def __init__(self, parent=None, file_main=None, file_abonds=None):
# State variables
a99.XLogMainWindow.__init__(self, parent)
# XRunnableManager instance
self._manager_form = None
# RunnableManager instance
self._rm = None
self.save_dir = None
self.load_dir = None
# # Synchronized sequences
# Used in generic operations where only certain parameters change
self.tab_texts = [
"Main configuration (Alt+&1)", "Abundances (Alt+&2)",
"Command-line options (Alt+&3)"
]
self.flags_changed = [False, False, False]
self.save_as_texts = [
"Save main configuration as...", "Save abundances as...",
"Save command-line options as..."
]
self.open_texts = [
"Load main configuration file", "Load abundances file",
"Load command-line options file"
]
self.clss = [pyfant.FileMain, pyfant.FileAbonds, pyfant.FileOptions]
self.wilds = ["*.dat", "*.dat", "*.py"]
# # Menu bar
b = self.menuBar()
m = self.menu_file = b.addMenu("&File")
ac = m.addAction("&Open...")
ac.setShortcut("Ctrl+O")
ac.triggered.connect(self.on_open)
m.addSeparator()
ac = m.addAction("&Save")
ac.setShortcut("Ctrl+S")
ac.triggered.connect(self.on_save)
ac = m.addAction("Save &as...")
ac.setShortcut("Ctrl+Shift+S")
ac.triggered.connect(self.on_save_as)
ac = m.addAction("Save a&ll...")
ac.setShortcut("Alt+Shift+S")
ac.triggered.connect(self.on_save_all)
m.addSeparator()
ac = m.addAction("Load &default")
ac.setStatusTip("Loads default")
ac.setShortcut("Ctrl+D")
ac.triggered.connect(self.on_reset)
m.addSeparator()
ac = m.addAction("&Quit")
ac.setShortcut("Ctrl+Q")
ac.triggered.connect(self.close)
m = self.menu_view = b.addMenu("&View")
ac = m.addAction("Runnables &Manager")
ac.setShortcut("Ctrl+M")
ac.triggered.connect(self.on_show_rm)
# # It is necessary to do a little more work to create this option
# ac = m.addAction("&Explorer")
# ac.setShortcut("Ctrl+E")
# ac.triggered.connect(self.on_show_explorer)
# # Central layout
cw = self.centralWidget = QWidget()
self.setCentralWidget(cw)
la = self.layout_main = QVBoxLayout(cw)
# ## Main control bar
# A layout is created and left blank for descendants to add
# widgets as needed
l = self.controlLayout = QHBoxLayout()
la.addLayout(l)
# ## Tabs
# tab "File"
tt = self.tabWidget = QTabWidget(self)
la.addWidget(tt)
tt.setFont(a99.MONO_FONT)
# ### Main configuration tab
w0 = self.c27272 = QWidget()
tt.addTab(w0, self.tab_texts[0])
l0 = self.c12842 = QVBoxLayout(w0)
# #### Main configuration file toolbar
l1 = self.c29378 = QHBoxLayout()
l0.addLayout(l1)
w = QLabel("<b>File:<b>")
l1.addWidget(w)
w = self.label_fn_main = QLabel()
l1.addWidget(w)
l1.addSpacerItem(
QSpacerItem(0, 0, QSizePolicy.Expanding, QSizePolicy.Minimum))
# #### Main file editor widget
me = self.me = WFileMain()
l0.addWidget(me)
me.changed.connect(self.on_main_edited)
# ### Abundances tab
w0 = self.c10101 = QWidget()
tt.addTab(w0, self.tab_texts[1])
l0 = self.c54354 = QVBoxLayout(w0)
# #### Abundances file toolbar
l1 = self.c65478 = QHBoxLayout()
w = QLabel("<b>File:</b>")
l0.addLayout(l1)
l1.addWidget(w)
w = self.label_fn_abonds = QLabel()
l1.addWidget(w)
l1.addSpacerItem(
QSpacerItem(0, 0, QSizePolicy.Expanding, QSizePolicy.Minimum))
# #### Abundances editor
ae = self.ae = WFileAbonds()
l0.addWidget(ae)
ae.changed.connect(self.on_abonds_edited)
# ### Command-line options tab
w0 = QWidget()
tt.addTab(w0, self.tab_texts[2])
l0 = QVBoxLayout(w0)
# # #### File label
# l1 = self.c293wd = QHBoxLayout()
# l0.addLayout(l1)
# w = QLabel("<b>File:<b>")
# l1.addWidget(w)
# w = self.label_fn_options = QLabel()
# l1.addWidget(w)
# l1.addSpacerItem(QSpacerItem(0, 0, QSizePolicy.Expanding, QSizePolicy.Minimum))
oe = self.oe = WOptionsEditor(self)
oe.changed.connect(self.on_options_edited)
l0.addWidget(oe)
# tt.tabBar()
# ### Final tabs setup
tt.setCurrentIndex(0)
# ### These sequences couldn't be set above because the widgets didn't exist yet
self.editors = [self.me, self.ae, self.oe]
self.labels_fn = [
self.label_fn_main, self.label_fn_abonds, self.oe.label_fn
]
assert len(self.tab_texts) == len(self.flags_changed) == \
len(self.save_as_texts) == len(self.open_texts) == len(self.clss) == \
len(self.editors) == len(self.labels_fn)
# # Loads default files
if os.path.isfile(pyfant.FileMain.default_filename):
f = pyfant.FileMain()
f.load()
self.me.load(f)
if os.path.isfile(pyfant.FileAbonds.default_filename):
f = pyfant.FileAbonds()
f.load()
self.ae.load(f)
if os.path.isfile(pyfant.FileOptions.default_filename):
f = pyfant.FileOptions()
f.load()
self.oe.load(f)
else:
self.oe.load(pyfant.FileOptions())
self._update_labels_fn()
def test_FileAbonds(tmpdir):
os.chdir(str(tmpdir))
obj = pyfant.FileAbonds()
obj.init_default()
obj.save_as()
#!/usr/bin/env python
"""Abundances file editor"""
import sys
import argparse
import logging
import a99
import pyfant
a99.logging_level = logging.INFO
a99.flag_log_file = True
if __name__ == "__main__":
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=a99.SmartFormatter)
parser.add_argument('fn',
type=str,
help='abundances file name',
default='abonds.dat',
nargs='?')
args = parser.parse_args()
m = pyfant.FileAbonds()
m.load(args.fn)
app = a99.get_QApplication([])
form = pyfant.XFileAbonds()
form.show()
form.load(m)
sys.exit(app.exec_())
def synth_plot_build(ax, name=None, st_dt=None):
#takes a name for the synthesis and the star data dictionary
global mainfile
global abondsfile
global atomsfile
#initialize main parameters
mainfile = pf.FileMain()
mainfile.load()
mainfile.pas = 0.01
#setting atmospherical parameters
if pflag or multiflag:
mainfile.fwhm = st_dt['fwhm']
teff = st_dt['teff']
logg = st_dt['logg']
met = st_dt['met']
vt = st_dt['vt']
if fflag:
mainfile.fwhm = fw
if pflag or multiflag:
mainfile.titrav = name
mainfile.teff = teff
mainfile.glog = logg
mainfile.asalog = mainfile.afstar = met
mainfile.vvt = [vt]
mainfile.flprefix = name[:3]
mainfile.nhe = 0.085
mainfile.llzero = linelambda - linerange / 2 - 3
mainfile.llfin = linelambda + linerange / 2 + 3
#initializing elemental abundance file and values
#note that if there's a file "abonds.dat" in the directory, it will be used
#if not, default values (solar) will be loaded
#additionally, if multirun is being used, the specified abonds file will be used
abondsfile = pf.FileAbonds()
if multiflag:
abondsfile.load(st_dt['ab_file'])
else:
abondsfile.load()
idx = abondsfile.ele.index(pf.adjust_atomic_symbol(element))
if pf.adjust_atomic_symbol(element) != "FE":
abondsfile.abol[abondsfile.ele.index("FE")] = -99.99
abondsfile.abol[idx] = -99.99
#initializing atomic data, based on filename passed or not
atomsfile = pf.FileAtoms()
atomsfile.load(atomdata)
#setting and interpolating atmospherical model
m = pf.Innewmarcs()
m.conf.flag_log_console = False
m.conf.file_main = mainfile
m.conf.opt.allow = True
m.conf.opt.absoru = True
m.conf.opt.opa = False
m.run()
#calculating hydrogen lines
h = pf.Hydro2()
h.conf.flag_log_console = False
h.conf.file_main = mainfile
h.run()
#running pfant only for atoms (except chosen element and Fe)
spec_atoms = pfant_cut(no_at=False, no_mol=True, fname='only_atoms')
#running pfant only for molecules
spec_molecules = pfant_cut(no_at=True, no_mol=False, fname='only_mols')
#running pfant for separate chosen element lines
#loading back true abundances
abondsfile = pf.FileAbonds()
if multiflag:
abondsfile.load(st_dt['ab_file'])
else:
abondsfile.load()
if element != 'Fe':
el_speclines, el_specval = el_multirun(element)
#running pfant for separate iron lines
fe_speclines, fe_specval = el_multirun("Fe")
#running pfant for the full spectrum
spec_full = pfant_cut(no_at=False, no_mol=False, fname='full')
#START PLOTTING
value_specat = [spec_atoms.x, spec_atoms.y]
value_specmol = [spec_molecules.x, spec_molecules.y]
value_total = [spec_full.x, spec_full.y]
ax.plot(value_total[0], value_total[1], 'b-')
ax.plot(value_specat[0], value_specat[1], 'g-')
ax.plot(value_specmol[0], value_specmol[1], 'c-')
if sflag or multiflag:
if multiflag:
global ospec
ospec = np.genfromtxt(st_dt['spec'], unpack=True)
obsplot = ax.plot(ospec[0]+st_dt['sp_adj'][0], ospec[1]/st_dt['sp_adj'][1], 'k--')
elif rflag:
ax.plot(ospec[0]+rel[0], ospec[1]/rel[1], 'k--')
else:
ax.plot(ospec[0], ospec[1], 'k--')
for l in fe_specval:
ax.plot(l[0], l[1], color='#FF8C00', ls='-.', lw=1.5)
if element != 'Fe':
for l in el_specval:
ax.plot(l[0], l[1], 'm-', lw=1.5)
if multiflag:
plt.text(0.04, 0.06, name, horizontalalignment='left',
verticalalignment='bottom', fontsize=16,
transform=plt.gca().transAxes)
plt.ylim((0., 1.05))
return [obsplot, ospec]