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DAMASK_EICMD
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adding ._hl method to modified h5py class 

Simple loading of module from importlib misses the extra methods and
attributes associated with h5py.
For h5py._hl is missing which is needed for nullterm strings in
attributes.
This commit is contained in:
Vitesh Shah 2023-11-28 09:45:16 +01:00
parent 1cf8696cbb
commit 05da811afe
1 changed files with 16 additions and 13 deletions
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29
python/damask/_result.py
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@ -2,6 +2,7 @@ import re
import fnmatch import fnmatch
import os import os
import sys import sys
import importlib
import importlib.util import importlib.util
import copy import copy
import datetime import datetime
@ -27,10 +28,12 @@ from . import tensor
from . import util from . import util
from ._typehints import FloatSequence, IntSequence, DADF5Dataset from ._typehints import FloatSequence, IntSequence, DADF5Dataset
#SPEC_H5PY = importlib.util.find_spec('h5py') SPEC_H5PY = importlib.util.find_spec('h5py')
#h5py_modified = importlib.util.module_from_spec(SPEC_H5PY) h5py_modified = importlib.util.module_from_spec(SPEC_H5PY)
#SPEC_H5PY.loader.exec_module(h5py_modified) SPEC_H5PY.loader.exec_module(h5py_modified)
#sys.modules['h5py_modified'] = h5py_modified sys.modules['h5py_modified'] = h5py_modified
h5py_modified.__dict__['_hl'] = h5py.__dict__['_hl']
h5py3 = h5py.__version__[0] == '3' h5py3 = h5py.__version__[0] == '3'
@ -69,7 +72,7 @@ def _empty_like(dataset: np.ma.core.MaskedArray,
fill_value = fill_float if dataset.dtype in np.sctypes['float'] else fill_int, fill_value = fill_float if dataset.dtype in np.sctypes['float'] else fill_int,
mask = True) mask = True)
class AttributeManagerNullterm(h5py.AttributeManager): class AttributeManagerNullterm(h5py_modified.AttributeManager):
""" """
Attribute management for DREAM.3D hdf5 files. Attribute management for DREAM.3D hdf5 files.
@ -90,7 +93,7 @@ class AttributeManagerNullterm(h5py.AttributeManager):
else: else:
super().create(name=name,data=data,shape=shape,dtype=dtype) super().create(name=name,data=data,shape=shape,dtype=dtype)
class ResetAttributeManager(h5py.AttributeManager): class ResetAttributeManager(h5py_modified.AttributeManager):
""" """
Reset the attribute management for DREAM.3D hdf5 files. Reset the attribute management for DREAM.3D hdf5 files.
@ -1990,7 +1993,7 @@ class Result:
Directory to save DREAM3D files. Will be created if non-existent. Directory to save DREAM3D files. Will be created if non-existent.
""" """
h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch' h5py_modified._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'
if self.N_constituents != 1 or not self.structured: if self.N_constituents != 1 or not self.structured:
raise TypeError('DREAM3D output requires structured grid with single constituent.') raise TypeError('DREAM3D output requires structured grid with single constituent.')
@ -2031,7 +2034,7 @@ class Result:
phase_ID_array[at_cell_ph[c][label]] = count + 1 phase_ID_array[at_cell_ph[c][label]] = count + 1
job_file_no_ext = self.fname.stem job_file_no_ext = self.fname.stem
o = h5py.File(f'{dream_dir}/{job_file_no_ext}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}.dream3d','w') o = h5py_modified.File(f'{dream_dir}/{job_file_no_ext}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}.dream3d','w')
o.attrs['DADF5toDREAM3D'] = '1.0' o.attrs['DADF5toDREAM3D'] = '1.0'
o.attrs['FileVersion'] = '7.0' o.attrs['FileVersion'] = '7.0'
@ -2093,10 +2096,10 @@ class Result:
.reshape((len(self.phases)+1,1)) .reshape((len(self.phases)+1,1))
phase_name_list = ['Unknown Phase Type'] phase_name_list = ['Unknown Phase Type']
phase_name_list.extend(i for i in self.visible['phases']) phase_name_list.extend(i for i in self.visible['phases'])
tid = h5py.h5t.C_S1.copy() tid = h5py_modified.h5t.C_S1.copy()
tid.set_size(h5py.h5t.VARIABLE) tid.set_size(h5py_modified.h5t.VARIABLE)
tid.set_cset(h5py.h5t.CSET_ASCII) tid.set_cset(h5py_modified.h5t.CSET_ASCII)
o[ensemble_label].create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py.Datatype(tid)) o[ensemble_label].create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py_modified.Datatype(tid))
# Attributes Ensemble Matrix # Attributes Ensemble Matrix
o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32) o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32)
@ -2128,7 +2131,7 @@ class Result:
o[geom_label].attrs['GeometryType'] = np.array([0],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['SpatialDimensionality'] = np.array([3],np.uint32)
o[geom_label].attrs['UnitDimensionality'] = 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: h5py_modified._hl.attrs.AttributeManager = ResetAttributeManager # Reset the attribute manager to original:
def export_DADF5(self, def export_DADF5(self,