def readVoxet(domain,
filename,
voproperty=1,
origin=None,
fillValue=0.,
referenceSystem=CartesianReferenceSystem()):
"""
Reads a single property from a GOCAD Voxet file and returns a data
object on the given domain with the property data.
Restrictions:
- Voxet origin in UVW space (i.e. AXIS_MIN) needs to be [0,0,0]
- samples size must be 4 (float32) or 8 (float64)
- data type must be IEEE
- format must be RAW
- domain resolution must be (approximately) a multiple of voxet resolution
:param domain: the domain to use for data (must be a ripley domain)
:type domain: `Domain`
:param filename: Voxet header filename (usually ends in .vo)
:type filename: ``string``
:param voproperty: identifier of the property to read. Either the numeric
property ID, the property name, or the filename of the
property data.
:type voproperty: ``int`` or ``string``
:param origin: if supplied will override the Voxet origin as read from the
file.
:type origin: ``list`` or ``tuple`` or ``None``
:param fillValue: value to use for cells that are not covered by property
data (if applicable)
:type fillValue: ``float``
:param referenceSystem: coordinate system of domain. Used to scale vertical
axis accordingly
:type referenceSystem: `ReferenceSystem`
"""
from esys.ripley import readBinaryGrid, BYTEORDER_BIG_ENDIAN, DATATYPE_FLOAT32, DATATYPE_FLOAT64
header = open(filename).readlines()
if not header[0].startswith('GOCAD Voxet'):
raise ValueError("Voxet header not found. Invalid Voxet file?!")
NE = None
axis_uvw = [None, None, None]
axis_min = [0., 0., 0.]
axis_max = [1., 1., 1.]
# props[id]=[name,file,datatype]
props = {}
for line in header:
if line.startswith('AXIS_O '):
if origin is None:
origin = [float(i) for i in line.split()[1:4]]
elif line.startswith('AXIS_U '):
u = [float(i) for i in line.split()[1:4]]
if (u[1] != 0) or (u[2] != 0):
raise ValueError('This coordinate system is not supported')
axis_uvw[0] = u[0]
elif line.startswith('AXIS_V '):
v = [float(i) for i in line.split()[1:4]]
if (v[0] != 0) or (v[2] != 0):
raise ValueError('This coordinate system is not supported')
axis_uvw[1] = v[1]
elif line.startswith('AXIS_W '):
w = [float(i) for i in line.split()[1:4]]
if (w[0] != 0) or (w[1] != 0):
raise ValueError('This coordinate system is not supported')
axis_uvw[2] = w[2]
elif line.startswith('AXIS_MIN '):
axis_min = [float(i) for i in line.split()[1:4]]
if axis_min != [0, 0, 0]:
raise ValueError('AXIS_MIN != [0,0,0] is not supported')
elif line.startswith('AXIS_MAX '):
axis_max = [float(i) for i in line.split()[1:4]]
elif line.startswith('AXIS_N '):
NE = [int(i) for i in line.split()[1:4]]
elif line.startswith('PROPERTY '):
propid = int(line.split()[1])
if not propid in props:
props[propid] = [None, None, None]
props[propid][0] = line.split()[2].strip()
elif line.startswith('PROP_ESIZE '):
propid = int(line.split()[1])
t = int(line.split()[2])
if t == 4:
props[propid][2] = DATATYPE_FLOAT32
elif t == 8:
props[propid][2] = DATATYPE_FLOAT64
else:
raise ValueError('Unsupported data size ' + t)
elif line.startswith('PROP_ETYPE '):
t = line.split()[2].strip()
if t != 'IEEE':
raise ValueError('Unsupported data type ' + t)
elif line.startswith('PROP_FORMAT '):
t = line.split()[2].strip()
if t != 'RAW':
raise ValueError('Unsupported data format ' + t)
elif line.startswith('PROP_OFFSET '):
dataoffset = int(line.split()[2])
if dataoffset != 0:
raise ValueError('data offset != 0 not supported')
elif line.startswith('PROP_FILE '):
propid = int(line.split()[1])
props[propid][1] = line.split()[2].strip()
if (axis_uvw[0] is None) or (axis_uvw[1] is None) or (axis_uvw[2] is None)\
or (NE is None) or (origin is None):
raise ValueError(
'Could not determine data configuration. Invalid file?!')
if len(props) == 0:
raise ValueError('No properties found.')
# voxets have these conventions:
# AXIS_N = number of samples (=cells!) in each dimension
# AXIS_UVW * AXIS_MAX = voxet length in each dimension
# AXIS_O = origin of voxet (cell centres!)
# see also http://paulbourke.net/dataformats/gocad/gocad.pdf
length = [axis_uvw[i] * axis_max[i] for i in range(3)]
# modify length and origin to account for the fact that Voxet cells are
# centred at the data points, i.e.:
# BEFORE: AFTER:
#
# O----length---->| O------length------>|
# ___________________ ___________________
# | * | * | * | * | * | | * | * | * | * | * |
# ------------------- -------------------
for i in range(3):
dz = length[i] / (NE[i] - 1)
origin[i] -= dz / 2.
length[i] += dz
if referenceSystem.isCartesian():
v_scale = 1.
else:
v_scale = 1. / referenceSystem.getHeightUnit()
origin[-1] = origin[-1] * v_scale
# retrieve domain configuration so we know where to place the voxet data
gridorigin, gridspacing, gridNE = domain.getGridParameters()
# determine base location of this dataset within the domain
first = [
int((origin[i] - gridorigin[i]) / gridspacing[i])
for i in range(domain.getDim())
]
# determine the resolution difference between domain and data.
# If domain has twice the resolution we can double up the data etc.
multiplier = [
int(round((abs(length[i]) / NE[i]) / gridspacing[i]))
for i in range(domain.getDim())
]
# NOTE: Depending on your data you might have to multiply your vertical
# multiplier by 1000. to convert km in meters.
#multiplier[-1] = int(multiplier[-1] * v_scale * 1000.)
multiplier[-1] = int(multiplier[-1] * v_scale)
datatype = None
propfile = None
for pid in props.keys():
p = props[pid]
if (isinstance(voproperty, int) and pid == voproperty) or \
(isinstance(voproperty, str) and (p[0]==voproperty or p[1]==voproperty)):
datatype = p[2]
name = p[1]
#remove quotes which GoCAD introduces for filenames with spaces
if name.startswith('"') and name.endswith('"'):
name = name[1:-1]
propfile = os.path.join(os.path.dirname(filename), name)
print("Voxet property file: %s" % propfile)
break
if propfile is None or datatype is None:
raise ValueError("Invalid property " + str(voproperty))
reverse = [0] * domain.getDim()
if axis_uvw[-1] < 0:
reverse[-1] = 1
print(
"calling readBinaryGrid with first=%s, nValues=%s, multiplier=%s, reverse=%s"
% (str(first), str(NE), str(multiplier), str(reverse)))
data = readBinaryGrid(propfile,
ReducedFunction(domain),
shape=(),
fill=fillValue,
byteOrder=BYTEORDER_BIG_ENDIAN,
dataType=p[2],
first=first,
numValues=NE,
multiplier=multiplier,
reverse=reverse)
return data
def readVoxet(domain, filename, voproperty=0, origin=None, fillValue=0.,
reference_system=None):
"""This subroutine reads in the Voxet and returns an escript Data object"""
header=open(filename).readlines()
if not header[0].startswith('GOCAD Voxet'):
raise ValueError("Invalid Voxet file")
NE=None
axis_uvw=[None,None,None]
axis_min=[0.,0.,0.]
axis_max=[1.,1.,1.]
# props[id]=[name,file,datatype]
props={}
for line in header:
if line.startswith('AXIS_O '):
if origin is None:
origin=[float(i) for i in line.split()[1:4]]
elif line.startswith('AXIS_U '):
u=[float(i) for i in line.split()[1:4]]
if (u[1] != 0) or (u[2] != 0):
raise ValueError('This coordinate system is not supported')
axis_uvw[0]=u[0]
elif line.startswith('AXIS_V '):
v=[float(i) for i in line.split()[1:4]]
if (v[0] != 0) or (v[2] != 0):
raise ValueError('This coordinate system is not supported')
axis_uvw[1]=v[1]
elif line.startswith('AXIS_W '):
w=[float(i) for i in line.split()[1:4]]
if (w[0] != 0) or (w[1] != 0):
raise ValueError('This coordinate system is not supported')
axis_uvw[2]=w[2]
elif line.startswith('AXIS_MIN '):
axis_min=[float(i) for i in line.split()[1:4]]
elif line.startswith('AXIS_MAX '):
axis_max=[float(i) for i in line.split()[1:4]]
elif line.startswith('AXIS_N '):
NE=[int(i) for i in line.split()[1:4]]
elif line.startswith('PROPERTY '):
propid=int(line.split()[1])
if not props.has_key(propid):
props[propid]=[None,None,None]
props[propid][0]=line.split()[2].strip()
elif line.startswith('PROP_ESIZE '):
propid=int(line.split()[1])
t=int(line.split()[2])
if t==4:
props[propid][2]=DATATYPE_FLOAT32
elif t==8:
props[propid][2]=DATATYPE_FLOAT64
else:
raise ValueError('Unsupported data size '+t)
elif line.startswith('PROP_ETYPE '):
t=line.split()[2].strip()
if t != 'IEEE':
raise ValueError('Unsupported data type '+t)
elif line.startswith('PROP_FORMAT '):
t=line.split()[2].strip()
if t != 'RAW':
raise ValueError('Unsupported data format '+t)
elif line.startswith('PROP_OFFSET '):
dataoffset=int(line.split()[2])
if dataoffset != 0:
raise ValueError('data offset != 0 not supported yet')
elif line.startswith('PROP_FILE '):
propid=int(line.split()[1])
props[propid][1]=line.split()[2].strip()
if (axis_uvw[0] is None) or (axis_uvw[1] is None) or (axis_uvw[2] is None)\
or (NE is None) or (origin is None):
raise ValueError('Could not determine data configuration. Invalid file?!')
if len(props)==0:
raise ValueError('No properties found.')
#l=[(origin[i], origin[i]+axis_uvw[i]*axis_max[i]) for i in range(3)]
gridorigin, gridspacing, gridNE = domain.getGridParameters()
if not reference_system:
reference_system = CartesianReferenceSystem()
if reference_system.isCartesian():
v_scale=1.
else:
v_scale=1./reference_system.getHeightUnit()
# add 2x half cells (top and bottom)
dz = axis_uvw[-1] / (NE[-1]-1)
axis_uvw = [x + dz for x in axis_uvw]
origin[-1] = origin[-1]*v_scale
# determine base location of this dataset within the domain
first=[int((origin[i]-gridorigin[i])/gridspacing[i]) for i in range(domain.getDim())]
datatype=None
propfile=None
for p in props.values():
if (isinstance(voproperty, int) and p[1] == voproperty) or \
(isinstance(voproperty, str) and p[0] == voproperty):
datatype=p[2]
name=p[1]
# remove quotes which GoCAD introduces for filenames with spaces
if name.startswith('"') and name.endswith('"'):
name=name[1:-1]
propfile=os.path.join(os.path.dirname(filename), name)
print("Voxet property file: %s"%propfile)
break
if propfile is None or datatype is None:
raise ValueError("Invalid property "+str(voproperty))
multiplier = [1,1,1]
reverse = [0]*domain.getDim()
if axis_uvw[-1] < 0:
reverse[-1]=1
data=readBinaryGrid(propfile, ReducedFunction(domain), shape=(),
fill=fillValue, byteOrder=BYTEORDER_BIG_ENDIAN,
dataType=p[2], first=first, numValues=NE, multiplier=multiplier,
reverse=reverse)
return data
def RegionalCalculation(reg_mask):
"""
Calculates the "regional" from the entire FEILDS model excluding the
selected region and outputs gravity at the specified altitude...
see above for the "residual"
"""
# read in a gravity data grid to define data computation space
G_DATA = os.path.join(DATADIR,'Final_BouguerTC_UC15K_qrtdeg.nc')
FS=ReducedFunction(dom)
nValues=[NX, NY, 1]
first = [0, 0, cell_at_altitude]
multiplier = [1, 1, 1]
reverse = [0, 0, 0]
byteorder = BYTEORDER_NATIVE
gdata = readBinaryGrid(G_DATA, FS, shape=(),
fill=-999999, byteOrder=byteorder,
dataType=DATATYPE_FLOAT32, first=first, numValues=nValues,
multiplier=multiplier, reverse=reverse)
print("Grid successfully read")
# get the masking and units sorted out for the data-space
g_mask = whereNonZero(gdata+999999)
gdata=gdata*g_mask * GRAV_UNITS
# if people choose to have air in their region we exclude it from the
# specified gravity calculation region
if h_top < 0.:
reg_mask = reg_mask+mask_air
live_model = initial_model* whereNonPositive(reg_mask)
dead_model = initial_model* wherePositive(reg_mask)
if UseMean is True:
# calculate the mean density within the selected region
BackgroundDensity = integrate(dead_model)/integrate(wherePositive(reg_mask))
print("Density mean for selected region equals = %s"%BackgroundDensity)
live_model = live_model + BackgroundDensity * wherePositive(reg_mask)
# create mapping
rho_mapping = DensityMapping(dom, rho0=live_model)
# invert sign of gravity field to account for escript's coordinate system
gdata = -GRAV_UNITS * gdata
# turn the scalars into vectors (vertical direction)
d=kronecker(DIM)[DIM-1]
w=safeDiv(1., g_mask)
gravity_model=GravityModel(dom, w*d, gdata*d, fixPotentialAtBottom=False, coordinates=COORDINATES)
gravity_model.rescaleWeights(rho_scale=rho_mapping.getTypicalDerivative())
phi,_ = gravity_model.getArguments(live_model)
g_init = -gravity_model.getCoordinateTransformation().getGradient(phi)
g_init = interpolate(g_init, gdata.getFunctionSpace())
print("Computed gravity: %s"%(g_init[2]))
fn=os.path.join(OUTPUTDIR,'regional-gravity')
if SiloOutput is True:
saveSilo(fn, density=live_model, gravity_init=g_init, g_initz=-g_init[2], gravitymask=g_mask, modelmask=reg_mask)
print('SILO file written with the following fields: density (kg/m^3), gravity vector (m/s^2), gz (m/s^2), gravitymask, modelmask')
# to compare calculated data against input dataset.
# Not used by default but should work if the input dataset is correct
#gslice = g_init[2]*wherePositive(g_mask)
#g_dash = integrate(gslice)/integrate(wherePositive(g_mask))
#gdataslice = gdata*wherePositive(g_mask)
#gdata_dash = integrate(gdataslice)/integrate(wherePositive(g_mask))
#misfit=(gdataslice-gdata_dash)-(gslice-g_dash)
saveDataCSV(fn+".csv", mask=g_mask, gz=-g_init[2], Long=datacoords[0], Lat=datacoords[1], h=datacoords[2])
print('CSV file written with the following fields: Longitude (degrees) Latitude (degrees), h (100km), gz (m/s^2)')
def readVoxet(domain, filename, voproperty=1, origin=None, fillValue=0.,
referenceSystem=CartesianReferenceSystem()):
"""
Reads a single property from a GOCAD Voxet file and returns a data
object on the given domain with the property data.
Restrictions:
- Voxet origin in UVW space (i.e. AXIS_MIN) needs to be [0,0,0]
- samples size must be 4 (float32) or 8 (float64)
- data type must be IEEE
- format must be RAW
- domain resolution must be (approximately) a multiple of voxet resolution
:param domain: the domain to use for data (must be a ripley domain)
:type domain: `Domain`
:param filename: Voxet header filename (usually ends in .vo)
:type filename: ``string``
:param voproperty: identifier of the property to read. Either the numeric
property ID, the property name, or the filename of the
property data.
:type voproperty: ``int`` or ``string``
:param origin: if supplied will override the Voxet origin as read from the
file.
:type origin: ``list`` or ``tuple`` or ``None``
:param fillValue: value to use for cells that are not covered by property
data (if applicable)
:type fillValue: ``float``
:param referenceSystem: coordinate system of domain. Used to scale vertical
axis accordingly
:type referenceSystem: `ReferenceSystem`
"""
from esys.ripley import readBinaryGrid, BYTEORDER_BIG_ENDIAN, DATATYPE_FLOAT32, DATATYPE_FLOAT64
header=open(filename).readlines()
if not header[0].startswith('GOCAD Voxet'):
raise ValueError("Voxet header not found. Invalid Voxet file?!")
NE=None
axis_uvw=[None,None,None]
axis_min=[0.,0.,0.]
axis_max=[1.,1.,1.]
# props[id]=[name,file,datatype]
props={}
for line in header:
if line.startswith('AXIS_O '):
if origin is None:
origin=[float(i) for i in line.split()[1:4]]
elif line.startswith('AXIS_U '):
u=[float(i) for i in line.split()[1:4]]
if (u[1] != 0) or (u[2] != 0):
raise ValueError('This coordinate system is not supported')
axis_uvw[0]=u[0]
elif line.startswith('AXIS_V '):
v=[float(i) for i in line.split()[1:4]]
if (v[0] != 0) or (v[2] != 0):
raise ValueError('This coordinate system is not supported')
axis_uvw[1]=v[1]
elif line.startswith('AXIS_W '):
w=[float(i) for i in line.split()[1:4]]
if (w[0] != 0) or (w[1] != 0):
raise ValueError('This coordinate system is not supported')
axis_uvw[2]=w[2]
elif line.startswith('AXIS_MIN '):
axis_min=[float(i) for i in line.split()[1:4]]
if axis_min != [0,0,0]:
raise ValueError('AXIS_MIN != [0,0,0] is not supported')
elif line.startswith('AXIS_MAX '):
axis_max=[float(i) for i in line.split()[1:4]]
elif line.startswith('AXIS_N '):
NE=[int(i) for i in line.split()[1:4]]
elif line.startswith('PROPERTY '):
propid=int(line.split()[1])
if not propid in props:
props[propid]=[None,None,None]
props[propid][0]=line.split()[2].strip()
elif line.startswith('PROP_ESIZE '):
propid=int(line.split()[1])
t=int(line.split()[2])
if t==4:
props[propid][2]=DATATYPE_FLOAT32
elif t==8:
props[propid][2]=DATATYPE_FLOAT64
else:
raise ValueError('Unsupported data size '+t)
elif line.startswith('PROP_ETYPE '):
t=line.split()[2].strip()
if t != 'IEEE':
raise ValueError('Unsupported data type '+t)
elif line.startswith('PROP_FORMAT '):
t=line.split()[2].strip()
if t != 'RAW':
raise ValueError('Unsupported data format '+t)
elif line.startswith('PROP_OFFSET '):
dataoffset=int(line.split()[2])
if dataoffset != 0:
raise ValueError('data offset != 0 not supported')
elif line.startswith('PROP_FILE '):
propid=int(line.split()[1])
props[propid][1]=line.split()[2].strip()
if (axis_uvw[0] is None) or (axis_uvw[1] is None) or (axis_uvw[2] is None)\
or (NE is None) or (origin is None):
raise ValueError('Could not determine data configuration. Invalid file?!')
if len(props)==0:
raise ValueError('No properties found.')
# voxets have these conventions:
# AXIS_N = number of samples (=cells!) in each dimension
# AXIS_UVW * AXIS_MAX = voxet length in each dimension
# AXIS_O = origin of voxet (cell centres!)
# see also http://paulbourke.net/dataformats/gocad/gocad.pdf
length = [axis_uvw[i]*axis_max[i] for i in range(3)]
# modify length and origin to account for the fact that Voxet cells are
# centred at the data points, i.e.:
# BEFORE: AFTER:
#
# O----length---->| O------length------>|
# ___________________ ___________________
# | * | * | * | * | * | | * | * | * | * | * |
# ------------------- -------------------
for i in range(3):
dz = length[i] / (NE[i]-1)
origin[i] -= dz/2.
length[i] += dz
if referenceSystem.isCartesian():
v_scale=1.
else:
v_scale=1./referenceSystem.getHeightUnit()
origin[-1] = origin[-1]*v_scale
# retrieve domain configuration so we know where to place the voxet data
gridorigin, gridspacing, gridNE = domain.getGridParameters()
# determine base location of this dataset within the domain
first=[int((origin[i]-gridorigin[i])/gridspacing[i]) for i in range(domain.getDim())]
# determine the resolution difference between domain and data.
# If domain has twice the resolution we can double up the data etc.
multiplier=[int(round((abs(length[i])/NE[i])/gridspacing[i])) for i in range(domain.getDim())]
# NOTE: Depending on your data you might have to multiply your vertical
# multiplier by 1000. to convert km in meters.
#multiplier[-1] = int(multiplier[-1] * v_scale * 1000.)
multiplier[-1] = int(multiplier[-1] * v_scale)
datatype=None
propfile=None
for pid in props.keys():
p=props[pid]
if (isinstance(voproperty, int) and pid == voproperty) or \
(isinstance(voproperty, str) and (p[0]==voproperty or p[1]==voproperty)):
datatype=p[2]
name=p[1]
#remove quotes which GoCAD introduces for filenames with spaces
if name.startswith('"') and name.endswith('"'):
name=name[1:-1]
propfile=os.path.join(os.path.dirname(filename), name)
print("Voxet property file: %s"%propfile)
break
if propfile is None or datatype is None:
raise ValueError("Invalid property "+str(voproperty))
reverse=[0]*domain.getDim()
if axis_uvw[-1] < 0:
reverse[-1]=1
print("calling readBinaryGrid with first=%s, nValues=%s, multiplier=%s, reverse=%s"%(str(first),str(NE),str(multiplier),str(reverse)))
data=readBinaryGrid(propfile, ReducedFunction(domain), shape=(),
fill=fillValue, byteOrder=BYTEORDER_BIG_ENDIAN,
dataType=p[2], first=first, numValues=NE, multiplier=multiplier,
reverse=reverse)
return data
