def __init__(self, file_name):
# ~~> 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.fle = {}
self.fle.update({'name': file_name})
# "<" means little-endian, ">" means big-endian
self.fle.update({'endian': ">"})
self.fle.update({'integer': ('i', 4)}) # 'i' size 4
self.fle.update({'float': ('f', 4)}) # 'f' size 4, 'd' = size 8
self.fle.update({'hook': open(file_name, 'r')})
fle = iter(self.fle['hook'])
# ~~ Read/Write dimensions ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Note:
# The section MeshFormat is mandatory
line = fle.next()
proc = re.match(self.frst_keys, line)
if proc:
if proc.group('key') != "MeshFormat":
raise TelemacException(
'... Could not recognise your MSH file format. '
'Missing MeshFormat key.')
line = fle.next().split()
if line[0] != "2.2":
raise TelemacException(
'... Could not read your MSH file format. '
'Only the version 2.2 is allowed.')
file_type = int(line[1])
if file_type == 1:
print('... I have never done this before. Do check it works')
line = fle.next()
_, _, _ = unpack('>i', line.read(4 + 4 + 4))
float_size = int(line[2])
if float_size == 8:
self.fle['float'] = ('d', 8)
line = fle.next()
proc = re.match(self.last_keys, line)
if proc:
if proc.group('key') != "MeshFormat":
raise TelemacException(
'... Could not complete reading the header of you MSH '
'file format. Missing EndMeshFormat key.')
# ~~ Loop on sections ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
while True:
try:
line = fle.next()
except StopIteration:
break
proc = re.match(self.frst_keys, line)
if not proc:
raise TelemacException(
'... Was expecting a new Section starter. '
'Found this instead: {}'.format(line))
key = proc.group('key')
# ~~ Section Nodes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
if key == "Nodes":
print(' +> mesh x,y,z')
npoin = int(fle.next())
if self.fle['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 = fle.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 = fle.next()
# ~~ Section Nodes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
elif proc.group('key') == "Elements":
print(' +> renumbered connectivity')
nelem = int(fle.next())
ikle2 = -np.ones((nelem, 3), dtype=np.int)
for i in range(nelem):
line = fle.next().split()
if int(line[1]) != 2:
continue
expr = line[int(line[2]) + 3:]
ikle2[i] = [
np.int(expr[0]),
np.int(expr[1]),
np.int(expr[2])
]
self.ikle2 = ikle2[np.not_equal(*(np.sort(ikle2).T[0::2]))] - 1
self.nelem2 = len(self.ikle2)
line = fle.next()
# TODO: fitting the unique node numbers with map_nodes ?
# ~~ Unnecessary section ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
else:
while True:
line = fle.next()
if re.match(self.last_keys, line):
break
proc = re.match(self.last_keys, line)
if proc:
if proc.group('key') != key:
raise TelemacException(
'... Could not complete reading the header of your '
'MSH file format. Missing {} end key.'.format(key))
# ~~> 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
_ = Triangulation(self.meshx, self.meshy, self.ikle3)\
.get_cpp_triangulation().get_neighbors()
# ~~> build the enssemble of boundary segments
# ~~> define ipobO from an arbitrary start point
self.ipob3 = np.ones(self.npoin3, dtype=np.int)
self.ipob2 = self.ipob3
def __init__(self, fname, vals=(None, None)):
"""
@brief Main class that fetches the GEBCO bathymetry data and puts it
into the SELAFIN data format
@param fname (string): the name of the GEBCO file
"""
# ~~> 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].lower() == "ncols":
nx1d = int(gline[-1][1])
else:
raise TelemacException(\
'.. Could not read this file format. '
'Key ncols expected here.')
gline.append(gebcofile.readline().split())
if gline[-1][0].lower() == "nrows":
ny1d = int(gline[-1][1])
else:
raise TelemacException(\
'.. Could not read this file format. '
'Key nrows expected here.')
gline.append(gebcofile.readline().split())
if gline[-1][0].lower() == "xllcorner":
xllcorner = np.float(gline[-1][1])
else:
raise TelemacException(\
'.. Could not read this file format. '
'Key xllcorner expected here.')
gline.append(gebcofile.readline().split())
if gline[-1][0].lower() == "yllcorner":
yllcorner = np.float(gline[-1][1])
else:
raise TelemacException(\
'.. Could not read this file format. '
'Key yllcorner expected here.')
gline.append(gebcofile.readline().split())
if gline[-1][0].lower() == "cellsize":
xdim = np.float(gline[-1][1])
ydim = xdim
elif gline[-1][0].lower() in ["xdim", "dx"]:
xdim = np.float(gline[-1][1])
gline.append(gebcofile.readline().split())
if gline[-1][0].lower() in ["ydim", "dy"]:
ydim = np.float(gline[-1][1])
else:
raise TelemacException(\
'.. Could not read this file format.'
' Key ydim expected here.')
else:
raise TelemacException(\
'.. Could not read this file format. '
'Key cellsize or xdim expected here.')
gline.append(gebcofile.readline().split())
if gline[-1][0].lower() == "nodata_value":
nodata_value = int(gline[-1][1])
else:
raise TelemacException(\
'.. Could not read this file format. '
'Key NODATA_value expected here.')
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.join_segments(ebounds)
# ~~> define ipobO from an arbitrary start point
print(' - set')
self.ipob3 = np.zeros(self.npoin3, dtype=np.int)
iptfr = 0
for bound in pbounds:
for n in bound[1:]:
iptfr += 1
self.ipob3[n] = iptfr
self.ipob2 = self.ipob3
def __init__(self, f):
Selafin.__init__(self, f)
self.ikle2, self.meshx, self.meshy, self.ipob2, \
self.interp, self.interp3 = \
subdivide_mesh4(self.ikle2, self.meshx, self.meshy)