def read_ascii_t(frame, path="./", file_prefix="fort"):
r"""Read only the fort.t file and return the data
:Input:
- *frame* - (int) Frame number to be read in
- *path* - (string) Path to the current directory of the file
- *file_prefix* - (string) Prefix of the files to be read in.
``default = 'fort'``
:Output:
- (list) List of output variables
- *t* - (int) Time of frame
- *meqn* - (int) Number of equations in the frame
- *ngrids* - (int) Number of grids
- *maux* - (int) Auxillary value in the frame
- *ndim* - (int) Number of dimensions in q and aux
"""
base_path = os.path.join(path, )
path = os.path.join(base_path, "%s.t" % file_prefix) + str(frame).zfill(4)
try:
logger.debug("Opening %s file." % path)
f = open(path, "r")
t = read_data_line(f)
meqn = read_data_line(f, type="int")
ngrids = read_data_line(f, type="int")
maux = read_data_line(f, type="int")
ndim = read_data_line(f, type="int")
f.close()
except (IOError):
raise
except:
logger.error("File " + t_fname +
" should contain t, meqn, ngrids, maux, ndim")
print(("File " + t_fname +
" should contain t, meqn, ngrids, maux, ndim"))
raise
return t, meqn, ngrids, maux, ndim
def read_ascii_t(frame, path='./', file_prefix='fort'):
r"""Read only the fort.t file and return the data
:Input:
- *frame* - (int) Frame number to be read in
- *path* - (string) Path to the current directory of the file
- *file_prefix* - (string) Prefix of the files to be read in.
``default = 'fort'``
:Output:
- (list) List of output variables
- *t* - (int) Time of frame
- *num_eqn* - (int) Number of equations in the frame
- *nstates* - (int) Number of states
- *num_aux* - (int) Auxillary value in the frame
- *num_dim* - (int) Number of dimensions in q and aux
"""
base_path = os.path.join(path, )
path = os.path.join(base_path, '%s.t' % file_prefix) + str(frame).zfill(4)
try:
logger.debug("Opening %s file." % path)
f = open(path, 'r')
t = read_data_line(f)
num_eqn = read_data_line(f, type='int')
nstates = read_data_line(f, type='int')
num_aux = read_data_line(f, type='int')
num_dim = read_data_line(f, type='int')
f.close()
except (IOError):
raise
except:
logger.error("File " + path +
" should contain t, num_eqn, nstates, num_aux, num_dim")
print "File " + path + " should contain t, num_eqn, nstates, num_aux, num_dim"
raise
return t, num_eqn, nstates, num_aux, num_dim
def read_ascii_t(frame,path='./',file_prefix='fort'):
r"""Read only the fort.t file and return the data
:Input:
- *frame* - (int) Frame number to be read in
- *path* - (string) Path to the current directory of the file
- *file_prefix* - (string) Prefix of the files to be read in.
``default = 'fort'``
:Output:
- (list) List of output variables
- *t* - (int) Time of frame
- *meqn* - (int) Number of equations in the frame
- *nstates* - (int) Number of states
- *maux* - (int) Auxillary value in the frame
- *ndim* - (int) Number of dimensions in q and aux
"""
base_path = os.path.join(path,)
path = os.path.join(base_path, '%s.t' % file_prefix) + str(frame).zfill(4)
try:
logger.debug("Opening %s file." % path)
f = open(path,'r')
t = read_data_line(f)
meqn = read_data_line(f,type='int')
nstates = read_data_line(f,type='int')
maux = read_data_line(f,type='int')
ndim = read_data_line(f,type='int')
f.close()
except(IOError):
raise
except:
logger.error("File " + t_fname + " should contain t, meqn, nstates, maux, ndim")
print "File " + t_fname + " should contain t, meqn, nstates, maux, ndim"
raise
return t,meqn,nstates,maux,ndim
def read_ascii(solution,frame,path='./',file_prefix='fort',read_aux=False,
options={}):
r"""
Read in a set of ascii formatted files
This routine reads the ascii formatted files corresponding to the classic
clawpack format 'fort.txxxx', 'fort.qxxxx', and 'fort.axxxx' or 'fort.aux'
Note that the fort prefix can be changed.
:Input:
- *solution* - (:class:`~pyclaw.solution.Solution`) Solution object to
read the data into.
- *frame* - (int) Frame number to be read in
- *path* - (string) Path to the current directory of the file
- *file_prefix* - (string) Prefix of the files to be read in.
``default = 'fort'``
- *read_aux* (bool) Whether or not an auxillary file will try to be read
in. ``default = False``
- *options* - (dict) Dictionary of options particular to this format
which in the case of ``ascii`` files is empty.
"""
import numpy as np
# Option parsing
option_defaults = {}
for (k,v) in option_defaults.iteritems():
if options.has_key(k):
exec("%s = options['%s']" % (k,k))
else:
exec('%s = v' % k)
if frame < 0:
# Don't construct file names with negative frameno values.
raise IOError("Frame " + str(frame) + " does not exist ***")
# Construct path names
base_path = os.path.join(path,)
# t_fname = os.path.join(base_path, '%s.t' % file_prefix) + str(frame).zfill(4)
q_fname = os.path.join(base_path, '%s.q' % file_prefix) + str(frame).zfill(4)
# Read in values from fort.t file:
[t,meqn,nstates,maux,ndim] = read_ascii_t(frame,path,file_prefix)
# Read in values from fort.q file:
try:
f = open(q_fname,'r')
# Loop through every grid setting the appropriate information
# for ng in range(len(solution.grids)):
for m in xrange(nstates):
# Read in base header for this grid
gridno = read_data_line(f,type='int')
level = read_data_line(f,type='int')
n = np.zeros((ndim))
lower = np.zeros((ndim))
d = np.zeros((ndim))
for i in xrange(ndim):
n[i] = read_data_line(f,type='int')
for i in xrange(ndim):
lower[i] = read_data_line(f)
for i in xrange(ndim):
d[i] = read_data_line(f)
blank = f.readline()
# Construct the grid
# Since we do not have names here, we will construct the grid with
# the assumed dimensions x,y,z
names = ['x','y','z']
dimensions = []
for i in xrange(ndim):
dimensions.append(
pyclaw.grid.Dimension(names[i],lower[i],lower[i] + n[i]*d[i],n[i]))
grid = pyclaw.grid.Grid(dimensions)
state= pyclaw.state.State(grid,meqn,maux)
state.t = t
# RJL 1/8/10: Changed empty_aux to zeros_aux below so aux won't
# be filled with random values if aux arrays not read in. Would
# like to delete this and initialize grid.aux only if it will be
# read in below, but for some reason that doesn't work.
if maux > 0:
state.aux[:]=0.
# Fill in q values
if grid.ndim == 1:
for i in xrange(grid.dimensions[0].n):
l = []
while len(l)<state.meqn:
line = f.readline()
l = l + line.split()
for m in xrange(state.meqn):
state.q[m,i] = float(l[m])
elif grid.ndim == 2:
for j in xrange(grid.dimensions[1].n):
for i in xrange(grid.dimensions[0].n):
l = []
while len(l)<state.meqn:
line = f.readline()
l = l + line.split()
for m in xrange(state.meqn):
state.q[m,i,j] = float(l[m])
blank = f.readline()
elif grid.ndim == 3:
raise NotImplementedError("3d still does not work!")
for k in xrange(grid.dimensions[2].n):
for j in xrange(grid.dimensions[1].n):
for i in xrange(grid.dimensions[0].n):
l=[]
while len(l) < state.meqn:
line = f.readline()
l = l + line.split()
for m in xrange(state.meqn):
state.q[m,i,j,k] = float(l[m])
blank = f.readline()
blank = f.readline()
else:
msg = "Read only supported up to 3d."
logger.critical(msg)
raise Exception(msg)
# Add AMR attributes:
grid.gridno = gridno
grid.level = level
# Add new grid to solution
solution.states.append(state)
except(IOError):
raise
except:
logger.error("File %s was not able to be read." % q_fname)
raise
# Read auxillary file if available and requested
if solution.states[0].maux > 0 and read_aux:
# Check for aux file
fname1 = os.path.join(base_path,'%s.a' % file_prefix)+str(frame).zfill(4)
fname2 = os.path.join(base_path,'%s.a' % file_prefix)
if os.path.exists(fname1):
fname = fname1
elif os.path.exists(fname2):
fname = fname2
else:
logger.info("Unable to open auxillary file %s or %s" % (fname1,fname2))
return
# Found a valid path, try to open and read it
try:
f = open(fname,'r')
# Read in aux file
for n in xrange(len(solution.states)):
# Fetch correct grid
gridno = read_data_line(f,type='int')
grid = solution.states[gridno-1].grid
# These should match this grid already, raise exception otherwise
if not (grid.level == read_data_line(f,type='int')):
raise IOError("Grid level in aux file header did not match grid no %s." % grid.gridno)
for dim in grid.dimensions:
if not (dim.n == read_data_line(f,type='int')):
raise IOError("Dimension %s's n in aux file header did not match grid no %s." % (dim.name,grid.gridno))
for dim in grid.dimensions:
if not (dim.lower == read_data_line(f,type='float')):
raise IOError("Dimension %s's lower in aux file header did not match grid no %s." % (dim.name,grid.gridno))
for dim in grid.dimensions:
if not (dim.d == read_data_line(f,type='float')):
raise IOError("Dimension %s's d in aux file header did not match grid no %s." % (dim.name,grid.gridno))
f.readline()
# Read in auxillary array
if grid.ndim == 1:
for i in xrange(grid.dimensions[0].n):
l = []
while len(l)<state.maux:
line = f.readline()
l = l + line.split()
for m in xrange(state.maux):
state.aux[i,m] = float(l[m])
elif grid.ndim == 2:
for j in xrange(grid.dimensions[1].n):
for i in xrange(grid.dimensions[0].n):
l = []
while len(l)<state.maux:
line = f.readline()
l = l + line.split()
for m in xrange(state.maux):
state.aux[i,j,m] = float(l[m])
blank = f.readline()
elif grid.ndim == 3:
for k in xrange(grid.dimensions[2].n):
for j in xrange(grid.dimensions[1].n):
for i in xrange(grid.dimensions[0].n):
l = []
while len(l)<state.maux:
line = f.readline()
l = l + line.split()
for m in xrange(state.maux):
state.aux[i,j,k,m] = float(l[m])
blank = f.readline()
blank = f.readline()
else:
logger.critical("Read aux only up to 3d is supported.")
raise Exception("Read aux only up to 3d is supported.")
except(IOError):
raise
except:
logger.error("File %s was not able to be read." % q_fname)
raise
def read_ascii(solution,
frame,
path='./',
file_prefix='fort',
read_aux=False,
options={}):
r"""
Read in a set of ascii formatted files
This routine reads the ascii formatted files corresponding to the classic
clawpack format 'fort.txxxx', 'fort.qxxxx', and 'fort.axxxx' or 'fort.aux'
Note that the fort prefix can be changed.
:Input:
- *solution* - (:class:`~pyclaw.solution.Solution`) Solution object to
read the data into.
- *frame* - (int) Frame number to be read in
- *path* - (string) Path to the current directory of the file
- *file_prefix* - (string) Prefix of the files to be read in.
``default = 'fort'``
- *read_aux* (bool) Whether or not an auxillary file will try to be read
in. ``default = False``
- *options* - (dict) Dictionary of options particular to this format
which in the case of ``ascii`` files is empty.
"""
# Option parsing
option_defaults = {}
for (k, v) in option_defaults.iteritems():
if options.has_key(k):
exec("%s = options['%s']" % (k, k))
else:
exec('%s = v' % k)
if frame < 0:
# Don't construct file names with negative frameno values.
raise IOError("Frame " + str(frame) + " does not exist ***")
# Construct path names
base_path = os.path.join(path, )
# t_fname = os.path.join(base_path, '%s.t' % file_prefix) + str(frame).zfill(4)
q_fname = os.path.join(base_path,
'%s.q' % file_prefix) + str(frame).zfill(4)
# Read in values from fort.t file:
[t, meqn, ngrids, maux, ndim] = read_ascii_t(frame, path, file_prefix)
# Read in values from fort.q file:
try:
f = open(q_fname, 'r')
# Loop through every grid setting the appropriate information
# for ng in range(len(solution.grids)):
for m in xrange(ngrids):
# Read in base header for this grid
gridno = read_data_line(f, type='int')
level = read_data_line(f, type='int')
n = np.zeros((ndim))
lower = np.zeros((ndim))
d = np.zeros((ndim))
for i in xrange(ndim):
n[i] = read_data_line(f, type='int')
for i in xrange(ndim):
lower[i] = read_data_line(f)
for i in xrange(ndim):
d[i] = read_data_line(f)
blank = f.readline()
# Construct the grid
# Since we do not have names here, we will construct the grid with
# the assumed dimensions x,y,z
names = ['x', 'y', 'z']
dimensions = []
for i in xrange(ndim):
dimensions.append(
pyclaw.solution.Dimension(names[i], lower[i],
lower[i] + n[i] * d[i], n[i]))
grid = pyclaw.solution.Grid(dimensions)
grid.t = t
grid.meqn = meqn
# RJL 1/8/10: Changed empty_aux to zeros_aux below so aux won't
# be filled with random values if aux arrays not read in. Would
# like to delete this and initialize grid.aux only if it will be
# read in below, but for some reason that doesn't work.
if maux > 0:
grid.zeros_aux(maux)
# Fill in q values
grid.empty_q()
if grid.ndim == 1:
for i in xrange(grid.dimensions[0].n):
l = []
while len(l) < grid.meqn:
line = f.readline()
l = l + line.split()
for m in xrange(grid.meqn):
grid.q[i, m] = float(l[m])
elif grid.ndim == 2:
for j in xrange(grid.dimensions[1].n):
for i in xrange(grid.dimensions[0].n):
l = []
while len(l) < grid.meqn:
line = f.readline()
l = l + line.split()
for m in xrange(grid.meqn):
grid.q[i, j, m] = float(l[m])
blank = f.readline()
elif grid.ndim == 3:
raise NotImplementedError("3d still does not work!")
for k in xrange(grid.dimensions[2].n):
for j in xrange(grid.dimensions[1].n):
for i in xrange(grid.dimensions[0].n):
l = []
while len(l) < grid.meqn:
line = f.readline()
l = l + line.split()
for m in xrange(grid.meqn):
grid.q[i, j, k, m] = float(l[m])
blank = f.readline()
blank = f.readline()
else:
msg = "Read only supported up to 3d."
logger.critical(msg)
raise Exception(msg)
# Add AMR attributes:
grid.gridno = gridno
grid.level = level
# Add new grid to solution
solution.grids.append(grid)
except (IOError):
raise
except:
logger.error("File %s was not able to be read." % q_fname)
raise
# Read auxillary file if available and requested
if solution.grids[0].maux > 0 and read_aux:
# Check for aux file
fname1 = os.path.join(base_path,
'%s.a' % file_prefix) + str(frame).zfill(4)
fname2 = os.path.join(base_path, '%s.a' % file_prefix)
if os.path.exists(fname1):
fname = fname1
elif os.path.exists(fname2):
fname = fname2
else:
logger.info("Unable to open auxillary file %s or %s" %
(fname1, fname2))
return
# Found a valid path, try to open and read it
try:
f = open(fname, 'r')
# Read in aux file
for n in xrange(len(solution.grids)):
# Fetch correct grid
gridno = read_data_line(f, type='int')
grid = solution.grids[gridno - 1]
# These should match this grid already, raise exception otherwise
if not (grid.level == read_data_line(f, type='int')):
raise IOError(
"Grid level in aux file header did not match grid no %s."
% grid.gridno)
for dim in grid.dimensions:
if not (dim.n == read_data_line(f, type='int')):
raise IOError(
"Dimension %s's n in aux file header did not match grid no %s."
% (dim.name, grid.gridno))
for dim in grid.dimensions:
if not (dim.lower == read_data_line(f, type='float')):
raise IOError(
"Dimension %s's lower in aux file header did not match grid no %s."
% (dim.name, grid.gridno))
for dim in grid.dimensions:
if not (dim.d == read_data_line(f, type='float')):
raise IOError(
"Dimension %s's d in aux file header did not match grid no %s."
% (dim.name, grid.gridno))
f.readline()
# Read in auxillary array
if grid.ndim == 1:
for i in xrange(grid.dimensions[0].n):
l = []
while len(l) < grid.maux:
line = f.readline()
l = l + line.split()
for m in xrange(grid.maux):
grid.aux[i, m] = float(l[m])
elif grid.ndim == 2:
for j in xrange(grid.dimensions[1].n):
for i in xrange(grid.dimensions[0].n):
l = []
while len(l) < grid.maux:
line = f.readline()
l = l + line.split()
for m in xrange(grid.maux):
grid.aux[i, j, m] = float(l[m])
blank = f.readline()
elif grid.ndim == 3:
for k in xrange(grid.dimensions[2].n):
for j in xrange(grid.dimensions[1].n):
for i in xrange(grid.dimensions[0].n):
l = []
while len(l) < grid.maux:
line = f.readline()
l = l + line.split()
for m in xrange(grid.maux):
grid.aux[i, j, k, m] = float(l[m])
blank = f.readline()
blank = f.readline()
else:
logger.critical("Read aux only up to 3d is supported.")
raise Exception("Read aux only up to 3d is supported.")
except (IOError):
raise
except:
logger.error("File %s was not able to be read." % q_fname)
raise
def read_ascii(solution,
frame,
path='./',
file_prefix='fort',
read_aux=False,
options={}):
r"""
Read in a set of ascii formatted files
This routine reads the ascii formatted files corresponding to the classic
clawpack format 'fort.txxxx', 'fort.qxxxx', and 'fort.axxxx' or 'fort.aux'
Note that the fort prefix can be changed.
:Input:
- *solution* - (:class:`~pyclaw.solution.Solution`) Solution object to
read the data into.
- *frame* - (int) Frame number to be read in
- *path* - (string) Path to the current directory of the file
- *file_prefix* - (string) Prefix of the files to be read in.
``default = 'fort'``
- *read_aux* (bool) Whether or not an auxillary file will try to be read
in. ``default = False``
- *options* - (dict) Dictionary of optional arguments dependent on
the format being read in. ``default = {}``
"""
import numpy as np
if frame < 0:
# Don't construct file names with negative frameno values.
raise IOError("Frame " + str(frame) + " does not exist ***")
# Construct path names
base_path = os.path.join(path, )
# t_fname = os.path.join(base_path, '%s.t' % file_prefix) + str(frame).zfill(4)
q_fname = os.path.join(base_path,
'%s.q' % file_prefix) + str(frame).zfill(4)
# Read in values from fort.t file:
[t, num_eqn, nstates, num_aux,
num_dim] = read_ascii_t(frame, path, file_prefix)
patches = []
# Read in values from fort.q file:
try:
f = open(q_fname, 'r')
# Loop through every patch setting the appropriate information
# for ng in range(len(solution.patchs)):
for m in xrange(nstates):
# Read in base header for this patch
patch_index = read_data_line(f, type='int')
level = read_data_line(f, type='int')
n = np.zeros((num_dim))
lower = np.zeros((num_dim))
d = np.zeros((num_dim))
for i in xrange(num_dim):
n[i] = read_data_line(f, type='int')
for i in xrange(num_dim):
lower[i] = read_data_line(f)
for i in xrange(num_dim):
d[i] = read_data_line(f)
blank = f.readline()
# Construct the patch
# Since we do not have names here, we will construct the patch with
# the assumed dimensions x,y,z
names = ['x', 'y', 'z']
dimensions = []
for i in xrange(num_dim):
dimensions.append(
pyclaw.geometry.Dimension(names[i], lower[i],
lower[i] + n[i] * d[i], n[i]))
patch = pyclaw.geometry.Patch(dimensions)
state = pyclaw.state.State(patch, num_eqn, num_aux)
state.t = t
# RJL 1/8/10: Changed empty_aux to zeros_aux below so aux won't
# be filled with random values if aux arrays not read in. Would
# like to delete this and initialize patch.aux only if it will be
# read in below, but for some reason that doesn't work.
if num_aux > 0:
state.aux[:] = 0.
# Fill in q values
if patch.num_dim == 1:
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l) < state.num_eqn:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_eqn):
state.q[m, i] = float(l[m])
elif patch.num_dim == 2:
for j in xrange(patch.dimensions[1].num_cells):
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l) < state.num_eqn:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_eqn):
state.q[m, i, j] = float(l[m])
blank = f.readline()
elif patch.num_dim == 3:
for k in xrange(patch.dimensions[2].num_cells):
for j in xrange(patch.dimensions[1].num_cells):
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l) < state.num_eqn:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_eqn):
state.q[m, i, j, k] = float(l[m])
blank = f.readline()
blank = f.readline()
else:
msg = "Read only supported up to 3d."
logger.critical(msg)
raise Exception(msg)
# Add AMR attributes:
patch.patch_index = patch_index
patch.level = level
# Add new patch to solution
solution.states.append(state)
patches.append(state.patch)
solution.domain = pyclaw.geometry.Domain(patches)
except (IOError):
raise
except:
logger.error("File %s was not able to be read." % q_fname)
raise
# Read auxillary file if available and requested
if solution.states[0].num_aux > 0 and read_aux:
# Check for aux file
fname1 = os.path.join(base_path,
'%s.a' % file_prefix) + str(frame).zfill(4)
fname2 = os.path.join(base_path, '%s.a' % file_prefix)
if os.path.exists(fname1):
fname = fname1
elif os.path.exists(fname2):
fname = fname2
else:
logger.info("Unable to open auxillary file %s or %s" %
(fname1, fname2))
return
# Found a valid path, try to open and read it
try:
f = open(fname, 'r')
# Read in aux file
for n in xrange(len(solution.states)):
# Fetch correct patch
patch_index = read_data_line(f, type='int')
patch = solution.states[patch_index - 1].patch
# These should match this patch already, raise exception otherwise
if not (patch.level == read_data_line(f, type='int')):
raise IOError(
"Patch level in aux file header did not match patch no %s."
% patch.patch_index)
for dim in patch.dimensions:
if not (dim.num_cells == read_data_line(f, type='int')):
raise IOError(
"Dimension %s's n in aux file header did not match patch no %s."
% (dim.name, patch.patch_index))
for dim in patch.dimensions:
if not (dim.lower == read_data_line(f, type='float')):
raise IOError(
"Dimension %s's lower in aux file header did not match patch no %s."
% (dim.name, patch.patch_index))
for dim in patch.dimensions:
if not (dim.delta == read_data_line(f, type='float')):
raise IOError(
"Dimension %s's d in aux file header did not match patch no %s."
% (dim.name, patch.patch_index))
f.readline()
# Read in auxillary array
if patch.num_dim == 1:
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l) < state.num_aux:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_aux):
state.aux[m, i] = float(l[m])
elif patch.num_dim == 2:
for j in xrange(patch.dimensions[1].num_cells):
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l) < state.num_aux:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_aux):
state.aux[m, i, j] = float(l[m])
blank = f.readline()
elif patch.num_dim == 3:
for k in xrange(patch.dimensions[2].num_cells):
for j in xrange(patch.dimensions[1].num_cells):
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l) < state.num_aux:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_aux):
state.aux[m, i, j, k] = float(l[m])
blank = f.readline()
blank = f.readline()
else:
logger.critical("Read aux only up to 3d is supported.")
raise Exception("Read aux only up to 3d is supported.")
except (IOError):
raise
except:
logger.error("File %s was not able to be read." % q_fname)
raise
def read_ascii(solution,frame,path='./',file_prefix='fort',read_aux=False,
options={}):
r"""
Read in a set of ascii formatted files
This routine reads the ascii formatted files corresponding to the classic
clawpack format 'fort.txxxx', 'fort.qxxxx', and 'fort.axxxx' or 'fort.aux'
Note that the fort prefix can be changed.
:Input:
- *solution* - (:class:`~pyclaw.solution.Solution`) Solution object to
read the data into.
- *frame* - (int) Frame number to be read in
- *path* - (string) Path to the current directory of the file
- *file_prefix* - (string) Prefix of the files to be read in.
``default = 'fort'``
- *read_aux* (bool) Whether or not an auxillary file will try to be read
in. ``default = False``
- *options* - (dict) Dictionary of optional arguments dependent on
the format being read in. ``default = {}``
"""
import numpy as np
if frame < 0:
# Don't construct file names with negative frameno values.
raise IOError("Frame " + str(frame) + " does not exist ***")
# Construct path names
base_path = os.path.join(path,)
# t_fname = os.path.join(base_path, '%s.t' % file_prefix) + str(frame).zfill(4)
q_fname = os.path.join(base_path, '%s.q' % file_prefix) + str(frame).zfill(4)
# Read in values from fort.t file:
[t,num_eqn,nstates,num_aux,num_dim] = read_ascii_t(frame,path,file_prefix)
patches = []
# Read in values from fort.q file:
try:
f = open(q_fname,'r')
# Loop through every patch setting the appropriate information
# for ng in range(len(solution.patchs)):
for m in xrange(nstates):
# Read in base header for this patch
patch_index = read_data_line(f,type='int')
level = read_data_line(f,type='int')
n = np.zeros((num_dim))
lower = np.zeros((num_dim))
d = np.zeros((num_dim))
for i in xrange(num_dim):
n[i] = read_data_line(f,type='int')
for i in xrange(num_dim):
lower[i] = read_data_line(f)
for i in xrange(num_dim):
d[i] = read_data_line(f)
blank = f.readline()
# Construct the patch
# Since we do not have names here, we will construct the patch with
# the assumed dimensions x,y,z
names = ['x','y','z']
dimensions = []
for i in xrange(num_dim):
dimensions.append(
pyclaw.geometry.Dimension(names[i],lower[i],lower[i] + n[i]*d[i],n[i]))
patch = pyclaw.geometry.Patch(dimensions)
state= pyclaw.state.State(patch,num_eqn,num_aux)
state.t = t
# RJL 1/8/10: Changed empty_aux to zeros_aux below so aux won't
# be filled with random values if aux arrays not read in. Would
# like to delete this and initialize patch.aux only if it will be
# read in below, but for some reason that doesn't work.
if num_aux > 0:
state.aux[:]=0.
# Fill in q values
if patch.num_dim == 1:
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l)<state.num_eqn:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_eqn):
state.q[m,i] = float(l[m])
elif patch.num_dim == 2:
for j in xrange(patch.dimensions[1].num_cells):
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l)<state.num_eqn:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_eqn):
state.q[m,i,j] = float(l[m])
blank = f.readline()
elif patch.num_dim == 3:
for k in xrange(patch.dimensions[2].num_cells):
for j in xrange(patch.dimensions[1].num_cells):
for i in xrange(patch.dimensions[0].num_cells):
l=[]
while len(l) < state.num_eqn:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_eqn):
state.q[m,i,j,k] = float(l[m])
blank = f.readline()
blank = f.readline()
else:
msg = "Read only supported up to 3d."
logger.critical(msg)
raise Exception(msg)
# Add AMR attributes:
patch.patch_index = patch_index
patch.level = level
# Add new patch to solution
solution.states.append(state)
patches.append(state.patch)
solution.domain = pyclaw.geometry.Domain(patches)
except(IOError):
raise
except:
logger.error("File %s was not able to be read." % q_fname)
raise
# Read auxillary file if available and requested
if solution.states[0].num_aux > 0 and read_aux:
# Check for aux file
fname1 = os.path.join(base_path,'%s.a' % file_prefix)+str(frame).zfill(4)
fname2 = os.path.join(base_path,'%s.a' % file_prefix)
if os.path.exists(fname1):
fname = fname1
elif os.path.exists(fname2):
fname = fname2
else:
logger.info("Unable to open auxillary file %s or %s" % (fname1,fname2))
return
# Found a valid path, try to open and read it
try:
f = open(fname,'r')
# Read in aux file
for n in xrange(len(solution.states)):
# Fetch correct patch
patch_index = read_data_line(f,type='int')
patch = solution.states[patch_index-1].patch
# These should match this patch already, raise exception otherwise
if not (patch.level == read_data_line(f,type='int')):
raise IOError("Patch level in aux file header did not match patch no %s." % patch.patch_index)
for dim in patch.dimensions:
if not (dim.num_cells == read_data_line(f,type='int')):
raise IOError("Dimension %s's n in aux file header did not match patch no %s." % (dim.name,patch.patch_index))
for dim in patch.dimensions:
if not (dim.lower == read_data_line(f,type='float')):
raise IOError("Dimension %s's lower in aux file header did not match patch no %s." % (dim.name,patch.patch_index))
for dim in patch.dimensions:
if not (dim.delta == read_data_line(f,type='float')):
raise IOError("Dimension %s's d in aux file header did not match patch no %s." % (dim.name,patch.patch_index))
f.readline()
# Read in auxillary array
if patch.num_dim == 1:
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l)<state.num_aux:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_aux):
state.aux[m,i] = float(l[m])
elif patch.num_dim == 2:
for j in xrange(patch.dimensions[1].num_cells):
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l)<state.num_aux:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_aux):
state.aux[m,i,j] = float(l[m])
blank = f.readline()
elif patch.num_dim == 3:
for k in xrange(patch.dimensions[2].num_cells):
for j in xrange(patch.dimensions[1].num_cells):
for i in xrange(patch.dimensions[0].num_cells):
l = []
while len(l)<state.num_aux:
line = f.readline()
l = l + line.split()
for m in xrange(state.num_aux):
state.aux[m,i,j,k] = float(l[m])
blank = f.readline()
blank = f.readline()
else:
logger.critical("Read aux only up to 3d is supported.")
raise Exception("Read aux only up to 3d is supported.")
except(IOError):
raise
except:
logger.error("File %s was not able to be read." % q_fname)
raise
