From 17e7b32b319c6d91fc14248d4990b6fb65fff657 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 17 Mar 2020 01:49:47 +0100 Subject: [PATCH] update to changes in Result class --- processing/post/DADF5_postResults.py | 59 +++++----- processing/post/DADF5toDREAM3D.py | 160 +++++++++++++-------------- 2 files changed, 104 insertions(+), 115 deletions(-) diff --git a/processing/post/DADF5_postResults.py b/processing/post/DADF5_postResults.py index 4fa237df8..22b91b57e 100755 --- a/processing/post/DADF5_postResults.py +++ b/processing/post/DADF5_postResults.py @@ -36,39 +36,34 @@ if options.con is None: options.con=[] # --- loop over input files ------------------------------------------------------------------------ for filename in options.filenames: - results = damask.DADF5(filename) - - if not results.structured: continue - if results.version_major == 0 and results.version_minor >= 5: - coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin) - else: - coords = damask.grid_filters.cell_coord0(results.grid,results.size) - - N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1 - N_digits = 5 # hack to keep test intact - for i,inc in enumerate(results.iter_visible('increments')): - print('Output step {}/{}'.format(i+1,len(results.increments))) + results = damask.Result(filename) - table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)}) - table.add('pos',coords.reshape((-1,3))) + if not results.structured: continue + coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin) - results.pick('materialpoints',False) - results.pick('constituents', True) - for label in options.con: - x = results.get_dataset_location(label) - if len(x) != 0: - table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1))) + N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1 + N_digits = 5 # hack to keep test intact + for inc in damask.util.show_progress(results.iter_visible('increments'),len(results.increments)): + table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)}) + table.add('pos',coords.reshape((-1,3))) - results.pick('constituents', False) - results.pick('materialpoints',True) - for label in options.mat: - x = results.get_dataset_location(label) - if len(x) != 0: - table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1))) + results.pick('materialpoints',False) + results.pick('constituents', True) + for label in options.con: + x = results.get_dataset_location(label) + if len(x) != 0: + table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1))) - dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir)) - if not os.path.isdir(dirname): - os.mkdir(dirname,0o755) - file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0], - inc[3:].zfill(N_digits)) - table.to_ASCII(os.path.join(dirname,file_out)) + results.pick('constituents', False) + results.pick('materialpoints',True) + for label in options.mat: + x = results.get_dataset_location(label) + if len(x) != 0: + table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1))) + + dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir)) + if not os.path.isdir(dirname): + os.mkdir(dirname,0o755) + file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0], + inc[3:].zfill(N_digits)) + table.to_ASCII(os.path.join(dirname,file_out)) diff --git a/processing/post/DADF5toDREAM3D.py b/processing/post/DADF5toDREAM3D.py index 7ab04b934..15f7c492c 100755 --- a/processing/post/DADF5toDREAM3D.py +++ b/processing/post/DADF5toDREAM3D.py @@ -55,94 +55,88 @@ parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string' options = parser.parse_args() -# -------------------------------------------------------------------- -# loop over input files for filename in options.filenames: - f = damask.DADF5(filename) #DAMASK output file - for increment in options.inc: - f.set_by_increment(increment,increment) - if len(f.visible['increments']) == 0: - continue + f = damask.Result(filename) + f.pick('increments',options.inc) + for increment in damask.util.show_progress(f.iter_selection('increments'),len(f.selection['increments'])): + #-------output file creation------------------------------------- + dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir)) + try: + os.mkdir(dirname) + except FileExistsError: + pass - #-------output file creation------------------------------------- - 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] + '_{}.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) - 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' + 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')) - # 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,)) + # 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')) + # 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) - # 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' - o[cell_data_label + '/Phases'].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' + o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = f.grid.astype(np.uint64) + + # Quats attributes + 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) + - # Quats attributes - 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' + # 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) - # 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) + 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)