def test_duplicates():
fname = datadir+'/linelists/lin4077new'
N = 50
ll1 = LineList.read_moog(fname)
ll2 = LineList.read_moog(fname)
ll = table.vstack([ll1,ll2[0:N]])
duplicate_indices,duplicate_lines = ll.find_duplicates(thresh=.01)
assert_equals(2*N,len(duplicate_indices))
def test_writeread(fname=datadir+'/linelists/masseron_linch.txt'):
ll = LineList.read(fname)
ll.write('line_list.fits',format='fits')
ll2 = LineList.read('line_list.fits',format='fits')
for i in range(len(ll)):
for col in ll[i].colnames:
if isinstance(ll[i][col], str): continue
diff = np.sum(np.abs(ll[i][col] - ll2[i][col]))
assert np.isnan(diff) or diff < .001, "{} {}".format(ll[i][col],ll2[i][col])
os.remove('line_list.fits')
def add_synth_list(self):
if self.session is None: return None
paths = self.open_file(caption="Select linelists for synths", dir="", filter="")
if not paths: return None
for path in paths:
transitions = LineList.read(path)
selectable_elements \
= list(set(transitions.unique_elements).difference(["H"]))
dialog = PeriodicTableDialog(
selectable_elements=selectable_elements,
explanation="Please select which element(s) will be measured"
" by synthesizing the transitions in {}:".format(
os.path.basename(path)),
multiple_select=True)
dialog.exec_()
if len(dialog.selected_elements) == 0:
# Nothing selected. Skip this filename.
continue
self.session.import_linelist_as_synthesis_model(path, dialog.selected_elements)
self.tableview.model().reset()
self.tableview.clearSelection()
return None
def test_exception():
ll = LineList.read(datadir+'/linelists/complete.list')
N = len(ll)
ll2 = LineList.read(datadir+'/linelists/complete.list')
ll.merge(ll2,skip_equal_loggf=True)
assert len(ll)==N,"{} {}".format(len(ll),N)
ll2[5]['loggf'] = -3.14159
ll2[200]['loggf'] = -3.14159
try:
ll.merge(ll2,skip_equal_loggf=True)
except linelists.LineListConflict as e:
assert len(e.conflicts1) == 2
assert len(e.conflicts2) == 2
else:
raise RuntimeError("Conflicts didn't work")
def test_get_needed_isotopes():
ll = LineList.read(datadir+'/linelists/lin4554new')
rproc = load_isotope_data('rproc')
isotopes, missing_isotopes = get_needed_isotopes(ll,rproc)
assert len(missing_isotopes) == 0, missing_isotopes
validate_isotopes(isotopes)
for elem in isotopes:
for mass in isotopes[elem]:
assert isotopes[elem][mass] == rproc[elem][mass]
def test_get_needed_isotopes2():
ll = LineList.read(datadir+'/linelists/masseron_linch.txt')
asplund = load_isotope_data('asplund')
asplund = add_molecules(asplund)
isotopes, missing_isotopes = get_needed_isotopes(ll,asplund,include_molecules=True)
assert len(missing_isotopes) == 0, missing_isotopes
validate_isotopes(isotopes)
for elem in isotopes:
for mass in isotopes[elem]:
assert isotopes[elem][mass] == asplund[elem][mass]
def test_identify_isotopes():
ll = LineList.read(datadir+'/linelists/lin4554new')
isotopes = identify_isotopes(ll)
for elem in isotopes:
for mass in isotopes[elem]:
if elem != 'Ba':
assert mass == 0
assert isotopes[elem][mass] == 1
needed_isotopes = identify_needed_isotopes(ll)
num_isotopes = 0
for elem in needed_isotopes:
for mass in needed_isotopes[elem]:
num_isotopes += 1
assert num_isotopes == 5
def test_identify_isotopes2():
ll = LineList.read(datadir+'/linelists/masseron_linch.txt')
isotopes = identify_isotopes(ll,include_molecules=True)
for elem in isotopes:
for mass in isotopes[elem]:
#print(elem,mass,isotopes[elem][mass])
if elem not in ['C','H-C','H']:
assert mass == 0
elif elem == 'H':
assert mass == 1
elif elem == 'C':
assert mass in [12,13]
elif elem == 'H-C':
assert mass in [112,113]
assert isotopes[elem][mass] == 1
needed_isotopes = identify_needed_isotopes(ll,include_molecules=True)
num_isotopes = 0
for elem in needed_isotopes:
for mass in needed_isotopes[elem]:
#print(elem,mass,isotopes[elem][mass])
num_isotopes += 1
assert num_isotopes == 4, num_isotopes
return None
sys.excepthook = exception_hook
# Run the main application window.
app.window = Ui_MainWindow(spectrum_filenames=[
datadir +
"/spectra/hd122563_1blue_multi_090205_oldbutgood.fits", datadir +
"/spectra/hd122563_1red_multi_090205_oldbutgood.fits"
])
# Enable all tabs
for i in range(app.window.tabs.count()):
app.window.tabs.setTabEnabled(i, True)
session = app.window.session
# TODO load a synthesis model here
transitions = LineList.read(datadir + '/linelists/lin4554new')
session.metadata["line_list"] = transitions
synth = sm.SpectralSynthesisModel(session, transitions['hash'], 'Ba')
session.metadata["spectral_models"] = [synth]
with open(smh.Session._default_settings_path, "rb") as fp:
defaults = yaml.load(fp)
app.window.chemical_abundances_tab.new_session_loaded()
app.window.tabs.setCurrentIndex(4)
app.window.chemical_abundances_tab.fit_all()
app.window.show()
sys.exit(app.exec_())
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'])
"/spectra/hd122563_1blue_multi_090205_oldbutgood.fits", datadir +
"/spectra/hd122563_1red_multi_090205_oldbutgood.fits"
])
# Enable all tabs
for i in range(app.window.tabs.count()):
app.window.tabs.setTabEnabled(i, True)
session = app.window.session
with open(smh.Session._default_settings_path, "rb") as fp:
defaults = yaml.load(fp)
datadir = os.path.dirname(
os.path.abspath(__file__)) + '/../tests/test_data'
# Load in line_list
ll = LineList.read(
os.path.dirname(os.path.abspath(__file__)) +
'/../tests/test_data/linelists/complete.list')
session.metadata['line_list'] = ll[190:200] #strong lines
#session.metadata['line_list'] = ll[90:100]
# Load in spectral_models from linelist
#from linelist_manager import TransitionsDialog
print("Loading spectral models...")
start = time.time()
sm = []
for hash in session.metadata["line_list"]["hash"]:
sm.append(smh.spectral_models.ProfileFittingModel(session, [hash]))
session.metadata['spectral_models'] = sm
print("Done! {:.1f}s".format(time.time() - start))
print("Fitting lines...")
def test_not_needed_isotopes():
ll = LineList.read(datadir+'/linelists/lin4554new')
isos = load_isotope_data('asplund') #Does not have Ba!
found_isos, missing_isos = get_needed_isotopes(ll,isos)
if len(missing_isos) != 1:
raise Error("{} {}".format(found_isos,missing_isos))
def test_merge():
ll1 = lls[0]
ll2 = lls[1]
ll1.merge(ll2,raise_exception=False)
lls[0] = LineList.read_moog(datadir+'/linelists/masseron_linch.txt')
from __future__ import (division, print_function, absolute_import,
unicode_literals)
import os
from smh import linelists, utils
from smh.linelists import LineList
from nose.tools import assert_equals, assert_almost_equals, ok_
from astropy import table
import numpy as np
ll_filenames = ['masseron_linch.txt']
ll_filenames = ['masseron_linch.txt','lin4077new','lin4554new']
datadir = os.path.dirname(os.path.abspath(__file__))+'/test_data'
lls = [LineList.read(datadir+'/linelists/'+filename) for filename in ll_filenames]
moog_lls = [LineList.read(datadir+'/linelists/'+filename,moog_columns=True) for filename in ll_filenames]
def test_species_converting():
# Species, elem1, isotope1, elem2, isotope2, ion
tests = [(56.1, 'Ba', 0, '', 0, 2),
(56.0, 'Ba', 0, '', 0, 1),
(56.1152, 'Ba', 152, '', 0, 2),
(106.0, 'H', 0, 'C', 0, 1),
(106.00112, 'H', 1, 'C', 12, 1),
(106.00113, 'H', 1, 'C', 13, 1)
]
failed = False
for test in tests:
species, elem1, isotope1, elem2, isotope2, ion = test
input = (elem1, elem2, isotope1, isotope2, ion)