def main(libpath, modeldir, overwrite):
ext = os.path.splitext(libpath)[-1].lower()
if ext == '.csv':
params = pd.read_csv(libpath)
maskpath = libpath[:-4] + '_mask.csv'
# Create mask dataframe
param_mask = pd.DataFrame()
for p in library.Library.STAR_PROPS:
param_mask[p] = np.isfinite(params[p])
param_mask['u_' + p] = np.isfinite(params[p])
params = get_isochrone_params(params, modeldir, overwrite)
params.to_csv(libpath)
param_mask.to_csv(maskpath)
elif ext == '.h5':
lib = library.read_hdf(libpath)
param_mask = pd.DataFrame()
for p in library.Library.STAR_PROPS:
param_mask[p] = np.isfinite(lib.library_params[p])
param_mask['u_' + p] = np.isfinite(lib.library_params[p])
lib.library_params = get_isochrone_params(lib.library_params, modeldir,
overwrite)
lib.param_mask = param_mask
lib.to_hdf(libpath)
else:
print("Library file was not in a valid format.")
sys.exit(1)
def main(libpath, modeldir, overwrite):
ext = os.path.splitext(libpath)[-1].lower()
if ext == '.csv':
params = pd.read_csv(libpath)
maskpath = libpath[:-4] + '_mask.csv'
# Create mask dataframe
param_mask = pd.DataFrame()
for p in library.Library.STAR_PROPS:
param_mask[p] = np.isfinite(params[p])
param_mask['u_'+p] = np.isfinite(params[p])
params = get_isochrone_params(params, modeldir, overwrite)
params.to_csv(libpath)
param_mask.to_csv(maskpath)
elif ext == '.h5':
lib = library.read_hdf(libpath)
param_mask = pd.DataFrame()
for p in library.Library.STAR_PROPS:
param_mask[p] = np.isfinite(lib.library_params[p])
param_mask['u_'+p] = np.isfinite(lib.library_params[p])
lib.library_params = get_isochrone_params(lib.library_params,
modeldir, overwrite)
lib.param_mask = param_mask
lib.to_hdf(libpath)
else:
print("Library file was not in a valid format.")
sys.exit(1)
def main(append, parampath, specdir, outdir):
library_params = pd.read_csv(parampath, index_col=0)
library_params['lib_index'] = None
# Read in NSO spectrum
nso = spectrum.read_fits(os.path.join(specdir, 'nso_adj.fits'))
nso = nso.cut(*WAVLIM)
# Use NSO wavelength scale as library wavelength scale
wav = nso.w
# Read in all spectra
spectra = np.empty((0, 3, len(wav)))
for idx, row in library_params.iterrows():
lib_obs = row['lib_obs']
spec_path = os.path.join(specdir, lib_obs+'_adj.fits')
spec = spectrum.read_fits(spec_path).cut(*WAVLIM)
# Check that shifted spectra are on same wavelength scale
if not np.allclose(spec.w, wav):
print("Spectrum {0} was not on the same wavelength scale".format(
row.lib_obs))
library_params.loc[idx, 'lib_obs'] = None
continue
# Add spectrum to library
library_params.loc[idx, 'lib_index'] = len(spectra)
spectra = np.vstack((spectra, [[spec.s, spec.serr, spec.mask]]))
# Read in parameter mask
maskpath = parampath[:-4] + '_mask.csv'
if os.path.exists(maskpath):
param_mask = pd.read_csv(maskpath, index_col=0)
else:
param_mask = pd.DataFrame()
for p in library.Library.STAR_PROPS:
param_mask[p] = np.isfinite(library_params[p])
param_mask['u_'+p] = np.isfinite(library_params[p])
# Drop stars with missing spectra
missing_spectra = pd.isnull(library_params.lib_obs)
missing_indices = library_params[missing_spectra].index.tolist()
print("Dropping {0:d} stars with no spectra".format(len(missing_indices)))
library_params.drop(missing_indices, inplace=True)
param_mask.drop(missing_indices, inplace=True)
libpath = os.path.join(outdir, 'library.h5')
if append:
lib = library.read_hdf(libpath)
lib.append(library_params, spectra, param_mask)
else:
lib = library.Library(wav, spectra, library_params, wavlim=WAVLIM,
param_mask=param_mask, nso=nso)
# Get allowed shift references
shift_obs = [row[0] for r in SHIFT_REFERENCES]
lib.header['shift_refs'] = shift_obs
# Save library
lib.to_hdf(libpath)
def specmatch_spectrum(args):
lib_subset = None
if args.debug:
lib = library.read_hdf(wavlim='none')
nspec = len(lib.library_params)
lib_subset = np.random.choice(np.arange(nspec),
size=args.n_lib_subset,
replace=False)
lib_subset = np.sort(lib_subset)
lib_subset = list(lib_subset)
core.specmatch_spectrum(args.spectrum,
plot_level=args.plots,
inlib=args.in_library,
outdir=args.outdir,
num_best=args.num_best,
suffix=args.suffix,
lib_subset=lib_subset)
def main(libpath, targ_name, outpath):
lib = library.read_hdf(libpath)
targ_idx = lib.get_index(targ_name)
targ_param, targ_spec = lib[targ_idx]
results = lib.library_params.copy()
for wl in range(WAVLIM[0], WAVLIM[1], WAVSTEP):
print("Matching region {0:d} - {1:d}".format(wl, wl + 100))
sm = specmatch.SpecMatch(targ_spec, lib, (wl, wl + WAVSTEP))
sm.match(ignore=targ_idx)
cs_col = 'chi_squared_{0:d}'.format(wl)
results[cs_col] = sm.match_results['chi_squared']
fit_col = 'fit_params_{0:d}'.format(wl)
results[fit_col] = sm.match_results['fit_params']
results.to_csv(outpath)
def main(libpath, targ_name, outpath):
lib = library.read_hdf(libpath)
targ_idx = lib.get_index(targ_name)
targ_param, targ_spec = lib[targ_idx]
results = lib.library_params.copy()
for wl in range(WAVLIM[0], WAVLIM[1], WAVSTEP):
print("Matching region {0:d} - {1:d}".format(wl, wl+100))
sm = specmatch.SpecMatch(targ_spec, lib, (wl, wl+WAVSTEP))
sm.match(ignore=targ_idx)
cs_col = 'chi_squared_{0:d}'.format(wl)
results[cs_col] = sm.match_results['chi_squared']
fit_col = 'fit_params_{0:d}'.format(wl)
results[fit_col] = sm.match_results['fit_params']
results.to_csv(outpath)
def main(libpath, targ_name, respath, outpath, num_best):
lib = library.read_hdf(libpath)
targ_idx = lib.get_index(targ_name)
targ_param, targ_spec = lib[targ_idx]
res_match = pd.read_csv(respath, index_col=0)
res_lincomb = targ_param.to_frame().transpose()
for wl in range(WAVLIM[0], WAVLIM[1], WAVSTEP):
matchcs_col = 'chi_squared_{0:d}'.format(wl)
res_match.sort_values(by=matchcs_col, inplace=True)
matchfit_col = 'fit_params_{0:d}'.format(wl)
sm = specmatch.SpecMatch(targ_spec, lib, (wl,wl+100), num_best)
sm.match(match_results=res_match.rename(\
columns={matchcs_col:'chi_squared', matchfit_col:'fit_params'}))
bestcs_col = 'best_cs_lincomb{0:d}_{1:d}'.format(num_best, wl)
bestcs = np.array(res_match.head(num_best)[matchcs_col])
res_lincomb[bestcs_col] = json.dumps(bestcs.tolist())
refidxs_col = 'ref_idxs_lincomb{0:d}_{1:d}'.format(num_best, wl)
ref_idxs = np.array(res_match.head(num_best).index)
res_lincomb[refidxs_col] = json.dumps(ref_idxs.tolist())
coeffs_col = 'coeffs_lincomb{0:d}_{1:d}'.format(num_best, wl)
coeffs = np.array(match.get_lincomb_coeffs(sm.mt_lincomb.best_params))
res_lincomb[coeffs_col] = json.dumps(coeffs.tolist())
cs_col = 'chi_squared_lincomb{0:d}_{1:d}'.format(num_best, wl)
res_lincomb[cs_col] = sm.mt_lincomb.best_chisq
fit_col = 'fit_params_lincomb{0:d}_{1:d}'.format(num_best, wl)
res_lincomb[fit_col] = sm.mt_lincomb.best_params.dumps()
res_lincomb.to_csv(outpath)
from specmatchemp import library
if __name__ == '__main__':
# Argument parser
psr = ArgumentParser(description="Combine match results")
psr.add_argument('libpath', type=str, help="Path to library file")
psr.add_argument('resdir', type=str, help="Path to results directory")
psr.add_argument('-s', '--suffix', type=str, default="", help="Suffix to append to results files")
args = psr.parse_args()
if not os.path.isdir(args.resdir):
print("Could not find folder at {0}".format(args.resdir))
sys.exit(1)
lib = library.read_hdf(args.libpath, wavlim='none')
# get names of stars
names = list(lib.library_params.cps_name)
# global dataframe to store
res_global = pd.DataFrame()
min_num = 2
max_num = 9
for name in names:
# combine results as one row for each star.
res_star = pd.DataFrame()
for num_best in range(min_num, max_num):
res_path = os.path.join(args.resdir, '{0}/{0}_lincomb{1:d}.csv'.format(name, num_best))
def main(resdir, suffix, plots):
lib = library.read_hdf(wavlim='none')
# Create global dataframe to store results
match_res_global = pd.DataFrame()
lincomb_res_global = pd.DataFrame()
for idx, row in lib.library_params.iterrows():
targ_name = row['cps_name']
res_path = os.path.join(
resdir,
targ_name + '/' + targ_name + args.suffix + '_lincomb_sm.hdf')
if not os.path.exists(res_path):
res_path = os.path.join(
resdir, targ_name + '/' + targ_name + args.suffix + '_sm.hdf')
if not os.path.exists(res_path):
print("Results file for {0} not found!".format(targ_name))
continue
print("Reading in results for {0}".format(targ_name))
sm = specmatch.SpecMatch.read_hdf(res_path, lib)
# Read in library grid search results
sm.match_results['targ_idx'] = idx
sm.match_results['ref_idx'] = sm.match_results.index
# Concatenate library grid search results
if match_res_global.empty:
match_res_global = sm.match_results
else:
match_res_global = pd.concat((match_res_global, sm.match_results),
ignore_index=True)
if lincomb_res_global.empty:
# Create global results dataframe containing final lincomb
# chi-squared and generated results
lincomb_res_global = lib.library_params.copy()
for i in range(len(sm.lincomb_regions)):
reg = sm.lincomb_regions[i]
suf = '_lincomb_{0:.0f}'.format(reg[0])
cs_col = 'chi_squared' + suf
lincomb_res_global[cs_col] = np.nan
for p in library.Library.STAR_PROPS:
p_col = p + suf
lincomb_res_global[p_col] = np.nan
suf = '_lincomb'
for p in library.Library.STAR_PROPS:
p_col = p + suf
p_nodetrend_col = p + '_nodetrend' + suf
lincomb_res_global[p_col] = np.nan
lincomb_res_global['u_' + p_col] = np.nan
lincomb_res_global[p_nodetrend_col] = np.nan
# Read in lincomb results for each wavelength region
for i in range(len(sm.lincomb_regions)):
mt = sm.lincomb_matches[i]
reg = sm.lincomb_regions[i]
suf = '_lincomb_{0:.0f}'.format(reg[0])
cs_col = 'chi_squared' + suf
lincomb_res_global.loc[idx, cs_col] = mt.best_chisq
for p in library.Library.STAR_PROPS:
p_col = p + suf
lincomb_res_global.loc[idx, p_col] = sm.lincomb_results[i][p]
# Read in averaged results
suf = '_lincomb'
for p in library.Library.STAR_PROPS:
p_col = p + suf
p_nodetrend_col = p + '_nodetrend' + suf
lincomb_res_global.loc[idx, p_col] = sm.results[p]
lincomb_res_global.loc[idx, 'u_' + p_col] = sm.results['u_' + p]
lincomb_res_global.loc[idx, p_nodetrend_col] = \
sm.results_nodetrend[p]
# Save results
outpath = os.path.join(resdir, 'match_results' + suffix + '.csv')
match_res_global.index.names = ['idx']
match_res_global.to_csv(outpath)
outpath = os.path.join(resdir, 'lincomb_results' + suffix + '.csv')
lincomb_res_global.to_csv(outpath)
if plots:
# Plots for individual regions
plotspath = os.path.join(resdir, 'library_plots_regions.pdf')
with PdfPages(plotspath) as pdf:
cols = list(lincomb_res_global.columns)
cscols = cscols = [
c for c in cols if re.search('chi_squared_lincomb_\d+', c)
]
regions = list(
set([
re.search('chi_squared_lincomb_(\d+)$', c).group(1)
for c in cscols
]))
for reg in regions:
reg = float(reg)
suf = '_lincomb_{0:.0f}'.format(reg)
title = 'Wavelength region: {0:.0f} - {1:.0f} A'\
.format(reg, reg + 100)
plot_diag(lincomb_res_global, suf, pdf, title)
# Plots for nodetrend parameters
plotspath = os.path.join(resdir, 'library_plots_nodetrend.pdf')
with PdfPages(plotspath) as pdf:
suf = '_nodetrend_lincomb'
title = 'Averaged over all wavelengths, not detrended'
# Plot all stars
plot_diag(lincomb_res_global, suf, pdf, title, trend=True)
# Plots for detrended parameters
plotspath = os.path.join(resdir, 'library_plots_lincomb.pdf')
with PdfPages(plotspath) as pdf:
suf = '_lincomb'
title = 'Averaged over all wavelengths, detrended'
# Plot all stars
plot_diag(lincomb_res_global, suf, pdf, title)
def main(append, parampath, specdir, outdir):
library_params = pd.read_csv(parampath, index_col=0)
library_params['lib_index'] = None
# Read in NSO spectrum
nso = spectrum.read_fits(os.path.join(specdir, 'nso_adj.fits'))
nso = nso.cut(*WAVLIM)
# Use NSO wavelength scale as library wavelength scale
wav = nso.w
# Read in all spectra
spectra = np.empty((0, 3, len(wav)))
for idx, row in library_params.iterrows():
lib_obs = row['lib_obs']
spec_path = os.path.join(specdir, lib_obs + '_adj.fits')
spec = spectrum.read_fits(spec_path).cut(*WAVLIM)
# Check that shifted spectra are on same wavelength scale
if not np.allclose(spec.w, wav):
print("Spectrum {0} was not on the same wavelength scale".format(
row.lib_obs))
library_params.loc[idx, 'lib_obs'] = None
continue
# Add spectrum to library
library_params.loc[idx, 'lib_index'] = len(spectra)
spectra = np.vstack((spectra, [[spec.s, spec.serr, spec.mask]]))
# Read in parameter mask
maskpath = parampath[:-4] + '_mask.csv'
if os.path.exists(maskpath):
param_mask = pd.read_csv(maskpath, index_col=0)
else:
param_mask = pd.DataFrame()
for p in library.Library.STAR_PROPS:
param_mask[p] = np.isfinite(library_params[p])
param_mask['u_' + p] = np.isfinite(library_params[p])
# Drop stars with missing spectra
missing_spectra = pd.isnull(library_params.lib_obs)
missing_indices = library_params[missing_spectra].index.tolist()
print("Dropping {0:d} stars with no spectra".format(len(missing_indices)))
library_params.drop(missing_indices, inplace=True)
param_mask.drop(missing_indices, inplace=True)
libpath = os.path.join(outdir, 'library.h5')
if append:
lib = library.read_hdf(libpath)
lib.append(library_params, spectra, param_mask)
else:
lib = library.Library(wav,
spectra,
library_params,
wavlim=WAVLIM,
param_mask=param_mask,
nso=nso)
# Get allowed shift references
shift_obs = [row[0] for r in SHIFT_REFERENCES]
lib.header['shift_refs'] = shift_obs
# Save library
lib.to_hdf(libpath)
psr.add_argument('formatstring', type=str, help="Format string")
psr.add_argument('cols', nargs='*', type=str, help="Columns to use")
psr.add_argument('-a',
'--append',
action='store_const',
const='a+',
default="w+",
help="Append to existing script")
args = psr.parse_args()
if not os.path.isfile(args.libpath):
print("Could not find {0}".format(args.libpath))
sys.exit(1)
if os.path.splitext(args.libpath)[1] == ".h5":
lib = library.read_hdf(args.libpath, wavlim='none')
df = lib.library_params
elif os.path.splitext(args.libpath)[1] == ".csv":
df = pd.read_csv(args.libpath)
else:
print("{0} was not a valid library format".format(args.libpath))
scriptfile = open(args.outpath, args.append)
for idx, row in df.iterrows():
s = "source ~/.bash_profile; "
s += args.formatstring.format(*(row[args.cols].values))
s += "\n"
scriptfile.write(s)
scriptfile.close()
def specmatch_spectrum(specpath, plot_level=0, inlib=False, outdir="./",
num_best=5, suffix="", wavlim='all', lib_subset=None,
name=None, n_lib_subset=None):
"""Perform the specmatch on a given spectrum
Args:
specpath (str): Path to target spectrum
plot_level (int, 0-2): Level of plots
0 - No plots saved, 1 - Representative plots, 2 - All plots
inlib (str or False): String to search within library for to exclude
from matching process
outdir (str): Output file directory
num_best (int): Number of best matches to use at lincomb stage
suffix (str): String to append to output file names
Returns:
specmatch.SpecMatch object
"""
if not os.path.exists(specpath):
raise ValueError(specpath + " does not exist!")
if wavlim == 'all':
target = spectrum.read_hires_fits(specpath)
else:
target = spectrum.read_hires_fits(specpath).cut(*wavlim)
# Determine the name of the target
if inlib:
name = inlib
elif name is None:
name = os.path.basename(specpath)[:-5]
if n_lib_subset is not None:
lib = library.read_hdf(wavlim='none')
lib_subset = lib.library_params.lib_index
lib_subset = np.random.choice(
lib_subset, size=n_lib_subset, replace=False
)
lib = library.read_hdf(wavlim=wavlim, lib_index_subset=lib_subset)
sm = specmatch.SpecMatch(target, lib)
sm.shift()
if inlib:
targ_idx = lib.get_index(inlib)
targ_param, targ_spec = lib[targ_idx]
sm.match(ignore=targ_idx, wavlim=wavlim)
else:
targ_param = None
sm.match(wavlim=wavlim)
sm.target.name = name # attach target name
sm.lincomb(num_best)
# Print results
print("SpecMatch Results for {0}".format(name))
sm.results_to_txt(sys.stdout)
outdir = os.path.join(outdir, name)
if not os.path.exists(outdir):
os.makedirs(outdir)
# Save final results
outpath = os.path.join(outdir, name + suffix + '_results.txt')
with open(outpath, 'w') as f:
if inlib:
f.write('Library Parameters\n')
f.write('------------------\n')
f.write('Teff: {0:.0f} +/- {1:.0f} K\n'.format(
targ_param['Teff'], targ_param['u_Teff']))
f.write('Radius: {0:.3f} +/- {1:.3f} Rsun\n'.format(
targ_param['radius'], targ_param['u_radius']))
f.write('[Fe/H]: {0:.2f} +/- {1:.2f} dex\n'.format(
targ_param['feh'], targ_param['u_feh']))
f.write('\n')
sm.results_to_txt(f, verbose=True)
print("created {}".format(outpath))
# Save full results
outpath = os.path.join(outdir, name + suffix + '_sm.hdf')
sm.to_hdf(outpath)
print("created {}".format(outpath))
# Create representative plots
if plot_level is not None and plot_level > 0:
plotspath = os.path.join(outdir, name + suffix + '_plots.pdf')
with PdfPages(plotspath) as pdf:
region = (5100, 5200)
wavlim = (5160, 5190)
order = 2
plot_shifts(sm, pdf, order, wavlim)
plot_match(sm, pdf, region, wavlim, targ_param)
plot_lincomb(sm, pdf, region, wavlim, targ_param)
print("created {}".format(plotspath))
# Create full plots
if plot_level == 2:
shiftplotspath = os.path.join(outdir, name + suffix +
'_shift_plots.pdf')
with PdfPages(shiftplotspath) as pdf:
for order in range(np.shape(sm.target_unshifted.w)[0]):
plot_shifts(sm, pdf, order, wavlim='all')
matchplotspath = os.path.join(outdir, name + suffix +
'_match_plots.pdf')
with PdfPages(matchplotspath) as pdf:
for reg in sm.regions:
plot_match(sm, pdf, reg, wavlim='all', targ_param=targ_param)
lincombplotspath = os.path.join(outdir, name + suffix +
'_lincomb_plots.pdf')
with PdfPages(lincombplotspath) as pdf:
for reg in sm.lincomb_regions:
plot_lincomb(sm, pdf, reg, wavlim='all', targ_param=targ_param)
print("created {}".format(plotspath))
return sm
def match_spectrum(specpath, indir="./", plot_level=0, inlib=False,
outdir="./", suffix=""):
"""Match a spectrum given its observation ID
Args:
specpath (str): Path to spectrum or its CPS observation id jXX.XXXX
indir (str): Directory to look in for target spectrum
plot_level (int, 0-2): Level of plotting to save
inlib (str or False): String to search within library for to exclude
from matching process
outdir (str): Output file directory
suffix (str): String to append to output file names
Returns:
specmatch.SpecMatch object
"""
# Check if specpath is a path or an observation ID
if os.path.exists(specpath):
targ_path = specpath
targid = os.path.splitext(os.path.basename(specpath))[0]
else:
targ_path = os.path.join(indir, 'r' + specpath + '_adj' + suffix +
'.fits')
if not os.path.exists(targ_path):
raise ValueError(specpath + " does not exist!")
targid = 'r' + specpath
# Load shifted spectrum
target = spectrum.read_fits(targ_path)
lib = library.read_hdf()
sm = specmatch.SpecMatch(target, lib)
if inlib:
name = inlib
sm.target.name = inlib
sm.target.attrs['obs'] = targid
targ_idx = lib.get_index(inlib)
targ_param, targ_spec = lib[targ_idx]
sm.match(ignore=targ_idx)
else:
name = targid
targ_param = None
sm.match()
# Save results
outdir = os.path.join(outdir, name)
if not os.path.exists(outdir):
os.mkdir(outdir)
outpath = os.path.join(outdir, name + suffix + '_match.csv')
sm.match_results.to_csv(outpath)
# Save SpecMatch object
outpath = os.path.join(outdir, name + suffix + '_sm.hdf')
sm.to_hdf(outpath)
# Generate representative plots
if plot_level == 1:
plotspath = os.path.join(outdir, name + suffix + '_match_plots.pdf')
with PdfPages(plotspath) as pdf:
region = (5100, 5200)
wavlim = (5160, 5190)
plot_match(sm, pdf, region, wavlim, targ_param)
# Generate full plots
if plot_level == 2:
plotspath = os.path.join(outdir, name + suffix + '_match_plots.pdf')
with PdfPages(plotspath) as pdf:
for reg in sm.regions:
plot_match(sm, pdf, reg, wavlim='all', targ_param=targ_param)
return sm
def lincomb_spectrum(respath,
plot_level=0,
inlib=False,
outdir="./",
num_best=5,
suffix=""):
"""Match a spectrum using the linear combination approach.
Can only be used to resume an existing SpecMatch object.
Args:
respath (str): Path to existing SpecMatch.hdf file
plot_level (int, 0-2): Level of plotting to save
inlib (str or False): String to search within library for to exclude
from matching process
outdir (str): Output file directory
num_best (int): Number of best matches to use at lincomb stage
suffix (str): String to append to output file names
Returns:
specmatch.SpecMatch object
"""
lib = library.read_hdf()
sm = specmatch.SpecMatch.read_hdf(respath, lib)
name = sm.target.name
if inlib:
targ_idx = lib.get_index(inlib)
targ_param, targ_spec = lib[targ_idx]
else:
targ_param = None
sm.lincomb(num_best=num_best)
# Print results
print("SpecMatch Results for {0}".format(name))
for p in library.Library.STAR_PROPS:
print("{0}: {1:.2f}".format(p, sm.results[p]))
outdir = os.path.join(outdir, name)
if not os.path.exists(outdir):
os.mkdir(outdir)
# Save final results
outpath = os.path.join(outdir, name + suffix + '_results.txt')
with open(outpath, 'w') as f:
if inlib:
f.write('Library Parameters\n')
f.write('------------------\n')
f.write('Teff: {0:.0f} +/- {1:.0f} K\n'.format(
targ_param['Teff'], targ_param['u_Teff']))
f.write('Radius: {0:.3f} +/- {1:.3f} Rsun\n'.format(
targ_param['radius'], targ_param['u_radius']))
f.write('[Fe/H]: {0:.2f} +/- {1:.2f} dex\n'.format(
targ_param['feh'], targ_param['u_feh']))
f.write('\n')
sm.results_to_txt(f, verbose=True)
# Save full results
outpath = os.path.join(outdir, name + suffix + '_lincomb_sm.hdf')
sm.to_hdf(outpath)
# Plot results
if plot_level == 1:
plotspath = os.path.join(outdir, name + suffix + '_lincomb_plots.pdf')
with PdfPages(plotspath) as pdf:
region = (5100, 5200)
wavlim = (5160, 5190)
plot_lincomb(sm, pdf, region, wavlim, targ_param)
if plot_level == 2:
plotspath = os.path.join(outdir, name + suffix + '_lincomb_plots.pdf')
with PdfPages(plotspath) as pdf:
for reg in sm.lincomb_regions:
plot_lincomb(sm, pdf, reg, wavlim='all', targ_param=targ_param)
return sm
def match_spectrum(specpath,
indir="./",
plot_level=0,
inlib=False,
outdir="./",
suffix=""):
"""Match a spectrum given its observation ID
Args:
specpath (str): Path to spectrum or its CPS observation id jXX.XXXX
indir (str): Directory to look in for target spectrum
plot_level (int, 0-2): Level of plotting to save
inlib (str or False): String to search within library for to exclude
from matching process
outdir (str): Output file directory
suffix (str): String to append to output file names
Returns:
specmatch.SpecMatch object
"""
# Check if specpath is a path or an observation ID
if os.path.exists(specpath):
targ_path = specpath
targid = os.path.splitext(os.path.basename(specpath))[0]
else:
targ_path = os.path.join(indir,
'r' + specpath + '_adj' + suffix + '.fits')
if not os.path.exists(targ_path):
raise ValueError(specpath + " does not exist!")
targid = 'r' + specpath
# Load shifted spectrum
target = spectrum.read_fits(targ_path)
lib = library.read_hdf()
sm = specmatch.SpecMatch(target, lib)
if inlib:
name = inlib
sm.target.name = inlib
sm.target.attrs['obs'] = targid
targ_idx = lib.get_index(inlib)
targ_param, targ_spec = lib[targ_idx]
sm.match(ignore=targ_idx)
else:
name = targid
targ_param = None
sm.match()
# Save results
outdir = os.path.join(outdir, name)
if not os.path.exists(outdir):
os.mkdir(outdir)
outpath = os.path.join(outdir, name + suffix + '_match.csv')
sm.match_results.to_csv(outpath)
# Save SpecMatch object
outpath = os.path.join(outdir, name + suffix + '_sm.hdf')
sm.to_hdf(outpath)
# Generate representative plots
if plot_level == 1:
plotspath = os.path.join(outdir, name + suffix + '_match_plots.pdf')
with PdfPages(plotspath) as pdf:
region = (5100, 5200)
wavlim = (5160, 5190)
plot_match(sm, pdf, region, wavlim, targ_param)
# Generate full plots
if plot_level == 2:
plotspath = os.path.join(outdir, name + suffix + '_match_plots.pdf')
with PdfPages(plotspath) as pdf:
for reg in sm.regions:
plot_match(sm, pdf, reg, wavlim='all', targ_param=targ_param)
return sm
def specmatch_spectrum(specpath,
plot_level=0,
inlib=False,
outdir="./",
num_best=5,
suffix="",
wavlim='all',
lib_subset=None,
name=None,
n_lib_subset=None):
"""Perform the specmatch on a given spectrum
Args:
specpath (str): Path to target spectrum
plot_level (int, 0-2): Level of plots
0 - No plots saved, 1 - Representative plots, 2 - All plots
inlib (str or False): String to search within library for to exclude
from matching process
outdir (str): Output file directory
num_best (int): Number of best matches to use at lincomb stage
suffix (str): String to append to output file names
Returns:
specmatch.SpecMatch object
"""
if not os.path.exists(specpath):
raise ValueError(specpath + " does not exist!")
if wavlim == 'all':
target = spectrum.read_hires_fits(specpath)
else:
target = spectrum.read_hires_fits(specpath).cut(*wavlim)
# Determine the name of the target
if inlib:
name = inlib
elif name is None:
name = os.path.basename(specpath)[:-5]
if n_lib_subset is not None:
lib = library.read_hdf(wavlim='none')
lib_subset = lib.library_params.lib_index
lib_subset = np.random.choice(lib_subset,
size=n_lib_subset,
replace=False)
lib = library.read_hdf(wavlim=wavlim, lib_index_subset=lib_subset)
sm = specmatch.SpecMatch(target, lib)
sm.shift()
if inlib:
targ_idx = lib.get_index(inlib)
targ_param, targ_spec = lib[targ_idx]
sm.match(ignore=targ_idx, wavlim=wavlim)
else:
targ_param = None
sm.match(wavlim=wavlim)
sm.target.name = name # attach target name
sm.lincomb(num_best)
# Print results
print("SpecMatch Results for {0}".format(name))
sm.results_to_txt(sys.stdout)
outdir = os.path.join(outdir, name)
if not os.path.exists(outdir):
os.makedirs(outdir)
# Save final results
outpath = os.path.join(outdir, name + suffix + '_results.txt')
with open(outpath, 'w') as f:
if inlib:
f.write('Library Parameters\n')
f.write('------------------\n')
f.write('Teff: {0:.0f} +/- {1:.0f} K\n'.format(
targ_param['Teff'], targ_param['u_Teff']))
f.write('Radius: {0:.3f} +/- {1:.3f} Rsun\n'.format(
targ_param['radius'], targ_param['u_radius']))
f.write('[Fe/H]: {0:.2f} +/- {1:.2f} dex\n'.format(
targ_param['feh'], targ_param['u_feh']))
f.write('\n')
sm.results_to_txt(f, verbose=True)
print("created {}".format(outpath))
# Save full results
outpath = os.path.join(outdir, name + suffix + '_sm.hdf')
sm.to_hdf(outpath)
print("created {}".format(outpath))
# Create representative plots
if plot_level is not None and plot_level > 0:
plotspath = os.path.join(outdir, name + suffix + '_plots.pdf')
with PdfPages(plotspath) as pdf:
region = (5100, 5200)
wavlim = (5160, 5190)
order = 2
plot_shifts(sm, pdf, order, wavlim)
plot_match(sm, pdf, region, wavlim, targ_param)
plot_lincomb(sm, pdf, region, wavlim, targ_param)
print("created {}".format(plotspath))
# Create full plots
if plot_level == 2:
shiftplotspath = os.path.join(outdir,
name + suffix + '_shift_plots.pdf')
with PdfPages(shiftplotspath) as pdf:
for order in range(np.shape(sm.target_unshifted.w)[0]):
plot_shifts(sm, pdf, order, wavlim='all')
matchplotspath = os.path.join(outdir,
name + suffix + '_match_plots.pdf')
with PdfPages(matchplotspath) as pdf:
for reg in sm.regions:
plot_match(sm, pdf, reg, wavlim='all', targ_param=targ_param)
lincombplotspath = os.path.join(outdir,
name + suffix + '_lincomb_plots.pdf')
with PdfPages(lincombplotspath) as pdf:
for reg in sm.lincomb_regions:
plot_lincomb(sm, pdf, reg, wavlim='all', targ_param=targ_param)
print("created {}".format(plotspath))
return sm
def lincomb_spectrum(respath, plot_level=0, inlib=False, outdir="./",
num_best=5, suffix=""):
"""Match a spectrum using the linear combination approach.
Can only be used to resume an existing SpecMatch object.
Args:
respath (str): Path to existing SpecMatch.hdf file
plot_level (int, 0-2): Level of plotting to save
inlib (str or False): String to search within library for to exclude
from matching process
outdir (str): Output file directory
num_best (int): Number of best matches to use at lincomb stage
suffix (str): String to append to output file names
Returns:
specmatch.SpecMatch object
"""
lib = library.read_hdf()
sm = specmatch.SpecMatch.read_hdf(respath, lib)
name = sm.target.name
if inlib:
targ_idx = lib.get_index(inlib)
targ_param, targ_spec = lib[targ_idx]
else:
targ_param = None
sm.lincomb(num_best=num_best)
# Print results
print("SpecMatch Results for {0}".format(name))
for p in library.Library.STAR_PROPS:
print("{0}: {1:.2f}".format(p, sm.results[p]))
outdir = os.path.join(outdir, name)
if not os.path.exists(outdir):
os.mkdir(outdir)
# Save final results
outpath = os.path.join(outdir, name + suffix + '_results.txt')
with open(outpath, 'w') as f:
if inlib:
f.write('Library Parameters\n')
f.write('------------------\n')
f.write('Teff: {0:.0f} +/- {1:.0f} K\n'.format(
targ_param['Teff'], targ_param['u_Teff']))
f.write('Radius: {0:.3f} +/- {1:.3f} Rsun\n'.format(
targ_param['radius'], targ_param['u_radius']))
f.write('[Fe/H]: {0:.2f} +/- {1:.2f} dex\n'.format(
targ_param['feh'], targ_param['u_feh']))
f.write('\n')
sm.results_to_txt(f, verbose=True)
# Save full results
outpath = os.path.join(outdir, name + suffix + '_lincomb_sm.hdf')
sm.to_hdf(outpath)
# Plot results
if plot_level == 1:
plotspath = os.path.join(outdir, name + suffix + '_lincomb_plots.pdf')
with PdfPages(plotspath) as pdf:
region = (5100, 5200)
wavlim = (5160, 5190)
plot_lincomb(sm, pdf, region, wavlim, targ_param)
if plot_level == 2:
plotspath = os.path.join(outdir, name + suffix + '_lincomb_plots.pdf')
with PdfPages(plotspath) as pdf:
for reg in sm.lincomb_regions:
plot_lincomb(sm, pdf, reg, wavlim='all', targ_param=targ_param)
return sm
import numpy as np
from collections import defaultdict
from specmatchemp import library
from specmatchemp import specmatch
# Noise selection path
lst = '/home/syee/specmatchemp-working/specmatchemp/tests/noise_selection.csv'
lc = '/home/syee/specmatchemp-working/specmatchemp/results/lincomb_results.csv'
res_path = '/home/syee/specmatchemp-working/specmatchemp/tests/resstudy_result.csv'
resdir = '/home/syee/specmatchemp-working/specmatchemp/results/'
RESOLUTION = [50000, 30000, 20000, 10000, 5000, 2500]
if __name__ == '__main__':
# Read library
lib = library.read_hdf()
# Get list of stars which were tested
starlist = pd.read_csv(lst)
# Open lincomb results
lincomb_res_table = pd.read_csv(lc)
for idx, row in starlist.iterrows():
star = row['cps_name']
# Get original lincomb result
lc_res = lincomb_res_table.query('cps_name == "' + star + '"').iloc[0]
suf = '_nodetrend_lincomb'
lincomb_result = {}
for p in library.Library.STAR_PROPS:
p_col = p + suf
starlist.loc[idx, p_col] = lc_res[p_col]
lincomb_result[p] = lc_res[p_col]
def main(resdir, suffix, plots):
lib = library.read_hdf(wavlim='none')
# Create global dataframe to store results
match_res_global = pd.DataFrame()
lincomb_res_global = pd.DataFrame()
for idx, row in lib.library_params.iterrows():
targ_name = row['cps_name']
res_path = os.path.join(resdir, targ_name + '/' + targ_name +
args.suffix + '_lincomb_sm.hdf')
if not os.path.exists(res_path):
res_path = os.path.join(resdir, targ_name + '/' + targ_name +
args.suffix + '_sm.hdf')
if not os.path.exists(res_path):
print("Results file for {0} not found!".format(targ_name))
continue
print("Reading in results for {0}".format(targ_name))
sm = specmatch.SpecMatch.read_hdf(res_path, lib)
# Read in library grid search results
sm.match_results['targ_idx'] = idx
sm.match_results['ref_idx'] = sm.match_results.index
# Concatenate library grid search results
if match_res_global.empty:
match_res_global = sm.match_results
else:
match_res_global = pd.concat((match_res_global, sm.match_results),
ignore_index=True)
if lincomb_res_global.empty:
# Create global results dataframe containing final lincomb
# chi-squared and generated results
lincomb_res_global = lib.library_params.copy()
for i in range(len(sm.lincomb_regions)):
reg = sm.lincomb_regions[i]
suf = '_lincomb_{0:.0f}'.format(reg[0])
cs_col = 'chi_squared' + suf
lincomb_res_global[cs_col] = np.nan
for p in library.Library.STAR_PROPS:
p_col = p + suf
lincomb_res_global[p_col] = np.nan
suf = '_lincomb'
for p in library.Library.STAR_PROPS:
p_col = p + suf
p_nodetrend_col = p + '_nodetrend' + suf
lincomb_res_global[p_col] = np.nan
lincomb_res_global['u_'+p_col] = np.nan
lincomb_res_global[p_nodetrend_col] = np.nan
# Read in lincomb results for each wavelength region
for i in range(len(sm.lincomb_regions)):
mt = sm.lincomb_matches[i]
reg = sm.lincomb_regions[i]
suf = '_lincomb_{0:.0f}'.format(reg[0])
cs_col = 'chi_squared' + suf
lincomb_res_global.loc[idx, cs_col] = mt.best_chisq
for p in library.Library.STAR_PROPS:
p_col = p + suf
lincomb_res_global.loc[idx, p_col] = sm.lincomb_results[i][p]
# Read in averaged results
suf = '_lincomb'
for p in library.Library.STAR_PROPS:
p_col = p + suf
p_nodetrend_col = p + '_nodetrend' + suf
lincomb_res_global.loc[idx, p_col] = sm.results[p]
lincomb_res_global.loc[idx, 'u_'+p_col] = sm.results['u_'+p]
lincomb_res_global.loc[idx, p_nodetrend_col] = \
sm.results_nodetrend[p]
# Save results
outpath = os.path.join(resdir, 'match_results' + suffix + '.csv')
match_res_global.index.names = ['idx']
match_res_global.to_csv(outpath)
outpath = os.path.join(resdir, 'lincomb_results' + suffix + '.csv')
lincomb_res_global.to_csv(outpath)
if plots:
# Plots for individual regions
plotspath = os.path.join(resdir, 'library_plots_regions.pdf')
with PdfPages(plotspath) as pdf:
cols = list(lincomb_res_global.columns)
cscols = cscols = [c for c in cols if re.search(
'chi_squared_lincomb_\d+', c)]
regions = list(set([re.search('chi_squared_lincomb_(\d+)$', c)
.group(1) for c in cscols]))
for reg in regions:
reg = float(reg)
suf = '_lincomb_{0:.0f}'.format(reg)
title = 'Wavelength region: {0:.0f} - {1:.0f} A'\
.format(reg, reg + 100)
plot_diag(lincomb_res_global, suf, pdf, title)
# Plots for nodetrend parameters
plotspath = os.path.join(resdir, 'library_plots_nodetrend.pdf')
with PdfPages(plotspath) as pdf:
suf = '_nodetrend_lincomb'
title = 'Averaged over all wavelengths, not detrended'
# Plot all stars
plot_diag(lincomb_res_global, suf, pdf, title, trend=True)
# Plots for detrended parameters
plotspath = os.path.join(resdir, 'library_plots_lincomb.pdf')
with PdfPages(plotspath) as pdf:
suf = '_lincomb'
title = 'Averaged over all wavelengths, detrended'
# Plot all stars
plot_diag(lincomb_res_global, suf, pdf, title)