def vtkDatasetToHdf5(g, name, ds):
"""
store a vtk dataset ds, formated as vtk file, within a hdf character array dataset.
The hdf dataset is created with name name under the group g.
"""
#assert False # lol this is just copy pasted from some old code. needs to be done properly
#assert type(ds) is vtk.vtkPolyData
assert ds.GetClassName(
) == 'vtkPolyData' # there needs to be a map from dataset type to writer type. Also the python type does not equal the wrapped c++ type.
writer = vtk.vtkPolyDataWriter()
writer.SetInput(ds)
writer.WriteToOutputStringOn()
writer.SetFileTypeToASCII()
writer.Update()
iso = writer.GetOutputString()
l = writer.GetOutputStringLength()
iso = iso[:l] # iso is a string, but only the content up to l is valid!
ds = g.create_dataset(name,
data=np.fromstring(iso, dtype=np.uint8),
compression='gzip',
compression_opts=9)
ds.attrs["TYPE"] = "VTK_FILE"
ds.attrs["VTK_DATASET_TYPE"] = type(ds).__name__
def __init__(self,
dataDir='data',
streamFileInit='streamInit.vtk',
streamFile='stream.vtk',
dumpFile='save.vtk',
interpolation='weighted',
s=[]):
"""
Maps the streamlines from X to x.
call signature:
mapStream(dataDir = 'data', streamFileInit = 'streamInit.vtk', streamFile = 'stream.vtk', dumpFile = 'save.vtk', interpolation = 'weighted')
Keyword arguments:
*dataDir*:
Data directory.
*streamFileInit*:
Read the initial streamline in this file.
*streamFile*:
Store the streamline in this file.
*dumpFile*:
Use this file for the mapping x(X,t).
*interpolation*:
Interpolation of the vector field.
'mean': takes the mean of the adjacent grid point.
'weighted': weights the adjacent grid points according to their distance.
*s*:
The streamlines object for t = 0. If not passed obtain it from 'streamFileInit'.
"""
# read the stream lines at t = 0
if (s == []):
s = gm.readStream(dataDir=dataDir, streamFile=streamFileInit)
#s = gm.readStream(dataDir = dataDir, streamFile = streamFileInit)
# convert x0 and y0 into array in case of scalars
try:
len(s.x0)
except:
s.x0 = np.array([s.x0])
s.y0 = np.array([s.y0])
# read the current state
data = gm.readDump(dataDir=dataDir, fileName=dumpFile)
p = data.p
xx = data.grid
# mapped tracers
tracersNew = np.zeros(s.tracers.shape, dtype=s.tracers.dtype)
# interpolate x(X,t) at S to get x(S,t), where S is the initial streamline
for i in range(len(s.x0)):
for j in range(len(s.y0)):
for sl in range(s.sl[i, j]):
tracersNew[:, i, j, sl] = vecInt(s.tracers[:, i, j, sl],
xx, p, interpolation)
self.x0 = s.x0
self.y0 = s.y0
self.sl = s.sl
self.tracers = tracersNew
self.p = p
#self.tracers = s.tracers
self.sub = s.sub
self.hMin = s.hMin
self.hMax = s.hMax
self.lMax = s.lMax
self.tol = s.tol
self.iterMax = s.iterMax
# save into vtk file
if (streamFile != []):
writer = vtk.vtkPolyDataWriter()
writer.SetFileName(dataDir + '/' + streamFile)
polyData = vtk.vtkPolyData()
fieldData = vtk.vtkFieldData()
# fields containing initial x and y values
field = VN.numpy_to_vtk(self.x0)
field.SetName('x0')
fieldData.AddArray(field)
field = VN.numpy_to_vtk(self.y0)
field.SetName('y0')
fieldData.AddArray(field)
# field containing length of stream lines for later decomposition
field = VN.numpy_to_vtk(self.sl)
field.SetName('sl')
fieldData.AddArray(field)
# streamline parameters
tmp = range(10)
tmp[0] = np.array([s.sub], dtype='int32')
field = VN.numpy_to_vtk(tmp[0])
field.SetName('sub')
fieldData.AddArray(field)
tmp[1] = np.array([s.hMin], dtype='float32')
field = VN.numpy_to_vtk(tmp[1])
field.SetName('hMin')
fieldData.AddArray(field)
tmp[2] = np.array([s.hMax], dtype='float32')
field = VN.numpy_to_vtk(tmp[2])
field.SetName('hMax')
fieldData.AddArray(field)
tmp[3] = np.array([s.lMax], dtype='float32')
field = VN.numpy_to_vtk(tmp[3])
field.SetName('lMax')
fieldData.AddArray(field)
tmp[4] = np.array([s.tol], dtype='float32')
field = VN.numpy_to_vtk(tmp[4])
field.SetName('tol')
fieldData.AddArray(field)
tmp[5] = np.array([s.iterMax], dtype='int32')
field = VN.numpy_to_vtk(tmp[5])
field.SetName('iterMax')
fieldData.AddArray(field)
# fields containing simulation parameters stored in paramFile
dic = dir(p)
params = range(len(dic))
i = 0
for attr in dic:
if (attr[0] != '_'):
params[i] = getattr(p, attr)
params[i] = np.array([params[i]], dtype=type(params[i]))
field = VN.numpy_to_vtk(params[i])
field.SetName(attr)
fieldData.AddArray(field)
i += 1
# all stremlines as continuous array of points
points = vtk.vtkPoints()
for i in range(len(s.x0)):
for j in range(len(s.y0)):
for k in range(self.sl[i, j]):
points.InsertNextPoint(self.tracers[:, i, j, k])
polyData.SetPoints(points)
polyData.SetFieldData(fieldData)
writer.SetInput(polyData)
writer.SetFileTypeToBinary()
writer.Write()
def __init__(self,
dataDir='data',
B0File='B0.vtk',
streamFileInit='streamInit.vtk',
paramFile='save.vtk',
interpolation='weighted',
integration='simple',
sub=1,
hMin=2e-3,
hMax=2e4,
lMax=500,
tol=1e-2,
iterMax=1e3,
x0=[],
y0=[]):
"""
Creates, saves and returns the initial streamline map.
call signature:
streamInit(dataDir = 'data', B0File = 'B0.vtk', streamFileInit = 'streamInit.vtk', paramFile = 'save.vtk', interpolation = 'weighted', integration = 'simple', sub = 1, hMin = 2e-3, hMax = 2e2, lMax = 500, tol = 2e-3, iterMax = 1e3, x0 = [], y0 = [])
Trace magnetic streamlines for t = 0 and store the positions in a file.
Keyword arguments:
*dataDir*:
Data directory.
*B0File*:
Name of the file storing B(X,0) = B0.
*streamFileInit*:
Store the streamline in this file. If it is empty [] don't write.
*paramFile*:
Dump file from where to read the simulation parameters.
*interpolation*:
Interpolation of the vector field.
'mean': takes the mean of the adjacent grid point.
'weighted': weights the adjacent grid points according to their distance.
*integration*:
Integration method.
'simple': low order method.
'RK6': Runge-Kutta 6th order.
*sub*:
Subsampling of the streamlines.
*hMin*:
Minimum step length for and underflow to occur.
*hMax*:
Parameter for the initial step length.
*lMax*:
Maximum length of the streamline. Integration will stop if l >= lMax.
*tol*:
Tolerance for each integration step. Reduces the step length if error >= tol.
*iterMax*:
Maximum number of iterations.
*x0*:
Initial seed in x-direction.
*y0*:
Initial seed in y-direction.
"""
data = gm.readB0(dataDir=dataDir, fileName=B0File)
B0 = data.bfield
p = gm.readParams(dataDir=dataDir, fileName=paramFile)
self.p = p
self.p.t = 0
# streamline parameters
self.sub = sub
self.hMin = hMin
self.hMax = hMax
self.lMax = lMax
self.tol = tol
self.iterMax = iterMax
# create initial seeds
if (x0 == []):
x0 = np.float32(
np.linspace(p.Ox - p.dx, p.Ox + p.Lx + p.dx,
np.round(1 + (2 * p.dx + p.Lx) / p.dx * sub)))
if (y0 == []):
y0 = np.float32(
np.linspace(p.Oy - p.dy, p.Oy + p.Ly + p.dy,
np.round(1 + (2 * p.dy + p.Ly) / p.dy * sub)))
self.x0 = x0
self.y0 = y0
try:
len(x0)
except:
x0 = np.array([x0])
y0 = np.array([y0])
self.tracers = np.zeros([3, len(x0), len(y0), iterMax],
dtype='float32') # tentative streamline length
self.sl = np.zeros([len(x0), len(y0)], dtype='int32')
tol2 = tol**2
# declare vectors
xMid = np.zeros(3)
xSingle = np.zeros(3)
xHalf = np.zeros(3)
xDouble = np.zeros(3)
# initialize the coefficient for the 6th order adaptive time step RK
a = np.zeros(6)
b = np.zeros((6, 5))
c = np.zeros(6)
cs = np.zeros(6)
k = np.zeros((6, 3))
a[1] = 0.2
a[2] = 0.3
a[3] = 0.6
a[4] = 1
a[5] = 0.875
b[1, 0] = 0.2
b[2, 0] = 3 / 40.
b[2, 1] = 9 / 40.
b[3, 0] = 0.3
b[3, 1] = -0.9
b[3, 2] = 1.2
b[4, 0] = -11 / 54.
b[4, 1] = 2.5
b[4, 2] = -70 / 27.
b[4, 3] = 35 / 27.
b[5, 0] = 1631 / 55296.
b[5, 1] = 175 / 512.
b[5, 2] = 575 / 13824.
b[5, 3] = 44275 / 110592.
b[5, 4] = 253 / 4096.
c[0] = 37 / 378.
c[2] = 250 / 621.
c[3] = 125 / 594.
c[5] = 512 / 1771.
cs[0] = 2825 / 27648.
cs[2] = 18575 / 48384.
cs[3] = 13525 / 55296.
cs[4] = 277 / 14336.
cs[5] = 0.25
# do the streamline tracing
r = 0
for u in x0:
s = 0
for v in y0:
# initialize the streamline
xx = np.array([u, v, p.Oz])
self.tracers[:, r, s, 0] = xx
dh = np.sqrt(hMax * hMin) # initial step size
sl = 0
l = 0
outside = False
if (integration == 'simple'):
while ((l < lMax) and (xx[2] < p.Oz + p.Lz)
and (sl < iterMax - 1) and (not (np.isnan(xx[0])))
and (outside == False)):
# (a) single step (midpoint method)
xMid = xx + 0.5 * dh * gm.vecInt(
xx, B0, p, interpolation)
xSingle = xx + dh * gm.vecInt(xMid, B0, p,
interpolation)
# (b) two steps with half stepsize
xMid = xx + 0.25 * dh * gm.vecInt(
xx, B0, p, interpolation)
xHalf = xx + 0.5 * dh * gm.vecInt(
xMid, B0, p, interpolation)
xMid = xHalf + 0.25 * dh * gm.vecInt(
xHalf, B0, p, interpolation)
xDouble = xHalf + 0.5 * dh * gm.vecInt(
xMid, B0, p, interpolation)
# (c) check error (difference between methods)
dist2 = np.sum((xSingle - xDouble)**2)
if (dist2 > tol2):
dh = 0.5 * dh
if (abs(dh) < hMin):
print("Error: stepsize underflow")
break
else:
l += np.sqrt(np.sum((xx - xDouble)**2))
xx = xDouble.copy()
if (abs(dh) < hMin):
dh = 2 * dh
sl += 1
self.tracers[:, r, s, sl] = xx.copy()
if ((dh > hMax) or (np.isnan(dh))):
dh = hMax
# check if this point lies outside the domain
if ((xx[0] < p.Ox - p.dx)
or (xx[0] > p.Ox + p.Lx + p.dx)
or (xx[1] < p.Oy - p.dy)
or (xx[1] > p.Oy + p.Ly + p.dy)
or (xx[2] < p.Oz)
or (xx[2] > p.Oz + p.Lz)):
outside = True
if (integration == 'RK6'):
while ((l < lMax) and (xx[2] < p.Oz + p.Lz)
and (sl < iterMax) and (not (np.isnan(xx[0])))
and (outside == False)):
k[0, :] = dh * gm.vecInt(xx, B0, p, interpolation)
k[1, :] = dh * gm.vecInt(xx + b[1, 0] * k[0, :], B0, p,
interpolation)
k[2, :] = dh * gm.vecInt(
xx + b[2, 0] * k[0, :] + b[2, 1] * k[1, :], B0, p,
interpolation)
k[3, :] = dh * gm.vecInt(
xx + b[3, 0] * k[0, :] + b[3, 1] * k[1, :] +
b[3, 2] * k[2, :], B0, p, interpolation)
k[4, :] = dh * gm.vecInt(
xx + b[4, 0] * k[0, :] + b[4, 1] * k[1, :] +
b[4, 2] * k[2, :] + b[4, 3] * k[3, :], B0, p,
interpolation)
k[5, :] = dh * gm.vecInt(
xx + b[5, 0] * k[0, :] + b[5, 1] * k[1, :] +
b[5, 2] * k[2, :] + b[5, 3] * k[3, :] +
b[5, 4] * k[4, :], B0, p, interpolation)
xNew = xx + c[0] * k[0, :] + c[1] * k[1, :] + c[2] * k[
2, :] + c[3] * k[3, :] + c[4] * k[4, :] + c[5] * k[
5, :]
xNewS = xx + cs[0] * k[0, :] + cs[1] * k[
1, :] + cs[2] * k[2, :] + cs[3] * k[
3, :] + cs[4] * k[4, :] + cs[5] * k[5, :]
delta2 = np.dot((xNew - xNewS), (xNew - xNewS))
delta = np.sqrt(delta2)
if (delta2 > tol2):
dh = dh * (0.9 * abs(tol / delta))**0.2
if (abs(dh) < hMin):
print("Error: step size underflow")
break
else:
l += np.sqrt(np.sum((xx - xNew)**2))
xx = xNew
if (abs(dh) < hMin):
dh = 2 * dh
sl += 1
self.tracers[:, r, s, sl] = xx
if ((dh > hMax) or (np.isnan(dh))):
dh = hMax
# check if this point lies outside the domain
if ((xx[0] < p.Ox - p.dx)
or (xx[0] > p.Ox + p.Lx + p.dx)
or (xx[1] < p.Oy - p.dy)
or (xx[1] > p.Oy + p.Ly + p.dy)
or (xx[2] < p.Oz)
or (xx[2] > p.Oz + p.Lz)):
outside = True
if ((dh > hMax) or (delta == 0) or (np.isnan(dh))):
dh = hMax
self.sl[r, s] = sl + 1
s += 1
r += 1
# save into vtk file
if (streamFileInit != []):
writer = vtk.vtkPolyDataWriter()
writer.SetFileName(dataDir + '/' + streamFileInit)
polyData = vtk.vtkPolyData()
fieldData = vtk.vtkFieldData()
# fields containing initial x and y values
field = VN.numpy_to_vtk(self.x0)
field.SetName('x0')
fieldData.AddArray(field)
field = VN.numpy_to_vtk(self.y0)
field.SetName('y0')
fieldData.AddArray(field)
# field containing length of stream lines for later decomposition
field = VN.numpy_to_vtk(self.sl)
field.SetName('sl')
fieldData.AddArray(field)
# streamline parameters
tmp = range(10)
tmp[0] = np.array([sub], dtype='int32')
field = VN.numpy_to_vtk(tmp[0])
field.SetName('sub')
fieldData.AddArray(field)
tmp[1] = np.array([hMin], dtype='float32')
field = VN.numpy_to_vtk(tmp[1])
field.SetName('hMin')
fieldData.AddArray(field)
tmp[2] = np.array([hMax], dtype='float32')
field = VN.numpy_to_vtk(tmp[2])
field.SetName('hMax')
fieldData.AddArray(field)
tmp[3] = np.array([lMax], dtype='float32')
field = VN.numpy_to_vtk(tmp[3])
field.SetName('lMax')
fieldData.AddArray(field)
tmp[4] = np.array([tol], dtype='float32')
field = VN.numpy_to_vtk(tmp[4])
field.SetName('tol')
fieldData.AddArray(field)
tmp[5] = np.array([iterMax], dtype='int32')
field = VN.numpy_to_vtk(tmp[5])
field.SetName('iterMax')
fieldData.AddArray(field)
# fields containing simulation parameters stored in paramFile
dic = dir(p)
params = range(len(dic))
i = 0
for attr in dic:
if (attr[0] != '_'):
params[i] = getattr(p, attr)
params[i] = np.array([params[i]], dtype=type(params[i]))
field = VN.numpy_to_vtk(params[i])
field.SetName(attr)
fieldData.AddArray(field)
i += 1
# all streamlines as continuous array of points
points = vtk.vtkPoints()
for r in range(len(x0)):
for s in range(len(y0)):
for sl in range(self.sl[r, s]):
points.InsertNextPoint(self.tracers[:, r, s, sl])
polyData.SetPoints(points)
polyData.SetFieldData(fieldData)
writer.SetInput(polyData)
writer.SetFileTypeToBinary()
writer.Write()
def __init__(self,
dataDir='data',
poincareInit='poincareInit.vtk',
poincare='poincare.vtk',
dumpFile='save.vtk',
interpolation='weighted',
po=[]):
"""
Maps the streamlines from X to x.
call signature:
mapPoincare(dataDir = 'data', poincareInit = 'poincareInit.vtk', poincareFile = 'poincare.vtk', dumpFile = 'save.vtk', interpolation = 'weighted', po = [])
Keyword arguments:
*dataDir*:
Data directory.
*poincareInit*:
Read the initial Poincare maps from this file.
*poincareFile*:
Store the Poincare map in this file.
*dumpFile*:
Use this file for the mapping x(X,t).
*interpolation*:
Interpolation of the vector field.
'mean': takes the mean of the adjacent grid point.
'weighted': weights the adjacent grid points according to their distance.
*po*:
The Poincare object for t = 0. If not passed obtain it from 'poincareInit'.
"""
# read the Poincare map at t = 0
if (po == []):
po = gm.readPoincare(dataDir=dataDir, poincare=poincareInit)
# read the current state
data = gm.readDump(dataDir=dataDir, fileName=dumpFile)
p = data.p
xx = data.grid
# mapped tracers
tracersNew = np.zeros(po.tracers.shape, dtype=po.tracers.dtype)
# mapped Poincare map
xNew = np.zeros(po.x.shape)
yNew = np.zeros(po.y.shape)
# interpolate x(X,t) at S to get x(S,t), where S is the initial streamline
for j in range(po.x.shape[1]):
for sl in range(po.sl[j]):
tracersNew[:, j, sl] = gm.vecInt(po.tracers[:, j, sl], xx, p,
interpolation)
for i in range(po.x.shape[0]):
if (i == 0):
#xyz = np.array([po.x[i,j], po.y[i,j], p.Oz-p.dz])
xyz = np.array([po.x[i, j], po.y[i, j], p.Oz])
else:
#xyz = np.array([po.x[i,j], po.y[i,j], p.Oz+p.Lz+p.dz])
xyz = np.array([po.x[i, j], po.y[i, j], p.Oz + p.Lz])
tmp = gm.vecInt(xyz, xx, p, interpolation)
xNew[i, j] = tmp[0]
yNew[i, j] = tmp[1]
self.x = xNew
self.y = yNew
self.sl = po.sl
self.tracers = tracersNew
self.p = p
self.hMin = po.hMin
self.hMax = po.hMax
self.lMax = po.lMax
self.tol = po.tol
self.iterMax = po.iterMax
self.nIter = po.nIter
self.nSeeds = po.nSeeds
# save into vtk file
if (poincare != []):
writer = vtk.vtkPolyDataWriter()
writer.SetFileName(dataDir + '/' + poincare)
polyData = vtk.vtkPolyData()
fieldData = vtk.vtkFieldData()
# fields containing x and y values
field = VN.numpy_to_vtk(self.x)
field.SetName('x')
fieldData.AddArray(field)
field = VN.numpy_to_vtk(self.y)
field.SetName('y')
fieldData.AddArray(field)
# field containing length of stream lines for later decomposition
field = VN.numpy_to_vtk(self.sl)
field.SetName('sl')
fieldData.AddArray(field)
# streamline parameters
tmp = range(10)
tmp[0] = np.array([po.hMin], dtype='float32')
field = VN.numpy_to_vtk(tmp[0])
field.SetName('hMin')
fieldData.AddArray(field)
tmp[1] = np.array([po.hMax], dtype='float32')
field = VN.numpy_to_vtk(tmp[1])
field.SetName('hMax')
fieldData.AddArray(field)
tmp[2] = np.array([po.lMax], dtype='float32')
field = VN.numpy_to_vtk(tmp[2])
field.SetName('lMax')
fieldData.AddArray(field)
tmp[3] = np.array([po.tol], dtype='float32')
field = VN.numpy_to_vtk(tmp[3])
field.SetName('tol')
fieldData.AddArray(field)
tmp[4] = np.array([po.iterMax], dtype='int32')
field = VN.numpy_to_vtk(tmp[4])
field.SetName('iterMax')
fieldData.AddArray(field)
tmp[5] = np.array([po.tol], dtype='int32')
field = VN.numpy_to_vtk(tmp[5])
field.SetName('nSeeds')
fieldData.AddArray(field)
tmp[6] = np.array([po.tol], dtype='int32')
field = VN.numpy_to_vtk(tmp[6])
field.SetName('nIter')
fieldData.AddArray(field)
# fields containing simulation parameters stored in paramFile
dic = dir(p)
params = range(len(dic))
i = 0
for attr in dic:
if (attr[0] != '_'):
params[i] = getattr(p, attr)
params[i] = np.array([params[i]], dtype=type(params[i]))
field = VN.numpy_to_vtk(params[i])
field.SetName(attr)
fieldData.AddArray(field)
i += 1
# all streamlines as continuous array of points
points = vtk.vtkPoints()
for q in range(self.x.shape[1]):
for l in range(self.sl[q]):
points.InsertNextPoint(self.tracers[:, q, l])
polyData.SetPoints(points)
polyData.SetFieldData(fieldData)
writer.SetInput(polyData)
writer.SetFileTypeToBinary()
writer.Write()
def __init__(self,
dataDir='data',
B0File='B0.vtk',
poincare='poincareInit.vtk',
paramFile='save.vtk',
dumpFile=[],
interpolation='weighted',
integration='simple',
hMin=2e-3,
hMax=2e2,
lMax=500,
tol=2e-3,
iterMax=1e3,
x0=[],
y0=[],
nSeeds=10,
nIter=10):
"""
Creates, saves and returns the initial streamline map for a few lines and the Poincare map.
call signature:
streamInit(dataDir = 'data', B0File = 'B0.vtk', poincare = 'poincareInit.vtk', paramFile = 'save.vtk', dumpFile = [], interpolation = 'weighted', integration = 'simple', sub = 1, hMin = 2e-3, hMax = 2e2, lMax = 500, tol = 2e-3, iterMax = 1e3, x0 = [], y0 = [])
Trace magnetic streamlines for t = 0 and store the positions in a file.
Keyword arguments:
*dataDir*:
Data directory.
*B0File*:
Name of the file storing B(X,0) = B0.
*poincare*:
Store the Poincare map in this file.
*paramFile*:
Dump file from where to read the simulation parameters.
*dumpFile*:
If not empty map the streamlines from B0.vtk to the time of dumpFile.
*interpolation*:
Interpolation of the vector field.
'mean': takes the mean of the adjacent grid point.
'weighted': weights the adjacent grid points according to their distance.
*integration*:
Integration method.
'simple': low order method.
'RK6': Runge-Kutta 6th order.
*hMin*:
Minimum step length for and underflow to occur.
*hMax*:
Parameter for the initial step length.
*lMax*:
Maximum length of the streamline. Integration will stop if l >= lMax.
*tol*:
Tolerance for each integration step. Reduces the step length if error >= tol.
*iterMax*:
Maximum number of iterations.
*x0*:
Initial seed in x-direction.
*y0*:
Initial seed in y-direction.
*nSeeds*:
Number of initial seeds.
*nIter*:
Number of times the streamlines go through the domain.
"""
p = gm.readParams(dataDir=dataDir, fileName=paramFile)
if (len(x0) != len(y0)):
print("error: length of x0 != length of y0.")
return -1
if ((len(x0) == 0) and (len(y0) == 0)):
x0 = np.random.random(nSeeds) * p.Lx + p.Ox
y0 = np.random.random(nSeeds) * p.Ly + p.Oy
else:
nSeeds = len(x0)
x = np.zeros((nIter + 1, nSeeds))
y = np.zeros((nIter + 1, nSeeds))
x[0, :] = x0
y[0, :] = y0
streams = range(nSeeds)
tracers = range(nSeeds)
sl = np.zeros(nSeeds, dtype='int32')
for q in range(len(x0)):
tracers[q] = []
for i in range(nIter):
# stream the lines until they hit the upper boundary
s = gm.streamInit(dataDir=dataDir,
B0File=B0File,
streamFileInit=[],
paramFile=paramFile,
interpolation=interpolation,
integration=integration,
hMin=hMin,
hMax=hMax,
lMax=lMax,
tol=tol,
iterMax=iterMax,
x0=x[i, q],
y0=y[i, q])
# in case the initial time is not 0, map the streamline accordingly
if (dumpFile != []):
s = gm.mapStream(dataDir=dataDir,
streamFileInit='streamInit.vtk',
streamFile=[],
dumpFile=dumpFile,
interpolation=interpolation,
s=s)
# interpolate the final values for points hitting through the boundary
l = (p.Oz + p.Lz - s.tracers[2, 0, 0, s.sl - 2]) / (
s.tracers[2, 0, 0, s.sl - 1] -
s.tracers[2, 0, 0, s.sl - 2])
x[i + 1,
q] = (s.tracers[0, 0, 0, s.sl - 1] -
s.tracers[0, 0, 0, s.sl - 2]) * l + s.tracers[0, 0, 0,
s.sl - 2]
y[i + 1,
q] = (s.tracers[1, 0, 0, s.sl - 1] -
s.tracers[1, 0, 0, s.sl - 2]) * l + s.tracers[1, 0, 0,
s.sl - 2]
# add the tracers to the existing ones
tracers[q].extend(
list(np.swapaxes(s.tracers[:, 0, 0, :s.sl], 0, 1)))
sl[q] += s.sl
p = s.p
self.p = p
self.x = x
self.y = y
self.sl = sl
maxLen = sl.max()
self.tracers = np.zeros((3, nSeeds, maxLen))
for q in range(len(x0)):
self.tracers[:, q, :sl[q]] = np.swapaxes(np.array(tracers[q]), 0,
1)
# streamline parameters
self.hMin = hMin
self.hMax = hMax
self.lMax = lMax
self.tol = tol
self.iterMax = iterMax
self.nSeeds = nSeeds
self.nIter = nIter
# safe in vtk file
if (poincare != []):
writer = vtk.vtkPolyDataWriter()
writer.SetFileName(dataDir + '/' + poincare)
polyData = vtk.vtkPolyData()
fieldData = vtk.vtkFieldData()
# fields containing x and y values
field = VN.numpy_to_vtk(self.x)
field.SetName('x')
fieldData.AddArray(field)
field = VN.numpy_to_vtk(self.y)
field.SetName('y')
fieldData.AddArray(field)
# field containing length of stream lines for later decomposition
field = VN.numpy_to_vtk(self.sl)
field.SetName('sl')
fieldData.AddArray(field)
# streamline parameters
tmp = range(10)
tmp[0] = np.array([s.hMin], dtype='float32')
field = VN.numpy_to_vtk(tmp[0])
field.SetName('hMin')
fieldData.AddArray(field)
tmp[1] = np.array([s.hMax], dtype='float32')
field = VN.numpy_to_vtk(tmp[1])
field.SetName('hMax')
fieldData.AddArray(field)
tmp[2] = np.array([s.lMax], dtype='float32')
field = VN.numpy_to_vtk(tmp[2])
field.SetName('lMax')
fieldData.AddArray(field)
tmp[3] = np.array([s.tol], dtype='float32')
field = VN.numpy_to_vtk(tmp[3])
field.SetName('tol')
fieldData.AddArray(field)
tmp[4] = np.array([s.iterMax], dtype='int32')
field = VN.numpy_to_vtk(tmp[4])
field.SetName('iterMax')
fieldData.AddArray(field)
tmp[5] = np.array([nSeeds], dtype='int32')
field = VN.numpy_to_vtk(tmp[5])
field.SetName('nSeeds')
fieldData.AddArray(field)
tmp[6] = np.array([nIter], dtype='int32')
field = VN.numpy_to_vtk(tmp[6])
field.SetName('nIter')
fieldData.AddArray(field)
# fields containing simulation parameters stored in paramFile
dic = dir(p)
params = range(len(dic))
i = 0
for attr in dic:
if (attr[0] != '_'):
params[i] = getattr(p, attr)
params[i] = np.array([params[i]], dtype=type(params[i]))
field = VN.numpy_to_vtk(params[i])
field.SetName(attr)
fieldData.AddArray(field)
i += 1
# all streamlines as continuous array of points
points = vtk.vtkPoints()
for q in range(len(x0)):
for l in range(self.sl[q]):
points.InsertNextPoint(self.tracers[:, q, l])
polyData.SetPoints(points)
polyData.SetFieldData(fieldData)
writer.SetInput(polyData)
writer.SetFileTypeToBinary()
writer.Write()