consistent and correct number of leading zeros

This commit is contained in:
Martin Diehl 2020-03-19 08:45:25 +01:00
parent b5899b51e1
commit 0871111c11
3 changed files with 32 additions and 29 deletions

View File

@ -8,18 +8,18 @@ import numpy as np
import damask
class AttributeManagerNullterm(h5py.AttributeManager):
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):
@ -28,7 +28,7 @@ class AttributeManagerNullterm(h5py.AttributeManager):
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'
@ -59,61 +59,64 @@ 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 increment in damask.util.show_progress(f.iterate('increments'),len(f.selection['increments'])):
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] + '_{}.dream3D'.format(increment),'w')
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'
o.attrs['FileVersion'] = '7.0'
for g in ['DataContainerBundles','Pipeline']: # empty groups (needed)
o.create_group(g)
data_container_label = 'DataContainers/ImageDataContainer'
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,))
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<int32_t>'
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<float>'
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'
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)
@ -121,15 +124,15 @@ for filename in options.filenames:
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)
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['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)

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@ -1039,7 +1039,7 @@ class Result:
elif mode.lower()=='point':
v = VTK.from_polyData(self.cell_coordinates())
N_digits = int(np.floor(np.log10(min(int(self.increments[-1][3:]),1))))+1
N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1
for i,inc in enumerate(util.show_progress(self.iterate('increments'),len(self.selection['increments']))):

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@ -258,7 +258,7 @@ def scale_to_coprime(v):
return m//reduce(np.gcd,m)
class return_message():
class return_message:
"""Object with formatted return message."""
def __init__(self,message):