Exemple #1
0
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()
Exemple #2
0
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()
Exemple #3
0
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()