From b208fa656566d9f480bada3b21c692b6b224cf6c Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 12 Oct 2019 08:00:12 +0200 Subject: [PATCH] takeover from Vitesh's work with small adoptions to current DADF5 --- processing/post/DADF5toDREAM3D.py | 149 ++++++++++++++++++++++++++++++ python/damask/dadf5.py | 13 +++ 2 files changed, 162 insertions(+) create mode 100755 processing/post/DADF5toDREAM3D.py diff --git a/processing/post/DADF5toDREAM3D.py b/processing/post/DADF5toDREAM3D.py new file mode 100755 index 000000000..885545297 --- /dev/null +++ b/processing/post/DADF5toDREAM3D.py @@ -0,0 +1,149 @@ +#!/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='HDF5 based output file') +parser.add_argument('--inc',nargs='+',help='Increment for which DREAM3D to be used, eg. 00025',type=int) +parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string', + help='name of subdirectory to hold output') + +options = parser.parse_args() + +# -------------------------------------------------------------------- +# loop over input files +for filename in options.filenames: + f = damask.DADF5(filename) #DAMASK output file + count = 0 + for increment in f.increments: + if int(increment[3:]) not in options.inc: + count = count + 1 + continue + + #-------output file creation------------------------------------- + dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir)) + print(dirname) + try: + os.mkdir(dirname) + except FileExistsError: + pass + + o = h5py.File(dirname + '/' + os.path.splitext(filename)[0] + '_{}.dream3D'.format(increment),'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,)) + # Data quaternions + DAMASK_quaternion = f.read_dataset(f.get_dataset_location('orientation'),0) + DREAM_3D_quaternion = np.empty((np.prod(f.grid),4),dtype=np.float32) + # 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'])) + 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) + + # phase attributes + o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64) + o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray' + + # Quats attributes + o[cell_data_label + '/Quats'].attrs['ComponentDimensions'] = np.array([4],np.uint64) + o[cell_data_label + '/Quats'].attrs['ObjectType'] = 'DataArray' + + # 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' + o[ensemble_label+'/'+group].attrs['TupleDimensions'] = np.array([2],np.uint64) + + + # Create geometry info + 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) diff --git a/python/damask/dadf5.py b/python/damask/dadf5.py index dae900755..72855051c 100644 --- a/python/damask/dadf5.py +++ b/python/damask/dadf5.py @@ -303,6 +303,19 @@ class DADF5(): return path + def get_constituent_ID(self,c=0): + """Pointwise constituent ID.""" + with h5py.File(self.filename,'r') as f: + names = f['/mapping/cellResults/constituent']['Name'][:,c].astype('str') + return np.array([int(n.split('_')[0]) for n in names.tolist()],dtype=np.int32) + + + def get_crystal_structure(self): # ToDo: extension to multi constituents/phase + """Info about the crystal structure.""" + with h5py.File(self.filename,'r') as f: + return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str') # np.bytes_ to string + + def read_dataset(self,path,c): """ Dataset for all points/cells.