update to changes in Result class

This commit is contained in:
Martin Diehl 2020-03-17 01:49:47 +01:00
parent 1e1fb35e14
commit 17e7b32b31
2 changed files with 104 additions and 115 deletions

View File

@ -36,39 +36,34 @@ if options.con is None: options.con=[]
# --- loop over input files ------------------------------------------------------------------------ # --- loop over input files ------------------------------------------------------------------------
for filename in options.filenames: for filename in options.filenames:
results = damask.DADF5(filename) results = damask.Result(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)))
table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)}) if not results.structured: continue
table.add('pos',coords.reshape((-1,3))) coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin)
results.pick('materialpoints',False) N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
results.pick('constituents', True) N_digits = 5 # hack to keep test intact
for label in options.con: for inc in damask.util.show_progress(results.iter_visible('increments'),len(results.increments)):
x = results.get_dataset_location(label) table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})
if len(x) != 0: table.add('pos',coords.reshape((-1,3)))
table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1)))
results.pick('constituents', False) results.pick('materialpoints',False)
results.pick('materialpoints',True) results.pick('constituents', True)
for label in options.mat: for label in options.con:
x = results.get_dataset_location(label) x = results.get_dataset_location(label)
if len(x) != 0: if len(x) != 0:
table.add(label,results.read_dataset(x,0,plain=True).reshape((results.grid.prod(),-1))) 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)) results.pick('constituents', False)
if not os.path.isdir(dirname): results.pick('materialpoints',True)
os.mkdir(dirname,0o755) for label in options.mat:
file_out = '{}_inc{}.txt'.format(os.path.splitext(os.path.split(filename)[-1])[0], x = results.get_dataset_location(label)
inc[3:].zfill(N_digits)) if len(x) != 0:
table.to_ASCII(os.path.join(dirname,file_out)) 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))

View File

@ -55,94 +55,88 @@ parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string'
options = parser.parse_args() options = parser.parse_args()
# --------------------------------------------------------------------
# loop over input files
for filename in options.filenames: for filename in options.filenames:
f = damask.DADF5(filename) #DAMASK output file f = damask.Result(filename)
for increment in options.inc: f.pick('increments',options.inc)
f.set_by_increment(increment,increment) for increment in damask.util.show_progress(f.iter_selection('increments'),len(f.selection['increments'])):
if len(f.visible['increments']) == 0: #-------output file creation-------------------------------------
continue dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
try:
os.mkdir(dirname)
except FileExistsError:
pass
#-------output file creation------------------------------------- o = h5py.File(dirname + '/' + os.path.splitext(filename)[0] + '_{}.dream3D'.format(increment),'w')
dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir)) #-----------------------------------------------------------------
try: o.attrs['DADF5toDREAM3D'] = '1.0'
os.mkdir(dirname) o.attrs['FileVersion'] = '7.0'
except FileExistsError: #-----------------------------------------------------------------
pass
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') data_container_label = 'DataContainers/ImageDataContainer'
#----------------------------------------------------------------- cell_data_label = data_container_label + '/CellData'
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 # Phase information of DREAM.3D is constituent ID in DAMASK
o[cell_data_label + '/Phases'] = f.get_constituent_ID().reshape(tuple(f.grid)+(1,)) o[cell_data_label + '/Phases'] = f.get_constituent_ID().reshape(tuple(f.grid)+(1,))
# Data quaternions # Data quaternions
DAMASK_quaternion = f.read_dataset(f.get_dataset_location('orientation')) 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 # 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'], DREAM_3D_quaternion = np.hstack((-DAMASK_quaternion['x'],-DAMASK_quaternion['y'],-DAMASK_quaternion['z'],
DAMASK_quaternion['w'])).astype(np.float32) DAMASK_quaternion['w'])).astype(np.float32)
o[cell_data_label + '/Quats'] = DREAM_3D_quaternion.reshape(tuple(f.grid)+(4,)) 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 # Common Attributes for groups in CellData
o[cell_data_label].attrs['AttributeMatrixType'] = np.array([3],np.uint32) for group in ['/Phases','/Quats']:
o[cell_data_label].attrs['TupleDimensions'] = f.grid.astype(np.uint64) 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)
# Common Attributes for groups in CellData
for group in ['/Phases','/Quats']: # phase attributes
o[cell_data_label + group].attrs['DataArrayVersion'] = np.array([2],np.int32) o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64)
o[cell_data_label + group].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*f.grid) o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray<int32_t>'
o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = f.grid.astype(np.uint64)
# phase attributes
o[cell_data_label + '/Phases'].attrs['ComponentDimensions'] = np.array([1],np.uint64) # Quats attributes
o[cell_data_label + '/Phases'].attrs['ObjectType'] = 'DataArray<int32_t>' o[cell_data_label + '/Quats'].attrs['ComponentDimensions'] = np.array([4],np.uint64)
o[cell_data_label + '/Phases'].attrs['TupleDimensions'] = f.grid.astype(np.uint64) o[cell_data_label + '/Quats'].attrs['ObjectType'] = 'DataArray<float>'
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<uint32_t>'
o[ensemble_label+'/'+group].attrs['TupleDimensions'] = np.array([2],np.uint64)
# Quats attributes # Create geometry info
o[cell_data_label + '/Quats'].attrs['ComponentDimensions'] = np.array([4],np.uint64) geom_label = data_container_label + '/_SIMPL_GEOMETRY'
o[cell_data_label + '/Quats'].attrs['ObjectType'] = 'DataArray<float>'
o[cell_data_label + '/Quats'].attrs['TupleDimensions'] = f.grid.astype(np.uint64) o[geom_label + '/DIMENSIONS'] = np.int64(f.grid)
o[geom_label + '/ORIGIN'] = np.float32(np.zeros(3))
# Create EnsembleAttributeMatrix o[geom_label + '/SPACING'] = np.float32(f.size)
ensemble_label = data_container_label + '/EnsembleAttributeMatrix'
# Data CrystalStructures o[geom_label].attrs['GeometryName'] = 'ImageGeometry'
o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array([999,\ o[geom_label].attrs['GeometryTypeName'] = 'ImageGeometry'
Crystal_structures[f.get_crystal_structure()]])).reshape((2,1)) o[geom_label].attrs['GeometryType'] = np.array([0],np.uint32)
o[ensemble_label + '/PhaseTypes'] = np.uint32(np.array([999,Phase_types['Primary']])).reshape((2,1)) # ToDo o[geom_label].attrs['SpatialDimensionality'] = np.array([3],np.uint32)
o[geom_label].attrs['UnitDimensionality'] = np.array([3],np.uint32)
# 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<uint32_t>'
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)