def set_fielddata_from_function(field,
subfieldname,
function,
pos_unit_length,
normalise=False,
scale_factor=1.0):
if type(function) != types.FunctionType:
raise NmagUserError("Expect function-object but got type '%s'" %
type(function))
log.log(
15, "set_fielddata_from_function: Entering, populate "
"subfield '%s' from function '%s'" % (subfieldname, function.__name__))
site_ids, site_pos, shape, site_vols = \
ocaml.mwe_subfield_metadata(field, subfieldname)
for pos, site in zip(site_pos, site_ids):
# convert position from mesh coordinates to meter
pos = [(x * pos_unit_length).in_units_of(SI("m")) for x in pos]
# sample function and set field at current site
value = function(pos)
set_field_at_site(field,
subfieldname,
site,
value,
normalise=normalise,
scale_factor=scale_factor)
log.debug("set_fielddata_from_function: Done.")
def set_fielddata_from_numpyarray_old(field,
subfieldname,
data,
normalise=False,
scale_factor=1.0):
if type(data) != numpy.ndarray:
raise NmagUserError, "Expect numpy array but got '%s'" % str(
type(data))
# check that length of data agrees with subfield
site_ids, site_pos, shape, site_vols = \
ocaml.mwe_subfield_metadata(field,subfieldname)
# check whether we have the same number of sites
if len(site_ids) != len(data):
raise NmagUserError("Subfield '%s' has %d sites but the data you "
"provided as a numpy array has %d site entries." %
(subfieldname, len(site_ids), len(data)))
# check whether the 'tensor' for each site has the correct shape
for i in range(len(data)):
site = site_ids[i]
tensor_value = data[i].tolist()
set_field_at_site(field,
subfieldname,
site,
tensor_value,
scale_factor=scale_factor,
normalise=normalise)
def set_fielddata_from_vector(field, subfieldname, data,
scale_factor=1.0, normalise=False):
# First check that shape of data and shape of this subfield agree:
log.debug("set_fielddata_from_vector: setting %s to '%s'."
% (_set_what_msg(subfieldname), data))
if True:
data = _prepare_set_field(field, subfieldname, data, None, # <- site
scale_factor, normalise)
exit_status = ocaml.set_field_uniformly(field, subfieldname, data)
if exit_status != 0:
raise NmagUserError("set_fielddata_from_vector: couldn't set "
"subfield '%s'." % subfieldname)
else:
site_ids, site_pos, shape, site_vols = \
ocaml.mwe_subfield_metadata(field, subfieldname)
for site in site_ids:
set_field_at_site(field, subfieldname, site, data,
normalise=normalise,
scale_factor=scale_factor)
log.debug("set_fielddata_from_vector: Done.")
def set_fielddata_from_vector(field,
subfieldname,
data,
scale_factor=1.0,
normalise=False):
# First check that shape of data and shape of this subfield agree:
log.debug("set_fielddata_from_vector: setting %s to '%s'." %
(_set_what_msg(subfieldname), data))
if True:
data = _prepare_set_field(
field,
subfieldname,
data,
None, # <- site
scale_factor,
normalise)
if type(data) == list:
pass
elif hasattr(data, "__iter__"):
data = list(data)
else:
data = [data]
exit_status = ocaml.set_field_uniformly(field, subfieldname, data)
if exit_status != 0:
raise NmagUserError("set_fielddata_from_vector: couldn't set "
"subfield '%s'." % subfieldname)
else:
site_ids, site_pos, shape, site_vols = \
ocaml.mwe_subfield_metadata(field, subfieldname)
for site in site_ids:
set_field_at_site(field,
subfieldname,
site,
data,
normalise=normalise,
scale_factor=scale_factor)
log.debug("set_fielddata_from_vector: Done.")
def set_fielddata_from_numpyarray_old(field, subfieldname, data,
normalise=False, scale_factor=1.0):
if type(data) != numpy.ndarray:
raise NmagUserError,"Expect numpy array but got '%s'" % str(type(data))
# check that length of data agrees with subfield
site_ids, site_pos, shape, site_vols = \
ocaml.mwe_subfield_metadata(field,subfieldname)
# check whether we have the same number of sites
if len(site_ids) != len(data):
raise NmagUserError("Subfield '%s' has %d sites but the data you "
"provided as a numpy array has %d site entries."
% (subfieldname, len(site_ids), len(data)))
# check whether the 'tensor' for each site has the correct shape
for i in range(len(data)):
site = site_ids[i]
tensor_value = data[i].tolist()
set_field_at_site(field, subfieldname, site, tensor_value,
scale_factor=scale_factor,
normalise=normalise)
def set_fielddata_from_function(field, subfieldname, function,
pos_unit_length, normalise=False,
scale_factor=1.0):
if type(function) != types.FunctionType:
raise NmagUserError("Expect function-object but got type '%s'"
% type(function))
log.log(15, "set_fielddata_from_function: Entering, populate "
"subfield '%s' from function '%s'"
% (subfieldname, function.__name__))
site_ids, site_pos, shape, site_vols = \
ocaml.mwe_subfield_metadata(field, subfieldname)
for pos, site in zip(site_pos, site_ids):
# convert position from mesh coordinates to meter
pos = [(x*pos_unit_length).in_units_of(SI("m")) for x in pos]
# sample function and set field at current site
value = function(pos)
set_field_at_site(field, subfieldname, site, value,
normalise=normalise, scale_factor=scale_factor)
log.debug("set_fielddata_from_function: Done.")
def _create_field(self, field_name, subfield_name=None, row=0):
# This is the real subfield name
full_field_name = build_full_field_name(field_name, subfield_name)
# Now we get the data
f = self.open_handler()
root_data_fields = self.get_root_data_fields()
dim = self.mesh.dim
field_stuff = f.getNode(root_data_fields, field_name)
field_shape = list(field_stuff.row[full_field_name].shape)[1:]
# Get the sites where the subfield is defined (sites) and the
# corresponding coordinates (ps) and values (vs)
ps, vs, sites = self.get_field_array(field_name, subfield_name, row)
# sites now contains the dof allocation for the subfield, i.e. in
# which sites the subfield is defined.
# We now want to build a numarray of one boolean value per each site
# which says whether for that site the field is defined or not
pointsregions = self.mesh.pointsregions
num_sites = len(pointsregions)
defined = numpy.ndarray(num_sites, dtype=numpy.bool)
defined.fill(False)
for site_where_defined in sites:
defined[site_where_defined] = True
# Run over all the sites and build a list of regions where the field
# is undefined
all_regions = range(1, self.mesh.numregions)
regions_where_defined = range(1, self.mesh.numregions)
for site in range(num_sites):
if not defined[site]:
regions_owning_this_site = pointsregions[site]
for region in regions_owning_this_site:
if region in regions_where_defined:
regions_where_defined.remove(region)
# Now we know in which regions of the mesh the field is defined
logmsg("'%s' has been found in regions %s" %
(full_field_name, regions_where_defined))
# Consistency check: there musn't be a region where the field
# is partially defined!
logmsg("Now checking that there the field is always present...")
for site in range(num_sites):
field_should_be_defined_here = \
(True in [rwd in pointsregions[site]
for rwd in regions_where_defined])
# ^^^ True when this site belongs to one region which is listed
# in 'regions_where_defined'
if field_should_be_defined_here != defined[site]:
logmsg("Inconsistency while checking the field definition "
"regions: site %d belongs to region %s, but the field "
"is defined in regions %s." %
(site, pointsregions[site], regions_where_defined))
raise NmagUserError("The given file seems to be corrupt!"
"Cannot proceed!")
logmsg("Check successful: definition regions are %s" %
regions_where_defined)
logmsg("Creating a new element '%s' for the field" % full_field_name)
element = ocaml.make_element(full_field_name, field_shape, dim,
self.field_order)
logmsg("Creating MWE")
element_assoc = zip(regions_where_defined,
[element] * len(regions_where_defined))
properties = zip(regions_where_defined,
[[full_field_name]] * len(regions_where_defined))
mwe = ocaml.make_mwe(field_name, self.mesh.raw_mesh, element_assoc, [],
properties)
logmsg("Creating the field")
field = ocaml.raw_make_field(mwe, [], "", "")
# We now try to understand how to map the data from file into the
# newly created field
metadata = ocaml.mwe_subfield_metadata(field, full_field_name)
new_site_ids, new_pos, new_shape, new_site_vols = metadata
num_new_sites = len(new_site_ids)
if num_new_sites != len(sites):
raise NmagUserError("The re-created field seems inconsistent "
"with the one saved to file. Number of "
"sites is %d for saved and %d for new field. "
"Cannot proceed!" % (num_sites, num_new_sites))
# Check that the new field is binary compatible with the old one
# this is really what we expect and allows us to set the field
# by just passing a numarray as retrieved from the file
need_map = False
for i in range(num_new_sites):
if new_site_ids[i] != sites[i]:
need_map = True
if need_map:
raise NmagUserError("need_map=True, not implemented because this"
"was not expected to happen, anyway! Contact"
"Matteo ([email protected])")
self.fields[full_field_name] = field
timer1.start("x")
ff.set_fielddata_from_numpyarray(field, full_field_name, vs)
timer1.stop("x")
return field
def _create_field(self, field_name, subfield_name=None, row=0):
# This is the real subfield name
full_field_name = build_full_field_name(field_name, subfield_name)
# Now we get the data
f = self.open_handler()
root_data_fields = self.get_root_data_fields()
dim = self.mesh.dim
field_stuff = f.getNode(root_data_fields, field_name)
field_shape = list(field_stuff.row[full_field_name].shape)[1:]
# Get the sites where the subfield is defined (sites) and the
# corresponding coordinates (ps) and values (vs)
ps, vs, sites = self.get_field_array(field_name, subfield_name, row)
# sites now contains the dof allocation for the subfield, i.e. in
# which sites the subfield is defined.
# We now want to build a numarray of one boolean value per each site
# which says whether for that site the field is defined or not
pointsregions = self.mesh.pointsregions
num_sites = len(pointsregions)
defined = numpy.ndarray(num_sites, dtype=numpy.bool)
defined.fill(False)
for site_where_defined in sites:
defined[site_where_defined] = True
# Run over all the sites and build a list of regions where the field
# is undefined
all_regions = range(1, self.mesh.numregions)
regions_where_defined = range(1, self.mesh.numregions)
for site in range(num_sites):
if not defined[site]:
regions_owning_this_site = pointsregions[site]
for region in regions_owning_this_site:
if region in regions_where_defined:
regions_where_defined.remove(region)
# Now we know in which regions of the mesh the field is defined
logmsg("'%s' has been found in regions %s"
% (full_field_name, regions_where_defined))
# Consistency check: there musn't be a region where the field
# is partially defined!
logmsg("Now checking that there the field is always present...")
for site in range(num_sites):
field_should_be_defined_here = \
(True in [rwd in pointsregions[site]
for rwd in regions_where_defined])
# ^^^ True when this site belongs to one region which is listed
# in 'regions_where_defined'
if field_should_be_defined_here != defined[site]:
logmsg("Inconsistency while checking the field definition "
"regions: site %d belongs to region %s, but the field "
"is defined in regions %s."
% (site, pointsregions[site], regions_where_defined))
raise NmagUserError("The given file seems to be corrupt!"
"Cannot proceed!")
logmsg("Check successful: definition regions are %s"
% regions_where_defined)
logmsg("Creating a new element '%s' for the field" % full_field_name)
element = ocaml.make_element(full_field_name, field_shape, dim,
self.field_order)
logmsg("Creating MWE")
element_assoc = zip(regions_where_defined,
[element]*len(regions_where_defined))
properties = zip(regions_where_defined,
[[full_field_name]]*len(regions_where_defined))
mwe = ocaml.make_mwe(field_name,
self.mesh.raw_mesh,
element_assoc,
[],
properties)
logmsg("Creating the field")
field = ocaml.raw_make_field(mwe, [], "", "")
# We now try to understand how to map the data from file into the
# newly created field
metadata = ocaml.mwe_subfield_metadata(field, full_field_name)
new_site_ids, new_pos, new_shape, new_site_vols = metadata
num_new_sites = len(new_site_ids)
if num_new_sites != len(sites):
raise NmagUserError("The re-created field seems inconsistent "
"with the one saved to file. Number of "
"sites is %d for saved and %d for new field. "
"Cannot proceed!" % (num_sites,num_new_sites))
# Check that the new field is binary compatible with the old one
# this is really what we expect and allows us to set the field
# by just passing a numarray as retrieved from the file
need_map = False
for i in range(num_new_sites):
if new_site_ids[i] != sites[i]:
need_map = True
if need_map:
raise NmagUserError("need_map=True, not implemented because this"
"was not expected to happen, anyway! Contact"
"Matteo ([email protected])")
self.fields[full_field_name] = field
timer1.start("x")
ff.set_fielddata_from_numpyarray(field, full_field_name, vs)
timer1.stop("x")
return field
