def DetectorArrays(stat):
"""
Return a dictionary of detector array lists contained in the supplied stat
"""
# Detector array data is divided in the stat into one path per array entry. We
# want to collapse this into a dictionary of one path per array. This involves
# lots of horrible parsing of stat paths.
# Find all detector array names and the paths for each entry in the array
arrays = {} # The arrays
notArrayNames = [] # List of candidate array names that are, in fact, not
# detector array names
for path in stat.PathLists():
if isinstance(stat[stat.FormPathFromList(path)], Stat):
# This isn't a leaf node
continue
# Look for an array marker in the path. This appears as:
# [path]%arrayname_index[%component]
# and for coordinates as:
# arrayname_index[%component]
if len(path) >= 2 and path[1] == "position":
# This might be a coordinate entry
firstKey = path[0]
keySplit = firstKey.split("_")
# We have an entry in an array if:
# 1. We have more than one entry in the split
# 2. The final entry in the split contains one of zero (for scalars) or
# two (for vector and tensors) array path delimiters
# 3. The first stat path split of the final entry is an integer (the
# index)
if len(keySplit) <= 1 \
or not len(stat.SplitPath(keySplit[-1])) in [1, 2] \
or not utils.IsIntString(stat.SplitPath(keySplit[-1])[0]):
# This definitely can't be an entry in a detector array
continue
# OK, we have something that looks a bit like an entry for a detector
# array
# Find the array name and the index for this entry
arrayName = utils.FormLine(
[utils.FormLine(keySplit[:-1], delimiter="_", newline=False)] +
path[1:],
delimiter=stat.GetDelimiter(),
newline=False)
index = int(keySplit[-1])
else:
# This might be a field entry
finalKey = path[-1]
keySplit = finalKey.split("_")
# We have an entry in an array if:
# 1. We have more than one entry in the split
# 2. The final entry in the split contains one of zero or one (for field
# components) array path delimiters
# 3. The first stat path split of the final entry is an integer (the
# index)
if len(keySplit) <= 1 \
or not len(stat.SplitPath(keySplit[-1])) in [1, 2] \
or not utils.IsIntString(stat.SplitPath(keySplit[-1])[0]):
# This definitely can't be an entry in a detector array
continue
# OK, we have something that looks a bit like an entry for a detector
# array
# Find the array name and the index for this entry
arrayName = utils.FormLine(
path[:-1] +
[utils.FormLine(keySplit[:-1], delimiter="_", newline=False)],
delimiter=stat.GetDelimiter(),
newline=False)
if len(stat.SplitPath(keySplit[-1])) > 1:
# This array name references a field component
# We need to append the component to the array name. This needs to be
# added to the last but one part of the stat path (the final entry is the
# name of this detector array as configured in Fluidity).
splitName = stat.SplitPath(arrayName)
splitName[-2] = stat.FormPath(splitName[-2],
stat.SplitPath(keySplit[-1])[1])
arrayName = stat.FormPathFromList(splitName)
index = int(stat.SplitPath(keySplit[-1])[0])
else:
# This array name references a field
index = int(keySplit[-1])
if arrayName in notArrayNames:
# We've already discovered that this candidate array name isn't in fact a
# detector array
continue
if index <= 0:
# This isn't a valid index
# This candidate array name isn't in fact a detector array
notArrayNames.append(arrayName)
if arrayName in arrays:
arrays.remove(arrayName)
continue
if arrayName in arrays and index in arrays[arrayName]:
# We've seen this index more than once for this array name
# This candidate apparent array name isn't in fact a detector array
notArrayNames.append(arrayName)
arrays.remove(arrayName)
continue
if arrayName in arrays:
arrays[arrayName][index] = stat[stat.FormPathFromList(path)]
else:
# This is a new array name
arrays[arrayName] = {}
arrays[arrayName][index] = stat[stat.FormPathFromList(path)]
# Convert the dictionaries of data to lists, and check for consecutive
# indices
for name in arrays:
array = arrays[name]
indices = array.keys()
data = [array[index] for index in indices]
indices, data = utils.KeyedSort(indices, data, returnSortedKeys=True)
arrays[name] = numpy.array(data)
for i, index in enumerate(indices):
if not i + 1 == index:
# The indices are not consecutive from one. After all the hard work
# above, we still have an array name that isn't in fact a detector
# array.
arrays.remove(name)
break
# Fantastic! We have our detectors dictionary!
debug.dprint("Detector keys:")
debug.dprint(arrays.keys())
return arrays
def ReadMsh(filename):
"""
Read a Gmsh msh file
"""
def ReadNonCommentLine(fileHandle):
line = fileHandle.readline()
while len(line) > 0:
line = line.strip()
if len(line) > 0:
return line
line = fileHandle.readline()
return line
fileHandle = open(filename, "r")
basename = filename.split(".")[0]
hasHalo = filehandling.FileExists(basename + ".halo")
# Read the MeshFormat section
line = ReadNonCommentLine(fileHandle)
assert(line == "$MeshFormat")
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert(len(lineSplit) == 3)
version = float(lineSplit[0])
fileType = int(lineSplit[1])
dataSize = int(lineSplit[2])
if fileType == 1:
# Binary format
if dataSize == 4:
realFormat = "f"
elif dataSize == 8:
realFormat = "d"
else:
raise Exception("Unrecognised real size " + str(dataSize))
iArr = array.array("i")
iArr.fromfile(fileHandle, 1)
if iArr[0] == 1:
swap = False
else:
iArr.byteswap()
if iArr[0] == 1:
swap = True
else:
raise Exception("Invalid one byte")
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndMeshFormat")
# Read the Nodes section
line = ReadNonCommentLine(fileHandle)
assert(line == "$Nodes")
line = ReadNonCommentLine(fileHandle)
nNodes = int(line)
# Assume dense node IDs, but not necessarily ordered
seenNode = [False for i in range(nNodes)]
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for i in range(nNodes):
iArr = array.array("i")
rArr = array.array(realFormat)
iArr.fromfile(fileHandle, 1)
rArr.fromfile(fileHandle, 3)
if swap:
iArr.byteswap()
rArr.byteswap()
nodeId = iArr[0]
coord = rArr
assert(nodeId > 0)
assert(not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# Read the Elements section
line = ReadNonCommentLine(fileHandle)
assert(line == "$Elements")
line = ReadNonCommentLine(fileHandle)
nEles = int(line)
i = 0
while i < nEles:
iArr = array.array("i")
iArr.fromfile(fileHandle, 3)
if swap:
iArr.byteswap()
typeId = iArr[0]
nSubEles = iArr[1]
nIds = iArr[2]
type = GmshElementType(gmshElementTypeId = typeId)
for j in range(nSubEles):
iArr = array.array("i")
iArr.fromfile(fileHandle, 1 + nIds + type.GetNodeCount())
if swap:
iArr.byteswap()
eleId = iArr[0]
assert(eleId > 0)
ids = iArr[1:1 + nIds]
nodes = FromGmshNodeOrder(utils.OffsetList(iArr[-type.GetNodeCount():], -1), type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) + " encountered in " + str(dim) + " dimensions")
i += nSubEles
assert(i == nEles)
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndElements")
elif fileType == 0:
# ASCII format
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndMeshFormat")
# Read the Nodes section
line = ReadNonCommentLine(fileHandle)
assert(line == "$Nodes")
line = ReadNonCommentLine(fileHandle)
nNodes = int(line)
# Assume dense node IDs, but not necessarily ordered
seenNode = [False for i in range(nNodes)]
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for i in range(nNodes):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert(len(lineSplit) == 4)
nodeId = int(lineSplit[0])
coord = [float(comp) for comp in lineSplit[1:]]
assert(nodeId > 0)
assert(not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# Read the Elements section
line = ReadNonCommentLine(fileHandle)
assert(line == "$Elements")
line = ReadNonCommentLine(fileHandle)
nEles = int(line)
for i in range(nEles):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert(len(lineSplit) > 3)
eleId = int(lineSplit[0])
assert(eleId > 0)
typeId = int(lineSplit[1])
nIds = int(lineSplit[2])
type = GmshElementType(gmshElementTypeId = typeId)
ids = [int(id) for id in lineSplit[3:3 + nIds]]
nodes = FromGmshNodeOrder([int(node) - 1 for node in lineSplit[-type.GetNodeCount():]], type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) + " encountered in " + str(dim) + " dimensions")
line = ReadNonCommentLine(fileHandle)
assert(line == "$EndElements")
# Ignore all remaining sections
else:
raise Exception("File type " + str(fileType) + " not recognised")
fileHandle.close()
if hasHalo:
# Read the .halo file
debug.dprint("Reading .halo file")
if mesh_halos.HaloIOSupport():
halos = mesh_halos.ReadHalos(basename + ".halo")
mesh.SetHalos(halos)
else:
debug.deprint("Warning: No .halo I/O support")
return mesh
def JoinStat(*args):
"""
Joins a series of stat files together. Useful for combining checkpoint .stat
files. Selects data in later stat files over earlier stat files. Assumes
data in stat files are sorted by ElapsedTime.
"""
nStat = len(args)
assert (nStat > 0)
times = [stat["ElapsedTime"] for stat in args]
startT = [t[0] for t in times]
permutation = utils.KeyedSort(startT, range(nStat))
stats = [args[index] for index in permutation]
startT = [startT[index] for index in permutation]
times = [times[index] for index in permutation]
endIndices = numpy.array([len(time) for time in times], dtype=int)
for i, t in enumerate(times[:-1]):
for j, time in enumerate(t):
if calc.AlmostEquals(startT[i + 1], time, tolerance=1.0e-6):
endIndices[i] = max(j - 1, 0)
break
elif startT[i + 1] < time:
endIndices[i] = j
break
debug.dprint("Time ranges:")
if len(times) > 0:
for i in range(nStat):
debug.dprint((startT[i], times[i][endIndices[i] - 1]))
else:
debug.dprint("No data")
dataIndices = numpy.empty(len(args) + 1, dtype=int)
dataIndices[0] = 0
for i, index in enumerate(endIndices):
dataIndices[i + 1] = dataIndices[i] + index
stat = stats[0]
data = {}
for key in stat.keys():
arr = stat[key]
shape = list(arr.shape)
shape[0] = dataIndices[-1]
data[key] = numpy.empty(shape, dtype=arr.dtype)
data[key][:dataIndices[1]] = arr[:endIndices[0]]
data[key][dataIndices[1]:] = calc.Nan()
delimiter = stat.GetDelimiter()
for i in range(1, nStat):
stat = stats[i]
for key in stat.keys():
arr = stat[key]
if not key in data:
shape = list(arr.shape)
shape[0] = dataIndices[-1]
data[key] = numpy.empty(shape, dtype=arr.dtype)
data[key][:dataIndices[i]] = calc.Nan()
data[key][dataIndices[i + 1]:] = calc.Nan()
data[key][dataIndices[i]:dataIndices[i + 1]] = arr[:endIndices[i]]
output = Stat(delimiter=delimiter)
for key in data.keys():
output[key] = numpy.array(data[key])
return output
def ReadAsciiMshV4(fileHandle):
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndMeshFormat")
# skip to the Nodes section
while line != "$Nodes":
line = ReadNonCommentLine(fileHandle)
assert (line == "$Nodes")
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
numBlocks = int(lineSplit[0])
numNodes = int(lineSplit[1])
seenNode = [False] * numNodes
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for b in range(numBlocks):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
subNodes = int(lineSplit[3])
tagArr = [int(ReadNonCommentLine(fileHandle)) for i in range(subNodes)]
for i in range(subNodes):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert (len(lineSplit) == 3)
nodeId = tagArr[i]
coord = [float(comp) for comp in lineSplit]
assert (nodeId > 0)
assert (not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# read the Elements section
line = ReadNonCommentLine(fileHandle)
assert (line == "$Elements")
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
numEntities = int(lineSplit[0])
numElems = int(lineSplit[1])
for i in range(numEntities):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
entityDim = int(lineSplit[0])
entityTag = int(lineSplit[1])
elementType = int(lineSplit[2])
elemsInBlock = int(lineSplit[3])
type = GmshElementType(gmshElementTypeId=elementType)
for j in range(elemsInBlock):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert (len(lineSplit) == 1 + type.GetNodeCount())
ids = [entityTag, int(lineSplit[0])]
nodes = FromGmshNodeOrder(
[int(node) - 1 for node in lineSplit[1:]], type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) +
" encountered in " + str(dim) + " dimensions")
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndElements")
return mesh
def ReadAsciiMshV2(fileHandle):
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndMeshFormat")
# Read the Nodes section
line = ReadNonCommentLine(fileHandle)
assert (line == "$Nodes")
line = ReadNonCommentLine(fileHandle)
nNodes = int(line)
# Assume dense node IDs, but not necessarily ordered
seenNode = [False for i in range(nNodes)]
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for i in range(nNodes):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert (len(lineSplit) == 4)
nodeId = int(lineSplit[0])
coord = [float(comp) for comp in lineSplit[1:]]
assert (nodeId > 0)
assert (not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# Read the Elements section
line = ReadNonCommentLine(fileHandle)
assert (line == "$Elements")
line = ReadNonCommentLine(fileHandle)
nEles = int(line)
for i in range(nEles):
line = ReadNonCommentLine(fileHandle)
lineSplit = line.split()
assert (len(lineSplit) > 3)
eleId = int(lineSplit[0])
assert (eleId > 0)
typeId = int(lineSplit[1])
nIds = int(lineSplit[2])
type = GmshElementType(gmshElementTypeId=typeId)
ids = [int(id) for id in lineSplit[3:3 + nIds]]
nodes = FromGmshNodeOrder(
[int(node) - 1 for node in lineSplit[-type.GetNodeCount():]], type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) +
" encountered in " + str(dim) + " dimensions")
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndElements")
return mesh
def ReadBinaryMshV4(fileHandle, dataSize):
if dataSize == 4:
sizeFormat = "i"
elif dataSize == 8:
sizeFormat = "l"
else:
raise Exception("Unrecognised size_t size " + str(dataSize))
swap = ByteSwap(fileHandle)
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndMeshFormat")
# skip ahead to Nodes section (possibly bypassing Entities)
while line != "$Nodes":
line = ReadNonCommentLine(fileHandle)
assert (line == "$Nodes")
# numEntityBlock(size_t) numNodes(size_t)
# minNodeTag(size_t) maxNodeTag(size_t)
#
# entityDim(int) entityTag(int) parametric(int) numNodes(size_t)
#
# nodeTag(size_t) ...
# x(double) y(double) z(double) ...
# ...
sArr = array.array(sizeFormat)
sArr.fromfile(fileHandle, 4)
if swap:
sArr.byteswap()
numBlocks = sArr[0]
numNodes = sArr[1]
# assume dense nodes (we can check using the min/max id fields)
seenNode = [False] * numNodes
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for b in range(numBlocks):
iArr = array.array("i")
sArr = array.array(sizeFormat)
iArr.fromfile(fileHandle, 3)
sArr.fromfile(fileHandle, 1)
if swap:
iArr.byteswap()
sArr.byteswap()
subNodes = sArr[0]
tagArr = array.array(sizeFormat)
tagArr.fromfile(fileHandle, subNodes)
if swap:
tagArr.byteswap()
for i in range(subNodes):
rArr = array.array("d")
rArr.fromfile(fileHandle, 3)
if swap:
rArr.byteswap()
nodeId = tagArr[i]
coord = rArr
assert (nodeId > 0)
assert (not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# read the Elements section
line = ReadNonCommentLine(fileHandle)
assert (line == "$Elements")
# numEntityBlocks(size_t) numElements(size_t)
# minElementTag(size_t) maxElementTag(size_t)
#
# entityDim(int) entityTag(int) elementType(int) numElems(size_t)
# elementTag(size_t) nodeTag(size_t) ...
# ...
# ...
sArr = array.array(sizeFormat)
sArr.fromfile(fileHandle, 4)
if swap:
sArr.byteswap()
numEntities = sArr[0]
numElems = sArr[1]
for i in range(numEntities):
iArr = array.array("i")
sArr = array.array(sizeFormat)
iArr.fromfile(fileHandle, 3)
sArr.fromfile(fileHandle, 1)
if swap:
iArr.byteswap()
sArr.byteswap()
entityDim = iArr[0]
entityTag = iArr[1]
elementType = iArr[2]
elemsInBlock = sArr[0]
type = GmshElementType(gmshElementTypeId=elementType)
for j in range(elemsInBlock):
sArr = array.array(sizeFormat)
sArr.fromfile(1 + type.GetNodeCount())
if swap:
sArr.byteswap()
ids = [entityTag, sArr[0]]
nodes = FromGmshNodeOrder(utils.OffsetList(sArr[1:], -1), type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) +
" encountered in " + str(dim) + " dimensions")
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndElements")
return mesh
def ReadBinaryMshV2(fileHandle, dataSize):
if dataSize == 4:
realFormat = "f"
elif dataSize == 8:
realFormat = "d"
else:
raise Exception("Unrecognised real size " + str(dataSize))
swap = ByteSwap(fileHandle)
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndMeshFormat")
# Read the Nodes section (no PhysicalNames section in binary)
line = ReadNonCommentLine(fileHandle)
assert (line == "$Nodes")
# number-of-nodes
# node-number x-coord y-coord z-coord
# ...
line = ReadNonCommentLine(fileHandle)
nNodes = int(line)
# Assume dense node IDs, but not necessarily ordered
seenNode = [False for i in range(nNodes)]
nodeIds = []
nodes = []
lbound = [calc.Inf() for i in range(3)]
ubound = [-calc.Inf() for i in range(3)]
for i in range(nNodes):
iArr = array.array("i")
rArr = array.array(realFormat)
iArr.fromfile(fileHandle, 1)
rArr.fromfile(fileHandle, 3)
if swap:
iArr.byteswap()
rArr.byteswap()
nodeId = iArr[0]
coord = rArr
assert (nodeId > 0)
assert (not seenNode[nodeId - 1])
seenNode[nodeId - 1] = True
nodeIds.append(nodeId)
nodes.append(coord)
for j in range(3):
lbound[j] = min(lbound[j], coord[j])
ubound[j] = max(ubound[j], coord[j])
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndNodes")
nodes = utils.KeyedSort(nodeIds, nodes)
bound = bounds.BoundingBox(lbound, ubound)
indices = bound.UsedDimIndices()
dim = len(indices)
if dim < 3:
nodes = [[coord[index] for index in indices] for coord in nodes]
mesh = meshes.Mesh(dim)
mesh.AddNodeCoords(nodes)
# Read the Elements section
line = ReadNonCommentLine(fileHandle)
assert (line == "$Elements")
# number-of-elements
# element-header-binary
# element-binary
# ...
# where element-header-binary is: elm-type num-elm num-tags
# where element-binary is:
# num-elm * (4 + num-tags*4 + node-num*4)
# node-num physical-tag elementary-tag node-nums ...
line = ReadNonCommentLine(fileHandle)
nEles = int(line)
i = 0
while i < nEles:
iArr = array.array("i")
iArr.fromfile(fileHandle, 3)
if swap:
iArr.byteswap()
typeId = iArr[0]
nSubEles = iArr[1]
nIds = iArr[2]
type = GmshElementType(gmshElementTypeId=typeId)
for j in range(nSubEles):
iArr = array.array("i")
iArr.fromfile(fileHandle, 1 + nIds + type.GetNodeCount())
if swap:
iArr.byteswap()
eleId = iArr[0]
assert (eleId > 0)
ids = iArr[1:1 + nIds]
nodes = FromGmshNodeOrder(
utils.OffsetList(iArr[-type.GetNodeCount():], -1), type)
element = elements.Element(nodes, ids)
if type.GetDim() == dim - 1:
mesh.AddSurfaceElement(element)
elif type.GetDim() == dim:
mesh.AddVolumeElement(element)
else:
debug.deprint("Warning: Element of type " + str(type) +
" encountered in " + str(dim) + " dimensions")
i += nSubEles
assert (i == nEles)
line = ReadNonCommentLine(fileHandle)
assert (line == "$EndElements")
return mesh
