Merge branch 'DREAM3D-merge' into development
This commit is contained in:
Martin Diehl
commit
14bbdb65c0
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#!/usr/bin/env python3
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import argparse
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import os
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import h5py
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import numpy as np
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import damask
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class AttributeManagerNullterm(h5py.AttributeManager):
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"""
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Attribute management for DREAM.3D hdf5 files.
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String attribute values are stored as fixed-length string with NULLTERM
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References
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----------
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https://stackoverflow.com/questions/38267076
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https://stackoverflow.com/questions/52750232
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"""
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def create(self, name, data, shape=None, dtype=None):
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if isinstance(data,str):
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tid = h5py.h5t.C_S1.copy()
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tid.set_size(len(data + ' '))
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super().create(name=name,data=data+' ',dtype = h5py.Datatype(tid))
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else:
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super().create(name=name,data=data,shape=shape,dtype=dtype)
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h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'
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# --------------------------------------------------------------------
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# Crystal structure specifications
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# --------------------------------------------------------------------
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Crystal_structures = {'fcc': 1,
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'bcc': 1,
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'hcp': 0,
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'bct': 7,
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'ort': 6} #TODO: is bct Tetragonal low/Tetragonal high?
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Phase_types = {'Primary': 0} #further additions to these can be done by looking at 'Create Ensemble Info' filter
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = argparse.ArgumentParser(description='Creating a file for DREAM3D from DAMASK data')
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parser.add_argument('filenames',nargs='+',help='HDF5 based output file')
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parser.add_argument('--inc',nargs='+',help='Increment for which DREAM3D to be used, eg. 00025',type=int)
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parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string',
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help='name of subdirectory to hold output')
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options = parser.parse_args()
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# --------------------------------------------------------------------
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# loop over input files
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for filename in options.filenames:
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f = damask.DADF5(filename) #DAMASK output file
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count = 0
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for increment in f.increments:
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if int(increment[3:]) not in options.inc:
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count = count + 1
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continue
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#-------output file creation-------------------------------------
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dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
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print(dirname)
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try:
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os.mkdir(dirname)
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except FileExistsError:
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pass
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o = h5py.File(dirname + '/' + os.path.splitext(filename)[0] + '_{}.dream3D'.format(increment),'w')
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#-----------------------------------------------------------------
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o.attrs['DADF5toDREAM3D'] = '1.0'
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o.attrs['FileVersion'] = '7.0'
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#-----------------------------------------------------------------
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for g in ['DataContainerBundles','Pipeline']: # empty groups (needed)
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o.create_group(g)
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data_container_label = 'DataContainers/ImageDataContainer'
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cell_data_label = data_container_label + '/CellData'
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# Phase information of DREAM.3D is constituent ID in DAMASK
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o[cell_data_label + '/Phases'] = f.get_constituent_ID().reshape(tuple(f.grid)+(1,))
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# Data quaternions
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DAMASK_quaternion = f.read_dataset(f.get_dataset_location('orientation'),0)
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DREAM_3D_quaternion = np.empty((np.prod(f.grid),4),dtype=np.float32)
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# Convert: DAMASK uses P = -1, DREAM.3D uses P = +1. Also change position of imagninary part
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DREAM_3D_quaternion = np.hstack((-DAMASK_quaternion['x'],-DAMASK_quaternion['y'],-DAMASK_quaternion['z'],
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DAMASK_quaternion['w']))
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o[cell_data_label + '/Quats'] = DREAM_3D_quaternion.reshape(tuple(f.grid)+(4,))
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# Attributes to CellData group
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o[cell_data_label].attrs['AttributeMatrixType'] = np.array([3],np.uint32)
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o[cell_data_label].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
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# Common Attributes for groups in CellData
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for group in ['/Phases','/Quats']:
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o[cell_data_label + group].attrs['DataArrayVersion'] = np.array([2],np.int32)
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o[cell_data_label + group].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*f.grid)
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# phase attributes
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o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64)
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o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray<int32_t>'
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# Quats attributes
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o[cell_data_label + '/Quats'].attrs['ComponentDimensions'] = np.array([4],np.uint64)
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o[cell_data_label + '/Quats'].attrs['ObjectType'] = 'DataArray<float>'
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# Create EnsembleAttributeMatrix
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ensemble_label = data_container_label + '/EnsembleAttributeMatrix'
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# Data CrystalStructures
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o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999,\
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Crystal_structures[f.get_crystal_structure()]])).reshape((2,1))
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o[ensemble_label + '/PhaseTypes'] = np.uint32(np.array([999,Phase_types['Primary']])).reshape((2,1)) # ToDo
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# Attributes Ensemble Matrix
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o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32)
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o[ensemble_label].attrs['TupleDimensions'] = np.array([2], np.uint64)
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# Attributes for data in Ensemble matrix
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for group in ['CrystalStructures','PhaseTypes']: # 'PhaseName' not required MD: But would be nice to take the phase name mapping
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o[ensemble_label+'/'+group].attrs['ComponentDimensions'] = np.array([1],np.uint64)
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o[ensemble_label+'/'+group].attrs['Tuple Axis Dimensions'] = 'x=2'
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o[ensemble_label+'/'+group].attrs['DataArrayVersion'] = np.array([2],np.int32)
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o[ensemble_label+'/'+group].attrs['ObjectType'] = 'DataArray<uint32_t>'
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o[ensemble_label+'/'+group].attrs['TupleDimensions'] = np.array([2],np.uint64)
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# Create geometry info
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geom_label = data_container_label + '/_SIMPL_GEOMETRY'
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o[geom_label + '/DIMENSIONS'] = np.int64(f.grid)
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o[geom_label + '/ORIGIN'] = np.float32(np.zeros(3))
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o[geom_label + '/SPACING'] = np.float32(f.size)
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o[geom_label].attrs['GeometryName'] = 'ImageGeometry'
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o[geom_label].attrs['GeometryTypeName'] = 'ImageGeometry'
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o[geom_label].attrs['GeometryType'] = np.array([0],np.uint32)
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o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32)
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o[geom_label].attrs['UnitDimensionality'] = np.array([3],np.uint32)
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@ -303,6 +303,19 @@ class DADF5():
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return path
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def get_constituent_ID(self,c=0):
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"""Pointwise constituent ID."""
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with h5py.File(self.filename,'r') as f:
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names = f['/mapping/cellResults/constituent']['Name'][:,c].astype('str')
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return np.array([int(n.split('_')[0]) for n in names.tolist()],dtype=np.int32)
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def get_crystal_structure(self): # ToDo: extension to multi constituents/phase
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"""Info about the crystal structure."""
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with h5py.File(self.filename,'r') as f:
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return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str') # np.bytes_ to string
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def read_dataset(self,path,c):
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"""
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Dataset for all points/cells.
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@ -312,7 +325,7 @@ class DADF5():
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with h5py.File(self.filename,'r') as f:
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shape = (self.Nmaterialpoints,) + np.shape(f[path[0]])[1:]
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if len(shape) == 1: shape = shape +(1,)
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dataset = np.full(shape,np.nan)
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dataset = np.full(shape,np.nan,dtype=np.dtype(f[path[0]]))
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for pa in path:
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label = pa.split('/')[2]
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