diff --git a/processing/DADF5toDREAM3D.py b/processing/DADF5toDREAM3D.py index 95b62c7ce..d1d87006c 100644 --- a/processing/DADF5toDREAM3D.py +++ b/processing/DADF5toDREAM3D.py @@ -7,6 +7,8 @@ import h5py import numpy as np import damask +from damask import Rotation +from damask import Orientation class AttributeManagerNullterm(h5py.AttributeManager): """ @@ -43,96 +45,143 @@ Crystal_structures = {'fcc': 1, '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 +class DAMASKtoDREAM3D(): + """ + This class can convert the DAMASK data to DREAM3D compatible data. + There can be various different types of ways DAMASK data can be represented. + Therefore, there are multiple functions available for different purposes. + """ + def __init__(self,simulation_folder,job_file,geom_file,load_file): + """ + Defining the common quantities for all the functions in this class. + + Parameters + ---------- + simulation_folder: str + Path of the simulation folder. + job_file: str + Name of the job file (DADF5 file). + geom_file : str + name of the geom file. + load_file : + name of the load file. + """ + self.simulation_folder = simulation_folder + self.job_file = job_file + self.geom_file = geom_file + self.load_file = load_file -# -------------------------------------------------------------------- -# 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') + def DAMASKtoDREAM3D(self,dx,inc): + """ + Creates a dream3D file from DAMASK output. + Without any regridding. + Considers the original grid from DAMASK. + + Parameters: + ----------- + dx : float + The grid spacing. + inc: int + increment of interest for DREAM3D processing. + """ + os.chdir(self.simulation_folder) + #-------------------------------------------------------------------------- + #Build array of euler angles for each cell + #-------------------------------------------------------------------------- + d = damask.Result(self.job_file) + inc_data = d.view(increments=inc) # selecting only relevant data to reduce overload + + f = h5py.File(self.job_file,'r') + cells = f['geometry'].attrs['cells'] + size = f['geometry'].attrs['size'] + dx = size/cells + + O_dict = inc_data.get('O') + + cell_orientation_array = np.zeros((np.prod(cells),3)) + + phase_ID_array = np.zeros((np.prod(cells)),dtype=np.int32) #need to reshape it later + + for count,p in enumerate(d.phases): + phase_index = np.where(f['cell_to/phase']['label'] == f'{p}'.encode())[0] + if len(d.phases) > 1: + cell_orientation_array[phase_index,:] = Rotation(O_dict[p]).as_Euler_angles() + else: + cell_orientation_array[phase_index,:] = Rotation(O_dict).as_Euler_angles() + phase_ID_array[phase_index] = count + 1 + + #-------------------------------------------------------------------------- + job_file_no_ext = os.path.splitext(self.job_file)[0] + o = h5py.File(f'{job_file_no_ext}_increment{inc}.dream3D','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' + o.create_group(g) + + data_container_label = 'DataContainers/SyntheticVolumeDataContainer' 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,)) - + + # Data phases + o[cell_data_label + '/Phases'] = np.reshape(phase_ID_array, \ + tuple(np.flip(cells))+(1,)) + + # Data eulers + orientation_data = cell_orientation_array.astype(np.float32) + o[cell_data_label + '/Eulers'] = orientation_data.reshape(tuple(np.flip(cells))+(3,)) + # 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) - + o[cell_data_label].attrs['TupleDimensions'] = np.array(cells,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) - + for group in ['/Phases','/Eulers']: + 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(*np.array(cells)) + + # phase attributes o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64) o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray' - 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' - o[cell_data_label + '/Quats'].attrs['TupleDimensions'] = f.grid.astype(np.uint64) - + o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = np.array(cells,np.uint64) + + # Eulers attributes + o[cell_data_label + '/Eulers'].attrs['ComponentDimensions'] = np.array([3],np.uint64) + o[cell_data_label + '/Eulers'].attrs['ObjectType'] = 'DataArray' + o[cell_data_label + '/Eulers'].attrs['TupleDimensions'] = np.array(cells,np.uint64) + # Create EnsembleAttributeMatrix - ensemble_label = data_container_label + '/EnsembleAttributeMatrix' - + ensemble_label = data_container_label + '/CellEnsembleData' + # 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 - + #o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999,1])) + o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999] + [1]*len(d.phases))) + # assuming only cubic crystal structures + # Damask can give the crystal structure info but need to look into dream3d which crystal structure corresponds to which number + o[ensemble_label + '/PhaseTypes'] = np.uint32(np.array([999] + [Phase_types['Primary']]*len(d.phases))).reshape((len(d.phases)+1,1)) + # also assuming Primary phases + # there can be precipitates etc as well + # Attributes Ensemble Matrix o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32) - o[ensemble_label].attrs['TupleDimensions'] = np.array([2], np.uint64) - + o[ensemble_label].attrs['TupleDimensions'] = np.array([len(d.phases) + 1], 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) - + o[ensemble_label+'/'+group].attrs['ComponentDimensions'] = np.array([1],np.uint64) + o[ensemble_label+'/'+group].attrs['Tuple Axis Dimensions'] = f'x={len(d.phases)+1}' + 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([len(d.phases) + 1],np.uint64) + + # Create geometry info geom_label = data_container_label + '/_SIMPL_GEOMETRY' - - o[geom_label + '/DIMENSIONS'] = np.int64(f.grid) + + o[geom_label + '/DIMENSIONS'] = np.int64(np.array(cells)) o[geom_label + '/ORIGIN'] = np.float32(np.zeros(3)) - o[geom_label + '/SPACING'] = np.float32(f.size) - + o[geom_label + '/SPACING'] = np.float32(dx) + 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) + 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/processing/legacy/DADF5toDREAM3D.py b/processing/legacy/DADF5toDREAM3D.py deleted file mode 100755 index 95b62c7ce..000000000 --- a/processing/legacy/DADF5toDREAM3D.py +++ /dev/null @@ -1,138 +0,0 @@ -#!/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' - 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' - 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' - 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)