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DAMASK_EICMD
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avoid monkey patching

This commit is contained in:
Martin Diehl 2023-12-04 21:50:02 +01:00
parent 7a5e08c14d
commit 213e8aa4be
1 changed files with 42 additions and 78 deletions
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116
python/damask/_result.py
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@ -62,41 +62,6 @@ def _empty_like(dataset: np.ma.core.MaskedArray,
fill_value = fill_float if dataset.dtype in np.sctypes['float'] else fill_int,
mask = True)
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)
class ResetAttributeManager(h5py.AttributeManager):
"""
Reset the attribute management for DREAM.3D hdf5 files.
References
----------
https://stackoverflow.com/questions/38267076
https://stackoverflow.com/questions/52750232
"""
def create(self, name, data, shape=None, dtype=None):
super().create(name=name,data=data,shape=shape,dtype=dtype)
class Result:
"""
@ -1983,7 +1948,15 @@ class Result:
Directory to save DREAM3D files. Will be created if non-existent.
"""
h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'
def add_attribute(obj,name,data):
"""DREAM.3D requires fixed length string."""
if isinstance(data,str):
tid = h5py.h5t.C_S1.copy()
tid.set_size(len(data)+1)
obj.attrs.create(name,data,dtype=h5py.Datatype(tid))
else:
obj.attrs.create(name,data)
if self.N_constituents != 1 or not self.structured:
raise TypeError('DREAM3D output requires structured grid with single constituent.')
@ -2000,16 +1973,15 @@ class Result:
with h5py.File(self.fname,'r') as f:
for inc in util.show_progress(self.visible['increments']):
cell_orientation_array = np.zeros((np.prod(self.cells),3))
cell_orientation = np.zeros((np.prod(self.cells),3))
phase_ID_array = np.zeros((np.prod(self.cells)),dtype=np.int32) #need to reshape it later
for c in range(self.N_constituents):
for count,label in enumerate(self.visible['phases']):
try:
data = ma.array(_read(f['/'.join([inc,'phase',label,'mechanical/O'])]))
lattice_dict[label] = f['/'.join([inc,'phase',label,'mechanical/O'])].attrs['lattice']
cell_orientation_array[at_cell_ph[c][label],:] = \
Rotation(data[in_data_ph[c][label],:]).as_Euler_angles()
# Dream3D handles euler angles better
data = _read(f['/'.join([inc,'phase',label,'mechanical/O'])])
lattice_dict[label] = data.dtype.metadata['lattice']
cell_orientation[at_cell_ph[c][label],:] = \
Rotation(data[in_data_ph[c][label],:]).as_Euler_angles().astype(np.float32)
except ValueError:
print("Orientation data is not present")
exit()
@ -2017,8 +1989,7 @@ class Result:
phase_ID_array[at_cell_ph[c][label]] = count + 1
o = h5py.File(f'{out_dir}/{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}.dream3d','w')
o.attrs['DADF5toDREAM3D'] = '1.0'
o.attrs['FileVersion'] = '7.0'
add_attribute(o,'FileVersion','7.0')
for g in ['DataContainerBundles','Pipeline']: # empty groups (needed)
o.create_group(g)
@ -2026,32 +1997,26 @@ class Result:
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(self.cells))+(1,))
o[cell_data_label + '/Phases'] = np.reshape(phase_ID_array,tuple(np.flip(self.cells))+(1,))
o[cell_data_label + '/EulerAngles'] = cell_orientation.reshape(tuple(np.flip(self.cells))+(3,))
# Data eulers
orientation_data = cell_orientation_array.astype(np.float32)
o[cell_data_label + '/EulerAngles'] = orientation_data.reshape(tuple(np.flip(self.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(self.cells,np.uint64)
# Common Attributes for groups in CellData
for dataset in ['/Phases','/EulerAngles']:
o[cell_data_label + dataset].attrs['DataArrayVersion'] = np.array([2],np.int32)
o[cell_data_label + dataset].attrs['Tuple Axis Dimensions'] = 'x={},y={},z={}'.format(*np.array(self.cells))
add_attribute(o[cell_data_label + dataset],'DataArrayVersion',np.array([2],np.int32))
add_attribute(o[cell_data_label + dataset],'Tuple Axis Dimensions','x={},y={},z={}'.format(*np.array(self.cells)))
# phase attributes
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'] = np.array(self.cells,np.uint64)
add_attribute(o[cell_data_label + '/Phases'], 'ComponentDimensions', np.array([1],np.uint64))
add_attribute(o[cell_data_label + '/Phases'], 'ObjectType', 'DataArray<int32_t>')
add_attribute(o[cell_data_label + '/Phases'], 'TupleDimensions', np.array(self.cells,np.uint64))
# Eulers attributes
o[cell_data_label + '/EulerAngles'].attrs['ComponentDimensions'] = np.array([3],np.uint64)
o[cell_data_label + '/EulerAngles'].attrs['ObjectType'] = 'DataArray<float>'
o[cell_data_label + '/EulerAngles'].attrs['TupleDimensions'] = np.array(self.cells,np.uint64)
add_attribute(o[cell_data_label + '/EulerAngles'], 'ComponentDimensions', np.array([3],np.uint64))
add_attribute(o[cell_data_label + '/EulerAngles'], 'ObjectType', 'DataArray<float>')
add_attribute(o[cell_data_label + '/EulerAngles'], 'TupleDimensions', np.array(self.cells,np.uint64))
# Create EnsembleAttributeMatrix
ensemble_label = data_container_label + '/CellEnsembleData'
@ -2081,17 +2046,17 @@ class Result:
# Attributes for data in Ensemble matrix
for group in ['CrystalStructures','PhaseTypes']:
o[ensemble_label+'/'+group].attrs['ComponentDimensions'] = np.array([1],np.uint64)
o[ensemble_label+'/'+group].attrs['Tuple Axis Dimensions'] = f'x={len(self.phases)+1}'
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([len(self.phases) + 1],np.uint64)
add_attribute(o[ensemble_label+'/'+group], 'ComponentDimensions', np.array([1],np.uint64))
add_attribute(o[ensemble_label+'/'+group], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}')
add_attribute(o[ensemble_label+'/'+group], 'DataArrayVersion', np.array([2],np.int32))
add_attribute(o[ensemble_label+'/'+group], 'ObjectType', 'DataArray<uint32_t>')
add_attribute(o[ensemble_label+'/'+group], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
o[ensemble_label+'/PhaseName'].attrs['ComponentDimensions'] = np.array([1],np.uint64)
o[ensemble_label+'/PhaseName'].attrs['Tuple Axis Dimensions'] = f'x={len(self.phases)+1}'
o[ensemble_label+'/PhaseName'].attrs['DataArrayVersion'] = np.array([2],np.int32)
o[ensemble_label+'/PhaseName'].attrs['ObjectType'] = 'StringDataArray'
o[ensemble_label+'/PhaseName'].attrs['TupleDimensions'] = np.array([len(self.phases) + 1],np.uint64)
add_attribute(o[ensemble_label+'/PhaseName'], 'ComponentDimensions', np.array([1],np.uint64))
add_attribute(o[ensemble_label+'/PhaseName'], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}')
add_attribute(o[ensemble_label+'/PhaseName'], 'DataArrayVersion', np.array([2],np.int32))
add_attribute(o[ensemble_label+'/PhaseName'], 'ObjectType', 'StringDataArray')
add_attribute(o[ensemble_label+'/PhaseName'], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
# Create geometry info
geom_label = data_container_label + '/_SIMPL_GEOMETRY'
@ -2100,12 +2065,11 @@ class Result:
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)
h5py._hl.attrs.AttributeManager = ResetAttributeManager # Reset the attribute manager to original:
add_attribute(o[geom_label], 'GeometryName', 'ImageGeometry')
add_attribute(o[geom_label], 'GeometryTypeName', 'ImageGeometry')
add_attribute(o[geom_label], 'GeometryType', np.array([0],np.uint32))
add_attribute(o[geom_label], 'SpatialDimensionality', np.array([3],np.uint32))
add_attribute(o[geom_label], 'UnitDimensionality', np.array([3],np.uint32))
def export_DADF5(self,