def testread(self):
# Section with digit
lines = ['[1section1]', 'option=value1', 'option2=value2',
'[section2]', 'option3=value3', 'option4=value4']
sobj = StringIO('\n'.join(lines))
c = ConfigParser()
self.assertRaises(IOError, c.read, sobj, False)
# Option with digit
lines = ['[section1]', '1option=value1', 'option2=value2',
'[section2]', 'option3=value3', 'option4=value4']
sobj = StringIO('\n'.join(lines))
c = ConfigParser()
self.assertRaises(IOError, c.read, sobj, False)
# Skip
lines = ['[1section1]', 'option=value1', 'option2=value2',
'[section2]', '1option3=value3', 'option4=value4']
sobj = StringIO('\n'.join(lines))
c = ConfigParser()
c.read(sobj, ignore_errors=True)
self.assertEqual(1, len(list(c)))
self.assertTrue('section2' in c)
self.assertTrue('option4' in c.section2)
def write(self):
dirpath = os.path.join(os.path.expanduser('~'), '.pymontecarlo')
if not os.path.exists(dirpath):
os.mkdir(dirpath)
with open(os.path.join(dirpath, 'settings.cfg'), 'w') as fileobj:
ConfigParser.write(self, fileobj)
reload_settings()
def load(cls, source):
"""
Loads results from a results ZIP.
:arg source: filepath or file-object
:return: results container
"""
zipfile = ZipFile(source, 'r')
# Check version
if zipfile.comment != 'version=%s' % VERSION:
raise IOError, "Incorrect version of results. Only version %s is accepted" % \
VERSION
# Read compositions
reader = csv.reader(zipfile.open('compositions.csv', 'r'))
header = reader.next()
zs = map(int, header[1:])
compositions = []
for row in reader:
wfs = map(float, row[1:])
composition = defaultdict(float)
composition.update(dict(zip(zs, wfs)))
compositions.append(composition)
# Read stats
config = ConfigParser()
config.read(zipfile.open('stats.cfg', 'r'))
section = config.stats
elapsed_time_s = float(section.elapsed_time_s)
iterations = int(section.iterations)
max_iterations = int(section.max_iterations)
iterator = section.iterator
convergor = section.convergor
assert iterations == len(compositions)
zipfile.close()
return cls(compositions, elapsed_time_s, max_iterations,
iterator, convergor)
def load(cls, source):
"""
Loads results from a results ZIP.
:arg source: filepath or file-object
:return: results container
"""
zipfile = ZipFile(source, 'r')
# Check version
if zipfile.comment != 'version=%s' % VERSION:
raise IOError, "Incorrect version of results. Only version %s is accepted" % \
VERSION
# Read compositions
reader = csv.reader(zipfile.open('compositions.csv', 'r'))
header = reader.next()
zs = map(int, header[1:])
compositions = []
for row in reader:
wfs = map(float, row[1:])
composition = defaultdict(float)
composition.update(dict(zip(zs, wfs)))
compositions.append(composition)
# Read stats
config = ConfigParser()
config.read(zipfile.open('stats.cfg', 'r'))
section = config.stats
elapsed_time_s = float(section.elapsed_time_s)
iterations = int(section.iterations)
max_iterations = int(section.max_iterations)
iterator = section.iterator
convergor = section.convergor
assert iterations == len(compositions)
zipfile.close()
return cls(compositions, elapsed_time_s, max_iterations, iterator,
convergor)
def setUp(self):
TestCase.setUp(self)
lines = ['[section1]', 'option1=value1', 'option2=value2',
'[section2]', 'option3=value3', 'option4=value4']
sobj = StringIO('\n'.join(lines))
self.c = ConfigParser()
self.c.read(sobj)
def _update_noversion(self, filepath):
logging.debug('Updating from "no version"')
oldzip = ZipFile(filepath, 'r')
newzip = ZipFile(filepath + ".new", 'w')
# Update keys.ini
config = ConfigParser()
fp = oldzip.open(KEYS_INI_FILENAME, 'r')
config.read(StringIO(fp.read().decode('ascii')))
for section, option, value in config:
value = value.replace('pymontecarlo.result.base.result.', '')
setattr(getattr(config, section), option, value)
fp = StringIO()
config.write(fp)
newzip.writestr(KEYS_INI_FILENAME, fp.getvalue())
# Add other files to new zip
for zipinfo in oldzip.infolist():
if zipinfo.filename == KEYS_INI_FILENAME:
continue
data = oldzip.read(zipinfo)
newzip.writestr(zipinfo, data)
# Add version
newzip.comment = b'version=2'
oldzip.close()
newzip.close()
# Remove old zip and replace with new one
os.remove(filepath)
os.rename(filepath + ".new", filepath)
return self._update_version2(filepath)
def _update_version1(self, filepath):
logging.debug('Updating from "version 1"')
oldzip = ZipFile(filepath, 'r')
newzip = ZipFile(filepath + ".new", 'w')
# Update stats.cfg
config = ConfigParser()
config.read(oldzip.open('stats.cfg', 'r'))
limit = config.stats.convergence_limit
del config.stats.convergence_limit
config.stats.convergor = '<CompositionConvergor(limit=%s)>' % limit
fp = StringIO()
config.write(fp)
newzip.writestr('stats.cfg', fp.getvalue())
# Add other files to new zip
for zipinfo in oldzip.infolist():
if zipinfo.filename == 'stats.cfg':
continue
data = oldzip.read(zipinfo)
newzip.writestr(zipinfo, data)
# Add version
newzip.comment = 'version=%s' % VERSION
oldzip.close()
newzip.close()
# Remove old zip and replace with new one
os.remove(filepath)
os.rename(filepath + ".new", filepath)
return filepath
def save(self, source):
"""
Saves results in a results ZIP.
:arg source: filepath or file-object
"""
zipfile = ZipFile(source, 'w', compression=ZIP_DEFLATED)
zipfile.comment = 'version=%s' % VERSION
# Save compositions
fp = StringIO()
writer = csv.writer(fp)
zs = self._compositions[0].keys()
writer.writerow(['iteration'] + zs)
for i, composition in enumerate(self._compositions):
writer.writerow([i + 1] + [composition.get(z, 0.0) for z in zs])
zipfile.writestr('compositions.csv', fp.getvalue())
# Save stats
config = ConfigParser()
section = config.add_section('stats')
section.elapsed_time_s = self.elapsed_time_s
section.iterations = self.iterations
section.max_iterations = self.max_iterations
section.iterator = self.iterator
section.convergor = self.convergor
fp = StringIO()
config.write(fp)
zipfile.writestr('stats.cfg', fp.getvalue())
zipfile.close()
def save(self, source):
"""
Saves results in a results ZIP.
:arg source: filepath or file-object
"""
zipfile = ZipFile(source, 'w', compression=ZIP_DEFLATED)
zipfile.comment = 'version=%s' % VERSION
# Save compositions
fp = StringIO()
writer = csv.writer(fp)
zs = self._compositions[0].keys()
writer.writerow(['iteration'] + zs)
for i, composition in enumerate(self._compositions):
writer.writerow([i + 1] + [composition.get(z, 0.0) for z in zs])
zipfile.writestr('compositions.csv', fp.getvalue())
# Save stats
config = ConfigParser()
section = config.add_section('stats')
section.elapsed_time_s = self.elapsed_time_s
section.iterations = self.iterations
section.max_iterations = self.max_iterations
section.iterator = self.iterator
section.convergor = self.convergor
fp = StringIO()
config.write(fp)
zipfile.writestr('stats.cfg', fp.getvalue())
zipfile.close()
def _update_version1(self, filepath):
logging.debug('Updating from "version 1"')
oldzip = ZipFile(filepath, 'r')
newzip = ZipFile(filepath + ".new", 'w')
# Update stats.cfg
config = ConfigParser()
config.read(oldzip.open('stats.cfg', 'r'))
limit = config.stats.convergence_limit
del config.stats.convergence_limit
config.stats.convergor = '<CompositionConvergor(limit=%s)>' % limit
fp = StringIO()
config.write(fp)
newzip.writestr('stats.cfg', fp.getvalue())
# Add other files to new zip
for zipinfo in oldzip.infolist():
if zipinfo.filename == 'stats.cfg':
continue
data = oldzip.read(zipinfo)
newzip.writestr(zipinfo, data)
# Add version
newzip.comment = 'version=%s' % VERSION
oldzip.close()
newzip.close()
# Remove old zip and replace with new one
os.remove(filepath)
os.rename(filepath + ".new", filepath)
return filepath
class TestConfigParser(TestCase):
def setUp(self):
TestCase.setUp(self)
lines = ['[section1]', 'option1=value1', 'option2=value2',
'[section2]', 'option3=value3', 'option4=value4']
sobj = StringIO('\n'.join(lines))
self.c = ConfigParser()
self.c.read(sobj)
def tearDown(self):
TestCase.tearDown(self)
def testskeleton(self):
self.assertEqual('value1', self.c.section1.option1)
self.assertEqual('value2', self.c.section1.option2)
self.assertEqual('value3', self.c.section2.option3)
self.assertEqual('value4', self.c.section2.option4)
self.assertRaises(AttributeError, getattr, self.c, 'section3')
self.assertRaises(AttributeError, getattr, self.c.section1, 'option3')
def testread(self):
# Section with digit
lines = ['[1section1]', 'option=value1', 'option2=value2',
'[section2]', 'option3=value3', 'option4=value4']
sobj = StringIO('\n'.join(lines))
c = ConfigParser()
self.assertRaises(IOError, c.read, sobj, False)
# Option with digit
lines = ['[section1]', '1option=value1', 'option2=value2',
'[section2]', 'option3=value3', 'option4=value4']
sobj = StringIO('\n'.join(lines))
c = ConfigParser()
self.assertRaises(IOError, c.read, sobj, False)
# Skip
lines = ['[1section1]', 'option=value1', 'option2=value2',
'[section2]', '1option3=value3', 'option4=value4']
sobj = StringIO('\n'.join(lines))
c = ConfigParser()
c.read(sobj, ignore_errors=True)
self.assertEqual(1, len(list(c)))
self.assertTrue('section2' in c)
self.assertTrue('option4' in c.section2)
def test__contains__(self):
self.assertTrue('section1' in self.c)
self.assertTrue('section2' in self.c)
self.assertFalse('section3' in self.c)
self.assertTrue('option1' in self.c.section1)
self.assertTrue('option2' in self.c.section1)
self.assertFalse('option3' in self.c.section1)
def testwrite(self):
# Add non-string value
self.c.section1.option3 = 1
# Write
output = StringIO()
self.c.write(output)
# Read and test
fp = StringIO(output.getvalue())
parser = SafeConfigParser()
parser.read_file(fp)
self.assertTrue(parser.has_section('section1'))
self.assertTrue(parser.has_option('section1', 'option1'))
self.assertTrue(parser.has_option('section1', 'option2'))
self.assertTrue(parser.has_option('section1', 'option3'))
self.assertEqual('value1', parser.get('section1', 'option1'))
self.assertEqual('value2', parser.get('section1', 'option2'))
self.assertEqual('1', parser.get('section1', 'option3'))
self.assertTrue(parser.has_section('section2'))
self.assertTrue(parser.has_option('section2', 'option3'))
self.assertTrue(parser.has_option('section2', 'option4'))
self.assertEqual('value3', parser.get('section2', 'option3'))
self.assertEqual('value4', parser.get('section2', 'option4'))
def test__setattr__(self):
self.assertEqual('value1', self.c.section1.option1)
self.c.section1.option1 = 'value99'
self.assertEqual('value99', self.c.section1.option1)
def testadd_section(self):
self.c.add_section('section3')
self.assertTrue('section3' in self.c)
def __init__(self):
ConfigParser.__init__(self)
self.add_section('pymontecarlo')
def _update_version3(self, filepath):
logging.debug('Updating from "version 3"')
manager = {}
def _load_photonintensity(zipfile, key):
fp = zipfile.open(key + '.csv', 'r')
reader = csv.reader(StringIO(fp.read().decode('ascii')))
next(reader)
intensities = {}
for row in reader:
transition = from_string(row[0])
# skip row[1] (energy)
intensities[PhotonKey(transition, False, PhotonKey.P)] = \
(float(row[6]), float(row[7]))
intensities[PhotonKey(transition, False, PhotonKey.C)] = \
(float(row[2]), float(row[3]))
intensities[PhotonKey(transition, False, PhotonKey.B)] = \
(float(row[4]), float(row[5]))
intensities[PhotonKey(transition, False, PhotonKey.T)] = \
(float(row[8]), float(row[9]))
intensities[PhotonKey(transition, True, PhotonKey.P)] = \
(float(row[14]), float(row[15]))
intensities[PhotonKey(transition, True, PhotonKey.C)] = \
(float(row[10]), float(row[11]))
intensities[PhotonKey(transition, True, PhotonKey.B)] = \
(float(row[12]), float(row[13]))
intensities[PhotonKey(transition, True, PhotonKey.T)] = \
(float(row[16]), float(row[17]))
return PhotonIntensityResult(intensities)
manager['PhotonIntensityResult'] = _load_photonintensity
def _load_photonspectrum(zipfile, key):
fp = zipfile.open(key + '.csv', 'r')
reader = csv.reader(StringIO(fp.read().decode('ascii')))
next(reader)
energies_eV = []
total_val = []
total_unc = []
background_val = []
background_unc = []
for row in reader:
energies_eV.append(float(row[0]))
total_val.append(float(row[1]))
total_unc.append(float(row[2]))
background_val.append(float(row[3]))
background_unc.append(float(row[4]))
total = np.array([energies_eV, total_val, total_unc]).T
background = np.array([energies_eV, background_val, background_unc]).T
return PhotonSpectrumResult(total, background)
manager['PhotonSpectrumResult'] = _load_photonspectrum
def _load_phirhoz(zipfile, key):
# Find all phi-rho-z files
arcnames = [name for name in zipfile.namelist() if name.startswith(key)]
# Read files
distributions = {}
for arcname in arcnames:
parts = os.path.splitext(arcname)[0].split('+')
transition = from_string(parts[-2].replace('_', ' '))
suffix = parts[-1]
absorption = suffix.startswith('e')
if suffix[1:] == 'nf':
flag = PhotonKey.PRIMARY
elif suffix[1:] == 'cf':
flag = PhotonKey.CHARACTERISTIC_FLUORESCENCE
elif suffix[1:] == 'bf':
flag = PhotonKey.BREMSSTRAHLUNG_FLUORESCENCE
elif suffix[1:] == 't':
flag = PhotonKey.TOTAL
elif suffix[1:] == 'f':
flag = PhotonKey.FLUORESCENCE
key = PhotonKey(transition, absorption, flag)
fp = zipfile.open(arcname, 'r')
reader = csv.reader(StringIO(fp.read().decode('ascii')))
next(reader)
zs = []
values = []
uncs = []
for row in reader:
zs.append(float(row[0]))
values.append(float(row[1]))
uncs.append(float(row[2]))
datum = np.array([zs, values, uncs]).T
distributions[key] = datum
return PhotonDepthResult(distributions)
manager['PhiRhoZResult'] = _load_phirhoz
def _load_time(zipfile, key):
element = xmlutil.parse(zipfile.open(key + '.xml', 'r'))
child = element.find('time')
if child is not None:
simulation_time = float(child.get('val', 0.0))
else:
simulation_time = 0.0
child = element.find('speed')
if child is not None:
simulation_speed = \
float(child.get('val', 0.0)), float(child.get('unc', 0.0))
else:
simulation_speed = (0.0, 0.0)
return TimeResult(simulation_time, simulation_speed)
manager['TimeResult'] = _load_time
def _load_showersstatistics(zipfile, key):
element = xmlutil.parse(zipfile.open(key + '.xml', 'r').read())
child = element.find('showers')
if child is not None:
showers = float(child.get('val', 0))
else:
showers = 0
return ShowersStatisticsResult(showers)
manager['ShowersStatisticsResult'] = _load_showersstatistics
def _load_electronfraction(zipfile, key):
element = xmlutil.parse(zipfile.open(key + '.xml', 'r'))
child = element.find('absorbed')
if child is not None:
absorbed = \
float(child.get('val', 0.0)), float(child.get('unc', 0.0))
else:
absorbed = (0.0, 0.0)
child = element.find('backscattered')
if child is not None:
backscattered = \
float(child.get('val', 0.0)), float(child.get('unc', 0.0))
else:
backscattered = (0.0, 0.0)
child = element.find('transmitted')
if child is not None:
transmitted = \
float(child.get('val', 0.0)), float(child.get('unc', 0.0))
else:
transmitted = (0.0, 0.0)
return ElectronFractionResult(absorbed, backscattered, transmitted)
manager['ElectronFractionResult'] = _load_electronfraction
def _load_trajectory(zipfile, key):
tmpdir = tempfile.mkdtemp()
filename = key + '.h5'
zipfile.extract(filename, tmpdir)
hdf5file = h5py.File(os.path.join(tmpdir, filename))
particles_ref = list(PARTICLES)
particles_ref = dict(zip(map(str, particles_ref), particles_ref))
collisions_ref = list(COLLISIONS)
collisions_ref = dict(zip(map(str, collisions_ref), collisions_ref))
trajectories = []
for dataset in hdf5file['trajectories'].values():
primary = bool(dataset.attrs['primary'])
particle = particles_ref.get(dataset.attrs['particle'].decode('ascii'))
collision = collisions_ref.get(dataset.attrs['collision'].decode('ascii'))
exit_state = int(dataset.attrs['exit_state'])
interactions = dataset[:]
trajectory = Trajectory(primary, particle, collision,
exit_state, interactions)
trajectories.append(trajectory)
hdf5file.close()
shutil.rmtree(tmpdir, ignore_errors=True)
return TrajectoryResult(trajectories)
manager['TrajectoryResult'] = _load_trajectory
def _load_backscatteredelectronenergy(zipfile, key):
data = np.loadtxt(zipfile.open(key + '.csv', 'r'), delimiter=',')
return BackscatteredElectronEnergyResult(data)
manager['BackscatteredElectronEnergyResult'] = _load_backscatteredelectronenergy
def _load_transmittedelectronenergy(zipfile, key):
data = np.loadtxt(zipfile.open(key + '.csv', 'r'), delimiter=',')
return TransmittedElectronEnergyResult(data)
manager['TransmittedElectronEnergyResult'] = _load_transmittedelectronenergy
# Create HDF5
newfilepath = os.path.splitext(filepath)[0] + '.h5'
hdf5file = h5py.File(newfilepath, 'w')
hdf5file.attrs['version'] = b'4'
zipfile = ZipFile(filepath, 'r', allowZip64=True)
## Read options
try:
zipinfo = zipfile.getinfo(OPTIONS_FILENAME)
except KeyError:
raise IOError("Zip file (%s) does not contain a %s" % \
(filepath, OPTIONS_FILENAME))
with zipfile.open(zipinfo, 'r') as fp:
source = fp.read()
source = _update_options(source)
hdf5file.attrs['options'] = source
## Parse keys.ini
try:
zipinfo = zipfile.getinfo(KEYS_INI_FILENAME)
except KeyError:
raise IOError("Zip file (%s) does not contain a %s" % \
(filepath, KEYS_INI_FILENAME))
config = ConfigParser()
config.read(StringIO(zipfile.open(zipinfo, 'r').read().decode('ascii')))
## Load each results
items = list(getattr(config, SECTION_KEYS))
for key, tag in items:
loader = manager[tag]
result = loader(zipfile, key)
handler = find_convert_handler('pymontecarlo.fileformat.results.result', result)
group = hdf5file.create_group(key)
handler.convert(result, group)
zipfile.close()
hdf5file.close()
# Create raw ZIP
oldzip = ZipFile(filepath, 'r')
if any([filename.startswith('raw/') for filename in oldzip.namelist()]):
zipfilepath = os.path.splitext(filepath)[0] + '_raw.zip'
newzip = ZipFile(zipfilepath, 'w', compression=ZIP_DEFLATED)
for filename in oldzip.namelist():
if not filename.startswith('raw/'): continue
data = oldzip.read(filename)
newzip.writestr(filename[4:], data)
newzip.close()
oldzip.close()
return self._update_version4(newfilepath)