def _read_log(self, path):
"""
Returns the last line of the :file:`penepma.csv` log file as a
:class:`dict` where the keys are the header of each column and the
values are the values of the last line.
:arg path: directory containing the simulation files
"""
filepath = os.path.join(path, 'penepma-res.dat')
if not os.path.exists(filepath):
raise ImporterException("Data file %s cannot be found" % filepath)
log = {}
with open(filepath, 'r') as fp:
for line in fp:
line = line.strip()
match = re.match(r'([^.]*) [\.]+ ([^ ]*)(?: \+\- )?([^ ]*)?',
line)
if not match:
continue
name = match.group(1).strip()
val = float(match.group(2))
unc = float(match.group(3) or 0.0)
log[name] = (val, unc)
return log
def _import_trajectory(self, options, key, detector, dirpath, *args,
**kwargs):
filepath = os.path.join(dirpath, 'pe-trajectories.dat')
if not os.path.exists(filepath):
raise ImporterException("Data file %s cannot be found" % filepath)
trajectories = {}
index = 0
primary = None
particle = None
collision = None
exit_state = None
interactions = []
with open(filepath, 'r') as fp:
for line in fp:
line = line.strip()
if not line or line.startswith("#"):
continue
if line == '0' * 80:
if index <= 0:
continue
traj = Trajectory(primary, particle, collision, exit_state,
np.array(interactions))
trajectories[index] = traj
primary = None
particle = None
collision = None
exit_state = None
interactions = []
elif line == '1' * 80:
continue
elif line.startswith('TRAJ'):
index = int(line.split()[1])
elif line.startswith('KPAR'):
particle = _PARTICLES_REF[int(line.split()[1])]
elif line.startswith('PARENT'):
primary = int(line.split()[1]) == 0
elif line.startswith('ICOL'):
collision = _COLLISIONS_REF[particle].get(
int(line.split()[1]), NO_COLLISION)
elif line.startswith('EXIT'):
exit_state = int(line.split()[1])
else:
values = line.split()
x = float(values[0]) * 0.01 # cm to m
y = float(values[1]) * 0.01 # cm to m
z = float(values[2]) * 0.01 # cm to m
e = float(values[3])
c = int(_COLLISIONS_REF[particle].get(
int(values[6]), NO_COLLISION))
interactions.append([x, y, z, e, c])
return TrajectoryResult(trajectories.values())
def _import_transmitted_electron_energy(self, options, key, detector, path,
*args):
filepath = os.path.join(path, 'pe-energy-el-down.dat')
if not os.path.exists(filepath):
raise ImporterException("Data file %s cannot be found" % filepath)
# Load distributions
bins, vals, uncs = _load_dat_files(filepath)
data = np.array([bins, vals, uncs]).T
return TransmittedElectronEnergyResult(data)
def _import_photon_spectrum(self, options, key, detector, path,
phdets_key_index, phdets_index_keys, *args):
index = phdets_key_index[key] + 1
# Find data files
spect_filepath = os.path.join(path,
'pe-spect-%s.dat' % str(index).zfill(2))
if not os.path.exists(spect_filepath):
raise ImporterException("Data file %s cannot be found" %
spect_filepath)
# Load total spectrum
energies, total_val, total_unc = _load_dat_files(spect_filepath)
total = np.array([energies, total_val, total_unc]).T
# Generate fake background
background = np.zeros(total.shape)
background[:, 0] = energies
return PhotonSpectrumResult(total, background)
def _import_photon_intensity(self, options, name, detector, jobdir):
intensities_filepath = os.path.join(jobdir, 'intensities_%s.csv' % name)
if not os.path.exists(intensities_filepath):
raise ImporterException('Result file "intensites_%s.csv" not found in job directory (%s)' % \
(name, jobdir))
intensities = {}
with open(intensities_filepath, 'r') as fp:
reader = csv.DictReader(fp, delimiter=';')
try:
row = next(reader)
except StopIteration:
row = {}
for transition, intensity in row.items():
transition = from_string(transition.strip())
enf = (float(intensity.strip().replace(',', '.')), 0.0) # FIXME: Hack to handle locale problem
intensities[PhotonKey(transition, True, PhotonKey.P)] = enf
return PhotonIntensityResult(intensities)
def _import_phi_z(self, options, name, detector, jobdir):
prz_filepath = os.path.join(jobdir, 'phi_%s.csv' % name)
if not os.path.exists(prz_filepath):
raise ImporterException('Result file "phi_%s.csv" not found in job directory (%s)' % \
(name, jobdir))
with open(prz_filepath, 'r') as fp:
reader = csv.reader(fp, delimiter=';')
header = next(reader)
data = {}
for row in reader:
for i, val in enumerate(row):
data.setdefault(header[i], []).append(float(val.replace(',', '.'))) # FIXME: Hack to handle locale problem
rzs = np.array(data.pop('rho z'))
distributions = {}
for transition, values in data.items():
transition = from_string(transition.strip())
enf = np.array([rzs, values]).transpose()
distributions[PhotonKey(transition, True, PhotonKey.P)] = enf
return PhiZResult(distributions)
def _import_photon_intensity(self, options, key, detector, path,
phdets_key_index, phdets_index_keys, *args):
def _read_intensities_line(line):
values = line.split()
try:
z = int(values[0])
src = Subshell(z, iupac=values[2].strip())
dst = Subshell(z, iupac=values[1].strip())
transition = Transition(z, src, dst)
except ValueError: # transition not supported
return None, 0.0, 0.0, 0.0, 0.0
nf = float(values[4]), float(values[5])
cf = float(values[6]), float(values[7])
bf = float(values[8]), float(values[9])
#tf = float(values[10]), float(values[11]) # skip not needed
t = float(values[12]), float(values[13])
return transition, cf, bf, nf, t
index = phdets_key_index[key] + 1
# Find data files
emitted_filepath = os.path.join(
path, 'pe-intens-%s.dat' % str(index).zfill(2))
if not os.path.exists(emitted_filepath):
raise ImporterException("Data file %s cannot be found" %
emitted_filepath)
generated_filepath = os.path.join(path, 'pe-gen-ph.dat')
if not os.path.exists(generated_filepath):
raise ImporterException("Data file %s cannot be found" %
generated_filepath)
# Load generated
intensities = {}
with open(generated_filepath, 'r') as fp:
for line in fp:
line = line.strip()
if line.startswith('#'): continue
transition, gcf, gbf, gnf, gt = _read_intensities_line(line)
if transition is None:
continue
intensities[PhotonKey(transition, False, PhotonKey.C)] = gcf
intensities[PhotonKey(transition, False, PhotonKey.B)] = gbf
intensities[PhotonKey(transition, False, PhotonKey.P)] = gnf
intensities[PhotonKey(transition, False, PhotonKey.T)] = gt
# Load emitted
with open(emitted_filepath, 'r') as fp:
for line in fp:
line = line.strip()
if line.startswith('#'): continue
transition, ecf, ebf, enf, et = _read_intensities_line(line)
if transition is None:
continue
intensities[PhotonKey(transition, True, PhotonKey.C)] = ecf
intensities[PhotonKey(transition, True, PhotonKey.B)] = ebf
intensities[PhotonKey(transition, True, PhotonKey.P)] = enf
intensities[PhotonKey(transition, True, PhotonKey.T)] = et
return PhotonIntensityResult(intensities)