DAMASK_EICMD/processing/post/DADF5_vtk_cells.py

#!/usr/bin/env python3

import os
import argparse
import re

import h5py
import numpy as np
import vtk
from vtk.util import numpy_support

import damask

scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID   = ' '.join([scriptName,damask.version])

# --------------------------------------------------------------------
#                                MAIN
# --------------------------------------------------------------------
parser = argparse.ArgumentParser()

#ToDo:  We need to decide on a way of handling arguments of variable lentght
#https://stackoverflow.com/questions/15459997/passing-integer-lists-to-python

#parser.add_argument('--version', action='version', version='%(prog)s {}'.format(scriptID))
parser.add_argument('filenames', nargs='+',
                    help='DADF5 files')
parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string',
                    help='name of subdirectory relative to the location of the DADF5 file to hold output')
parser.add_argument('--mat', nargs='+',
                    help='labels for materialpoint',dest='mat')
parser.add_argument('--con', nargs='+',
                    help='labels for constituent',dest='con')

options = parser.parse_args()

if options.mat is None: options.mat=[]
if options.con is None: options.con=[]

# --- loop over input files ------------------------------------------------------------------------

for filename in options.filenames:
  results = damask.DADF5(filename)
  
  if results.structured:                                                                            # for grid solvers use rectilinear grid
    grid = vtk.vtkRectilinearGrid()
    coordArray = [vtk.vtkDoubleArray(),
                  vtk.vtkDoubleArray(),
                  vtk.vtkDoubleArray(),
                 ]

    grid.SetDimensions(*(results.grid+1))
    for dim in [0,1,2]:
      for c in np.linspace(0,results.size[dim],1+results.grid[dim]):
        coordArray[dim].InsertNextValue(c)

    grid.SetXCoordinates(coordArray[0])
    grid.SetYCoordinates(coordArray[1])
    grid.SetZCoordinates(coordArray[2])
  else:
    nodes = vtk.vtkPoints()
    with h5py.File(filename) as f:
      nodes.SetData(numpy_support.numpy_to_vtk(f['/geometry/x_n'][()],deep=True))
      grid = vtk.vtkUnstructuredGrid()
      grid.SetPoints(nodes)
      grid.Allocate(f['/geometry/T_c'].shape[0])
      for i in f['/geometry/T_c']:
        grid.InsertNextCell(vtk.VTK_HEXAHEDRON,8,i-1)

  N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
  for i,inc in enumerate(results.iter_visible('increments')):
    print('Output step {}/{}'.format(i+1,len(results.increments)))
    vtk_data = []
    
    results.set_visible('materialpoints',False)
    results.set_visible('constituents',  True)
    for label in options.con:
      for p in results.iter_visible('con_physics'):
        if p != 'generic':
          for c in results.iter_visible('constituents'):
            x = results.get_dataset_location(label)
            if len(x) == 0:
              continue
            array = results.read_dataset(x,0)
            shape = [array.shape[0],np.product(array.shape[1:])]
            vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
            vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
            grid.GetCellData().AddArray(vtk_data[-1])
        else:
          x = results.get_dataset_location(label)
          if len(x) == 0:
            continue
          ph_name = re.compile(r'(?<=(constituent\/))(.*?)(?=(generic))') #looking for phase name in dataset name
          array = results.read_dataset(x,0)
          shape = [array.shape[0],np.product(array.shape[1:])]
          vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
          dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1])           #removing phase name from generic dataset
          vtk_data[-1].SetName(dset_name)
          grid.GetCellData().AddArray(vtk_data[-1])
    
    results.set_visible('constituents',  False)
    results.set_visible('materialpoints',True)
    for label in options.mat:
      for p in results.iter_visible('mat_physics'):
        if p != 'generic':
          for m in results.iter_visible('materialpoints'):
            x = results.get_dataset_location(label)
            if len(x) == 0:
              continue
            array = results.read_dataset(x,0)
            shape = [array.shape[0],np.product(array.shape[1:])]
            vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
            vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
            grid.GetCellData().AddArray(vtk_data[-1])
        else:
          x = results.get_dataset_location(label)
          if len(x) == 0:
            continue
          array = results.read_dataset(x,0)
          shape = [array.shape[0],np.product(array.shape[1:])]
          vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
          vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
          grid.GetCellData().AddArray(vtk_data[-1])
          
    writer = vtk.vtkXMLRectilinearGridWriter() if results.structured else \
             vtk.vtkXMLUnstructuredGridWriter()

    results.set_visible('constituents',  False)
    results.set_visible('materialpoints',False)
    x = results.get_dataset_location('u_n')
    vtk_data.append(numpy_support.numpy_to_vtk(num_array=results.read_dataset(x,0),deep=True,array_type=vtk.VTK_DOUBLE))
    vtk_data[-1].SetName('u')
    grid.GetPointData().AddArray(vtk_data[-1])
    
    dirname  = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
    if not os.path.isdir(dirname):
      os.mkdir(dirname,0o755)
    file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.split(filename)[-1])[0],
                                    inc[3:].zfill(N_digits),
                                    writer.GetDefaultFileExtension())
    
    writer.SetCompressorTypeToZLib()
    writer.SetDataModeToBinary()
    writer.SetFileName(os.path.join(dirname,file_out))
    writer.SetInputData(grid)
    
    writer.Write()