def BoundingBox(self):
lbound = [calc.Inf() for i in range(self.GetDim())]
ubound = [-calc.Inf() for i in range(self.GetDim())]
for nodeCoord in self.GetNodeCoords():
for i, val in enumerate(nodeCoord):
if val < lbound[i]:
lbound[i] = val
if val > ubound[i]:
ubound[i] = val
return bounds.BoundingBox(lbound, ubound)
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 ReadGid(filename):
"""
Read a GiD file with the given filename, and return it as a mesh
"""
debug.dprint("Reading GiD mesh with filename " + filename)
fileHandle = open(filename, "r")
# Read the header
header = fileHandle.readline()
lineSplit = header.split()
assert(lineSplit[0] == "MESH")
dimension = None
elemType = None
nnode = None
for i, word in enumerate(lineSplit[:len(lineSplit) - 1]):
if word == "dimension":
dimension = int(lineSplit[i + 1])
assert(dimension >= 0)
elif word == "ElemType":
elemType = lineSplit[i + 1]
elif word == "Nnode":
nnode = int(lineSplit[i + 1])
assert(nnode >= 0)
assert(not dimension is None)
assert(not elemType is None)
assert(not nnode is None)
debug.dprint("Dimension = " + str(dimension))
debug.dprint("Element type = " + elemType)
debug.dprint("Element nodes = " + str(nnode))
# Read the nodes
nodeCoords = []
line = fileHandle.readline()
index = 0
while len(line) > 0:
if line.strip() == "Coordinates":
line = fileHandle.readline()
while not line.strip() == "end coordinates":
assert(len(line) > 0)
index += 1
lineSplit = line.split()
assert(len(lineSplit) == 1 + dimension)
assert(int(lineSplit[0]) == index)
nodeCoords.append([float(coord) for coord in lineSplit[1:]])
line = fileHandle.readline()
break
line = fileHandle.readline()
debug.dprint("Nodes: " + str(index))
# Check for unused dimensions
lbound = [calc.Inf() for i in range(dimension)]
ubound = [-calc.Inf() for i in range(dimension)]
for nodeCoord in nodeCoords:
for i, val in enumerate(nodeCoord):
lbound[i] = min(lbound[i], val)
ubound[i] = max(ubound[i], val)
boundingBox = bounds.BoundingBox(lbound, ubound)
actualDimension = boundingBox.UsedDim()
if not dimension == actualDimension:
debug.deprint("Dimension suggested by bounds = " + str(actualDimension))
debug.deprint("Warning: Header dimension inconsistent with bounds")
dimension = actualDimension
coordMask = boundingBox.UsedDimCoordMask()
nodeCoords = [utils.MaskList(nodeCoord, coordMask) for nodeCoord in nodeCoords]
mesh = meshes.Mesh(dimension)
mesh.AddNodeCoords(nodeCoords)
fileHandle.seek(0)
# Read the volume elements
line = fileHandle.readline()
index = 0
while len(line) > 0:
if line.strip() == "Elements":
line = fileHandle.readline()
while not line.strip() == "end elements":
assert(len(line) > 0)
index += 1
lineSplit = line.split()
assert(len(lineSplit) == 1 + nnode)
assert(int(lineSplit[0]) == index)
# Note: GiD file indexes nodes from 1, Mesh s index nodes from 0
mesh.AddVolumeElement(elements.Element(nodes = FromGidNodeOrder([int(node) - 1 for node in lineSplit[1:]], elements.ElementType(dim = dimension, nodeCount = nnode))))
line = fileHandle.readline()
break
line = fileHandle.readline()
debug.dprint("Elements: " + str(index))
fileHandle.close()
debug.dprint("Finished reading GiD mesh")
return mesh
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