DAMASK_EICMD/processing/legacy/DADF5toDREAM3D.py

#!/usr/bin/env python3

import argparse
import os

import h5py
import numpy as np

import damask

class AttributeManagerNullterm(h5py.AttributeManager):
  """
  Attribute management for DREAM.3D hdf5 files.

  String attribute values are stored as fixed-length string with NULLTERM

  References
  ----------
    https://stackoverflow.com/questions/38267076
    https://stackoverflow.com/questions/52750232

  """

  def create(self, name, data, shape=None, dtype=None):
    if isinstance(data,str):
      tid = h5py.h5t.C_S1.copy()
      tid.set_size(len(data + ' '))
      super().create(name=name,data=data+' ',dtype = h5py.Datatype(tid))
    else:
      super().create(name=name,data=data,shape=shape,dtype=dtype)


h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'


# --------------------------------------------------------------------
# Crystal structure specifications
# --------------------------------------------------------------------
Crystal_structures = {'fcc': 1,
                      'bcc': 1,
                      'hcp': 0,
                      'bct': 7,
                      'ort': 6} #TODO: is bct Tetragonal low/Tetragonal high?
Phase_types = {'Primary': 0} #further additions to these can be done by looking at 'Create Ensemble Info' filter


# --------------------------------------------------------------------
#                                MAIN
# --------------------------------------------------------------------
parser = argparse.ArgumentParser(description='Creating a file for DREAM3D from DAMASK data')
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('--inc',nargs='+',
                    help='Increment for which DREAM3D to be used, eg. 25',type=int)

options = parser.parse_args()

for filename in options.filenames:
    f = damask.Result(filename)
    N_digits = int(np.floor(np.log10(int(f.increments[-1][3:]))))+1

    f.pick('increments',options.inc)
    for inc in damask.util.show_progress(f.iterate('increments'),len(f.selection['increments'])):
        dirname  = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
        try:
            os.mkdir(dirname)
        except FileExistsError:
            pass

        o = h5py.File(dirname + '/' + os.path.splitext(filename)[0] \
          + '_inc_{}.dream3D'.format(inc[3:].zfill(N_digits)),'w')
        o.attrs['DADF5toDREAM3D'] = '1.0'
        o.attrs['FileVersion']    = '7.0'

        for g in ['DataContainerBundles','Pipeline']: # empty groups (needed)
            o.create_group(g)

        data_container_label = 'DataContainers/ImageDataContainer'
        cell_data_label      = data_container_label + '/CellData'

        # Phase information of DREAM.3D is constituent ID in DAMASK
        o[cell_data_label + '/Phases'] = f.get_constituent_ID().reshape(tuple(f.grid)+(1,))
        DAMASK_quaternion = f.read_dataset(f.get_dataset_location('orientation'))
        # Convert: DAMASK uses P = -1, DREAM.3D uses P = +1. Also change position of imagninary part
        DREAM_3D_quaternion = np.hstack((-DAMASK_quaternion['x'],-DAMASK_quaternion['y'],-DAMASK_quaternion['z'],
                                          DAMASK_quaternion['w'])).astype(np.float32)
        o[cell_data_label + '/Quats'] = DREAM_3D_quaternion.reshape(tuple(f.grid)+(4,))

        # Attributes to CellData group
        o[cell_data_label].attrs['AttributeMatrixType'] = np.array([3],np.uint32)
        o[cell_data_label].attrs['TupleDimensions']     = f.grid.astype(np.uint64)

        # Common Attributes for groups in CellData
        for group in ['/Phases','/Quats']:
            o[cell_data_label + group].attrs['DataArrayVersion']      = np.array([2],np.int32)
            o[cell_data_label + group].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*f.grid)

        o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64)
        o[cell_data_label + '/Phases'].attrs['ObjectType']          = 'DataArray<int32_t>'
        o[cell_data_label + '/Phases'].attrs['TupleDimensions']     = f.grid.astype(np.uint64)

        o[cell_data_label + '/Quats'].attrs['ComponentDimensions'] = np.array([4],np.uint64)
        o[cell_data_label + '/Quats'].attrs['ObjectType']          = 'DataArray<float>'
        o[cell_data_label + '/Quats'].attrs['TupleDimensions']     = f.grid.astype(np.uint64)

        # Create EnsembleAttributeMatrix
        ensemble_label = data_container_label + '/EnsembleAttributeMatrix'

        # Data CrystalStructures
        o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999,\
                                                       Crystal_structures[f.get_crystal_structure()]])).reshape(2,1)
        o[ensemble_label + '/PhaseTypes']        = np.uint32(np.array([999,Phase_types['Primary']])).reshape(2,1)    # ToDo

        # Attributes Ensemble Matrix
        o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32)
        o[ensemble_label].attrs['TupleDimensions']     = np.array([2], np.uint64)

        # Attributes for data in Ensemble matrix
        for group in ['CrystalStructures','PhaseTypes']: # 'PhaseName' not required MD: But would be nice to take the phase name mapping
            o[ensemble_label+'/'+group].attrs['ComponentDimensions']   = np.array([1],np.uint64)
            o[ensemble_label+'/'+group].attrs['Tuple Axis Dimensions'] = 'x=2'
            o[ensemble_label+'/'+group].attrs['DataArrayVersion']      = np.array([2],np.int32)
            o[ensemble_label+'/'+group].attrs['ObjectType']            = 'DataArray<uint32_t>'
            o[ensemble_label+'/'+group].attrs['TupleDimensions']       = np.array([2],np.uint64)

        geom_label = data_container_label + '/_SIMPL_GEOMETRY'

        o[geom_label + '/DIMENSIONS'] = np.int64(f.grid)
        o[geom_label + '/ORIGIN']     = np.float32(np.zeros(3))
        o[geom_label + '/SPACING']    = np.float32(f.size)

        o[geom_label].attrs['GeometryName']     = 'ImageGeometry'
        o[geom_label].attrs['GeometryTypeName'] = 'ImageGeometry'
        o[geom_label].attrs['GeometryType']          = np.array([0],np.uint32)
        o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32)
        o[geom_label].attrs['UnitDimensionality']    = np.array([3],np.uint32)