def test_update_masters():
# Dummy self
arut.dummy_settings(spectrograph='shane_kast_blue', set_idx=True)
slf1 = arut.dummy_self()
slf1._idx_arcs = np.array([0, 1])
slf2 = arut.dummy_self()
sciexp = [slf1, slf2]
# Not actually filling anything
armb.UpdateMasters(sciexp, 0, 1, 'arc')
def test_gen_sensfunc():
# Load a random spectrum for the sensitivity function
sfile = data_path('spec1d_J0025-0312_KASTr_2015Jan23T025323.85.fits')
specobjs = arload.load_specobj(sfile)
# Settings, etc.
arutils.dummy_settings()
settings.argflag['run']['spectrograph'] = 'shane_kast_blue'
settings.argflag['reduce']['masters']['setup'] = 'C_01_aa'
settings.spect['arc'] = {}
settings.spect['arc']['index'] = [[0]]
fitsdict = arutils.dummy_fitsdict()
slf = arutils.dummy_self()
slf._msstd[0]['RA'] = '05:06:36.6'
slf._msstd[0]['DEC'] = '52:52:01.0'
# Generate
slf._sensfunc = arflx.generate_sensfunc(slf, 4, [specobjs], fitsdict)
# Save
try:
os.mkdir('MF_shane_kast_blue')
except FileExistsError:
pass
armasters.save_sensfunc(slf, 'C_01_aa')
# Test
assert isinstance(slf._sensfunc, dict)
assert isinstance(slf._sensfunc['wave_min'], Quantity)
def load_arcline_list(slf, idx, lines, disperser, wvmnx=None, modify_parse_dict=None):
"""Loads arc line list from NIST files
Parses and rejects
Parameters
----------
idx : list
indices of the arc
lines : list
List of ions to load
wvmnx : list or tuple
wvmin, wvmax for line list
disperser : str
Name of the disperser
modify_parse_dict : dict, optional
Used to over-ride default settings of parse_dict
Returns
-------
alist : Table
Table of arc lines
"""
# Get the parse dict
parse_dict = load_parse_dict(modify_dict=modify_parse_dict)
# Read rejection file
if slf is None:
from pypit import arutils as arut
msgs.warn("Using arutils.dummy_self. Better know what you are doing.")
slf = arut.dummy_self()
root = slf._argflag['run']['pypitdir']
with open(root+'/data/arc_lines/rejected_lines.yaml', 'r') as infile:
rej_dict = yaml.load(infile)
# Loop through the NIST Tables
tbls = []
for iline in lines:
# Load
tbl = parse_nist(slf,iline)
# Parse
if iline in parse_dict.keys():
tbl = parse_nist_tbl(tbl,parse_dict[iline])
# Reject
if iline in rej_dict.keys():
msgs.info("Rejecting select {:s} lines".format(iline))
tbl = reject_lines(slf,tbl,idx,rej_dict[iline],disperser)
tbls.append(tbl[['Ion','wave','RelInt']])
# Stack
alist = vstack(tbls)
# wvmnx?
if wvmnx is not None:
msgs.info('Cutting down line list by wvmnx: {:g},{:g}'.format(wvmnx[0],wvmnx[1]))
gdwv = (alist['wave'] >= wvmnx[0]) & (alist['wave'] <= wvmnx[1])
alist = alist[gdwv]
# Return
return alist
def parse_nist(slf, ion):
"""Parse a NIST ASCII table. Note that the long ---- should have
been commented out and also the few lines at the start.
Parameters
----------
ion : str
Name of ion
"""
# Root (for development only)
if slf is None:
from pypit import arutils as arut
msgs.warn("Using arutils.dummy_self. Better know what you are doing.")
slf = arut.dummy_self()
root = settings.argflag['run']['pypitdir']
# Find file
srch_file = root + '/data/arc_lines/NIST/' + ion + '_vacuum.ascii'
nist_file = glob.glob(srch_file)
if len(nist_file) == 0:
msgs.error("Cannot find NIST file {:s}".format(srch_file))
elif len(nist_file) != 1:
msgs.error("Multiple NIST files for {:s}".format(srch_file))
# Read
nist_tbl = Table.read(nist_file[0],
format='ascii.fixed_width',
comment='#')
gdrow = nist_tbl['Observed'] > 0. # Eliminate dummy lines
nist_tbl = nist_tbl[gdrow]
# Now unique values only (no duplicates)
uniq, indices = np.unique(nist_tbl['Observed'], return_index=True)
nist_tbl = nist_tbl[indices]
# Deal with Rel
agdrel = []
for row in nist_tbl:
try:
gdrel = int(row['Rel.'])
except:
try:
gdrel = int(row['Rel.'][:-1])
except:
gdrel = 0
agdrel.append(gdrel)
agdrel = np.array(agdrel)
# Remove and add
nist_tbl.remove_column('Rel.')
nist_tbl.remove_column('Ritz')
nist_tbl.add_column(Column(agdrel, name='RelInt'))
nist_tbl.remove_column('Acc.')
nist_tbl.remove_column('Type')
#nist_tbl.add_column(Column([ion]*len(nist_tbl), name='Ion', dtype='S5'))
nist_tbl.add_column(Column([ion] * len(nist_tbl), name='Ion', dtype='U5'))
nist_tbl.rename_column('Observed', 'wave')
# Return
return nist_tbl
def test_save1d_fits():
""" save1d to FITS and HDF5
"""
arut.dummy_settings()
fitsdict = arut.dummy_fitsdict(nfile=10, spectrograph='shane_kast_blue', directory=data_path(''))
# Dummy self
slf = arut.dummy_self()
slf._specobjs = []
slf._specobjs.append([])
slf._specobjs[0].append([mk_specobj()])
# Write to FITS
arsv.save_1d_spectra_fits(slf, fitsdict)
def test_save1d_hdf5():
""" save1d to FITS and HDF5
"""
# Dummy self
slf = arut.dummy_self()
fitsdict = arut.dummy_fitsdict(nfile=1, spectrograph='none')
# specobj
slf._specobjs = []
slf._specobjs.append([])
slf._specobjs[0].append([mk_specobj(objid=455), mk_specobj(flux=3., objid=555)])
# Write to HDF5
arsv.save_1d_spectra_hdf5(slf, fitsdict)
def test_instr_config():
from pypit import arutils as arut
from pypit import armlsd
# Dummy self
slf = arut.dummy_self()
# Grab
fits_dict = {'slitwid': [0.5], 'dichroic': ['d55'],
'disperser': ['B600/400'], 'cdangle': [11000.]}
det, scidx = 1, 0
#
config = armlsd.instconfig(slf, det, scidx, fits_dict)
# Test
assert config == 'S05-D55-G600400-T110000-B11'
def parse_nist(slf,ion):
"""Parse a NIST ASCII table. Note that the long ---- should have
been commented out and also the few lines at the start.
Parameters
----------
ion : str
Name of ion
"""
# Root (for development only)
if slf is None:
from pypit import arutils as arut
msgs.warn("Using arutils.dummy_self. Better know what you are doing.")
slf = arut.dummy_self()
root = slf._argflag['run']['pypitdir']
# Find file
srch_file = root + '/data/arc_lines/NIST/'+ion+'_vacuum.ascii'
nist_file = glob.glob(srch_file)
if len(nist_file) == 0:
msgs.error("Cannot find NIST file {:s}".format(srch_file))
elif len(nist_file) != 1:
msgs.error("Multiple NIST files for {:s}".format(srch_file))
# Read
nist_tbl = Table.read(nist_file[0], format='ascii.fixed_width')
gdrow = nist_tbl['Observed'] > 0. # Eliminate dummy lines
nist_tbl = nist_tbl[gdrow]
# Now unique values only (no duplicates)
uniq, indices = np.unique(nist_tbl['Observed'],return_index=True)
nist_tbl = nist_tbl[indices]
# Deal with Rel
agdrel = []
for row in nist_tbl:
try:
gdrel = int(row['Rel.'])
except:
try:
gdrel = int(row['Rel.'][:-1])
except:
gdrel = 0
agdrel.append(gdrel)
agdrel = np.array(agdrel)
# Remove and add
nist_tbl.remove_column('Rel.')
nist_tbl.remove_column('Ritz')
nist_tbl.add_column(Column(agdrel,name='RelInt'))
#nist_tbl.add_column(Column([ion]*len(nist_tbl), name='Ion', dtype='S5'))
nist_tbl.add_column(Column([ion]*len(nist_tbl), name='Ion', dtype='U5'))
nist_tbl.rename_column('Observed','wave')
# Return
return nist_tbl
def test_ampsec(fitsdict):
""" Test sort_data
"""
arutils.dummy_settings(spectrograph='shane_kast_blue')
slf = arutils.dummy_self()
# Run
det, scidx = 1, 5
arproc.get_datasec_trimmed(slf, fitsdict, det, scidx)
# Test
assert slf._datasec[det - 1].shape == (2112, 2048)
assert np.sum(np.isclose(slf._datasec[0], 1)) == 2162688 # Data region
assert np.sum(np.isclose(slf._datasec[0], 2)) == 2162688 # second amp
assert settings.spect['det01']['oscansec01'] == [[0, 0], [2049, 2080]]
assert settings.spect['det01']['datasec01'] == [[0, 0], [0, 1024]]
def test_extinction_correction():
from pypit import arflux as arflx
from pypit import arutils as arut
# Dummy self
slf = arut.dummy_self()
slf._spect['mosaic']['latitude'] = 37.3413889
slf._spect['mosaic']['longitude'] = 121.6428
# Load
extinct = arflx.load_extinction_data(slf)
# Correction
wave = np.arange(3000., 10000.) * u.AA
AM = 1.5
flux_corr = arflx.extinction_correction(wave, AM, extinct)
# Test
np.testing.assert_allclose(flux_corr[0], 4.47095192)
def test_flex_shift():
if not os.getenv('PYPIT'):
pass
else:
# Dummy slf
arut.dummy_settings()
settings.argflag['reduce']['flexure']['maxshift'] = 50
slf = arut.dummy_self()
# Read spectra
obj_spec = lsio.readspec(data_path('obj_lrisb_600_sky.fits'))
arx_file = pypit.__path__[0]+'/data/sky_spec/sky_LRISb_600.fits'
arx_spec = lsio.readspec(arx_file)
# Call
#msgs._debug['flexure'] = True
flex_dict = arwave.flex_shift(slf, 1, obj_spec, arx_spec)
assert np.abs(flex_dict['shift'] - 43.7) < 0.1
def test_detect_lines():
if os.getenv('RUN_ALL_PYPIT_TESTS'
) is None: # REMOVE WHEN WORKING WITH Python 3
assert True
return
from linetools.spectra import xspectrum1d
import pypit
slf = arut.dummy_self()
det = 1
# Using Paranal night sky as an 'arc'
arx_sky = xspectrum1d.XSpectrum1D.from_file(
pypit.__path__[0] + '/data/sky_spec/paranal_sky.fits')
arx_amp, arx_cent, arx_wid, arx_w, arx_satsnd, arx_yprep = pyarc.detect_lines(
slf, det, msarc=None, censpec=arx_sky.flux.value, MK_SATMASK=False)
# Test
assert len(arx_w[0]) == 1767
def test_extinction_correction():
from pypit import arflux as arflx
from pypit import arutils as arut
# Dummy self
slf = arut.dummy_self()
slf._spect["mosaic"]["latitude"] = 37.3413889
slf._spect["mosaic"]["longitude"] = 121.6428
# Load
extinct = arflx.load_extinction_data(slf)
# Correction
wave = np.arange(3000.0, 10000.0) * u.AA
AM = 1.5
flux_corr = arflx.extinction_correction(wave, AM, extinct)
# Test
np.testing.assert_allclose(flux_corr[0], 4.47095192)
def test_instr_config():
from pypit import arutils as arut
from pypit import armlsd
# Dummy self
slf = arut.dummy_self()
# Grab
fits_dict = {
'slitwid': [0.5],
'dichroic': ['d55'],
'disperser': ['B600/400'],
'cdangle': [11000.]
}
det, scidx = 1, 0
#
config = armlsd.instconfig(slf, det, scidx, fits_dict)
# Test
assert config == 'S05-D55-G600400-T110000-B11'
def test_setup_param():
""" Run the parameter setup script
Returns
-------
"""
# Initialize some settings
arut.dummy_settings()
# Load Dummy self
slf = arut.dummy_self()
settings.argflag['run']['spectrograph'] = 'shane_kast_blue'
settings.spect['arc'] = {}
settings.spect['arc']['index'] = [[0]]
fitsdict = arut.dummy_fitsdict()
# Run
arcparm = pyarc.setup_param(slf, 0, 1, fitsdict)
for key in ['llist', 'disp', 'wvmnx']:
assert key in arcparm
def test_geocorrect(fitsdict):
"""
"""
# Initialize some settings
arutils.dummy_settings(spectrograph='shane_kast_blue') #, set_idx=False)
# Load Dummy self
slf = arutils.dummy_self(fitsdict=fitsdict)
# Specobjs
specobjs = arutils.dummy_specobj(fitsdict, extraction=True)
slf._specobjs[0] = [specobjs]
# Run
# vhel = x_keckhelio(106.59770833333332, 30.34736111111111, 2000., jd=2457046.5036, OBS='lick') 9.3166 km/s
helio, hel_corr = py_arwave.geomotion_correct(slf, 1, fitsdict)
assert np.isclose(helio, -9.3344957,
rtol=1e-5) # Checked against x_keckhelio
assert np.isclose(slf._specobjs[0][0][0].boxcar['wave'][0].value,
3999.8754558341816,
rtol=1e-8)
def test_load_extinction():
from pypit import arflux as arflx
from pypit import arutils as arut
# Dummy self
slf = arut.dummy_self()
slf._spect['mosaic']['latitude'] = 37.3413889
slf._spect['mosaic']['longitude'] = 121.6428
# Load
extinct = arflx.load_extinction_data(slf)
np.testing.assert_allclose(extinct['wave'][0], 3200.)
assert extinct['wave'].unit == u.AA
np.testing.assert_allclose(extinct['mag_ext'][0], 1.084)
# Fail
slf._spect['mosaic']['latitude'] = 37.3413889
slf._spect['mosaic']['longitude'] = 0.
#
extinct = arflx.load_extinction_data(slf)
assert extinct is None
def test_load_extinction():
from pypit import arflux as arflx
from pypit import arutils as arut
# Dummy self
slf = arut.dummy_self()
slf._spect["mosaic"]["latitude"] = 37.3413889
slf._spect["mosaic"]["longitude"] = 121.6428
# Load
extinct = arflx.load_extinction_data(slf)
np.testing.assert_allclose(extinct["wave"][0], 3200.0)
assert extinct["wave"].unit == u.AA
np.testing.assert_allclose(extinct["mag_ext"][0], 1.084)
# Fail
slf._spect["mosaic"]["latitude"] = 37.3413889
slf._spect["mosaic"]["longitude"] = 0.0
#
extinct = arflx.load_extinction_data(slf)
assert extinct is None
def test_setup_param():
""" Run the parameter setup script
Returns
-------
"""
# Load
# Dummy self
slf = arut.dummy_self()
slf._argflag['run']['spectrograph'] = 'kast_blue'
slf._spect['arc'] = {}
slf._spect['arc']['index'] = [[0]]
fitsdict = {}
fitsdict["disperser"] = ['600/4310']
fitsdict["binning"] = [[None]]
# Run
arcparm = pyarc.setup_param(slf, 0, 1, fitsdict)
for key in ['llist','disp','wvmnx']:
assert key in arcparm
def test_find_standard():
from pypit import arutils as arut
from pypit import arflux as arflx
# Dummy self
slf = arut.dummy_self()
# G191b2b
std_ra = '05:06:36.6'
std_dec = '52:52:01.0'
# Grab
std_dict = arflx.find_standard_file(slf._argflag, (std_ra, std_dec))
# Test
assert std_dict['name'] == 'G191B2B'
assert std_dict['file'] == '/data/standards/calspec/g191b2b_mod_005.fits'
assert std_dict['fmt'] == 1
# Fail to find
# near G191b2b
std_ra = '05:06:36.6'
std_dec = '52:22:01.0'
std_dict = arflx.find_standard_file(slf._argflag, (std_ra, std_dec))
assert std_dict is None
def test_find_standard():
from pypit import arutils as arut
from pypit import arflux as arflx
# Dummy self
slf = arut.dummy_self()
# G191b2b
std_ra = "05:06:36.6"
std_dec = "52:52:01.0"
# Grab
std_dict = arflx.find_standard_file(slf._argflag, (std_ra, std_dec))
# Test
assert std_dict["name"] == "G191B2B"
assert std_dict["file"] == "/data/standards/calspec/g191b2b_mod_005.fits"
assert std_dict["fmt"] == 1
# Fail to find
# near G191b2b
std_ra = "05:06:36.6"
std_dec = "52:22:01.0"
std_dict = arflx.find_standard_file(slf._argflag, (std_ra, std_dec))
assert std_dict is None
def test_save2d_fits():
arut.dummy_settings()
# Dummy self
slf = arut.dummy_self()
fitsdict = arut.dummy_fitsdict(nfile=1, spectrograph='none', directory=data_path(''))
fitsdict['filename'] = np.array(['b1.fits.gz'])
# Settings
settings.argflag['run']['directory']['science'] = data_path('')
settings.argflag['reduce']['masters']['setup'] = 'A_01_aa'
# Fill with dummy images
dum = np.ones((100,100))
slf._sciframe[0] = dum
slf._modelvarframe[0] = dum * 2
slf._bgframe[0] = dum + 0.1
slf._basename = 'test'
slf._idx_sci[0] = 0
# Call
arsv.save_2d_images(slf, fitsdict)
# Read and test
head0 = pyfits.getheader(data_path('spec2d_test.fits'))
assert head0['PYPCNFIG'] == 'A'
assert head0['PYPCALIB'] == 'aa'
assert 'PYPIT' in head0['PIPELINE']
def load_arcline_list(slf,
idx,
lines,
disperser,
wvmnx=None,
modify_parse_dict=None):
"""Loads arc line list from NIST files
Parses and rejects
Parameters
----------
idx : list
indices of the arc
lines : list
List of ions to load
wvmnx : list or tuple
wvmin, wvmax for line list
disperser : str
Name of the disperser
modify_parse_dict : dict, optional
Used to over-ride default settings of parse_dict
Returns
-------
alist : Table
Table of arc lines
"""
# Get the parse dict
parse_dict = load_parse_dict(modify_dict=modify_parse_dict)
# Read rejection file
if slf is None:
from pypit import arutils as arut
msgs.warn("Using arutils.dummy_self. Better know what you are doing.")
slf = arut.dummy_self()
root = settings.argflag['run']['pypitdir']
with open(root + '/data/arc_lines/rejected_lines.yaml', 'r') as infile:
rej_dict = yaml.load(infile)
# Loop through the NIST Tables
tbls = []
for iline in lines:
# Load
tbl = parse_nist(slf, iline)
# Parse
if iline in parse_dict.keys():
tbl = parse_nist_tbl(tbl, parse_dict[iline])
# Reject
if iline in rej_dict.keys():
msgs.info("Rejecting select {:s} lines".format(iline))
tbl = reject_lines(slf, tbl, idx, rej_dict[iline], disperser)
tbls.append(tbl[['Ion', 'wave', 'RelInt']])
# Stack
alist = vstack(tbls)
# wvmnx?
if wvmnx is not None:
msgs.info('Cutting down line list by wvmnx: {:g},{:g}'.format(
wvmnx[0], wvmnx[1]))
gdwv = (alist['wave'] >= wvmnx[0]) & (alist['wave'] <= wvmnx[1])
alist = alist[gdwv]
# Return
return alist
