From 9e51ab160cb4095c7b49278cccbe596af38d2bce Mon Sep 17 00:00:00 2001 From: Vitesh Shah Date: Fri, 1 Dec 2023 12:20:36 +0100 Subject: [PATCH] ditching the patched copy approach Further details or things to look at: https://git.damask.mpie.de/damask/DAMASK/-/commit/2a48bf504e8decda0cb1dfe66c84033411c60066#note_12028 --- python/damask/_result.py | 48 +++++++++++----------------------------- 1 file changed, 13 insertions(+), 35 deletions(-) diff --git a/python/damask/_result.py b/python/damask/_result.py index faa2c1fbd..99fef3d79 100644 --- a/python/damask/_result.py +++ b/python/damask/_result.py @@ -1,9 +1,6 @@ import re import fnmatch import os -import sys -import importlib -import importlib.util import copy import datetime import xml.etree.ElementTree as ET # noqa @@ -28,27 +25,6 @@ from . import tensor from . import util from ._typehints import FloatSequence, IntSequence, DADF5Dataset -h5py_module_list = ['h5py','h5py._hl','h5py._hl.attrs'] -module_dict = {} - -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 - -SPEC_H5PY_HL = importlib.util.find_spec('h5py._hl') -h5py_hl_modified = importlib.util.module_from_spec(SPEC_H5PY_HL) -SPEC_H5PY_HL.loader.exec_module(h5py_hl_modified) -sys.modules['h5py_hl_modified'] = h5py_hl_modified - -SPEC_H5PY_HL_attrs = importlib.util.find_spec('h5py._hl.attrs') -h5py_hl_attrs_modified = importlib.util.module_from_spec(SPEC_H5PY_HL_attrs) -SPEC_H5PY_HL_attrs.loader.exec_module(h5py_hl_attrs_modified) -sys.modules['h5py_hl_attrs_modified'] = h5py_hl_attrs_modified - -h5py_hl_modified.__dict__['attrs'] = h5py_hl_attrs_modified -h5py_modified.__dict__['_hl'] = h5py_hl_modified - h5py3 = h5py.__version__[0] == '3' chunk_size = 1024**2//8 # for compression in HDF5 @@ -86,7 +62,7 @@ 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_modified.AttributeManager): +class AttributeManagerNullterm(h5py.AttributeManager): """ Attribute management for DREAM.3D hdf5 files. @@ -107,7 +83,7 @@ class AttributeManagerNullterm(h5py_modified.AttributeManager): else: super().create(name=name,data=data,shape=shape,dtype=dtype) -class ResetAttributeManager(h5py_modified.AttributeManager): +class ResetAttributeManager(h5py.AttributeManager): """ Reset the attribute management for DREAM.3D hdf5 files. @@ -2007,13 +1983,14 @@ class Result: Directory to save DREAM3D files. Will be created if non-existent. """ - h5py_modified._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch' + h5py._hl.attrs.AttributeManager = AttributeManagerNullterm # 'Monkey patch' if self.N_constituents != 1 or not self.structured: raise TypeError('DREAM3D output requires structured grid with single constituent.') N_digits = int(np.floor(np.log10(max(1,self.incs[-1]))))+1 - Crystal_structure_types = {'Hexagonal': 0, 'Cubic': 1, 'Triclinic': 4, 'Monoclinic': 5, 'Orthorhombic': 6, 'Tetrogonal': 8} + Crystal_structure_types = {'Hexagonal': 0, 'Cubic': 1, 'Triclinic': 4, 'Monoclinic': 5, \ + 'Orthorhombic': 6, 'Tetrogonal': 8} # crystal structure map according to Dream3D Phase_types = {'Primary': 0} @@ -2048,7 +2025,7 @@ class Result: phase_ID_array[at_cell_ph[c][label]] = count + 1 job_file_no_ext = self.fname.stem - o = h5py_modified.File(f'{dream_dir}/{job_file_no_ext}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}.dream3d','w') + o = h5py.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' @@ -2105,15 +2082,16 @@ class Result: elif lattice_dict[label] in ['tP','tI']: crystal_structure = 'tetragonal' crystal_structure_list.append(Crystal_structure_types[crystal_structure]) - o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array(crystal_structure_list)).reshape((len(self.phases)+1,1)) + o[ensemble_label + '/CrystalStructures'] = np.uint32(np.array(crystal_structure_list)).reshape((len(self.phases)\ + +1,1)) o[ensemble_label + '/PhaseTypes'] = np.uint32(np.array([999] + [Phase_types['Primary']]*len(self.phases)))\ .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_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)) + 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)) # Attributes Ensemble Matrix o[ensemble_label].attrs['AttributeMatrixType'] = np.array([11],np.uint32) @@ -2145,7 +2123,7 @@ class Result: 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_modified._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,