From 556ac6bfed15f1527081bd71c6a738fe2a186aea Mon Sep 17 00:00:00 2001 From: Vitesh Shah Date: Fri, 13 Oct 2023 11:27:35 +0200 Subject: [PATCH] legacy code not needed anymore --- processing/DADF5toDREAM3D.py | 185 ----------------------------------- 1 file changed, 185 deletions(-) delete mode 100644 processing/DADF5toDREAM3D.py diff --git a/processing/DADF5toDREAM3D.py b/processing/DADF5toDREAM3D.py deleted file mode 100644 index e41bee9d3..000000000 --- a/processing/DADF5toDREAM3D.py +++ /dev/null @@ -1,185 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import os -from pathlib import Path - -import h5py -import numpy as np - -import damask -from damask import Rotation -from damask import Orientation - -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 - -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,job_file,geom_file,load_file): - """ - Defining the common quantities for all the functions in this class. - - Parameters - ---------- - job_file: str or pathlib.Path - Full path of the DAMASK results file. - geom_file : str - name of the geom file. - load_file : - name of the load file. - """ - self.job_file = Path(job_file).expanduser().absolute() - self.geom_file = geom_file - self.load_file = load_file - - 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.job_file.parents[0]) - #-------------------------------------------------------------------------- - #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/SyntheticVolumeDataContainer' - cell_data_label = data_container_label + '/CellData' - - # 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'] = np.array(cells,np.uint64) - - # Common Attributes for groups in CellData - 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'] = 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 + '/CellEnsembleData' - - # Data CrystalStructures - #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([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'] = 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(np.array(cells)) - o[geom_label + '/ORIGIN'] = np.float32(np.zeros(3)) - 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)