def ReadMsh(filename):
"""
Read a Gmsh msh file
"""
fileHandle = open(filename, "rb")
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 = lineSplit[0]
fileType = int(lineSplit[1])
dataSize = int(lineSplit[2])
if version[0] == "4" and version < "4.1":
raise Exception("gmshtools doesn't handle msh4 with minor version 0")
if fileType == 1:
# Binary format
if version[0] == "4":
mesh = ReadBinaryMshV4(fileHandle, dataSize)
elif version[0] == "2":
mesh = ReadBinaryMshV2(fileHandle, dataSize)
else:
raise Exception("Unknown gmsh major version")
elif fileType == 0:
# ASCII format
if version[0] == "4":
mesh = ReadAsciiMshV4(fileHandle)
elif version[0] == "2":
mesh = ReadAsciiMshV2(fileHandle)
else:
raise Exception("Unknown gmsh major version")
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 FindPFilenames(basename, extension):
filenames = []
i = 0
while True:
filename = basename + "_" + str(i)
if filehandling.FileExists(filename + extension):
filenames.append(filename)
else:
break
i += 1
return filenames
def hasFaceFile(basename): return filehandling.FileExists(basename + ".face")
def hasEdgeFile(basename): return filehandling.FileExists(basename + ".edge")
def ReadTriangle(baseName):
"""
Read triangle files with the given base name, and return it as a mesh
"""
def StripComment(line):
if "#" in line:
return line.split("#")[0]
else:
return line
def ReadNonCommentLine(fileHandle):
line = fileHandle.readline()
while len(line) > 0:
line = StripComment(line).strip()
if len(line) > 0:
return line
line = fileHandle.readline()
return line
# Determine which files exist
assert(filehandling.FileExists(baseName + ".node"))
hasBound = filehandling.FileExists(baseName + ".bound")
hasEdge = filehandling.FileExists(baseName + ".edge")
hasFace = filehandling.FileExists(baseName + ".face")
hasEle = filehandling.FileExists(baseName + ".ele")
hasHalo = filehandling.FileExists(baseName + ".halo")
# Read the .node file
nodeHandle = open(baseName + ".node", "r")
# Extract the meta data
line = ReadNonCommentLine(nodeHandle)
lineSplit = line.split()
assert(len(lineSplit) == 4)
nNodes = int(lineSplit[0])
assert(nNodes >= 0)
dim = int(lineSplit[1])
assert(dim >= 0)
nNodeAttrs = int(lineSplit[2])
assert(nNodeAttrs >= 0)
nNodeIds = int(lineSplit[3])
assert(nNodeIds >= 0)
mesh = meshes.Mesh(dim)
# Read the nodes
debug.dprint("Reading .node file")
for line in nodeHandle.readlines():
line = StripComment(line)
if len(line.strip()) == 0:
continue
lineSplit = line.split()
assert(len(lineSplit) == 1 + dim + nNodeAttrs + nNodeIds)
mesh.AddNodeCoord([float(coord) for coord in lineSplit[1:dim + 1]])
assert(mesh.NodeCoordsCount() == nNodes)
nodeHandle.close()
if hasBound and dim == 1:
# Read the .bound file
debug.dprint("Reading .bound file")
boundHandle = open(baseName + ".bound", "r")
# Extract the meta data
line = ReadNonCommentLine(boundHandle)
lineSplit = line.split()
assert(len(lineSplit) == 2)
nBounds = int(lineSplit[0])
assert(nBounds >= 0)
nBoundIds = int(lineSplit[1])
assert(nBoundIds >= 0)
# Read the bounds
for line in boundHandle.readlines():
line = StripComment(line)
if len(line.strip()) == 0:
continue
lineSplit = line.split()
assert(len(lineSplit) == 2 + nBoundIds)
element = elements.Element()
for node in lineSplit[1:2]:
element.AddNode(int(node) - 1)
element.SetIds([int(boundId) for boundId in lineSplit[2:]])
mesh.AddSurfaceElement(element)
assert(mesh.SurfaceElementCount() == nBounds)
boundHandle.close()
if hasEdge and dim == 2:
# Read the .edge file
debug.dprint("Reading .edge file")
edgeHandle = open(baseName + ".edge", "r")
# Extract the meta data
line = ReadNonCommentLine(edgeHandle)
lineSplit = line.split()
assert(len(lineSplit) == 2)
nEdges = int(lineSplit[0])
assert(nEdges >= 0)
nEdgeIds = int(lineSplit[1])
assert(nEdgeIds >= 0)
# Read the edges
for line in edgeHandle.readlines():
line = StripComment(line)
if len(line.strip()) == 0:
continue
lineSplit = line.split()
assert(len(lineSplit) == 3 + nEdgeIds)
element = elements.Element()
for node in lineSplit[1:3]:
element.AddNode(int(node) - 1)
element.SetIds([int(edgeId) for edgeId in lineSplit[3:]])
mesh.AddSurfaceElement(element)
assert(mesh.SurfaceElementCount() == nEdges)
edgeHandle.close()
if hasFace and dim > 2:
# Read the .face file
debug.dprint("Reading .face file")
faceHandle = open(baseName + ".face", "r")
# Extract the meta data
line = ReadNonCommentLine(faceHandle)
lineSplit = line.split()
assert(len(lineSplit) == 2)
nFaces = int(lineSplit[0])
assert(nFaces >= 0)
nFaceIds = int(lineSplit[1])
assert(nFaceIds >= 0)
# Read the faces
for line in faceHandle.readlines():
line = StripComment(line)
if len(line.strip()) == 0:
continue
lineSplit = line.split()
assert(len(lineSplit) >= 4 + nFaceIds)
element = elements.Element()
for node in lineSplit[1:len(lineSplit) - nFaceIds]:
element.AddNode(int(node) - 1)
element.SetIds([int(faceId) for faceId in lineSplit[len(lineSplit) - nFaceIds:]])
mesh.AddSurfaceElement(element)
assert(mesh.SurfaceElementCount() == nFaces)
faceHandle.close()
if hasEle:
# Read the .ele file
debug.dprint("Reading .ele file")
eleHandle = open(baseName + ".ele", "r")
# Extract the meta data
line = ReadNonCommentLine(eleHandle)
lineSplit = line.split()
assert(len(lineSplit) == 3)
nEles = int(lineSplit[0])
assert(nEles >= 0)
nNodesPerEle = int(lineSplit[1])
assert(nNodesPerEle >= 0)
nEleIds = int(lineSplit[2])
assert(nEleIds >= 0)
# Read the eles
for line in eleHandle.readlines():
line = StripComment(line)
if len(line.strip()) == 0:
continue
lineSplit = line.split()
assert(len(lineSplit) == 1 + nNodesPerEle + nEleIds)
element = elements.Element()
for node in lineSplit[1:len(lineSplit) - nEleIds]:
element.AddNode(int(node) - 1)
element.SetIds([int(eleId) for eleId in lineSplit[len(lineSplit) - nEleIds:]])
mesh.AddVolumeElement(element)
assert(mesh.VolumeElementCount() == nEles)
eleHandle.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 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 Read(self, filename, includeMc=False, subsample=1):
"""
Read a .stat file
"""
def ParseRawS(s, delimiter):
newS = {}
for key1 in s.keys():
assert (not key1 in ["val", "value"])
if isinstance(s[key1], dict):
if len(s[key1]) == 1 and ("val" in s[key1]
or "value" in s[key1]):
newS[str(key1)] = list(s[key1].values())[0]
else:
subS = ParseRawS(s[key1], delimiter)
newS[str(key1)] = {}
for key2 in subS.keys():
newS[str(key1)][str(key2)] = subS[key2]
else:
rank = len(s[key1].shape)
if rank > 1:
assert (rank == 2)
if includeMc:
# Add in this vector
# stat_parser gives this in an inconvenient matrix order. Take the
# transpose here to make life easier.
newS[str(key1)] = s[key1].transpose()
# Add in the vector field components
for i in range(len(s[key1])):
newS[str(key1) + delimiter +
str(i + 1)] = s[key1][i]
else:
try:
# Add in this scalar
newS[str(key1)] = s[key1]
except TypeError:
debug.deprint(
"Type error for data " + str(s[key1]), 0)
raise Exception("ParseRawS failure")
except ValueError:
debug.deprint(
"Value error for data " + str(s[key1]), 0)
raise Exception("ParseRawS failure")
return newS
debug.dprint("Reading .stat file: " + filename)
if filehandling.FileExists(filename + ".dat"):
debug.dprint("Format: binary")
else:
debug.dprint("Format: plain text")
if subsample == 1:
# Handle this case separately, as it's convenient to be backwards
# compatible
statParser = stat_parser(filename)
else:
statParser = stat_parser(filename, subsample=subsample)
self._s = ParseRawS(statParser, self._delimiter)
if "ElapsedTime" in self.keys():
t = self["ElapsedTime"]
if t.shape[0] > 0:
debug.dprint("Time range: " + str((t[0], t[-1])))
else:
debug.dprint("Time range: No data")
return
