def example_nc2vtk_domain():
'''
given .nc (MPAS NETCDF) file, output data into classic vtk format.
This way, we can read into VisIt
'''
import conn
#file properties
ncfname = '/home/nickszap/research/mpas/output.2010-10-23_00:00:00.nc' #input file
vtkfname = 'domainTest5.vtk' #output file
data = open_netcdf_data(ncfname)
#partition mesh
seed0 = 0; nSeeds = 10
nCellsTotal = len(data.dimensions['nCells']); nVerticesTotal = len(data.dimensions['nVertices']);
nEdgesOnCell = data.variables['nEdgesOnCell'][:];
cellsOnCell = data.variables['cellsOnCell'][:]-1;
cell2Site,seeds = conn.partition_max(seed0, cellsOnCell, nEdgesOnCell, nCellsTotal, nSeeds)
#let's pick out a specific domain
domainInd = 5; countThreshold=1
cells = np.array(xrange(nCellsTotal))[cell2Site==seeds[domainInd]]
nCells=len(cells)
vOnCell = data.variables['verticesOnCell'][cells,:]-1
verts = conn.gatherVerticesInRegion(nCells, vOnCell,
nEdgesOnCell[cells,:], nVerticesTotal, countThreshold)
#open the output vtk file and write header.
fvtk = write_vtk_header_polydata(vtkfname, ncfname)
#write nodes and cells
nNodes = write_vtk_xyzNodes_domain(fvtk, data, verts)
#need local indices for polygon vertices
g2lVertex = conn.make_global2localMap(verts, [], nVerticesTotal)
vOnCell = conn.make_localDomainNbrs(nCells, vOnCell, nEdgesOnCell[cells,:], g2lVertex)
write_vtk_polygons_domain(fvtk, nCells, vOnCell, nEdgesOnCell[cells,:])
#write some cell data
fvtk.write('\nCELL_DATA '+str(nCells)+'\n')
write_vtk_cellLandType_domain(fvtk, data, cells)
#write some node data
#close the files
data.close()
fvtk.close()
def write_vtk_polyHorizConn_domain(data, fvtk, cells, nEdgesOnCell,nVerticesTotal): #write the polygons in this domain to file in legacy vtk format import conn #write nodes and cells nCells = len(cells) vOnCell = data.variables['verticesOnCell'][cells,:]-1 verts = conn.gatherVerticesInRegion(nCells, vOnCell,nEdgesOnCell[cells,:], nVerticesTotal, 1) nNodes = write_vtk_xyzNodes_domain(fvtk, data, verts) #need local indices for polygon vertices g2lVertex = conn.make_global2localMap(verts, [], nVerticesTotal) vOnCell = conn.make_localDomainNbrs(nCells, vOnCell, nEdgesOnCell[cells,:], g2lVertex) write_vtk_polygons_domain(fvtk, nCells, vOnCell, nEdgesOnCell[cells,:])
def test_deriv():
#we'll use analytic functions to test derivs
ncfname = '/arctic1/mduda/60km/x1.163842.output.2006-07-08_00.00.00.nc'
#ncfname = '/home/nickszap/research/mpas/output.2010-10-23_00:00:00.nc'
data = netCDF4.Dataset(ncfname,'r')
nCellsTotal = len(data.dimensions['nCells'])
nVerticesTotal = len(data.dimensions['nVertices']);
nLevels = len(data.dimensions['nVertLevels'])
nEdgesOnCell = data.variables['nEdgesOnCell'][:];
cellsOnCell = data.variables['cellsOnCell'][:]-1;
c0 = 0
cells = np.array([c0])
nCells = len(cells)
haloCells = cellsOnCell[c0,0:nEdgesOnCell[c0]]
#cell values and connectivity for this domain
g2lCell = conn.make_global2localMap(cells, haloCells, nCellsTotal)
c2c = conn.make_localDomainNbrs(nCells, cellsOnCell[cells,:], nEdgesOnCell[cells], g2lCell)
neededCells = cells.tolist(); neededCells.extend(haloCells) #has to be domain then halo (as in g2l map)
#I'm having memory errors.
#gc.collect()
#load data for domain and halo -----------------------------
timeInd = 0
print "Loading data for domain {0} with {1} cells\n".format('arctic', len(neededCells))
#print neededCells
state = loadFields(data, timeInd, neededCells, nLevels)
#edit state with analytic functions
state.ux[:,:] = state.xyz[:,:,0]; print state.ux
state.uy[:,:] = state.xyz[:,:,1]
state.uz[:,:] = state.xyz[:,:,2]
out = [None]*nCells
for hCell in xrange(nCells):
grads = []
gInd = cells[hCell]
hNbrs = c2c[hCell,0:nEdgesOnCell[gInd]]
nHNbrs = len(hNbrs)
nVars = 4 #u's and theta
vals0 = [None]*nVars
vals0[0] = state.ux[hCell,:]
vals0[1] = state.uy[hCell,:]
vals0[2] = state.uz[hCell,:]
vals0[3] = state.theta[hCell,:]
xyz0 = state.xyz[hCell,:,:] #.copy() #these get altered!
#ht0 = state.ht[hCell,:]
valsNbrs = [None]*nVars
valsNbrs[0] = state.ux[hNbrs,:]
valsNbrs[1] = state.uy[hNbrs,:]
valsNbrs[2] = state.uz[hNbrs,:]
valsNbrs[3] = state.theta[hNbrs,:]
xyzNbrs = state.xyz[hNbrs,:,:] #.copy()
#htNbrs = state.ht[hNbrs,:]
for l in xrange(nLevels):
grads.append(calc_varsGradients_leastSquare(l, nVars, xyz0, xyzNbrs,vals0,valsNbrs,nHNbrs, nLevels))
#grads = calc_varsGradients_leastSquare_column(ht0, htNbrs, nVars, xyz0, xyzNbrs,vals0,valsNbrs,nHNbrs, nLevels)
out[hCell] = grads
print grads
data.close()
return out
def driver_arctic():
#plot epv on a polar cap
ncfname = '/arctic1/nick/cases/163842/testDuda/x1.163842.output.2006-07-15_00.00.00.nc'
#ncfname = '/arctic1/mduda/60km/x1.163842.output.2006-07-08_00.00.00.nc'
#ncfname = '/home/nickszap/research/mpas/output.2010-10-23_00:00:00.nc'
data = netCDF4.Dataset(ncfname,'r')
nCellsTotal = len(data.dimensions['nCells'])
nVerticesTotal = len(data.dimensions['nVertices']);
nLevels = len(data.dimensions['nVertLevels'])
nEdgesOnCell = data.variables['nEdgesOnCell'][:];
cellsOnCell = data.variables['cellsOnCell'][:]-1;
latThresh = 45.*np.pi/180.
#latThresh = 70.*np.pi/180.
latCell = data.variables['latCell'][:]
cells = conn.gatherArcticCells(latCell, nCellsTotal, latThresh)
nCells = len(cells)
#open the output vtk file and write header.
vtkfname = 'test.arctic.pv_approx.vtk'
fvtk = output_data.write_vtk_header_polydata(vtkfname, ncfname)
#write nodes and cells
output_data.write_vtk_polyHorizConn_domain(data, fvtk, cells, nEdgesOnCell,nVerticesTotal)
#cell values and connectivity for this domain
haloCells = conn.get_arcticHalo(cells, latCell, latThresh, cellsOnCell, nEdgesOnCell)
g2lCell = conn.make_global2localMap(cells, haloCells, nCellsTotal)
c2c = conn.make_localDomainNbrs(nCells, cellsOnCell[cells,:], nEdgesOnCell[cells], g2lCell)
neededCells = cells.tolist(); neededCells.extend(haloCells) #has to be domain then halo (as in g2l map)
#I'm having memory errors.
#gc.collect()
#load data for domain and halo -----------------------------
timeInd = 0
print "Loading data for domain {0} with {1} cells\n".format('arctic', len(neededCells))
#print neededCells
state = loadFields(data, timeInd, neededCells, nLevels)
#compute derived variables -------------------------------
#theta on dynamic tropopause
pv = np.empty((nCells,nLevels), dtype=float)
#make_localDomainNbrs(nCells, cellsOnCell_local, nEdgesOnCell_local, g2lMap)
for hCell in xrange(nCells):
hNbrs = c2c[hCell,0:nEdgesOnCell[cells[hCell]]]
pvColumn = driverErtel(state, hCell, hNbrs, nLevels)
#pvColumn = driverErtel_column(state, hCell, hNbrs, nLevels)
for l in range(nLevels):
pv[hCell,l] = pvColumn[l]
#
pvuVal = 2.; #pv = np.abs(pv) #don't need questionable hack for southern hemisphere
thetaVal = np.empty(nCells)
for hCell in xrange(nCells):
(l,dl) = output_data.calcIndexOfValue(pvuVal,pv[hCell,:], nLevels)
thetaVal[hCell] = output_data.calcValueOfIndex(l,dl,state.theta[hCell,:])
#write some cell data ----------------
fvtk.write('\nCELL_DATA '+str(nCells)+'\n')
output_data.write_levelData_float('theta_2pvu', fvtk, thetaVal, nCells)
fvtk.close()
data.close()
def driver_domains(nSeeds):
#
ncfname = '/arctic1/mduda/60km/x1.163842.output.2006-07-09_12.00.00.nc'
#ncfname = '/home/nickszap/research/mpas/output.2010-10-23_00:00:00.nc'
data = netCDF4.Dataset(ncfname,'r')
nCellsTotal = len(data.dimensions['nCells'])
nVerticesTotal = len(data.dimensions['nVertices']);
nLevels = len(data.dimensions['nVertLevels'])
nEdgesOnCell = data.variables['nEdgesOnCell'][:];
cellsOnCell = data.variables['cellsOnCell'][:]-1;
seed0 = 0
#seed0 = np.argmax(data.variables['meshDensity'][:]) #seems like a decent heuristic
cell2Site,seeds = conn.partition_max(seed0, cellsOnCell, nEdgesOnCell,nCellsTotal, nSeeds)
for domainInd in xrange(nSeeds):
#output domain mesh ------------------------
cells = np.array(xrange(nCellsTotal))[cell2Site==seeds[domainInd]]
nCells = len(cells)
#open the output vtk file and write header.
vtkfname = 'test'+str(domainInd)+'.vtk'
fvtk = output_data.write_vtk_header_polydata(vtkfname, ncfname)
#write nodes and cells
output_data.write_vtk_polyHorizConn_domain(data, fvtk, cells, nEdgesOnCell,nVerticesTotal)
#cell values and connectivity for this domain
haloCells = conn.getHalo(seeds[domainInd], cell2Site, cellsOnCell, nEdgesOnCell, nCellsTotal)
g2lCell = conn.make_global2localMap(cells, haloCells, nCellsTotal)
c2c = conn.make_localDomainNbrs(nCells, cellsOnCell[cells,:], nEdgesOnCell[cells], g2lCell)
neededCells = cells.tolist(); neededCells.extend(haloCells) #has to be domain then halo (as in g2l map)
#I'm having memory errors.
#gc.collect()
#load data for domain and halo -----------------------------
timeInd = 0
print "Loading data for domain {0} with {1} cells\n".format(domainInd, len(neededCells))
#print neededCells
state = loadFields(data, timeInd, neededCells, nLevels)
#compute derived variables -------------------------------
#theta on dynamic tropopause
pv = np.empty((nCells,nLevels), dtype=float)
#make_localDomainNbrs(nCells, cellsOnCell_local, nEdgesOnCell_local, g2lMap)
for hCell in xrange(nCells):
hNbrs = c2c[hCell,0:nEdgesOnCell[cells[hCell]]]
pvColumn = driverErtel(state, hCell, hNbrs, nLevels)
for l in range(nLevels):
pv[hCell,l] = pvColumn[l]
#
pvuVal = 2.; pv = np.abs(pv) #questionable hack for southern hemisphere
thetaVal = np.empty(nCells)
for hCell in range(nCells):
(l,dl) = output_data.calcIndexOfValue(pvuVal,pv[hCell,:], nLevels)
thetaVal[hCell] = output_data.calcValueOfIndex(l,dl,state.theta[hCell,:])
#write some cell data ----------------
fvtk.write('\nCELL_DATA '+str(nCells)+'\n')
output_data.write_levelData_float('theta_2pvu', fvtk, thetaVal, nCells)
fvtk.close()
data.close()