def __init__(self, fileName):
# ~~> empty SELAFIN
SELAFIN.__init__(self, '')
self.DATETIME = []
# ~~> variables
self.TITLE = ''
self.NBV1 = 1
self.NVAR = self.NBV1
self.VARINDEX = range(self.NVAR)
self.VARNAMES = ['BOTTOM ']
self.VARUNITS = ['M ']
# ~~ Openning files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
self.file = {}
self.file.update({'name': fileName})
self.file.update({'endian': ">"
}) # "<" means little-endian, ">" means big-endian
self.file.update({'integer': ('i', 4)}) #'i' size 4
self.file.update({'float': ('f', 4)}) #'f' size 4, 'd' = size 8
self.file.update({'hook': open(fileName, 'rt')})
file = iter(self.file['hook'])
# ~~ Read/Write dimensions ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Note:
# The section MeshFormat is mandatory
line = file.next()
proc = re.match(self.frst_keys, line)
if proc:
if proc.group('key') != "MeshFormat":
print '... Could not recognise your MSH file format. Missing MeshFormat key.'
sys.exit(1)
line = file.next().split()
if line[0] != "2.2":
print '... Could not read your MSH file format. Only the version 2.2 is allowed.'
sys.exit(1)
fileType = int(line[1])
if fileType == 1:
print '... I have never done this before. Do check it works'
line = file.next()
l, isize, chk = unpack('>i', line.read(4 + 4 + 4))
floatSize = int(line[2])
if floatSize == 8: self.file['float'] = ('d', 8)
line = file.next()
proc = re.match(self.last_keys, line)
if proc:
if proc.group('key') != "MeshFormat":
print '... Could not complete reading the header of you MSH file format. Missing EndMeshFormat key.'
sys.exit(1)
# ~~ Loop on sections ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
while True:
try:
line = file.next()
except:
break
proc = re.match(self.frst_keys, line)
if not proc:
print '... Was expecting a new Section starter. Found this instead: ', line
sys.exit(1)
key = proc.group('key')
# ~~ Section Nodes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
if key == "Nodes":
print ' +> mesh x,y,z'
NPOIN = int(file.next())
if self.file['float'][0] == 'd':
MESHX = np.zeros(NPOIN, dtype=np.float64)
MESHY = np.zeros(NPOIN, dtype=np.float64)
MESHZ = np.zeros(NPOIN, dtype=np.float64)
else:
MESHX = np.zeros(NPOIN, dtype=np.float)
MESHY = np.zeros(NPOIN, dtype=np.float)
MESHZ = np.zeros(NPOIN, dtype=np.float)
#map_nodes = []
for i in range(NPOIN):
line = file.next().split()
#map_nodes.append(int(line[0]))
MESHX[i] = np.float(line[1])
MESHY[i] = np.float(line[2])
MESHZ[i] = np.float(line[3])
# TODO: renumbering nodes according to map_nodes ?
#map_nodes = np.asarray(map_nodes)
self.NPOIN2 = NPOIN
self.MESHX = MESHX
self.MESHY = MESHY
self.MESHZ = MESHZ
line = file.next()
# ~~ Section Nodes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
elif proc.group('key') == "Elements":
print ' +> renumbered connectivity'
NELEM = int(file.next())
IKLE2 = -np.ones((NELEM, 3), dtype=np.int)
for i in range(NELEM):
line = file.next().split()
if int(line[1]) != 2: continue
e = line[int(line[2]) + 3:]
IKLE2[i] = [np.int(e[0]), np.int(e[1]), np.int(e[2])]
self.IKLE2 = IKLE2[np.not_equal(*(np.sort(IKLE2).T[0::2]))] - 1
self.NELEM2 = len(self.IKLE2)
line = file.next()
# TODO: fitting the unique node numbers with map_nodes ?
# ~~ Unnecessary section ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
else:
while True:
line = file.next()
if re.match(self.last_keys, line): break
proc = re.match(self.last_keys, line)
if proc:
if proc.group('key') != key:
print '... Could not complete reading the header of you MSH file format. Missing ', key, ' end key.'
sys.exit(1)
# ~~> sizes
print ' +> sizes'
self.NDP3 = 3
self.NDP2 = 3
self.NPLAN = 1
self.NELEM3 = self.NELEM2
self.NPOIN3 = self.NPOIN2
self.IKLE3 = self.IKLE2
self.IPARAM = [0, 0, 0, 0, 0, 0, 1, 0, 0, 0]
print ' +> boundaries'
# ~~> establish neighborhood
neighbours = Triangulation(
self.MESHX, self.MESHY,
self.IKLE3).get_cpp_triangulation().get_neighbors()
# ~~> build the enssemble of boundary segments
ebounds = []
#print ' - identify'
#pbar = ProgressBar(maxval=self.NELEM3).start()
#for i in range(self.NELEM3):
# if neighbours[i,0] < 0: ebounds.append([self.IKLE3[i][0],self.IKLE3[i][1]])
# if neighbours[i,1] < 0: ebounds.append([self.IKLE3[i][1],self.IKLE3[i][2]])
# if neighbours[i,2] < 0: ebounds.append([self.IKLE3[i][2],self.IKLE3[i][0]])
# pbar.update(i)
#pbar.finish()
# ~~> assemble the enssemble of boundary segments
#print ' - assemble'
#pbounds = polygons.joinSegments(ebounds)
# ~~> define IPOBO from an arbitrary start point
#print ' - set'
self.IPOB3 = np.ones(self.NPOIN3, dtype=np.int)
#self.IPOB3 = np.zeros(self.NPOIN3,dtype=np.int)
#iptfr = 0
#for p in pbounds:
# for n in p[1:]:
# iptfr += 1
# self.IPOB3[n] = iptfr
self.IPOB2 = self.IPOB3
def __init__(self, fname, vals=(None, None)):
# ~~> empty SELAFIN
SELAFIN.__init__(self, '')
self.DATETIME = []
# ~~> variables
self.TITLE = ''
self.NBV1 = 1 # bathymetry only
self.NVAR = self.NBV1
self.VARINDEX = range(self.NVAR)
self.VARNAMES = ['BOTTOM ']
self.VARUNITS = ['M ']
print ' +> header'
# ~~> load header (ASC type)
gebcofile = open(fname, 'r')
# ~~
gline = []
gline.append(gebcofile.readline().split())
if gline[-1][0] == "ncols": NX1D = int(gline[-1][1])
else:
print '.. Could not read this file format. Key ncols expected here.'
sys.exit(1)
gline.append(gebcofile.readline().split())
if gline[-1][0] == "nrows": NY1D = int(gline[-1][1])
else:
print '.. Could not read this file format. Key nrows expected here.'
sys.exit(1)
gline.append(gebcofile.readline().split())
if gline[-1][0] == "xllcorner": xllcorner = np.float(gline[-1][1])
else:
print '.. Could not read this file format. Key xllcorner expected here.'
sys.exit(1)
gline.append(gebcofile.readline().split())
if gline[-1][0] == "yllcorner": yllcorner = np.float(gline[-1][1])
else:
print '.. Could not read this file format. Key yllcorner expected here.'
sys.exit(1)
gline.append(gebcofile.readline().split())
if gline[-1][0] == "cellsize":
xdim = np.float(gline[-1][1])
ydim = xdim
elif gline[-1][0] in ["xdim", "dx"]:
xdim = np.float(gline[-1][1])
gline.append(gebcofile.readline().split())
if gline[-1][0] in ["ydim", "dy"]: ydim = np.float(gline[-1][1])
else:
print '.. Could not read this file format. Key ydim expected here.'
sys.exit(1)
else:
print '.. Could not read this file format. Key cellsize or xdim expected here.'
sys.exit(1)
gline.append(gebcofile.readline().split())
if gline[-1][0] == "NODATA_value": NODATA_value = int(gline[-1][1])
else:
print '.. Could not read this file format. Key NODATA_value expected here.'
sys.exit(1)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gebcofile.close()
print ' +> bathymetry'
# ~~> load ASCII content, ignoring the header lines
z = np.loadtxt(fname, skiprows=len(gline)).T.ravel()
print ' +> filtered connectivity'
# ~~> temporary IKLE
aval = min(z) - 1
if vals[0] != None: aval = float(vals[0])
bval = max(z) + 1
if vals[1] != None: bval = float(vals[1])
ielem = 0
pbar = ProgressBar(maxval=2 * (NX1D - 1) * (NY1D - 1)).start()
ikle3 = -np.ones((2 * (NX1D - 1) * (NY1D - 1), 3), dtype=np.int)
for i in range(1, NX1D):
for j in range(1, NY1D):
ipoin = (i - 1) * NY1D + j - 1
# ~~> first triangle
if ( aval < z[ipoin] < bval ) and \
( aval < z[ipoin + NY1D] < bval ) and \
( aval < z[ipoin + 1] < bval ):
ikle3[ielem] = [ipoin, ipoin + 1, ipoin + NY1D]
ielem = ielem + 1
pbar.update(ielem)
# ~~> second triangle
if ( aval < z[ipoin + NY1D] < bval ) and \
( aval < z[ipoin + NY1D + 1] < bval ) and \
( aval < z[ipoin + 1] < bval ):
ikle3[ielem] = [ipoin + NY1D, ipoin + 1, ipoin + NY1D + 1]
ielem = ielem + 1
pbar.update(ielem)
pbar.finish()
print ' +> renumbered connectivity'
# ~~> intermediate connectivity
GIKLE = ikle3[np.not_equal(*(np.sort(ikle3).T[0::2]))]
KNOLG = np.unique(np.ravel(GIKLE))
KNOGL = dict(zip(KNOLG, range(len(KNOLG))))
# ~~> final connectivity
self.IKLE3 = -np.ones_like(GIKLE, dtype=np.int)
pbar = ProgressBar(maxval=len(GIKLE)).start()
for k in range(len(GIKLE)):
self.IKLE3[k] = [
KNOGL[GIKLE[k][0]], KNOGL[GIKLE[k][1]], KNOGL[GIKLE[k][2]]
]
pbar.update(k)
pbar.finish()
print ' +> mesh x,y,z'
# ~~> defines grid
x = xllcorner + xdim * np.arange(NX1D, dtype=np.float) - xdim / 2.
y = yllcorner - ydim * np.arange(
NY1D, dtype=np.float) + ydim * NY1D - ydim / 2.
self.MESHX = np.tile(x, NY1D).reshape(NY1D, NX1D).T.ravel()[KNOLG]
self.MESHY = np.tile(y, NX1D)[KNOLG]
self.z = z[KNOLG]
print ' +> sizes'
# ~~> sizes
self.NPLAN = 1
self.NDP2 = 3
self.NDP3 = self.NDP2
self.NPOIN2 = len(self.MESHX)
self.NPOIN3 = self.NPOIN2
self.NELEM2 = len(self.IKLE3)
self.NELEM3 = self.NELEM2
self.IPARAM = [0, 0, 0, 0, 0, 0, 1, 0, 0, 0]
print ' +> boundaries'
# ~~> establish neighborhood
neighbours = Triangulation(
self.MESHX, self.MESHY,
self.IKLE3).get_cpp_triangulation().get_neighbors()
# ~~> build the enssemble of boundary segments
ebounds = []
print ' - identify'
pbar = ProgressBar(maxval=self.NELEM3).start()
for i in range(self.NELEM3):
if neighbours[i, 0] < 0:
ebounds.append([self.IKLE3[i][0], self.IKLE3[i][1]])
if neighbours[i, 1] < 0:
ebounds.append([self.IKLE3[i][1], self.IKLE3[i][2]])
if neighbours[i, 2] < 0:
ebounds.append([self.IKLE3[i][2], self.IKLE3[i][0]])
pbar.update(i)
pbar.finish()
# ~~> assemble the enssemble of boundary segments
print ' - assemble'
pbounds = polygons.joinSegments(ebounds)
# ~~> define IPOBO from an arbitrary start point
print ' - set'
self.IPOB3 = np.zeros(self.NPOIN3, dtype=np.int)
iptfr = 0
for p in pbounds:
for n in p[1:]:
iptfr += 1
self.IPOB3[n] = iptfr
self.IPOB2 = self.IPOB3
