def test_run_parallel(tmpdir):
os.chdir(str(tmpdir))
pyfant.copy_star(pyfant.get_pfant_data_path('arcturus'))
pyfant.link_to_data(pyfant.get_pfant_data_path("common"))
cc = []
c = pyfant.Combo()
c.conf.flag_output_to_dir = True
cc.append(c)
c = pyfant.Combo()
c.conf.flag_output_to_dir = True
cc.append(c)
pyfant.run_parallel(cc, flag_console=False)
def el_multirun(elm):
#separating each line from atom data
atomtrim = pf.FileAtoms()
atomtrim.load(atomdata)
atomtrim.cut(mainfile.llzero, mainfile.llfin)
atomel = pf.FileAtoms()
atomel.atoms = [a for a in atomtrim.atoms if a.elem == pf.adjust_atomic_symbol(elm)]
speclines = []
line_num_specs = []
#configuring multi-running for each line
el_combos = []
for atom in atomel.atoms:
for line in atom.lines:
singline = pf.FileAtoms()
a = copy.copy(atom)
a.lines = [line]
singline.atoms = [a]
cm = pf.Combo([pf.FOR_PFANT, pf.FOR_NULBAD])
cm.conf.flag_output_to_dir = True
cm.conf.flag_log_console = False
cm.conf.opt.no_molecules = True
cm.conf.opt.absoru = True
cm.conf.opt.opa = False
cm.conf.file_main = mainfile
cm.conf.file_abonds = abondsfile
cm.conf.file_atoms = singline
cm.conf.file_main = mainfile
cm.conf.opt.fn_cv = cm.conf.file_main.flprefix + ".norm.nulbad.%5.3f" % mainfile.fwhm
el_combos.append(cm)
#run pfant-multi
pf.run_parallel(el_combos, flag_console=False)
#load results and save spectra into lists
i = 0
for atom in atomel.atoms:
for line in atom.lines:
pl = el_combos[i].pfant
n = el_combos[i].nulbad
n.load_result()
n.convolved.filename = str(line.lambda_)
speclines.append(n.convolved)
lbdfluxpec = [n.convolved.x, n.convolved.y]
line_num_specs.append(lbdfluxpec)
pl.conf.sid.clean()
i += 1
return speclines, line_num_specs
def get_combo():
c = pyfant.Combo(["pfant", "nulbad"])
if os.path.isfile(pyfant.FileOptions.default_filename):
opt = pyfant.FileOptions()
opt.load()
c.conf.opt = opt
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
def __submit_job(self):
import pyfant as pf
r = pyfant.Combo()
if self.checkbox_custom_id.isChecked():
custom_id = self.__get_custom_session_id()
r.conf.sid.id = custom_id
if _get_custom_dirname(custom_id) == custom_id:
# Understands that session dirname prefix must be cleared
r.sid.id_maker.session_prefix_singular = ""
r.conf.opt = copy.copy(self.oe.f)
r.conf.file_main = self.me.f
r.conf.file_abonds = self.ae.f
r.conf.file_dissoc = self.ae.f.get_file_dissoc()
r.conf.flag_output_to_dir = True
self._rm.add_runnables([r])
a99.logging_level = logging.INFO
a99.flag_log_file = True
if __name__ == "__main__":
parser = argparse.ArgumentParser(description=__doc__,
formatter_class=a99.SmartFormatter)
names = pyfant.Conf().opt.get_names() # option names
for name in names:
# name = name.replace('_', '-')
parser.add_argument("--" + name, type=str, help='')
args = parser.parse_args()
# Configuration for Python logging messages.
logger = a99.get_python_logger()
c = pyfant.Combo()
c.conf.flag_log_file = True # Configuration for Fortran messages
c.conf.flag_log_console = True # "
c.conf.flag_output_to_dir = False # Will generate outputs in current directory
for name in names:
x = args.__getattribute__(name)
if x is not None:
c.conf.opt.__setattr__(name, x)
c.run()
logger.info("Session directory: %s" % c.conf.sid.dir)
"""Runs synthesis over large wavelength range, then plots continuum"""
import pyfant
import f311
import matplotlib.pyplot as plt
import a99
if __name__ == "__main__":
# Copies files main.dat and abonds.dat to local directory (for given star)
pyfant.copy_star(starname="sun-grevesse-1996")
# Creates symbolic links to all non-star-specific files, such as atomic & molecular lines,
# partition functions, etc.
pyfant.link_to_data()
# Creates object that will run the four Fortran executables (innewmarcs, hydro2, pfant, nulbad)
obj = pyfant.Combo()
oo = obj.conf.opt
# synthesis interval start (angstrom)
oo.llzero = 2500
# synthesis interval end (angstrom)
oo.llfin = 30000
# savelength step (angstrom)
oo.pas = 1.
# Turns off hydrogen lines
oo.no_h = True
# Turns off atomic lines
oo.no_atoms = True
# Turns off molecular lines
oo.no_molecules = True
obj.run()
pyfant.copy_star(starname="sun-grevesse-1996")
pyfant.link_to_data()
# Loads full atomic lines file
fatoms = pyfant.FileAtoms()
fatoms.load()
runnables = []
for elem_ioni in MY_SPECIES:
atom = fatoms.find_atom(elem_ioni)
# Creates atomic lines file object containing only one atom
fatoms2 = pyfant.FileAtoms()
fatoms2.atoms = [atom]
ecombo = pyfant.Combo()
# Overrides file "atoms.dat" with in-memory object
ecombo.conf.file_atoms = fatoms2
ecombo.conf.flag_output_to_dir = True
oo = ecombo.conf.opt
# Assigns synthesis range to match atomic lines range
oo.llzero, oo.llfin = fatoms2.llzero, fatoms2.llfin
# Turns off hydrogen lines
oo.no_h = True
# Turns off molecular lines
oo.no_molecules = True
runnables.append(ecombo)
pyfant.run_parallel(runnables)
def test_run_combo(tmpdir):
os.chdir(str(tmpdir))
pyfant.copy_star(pyfant.get_pfant_data_path('arcturus'))
pyfant.link_to_data(pyfant.get_pfant_data_path("common"))
c = pyfant.Combo()
c.run()
# logger.info("%d abundance(s) changed" % cnt)
# ## Creates the Runnable instances
PAS = 0.04
logger.info("Calculation step will be set to %g" % PAS)
logger.info("Preparing pfant's...")
combos, ll, i = [], [], 0
ii = 0
n = file_atoms.num_lines
for atom in file_atoms.atoms:
for line in atom.lines:
a = copy.copy(atom) # shallow copy
a.lines = [line]
f = pyfant.FileAtoms()
f.atoms = [a]
combo = pyfant.Combo([pyfant.FOR_PFANT])
# Fortran messages will not be displayed in terminal
combo.conf.flag_log_console = False
combo.conf.sid.flag_split_dirs = True
# Forces pfant to run one single iteration (ikeytot will be =1)
combo.conf.opt.aint = args.max + 10
combo.conf.file_atoms = f
combo.conf.file_abonds = fa
combo.conf.opt.logging_level = "warning"
combo.conf.opt.pas = PAS
combo.conf.flag_output_to_dir = True
combo.conf.opt.zinf = args.max
combo.conf.opt.no_molecules = True
combo.conf.opt.opa = False
combo.conf.opt.no_h = True
# Note that half of the line (needs to)/(will be) calculated
def __run(self):
# Called from run() to lower one indentation lever.
# **Note** If something is not right here: *raise*.
#
# **Note** It plays around with Conf, SID, IdMaker objects
import pyfant as pf
# # Preparation
self.__status.stage = "preparing"
if self.__custom_id:
self.__sid.id = self.__custom_id
else:
self.__sid.make_id()
# This id maker will create directories inside the
# multi-session directory.
# It will replace the Pfant's default id maker
custom_id_maker = pyfant.IdMaker()
custom_id_maker.session_prefix_singular = os.path.join(
self.__sid.dir, "session-")
# # Runs innewmarcs and hydro2
ih = pyfant.Combo([pyfant.FOR_INNEWMARCS, pyfant.FOR_HYDRO2])
ih.conf.flag_output_to_dir = True
ih.conf.logger = self.__logger
ih.conf.opt = copy.copy(self.__options)
ih.conf.sid = self.__sid
ih.conf.file_main = copy.copy(self.__file_main)
# Runs innewmarcs and hydro2;
# it is also expected to create the "multi-session" directory
ih.run()
####
# # Runs pfant, pfant creates several .norm files
self.__status.stage = "pfant stage"
self.__logger.info("+++ pfant stage...")
pfant_list = []
symbols = list(self.__file_abxfwhm.ab.keys())
abdiffss = list(self.__file_abxfwhm.ab.values())
n_abdif = len(abdiffss[0])
fwhms = self.__file_abxfwhm.get_fwhms()
for fwhm in fwhms:
if fwhm > 9.99:
raise RuntimeError("fhwm maximum is 9.99")
for j in range(n_abdif):
file_abonds_ = copy.deepcopy(self.__file_abonds)
for i, symbol in enumerate(symbols):
found = False
for k in range(len(file_abonds_.ele)):
if file_abonds_.ele[k] == symbol:
abdif = abdiffss[i][j]
file_abonds_.abol[k] += abdif
self.__logger.debug(j, " - ", symbol, "with abundance",
file_abonds_.abol[k])
found = True
if not found:
raise RuntimeError("Atom '%s' not found" % symbol)
pfant_name = self.__file_abxfwhm.pfant_names[j] \
if self.__file_abxfwhm.pfant_names \
else "%02d" % j
flprefix = "%s_%s" % (self.__file_main.titrav, pfant_name)
pfant = pyfant.Pfant()
pfant.conf.flag_output_to_dir = False
pfant.conf.opt = copy.copy(self.__options)
pfant.conf.rename_outputs(
[pyfant.FOR_INNEWMARCS, pyfant.FOR_HYDRO2], sid=self.sid)
pfant.conf.sid.id_maker = custom_id_maker
pfant.conf.sid.id = flprefix
pfant.conf.opt.flprefix = self.__sid.join_with_session_dir(
flprefix)
pfant.conf.file_main = copy.copy(self.__file_main)
pfant.conf.file_abonds = file_abonds_
pfant.conf.file_dissoc = file_abonds_.get_file_dissoc()
self.__logger.debug("LOOK FLPREFIX " +
str(pfant.conf.opt.flprefix))
pfant_list.append(pfant)
rm = self.__runnable_manager = pyfant.RunnableManager()
pyfant.run_parallel(pfant_list,
flag_console=False,
runnable_manager=rm)
if self._flag_killed:
return
if not rm.flag_success:
raise RuntimeError("Not all pfant's succeeded running.")
####
# # Runs nulbad, saves .sp and .spl files
# function to convert given FWHM to string to use as part of a file name
fmt_fwhm = lambda x: "%03d" % round(x * 100)
# ## Prepares nulbad's
nulbad_list = []
sp_filenames_by_fwhm = {
} # dictionary containing a list of .sp filenames for each FWHM
for pfant in pfant_list:
# prefix is sth like: multi-session-1/Sun_00
prefix = pfant.conf.opt.flprefix
for fwhm in fwhms:
nulbad = pyfant.Nulbad()
nulbad.conf.flag_output_to_dir = False
nulbad.conf.sid.id_maker = custom_id_maker
nulbad.conf.opt = copy.copy(self.__options)
nulbad.conf.opt.fn_flux = pfant.conf.opt.flprefix + ".norm"
nulbad.conf.opt.fwhm = fwhm
nulbad.conf.opt.fn_cv = "%s_%s.sp" % (prefix, fmt_fwhm(fwhm))
nulbad_list.append(nulbad)
if not fwhm in sp_filenames_by_fwhm:
sp_filenames_by_fwhm[fwhm] = []
sp_filenames_by_fwhm[fwhm].append(nulbad.conf.opt.fn_cv)
# ## Saves files for lineplot.py (lists of spectra)
# Each item of each list is a full path to a spectrum file
for fwhm, sp_filenames in list(sp_filenames_by_fwhm.items()):
spl_filename = os.path.join(self.__sid.dir,
"cv_%s.spl" % fmt_fwhm(fwhm))
with open(spl_filename, "w") as h:
for sp_filename in sp_filenames:
h.write(
os.path.abspath(
os.path.join(self.__sid.dir,
os.path.basename(sp_filename) +
"\n")))
# ## Runs nulbads
self.__status.stage = "nulbad stage"
self.__logger.info("+++ nulbad stage...")
rm = self.__runnable_manager = pyfant.RunnableManager()
pyfant.run_parallel(nulbad_list,
flag_console=False,
runnable_manager=rm)
if self._flag_killed:
return
if not rm.flag_success:
raise RuntimeError("Not all nulbad's succeeded running.")
####
# # Deletes session-* directories if successful
FLAG_CLEAN = True
if FLAG_CLEAN:
self.__logger.info("+++ Cleaning up...")
for pfant in pfant_list:
pfant.sid.clean()
for nulbad in nulbad_list:
nulbad.sid.clean()
else:
self.__logger.info("+++ NOT cleaning up...")