def main(fns_input, fn_output):
ffmol = []
for fn in fns_input:
fmol = pyfant.FileMolecules()
try:
fmol.load(fn)
print("File '{}': {} molecule{}".format(
fn, len(fmol), "" if len(fmol) == 1 else "s"))
ffmol.append(fmol)
except:
a99.get_python_logger().exception("Skipping file '{}'".format(fn))
n = len(ffmol)
fout = pyfant.FileMolecules()
fout.titm = "Merge of {} file{}: {}".format(
n, "s" if n != 1 else "",
", ".join([os.path.split(fmol.filename)[1] for fmol in ffmol]))
for fmol in ffmol:
fout.molecules.extend(fmol.molecules)
print("Number of molecules in output: {}".format(len(fout)))
if fn_output is None:
fn_output = a99.new_filename(_PREFIX, ".dat")
fout.save_as(fn_output)
print("Saved file '{}'".format(fn_output))
def make_file_molecules(self, lines):
"""
Builds a FileMolecules object
Args:
lines: in most cases, a DataFile instance, but may be anything, since the molecular
lines data extraction is performed by a particular descendant class.
For example, the HITRAN converter expects a structure from the HAPI
Returns:
f, log: FileMolecules, MolConversionLog instances
"""
# Runs specific conversor to SetOfLines
sols, log = self._make_sols(lines)
assert isinstance(sols, ConvSols)
assert isinstance(log, MolConversionLog)
sols_list = list(sols.values())
sols_list.sort(key= lambda sol: sol.vl*1000+sol.v2l)
mol = pyfant.molconsts_to_molecule(self.molconsts)
mol.sol = sols_list
f = pyfant.FileMolecules()
now = datetime.datetime.now()
f.titm = "PFANT molecular lines file. Created by f311.convmol.Conv.make_file_molecules() @ {}".format(now.isoformat())
f.molecules = [mol]
return f, log
def _open_mol_clicked(self):
filename = self.w_out.value
if len(filename) > 0:
f = pyfant.FileMolecules()
f.load(filename)
vis = pyfant.VisMolecules()
vis.use(f)
def test_FileMolecules(tmpdir):
os.chdir(str(tmpdir))
m = pyfant.Molecule()
sol = pyfant.SetOfLines()
sol.append_line(2000., .25, 10.5, "P")
sol.append_line(1000., .25, 10.5, "Q1")
m.sol = [sol]
sol = pyfant.SetOfLines()
sol.append_line(3000., .125, 13.5, "R21")
m.sol.append(sol)
f = pyfant.FileMolecules()
f.molecules = [m]
assert f.llzero == 1000.
assert f.llfin == 3000.
assert f.num_lines == 3
assert f.num_sols == 2
f.lmbdam
f.sj
f.jj
f.branch
f.qqv
f.ggv
f.bbv
f.ddv
f.fe
f.do
f.mm
f.am
f.ua
f.ub
f.te
f.cro
f.s
f.cut(500, 1500)
assert f.num_lines == 1
assert f.num_sols == 1
m.symbols = ["We", "Ur"]
assert m.formula == "WeUr"
f.save_as("qq")
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=a99.SmartFormatter)
parser.add_argument('llzero',
type=float,
nargs=1,
help='lower wavelength boundary (angstrom)')
parser.add_argument('llfin',
type=float,
nargs=1,
help='upper wavelength boundary (angstrom)')
parser.add_argument('fn_input', type=str, help='input file name', nargs=1)
parser.add_argument('fn_output',
type=str,
help='output file name',
nargs=1)
args = parser.parse_args()
file_molecules = pyfant.FileMolecules()
file_molecules.load(args.fn_input[0])
lmbdam = file_molecules.lmbdam
m, M = min(lmbdam), max(lmbdam)
print("Original interval: [%g, %g]" % (m, M))
print("New interval: [%g, %g]" % (args.llzero[0], args.llfin[0]))
file_molecules.cut(args.llzero[0], args.llfin[0])
file_molecules.save_as(args.fn_output[0])
print("Successfully created file '%s'" % args.fn_output[0])
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('fn1', type=str, help='input file name', nargs=1)
parser.add_argument('fn2', type=str, help='output file name', nargs=1)
args = parser.parse_args()
fn1 = args.fn1[0]
fn2 = args.fn2[0]
fa = pyfant.FileMolecules()
fa.load(fn1)
fb = pyfant.FileMolecules()
fb.load(fn2)
data = []
header = [fn1, fn2]
def append_data(objname, attrname, value0, value1):
"""Appends difference"""
data.append([
"{}.{} = {}".format(objname, attrname, value0),
"{}.{} = {}".format(objname, attrname, value1)
])
c.conf.opt.no_h = True
c.conf.opt.no_atoms = True
c.conf.opt.allow = True
c.conf.opt.fwhm = 0.14
return c
if __name__ == "__main__":
print("loading '{}'...".format(FN_OBS))
sp = f311.load_spectrum(FN_OBS)
sp_lam_min = min(sp.wavelength)
sp_lam_max = max(sp.wavelength)
c = get_combo()
f = pyfant.FileMolecules()
f.load(c.conf.opt.fn_molecules)
formulas = Counter()
jobs = []
for molecule in f:
llzero = max(sp_lam_min, min(molecule.lmbdam))
llfin = min(sp_lam_max, max(molecule.lmbdam))
if llzero >= llfin:
print(
"Molecule {} - {} skipped because of wavelength range being out of that of observed spectrum"
.format(molecule.formula, molecule.description))
f1 = pyfant.FileMolecules()
f1.molecules.append(molecule)
#!/usr/bin/env python
"""Molecular lines file editor."""
import sys
import argparse
import logging
import pyfant
import a99
if __name__ == "__main__":
a99.logging_level = logging.INFO
a99.flag_log_file = True
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=a99.SmartFormatter)
parser.add_argument('fn',
type=str,
help='molecules file name',
default=pyfant.FileMolecules.default_filename,
nargs='?')
args = parser.parse_args()
m = pyfant.FileMolecules()
m.load(args.fn)
app = a99.get_QApplication([])
form = pyfant.XFileMolecules()
form.show()
form.load(m)
sys.exit(app.exec_())
"""Runs synthesis for molecular species separately. No atomic nor hydrogen lines."""
import matplotlib.pyplot as plt
import a99
import pyfant
import f311
SUBPLOT_NUM_ROWS = 2
SUBPLOT_NUM_COLS = 2
if __name__ == "__main__":
pyfant.copy_star(starname="sun-grevesse-1996")
pyfant.link_to_data()
# Loads full molecular lines file
fmol = pyfant.FileMolecules()
fmol.load()
runnables = []
for molecule in fmol:
fmol2 = pyfant.FileMolecules()
fmol2.molecules = [molecule]
ecombo = pyfant.Combo()
# Overrides file "molecules.dat" with in-memory object
ecombo.conf.file_molecules = fmol2
ecombo.conf.flag_output_to_dir = True
oo = ecombo.conf.opt
# Assigns synthesis range to match atomic lines range
oo.llzero, oo.llfin = fmol2.llzero, fmol2.llfin
# Turns off hydrogen lines