outdir)
# Perform the setup
droot = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA/shane_kast_blue/600_4310_d55')
droot += '/'
setup.main(setup.parser(['-r', droot, '-s', 'shane_kast_blue', '-c', 'all']))
# Define the pypeit file (HARDCODED!!)
pypeit_file = os.path.join(outdir, 'shane_kast_blue_A.pypeit')
# Run the tracing
trace_edges.main(trace_edges.parser(['-f', pypeit_file]))
# Define the edges master file (HARDCODED!!)
trace_file = os.path.join(outdir, 'Masters', 'MasterEdges_A_1_01.fits.gz')
# Check that the correct number of traces were found
edges = edgetrace.EdgeTraceSet.from_file(trace_file)
assert edges.ntrace == 2, 'Did not find the expected number of traces.'
# Clean up
shutil.rmtree(setupdir)
shutil.rmtree(outdir)
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 make_example_pypeit_file():
oroot = os.path.join(
os.path.split(os.path.abspath(resource_filename('pypeit', '')))[0],
'doc', 'include')
droot = os.path.join(os.getenv('PYPEIT_DEV'),
'RAW_DATA/shane_kast_blue/600_4310_d55')
droot += '/'
pargs = setup.parse_args(
['-r', droot, '-s', 'shane_kast_blue', '-c', 'all', '-d', oroot])
setup.main(pargs)
shutil.rmtree(os.path.join(oroot, 'setup_files'))
ofile = os.path.join(oroot, 'shane_kast_blue_A.pypeit.rst')
with open(ofile, 'w') as f:
with open(
os.path.join(oroot, 'shane_kast_blue_A',
'shane_kast_blue_A.pypeit'), 'r') as p:
lines = p.readlines()
f.write('.. code-block:: console\n')
f.write('\n')
for l in lines:
f.write(' ' + l)
f.write('\n\n')
shutil.rmtree(os.path.join(oroot, 'shane_kast_blue_A'))
def test_run_pypeit():
# 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'
# Just get a few files
testrawdir = os.path.join(rawdir, 'TEST')
if os.path.isdir(testrawdir):
shutil.rmtree(testrawdir)
os.makedirs(testrawdir)
files = [
'b21.fits.gz', 'b22.fits.gz', 'b23.fits.gz', 'b27.fits.gz',
'b1.fits.gz', 'b11.fits.gz', 'b12.fits.gz', 'b13.fits.gz'
]
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.parser([
'-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 original reductions
pargs = run_pypeit.parser([pyp_file, '-o'])
run_pypeit.main(pargs)
# Now try to reuse the old masters
pargs = run_pypeit.parser([pyp_file, '-o', '-m'])
run_pypeit.main(pargs)
# Now try not overwriting and using the old masters
pargs = run_pypeit.parser([pyp_file, '-m'])
run_pypeit.main(pargs)
# Clean-up
shutil.rmtree(outdir)
shutil.rmtree(testrawdir)
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'][~indx] == [-1], 'Incorrect combination group ID'
shutil.rmtree(config_dir)
def test_setup_keck_lris_red():
droot = os.path.join(os.environ['PYPEIT_DEV'],
'RAW_DATA/Keck_LRIS_red/multi_400_8500_d560')
droot += '/'
pargs = setup.parser(['-r', droot, '-s', 'keck_lris_red'])
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*'))
ext = [f.split('.')[-1] for f in files]
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_vlt_xshooter_nir():
droot = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA/VLT_XSHOOTER/NIR')
droot += '/XSHO'
pargs = setup.parser(['-r', droot, '-s', 'vlt_xshooter_nir'])
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_xshooter_nir*'))
ext = [f.split('.')[-1] for f in files]
#expected = ['lst', 'pypeit', 'setups', 'sorted']
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_wht_isis_blue():
droot = os.path.join(os.environ['PYPEIT_DEV'], 'RAW_DATA/wht_isis_blue/long_R300B_d5300')
droot += '/'
pargs = setup.parse_args(['-r', droot, '-s', 'wht_isis_blue', '--extension', '.fit'])
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, 'wht_isis_blue*'))
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_shane_kast_blue():
droot = os.path.join(os.environ['PYPEIT_DEV'],
'RAW_DATA/Shane_Kast_blue/600_4310_d55')
droot += '/'
pargs = setup.parser(['-r', droot, '-s', 'shane_kast_blue'])
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, 'shane_kast_blue*'))
ext = [f.split('.')[-1] for f in files]
#expected = ['lst', 'pypeit', 'setups', 'sorted']
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_keck_nirspec():
droot = os.path.join(os.environ['PYPEIT_DEV'],
'RAW_DATA/keck_nirspec/LOW_NIRSPEC-1')
droot += '/'
pargs = setup.parse_args(['-r', droot, '-s', 'keck_nirspec_low'])
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_nirspec*'))
ext = [f.split('.')[-1] for f in files]
#expected = ['lst', 'pypeit', 'setups', 'sorted']
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_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 = chk_for_calibs.parse_args([droot, '-s', 'vlt_fors2'])
answers, ps = chk_for_calibs.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'
# 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 = [
'MasterArc_A_1_01.fits', 'MasterTiltimg_A_1_01.fits',
'MasterBias_A_1_01.fits', 'MasterTilts_A_1_01.fits',
'MasterEdges_A_1_01.fits.gz', 'MasterFlat_A_1_01.fits',
'MasterWaveCalib_A_1_01.json'
]
# Just get a few files
for ss, sub_files, masters in zip(
range(3),
[['arcs', 'flats', 'bias'], ['arcs', 'bias'], ['flats', 'bias']], [
all_masters, [
'MasterArc_A_1_01.fits', 'MasterTiltimg_A_1_01.fits'
], ['MasterEdges_A_1_01.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.parser([
'-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 = run_pypeit.parser([pyp_file, '-c', '-r', configdir])
run_pypeit.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)
# Clean-up
shutil.rmtree(outdir)
shutil.rmtree(testrawdir)
def test_run_pypeit():
# 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'
# Just get a few files
testrawdir = os.path.join(rawdir, 'TEST')
if os.path.isdir(testrawdir):
shutil.rmtree(testrawdir)
os.makedirs(testrawdir)
files = [
'b21.fits.gz', 'b22.fits.gz', 'b23.fits.gz', 'b27.fits.gz',
'b1.fits.gz', 'b11.fits.gz', 'b12.fits.gz', 'b13.fits.gz'
]
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.parser([
'-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.'
# Try to run with -m and -o
pargs = run_pypeit.parser([pyp_file, '-o', '-m', '-r', configdir])
run_pypeit.main(pargs)
# #########################################################33
# Test!!
# Files exist
assert os.path.isfile(
os.path.join(configdir, 'Science',
'spec2d_b27-J1217p3905_KASTb_2015May20T045733.560.fits'))
# spec1d
spec1d_file = os.path.join(
configdir, 'Science',
'spec1d_b27-J1217p3905_KASTb_2015May20T045733.560.fits')
assert os.path.isfile(spec1d_file)
specObjs = specobjs.SpecObjs.from_fitsfile(spec1d_file)
# Flexure
assert specObjs[0].FLEX_SHIFT != 0., 'Flexure not calculated!'
# Helio
assert specObjs[0].VEL_CORR != 0., 'Heliocentric not calculated!'
# Now re-use those master files
pargs = run_pypeit.parser([pyp_file, '-o', '-m', '-r', configdir])
run_pypeit.main(pargs)
# Clean-up
shutil.rmtree(outdir)
shutil.rmtree(testrawdir)