def photon_sampling_setup(mesh, phtn_src, tags):
"""This function reads in an ALARA photon source file and creates and tags
photon source densities onto a Mesh object for the second R2S transport
step.
Parameters
----------
mesh : PyNE Mesh
The object containing the mesh instance to be tagged.
phtn_src : str
The path of the ALARA phtn_file.
tags: dict
A dictionary were the keys are tuples with two values. The first is a
string denoting an nuclide in any form that is understood by
pyne.nucname (e.g. '1001', 'U-235', '242Am') or 'TOTAL' for all
nuclides. The second is a string denoting the decay time as it appears
in the phtn_src file (e.g. 'shutdown', '1 h' '3 d'). The values of the
dictionary are the requested tag names for the combination of nuclide
and decay time. These tag names should be the tag names that are read
by the sampling subroutine. For example:
tags = {('U-235', 'shutdown'): 'tag1', ('TOTAL', '1 h'): 'tag2'}
"""
photon_source_to_hdf5(phtn_src)
h5_file = phtn_src + ".h5"
photon_source_hdf5_to_mesh(mesh, h5_file, tags)
def photon_sampling_setup(mesh, phtn_src, tags):
"""This function reads in an ALARA photon source file and creates and tags
photon source densities onto a Mesh object for the second R2S transport
step.
Parameters
----------
mesh : PyNE Mesh
The object containing the iMesh instance to be tagged.
phtn_src : str
The path of the ALARA phtn_file.
tags: dict
A dictionary were the keys are tuples with two values. The first is a
string denoting an nuclide in any form that is understood by
pyne.nucname (e.g. '1001', 'U-235', '242Am') or 'TOTAL' for all
nuclides. The second is a string denoting the decay time as it appears
in the phtn_src file (e.g. 'shutdown', '1 h' '3 d'). The values of the
dictionary are the requested tag names for the combination of nuclide
and decay time. These tag names should be the tag names that are read
by the sampling subroutine. For example:
tags = {('U-235', 'shutdown'): 'tag1', ('TOTAL', '1 h'): 'tag2'}
"""
photon_source_to_hdf5(phtn_src)
h5_file = phtn_src + ".h5"
photon_source_hdf5_to_mesh(mesh, h5_file, tags)
def test_photon_source_to_hdf5():
"""Tests the function photon_source_to_hdf5.
"""
filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
photon_source_to_hdf5(filename, chunkshape=(10, ))
assert_true(os.path.exists(filename + '.h5'))
with tb.openFile(filename + '.h5') as h5f:
obs = h5f.root.data[:]
with open(filename, 'r') as f:
lines = f.readlines()
count = 0
old = ""
for i, row in enumerate(obs):
ls = lines[i].strip().split('\t')
if ls[0] != 'TOTAL' and old == 'TOTAL':
count += 1
assert_equal(count, row['idx'])
assert_equal(ls[0].strip(), row['nuc'].decode())
assert_equal(ls[1].strip(), row['time'].decode())
assert_array_equal(np.array(ls[2:], dtype=np.float64),
row['phtn_src'])
old = ls[0]
if os.path.isfile(filename + '.h5'):
os.remove(filename + '.h5')
def test_photon_source_hdf5_to_mesh():
"""Tests the function photon source_h5_to_mesh."""
if not HAVE_PYTAPS:
raise SkipTest
filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
photon_source_to_hdf5(filename, chunkshape=(10, ))
assert_true(os.path.exists(filename + '.h5'))
mesh = Mesh(structured=True,
structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])
tags = {('1001', 'shutdown'): 'tag1', ('TOTAL', '1 h'): 'tag2'}
photon_source_hdf5_to_mesh(mesh, filename + '.h5', tags)
# create lists of lists of expected results
tag1_answers = [[1] + [0] * 41, [2] + [0] * 41, [3] + [0] * 41,
[4] + [0] * 41]
tag2_answers = [[5] + [0] * 41, [6] + [0] * 41, [7] + [0] * 41,
[8] + [0] * 41]
ves = list(mesh.structured_iterate_hex("xyz"))
for i, ve in enumerate(ves):
assert_array_equal(mesh.mesh.getTagHandle("tag1")[ve], tag1_answers[i])
assert_array_equal(mesh.mesh.getTagHandle("tag2")[ve], tag2_answers[i])
if os.path.isfile(filename + '.h5'):
os.remove(filename + '.h5')
def test_photon_source_to_hdf5():
"""Tests the function photon_source_to_hdf5.
"""
filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
photon_source_to_hdf5(filename, chunkshape=(10,))
assert_true(os.path.exists(filename + ".h5"))
with tb.openFile(filename + ".h5") as h5f:
obs = h5f.root.data[:]
with open(filename, "r") as f:
lines = f.readlines()
count = 0
old = ""
for i, row in enumerate(obs):
ls = lines[i].strip().split("\t")
if ls[0] != "TOTAL" and old == "TOTAL":
count += 1
assert_equal(count, row["idx"])
assert_equal(ls[0].strip(), row["nuc"].decode())
assert_equal(ls[1].strip(), row["time"].decode())
assert_array_equal(np.array(ls[2:], dtype=np.float64), row["phtn_src"])
old = ls[0]
if os.path.isfile(filename + ".h5"):
os.remove(filename + ".h5")
def test_photon_source_hdf5_to_mesh():
"""Tests the function photon source_h5_to_mesh."""
if not HAVE_PYTAPS:
raise SkipTest
filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
photon_source_to_hdf5(filename, chunkshape=(10,))
assert_true(os.path.exists(filename + ".h5"))
mesh = Mesh(structured=True, structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])
tags = {("1001", "shutdown"): "tag1", ("TOTAL", "1 h"): "tag2"}
photon_source_hdf5_to_mesh(mesh, filename + ".h5", tags)
# create lists of lists of expected results
tag1_answers = [[1] + [0] * 41, [2] + [0] * 41, [3] + [0] * 41, [4] + [0] * 41]
tag2_answers = [[5] + [0] * 41, [6] + [0] * 41, [7] + [0] * 41, [8] + [0] * 41]
ves = list(mesh.structured_iterate_hex("xyz"))
for i, ve in enumerate(ves):
assert_array_equal(mesh.mesh.getTagHandle("tag1")[ve], tag1_answers[i])
assert_array_equal(mesh.mesh.getTagHandle("tag2")[ve], tag2_answers[i])
if os.path.isfile(filename + ".h5"):
os.remove(filename + ".h5")
def test_photon_source_to_hdf5():
"""Tests the function photon_source_to_hdf5."""
filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
photon_source_to_hdf5(filename, chunkshape=(10, ))
assert_true(os.path.exists(filename + ".h5"))
with tb.open_file(filename + ".h5") as h5f:
obs = h5f.root.data[:]
with open(filename, "r") as f:
lines = f.readlines()
count = 0
old = ""
for i, row in enumerate(obs):
tokens = lines[i].strip().split("\t")
if tokens[0] != "TOTAL" and old == "TOTAL":
count += 1
assert_equal(count, row["idx"])
assert_equal(tokens[0].strip(), row["nuc"].decode())
assert_equal(tokens[1].strip(), row["time"].decode())
assert_array_equal(np.array(tokens[2:], dtype=np.float64),
row["phtn_src"])
old = tokens[0]
if os.path.isfile(filename + ".h5"):
os.remove(filename + ".h5")
# wrong nuc option raise test
assert_raises(ValueError, photon_source_to_hdf5, filename, "test")
def step2():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean("general", "structured")
sub_voxel = config.getboolean("general", "sub_voxel")
decay_times = config.get("step2", "decay_times").split(",")
output = config.get("step2", "output")
tot_phtn_src_intensities = config.get("step2", "tot_phtn_src_intensities")
tag_name = "source_density"
if sub_voxel:
geom = config.get("step1", "geom")
load(geom)
cell_mats = cell_materials(geom)
else:
cell_mats = None
h5_file = "phtn_src.h5"
if not isfile(h5_file):
photon_source_to_hdf5(filename="phtn_src", nucs="total")
intensities = "Total photon source intensities (p/s)\n"
e_bounds = phtn_src_energy_bounds("alara_inp")
for i in range(len(e_bounds)):
e_bounds[i] /= 1.0e6 # convert unit from eV to MeV
for i, dt in enumerate(decay_times):
print("Writing source for decay time: {0} to mesh".format(dt))
mesh = Mesh(structured=structured, mesh="blank_mesh.h5m")
tags = {("TOTAL", dt): tag_name}
photon_source_hdf5_to_mesh(mesh,
h5_file,
tags,
sub_voxel=sub_voxel,
cell_mats=cell_mats)
p_src_filename = "{0}_{1}.h5m".format(output, i + 1)
intensity = total_photon_source_intensity(mesh,
tag_name,
sub_voxel=sub_voxel)
mesh = tag_e_bounds(mesh, e_bounds)
mesh = tag_source_intensity(mesh, intensity)
# get and tag decay time
decay_time = to_sec(float(dt.split()[0]), dt.split()[1])
mesh = tag_decay_time(mesh, decay_time)
# set version manually when changing the information of source.h5m
mesh = tag_version(mesh)
mesh.write_hdf5("{0}_{1}.h5m".format(output, i + 1))
intensities += "{0}: {1}\n".format(dt, intensity)
with open(tot_phtn_src_intensities, "w") as f:
f.write(intensities)
print("R2S step2 complete.")
def test_photon_source_hdf5_to_mesh_subvoxel():
"""Tests the function photon source_h5_to_mesh
under sub-voxel r2s condition."""
if not HAVE_PYMOAB:
raise SkipTest
filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
photon_source_to_hdf5(filename, chunkshape=(10, ))
assert_true(os.path.exists(filename + '.h5'))
sub_voxel = True
mesh = Mesh(structured=True,
structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])
cell_fracs = np.zeros(6,
dtype=[('idx', np.int64), ('cell', np.int64),
('vol_frac', np.float64),
('rel_error', np.float64)])
cell_fracs[:] = [(0, 11, 1.0, 0.0), (1, 11, 0.5, 0.0), (1, 12, 0.5, 0.0),
(2, 11, 0.5, 0.0), (2, 13, 0.5, 0.0), (3, 13, 1.0, 0.0)]
cell_mats = {
11: Material({'H': 1.0}, density=1.0),
12: Material({'He': 1.0}, density=1.0),
13: Material({}, density=0.0, metadata={'name': 'void'})
}
mesh.tag_cell_fracs(cell_fracs)
tags = {('1001', 'shutdown'): 'tag1', ('TOTAL', '1 h'): 'tag2'}
photon_source_hdf5_to_mesh(mesh,
filename + '.h5',
tags,
sub_voxel=sub_voxel,
cell_mats=cell_mats)
# create lists of lists of expected results
tag1_answers = [[1.0] + [0.0] * 41 + [0.0] * 42,
[2.0] + [0.0] * 41 + [3.0] + [0.0] * 41,
[4.0] + [0.0] * 41 + [0.0] * 42, [0.0] * 42 * 2]
tag2_answers = [[5.0] + [0.0] * 41 + [0.0] * 42,
[6.0] + [0.0] * 41 + [7.0] + [0.0] * 41,
[8.0] + [0.0] * 41 + [0.0] * 42, [0.0] * 42 * 2]
for i, _, ve in mesh:
assert_array_equal(mesh.tag1[ve], tag1_answers[i])
assert_array_equal(mesh.tag2[ve], tag2_answers[i])
if os.path.isfile(filename + '.h5'):
os.remove(filename + '.h5')
def step2():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean('general', 'structured')
sub_voxel = config.getboolean('general', 'sub_voxel')
decay_times = config.get('step2', 'decay_times').split(',')
output = config.get('step2', 'output')
tot_phtn_src_intensities = config.get('step2', 'tot_phtn_src_intensities')
tag_name = "source_density"
if sub_voxel:
geom = config.get('step1', 'geom')
load(geom)
cell_mats = cell_materials(geom)
else:
cell_mats = None
h5_file = 'phtn_src.h5'
if not isfile(h5_file):
photon_source_to_hdf5('phtn_src')
intensities = "Total photon source intensities (p/s)\n"
for i, dc in enumerate(decay_times):
print('Writing source for decay time: {0}'.format(dc))
mesh = Mesh(structured=structured, mesh='blank_mesh.h5m')
tags = {('TOTAL', dc): tag_name}
photon_source_hdf5_to_mesh(mesh,
h5_file,
tags,
sub_voxel=sub_voxel,
cell_mats=cell_mats)
mesh.write_hdf5('{0}_{1}.h5m'.format(output, i + 1))
intensity = total_photon_source_intensity(mesh,
tag_name,
sub_voxel=sub_voxel)
intensities += "{0}: {1}\n".format(dc, intensity)
with open(tot_phtn_src_intensities, 'w') as f:
f.write(intensities)
e_bounds = phtn_src_energy_bounds("alara_inp")
e_bounds_str = ""
for e in e_bounds:
e = e / 1e6 # convert unit to MeV
e_bounds_str += "{0}\n".format(e)
with open("e_bounds", 'w') as f:
f.write(e_bounds_str)
print('R2S step2 complete.')
def step2():
config = ConfigParser.ConfigParser()
config.read(config_filename)
structured = config.getboolean('general', 'structured')
sub_voxel = config.getboolean('general', 'sub_voxel')
decay_times = config.get('step2', 'decay_times').split(',')
output = config.get('step2', 'output')
tot_phtn_src_intensities = config.get('step2', 'tot_phtn_src_intensities')
tag_name = "source_density"
if sub_voxel:
geom = config.get('step1', 'geom')
load(geom)
cell_mats = cell_materials(geom)
else:
cell_mats = None
h5_file = 'phtn_src.h5'
if not isfile(h5_file):
photon_source_to_hdf5(filename='phtn_src', nucs='total')
intensities = "Total photon source intensities (p/s)\n"
e_bounds = phtn_src_energy_bounds("alara_inp")
for i in range(len(e_bounds)):
e_bounds[i] /= 1.0e6 # convert unit from eV to MeV
for i, dt in enumerate(decay_times):
print('Writing source for decay time: {0} to mesh'.format(dt))
mesh = Mesh(structured=structured, mesh='blank_mesh.h5m')
tags = {('TOTAL', dt): tag_name}
photon_source_hdf5_to_mesh(mesh, h5_file, tags, sub_voxel=sub_voxel,
cell_mats=cell_mats)
intensity = total_photon_source_intensity(mesh, tag_name,
sub_voxel=sub_voxel)
mesh = tag_e_bounds(mesh, e_bounds)
mesh = tag_source_intensity(mesh, intensity)
# get and tag decay time
decay_time = to_sec(float(dt.split()[0]), dt.split()[1])
mesh = tag_decay_time(mesh, decay_time)
# set version manually when changing the information of source.h5m
mesh = tag_version(mesh)
mesh.write_hdf5('{0}_{1}.h5m'.format(output, i+1))
intensities += "{0}: {1}\n".format(dt, intensity)
with open(tot_phtn_src_intensities, 'w') as f:
f.write(intensities)
print('R2S step2 complete.')
def test_photon_source_hdf5_to_mesh_subvoxel_size1():
"""Tests the function photon source_h5_to_mesh
under sub-voxel r2s condition."""
if not HAVE_PYMOAB:
raise SkipTest
filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
photon_source_to_hdf5(filename, chunkshape=(10, ))
assert_true(os.path.exists(filename + ".h5"))
sub_voxel = True
mesh = Mesh(structured=True,
structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])
cell_fracs = np.zeros(
4,
dtype=[
("idx", np.int64),
("cell", np.int64),
("vol_frac", np.float64),
("rel_error", np.float64),
],
)
cell_fracs[:] = [
(0, 11, 1.0, 0.0),
(1, 12, 1.0, 0.0),
(2, 13, 1.0, 0.0),
(3, 14, 1.0, 0.0),
]
cell_mats = {
11: Material({"H": 1.0}, density=1.0),
12: Material({"He": 1.0}, density=1.0),
13: Material({"He": 1.0}, density=1.0),
14: Material({}, density=0.0, metadata={"name": "void"}),
}
mesh.tag_cell_fracs(cell_fracs)
tags = {("1001", "shutdown"): "tag1", ("TOTAL", "1 h"): "tag2"}
photon_source_hdf5_to_mesh(mesh,
filename + ".h5",
tags,
sub_voxel=sub_voxel,
cell_mats=cell_mats)
# create lists of lists of expected results
tag1_answers = [
[1.0] + [0.0] * 41,
[2.0] + [0.0] * 41,
[3.0] + [0.0] * 41,
[0.0] * 42,
]
tag2_answers = [
[5.0] + [0.0] * 41,
[6.0] + [0.0] * 41,
[7.0] + [0.0] * 41,
[0.0] * 42,
]
for i, _, ve in mesh:
assert_array_equal(mesh.tag1[ve], tag1_answers[i])
assert_array_equal(mesh.tag2[ve], tag2_answers[i])
if os.path.isfile(filename + ".h5"):
os.remove(filename + ".h5")