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DAMASK_EICMD
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attempting patched copy of h5py 

https://stackoverflow.com/questions/11170949/how-to-make-a-copy-of-a-python-module-at-runtime
This commit is contained in:
Vitesh Shah 2023-11-17 12:18:35 +01:00
parent 597175d8fd
commit 2a48bf504e
1 changed files with 18 additions and 12 deletions
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30
python/damask/_result.py
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@ -1,6 +1,8 @@
import re
import fnmatch
import os
import sys
import importlib.util
import copy
import datetime
import xml.etree.ElementTree as ET # noqa
@ -11,7 +13,6 @@ from collections import defaultdict
from collections.abc import Iterable
from typing import Optional, Union, Callable, Any, Sequence, Literal, Dict, List, Tuple
import h5py
import numpy as np
from numpy import ma
@ -25,6 +26,11 @@ from . import tensor
from . import util
from ._typehints import FloatSequence, IntSequence, DADF5Dataset
SPEC_H5PY = importlib.util.find_spec('h5py')
h5py_modified = importlib.util.module_from_spec(SPEC_H5PY)
SPEC_H5PY.loader.exec_module(h5py_modified)
sys.modules['h5py_modified'] = h5py_modified
h5py3 = h5py.__version__[0] == '3'
chunk_size = 1024**2//8 # for compression in HDF5
@ -62,7 +68,7 @@ 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):
class AttributeManagerNullterm(h5py_modified.AttributeManager):
"""
Attribute management for DREAM.3D hdf5 files.
@ -77,9 +83,9 @@ class AttributeManagerNullterm(h5py.AttributeManager):
def create(self, name, data, shape=None, dtype=None):
if isinstance(data,str):
tid = h5py.h5t.C_S1.copy()
tid = h5py_modified.h5t.C_S1.copy()
tid.set_size(len(data + ' '))
super().create(name=name,data=data+' ',dtype = h5py.Datatype(tid))
super().create(name=name,data=data+' ',dtype = h5py_modified.Datatype(tid))
else:
super().create(name=name,data=data,shape=shape,dtype=dtype)
@ -1983,7 +1989,7 @@ class Result:
Directory to save DREAM3D files. Will be created if non-existent.
"""
h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'
#h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch'
N_digits = int(np.floor(np.log10(max(1,self.incs[-1]))))+1
@ -2002,7 +2008,7 @@ class Result:
dream_dir = Path.cwd() if target_dir is None else Path(target_dir)
dream_dir.mkdir(parents=True,exist_ok=True)
with h5py.File(self.fname,'r') as f:
with h5py_modified.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))
phase_ID_array = np.zeros((np.prod(self.cells)),dtype=np.int32) #need to reshape it later
@ -2021,7 +2027,7 @@ class Result:
phase_ID_array[at_cell_ph[c][label]] = count + 1
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['FileVersion'] = '7.0'
@ -2083,10 +2089,10 @@ class Result:
.reshape((len(self.phases)+1,1))
phase_name_list = ['Unknown Phase Type']
phase_name_list.extend(i for i in self.visible['phases'])
tid = h5py.h5t.C_S1.copy()
tid.set_size(h5py.h5t.VARIABLE)
tid.set_cset(h5py.h5t.CSET_ASCII)
o[ensemble_label].create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py.Datatype(tid))
tid = h5py_modified.h5t.C_S1.copy()
tid.set_size(h5py_modified.h5t.VARIABLE)
tid.set_cset(h5py_modified.h5t.CSET_ASCII)
o[ensemble_label].create_dataset(name='PhaseName',data = phase_name_list, dtype=h5py_modified.Datatype(tid))
# also assuming Primary phases
# there can be precipitates etc as well
@ -2121,7 +2127,7 @@ class Result:
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
#h5py._hl.attrs.AttributeManager = ResetAttributeManager # Reset the attribute manager to original
def export_DADF5(self,