def get_parameter(self, key, try_json=True, parameters=None):
if parameters is None:
parameters = self._parameters
if key not in parameters:
return None
parameter, typ = parameters[key]
return convert_parameter(parameter, typ, try_json)
def get_parameter(self, key, try_json=True, parameters=None):
if parameters is None:
parameters = self._parameters
if key not in parameters:
return None
parameter, typ = parameters[key]
return convert_parameter(parameter, typ, try_json)
def to_mesh_xml(self):
root = lxml.etree.Element('gssf')
root.set('name', 'elmer_libnuma')
root.set('version', '1.0.2')
# Start by creating a geometry section
geometry = lxml.etree.Element('geometry')
root.append(geometry)
# We get the location of the simulation centre from the parameters
centre_location = self.get_parameter("CENTRE_LOCATION")
# If it isn't there, then the centre will be the first needle tip, or
# if we have been given "centroid-of-tips" instead of a set of
# coordinates, calculate the centroid of all the tips
if centre_location is None or centre_location == "first-needle":
if self._needles:
centre_location = self.get_needle_parameter(0, "NEEDLE_TIP_LOCATION")
elif centre_location == "centroid-of-tips":
if self._needles:
needle_tips = [self.get_needle_parameter(i, "NEEDLE_TIP_LOCATION") for i in range(len(self._needles))]
needle_tips = zip(*needle_tips)
centre_location = [sum(tips) / len(self._needles) for tips in needle_tips]
# If we have a needle, then use it to set the `needleaxis`
if self._needles:
needle_axis_node = lxml.etree.Element('needleaxis')
# Get the entry and tip of the first needle
tip_location = self.get_needle_parameter(0, "NEEDLE_TIP_LOCATION")
entry_location = self.get_needle_parameter(0, "NEEDLE_ENTRY_LOCATION")
norm = 0
vec = []
for c, vt, ve in zip(('x', 'y', 'z'), tip_location, entry_location):
needle_axis_node.set(c, str(ve - vt))
vec.append(ve - vt)
norm += (ve - vt) * (ve - vt)
# Based on the calculated axis, add this to the geometry
geometry.append(needle_axis_node)
# FIXME: is this supposed to be inside this if??
# Use the CENTRE_OFFSET parameter to shift the geometry if required
offset = self.get_parameter("CENTRE_OFFSET")
if offset is not None:
for c, v in enumerate(centre_location):
centre_location[c] = v + offset * vec[c] / math.sqrt(norm)
# After all the calculations above, use the finally chosen centre in the
# geometry section
centre_location_node = lxml.etree.Element("centre")
for c, v in zip(('x', 'y', 'z'), centre_location):
centre_location_node.set(c, str(v))
geometry.append(centre_location_node)
# If we have a simulation scaling parameter, that goes into the geometry
# section also
if self.get_parameter("SIMULATION_SCALING") is not None:
lxml.etree.SubElement(geometry, "simulationscaling") \
.set("ratio",
str(self.get_parameter("SIMULATION_SCALING")))
# Each region goes into the regions section, fairly intuitively
regions = lxml.etree.SubElement(root, "regions")
for name, region in self._regions.items():
regionNode = lxml.etree.SubElement(regions, region["format"])
regionNode.set("name", name)
regionNode.set("input", os.path.join("input/", region["input"]))
regionNode.set("groups", "; ".join(region["groups"]))
# Add the parameters wholesale
parameters = lxml.etree.SubElement(root, "constants")
for key, parameterPair in self._parameters.items():
parameter, typ = parameterPair
parameterNode = lxml.etree.SubElement(parameters, "parameter")
parameterNode.set("name", key)
p = convert_parameter(parameter, typ)
parameterNode.set("value", json.dumps(p))
if typ is not None:
parameterNode.set("type", typ)
name_needle_regions = False
# The needlelibrary needs to know if we have solid needles
needlelibrary = lxml.etree.SubElement(root, 'needlelibrary')
solid_needles = self.get_parameter("SETTING_SOLID_NEEDLES")
if solid_needles is not None:
needlelibrary.set("zones", "true" if solid_needles is True else "false")
name_needle_regions = True
# The outer mesh, as far as we are concerned, is always CGAL
mesher = lxml.etree.SubElement(root, "mesher")
mesher.set('type', 'CGAL')
# RMV: should this be reinserted?
# if self.get_parameter("SETTING_SOLID_NEEDLES") is True or self.get_parameter("SETTING_ZONE_BOUNDARIES") is True:
mesher.set("zone_boundaries", "true")
# If we have an inner mesh, add it to the mesher
mesher_inner = self.get_parameter("SETTING_AXISYMMETRIC_INNER")
if mesher_inner is not None:
innerNode = lxml.etree.SubElement(mesher, "inner")
innerNode.set("type", "axisymmetric")
innerNode.set("template", mesher_inner)
# Coarse inner, similarly
mesher_inner_coarse = self.get_parameter("SETTING_AXISYMMETRIC_INNER_COARSE")
if mesher_inner_coarse is not None:
innerNode = lxml.etree.SubElement(mesher, "inner")
innerNode.set("type", "axisymmetric")
innerNode.set("name", "coarse")
innerNode.set("template", mesher_inner_coarse)
# The extent we assume is a sphere of radius in parameters
extent = lxml.etree.SubElement(mesher, 'extent')
radius = self.get_parameter("SIMULATION_DOMAIN_RADIUS")
if radius is not None:
extent.set('radius', str(radius))
else:
extent.set('radius', '50')
# Adding the empty centre element tells the mesher we want a denser
# centre than the boundaries
lxml.etree.SubElement(mesher, 'centre')
# Start going through the length scales
lengthscales = lxml.etree.SubElement(mesher, 'lengthscales')
# Two sets of fairly sensible defaults for the usual meshing case
if self.get_parameter('RESOLUTION_HIGH'):
lengthscale_settings = [
('nearfield', '1.0'), ('farfield', '2.0'), ('zonefield', '1.0'),
('vessels', 'far')
]
else:
lengthscale_settings = [
('nearfield', '2.0'), ('farfield', '5.0'), ('zonefield', '2.0'),
('vessels', 'far')
]
# Allow them to be overridden
nearfield = self.get_parameter('RESOLUTION_FIELD_NEAR')
needlezonefield = self.get_parameter('RESOLUTION_FIELD_NEEDLE_ZONE')
if not needlezonefield:
needlezonefield = self.get_parameter('RESOLUTION_NEEDLE_ZONE_FIELD')
farfield = self.get_parameter('RESOLUTION_FIELD_FAR')
zonefield = self.get_parameter('RESOLUTION_FIELD_ZONE')
if nearfield:
lengthscale_settings[0] = ('nearfield', nearfield)
if farfield:
lengthscale_settings[1] = ('farfield', farfield)
if zonefield:
lengthscale_settings[2] = ('zonefield', zonefield)
for k, v in lengthscale_settings:
lengthscales.set(k, str(v))
if needlezonefield:
lengthscales.set("needlezonefield", str(needlezonefield))
farfield = str(lengthscale_settings[1][1])
zonefield = str(lengthscale_settings[2][1])
# Each region may need to be added to the mesher section
for idx, region in self._regions.items():
# If we have an organ, it should appear as a zone or organ
if region['meaning'] == 'organ':
if self.get_parameter('SETTING_ORGAN_AS_SUBDOMAIN'):
zone = lxml.etree.SubElement(mesher, 'zone')
zone.set('region', idx)
zone.set('priority', '100')
zone.set('characteristic_length', farfield)
else:
lxml.etree.SubElement(mesher, 'organ').set('region', idx)
# If we have a zone, not excluded from meshing, then it goes in too
elif region['format'] == 'zone' and not (set(region['groups']) & self._nonmeshing_groups):
zone = lxml.etree.SubElement(mesher, 'zone')
zone.set('region', idx)
zone.set('priority', '1')
zone.set('characteristic_length', zonefield)
# If we have vessels, they get added also
elif 'vessels' in region['groups'] or 'bronchi' in region['groups']:
# FIXME: surely this should be a surface/vessel tag?
zone = lxml.etree.SubElement(mesher, 'zone')
zone.set('region', idx)
zone.set('priority', '2')
zone.set('characteristic_length', zonefield)
# These are standard entries
lxml.etree.SubElement(root, 'optimizer')
# The register of needles must be filled in
globalNeedlesNode = lxml.etree.SubElement(root, "needles")
if not needlezonefield:
needlezonefield = zonefield
# Make sure all needles are int-castable, or, if not,
# just make up our own ordering
try:
needle_indices = [int(ix.replace('needle', '')) for ix in self._needles]
except ValueError:
self._needles = {str(i + 1): v for i, v in enumerate(self._needles.values())}
needle_indices = [int(ix) for ix in self._needles]
augment = (0 in needle_indices)
for ix, needle in self._needles.items():
# Add a needle node and set the name to be our index (if we have
# been given, say, 'needle-3' as an index, it becomes '3')
globalNeedleNode = lxml.etree.SubElement(globalNeedlesNode, "needle")
l = int(ix.replace('needle', ''))
if augment:
l += 1
globalNeedleNode.set("name", str(l))
# If this needle is a boundary type (the only type for the
# moment)...
if needle['class'] in ('solid-boundary', 'boundary'):
# The 'file' attribute in GSSA should be a colon-separated pair
# indicating what type of definition it is and the specifics
# required
location = needle['file'].split(':', 1)
needle_mesh = None
# If we aren't using a library type, then we need to get the
# region
if location[0] in ('surface', 'zone', 'both'):
needleNode = lxml.etree.SubElement(regions, location[0])
needleNode.set("name", str(l))
needleNode.set("input", os.path.join("input/", location[1]))
needleNode.set("groups", "needles")
# TODO: surely this might be a surface?
needle_mesh = lxml.etree.SubElement(mesher, 'zone')
needle_mesh.set('region', str(l))
needle_mesh.set('characteristic_length', str(needlezonefield))
needle_mesh.set('priority', '0')
else:
needleNode = lxml.etree.SubElement(needlelibrary, 'needle')
if name_needle_regions:
needleNode.set("name", str(l))
# If this is a library type, set its ID
if location[0] == 'library':
needleNode.set("id", location[1])
needleNode.set("name", str(l))
# Calculate the offset and axis for this needle
tip_location = self.get_needle_parameter(ix, "NEEDLE_TIP_LOCATION")
entry_location = self.get_needle_parameter(ix, "NEEDLE_ENTRY_LOCATION")
needleNode.set("offset", " ".join(map(lambda c: str(c[0] - c[1]), zip(tip_location, centre_location))))
needleNode.set("axis", " ".join(map(lambda c: str(c[0] - c[1]), zip(entry_location, tip_location))))
# Add any needle-specific parameters
parameters = lxml.etree.SubElement(globalNeedleNode, "parameters")
for key, parameterPair in needle["parameters"].items():
parameter, typ = parameterPair
parameterNode = lxml.etree.SubElement(parameters, "constant")
parameterNode.set("name", key)
parameterNode.set("value", str(convert_parameter(parameter, typ)))
# Set active region if needs be
needle_active_length = self.get_needle_parameter(ix, "NEEDLE_ACTIVE_LENGTH")
global_active_length = self.get_needle_parameter(ix, "CONSTANT_GLOBAL_ACTIVE_LENGTH")
if needle_active_length is None:
needle_active_length = global_active_length
if needle_active_length is not None:
if needle_mesh is None:
needle_mesh = lxml.etree.SubElement(mesher, 'zone')
needle_mesh.set('characteristic_length', str(needlezonefield))
needle_mesh.set('priority', '0')
needle_mesh.set('region', 'needle-' + str(l))
activity = lxml.etree.SubElement(needle_mesh, 'activity')
tip_location = self.get_needle_parameter(ix, "NEEDLE_TIP_LOCATION")
for c, vt, vc in zip(('x', 'y', 'z'), tip_location, centre_location):
activity.set(c, str(vt - vc))
activity.set('r', str(needle_active_length))
self._mesher_xml = root
return self._mesher_xml
def to_mesh_xml(self):
root = lxml.etree.Element('gssf')
root.set('name', 'elmer_libnuma')
root.set('version', '1.0.2')
# Start by creating a geometry section
geometry = lxml.etree.Element('geometry')
root.append(geometry)
# We get the location of the simulation centre from the parameters
centre_location = self.get_parameter("CENTRE_LOCATION")
# If it isn't there, then the centre will be the first needle tip, or
# if we have been given "centroid-of-tips" instead of a set of
# coordinates, calculate the centroid of all the tips
if centre_location is None or centre_location == "first-needle":
if self._needles:
centre_location = self.get_needle_parameter(
0, "NEEDLE_TIP_LOCATION")
elif centre_location == "centroid-of-tips":
if self._needles:
needle_tips = [
self.get_needle_parameter(i, "NEEDLE_TIP_LOCATION")
for i in range(len(self._needles))
]
needle_tips = zip(*needle_tips)
centre_location = [
sum(tips) / len(self._needles) for tips in needle_tips
]
# If we have a needle, then use it to set the `needleaxis`
if self._needles:
needle_axis_node = lxml.etree.Element('needleaxis')
# Get the entry and tip of the first needle
tip_location = self.get_needle_parameter(0, "NEEDLE_TIP_LOCATION")
entry_location = self.get_needle_parameter(
0, "NEEDLE_ENTRY_LOCATION")
norm = 0
vec = []
for c, vt, ve in zip(('x', 'y', 'z'), tip_location,
entry_location):
needle_axis_node.set(c, str(ve - vt))
vec.append(ve - vt)
norm += (ve - vt) * (ve - vt)
# Based on the calculated axis, add this to the geometry
geometry.append(needle_axis_node)
# FIXME: is this supposed to be inside this if??
# Use the CENTRE_OFFSET parameter to shift the geometry if required
offset = self.get_parameter("CENTRE_OFFSET")
if offset is not None:
for c, v in enumerate(centre_location):
centre_location[c] = v + offset * vec[c] / math.sqrt(norm)
# After all the calculations above, use the finally chosen centre in the
# geometry section
centre_location_node = lxml.etree.Element("centre")
for c, v in zip(('x', 'y', 'z'), centre_location):
centre_location_node.set(c, str(v))
geometry.append(centre_location_node)
# If we have a simulation scaling parameter, that goes into the geometry
# section also
if self.get_parameter("SIMULATION_SCALING") is not None:
lxml.etree.SubElement(geometry, "simulationscaling") \
.set("ratio",
str(self.get_parameter("SIMULATION_SCALING")))
# Each region goes into the regions section, fairly intuitively
regions = lxml.etree.SubElement(root, "regions")
for name, region in self._regions.items():
regionNode = lxml.etree.SubElement(regions, region["format"])
regionNode.set("name", name)
regionNode.set("input", os.path.join("input/", region["input"]))
regionNode.set("groups", "; ".join(region["groups"]))
# Add the parameters wholesale
parameters = lxml.etree.SubElement(root, "constants")
for key, parameterPair in self._parameters.items():
parameter, typ = parameterPair
parameterNode = lxml.etree.SubElement(parameters, "parameter")
parameterNode.set("name", key)
p = convert_parameter(parameter, typ)
parameterNode.set("value", json.dumps(p))
if typ is not None:
parameterNode.set("type", typ)
name_needle_regions = False
# The needlelibrary needs to know if we have solid needles
needlelibrary = lxml.etree.SubElement(root, 'needlelibrary')
solid_needles = self.get_parameter("SETTING_SOLID_NEEDLES")
if solid_needles is not None:
needlelibrary.set("zones",
"true" if solid_needles is True else "false")
name_needle_regions = True
# The outer mesh, as far as we are concerned, is always CGAL
mesher = lxml.etree.SubElement(root, "mesher")
mesher.set('type', 'CGAL')
# RMV: should this be reinserted?
# if self.get_parameter("SETTING_SOLID_NEEDLES") is True or self.get_parameter("SETTING_ZONE_BOUNDARIES") is True:
mesher.set("zone_boundaries", "true")
# If we have an inner mesh, add it to the mesher
mesher_inner = self.get_parameter("SETTING_AXISYMMETRIC_INNER")
if mesher_inner is not None:
innerNode = lxml.etree.SubElement(mesher, "inner")
innerNode.set("type", "axisymmetric")
innerNode.set("template", mesher_inner)
# Coarse inner, similarly
mesher_inner_coarse = self.get_parameter(
"SETTING_AXISYMMETRIC_INNER_COARSE")
if mesher_inner_coarse is not None:
innerNode = lxml.etree.SubElement(mesher, "inner")
innerNode.set("type", "axisymmetric")
innerNode.set("name", "coarse")
innerNode.set("template", mesher_inner_coarse)
# The extent we assume is a sphere of radius in parameters
extent = lxml.etree.SubElement(mesher, 'extent')
radius = self.get_parameter("SIMULATION_DOMAIN_RADIUS")
if radius is not None:
extent.set('radius', str(radius))
else:
extent.set('radius', '50')
# Adding the empty centre element tells the mesher we want a denser
# centre than the boundaries
lxml.etree.SubElement(mesher, 'centre')
# Start going through the length scales
lengthscales = lxml.etree.SubElement(mesher, 'lengthscales')
# Two sets of fairly sensible defaults for the usual meshing case
if self.get_parameter('RESOLUTION_HIGH'):
lengthscale_settings = [('nearfield', '1.0'), ('farfield', '2.0'),
('zonefield', '1.0'), ('vessels', 'far')]
else:
lengthscale_settings = [('nearfield', '2.0'), ('farfield', '5.0'),
('zonefield', '2.0'), ('vessels', 'far')]
# Allow them to be overridden
nearfield = self.get_parameter('RESOLUTION_FIELD_NEAR')
needlezonefield = self.get_parameter('RESOLUTION_FIELD_NEEDLE_ZONE')
if not needlezonefield:
needlezonefield = self.get_parameter(
'RESOLUTION_NEEDLE_ZONE_FIELD')
farfield = self.get_parameter('RESOLUTION_FIELD_FAR')
zonefield = self.get_parameter('RESOLUTION_FIELD_ZONE')
if nearfield:
lengthscale_settings[0] = ('nearfield', nearfield)
if farfield:
lengthscale_settings[1] = ('farfield', farfield)
if zonefield:
lengthscale_settings[2] = ('zonefield', zonefield)
for k, v in lengthscale_settings:
lengthscales.set(k, str(v))
if needlezonefield:
lengthscales.set("needlezonefield", str(needlezonefield))
farfield = str(lengthscale_settings[1][1])
zonefield = str(lengthscale_settings[2][1])
# Each region may need to be added to the mesher section
for idx, region in self._regions.items():
# If we have an organ, it should appear as a zone or organ
if region['meaning'] == 'organ':
if self.get_parameter('SETTING_ORGAN_AS_SUBDOMAIN'):
zone = lxml.etree.SubElement(mesher, 'zone')
zone.set('region', idx)
zone.set('priority', '100')
zone.set('characteristic_length', farfield)
else:
lxml.etree.SubElement(mesher, 'organ').set('region', idx)
# If we have a zone, not excluded from meshing, then it goes in too
elif region['format'] == 'zone' and not (
set(region['groups']) & self._nonmeshing_groups):
zone = lxml.etree.SubElement(mesher, 'zone')
zone.set('region', idx)
zone.set('priority', '1')
zone.set('characteristic_length', zonefield)
# If we have vessels, they get added also
elif 'vessels' in region['groups'] or 'bronchi' in region['groups']:
# FIXME: surely this should be a surface/vessel tag?
zone = lxml.etree.SubElement(mesher, 'zone')
zone.set('region', idx)
zone.set('priority', '2')
zone.set('characteristic_length', zonefield)
# These are standard entries
lxml.etree.SubElement(root, 'optimizer')
# The register of needles must be filled in
globalNeedlesNode = lxml.etree.SubElement(root, "needles")
if not needlezonefield:
needlezonefield = zonefield
# Make sure all needles are int-castable, or, if not,
# just make up our own ordering
try:
needle_indices = [
int(ix.replace('needle', '')) for ix in self._needles
]
except ValueError:
self._needles = {
str(i + 1): v
for i, v in enumerate(self._needles.values())
}
needle_indices = [int(ix) for ix in self._needles]
augment = (0 in needle_indices)
for ix, needle in self._needles.items():
# Add a needle node and set the name to be our index (if we have
# been given, say, 'needle-3' as an index, it becomes '3')
globalNeedleNode = lxml.etree.SubElement(globalNeedlesNode,
"needle")
l = int(ix.replace('needle', ''))
if augment:
l += 1
globalNeedleNode.set("name", str(l))
# If this needle is a boundary type (the only type for the
# moment)...
if needle['class'] in ('solid-boundary', 'boundary'):
# The 'file' attribute in GSSA should be a colon-separated pair
# indicating what type of definition it is and the specifics
# required
location = needle['input'].split(':', 1)
needle_mesh = None
# If we aren't using a library type, then we need to get the
# region
if location[0] in ('surface', 'zone', 'both'):
needleNode = lxml.etree.SubElement(regions, location[0])
needleNode.set("name", str(l))
needleNode.set("input",
os.path.join("input/", location[1]))
needleNode.set("groups", "needles")
# TODO: surely this might be a surface?
needle_mesh = lxml.etree.SubElement(mesher, 'zone')
needle_mesh.set('region', str(l))
needle_mesh.set('characteristic_length',
str(needlezonefield))
needle_mesh.set('priority', '0')
else:
needleNode = lxml.etree.SubElement(needlelibrary, 'needle')
if name_needle_regions:
needleNode.set("name", str(l))
# If this is a library type, set its ID
if location[0] == 'library':
needleNode.set("id", location[1])
else:
needleNode.set("input", location[1])
needleNode.set("name", str(l))
# Calculate the offset and axis for this needle
tip_location = self.get_needle_parameter(
ix, "NEEDLE_TIP_LOCATION")
entry_location = self.get_needle_parameter(
ix, "NEEDLE_ENTRY_LOCATION")
needleNode.set(
"offset", " ".join(
map(lambda c: str(c[0] - c[1]),
zip(tip_location, centre_location))))
needleNode.set(
"axis", " ".join(
map(lambda c: str(c[0] - c[1]),
zip(entry_location, tip_location))))
needle_scaling = self.get_needle_parameter(
ix, "NEEDLE_SCALING")
if needle_scaling:
needleNode.set("scaling", str(needle_scaling))
# Add any needle-specific parameters
parameters = lxml.etree.SubElement(globalNeedleNode,
"parameters")
for key, parameterPair in needle["parameters"].items():
parameter, typ = parameterPair
parameterNode = lxml.etree.SubElement(
parameters, "constant")
parameterNode.set("name", key)
parameterNode.set(
"value", str(convert_parameter(parameter, typ)))
# Set active region if needs be
needle_active_length = self.get_needle_parameter(
ix, "NEEDLE_ACTIVE_LENGTH")
global_active_length = self.get_needle_parameter(
ix, "CONSTANT_GLOBAL_ACTIVE_LENGTH")
if needle_active_length is None:
needle_active_length = global_active_length
if needle_active_length is not None:
if needle_mesh is None:
needle_mesh = lxml.etree.SubElement(mesher, 'zone')
needle_mesh.set('characteristic_length',
str(needlezonefield))
needle_mesh.set('priority', '0')
needle_mesh.set('region', 'needle-' + str(l))
activity = lxml.etree.SubElement(needle_mesh, 'activity')
tip_location = self.get_needle_parameter(
ix, "NEEDLE_TIP_LOCATION")
for c, vt, vc in zip(('x', 'y', 'z'), tip_location,
centre_location):
activity.set(c, str(vt - vc))
activity.set('r', str(needle_active_length))
self._mesher_xml = root
return self._mesher_xml
