def new_to_old(filename):
f = DataFile(filename)
newfile = DataFile(os.path.splitext(filename)[0] + str(".BOUT_metrics.nc"),
create=True)
name_changes = {
"g_yy": "g_22",
"gyy": "g22",
"gxx": "g11",
"gxz": "g13",
"gzz": "g33",
"g_xx": "g_11",
"g_xz": "g_13",
"g_zz": "g_33"
}
for key in f.keys():
name = key
if name in name_changes:
name = name_changes[name]
newfile.write(name, np.asarray(f.read(key)))
f.close()
newfile.close()
newfile.list()
def listKeys(self, simIndex=0, simType='1-base'):
if simType == '1-base':
os.chdir('{}/{}'.format(self.outDir, simIndex))
else:
os.chdir('{}/{}/{}'.format(self.outDir, simIndex, simType))
datFile = DataFile('BOUT.dmp.0.nc')
self.datFile = datFile
return datFile.keys()
def change_variable(filename, variable, new_value):
f = DataFile(filename)
newfile = DataFile(os.path.splitext(filename)[0] + str(variable) + "." +
str(new_value),
create=True)
var_changes = {str(variable)}
for key in f.keys():
name = key
if name in var_changes:
name = name_changes[name]
newfile.write(name, np.asarray(f.read(key)))
f.close()
newfile.close()
newfile.list()
def slice(infile, outfile, region = None, xind=None, yind=None):
"""
xind, yind - index ranges. Range includes first point, but not last point
"""
# Open input and output files
indf = DataFile(infile)
outdf = DataFile(outfile, create=True)
nx = indf["nx"][0]
ny = indf["ny"][0]
if region:
# Select a region of the mesh
xind = [0, nx]
if region == 0:
# Lower inner leg
yind = [0, indf["jyseps1_1"][0]+1]
elif region == 1:
# Inner core
yind = [indf["jyseps1_1"][0]+1, indf["jyseps2_1"][0]+1]
elif region == 2:
# Upper inner leg
yind = [indf["jyseps2_1"][0]+1, indf["ny_inner"][0]]
elif region == 3:
# Upper outer leg
yind = [indf["ny_inner"][0], indf["jyseps1_2"][0]+1]
elif region == 4:
# Outer core
yind = [indf["jyseps1_2"][0]+1, indf["jyseps2_2"][0]+1]
else:
# Lower outer leg
yind = [indf["jyseps2_2"][0]+1, ny]
else:
# Use indices
if not xind:
xind = [0, nx]
if not yind:
yind = [0, ny]
print("Indices: [%d:%d, %d:%d]" % (xind[0], xind[1], yind[0], yind[1]))
# List of variables requiring special handling
special = ["nx", "ny", "ny_inner",
"ixseps1", "ixseps2",
"jyseps1_1", "jyseps1_2", "jyseps2_1", "jyseps2_2",
"ShiftAngle"]
outdf["nx"] = xind[1] - xind[0]
outdf["ny"] = yind[1] - yind[0]
outdf["ny_inner"] = indf["ny_inner"][0] - yind[0]
outdf["ixseps1"] = indf["ixseps1"][0]
outdf["ixseps2"] = indf["ixseps2"][0]
outdf["jyseps1_1"] = indf["jyseps1_1"][0] - yind[0]
outdf["jyseps2_1"] = indf["jyseps2_1"][0] - yind[0]
outdf["jyseps1_2"] = indf["jyseps1_2"][0] - yind[0]
outdf["jyseps2_2"] = indf["jyseps2_2"][0] - yind[0]
outdf["ShiftAngle"] = indf["ShiftAngle"][xind[0]:xind[1]]
# Loop over all variables
for v in list(indf.keys()):
if v in special:
continue # Skip these variables
ndims = indf.ndims(v)
if ndims == 0:
# Copy scalars
print("Copying variable: " + v)
outdf[v] = indf[v][0]
elif ndims == 2:
# Assume [x,y]
print("Slicing variable: " + v);
outdf[v] = indf[v][xind[0]:xind[1], yind[0]:yind[1]]
else:
# Skip
print("Skipping variable: " + v)
indf.close()
outdf.close()
def slice(infile, outfile, region=None, xind=None, yind=None):
"""
xind, yind - index ranges. Range includes first point, but not last point
"""
# Open input and output files
indf = DataFile(infile)
outdf = DataFile(outfile, create=True)
nx = indf["nx"][0]
ny = indf["ny"][0]
if region:
# Select a region of the mesh
xind = [0, nx]
if region == 0:
# Lower inner leg
yind = [0, indf["jyseps1_1"][0] + 1]
elif region == 1:
# Inner core
yind = [indf["jyseps1_1"][0] + 1, indf["jyseps2_1"][0] + 1]
elif region == 2:
# Upper inner leg
yind = [indf["jyseps2_1"][0] + 1, indf["ny_inner"][0]]
elif region == 3:
# Upper outer leg
yind = [indf["ny_inner"][0], indf["jyseps1_2"][0] + 1]
elif region == 4:
# Outer core
yind = [indf["jyseps1_2"][0] + 1, indf["jyseps2_2"][0] + 1]
else:
# Lower outer leg
yind = [indf["jyseps2_2"][0] + 1, ny]
else:
# Use indices
if not xind:
xind = [0, nx]
if not yind:
yind = [0, ny]
print("Indices: [%d:%d, %d:%d]" % (xind[0], xind[1], yind[0], yind[1]))
# List of variables requiring special handling
special = [
"nx", "ny", "ny_inner", "ixseps1", "ixseps2", "jyseps1_1", "jyseps1_2",
"jyseps2_1", "jyseps2_2", "ShiftAngle"
]
outdf["nx"] = xind[1] - xind[0]
outdf["ny"] = yind[1] - yind[0]
outdf["ny_inner"] = indf["ny_inner"][0] - yind[0]
outdf["ixseps1"] = indf["ixseps1"][0]
outdf["ixseps2"] = indf["ixseps2"][0]
outdf["jyseps1_1"] = indf["jyseps1_1"][0] - yind[0]
outdf["jyseps2_1"] = indf["jyseps2_1"][0] - yind[0]
outdf["jyseps1_2"] = indf["jyseps1_2"][0] - yind[0]
outdf["jyseps2_2"] = indf["jyseps2_2"][0] - yind[0]
outdf["ShiftAngle"] = indf["ShiftAngle"][xind[0]:xind[1]]
# Loop over all variables
for v in list(indf.keys()):
if v in special:
continue # Skip these variables
ndims = indf.ndims(v)
if ndims == 0:
# Copy scalars
print("Copying variable: " + v)
outdf[v] = indf[v][0]
elif ndims == 2:
# Assume [x,y]
print("Slicing variable: " + v)
outdf[v] = indf[v][xind[0]:xind[1], yind[0]:yind[1]]
else:
# Skip
print("Skipping variable: " + v)
indf.close()
outdf.close()
def slice(infile, outfile, region=None, xind=None, yind=None):
"""Copy an X-Y slice from one DataFile to another
Parameters
----------
infile : str
Name of DataFile to read slice from
outfile : str
Name of DataFile to write slice to. File will be created, and
will be overwritten if it already exists
region : {0, 1, 2, 3, 4, 5, None}, optional
Copy a whole region. The available regions are:
- 0: Lower inner leg
- 1: Inner core
- 2: Upper inner leg
- 3: Upper outer leg
- 4: Outer core
- 5: Lower outer leg
xind, yind : (int, int), optional
Index ranges for x and y. Range includes first point, but not
last point
TODO
----
- Rename to not clobber builtin `slice`
- Better regions?
"""
# Open input and output files
indf = DataFile(infile)
outdf = DataFile(outfile, create=True)
nx = indf["nx"][0]
ny = indf["ny"][0]
if region:
# Select a region of the mesh
xind = [0, nx]
if region == 0:
# Lower inner leg
yind = [0, indf["jyseps1_1"][0] + 1]
elif region == 1:
# Inner core
yind = [indf["jyseps1_1"][0] + 1, indf["jyseps2_1"][0] + 1]
elif region == 2:
# Upper inner leg
yind = [indf["jyseps2_1"][0] + 1, indf["ny_inner"][0]]
elif region == 3:
# Upper outer leg
yind = [indf["ny_inner"][0], indf["jyseps1_2"][0] + 1]
elif region == 4:
# Outer core
yind = [indf["jyseps1_2"][0] + 1, indf["jyseps2_2"][0] + 1]
else:
# Lower outer leg
yind = [indf["jyseps2_2"][0] + 1, ny]
else:
# Use indices
if not xind:
xind = [0, nx]
if not yind:
yind = [0, ny]
print("Indices: [%d:%d, %d:%d]" % (xind[0], xind[1], yind[0], yind[1]))
# List of variables requiring special handling
special = [
"nx",
"ny",
"ny_inner",
"ixseps1",
"ixseps2",
"jyseps1_1",
"jyseps1_2",
"jyseps2_1",
"jyseps2_2",
"ShiftAngle",
]
outdf["nx"] = xind[1] - xind[0]
outdf["ny"] = yind[1] - yind[0]
outdf["ny_inner"] = indf["ny_inner"][0] - yind[0]
outdf["ixseps1"] = indf["ixseps1"][0]
outdf["ixseps2"] = indf["ixseps2"][0]
outdf["jyseps1_1"] = indf["jyseps1_1"][0] - yind[0]
outdf["jyseps2_1"] = indf["jyseps2_1"][0] - yind[0]
outdf["jyseps1_2"] = indf["jyseps1_2"][0] - yind[0]
outdf["jyseps2_2"] = indf["jyseps2_2"][0] - yind[0]
outdf["ShiftAngle"] = indf["ShiftAngle"][xind[0]:xind[1]]
# Loop over all variables
for v in list(indf.keys()):
if v in special:
continue # Skip these variables
ndims = indf.ndims(v)
if ndims == 0:
# Copy scalars
print("Copying variable: " + v)
outdf[v] = indf[v][0]
elif ndims == 2:
# Assume [x,y]
print("Slicing variable: " + v)
outdf[v] = indf[v][xind[0]:xind[1], yind[0]:yind[1]]
else:
# Skip
print("Skipping variable: " + v)
indf.close()
outdf.close()
def slice(infile, outfile, region=None, xind=None, yind=None):
"""Copy an X-Y slice from one DataFile to another
Parameters
----------
infile : str
Name of DataFile to read slice from
outfile : str
Name of DataFile to write slice to. File will be created, and
will be overwritten if it already exists
region : {0, 1, 2, 3, 4, 5, None}, optional
Copy a whole region. The available regions are:
- 0: Lower inner leg
- 1: Inner core
- 2: Upper inner leg
- 3: Upper outer leg
- 4: Outer core
- 5: Lower outer leg
xind, yind : (int, int), optional
Index ranges for x and y. Range includes first point, but not
last point
TODO
----
- Rename to not clobber builtin `slice`
- Better regions?
"""
# Open input and output files
indf = DataFile(infile)
outdf = DataFile(outfile, create=True)
nx = indf["nx"][0]
ny = indf["ny"][0]
if region:
# Select a region of the mesh
xind = [0, nx]
if region == 0:
# Lower inner leg
yind = [0, indf["jyseps1_1"][0]+1]
elif region == 1:
# Inner core
yind = [indf["jyseps1_1"][0]+1, indf["jyseps2_1"][0]+1]
elif region == 2:
# Upper inner leg
yind = [indf["jyseps2_1"][0]+1, indf["ny_inner"][0]]
elif region == 3:
# Upper outer leg
yind = [indf["ny_inner"][0], indf["jyseps1_2"][0]+1]
elif region == 4:
# Outer core
yind = [indf["jyseps1_2"][0]+1, indf["jyseps2_2"][0]+1]
else:
# Lower outer leg
yind = [indf["jyseps2_2"][0]+1, ny]
else:
# Use indices
if not xind:
xind = [0, nx]
if not yind:
yind = [0, ny]
print("Indices: [%d:%d, %d:%d]" % (xind[0], xind[1], yind[0], yind[1]))
# List of variables requiring special handling
special = ["nx", "ny", "ny_inner",
"ixseps1", "ixseps2",
"jyseps1_1", "jyseps1_2", "jyseps2_1", "jyseps2_2",
"ShiftAngle"]
outdf["nx"] = xind[1] - xind[0]
outdf["ny"] = yind[1] - yind[0]
outdf["ny_inner"] = indf["ny_inner"][0] - yind[0]
outdf["ixseps1"] = indf["ixseps1"][0]
outdf["ixseps2"] = indf["ixseps2"][0]
outdf["jyseps1_1"] = indf["jyseps1_1"][0] - yind[0]
outdf["jyseps2_1"] = indf["jyseps2_1"][0] - yind[0]
outdf["jyseps1_2"] = indf["jyseps1_2"][0] - yind[0]
outdf["jyseps2_2"] = indf["jyseps2_2"][0] - yind[0]
outdf["ShiftAngle"] = indf["ShiftAngle"][xind[0]:xind[1]]
# Loop over all variables
for v in list(indf.keys()):
if v in special:
continue # Skip these variables
ndims = indf.ndims(v)
if ndims == 0:
# Copy scalars
print("Copying variable: " + v)
outdf[v] = indf[v][0]
elif ndims == 2:
# Assume [x,y]
print("Slicing variable: " + v);
outdf[v] = indf[v][xind[0]:xind[1], yind[0]:yind[1]]
else:
# Skip
print("Skipping variable: " + v)
indf.close()
outdf.close()
