def CalcAge(self):
"""
Calculate the age of a particle inside of the age polygon
"""
#print '\t\tCalculating the particle age...'
#inpoly = nxutils.points_inside_poly(np.vstack((self.particles['X'],self.particles['Y'])).T,self.agepoly)
inpoly = inpolygon(np.vstack((self.particles['X'],self.particles['Y'])).T,self.agepoly)
self.particles['age'][inpoly] = self.particles['age'][inpoly] + self.dt
self.particles['age'][inpoly==False]=0.0
# Update the agemax attribute
self.particles['agemax'] = np.max([self.particles['age'],self.particles['agemax']],axis=0)
def CalcAge(self):
"""
Calculate the age of a particle inside of the age polygon
"""
#print '\t\tCalculating the particle age...'
#inpoly = nxutils.points_inside_poly(np.vstack((self.particles['X'],self.particles['Y'])).T,self.agepoly)
inpoly = inpolygon(np.vstack((self.particles['X'],self.particles['Y'])).T,self.agepoly)
self.particles['age'][inpoly] = self.particles['age'][inpoly] + self.dt
self.particles['age'][inpoly==False]=0.0
# Update the agemax attribute
self.particles['agemax'] = np.max([self.particles['age'],self.particles['agemax']],axis=0)
def setAgeSource(self,shpfile):
"""
Sets the age source term using a polygon shapefile
"""
# Read the shapefile
XY,tmp = readShpPoly(shpfile,FIELDNAME=None)
if len(XY)<1:
raise Exception, ' could not find any polygons in shapefile: %s'%shpfile
for xpoly in XY:
xycells = np.asarray([self.xv,self.yv])
#ind1 = nxutils.points_inside_poly(xycells.T,xpoly)
ind1 = inpolygon(xycells.T,xpoly)
# Sets all vertical layers for now...
self.agesource[:,ind1] = 1.
def curv_ugrid_gen(X,Y,suntanspath=None,maskpoly=None):
"""
Creates a curvilinear mesh from grid corners points stored
in arrays X and Y.
"""
ny,nx = X.shape
XY = np.vstack((X.ravel(),Y.ravel())).T
if not maskpoly is None:
mask = inpolygon(XY,maskpoly)
mask = mask.reshape((ny,nx))
else:
mask = np.ones((ny,nx),dtype=np.bool) # all false
cells=[]
xp = []
yp = []
def pntindx(j,i,nrows):
return j*nrows + i
for jj in range(ny):
for ii in range(nx):
#if mask[jj,ii]:
#xp.append(xgrd[ii])
#yp.append(ygrd[jj])
xp.append(X[jj,ii])
yp.append(Y[jj,ii])
for jj in range(ny-1):
for ii in range(nx-1):
if mask[jj,ii] and mask[jj+1,ii] and mask[jj+1,ii+1] and mask[jj,ii+1]:
cells.append([pntindx(jj,ii,nx), pntindx(jj+1,ii,nx),\
pntindx(jj+1,ii+1,nx),pntindx(jj,ii+1,nx)])
Nc = len(cells)
nfaces = 4*np.ones((Nc,),np.int)
cells = np.array(cells,dtype=np.int32)
# Convert to a suntans grid
grd = HybridGrid(np.array(xp),np.array(yp),cells,nfaces=nfaces)
if not suntanspath is None:
grd.write2suntans(suntanspath)
return grd
def curv_ugrid_gen(X,Y,suntanspath=None,maskpoly=None):
"""
Creates a curvilinear mesh from grid corners points stored
in arrays X and Y.
"""
ny,nx = X.shape
XY = np.vstack((X.ravel(),Y.ravel())).T
if not maskpoly is None:
mask = inpolygon(XY,maskpoly)
mask = mask.reshape((ny,nx))
else:
mask = np.ones((ny,nx),dtype=np.bool) # all false
cells=[]
xp = []
yp = []
def pntindx(j,i,nrows):
return j*nrows + i
for jj in range(ny):
for ii in range(nx):
#if mask[jj,ii]:
#xp.append(xgrd[ii])
#yp.append(ygrd[jj])
xp.append(X[jj,ii])
yp.append(Y[jj,ii])
for jj in range(ny-1):
for ii in range(nx-1):
if mask[jj,ii] and mask[jj+1,ii] and mask[jj+1,ii+1] and mask[jj,ii+1]:
cells.append([pntindx(jj,ii,nx), pntindx(jj+1,ii,nx),\
pntindx(jj+1,ii+1,nx),pntindx(jj,ii+1,nx)])
Nc = len(cells)
nfaces = 4*np.ones((Nc,),np.int)
cells = np.array(cells,dtype=np.int32)
# Convert to a suntans grid
grd = HybridGrid(np.array(xp),np.array(yp),cells,nfaces=nfaces)
if not suntanspath is None:
grd.write2suntans(suntanspath)
return grd
def inCell(self, cellind, xy):
"""
Check whether a point is inside a cell
Basically a wrapper for points_inside_polyo function
"""
xyverts = np.zeros((4, 2))
xyverts[:,0]= [self.xp[self.cells[cellind,0]],\
self.xp[self.cells[cellind,1]],\
self.xp[self.cells[cellind,2]],\
self.xp[self.cells[cellind,0]]]
xyverts[:,1]= [self.yp[self.cells[cellind,0]],\
self.yp[self.cells[cellind,1]],\
self.yp[self.cells[cellind,2]],\
self.yp[self.cells[cellind,0]] ]
#return points_inside_poly(xy.reshape(1,2),xyverts)
return inpolygon(xy.reshape(1, 2), xyverts)
def inCell(self,cellind,xy):
"""
Check whether a point is inside a cell
Basically a wrapper for points_inside_polyo function
"""
xyverts=np.zeros((4,2))
xyverts[:,0]= [self.xp[self.cells[cellind,0]],\
self.xp[self.cells[cellind,1]],\
self.xp[self.cells[cellind,2]],\
self.xp[self.cells[cellind,0]]]
xyverts[:,1]= [self.yp[self.cells[cellind,0]],\
self.yp[self.cells[cellind,1]],\
self.yp[self.cells[cellind,2]],\
self.yp[self.cells[cellind,0]] ]
#return points_inside_poly(xy.reshape(1,2),xyverts)
return inpolygon(xy.reshape(1,2),xyverts)
def inCellVecOld(self, cellinds, x, y):
"""
Check whether a point is inside a cell
Basically a wrapper for points_inside_poly function
"""
nx = x.shape[0]
xyvertsall = np.zeros((nx, 4, 2))
xyvertsall[:, 0, 0] = self.xp[self.cells[cellinds, 0]]
xyvertsall[:, 1, 0] = self.xp[self.cells[cellinds, 1]]
xyvertsall[:, 2, 0] = self.xp[self.cells[cellinds, 2]]
xyvertsall[:, 3, 0] = self.xp[self.cells[cellinds, 0]]
xyvertsall[:, 0, 1] = self.yp[self.cells[cellinds, 0]]
xyvertsall[:, 1, 1] = self.yp[self.cells[cellinds, 1]]
xyvertsall[:, 2, 1] = self.yp[self.cells[cellinds, 2]]
xyvertsall[:, 3, 1] = self.yp[self.cells[cellinds, 0]]
xyverts = np.zeros((4, 2))
def _xyverts(ii):
xyverts[:, :] = xyvertsall[ii, :, :]
return xyverts
xy = np.zeros((1, 2))
def _xy(ii):
xy[0, 0] = x[ii]
xy[0, 1] = y[ii]
return xy
nx = x.shape[0]
inpoly = np.zeros((x.shape), dtype=np.bool)
for ii in range(nx):
#inpoly[ii] = points_inside_poly(_xy(ii),_xyverts(ii))
inpoly[ii] = inpolygon(_xy(ii), _xyverts(ii))
return inpoly
def inCellVecOld(self,cellinds,x,y):
"""
Check whether a point is inside a cell
Basically a wrapper for points_inside_poly function
"""
nx = x.shape[0]
xyvertsall=np.zeros((nx,4,2))
xyvertsall[:,0,0]= self.xp[self.cells[cellinds,0]]
xyvertsall[:,1,0]= self.xp[self.cells[cellinds,1]]
xyvertsall[:,2,0]= self.xp[self.cells[cellinds,2]]
xyvertsall[:,3,0]= self.xp[self.cells[cellinds,0]]
xyvertsall[:,0,1]= self.yp[self.cells[cellinds,0]]
xyvertsall[:,1,1]= self.yp[self.cells[cellinds,1]]
xyvertsall[:,2,1]= self.yp[self.cells[cellinds,2]]
xyvertsall[:,3,1]= self.yp[self.cells[cellinds,0]]
xyverts=np.zeros((4,2))
def _xyverts(ii):
xyverts[:,:] = xyvertsall[ii,:,:]
return xyverts
xy = np.zeros((1,2))
def _xy(ii):
xy[0,0]=x[ii]
xy[0,1]=y[ii]
return xy
nx = x.shape[0]
inpoly = np.zeros((x.shape),dtype=np.bool)
for ii in range(nx):
#inpoly[ii] = points_inside_poly(_xy(ii),_xyverts(ii))
inpoly[ii] = inpolygon(_xy(ii),_xyverts(ii))
return inpoly
def modifyBCmarker(suntanspath, bcfile, saveplot=False):
"""
Modifies SUNTANS boundary markers with a shapefile
The shapefile must contain polygons with the integer-type field "marker"
"""
print '#######################################################'
print ' Modifying the boundary markers for grid in folder:'
print ' %s'%suntanspath
# Load the grid into an object
grd = sunpy.Grid(suntanspath)
# Find the edge points
xe = np.mean(grd.xp[grd.edges],axis=1)
ye = np.mean(grd.yp[grd.edges],axis=1)
# Read the shapefile
if not bcfile==None:
XY,newmarker = readShpPoly(bcfile,FIELDNAME='marker')
if len(XY)<1:
print 'Error - could not find any polygons with the field name "marker" in shapefile: %s'%bcfile
return
XY,edge_id = readShpPoly(bcfile,FIELDNAME='edge_id')
if len(XY)<1:
print 'Error - could not find any polygons with the field name "edge_id" in shapefile: %s'%bcfile
return
else:
XY=[]
newmarker=[]
edge_id=[]
# Plot before updates
#plt.figure()
#grd.plotBC()
#plt.plot(XY[0][:,0],XY[0][:,1],'m',linewidth=2)
#plt.show()
# Reset all markers to one (closed)
ind0 = grd.mark>0
grd.mark[ind0]=1
# Find the points inside each of the polygon and assign new bc
grd.edge_id = grd.mark*0 # Flag to identify linked edges/segments (marker=4 only)
for xpoly, bctype,segmentID in zip(XY,newmarker,edge_id):
ind0 = grd.mark>0
edges = np.asarray([xe[ind0],ye[ind0]])
mark = grd.mark[ind0]
#ind1 = nxutils.points_inside_poly(edges.T,xpoly)
ind1 = inpolygon(edges.T,xpoly)
if bctype==4:
eflag = grd.edge_id[ind0]
eflag[ind1]=segmentID
grd.edge_id[ind0]=eflag
bctype=2
mark[ind1]=bctype
grd.mark[ind0]=mark
# Save the new markers to edges.dat
edgefile = suntanspath+'/edges.dat'
grd.saveEdges(edgefile)
print 'Updated markers written to: %s'%(edgefile)
# Plot the markers
if saveplot:
plt.figure()
grd.plotBC()
if len(XY)>0:
plt.plot(XY[0][:,0],XY[0][:,1],'m',linewidth=2)
figfile = suntanspath+'/BoundaryMarkerTypes.pdf'
plt.savefig(figfile)
print 'Marker plot saved to: %s'%(figfile)
print 'Done.'
print '#######################################################'
def GridParticles(grdfile,dx,dy,nz,xypoly=None,splitvec=1):
"""
Returns the locations of particles on a regular grid inside of suntans grid
Inputs:
grdfile - netcdf filename containing the suntans grid
dx,dy - resolution in x and y component respectively.
nz - number of particles in the vertical. Particles are arranged in sigma layers.
xypoly - [optional] coordinates of an additional bounding polygon [Nx2 array]
"""
# Load the suntans grid
sun = Grid(grdfile)
# Load a trisearch object
tri = GridSearch(sun.xp,sun.yp,sun.cells,nfaces=sun.nfaces,verbose=False)
if xypoly == None:
xlims = [sun.xlims[0],sun.xlims[1]]
ylims = [sun.ylims[0],sun.ylims[1]]
else:
xlims = [xypoly[:,0].min(),xypoly[:,0].max()]
ylims = [xypoly[:,1].min(),xypoly[:,1].max()]
# Construct a 2D mesh of particles
x = np.arange(xlims[0],xlims[1],dx)
y = np.arange(ylims[0],ylims[1],dy)
X,Y = np.meshgrid(x,y)
X=X.ravel()
Y=Y.ravel()
# Check which particles are inside the grid
cellind = tri(X,Y)
mask = cellind!=-1
# Check which particles are also inside of the polygon
if not xypoly == None:
inpoly = inpolygon(np.vstack((X,Y)).T,xypoly)
mask = operator.and_(mask,inpoly)
xout = X[mask]
yout = Y[mask]
nx = xout.shape[0]
# Construct the 3D mesh
xout = np.repeat(xout.reshape((nx,1)),nz,axis=1)
yout = np.repeat(yout.reshape((nx,1)),nz,axis=1)
zout = np.linspace(0.05,0.95,nz)
zout = np.repeat(zout.reshape((nz,1)),nx,axis=1)
zout *= -sun.dv[cellind[mask]]
zout = zout.T
xout = xout.ravel()
yout = yout.ravel()
zout = zout.ravel()
# Rearrange the vectors to avoid clustering (this helps even the MPI workload)
#xout_split=[]
#yout_split=[]
#zout_split=[]
#for start in range(splitvec):
# xout_split.append(xout[start::splitvec])
# yout_split.append(yout[start::splitvec])
# zout_split.append(zout[start::splitvec])
#xout = np.hstack(xout_split)
#yout = np.hstack(yout_split)
#zout = np.hstack(zout_split)
return xout, yout, zout
def GridParticles(grdfile,dx,dy,nz,xypoly=None,splitvec=1):
"""
Returns the locations of particles on a regular grid inside of suntans grid
Inputs:
grdfile - netcdf filename containing the suntans grid
dx,dy - resolution in x and y component respectively.
nz - number of particles in the vertical. Particles are arranged in sigma layers.
xypoly - [optional] coordinates of an additional bounding polygon [Nx2 array]
"""
# Load the suntans grid
sun = Grid(grdfile)
# Load a trisearch object
tri = GridSearch(sun.xp,sun.yp,sun.cells,nfaces=sun.nfaces,verbose=False)
if xypoly == None:
xlims = [sun.xlims[0],sun.xlims[1]]
ylims = [sun.ylims[0],sun.ylims[1]]
else:
xlims = [xypoly[:,0].min(),xypoly[:,0].max()]
ylims = [xypoly[:,1].min(),xypoly[:,1].max()]
# Construct a 2D mesh of particles
x = np.arange(xlims[0],xlims[1],dx)
y = np.arange(ylims[0],ylims[1],dy)
X,Y = np.meshgrid(x,y)
X=X.ravel()
Y=Y.ravel()
# Check which particles are inside the grid
cellind = tri(X,Y)
mask = cellind!=-1
# Check which particles are also inside of the polygon
if not xypoly == None:
inpoly = inpolygon(np.vstack((X,Y)).T,xypoly)
mask = operator.and_(mask,inpoly)
xout = X[mask]
yout = Y[mask]
nx = xout.shape[0]
# Construct the 3D mesh
xout = np.repeat(xout.reshape((nx,1)),nz,axis=1)
yout = np.repeat(yout.reshape((nx,1)),nz,axis=1)
zout = np.linspace(0.05,0.95,nz)
zout = np.repeat(zout.reshape((nz,1)),nx,axis=1)
zout *= -sun.dv[cellind[mask]]
zout = zout.T
xout = xout.ravel()
yout = yout.ravel()
zout = zout.ravel()
# Rearrange the vectors to avoid clustering (this helps even the MPI workload)
#xout_split=[]
#yout_split=[]
#zout_split=[]
#for start in range(splitvec):
# xout_split.append(xout[start::splitvec])
# yout_split.append(yout[start::splitvec])
# zout_split.append(zout[start::splitvec])
#xout = np.hstack(xout_split)
#yout = np.hstack(yout_split)
#zout = np.hstack(zout_split)
return xout, yout, zout
