def example_prism_column():
#write out a column of the mesh as prisms.
#the column is a triangle radially out identified by primal (eg hexagonal) vertex
import vars_column
ncfname = '/home/nickszap/research/mpas/output.2010-10-23_00:00:00.nc' #input file
vtkfname = 'prismTest.vtk' #output file
data = open_netcdf_data(ncfname)
nCells = len(data.dimensions['nCells']); nLevels = len(data.dimensions['nVertLevels'])
nVertices = len(data.dimensions['nVertices'])
f = write_vtk_header_unstructured(vtkfname, ncfname)
#hack for this case ---------------
nVertices = 1; vertexId = 10
nCells = 3; cells = data.variables['cellsOnVertex'][vertexId]-1 #0-indexing
xyzc = vars_column.calc_cellCenterColumn(data,cells,nLevels) #index as xyzc[celli,level,dirs]
#end hack ----------------
numPts = nCells*nLevels
s = 'POINTS '+str(numPts)+' float\n'
f.write(s)
for c in xrange(nCells):
for l in xrange(nLevels):
s = str(float(xyzc[c,l,0]))+' '+str(float(xyzc[c,l,1]))+' '+str(float(xyzc[c,l,2]))+'\n'
f.write(s)
#
nPrisms = nVertices*(nLevels-1) #1 triangle per vertex with prisms centered over interfaces
s = '\nCELLS '+str(nPrisms)+' '+str(nPrisms*(6+1))+'\n' #6 pts per prism +1 int for #conn, ie '6 vertex0 v1...v5' for prism
f.write(s)
for v in xrange(nVertices):
for l in xrange(nLevels-1):
s = '6'
for i in xrange(3): #visit 3 cells on vertex at base. unchecked winding
c = cells[i] #would be cells[v,i] for multiple vertices
ind = cellToTriangleInd(i,l, nLevels) #would be cellToTriangleInd(c,l, nLevels)
s+= ' '+str(ind)
for i in xrange(3): #visit 3 cells on vertex at top. unchecked winding
c = cells[i] #would be cells[v,i] for multiple vertices
ind = cellToTriangleInd(i,l+1, nLevels) #would be cellToTriangleInd(c,l, nLevels)
s+= ' '+str(ind)
s+='\n'
f.write(s)
#
s = '\nCELL_TYPES '+str(nPrisms)+'\n'
for i in range(nPrisms):
s+= '13\n'
f.write(s)
data.close()
f.close()
def example_plot3d_epv_arctic():
import vars_column
import conn
#ncfname = '/home/nickszap/research/mpas/output.2010-10-23_00:00:00.nc' #input file
#ncfname = '/arctic1/nick/cases/cfsr/output/x4.cfsr.output.2006-08-01_00.00.00.nc'
#ncfname = '/arctic1/nick/cases/v1.0/x4/longer/x4.kf.output.2006-08-15_00.00.00.nc'
ncfname = '/arctic1/nick/cases/650k/x1.t.output.2006-08-15_00.00.00.nc'
#vtkfname = '/data01/epv-prismTestArctic.vtk' #output file
data = open_netcdf_data(ncfname)
nCellsTotal = len(data.dimensions['nCells']); nLevels = len(data.dimensions['nVertLevels'])
nVerticesTotal = len(data.dimensions['nVertices']); nTimes = len(data.dimensions['Time'])
nEdgesOnCell = data.variables['nEdgesOnCell'][:]
#hack for this case ---------------
latCell = data.variables['latCell'][:]
#latThresh = 85.*np.pi/180.
latThresh = 75.*np.pi/180.
cells = conn.gatherArcticCells(latCell, nCellsTotal, latThresh)
#should get halo as well
#conn.get_arcticHalo(cells, latCell, latThresh, cellsOnCell, nEdgesOnCell)
verticesOnCell = data.variables['verticesOnCell'][cells,:]-1
vertices = conn.gatherVerticesInRegion(len(cells), verticesOnCell, nEdgesOnCell[cells], nVerticesTotal, 3)
nVertices = len(vertices);
nCells = len(cells);
print "Number of cells in region: ", nCells
xyzc = vars_column.calc_cellCenterColumn(data,cells,nLevels) #index as xyzc[celli,level,dirs]
#end hack ----------------
for timeInd in xrange(nTimes):
vtkfname = '/data01/epv-prismTestArctic_650k-'+str(timeInd)+'.vtk' #output file
f = write_vtk_header_unstructured(vtkfname, ncfname)
#Here we'll manipulate xyz for more clear viz
#ince we're in shallow water land, the vertical is quite scrunched wrt horizontal.
#We could do this anywhere over earth by taking a "central" cell in the region's
#tangent plane as the reference.
#We'll stretch it a bit to help with viz, since over arctic magnify z
zFactor = 100.
numPts = nCells*nLevels
s = 'POINTS '+str(numPts)+' float\n'
f.write(s)
zgrid = data.variables['zgrid'][cells,:]
for c in xrange(nCells):
s = ''
for l in xrange(nLevels):
#s += str(float(xyzc[c,l,0]))+' '+str(float(xyzc[c,l,1]))+' '+str(float(xyzc[c,l,2]))+'\n'
s += str(float(xyzc[c,l,0]))+' '+str(float(xyzc[c,l,1]))+' '+str(float(zFactor*zgrid[c,l]))+'\n'
f.write(s)
#
#for prisms need global cell index to local map.
#only need map for cells in region so can possibly save a bit on memory
g2lCell = np.zeros(np.max(cells)+1,dtype=int) #global to local map for cells on horizontal
for i,c in enumerate(cells):
g2lCell[c]=i
cellsOnVertex = data.variables['cellsOnVertex'][vertices,:]-1
nPrisms = nVertices*(nLevels-1) #1 triangle per vertex with prisms centered over interfaces
s = '\nCELLS '+str(nPrisms)+' '+str(nPrisms*(6+1))+'\n' #6 pts per prism +1 int for #conn, ie '6 vertex0 v1...v5' for prism
f.write(s)
for v in xrange(nVertices):
for l in xrange(nLevels-1):
s = '6'
for i in xrange(3): #visit 3 cells on vertex at base. unchecked winding
c = cellsOnVertex[v,i] #would be cells[v,i] for multiple vertices
ind = g2lCell[c]
ind = cellToTriangleInd(ind,l, nLevels) #would be cellToTriangleInd(c,l, nLevels)
s+= ' '+str(ind)
for i in xrange(3): #what happens if 4 equidistant cell centers. still 3???
c = cellsOnVertex[v,i] #would be cells[v,i] for multiple vertices
ind = g2lCell[c]
ind = cellToTriangleInd(ind,l+1, nLevels) #would be cellToTriangleInd(c,l, nLevels)
s+= ' '+str(ind)
s+='\n'
f.write(s)
#
s = '\nCELL_TYPES '+str(nPrisms)+'\n'
for i in xrange(nPrisms):
s+= '13\n'
f.write(s)
f.write('\nPOINT_DATA '+str(numPts)+'\n')
s = '\nSCALARS epv float 1\nLOOKUP_TABLE default\n'
f.write(s)
#timeInd=0
ertel_pv = data.variables['ertel_pv'][timeInd,cells,:]
for c in xrange(nCells):
s = ''
for l in xrange(nLevels):
s += str(float(ertel_pv[c,l]))+'\n'
f.write(s)
f.close()
data.close()
def example_prismsRegion():
import vars_column
import conn
ncfname = '/home/nickszap/research/mpas/output.2010-10-23_00:00:00.nc' #input file
vtkfname = 'prismTestRegion.vtk' #output file
data = open_netcdf_data(ncfname)
nCellsTotal = len(data.dimensions['nCells']); nLevels = len(data.dimensions['nVertLevels'])
nVerticesTotal = len(data.dimensions['nVertices'])
f = write_vtk_header_unstructured(vtkfname, ncfname)
#hack for this case ---------------
c0 = 10 #do cell and nbrs
nEdgesOnCell = data.variables['nEdgesOnCell'][:]
nNbrs = nEdgesOnCell[c0]
nbrs = data.variables['cellsOnCell'][c0,0:nNbrs]-1
cells = [c0]+nbrs.tolist()
verticesOnCell = data.variables['verticesOnCell'][cells,:]-1
vertices = conn.gatherVerticesInRegion(len(cells), verticesOnCell, nEdgesOnCell[cells], nVerticesTotal, 3)
nVertices = len(vertices);
nCells = len(cells);
xyzc = vars_column.calc_cellCenterColumn(data,cells,nLevels) #index as xyzc[celli,level,dirs]
#end hack ----------------
numPts = nCells*nLevels
s = 'POINTS '+str(numPts)+' float\n'
f.write(s)
for c in xrange(nCells):
for l in xrange(nLevels):
s = str(float(xyzc[c,l,0]))+' '+str(float(xyzc[c,l,1]))+' '+str(float(xyzc[c,l,2]))+'\n'
f.write(s)
#
#for prisms need global cell index to local map.
#only need map for cells in region so can possibly save a bit on memory
g2lCell = np.zeros(np.max(cells),dtype=int) #global to local map for cells on horizontal
for i,c in enumerate(cells):
g2lCell[c]=i
cellsOnVertex = data.variables['cellsOnVertex'][vertices,:]-1
nPrisms = nVertices*(nLevels-1) #1 triangle per vertex with prisms centered over interfaces
s = '\nCELLS '+str(nPrisms)+' '+str(nPrisms*(6+1))+'\n' #6 pts per prism +1 int for #conn, ie '6 vertex0 v1...v5' for prism
f.write(s)
for v in xrange(nVertices):
for l in xrange(nLevels-1):
s = '6'
for i in xrange(3): #visit 3 cells on vertex at base. unchecked winding
c = cellsOnVertex[v,i] #would be cells[v,i] for multiple vertices
ind = g2lCell[c]
ind = cellToTriangleInd(ind,l, nLevels) #would be cellToTriangleInd(c,l, nLevels)
s+= ' '+str(ind)
for i in xrange(3): #what happens if 4 equidistant cell centers. still 3???
c = cellsOnVertex[v,i] #would be cells[v,i] for multiple vertices
ind = g2lCell[c]
ind = cellToTriangleInd(ind,l+1, nLevels) #would be cellToTriangleInd(c,l, nLevels)
s+= ' '+str(ind)
s+='\n'
f.write(s)
#
s = '\nCELL_TYPES '+str(nPrisms)+'\n'
for i in range(nPrisms):
s+= '13\n'
f.write(s)
data.close()
f.close()