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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 re
import fnmatch import fnmatch
import os import os
import sys
import importlib.util
import copy import copy
import datetime import datetime
import xml.etree.ElementTree as ET # noqa import xml.etree.ElementTree as ET # noqa
@ -11,7 +13,6 @@ from collections import defaultdict
from collections.abc import Iterable from collections.abc import Iterable
from typing import Optional, Union, Callable, Any, Sequence, Literal, Dict, List, Tuple from typing import Optional, Union, Callable, Any, Sequence, Literal, Dict, List, Tuple
import h5py
import numpy as np import numpy as np
from numpy import ma from numpy import ma
@ -25,6 +26,11 @@ 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')
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' h5py3 = h5py.__version__[0] == '3'
chunk_size = 1024**2//8 # for compression in HDF5 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, 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.
@ -77,9 +83,9 @@ class AttributeManagerNullterm(h5py.AttributeManager):
def create(self, name, data, shape=None, dtype=None): def create(self, name, data, shape=None, dtype=None):
if isinstance(data,str): if isinstance(data,str):
tid = h5py.h5t.C_S1.copy() tid = h5py_modified.h5t.C_S1.copy()
tid.set_size(len(data + ' ')) 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: else:
super().create(name=name,data=data,shape=shape,dtype=dtype) 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. 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 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 = Path.cwd() if target_dir is None else Path(target_dir)
dream_dir.mkdir(parents=True,exist_ok=True) 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']): for inc in util.show_progress(self.visible['increments']):
cell_orientation_array = np.zeros((np.prod(self.cells),3)) 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 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 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'
@ -2083,10 +2089,10 @@ 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))
# also assuming Primary phases # also assuming Primary phases
# there can be precipitates etc as well # 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['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._hl.attrs.AttributeManager = ResetAttributeManager # Reset the attribute manager to original
def export_DADF5(self, def export_DADF5(self,