def addFoamVectorField(self, fieldpath, name, time, projectedField=False):
"""
"""
tSurf = TriSurfaceVector.readFromFoamFile(
fieldpath, self.triSurfaceMesh, time=time, projectedField=projectedField
)
self.fields[name] = tSurf
def addFoamVectorField(self, fieldpath, name, time, projectedField=False):
'''
'''
tSurf = TriSurfaceVector.readFromFoamFile(
fieldpath,
self.triSurfaceMesh,
time=time,
projectedField=projectedField)
self.fields[name] = tSurf
def readVelFromFoamFile(self,
varsFile,
pointsFile,
facesFile,
viewAnchor=(0,0,0),
xViewBasis=(1,0,0),
yViewBasis=(0,1,0),
dx=None,
dy=None,
interpolationMethod='cubic',
kind='min_E'):
'''
'''
tsm = TriSurfaceMesh.readFromFoamFile(pointsFile=pointsFile,
facesFile=facesFile,
viewAnchor=viewAnchor,
xViewBasis=xViewBasis,
yViewBasis=yViewBasis)
tsv = TriSurfaceVector.readFromFoamFile(varsFile=varsFile,
triSurfaceMesh=tsm,
time=0,
projectedField=False)
points = np.vstack((tsv.x,tsv.y)).T
print 'Creating Grid and Interpolator'
if dx==None:
dxlist=[a for a in np.abs(np.diff(points[:,0])) if a>0]
dx=np.min(dxlist)
if dy==None:
dylist=[a for a in np.abs(np.diff(points[:,1])) if a>0]
dy=np.min(dylist)
MaxX=np.max(points[:,0])
MinX=np.min(points[:,0])
MaxY=np.max(points[:,1])
MinY=np.min(points[:,1])
extent=[MinX-dx/2,MaxX+dx/2,MinY-dy/2,MaxY+dy/2]
cellsX=int((MaxX-MinX)/dx)+1
cellsY=int((MaxY-MinY)/dy)+1
grid_y, grid_x = np.mgrid[MinY:MaxY:np.complex(0,cellsY),MinX:MaxX:np.complex(0,cellsX)]
triang = tsv.triangulation
vx_i=self.interpolateField(tsv.vx,grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
vy_i=self.interpolateField(tsv.vx,grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
vz_i=self.interpolateField(tsv.vx,grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
self.vx=np.flipud(vx_i)
self.vy=np.flipud(vy_i)
self.vz=np.flipud(vz_i)
self.dx=dx
self.dy=dy
self.minX=MinX
self.maxX=MaxX
self.minY=MinY
self.maxY=MaxY
self.createDataDict()
self.extent=extent
def readFromFoamFile(self,
pointsFile,
facesFile,
velFile,
scalarFileList=[],
symTensorFileList=[],
viewAnchor=(0,0,0),
xViewBasis=(1,0,0),
yViewBasis=(0,1,0),
dx=None,
dy=None,
interpolationMethod='cubic',
kind='min_E'):
'''
Read an OpenFOAM surface (triangulated grid) in the current Surface
object (cartesian grid). As the "grid" change (tri to cartesian), the
value must be interpolated.
Arguments:
*pointFile*: python string.
Point file generate by OpenFOAM. This is the grid point
coordinates.
*facesFile*: python string.
Face file generate by OpenFOAM. It is a list of triangles, which
compose the grid.
*velFile*: python string.
Vector file generate by OpenFOAM. This is the data associated with
each grid point.
*scalarFileList*: python list.
*symTensorFileList*: python list.
*dx*: python float.
Physical size of a pixel in the Surface class (x discretisation).
Must be given in mm.
*dy*: python float.
Physical size of a pixel in the Surface class (y discretisation).
Must be given in mm.
*interpolationMethod*: python string.
Interpolation method used to interpolate from the triangulated
grid to the cartesian grid. "cubic" or "linear". Default="cubic"
*kind*: python string.
Defines the algorithm used for the cubic interpolation. Choices:
"min_E" or "geom". "min_E" should be the more accurate, but it is
also the most time time consuming.
Returns:
none
'''
print 'Reading Velocity'
tsm = TriSurfaceMesh.readFromFoamFile(pointsFile=pointsFile,
facesFile=facesFile,
viewAnchor=viewAnchor,
xViewBasis=xViewBasis,
yViewBasis=yViewBasis)
tsv = TriSurfaceVector.readFromFoamFile(varsFile=velFile,
triSurfaceMesh=tsm,
time=0,
projectedField=False)
points = np.vstack((tsv.x,tsv.y)).T
print 'Creating Grid and Interpolator'
if dx==None:
dxlist=[a for a in np.abs(np.diff(points[:,0])) if a>0]
dx=np.min(dxlist)
if dy==None:
dylist=[a for a in np.abs(np.diff(points[:,1])) if a>0]
dy=np.min(dylist)
MaxX=np.max(points[:,0])
MinX=np.min(points[:,0])
MaxY=np.max(points[:,1])
MinY=np.min(points[:,1])
extent=[MinX-dx/2,MaxX+dx/2,MinY-dy/2,MaxY+dy/2]
cellsX=int((MaxX-MinX)/dx)+1
cellsY=int((MaxY-MinY)/dy)+1
grid_y, grid_x = np.mgrid[MinY:MaxY:np.complex(0,cellsY),MinX:MaxX:np.complex(0,cellsX)]
triang = tsv.triangulation
print 'Interpolating Velocity'
vx_i=self.interpolateField(tsv.vx,grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
vy_i=self.interpolateField(tsv.vy,grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
vz_i=self.interpolateField(tsv.vz,grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
self.vx=np.flipud(vx_i)
self.vy=np.flipud(vy_i)
self.vz=np.flipud(vz_i)
self.dx=dx
self.dy=dy
self.minX=MinX
self.maxX=MaxX
self.minY=MinY
self.maxY=MaxY
self.extent=extent
self.createDataDict()
for scalarFile in scalarFileList:
varName=os.path.basename(scalarFile)
print 'Reading Scalar',varName
tsv.addFieldFromFoamFile(fieldFile=scalarFile,fieldname=varName)
scalar_i=self.interpolateField(tsv[varName],grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
self.data[varName]=np.flipud(scalar_i)
for symTensorFile in symTensorFileList:
varName=os.path.basename(symTensorFile)
print 'Reading Tenstor',varName
tsv.addFieldFromFoamFile(fieldFile=symTensorFile,fieldname=varName)
tensor_11=self.interpolateField(tsv[varName][:,0],grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
tensor_12=self.interpolateField(tsv[varName][:,1],grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
tensor_13=self.interpolateField(tsv[varName][:,2],grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
tensor_22=self.interpolateField(tsv[varName][:,3],grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
tensor_23=self.interpolateField(tsv[varName][:,4],grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
tensor_33=self.interpolateField(tsv[varName][:,5],grid_x, grid_y, triang, method=interpolationMethod, kind=kind)
tensor_11=np.flipud(tensor_11)
tensor_12=np.flipud(tensor_12)
tensor_13=np.flipud(tensor_13)
tensor_22=np.flipud(tensor_22)
tensor_23=np.flipud(tensor_23)
tensor_33=np.flipud(tensor_33)
if varName=='UPrime2Mean':
print 'Adding UPrime2Mean'
self.data['uu_bar']=tensor_11
self.data['uv_bar']=tensor_12
self.data['uw_bar']=tensor_13
self.data['vv_bar']=tensor_22
self.data['vw_bar']=tensor_23
self.data['ww_bar']=tensor_33
self.data['TKE_bar']=0.5*(self.data['uu_bar']+self.data['vv_bar']+self.data['ww_bar'])
else:
print 'Adding symTensor',varName
self.data[varName+'_ii']=[tensor_11,tensor_12,tensor_13,tensor_22,tensor_23,tensor_33]
def addFieldFromHdf5(self,
hdf5Parser,
key,
names=[],
projectedField=False):
'''
Add a list field stored in a hdf5 to the TriSurfaceContainer.
Arguments:
*hdf5Parser*: h5py parser object.
Parser object of the source hdf5 file.
*key*: python string.
The time (as a key) to extract from the HDF5. If it does not exist, IOError
is returned.
*names*: python list of string.
Name of the fields to extract from the HDF5. It can be a single
field (names=['oneField']) or multiple. if names=[], all the
fields are loaded. Default: names=[].
*projectedField*: python bool
Project the fields in the surface coordinate system.
Default: projectedField=False.
Usages:
>>> import h5py
>>> parser = h5py.File('myfile.h5','r')
>>> tsc = TriSurfaceContainer.createFromHdf5(parser,xViewBasis=[1,0,0])
>>> tsc.addFieldFromHdf5(parser,time=1.5,names=['U','S'])
'''
gTime = key
time = float(key)
if len(names) == 0:
names = hdf5Parser[gTime].keys()
names.pop(names.index('time'))
for name in names:
try:
dataShape = hdf5Parser[gTime][name].value.shape
if len(dataShape) == 1: #data is a scalar
tss = TriSurfaceScalar.readFromHdf5(
hdf5Parser=hdf5Parser,
varName=name,
triSurfaceMesh=self.triSurfaceMesh,
key=key,
projectedField=projectedField)
self.fields[name] = tss
elif len(dataShape
) == 2 and dataShape[1] == 3: #data is a vector
tsv = TriSurfaceVector.readFromHdf5(
hdf5Parser=hdf5Parser,
varName=name,
triSurfaceMesh=self.triSurfaceMesh,
key=key,
projectedField=projectedField)
self.fields[name] = tsv
elif len(dataShape
) == 2 and dataShape[1] == 6: #data is a symmtensor
tsst = TriSurfaceSymmTensor.readFromHdf5(
hdf5Parser=hdf5Parser,
varName=name,
triSurfaceMesh=self.triSurfaceMesh,
key=key,
projectedField=projectedField)
self.fields[name] = tsst
else:
raise IOError('variable of name "' + name + '" is not a'
'scalar, not a vector, not a symmTensor.')
except KeyError as e:
'time "' + gTime + '" and/or name "' + name + '" does not exist as key in the HDF5 parser. Not read, but continuing'
print e
except KeyboardInterrupt as e:
print e
return False
except MemoryError as e:
print e
return False
except:
print "Unexpected error:", sys.exc_info()[0]
#raise IOError('time "'+gTime+'" and/or name "'+name+'" does not '
#'exist as key in the HDF5 parser.')
return False
return True
def addFieldFromHdf5(self, hdf5Parser, key, names=[], projectedField=False):
"""
Add a list field stored in a hdf5 to the TriSurfaceContainer.
Arguments:
*hdf5Parser*: h5py parser object.
Parser object of the source hdf5 file.
*key*: python string.
The time (as a key) to extract from the HDF5. If it does not exist, IOError
is returned.
*names*: python list of string.
Name of the fields to extract from the HDF5. It can be a single
field (names=['oneField']) or multiple. if names=[], all the
fields are loaded. Default: names=[].
*projectedField*: python bool
Project the fields in the surface coordinate system.
Default: projectedField=False.
Usages:
>>> import h5py
>>> parser = h5py.File('myfile.h5','r')
>>> tsc = TriSurfaceContainer.createFromHdf5(parser,xViewBasis=[1,0,0])
>>> tsc.addFieldFromHdf5(parser,time=1.5,names=['U','S'])
"""
gTime = key
time = float(key)
if len(names) == 0:
names = hdf5Parser[gTime].keys()
names.pop(names.index("time"))
for name in names:
try:
dataShape = hdf5Parser[gTime][name].value.shape
if len(dataShape) == 1: # data is a scalar
tss = TriSurfaceScalar.readFromHdf5(
hdf5Parser=hdf5Parser,
varName=name,
triSurfaceMesh=self.triSurfaceMesh,
key=key,
projectedField=projectedField,
)
self.fields[name] = tss
elif len(dataShape) == 2 and dataShape[1] == 3: # data is a vector
tsv = TriSurfaceVector.readFromHdf5(
hdf5Parser=hdf5Parser,
varName=name,
triSurfaceMesh=self.triSurfaceMesh,
key=key,
projectedField=projectedField,
)
self.fields[name] = tsv
elif len(dataShape) == 2 and dataShape[1] == 6: # data is a symmtensor
tsst = TriSurfaceSymmTensor.readFromHdf5(
hdf5Parser=hdf5Parser,
varName=name,
triSurfaceMesh=self.triSurfaceMesh,
key=key,
projectedField=projectedField,
)
self.fields[name] = tsst
else:
raise IOError('variable of name "' + name + '" is not a' "scalar, not a vector, not a symmTensor.")
except KeyError as e:
'time "' + gTime + '" and/or name "' + name + '" does not exist as key in the HDF5 parser. Not read, but continuing'
print e
except KeyboardInterrupt as e:
print e
return False
except MemoryError as e:
print e
return False
except:
print "Unexpected error:", sys.exc_info()[0]
# raise IOError('time "'+gTime+'" and/or name "'+name+'" does not '
#'exist as key in the HDF5 parser.')
return False
return True
