update to changes in Result class
This commit is contained in:
Martin Diehl
parent
1e1fb35e14
commit
17e7b32b31
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@ -36,39 +36,34 @@ if options.con is None: options.con=[]
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# --- loop over input files ------------------------------------------------------------------------
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# --- loop over input files ------------------------------------------------------------------------
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for filename in options.filenames:
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for filename in options.filenames:
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results = damask.DADF5(filename)
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results = damask.Result(filename)
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if not results.structured: continue
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if not results.structured: continue
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if results.version_major == 0 and results.version_minor >= 5:
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coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin)
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coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin)
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else:
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coords = damask.grid_filters.cell_coord0(results.grid,results.size)
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N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
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N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
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N_digits = 5 # hack to keep test intact
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N_digits = 5 # hack to keep test intact
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for i,inc in enumerate(results.iter_visible('increments')):
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for inc in damask.util.show_progress(results.iter_visible('increments'),len(results.increments)):
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print('Output step {}/{}'.format(i+1,len(results.increments)))
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table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})
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table.add('pos',coords.reshape((-1,3)))
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table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})
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results.pick('materialpoints',False)
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table.add('pos',coords.reshape((-1,3)))
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results.pick('constituents', True)
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for label in options.con:
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x = results.get_dataset_location(label)
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if len(x) != 0:
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table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1)))
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results.pick('materialpoints',False)
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results.pick('constituents', False)
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results.pick('constituents', True)
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results.pick('materialpoints',True)
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for label in options.con:
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for label in options.mat:
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x = results.get_dataset_location(label)
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x = results.get_dataset_location(label)
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if len(x) != 0:
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if len(x) != 0:
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table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1)))
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table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1)))
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results.pick('constituents', False)
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dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
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results.pick('materialpoints',True)
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if not os.path.isdir(dirname):
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for label in options.mat:
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os.mkdir(dirname,0o755)
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x = results.get_dataset_location(label)
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file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0],
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if len(x) != 0:
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inc[3:].zfill(N_digits))
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table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1)))
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table.to_ASCII(os.path.join(dirname,file_out))
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dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
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if not os.path.isdir(dirname):
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os.mkdir(dirname,0o755)
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file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0],
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inc[3:].zfill(N_digits))
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table.to_ASCII(os.path.join(dirname,file_out))
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@ -55,94 +55,88 @@ parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string'
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options = parser.parse_args()
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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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for filename in options.filenames:
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f = damask.DADF5(filename) #DAMASK output file
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f = damask.Result(filename)
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for increment in options.inc:
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f.pick('increments',options.inc)
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f.set_by_increment(increment,increment)
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for increment in damask.util.show_progress(f.iter_selection('increments'),len(f.selection['increments'])):
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if len(f.visible['increments']) == 0:
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#-------output file creation-------------------------------------
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continue
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dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
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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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#-------output file creation-------------------------------------
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o = h5py.File(dirname + '/' + os.path.splitext(filename)[0] + '_{}.dream3D'.format(increment),'w')
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dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
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#-----------------------------------------------------------------
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try:
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o.attrs['DADF5toDREAM3D'] = '1.0'
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os.mkdir(dirname)
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o.attrs['FileVersion'] = '7.0'
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except FileExistsError:
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#-----------------------------------------------------------------
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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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for g in ['DataContainerBundles','Pipeline']: # empty groups (needed)
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#-----------------------------------------------------------------
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o.create_group(g)
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o.attrs['DADF5toDREAM3D'] = '1.0'
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o.attrs['FileVersion'] = '7.0'
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data_container_label = 'DataContainers/ImageDataContainer'
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#-----------------------------------------------------------------
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cell_data_label = data_container_label + '/CellData'
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for g in ['DataContainerBundles','Pipeline']: # empty groups (needed)
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# Phase information of DREAM.3D is constituent ID in DAMASK
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o.create_group(g)
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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'))
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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'])).astype(np.float32)
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o[cell_data_label + '/Quats'] = DREAM_3D_quaternion.reshape(tuple(f.grid)+(4,))
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data_container_label = 'DataContainers/ImageDataContainer'
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# Attributes to CellData group
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cell_data_label = data_container_label + '/CellData'
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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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o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
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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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o[cell_data_label + '/Quats'].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
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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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# Phase information of DREAM.3D is constituent ID in DAMASK
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# Create geometry info
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o[cell_data_label + '/Phases'] = f.get_constituent_ID().reshape(tuple(f.grid)+(1,))
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geom_label = data_container_label + '/_SIMPL_GEOMETRY'
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# Data quaternions
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DAMASK_quaternion = f.read_dataset(f.get_dataset_location('orientation'))
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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'])).astype(np.float32)
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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[geom_label + '/DIMENSIONS'] = np.int64(f.grid)
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o[cell_data_label].attrs['AttributeMatrixType'] = np.array([3],np.uint32)
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o[geom_label + '/ORIGIN'] = np.float32(np.zeros(3))
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o[cell_data_label].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
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o[geom_label + '/SPACING'] = np.float32(f.size)
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# Common Attributes for groups in CellData
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o[geom_label].attrs['GeometryName'] = 'ImageGeometry'
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for group in ['/Phases','/Quats']:
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o[geom_label].attrs['GeometryTypeName'] = 'ImageGeometry'
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o[cell_data_label + group].attrs['DataArrayVersion'] = np.array([2],np.int32)
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o[geom_label].attrs['GeometryType'] = np.array([0],np.uint32)
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o[cell_data_label + group].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*f.grid)
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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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# 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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o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
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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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o[cell_data_label + '/Quats'].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
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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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