def test_convert_v01():
fname_in = datadir + "/hd122563_v0.1.smh"
fname_out = datadir + "/.converted.hd122563_v0.1.smh"
legacy.convert_v0_1_to_v0_2(fname_in, fname_out, overwrite=True)
session = Session.load(fname_out)
session.measure_abundances()
def test_ReviewTab(session=None):
if session is None:
session = Session.load(datadir + "/test_G64-12_v02.smh")
session.measure_abundances()
window, cw = create_blank_window(width=1000, height=600)
window.session = session
tab = ReviewTab(window)
vbox = QtGui.QVBoxLayout(cw)
vbox.addWidget(tab)
return window
def test_import_models_into_session():
session = Session([datadir + '/spectra/hd122563.fits'])
session.import_linelist_as_profile_models(eqw_ll_fname)
print("Loaded profiles into session")
for fname, elem in zip(synth_ll_filenames, synth_elems):
session.import_linelist_as_synthesis_model(fname, elem)
print("Loaded syntheses into session")
options, args = parser.parse_args()
origfname, datafname, outfname = args
tmpfname = "./.tmp.pkl"
while os.path.exists(tmpfname):
tmpfname = tmpfname[:-4] + "p.pkl"
assert os.path.exists(origfname), "input 1 {} does not exist".format(
origfname)
assert os.path.exists(datafname), "input 2 {} does not exist".format(
datafname)
assert options.force or (not os.path.exists(outfname)
), "output {} already exists".format(outfname)
session1 = Session.load(origfname)
session2 = Session.load(datafname)
profile_keys = [
"profile", "central_weighting", "window", "continuum_order",
"detection_sigma", "detection_pixels", "max_iterations",
"velocity_tolerance", "mask", "antimask_flag", "elements", "species"
]
synthesis_keys = [
"mask", "window", "continuum_order", "velocity_tolerance",
"smoothing_kernel", "initial_abundance_bounds", "elements", "species",
"manual_continuum", "manual_sigma_smooth", "manual_rv"
]
new_spectral_models = []
for model in session1.spectral_models:
return None
if __name__=="__main__":
app = QtGui.QApplication(sys.argv)
import main_ui
app.window = main_ui.Ui_MainWindow()
for i in range(app.window.tabs.count()):
app.window.tabs.setTabEnabled(i, True)
app.window.show()
import yaml
with open(Session._default_settings_path, "rb") as fp:
defaults = yaml.load(fp)
datadir = os.path.dirname(os.path.abspath(__file__))+"/../tests/test_data"
session = Session([datadir+"/spectra/hd122563.fits"])
session.metadata.update(defaults)
ll = LineList.read(os.path.dirname(os.path.abspath(__file__))+"/../tests/test_data/linelists/complete.list")
session.metadata["line_list"] = ll
import cPickle as pickle
print("Loading pre-saved spectral models"); start = time.time()
with open(datadir+"/ewtest.pkl","rb") as fp:
session.metadata["spectral_models"] = pickle.load(fp)
print("Done!",time.time()-start)
app.window.session = session
chemical_abundances_tab = app.window.chemical_abundances_tab
abundtree = chemical_abundances_tab.abundtree
model = abundtree.model()
#abundtree = AbundTreeView(None)
#prefixred = prefix+"/red/Final-Products"
prefix="/Users/alexji/Dropbox/Observing/2016_8/reduced_data/rproc"
prefixblue=prefix
prefixred=prefix
#outpath = "./n3"
outpath = "/Users/alexji/Dropbox/Observing/2016_8/reduced_data/rproc/summaries"
rv_fix = {} #{"retii-09":60.0}
specnames = [x[:-15] for x in glob.glob(prefixblue+"/*blue*")]
specnames = [os.path.basename(x) for x in specnames]
print(specnames)
for specname in specnames:
bluespec = prefixblue+"/"+specname+"blue_multi.fits"
redspec = prefixred +"/"+specname+"red_multi.fits"
session = Session([bluespec,redspec])
#with open(smh.Session._default_settings_path, "rb") as fp:
# defaults = yaml.load(fp)
#session.metadata.update(defaults)
if specname in rv_fix:
rv = rv_fix[specname]
else:
rv,rve = session.rv_measure()
print("RV:",rv)
session.rv_correct(rv)
#session.normalize_input_spectra()
for index,order in enumerate(session.input_spectra):
fit_continuum(session,index)
session.stitch_and_stack()
from __future__ import (division, print_function, absolute_import,
unicode_literals)
import numpy as np
import matplotlib.pyplot as plt
import time
import smh
from smh import Session
from smh.spectral_models import (ProfileFittingModel, SpectralSynthesisModel)
from smh.linelists import LineList
if __name__ == "__main__":
path = "/Users/alexji/lib/smhr/smh/tests/test_data/test2.smh"
session = Session.load(path)
# Already normalized and rv-corrected, but not stitched
normalized_spectrum = session.stitch_and_stack()
metadata = session.metadata
line_list = metadata["line_list"]
spectral_models = metadata["spectral_models"]
"""
# Everything is fit already, but you can run fit again
print("Fitting models..."); start = time.time()
for model in spectral_models:
try:
res = model.fit()
except Exception as e:
print(model.elements, model.species, model._repr_wavelength, e)
print("Time to fit all models: {:.1f}".format(time.time()-start))
"""
self.mpl_figure.draw()
return True
if __name__ == "__main__":
import sys
from smh import linelists, Session, specutils
transitions = linelists.LineList.read(
"/Users/arc/research/ges/linelist/vilnius.ew.fe")
session = Session([
"/Users/arc/codes/smh/hd44007red_multi.fits",
"/Users/arc/codes/smh/hd44007blue_multi.fits",
])
session.normalized_spectrum = specutils.Spectrum1D.read(
"../smh/hd44007-rest.fits")
session.metadata["line_list"] = transitions
from smh import spectral_models as sm
foo = []
for i in range(len(transitions)):
if i % 2:
foo.append(
sm.ProfileFittingModel(session, transitions["hash"][[i]]))
else:
foo.append(
except RuntimeError:
None
# Load some spectra.
spectra = [] + \
Spectrum1D.read("/Users/arc/Downloads/hd122563_1blue_multi_090205_oldbutgood.fits") + \
Spectrum1D.read("/Users/arc/Downloads/hd122563_1red_multi_090205_oldbutgood.fits") + \
[Spectrum1D.read("smh/balmer/hd122563.fits")]
for spectrum in spectra[:-1]:
spectrum._dispersion = (1 + +52.1 / 299792.458) * spectrum.dispersion
#spectra = [Spectrum1D.read("hd140283.fits")]
#spectra = [Spectrum1D.read("/Users/arc/research/fe-rich-stars/sm0342-2842.rest.fits")]
sigma = 0.01 * np.ones_like(spectra[-1].dispersion)
spectra[-1]._ivar = sigma**(-2)
from smh import Session
session = Session.load("hd122563.smh")
window = BalmerLineFittingDialog(spectra,
observed_spectra_labels=[
"Order {}".format(i)
for i in range(1, len(spectra))
] + ["Normalized rest-frame spectrum"],
session=session)
window.exec_()
def test_import_eqw_into_session():
session = Session([datadir + '/spectra/hd122563.fits'])
session.import_linelist_as_profile_models(
datadir + "/linelists/frebel13_HD122563.moog2",
import_equivalent_widths=True)
print("Loaded eqws into session")
def test_create_synthesis():
session = Session([datadir + '/spectra/hd122563.fits'])
for ll, elem in zip(synth_lls, synth_elems):
model = sm.SpectralSynthesisModel(session, ll, elem)
print("Created synthesis models!")
def test_create_profile():
session = Session([datadir + '/spectra/hd122563.fits'])
model = sm.ProfileFittingModel(session, eqw_ll[0])
model = sm.ProfileFittingModel(session, eqw_ll[0])
print("Created profile model!")
def test_load_session():
file_to_load = datadir + "/test_create_session.smh"
session = Session.load(file_to_load)
def test_create_session_and_analyze():
file_to_write_to = datadir + "/.test_create_session.smh"
#file_to_write_to = datadir+"/test_create_session.smh"
session = Session([datadir + '/spectra/hd122563.fits'])
session.import_linelist_as_profile_models(datadir +
'/linelists/complete.list')
#rv, e_rv = session.rv_measure()
#print( rv, e_rv )
session.rv_correct(0.0)
# TODO put this in somewhere nice, as well as the rest of the normalization tab
session.metadata["normalization"] = {
"continuum": [1.0],
"normalization_kwargs": [{}]
}
session.stitch_and_stack()
start = time.time()
num_fit = 0
for model in session.spectral_models:
try:
res = model.fit()
except (ValueError, RuntimeError, TypeError) as e:
print("Fitting error", model)
print(e)
else:
num_fit += 1
print("Time to fit {}/{} models: {:.1f}".format(
num_fit, len(session.spectral_models),
time.time() - start))
session.measure_abundances()
session.save(file_to_write_to, overwrite=True)
self.endRemoveRows()
class IsotopeLog(QtGui.QPlainTextEdit):
def log(self, msg):
self.appendMessage(msg)
def appendMessage(self, msg):
self.appendPlainText(msg)
self.verticalScrollBar().setValue(self.verticalScrollBar().maximum())
if __name__ == "__main__":
# For development
datadir = os.path.dirname(
os.path.abspath(__file__)) + '/../tests/test_data'
session = Session([datadir + "/spectra/hd122563.fits"])
orig_isotopes = isoutils.load_isotope_data('rproc')
ll = LineList.read(
os.path.dirname(os.path.abspath(__file__)) +
'/../tests/test_data/linelists/lin4554new')
session.metadata['isotopes'] = orig_isotopes
session.metadata['line_list'] = ll
app = QtGui.QApplication(sys.argv)
window = IsotopeDialog(session) #orig_isotopes=orig_isotopes, linelist=ll)
window.exec_()
#print(session.metadata['isotopes'])
#print('U in isotopes?', 'U' in session.metadata['isotopes'])
return None
if __name__ == "__main__":
# This is just for development testing.
app = QtGui.QApplication(sys.argv)
#window = RVRegionDialog(None)
#window.exec_()
widget = QtGui.QWidget(None)
with open(Session._default_settings_path, "rb") as fp:
defaults = yaml.load(fp)
datadir = os.path.dirname(
os.path.abspath(__file__)) + '/../tests/test_data'
session = Session([datadir + "/spectra/hd122563.fits"])
widget.session = session
session.metadata.update(defaults)
ll = LineList.read(
os.path.dirname(os.path.abspath(__file__)) +
'/../tests/test_data/linelists/lin4554new')
session.metadata['line_list'] = ll
rv_tab = RVTab(widget)
rv_tab.update_from_new_session()
rv_tab.template_path = QtGui.QLineEdit()
rv_tab.template_path.setText(datadir + '/spectra/hd122563.fits')
dialog = RVRegionDialog(rv_tab)
rhomat = utils._make_rhomat(rho_Tg=rho_Tg,
rho_Tv=rho_Tv,
rho_gv=rho_gv,
rho_TM=rho_TM,
rho_gM=rho_gM,
rho_vM=rho_vM)
version_out = "v1" # Submitted version
fnames = glob.glob("smhr_errors/*_errors.smh")
print(fnames)
all_lines = []
all_abunds = []
for fname in fnames:
name = os.path.basename(fname)[:-11]
print(name)
session = Session.load(fname)
## Extract line info
linetab = utils.process_session_uncertainties_lines(session, rhomat)
## Manual updates to line info
try:
linetab = fix_ch_lines(name, linetab)
except Exception as e:
print("CH", e)
linetab = add_ba_errors(name, linetab)
linetab = add_cn_errors(name, linetab)
linetab = fix_o_loggf(name, linetab)
linetab = add_al_errors(name, linetab)
linetab = add_hfs_errors(name, linetab)
for species in [8.0, 106.0, 56.1, 607.0, 13.0] + hfs_species:
ix = np.where((linetab["species"] == species)
def create_blank_window(width=800, height=400):
window = QtGui.QMainWindow()
window.resize(width, height)
cw = QtGui.QWidget(window)
window.setCentralWidget(cw)
return window, cw
def test_ReviewTab(session=None):
if session is None:
session = Session.load(datadir + "/test_G64-12_v02.smh")
session.measure_abundances()
window, cw = create_blank_window(width=1000, height=600)
window.session = session
tab = ReviewTab(window)
vbox = QtGui.QVBoxLayout(cw)
vbox.addWidget(tab)
return window
if __name__ == "__main__":
session = Session.load(datadir + "/test_G64-12_v02.smh")
w1 = test_ReviewTab(session)
ws = [w1]
for w in ws:
w.show()
w.raise_()
sys.exit(app.exec_())