DAMASK_EICMD/python/damask/_result.py

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import multiprocessing as mp
import re
import fnmatch
import os
import copy
import datetime
import xml.etree.ElementTree as ET
import xml.dom.minidom
from pathlib import Path
from functools import partial
from collections import defaultdict
from collections.abc import Iterable
import h5py
import numpy as np
import numpy.ma as ma
from numpy.lib import recfunctions as rfn
import damask
from . import VTK
from . import Orientation
from . import grid_filters
from . import mechanics
from . import tensor
from . import util
h5py3 = h5py.__version__[0] == '3'
def _read(dataset):
"""Read a dataset and its metadata into a numpy.ndarray."""
metadata = {k:(v.decode() if not h5py3 and type(v) is bytes else v) for k,v in dataset.attrs.items()}
dtype = np.dtype(dataset.dtype,metadata=metadata)
return np.array(dataset,dtype=dtype)
def _match(requested,existing):
"""Find matches among two sets of labels."""
def flatten_list(list_of_lists):
return [e for e_ in list_of_lists for e in e_]
if requested is True:
requested = '*'
elif requested is False or requested is None:
requested = []
requested_ = requested if hasattr(requested,'__iter__') and not isinstance(requested,str) else \
[requested]
return sorted(set(flatten_list([fnmatch.filter(existing,r) for r in requested_])),
key=util.natural_sort)
def _empty_like(dataset,N_materialpoints,fill_float,fill_int):
"""Create empty numpy.ma.MaskedArray."""
return ma.array(np.empty((N_materialpoints,)+dataset.shape[1:],dataset.dtype),
fill_value = fill_float if dataset.dtype in np.sctypes['float'] else fill_int,
mask = True)
class Result:
"""
Manipulate and read DADF5 files.
DADF5 (DAMASK HDF5) files contain DAMASK results.
The group/folder structure reflects the input data
in material.yaml.
"""
def __init__(self,fname):
"""
New result view bound to a HDF5 file.
Parameters
----------
fname : str or pathlib.Path
Name of the DADF5 file to be opened.
"""
with h5py.File(fname,'r') as f:
self.version_major = f.attrs['DADF5_version_major']
self.version_minor = f.attrs['DADF5_version_minor']
if self.version_major != 0 or not 7 <= self.version_minor <= 12:
raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}')
self.structured = 'grid' in f['geometry'].attrs.keys() or \
'cells' in f['geometry'].attrs.keys()
if self.structured:
try:
self.cells = f['geometry'].attrs['cells']
except KeyError:
self.cells = f['geometry'].attrs['grid']
self.size = f['geometry'].attrs['size']
self.origin = f['geometry'].attrs['origin']
r=re.compile('inc[0-9]+' if self.version_minor < 12 else 'increment_[0-9]+')
self.increments = sorted([i for i in f.keys() if r.match(i)],key=util.natural_sort)
self.times = [round(f[i].attrs['time/s' if self.version_minor < 12 else
't/s'],12) for i in self.increments]
grp = 'mapping' if self.version_minor < 12 else 'cell_to'
self.N_materialpoints, self.N_constituents = np.shape(f[f'{grp}/phase'])
self.homogenizations = [m.decode() for m in np.unique(f[f'{grp}/homogenization']
['Name' if self.version_minor < 12 else 'label'])]
self.homogenizations = sorted(self.homogenizations,key=util.natural_sort)
self.phases = [c.decode() for c in np.unique(f[f'{grp}/phase']
['Name' if self.version_minor < 12 else 'label'])]
self.phases = sorted(self.phases,key=util.natural_sort)
self.fields = []
for c in self.phases:
self.fields += f['/'.join([self.increments[0],'phase',c])].keys()
for m in self.homogenizations:
self.fields += f['/'.join([self.increments[0],'homogenization',m])].keys()
self.fields = sorted(set(self.fields),key=util.natural_sort) # make unique
self.visible = {'increments': self.increments,
'phases': self.phases,
'homogenizations': self.homogenizations,
'fields': self.fields,
}
self.fname = Path(fname).absolute()
self._allow_modification = False
def __copy__(self):
"""Create deep copy."""
return copy.deepcopy(self)
copy = __copy__
def __repr__(self):
"""Show summary of file content."""
visible_increments = self.visible['increments']
first = self.view('increments',visible_increments[0:1]).list_data()
last = '' if len(visible_increments) < 2 else \
self.view('increments',visible_increments[-1:]).list_data()
in_between = '' if len(visible_increments) < 3 else \
''.join([f'\n{inc}\n ...\n' for inc in visible_increments[1:-1]])
return util.srepr(first + in_between + last)
def _manage_view(self,action,what,datasets):
"""
Manages the visibility of the groups.
Parameters
----------
action : str
Select from 'set', 'add', and 'del'.
what : str
Attribute to change (must be from self.visible).
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards.
True is equivalent to '*', False is equivalent to [].
"""
# allow True/False and string arguments
if datasets is True:
datasets = '*'
elif datasets is False or datasets is None:
datasets = []
choice = list(datasets).copy() if hasattr(datasets,'__iter__') and not isinstance(datasets,str) else \
[datasets]
inc = 'inc' if self.version_minor < 12 else 'increment_' # compatibility hack
if what == 'increments':
choice = [c if isinstance(c,str) and c.startswith(inc) else
f'{inc}{c}' for c in choice]
elif what == 'times':
what = 'increments'
if choice == ['*']:
choice = self.increments
else:
iterator = map(float,choice)
choice = []
for c in iterator:
idx = np.searchsorted(self.times,c)
if idx >= len(self.times): continue
if np.isclose(c,self.times[idx]):
choice.append(self.increments[idx])
elif np.isclose(c,self.times[idx+1]):
choice.append(self.increments[idx+1])
valid = _match(choice,getattr(self,what))
existing = set(self.visible[what])
dup = self.copy()
if action == 'set':
dup.visible[what] = sorted(set(valid), key=util.natural_sort)
elif action == 'add':
add = existing.union(valid)
dup.visible[what] = sorted(add, key=util.natural_sort)
elif action == 'del':
diff = existing.difference(valid)
dup.visible[what] = sorted(diff, key=util.natural_sort)
return dup
def allow_modification(self):
"""Allow to overwrite existing data."""
print(util.warn('Warning: Modification of existing datasets allowed!'))
dup = self.copy()
dup._allow_modification = True
return dup
def disallow_modification(self):
"""Disallow to overwrite existing data (default case)."""
dup = self.copy()
dup._allow_modification = False
return dup
def increments_in_range(self,start,end):
"""
Select all increments within a given range.
Parameters
----------
start : int or str
Start increment.
end : int or str
End increment.
"""
# compatibility hack
ln = 3 if self.version_minor < 12 else 10
selected = []
for i,inc in enumerate([int(i[ln:]) for i in self.increments]):
s,e = map(lambda x: int(x[ln:] if isinstance(x,str) and x.startswith('inc') else x), (start,end))
if s <= inc <= e:
selected.append(self.increments[i])
return selected
def times_in_range(self,start,end):
"""
Select all increments within a given time range.
Parameters
----------
start : float
Time of start increment.
end : float
Time of end increment.
"""
selected = []
for i,time in enumerate(self.times):
if start <= time <= end:
selected.append(self.times[i])
return selected
def view(self,what,datasets):
"""
Set view.
Parameters
----------
what : {'increments', 'times', 'phases', 'homogenizations', 'fields'}
Attribute to change.
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards.
True is equivalent to '*', False is equivalent to [].
"""
return self._manage_view('set',what,datasets)
def view_more(self,what,datasets):
"""
Add to view.
Parameters
----------
what : {'increments', 'times', 'phases', 'homogenizations', 'fields'}
Attribute to change.
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards.
True is equivalent to '*', False is equivalent to [].
"""
return self._manage_view('add',what,datasets)
def view_less(self,what,datasets):
"""
Delete from view.
Parameters
----------
what : {'increments', 'times', 'phases', 'homogenizations', 'fields'}
Attribute to change.
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards.
True is equivalent to '*', False is equivalent to [].
"""
return self._manage_view('del',what,datasets)
def rename(self,name_old,name_new):
"""
Rename dataset.
Parameters
----------
name_old : str
Name of the dataset to be renamed.
name_new : str
New name of the dataset.
"""
if not self._allow_modification:
raise PermissionError('Rename operation not permitted')
with h5py.File(self.fname,'a') as f:
for inc in self.visible['increments']:
for ty in ['phase','homogenization']:
for label in self.visible[ty+'s']:
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
path_old = '/'.join([inc,ty,label,field,name_old])
path_new = '/'.join([inc,ty,label,field,name_new])
if path_old in f.keys():
f[path_new] = f[path_old]
f[path_new].attrs['renamed'] = f'original name: {name_old}' if h5py3 else \
f'original name: {name_old}'.encode()
del f[path_old]
def list_data(self):
"""Return information on all active datasets in the file."""
# compatibility hack
de = 'Description' if self.version_minor < 12 else 'description'
un = 'Unit' if self.version_minor < 12 else 'unit'
msg = ''
with h5py.File(self.fname,'r') as f:
for inc in self.visible['increments']:
msg = ''.join([msg,f'\n{inc} ({self.times[self.increments.index(inc)]}s)\n'])
for ty in ['phase','homogenization']:
msg = ' '.join([msg,f'{ty}\n'])
for label in self.visible[ty+'s']:
msg = ' '.join([msg,f'{label}\n'])
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
msg = ' '.join([msg,f'{field}\n'])
for d in f['/'.join([inc,ty,label,field])].keys():
dataset = f['/'.join([inc,ty,label,field,d])]
unit = f' / {dataset.attrs[un]}' if h5py3 else \
f' / {dataset.attrs[un].decode()}'
description = dataset.attrs[de] if h5py3 else \
dataset.attrs[de].decode()
msg = ' '.join([msg,f'{d}{unit}: {description}\n'])
return msg
def enable_user_function(self,func):
globals()[func.__name__]=func
print(f'Function {func.__name__} enabled in add_calculation.')
@property
def coordinates0_point(self):
"""Return initial coordinates of the cell centers."""
if self.structured:
return grid_filters.coordinates0_point(self.cells,self.size,self.origin).reshape(-1,3,order='F')
else:
with h5py.File(self.fname,'r') as f:
return f['geometry/x_c'][()]
@property
def coordinates0_node(self):
"""Return initial coordinates of the cell centers."""
if self.structured:
return grid_filters.coordinates0_node(self.cells,self.size,self.origin).reshape(-1,3,order='F')
else:
with h5py.File(self.fname,'r') as f:
return f['geometry/x_n'][()]
@property
def geometry0(self):
if self.structured:
return VTK.from_rectilinear_grid(self.cells,self.size,self.origin)
else:
with h5py.File(self.fname,'r') as f:
return VTK.from_unstructured_grid(f['/geometry/x_n'][()],
f['/geometry/T_c'][()]-1,
f['/geometry/T_c'].attrs['VTK_TYPE'] if h5py3 else \
f['/geometry/T_c'].attrs['VTK_TYPE'].decode())
@staticmethod
def _add_absolute(x):
return {
'data': np.abs(x['data']),
'label': f'|{x["label"]}|',
'meta': {
'unit': x['meta']['unit'],
'description': f"absolute value of {x['label']} ({x['meta']['description']})",
'creator': 'add_absolute'
}
}
def add_absolute(self,x):
"""
Add absolute value.
Parameters
----------
x : str
Label of scalar, vector, or tensor dataset to take absolute value of.
"""
self._add_generic_pointwise(self._add_absolute,{'x':x})
@staticmethod
def _add_calculation(**kwargs):
formula = kwargs['formula']
for d in re.findall(r'#(.*?)#',formula):
formula = formula.replace(f'#{d}#',f"kwargs['{d}']['data']")
return {
'data': eval(formula),
'label': kwargs['label'],
'meta': {
'unit': kwargs['unit'],
'description': f"{kwargs['description']} (formula: {kwargs['formula']})",
'creator': 'add_calculation'
}
}
def add_calculation(self,label,formula,unit='n/a',description=None):
"""
Add result of a general formula.
Parameters
----------
label : str
Label of resulting dataset.
formula : str
Formula to calculate resulting dataset. Existing datasets are referenced by '#TheirLabel#'.
unit : str, optional
Physical unit of the result.
description : str, optional
Human-readable description of the result.
"""
dataset_mapping = {d:d for d in set(re.findall(r'#(.*?)#',formula))} # datasets used in the formula
args = {'formula':formula,'label':label,'unit':unit,'description':description}
self._add_generic_pointwise(self._add_calculation,dataset_mapping,args)
@staticmethod
def _add_stress_Cauchy(P,F):
return {
'data': mechanics.stress_Cauchy(P['data'],F['data']),
'label': 'sigma',
'meta': {
'unit': P['meta']['unit'],
'description': "Cauchy stress calculated "
f"from {P['label']} ({P['meta']['description']})"
f" and {F['label']} ({F['meta']['description']})",
'creator': 'add_stress_Cauchy'
}
}
def add_stress_Cauchy(self,P='P',F='F'):
"""
Add Cauchy stress calculated from first Piola-Kirchhoff stress and deformation gradient.
Parameters
----------
P : str, optional
Label of the dataset containing the first Piola-Kirchhoff stress. Defaults to 'P'.
F : str, optional
Label of the dataset containing the deformation gradient. Defaults to 'F'.
"""
self._add_generic_pointwise(self._add_stress_Cauchy,{'P':P,'F':F})
@staticmethod
def _add_determinant(T):
return {
'data': np.linalg.det(T['data']),
'label': f"det({T['label']})",
'meta': {
'unit': T['meta']['unit'],
'description': f"determinant of tensor {T['label']} ({T['meta']['description']})",
'creator': 'add_determinant'
}
}
def add_determinant(self,T):
"""
Add the determinant of a tensor.
Parameters
----------
T : str
Label of tensor dataset.
"""
self._add_generic_pointwise(self._add_determinant,{'T':T})
@staticmethod
def _add_deviator(T):
return {
'data': tensor.deviatoric(T['data']),
'label': f"s_{T['label']}",
'meta': {
'unit': T['meta']['unit'],
'description': f"deviator of tensor {T['label']} ({T['meta']['description']})",
'creator': 'add_deviator'
}
}
def add_deviator(self,T):
"""
Add the deviatoric part of a tensor.
Parameters
----------
T : str
Label of tensor dataset.
"""
self._add_generic_pointwise(self._add_deviator,{'T':T})
@staticmethod
def _add_eigenvalue(T_sym,eigenvalue):
if eigenvalue == 'max':
label,p = 'maximum',2
elif eigenvalue == 'mid':
label,p = 'intermediate',1
elif eigenvalue == 'min':
label,p = 'minimum',0
return {
'data': tensor.eigenvalues(T_sym['data'])[:,p],
'label': f"lambda_{eigenvalue}({T_sym['label']})",
'meta' : {
'unit': T_sym['meta']['unit'],
'description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['description']})",
'creator': 'add_eigenvalue'
}
}
def add_eigenvalue(self,T_sym,eigenvalue='max'):
"""
Add eigenvalues of symmetric tensor.
Parameters
----------
T_sym : str
Label of symmetric tensor dataset.
eigenvalue : str, optional
Eigenvalue. Select from 'max', 'mid', 'min'. Defaults to 'max'.
"""
self._add_generic_pointwise(self._add_eigenvalue,{'T_sym':T_sym},{'eigenvalue':eigenvalue})
@staticmethod
def _add_eigenvector(T_sym,eigenvalue):
if eigenvalue == 'max':
label,p = 'maximum',2
elif eigenvalue == 'mid':
label,p = 'intermediate',1
elif eigenvalue == 'min':
label,p = 'minimum',0
return {
'data': tensor.eigenvectors(T_sym['data'])[:,p],
'label': f"v_{eigenvalue}({T_sym['label']})",
'meta' : {
'unit': '1',
'description': f"eigenvector corresponding to {label} eigenvalue"
f" of {T_sym['label']} ({T_sym['meta']['description']})",
'creator': 'add_eigenvector'
}
}
def add_eigenvector(self,T_sym,eigenvalue='max'):
"""
Add eigenvector of symmetric tensor.
Parameters
----------
T_sym : str
Label of symmetric tensor dataset.
eigenvalue : str, optional
Eigenvalue to which the eigenvector corresponds.
Select from 'max', 'mid', 'min'. Defaults to 'max'.
"""
self._add_generic_pointwise(self._add_eigenvector,{'T_sym':T_sym},{'eigenvalue':eigenvalue})
@staticmethod
def _add_IPF_color(l,q):
m = util.scale_to_coprime(np.array(l))
try:
lattice = {'fcc':'cF','bcc':'cI','hex':'hP'}[q['meta']['lattice']]
except KeyError:
lattice = q['meta']['lattice']
try:
o = Orientation(rotation = (rfn.structured_to_unstructured(q['data'])),lattice=lattice)
except ValueError:
o = Orientation(rotation = q['data'],lattice=lattice)
return {
'data': np.uint8(o.IPF_color(l)*255),
'label': 'IPFcolor_({} {} {})'.format(*m),
'meta' : {
'unit': '8-bit RGB',
'lattice': q['meta']['lattice'],
'description': 'Inverse Pole Figure (IPF) colors along sample direction ({} {} {})'.format(*m),
'creator': 'add_IPF_color'
}
}
def add_IPF_color(self,l,q='O'):
"""
Add RGB color tuple of inverse pole figure (IPF) color.
Parameters
----------
l : numpy.array of shape (3)
Lab frame direction for inverse pole figure.
q : str
Label of the dataset containing the crystallographic orientation as quaternions.
Defaults to 'O'.
"""
self._add_generic_pointwise(self._add_IPF_color,{'q':q},{'l':l})
@staticmethod
def _add_maximum_shear(T_sym):
return {
'data': mechanics.maximum_shear(T_sym['data']),
'label': f"max_shear({T_sym['label']})",
'meta': {
'unit': T_sym['meta']['unit'],
'description': f"maximum shear component of {T_sym['label']} ({T_sym['meta']['description']})",
'creator': 'add_maximum_shear'
}
}
def add_maximum_shear(self,T_sym):
"""
Add maximum shear components of symmetric tensor.
Parameters
----------
T_sym : str
Label of symmetric tensor dataset.
"""
self._add_generic_pointwise(self._add_maximum_shear,{'T_sym':T_sym})
@staticmethod
def _add_equivalent_Mises(T_sym,kind):
k = kind
if k is None:
if T_sym['meta']['unit'] == '1':
k = 'strain'
elif T_sym['meta']['unit'] == 'Pa':
k = 'stress'
if k not in ['stress', 'strain']:
raise ValueError(f'invalid von Mises kind {kind}')
return {
'data': (mechanics.equivalent_strain_Mises if k=='strain' else \
mechanics.equivalent_stress_Mises)(T_sym['data']),
'label': f"{T_sym['label']}_vM",
'meta': {
'unit': T_sym['meta']['unit'],
'description': f"Mises equivalent {k} of {T_sym['label']} ({T_sym['meta']['description']})",
'creator': 'add_Mises'
}
}
def add_equivalent_Mises(self,T_sym,kind=None):
"""
Add the equivalent Mises stress or strain of a symmetric tensor.
Parameters
----------
T_sym : str
Label of symmetric tensorial stress or strain dataset.
kind : {'stress', 'strain', None}, optional
Kind of the von Mises equivalent. Defaults to None, in which case
it is selected based on the unit of the dataset ('1' -> strain, 'Pa' -> stress).
"""
self._add_generic_pointwise(self._add_equivalent_Mises,{'T_sym':T_sym},{'kind':kind})
@staticmethod
def _add_norm(x,ord):
o = ord
if len(x['data'].shape) == 2:
axis = 1
t = 'vector'
if o is None: o = 2
elif len(x['data'].shape) == 3:
axis = (1,2)
t = 'tensor'
if o is None: o = 'fro'
else:
raise ValueError
return {
'data': np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
'label': f"|{x['label']}|_{o}",
'meta': {
'unit': x['meta']['unit'],
'description': f"{o}-norm of {t} {x['label']} ({x['meta']['description']})",
'creator': 'add_norm'
}
}
def add_norm(self,x,ord=None):
"""
Add the norm of vector or tensor.
Parameters
----------
x : str
Label of vector or tensor dataset.
ord : {non-zero int, inf, -inf, 'fro', 'nuc'}, optional
Order of the norm. inf means NumPys inf object. For details refer to numpy.linalg.norm.
"""
self._add_generic_pointwise(self._add_norm,{'x':x},{'ord':ord})
@staticmethod
def _add_stress_second_Piola_Kirchhoff(P,F):
return {
'data': mechanics.stress_second_Piola_Kirchhoff(P['data'],F['data']),
'label': 'S',
'meta': {
'unit': P['meta']['unit'],
'description': "second Piola-Kirchhoff stress calculated "
f"from {P['label']} ({P['meta']['description']})"
f" and {F['label']} ({F['meta']['description']})",
'creator': 'add_stress_second_Piola_Kirchhoff'
}
}
def add_stress_second_Piola_Kirchhoff(self,P='P',F='F'):
"""
Add second Piola-Kirchhoff stress calculated from first Piola-Kirchhoff stress and deformation gradient.
Parameters
----------
P : str, optional
Label of first Piola-Kirchhoff stress dataset. Defaults to 'P'.
F : str, optional
Label of deformation gradient dataset. Defaults to 'F'.
"""
self._add_generic_pointwise(self._add_stress_second_Piola_Kirchhoff,{'P':P,'F':F})
# The add_pole functionality needs discussion.
# The new Crystal object can perform such a calculation but the outcome depends on the lattice parameters
# as well as on whether a direction or plane is concerned (see the DAMASK_examples/pole_figure notebook).
# Below code appears to be too simplistic.
# @staticmethod
# def _add_pole(q,p,polar):
# pole = np.array(p)
# unit_pole = pole/np.linalg.norm(pole)
# m = util.scale_to_coprime(pole)
# rot = Rotation(q['data'].view(np.double).reshape(-1,4))
#
# rotatedPole = rot @ np.broadcast_to(unit_pole,rot.shape+(3,)) # rotate pole according to crystal orientation
# xy = rotatedPole[:,0:2]/(1.+abs(unit_pole[2])) # stereographic projection
# coords = xy if not polar else \
# np.block([np.sqrt(xy[:,0:1]*xy[:,0:1]+xy[:,1:2]*xy[:,1:2]),np.arctan2(xy[:,1:2],xy[:,0:1])])
# return {
# 'data': coords,
# 'label': 'p^{}_[{} {} {})'.format(u'rφ' if polar else 'xy',*m),
# 'meta' : {
# 'unit': '1',
# 'description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
# .format('Polar' if polar else 'Cartesian'),
# 'creator': 'add_pole'
# }
# }
# def add_pole(self,q,p,polar=False):
# """
# Add coordinates of stereographic projection of given pole in crystal frame.
#
# Parameters
# ----------
# q : str
# Label of the dataset containing the crystallographic orientation as quaternions.
# p : numpy.array of shape (3)
# Crystallographic direction or plane.
# polar : bool, optional
# Give pole in polar coordinates. Defaults to False.
#
# """
# self._add_generic_pointwise(self._add_pole,{'q':q},{'p':p,'polar':polar})
@staticmethod
def _add_rotation(F):
return {
'data': mechanics.rotation(F['data']).as_matrix(),
'label': f"R({F['label']})",
'meta': {
'unit': F['meta']['unit'],
'description': f"rotational part of {F['label']} ({F['meta']['description']})",
'creator': 'add_rotation'
}
}
def add_rotation(self,F):
"""
Add rotational part of a deformation gradient.
Parameters
----------
F : str, optional
Label of deformation gradient dataset.
"""
self._add_generic_pointwise(self._add_rotation,{'F':F})
@staticmethod
def _add_spherical(T):
return {
'data': tensor.spherical(T['data'],False),
'label': f"p_{T['label']}",
'meta': {
'unit': T['meta']['unit'],
'description': f"spherical component of tensor {T['label']} ({T['meta']['description']})",
'creator': 'add_spherical'
}
}
def add_spherical(self,T):
"""
Add the spherical (hydrostatic) part of a tensor.
Parameters
----------
T : str
Label of tensor dataset.
"""
self._add_generic_pointwise(self._add_spherical,{'T':T})
@staticmethod
def _add_strain(F,t,m):
return {
'data': mechanics.strain(F['data'],t,m),
'label': f"epsilon_{t}^{m}({F['label']})",
'meta': {
'unit': F['meta']['unit'],
'description': f"strain tensor of {F['label']} ({F['meta']['description']})",
'creator': 'add_strain'
}
}
def add_strain(self,F='F',t='V',m=0.0):
"""
Add strain tensor of a deformation gradient.
For details, see damask.mechanics.strain.
Parameters
----------
F : str, optional
Label of deformation gradient dataset. Defaults to 'F'.
t : {'V', 'U'}, optional
Type of the polar decomposition, 'V' for left stretch tensor and 'U' for right stretch tensor.
Defaults to 'V'.
m : float, optional
Order of the strain calculation. Defaults to 0.0.
"""
self._add_generic_pointwise(self._add_strain,{'F':F},{'t':t,'m':m})
@staticmethod
def _add_stretch_tensor(F,t):
return {
'data': (mechanics.stretch_left if t.upper() == 'V' else mechanics.stretch_right)(F['data']),
'label': f"{t}({F['label']})",
'meta': {
'unit': F['meta']['unit'],
'description': '{} stretch tensor of {} ({})'.format('left' if t.upper() == 'V' else 'right',
F['label'],F['meta']['description']),
'creator': 'add_stretch_tensor'
}
}
def add_stretch_tensor(self,F='F',t='V'):
"""
Add stretch tensor of a deformation gradient.
Parameters
----------
F : str, optional
Label of deformation gradient dataset. Defaults to 'F'.
t : {'V', 'U'}, optional
Type of the polar decomposition, 'V' for left stretch tensor and 'U' for right stretch tensor.
Defaults to 'V'.
"""
self._add_generic_pointwise(self._add_stretch_tensor,{'F':F},{'t':t})
def _job(self,group,func,datasets,args,lock):
"""Execute job for _add_generic_pointwise."""
try:
datasets_in = {}
lock.acquire()
with h5py.File(self.fname,'r') as f:
for arg,label in datasets.items():
loc = f[group+'/'+label]
datasets_in[arg]={'data' :loc[()],
'label':label,
'meta': {k:(v if h5py3 else v.decode()) for k,v in loc.attrs.items()}}
lock.release()
r = func(**datasets_in,**args)
return [group,r]
except Exception as err:
print(f'Error during calculation: {err}.')
return None
def _add_generic_pointwise(self,func,datasets,args={}):
"""
General function to add pointwise data.
Parameters
----------
func : function
Callback function that calculates a new dataset from one or
more datasets per HDF5 group.
datasets : dictionary
Details of the datasets to be used:
{arg (name to which the data is passed in func): label (in HDF5 file)}.
args : dictionary, optional
Arguments parsed to func.
"""
chunk_size = 1024**2//8
pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',1)))
lock = mp.Manager().Lock()
groups = []
with h5py.File(self.fname,'r') as f:
for inc in self.visible['increments']:
for ty in ['phase','homogenization']:
for label in self.visible[ty+'s']:
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
group = '/'.join([inc,ty,label,field])
if set(datasets.values()).issubset(f[group].keys()): groups.append(group)
if len(groups) == 0:
print('No matching dataset found, no data was added.')
return
default_arg = partial(self._job,func=func,datasets=datasets,args=args,lock=lock)
for result in util.show_progress(pool.imap_unordered(default_arg,groups),len(groups)):
if not result:
continue
lock.acquire()
with h5py.File(self.fname, 'a') as f:
try:
if self._allow_modification and result[0]+'/'+result[1]['label'] in f:
dataset = f[result[0]+'/'+result[1]['label']]
dataset[...] = result[1]['data']
dataset.attrs['overwritten'] = True
else:
if result[1]['data'].size >= chunk_size*2:
shape = result[1]['data'].shape
chunks = (chunk_size//np.prod(shape[1:]),)+shape[1:]
dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'],
maxshape=shape, chunks=chunks,
compression='gzip', compression_opts=6,
shuffle=True,fletcher32=True)
else:
dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'])
now = datetime.datetime.now().astimezone()
dataset.attrs['created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \
now.strftime('%Y-%m-%d %H:%M:%S%z').encode()
for l,v in result[1]['meta'].items():
dataset.attrs[l.lower()]=v if h5py3 else v.encode()
creator = dataset.attrs['creator'] if h5py3 else \
dataset.attrs['creator'].decode()
dataset.attrs['creator'] = f'damask.Result.{creator} v{damask.version}' if h5py3 else \
f'damask.Result.{creator} v{damask.version}'.encode()
except (OSError,RuntimeError) as err:
print(f'Could not add dataset: {err}.')
lock.release()
pool.close()
pool.join()
def save_XDMF(self,output='*'):
"""
Write XDMF file to directly visualize data in DADF5 file.
Parameters
----------
output : (list of) str
Labels of the datasets to read.
Defaults to '*', in which case all datasets are considered.
"""
u = 'Unit' if self.version_minor < 12 else 'unit' # compatibility hack
if self.N_constituents != 1 or len(self.phases) != 1 or not self.structured:
raise TypeError('XDMF output requires structured grid with single phase and single constituent.')
attribute_type_map = defaultdict(lambda:'Matrix', ( ((),'Scalar'), ((3,),'Vector'), ((3,3),'Tensor')) )
def number_type_map(dtype):
if dtype in np.sctypes['int']: return 'Int'
if dtype in np.sctypes['uint']: return 'UInt'
if dtype in np.sctypes['float']: return 'Float'
xdmf = ET.Element('Xdmf')
xdmf.attrib={'Version': '2.0',
'xmlns:xi': 'http://www.w3.org/2001/XInclude'}
domain = ET.SubElement(xdmf, 'Domain')
collection = ET.SubElement(domain, 'Grid')
collection.attrib={'GridType': 'Collection',
'CollectionType': 'Temporal',
'Name': 'Increments'}
time = ET.SubElement(collection, 'Time')
time.attrib={'TimeType': 'List'}
time_data = ET.SubElement(time, 'DataItem')
times = [self.times[self.increments.index(i)] for i in self.visible['increments']]
time_data.attrib={'Format': 'XML',
'NumberType': 'Float',
'Dimensions': f'{len(times)}'}
time_data.text = ' '.join(map(str,times))
attributes = []
data_items = []
with h5py.File(self.fname,'r') as f:
for inc in self.visible['increments']:
grid = ET.SubElement(collection,'Grid')
grid.attrib = {'GridType': 'Uniform',
'Name': inc}
topology = ET.SubElement(grid, 'Topology')
topology.attrib = {'TopologyType': '3DCoRectMesh',
'Dimensions': '{} {} {}'.format(*(self.cells+1))}
geometry = ET.SubElement(grid, 'Geometry')
geometry.attrib = {'GeometryType':'Origin_DxDyDz'}
origin = ET.SubElement(geometry, 'DataItem')
origin.attrib = {'Format': 'XML',
'NumberType': 'Float',
'Dimensions': '3'}
origin.text = "{} {} {}".format(*self.origin)
delta = ET.SubElement(geometry, 'DataItem')
delta.attrib = {'Format': 'XML',
'NumberType': 'Float',
'Dimensions': '3'}
delta.text="{} {} {}".format(*(self.size/self.cells))
attributes.append(ET.SubElement(grid, 'Attribute'))
attributes[-1].attrib = {'Name': 'u / m',
'Center': 'Node',
'AttributeType': 'Vector'}
data_items.append(ET.SubElement(attributes[-1], 'DataItem'))
data_items[-1].attrib = {'Format': 'HDF',
'Precision': '8',
'Dimensions': '{} {} {} 3'.format(*(self.cells+1))}
data_items[-1].text = f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n'
for ty in ['phase','homogenization']:
for label in self.visible[ty+'s']:
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
for out in _match(output,f['/'.join([inc,ty,label,field])].keys()):
name = '/'.join([inc,ty,label,field,out])
shape = f[name].shape[1:]
dtype = f[name].dtype
unit = f[name].attrs[u] if h5py3 else f[name].attrs[u].decode()
attributes.append(ET.SubElement(grid, 'Attribute'))
attributes[-1].attrib = {'Name': '/'.join([ty,field,out])+f' / {unit}',
'Center': 'Cell',
'AttributeType': attribute_type_map[shape]}
data_items.append(ET.SubElement(attributes[-1], 'DataItem'))
data_items[-1].attrib = {'Format': 'HDF',
'NumberType': number_type_map(dtype),
'Precision': f'{dtype.itemsize}',
'Dimensions': '{} {} {} {}'.format(*self.cells,1 if shape == () else
np.prod(shape))}
data_items[-1].text = f'{os.path.split(self.fname)[1]}:{name}'
with open(self.fname.with_suffix('.xdmf').name,'w',newline='\n') as f:
f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
def _mappings(self):
grp = 'mapping' if self.version_minor < 12 else 'cell_to' # compatibility hack
name = 'Name' if self.version_minor < 12 else 'label' # compatibility hack
member = 'member' if self.version_minor < 12 else 'entry' # compatibility hack
with h5py.File(self.fname,'r') as f:
at_cell_ph = []
in_data_ph = []
for c in range(self.N_constituents):
at_cell_ph.append({label: np.where(f['/'.join([grp,'phase'])][:,c][name] == label.encode())[0] \
for label in self.visible['phases']})
in_data_ph.append({label: f['/'.join([grp,'phase'])][member][at_cell_ph[c][label]][:,c] \
for label in self.visible['phases']})
at_cell_ho = {label: np.where(f['/'.join([grp,'homogenization'])][:][name] == label.encode())[0] \
for label in self.visible['homogenizations']}
in_data_ho = {label: f['/'.join([grp,'homogenization'])][member][at_cell_ho[label]] \
for label in self.visible['homogenizations']}
return at_cell_ph,in_data_ph,at_cell_ho,in_data_ho
def save_VTK(self,output='*',mode='cell',constituents=None,fill_float=np.nan,fill_int=0,parallel=True):
"""
Export to VTK cell/point data.
Parameters
----------
output : (list of) str, optional
Labels of the datasets to place.
Defaults to '*', in which case all datasets are exported.
mode : {'cell', 'point'}
Export in cell format or point format.
Defaults to 'cell'.
constituents : (list of) int, optional
Constituents to consider.
Defaults to None, in which case all constituents are considered.
fill_float : float
Fill value for non-existent entries of floating point type.
Defaults to NaN.
fill_int : int
Fill value for non-existent entries of integer type.
Defaults to 0.
parallel : bool
Write out VTK files in parallel in a separate background process.
Defaults to True.
"""
if mode.lower()=='cell':
v = self.geometry0
elif mode.lower()=='point':
v = VTK.from_poly_data(self.coordinates0_point)
ln = 3 if self.version_minor < 12 else 10 # compatibility hack
N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][ln:])))))+1
constituents_ = constituents if isinstance(constituents,Iterable) else \
(range(self.N_constituents) if constituents is None else [constituents])
suffixes = [''] if self.N_constituents == 1 or isinstance(constituents,int) else \
[f'#{c}' for c in constituents_]
at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings()
with h5py.File(self.fname,'r') as f:
for inc in util.show_progress(self.visible['increments']):
u = _read(f['/'.join([inc,'geometry','u_n' if mode.lower() == 'cell' else 'u_p'])])
v.add(u,'u')
for ty in ['phase','homogenization']:
for field in self.visible['fields']:
outs = {}
for label in self.visible[ty+'s']:
if field not in f['/'.join([inc,ty,label])].keys(): continue
for out in _match(output,f['/'.join([inc,ty,label,field])].keys()):
data = ma.array(_read(f['/'.join([inc,ty,label,field,out])]))
if ty == 'phase':
if out+suffixes[0] not in outs.keys():
for c,suffix in zip(constituents_,suffixes):
outs[out+suffix] = \
_empty_like(data,self.N_materialpoints,fill_float,fill_int)
for c,suffix in zip(constituents_,suffixes):
outs[out+suffix][at_cell_ph[c][label]] = data[in_data_ph[c][label]]
if ty == 'homogenization':
if out not in outs.keys():
outs[out] = _empty_like(data,self.N_materialpoints,fill_float,fill_int)
outs[out][at_cell_ho[label]] = data[in_data_ho[label]]
for label,dataset in outs.items():
v.add(dataset,' / '.join(['/'.join([ty,field,label]),dataset.dtype.metadata['unit']]))
v.save(f'{self.fname.stem}_inc{inc[ln:].zfill(N_digits)}',parallel=parallel)
def get(self,output='*',flatten=True,prune=True):
"""
Collect data per phase/homogenization reflecting the group/folder structure in the DADF5 file.
Parameters
----------
output : (list of) str
Labels of the datasets to read.
Defaults to '*', in which case all datasets are read.
flatten : bool
Remove singular levels of the folder hierarchy.
This might be beneficial in case of single increment,
phase/homogenization, or field. Defaults to True.
prune : bool
Remove branches with no data. Defaults to True.
Returns
-------
data : dict of numpy.ndarray
Datasets structured by phase/homogenization and according to selected view.
"""
r = {}
with h5py.File(self.fname,'r') as f:
for inc in util.show_progress(self.visible['increments']):
r[inc] = {'phase':{},'homogenization':{},'geometry':{}}
for out in _match(output,f['/'.join([inc,'geometry'])].keys()):
r[inc]['geometry'][out] = _read(f['/'.join([inc,'geometry',out])])
for ty in ['phase','homogenization']:
for label in self.visible[ty+'s']:
r[inc][ty][label] = {}
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
r[inc][ty][label][field] = {}
for out in _match(output,f['/'.join([inc,ty,label,field])].keys()):
r[inc][ty][label][field][out] = _read(f['/'.join([inc,ty,label,field,out])])
if prune: r = util.dict_prune(r)
if flatten: r = util.dict_flatten(r)
return None if (type(r) == dict and r == {}) else r
def place(self,output='*',flatten=True,prune=True,constituents=None,fill_float=np.nan,fill_int=0):
"""
Merge data into spatial order that is compatible with the damask.VTK geometry representation.
The returned data structure reflects the group/folder structure
in the DADF5 file.
Multi-phase data is fused into a single output.
`place` is equivalent to `read` if only one phase/homogenization
and one constituent is present.
Parameters
----------
output : (list of) str, optional
Labels of the datasets to place.
Defaults to '*', in which case all datasets are placed.
flatten : bool
Remove singular levels of the folder hierarchy.
This might be beneficial in case of single increment or field.
Defaults to True.
prune : bool
Remove branches with no data. Defaults to True.
constituents : (list of) int, optional
Constituents to consider.
Defaults to 'None', in which case all constituents are considered.
fill_float : float
Fill value for non-existent entries of floating point type.
Defaults to NaN.
fill_int : int
Fill value for non-existent entries of integer type.
Defaults to 0.
Returns
-------
data : dict of numpy.ma.MaskedArray
Datasets structured by spatial position and according to selected view.
"""
r = {}
constituents_ = constituents if isinstance(constituents,Iterable) else \
(range(self.N_constituents) if constituents is None else [constituents])
suffixes = [''] if self.N_constituents == 1 or isinstance(constituents,int) else \
[f'#{c}' for c in constituents_]
at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings()
with h5py.File(self.fname,'r') as f:
for inc in util.show_progress(self.visible['increments']):
r[inc] = {'phase':{},'homogenization':{},'geometry':{}}
for out in _match(output,f['/'.join([inc,'geometry'])].keys()):
r[inc]['geometry'][out] = ma.array(_read(f['/'.join([inc,'geometry',out])]),fill_value = fill_float)
for ty in ['phase','homogenization']:
for label in self.visible[ty+'s']:
for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
if field not in r[inc][ty].keys():
r[inc][ty][field] = {}
for out in _match(output,f['/'.join([inc,ty,label,field])].keys()):
data = ma.array(_read(f['/'.join([inc,ty,label,field,out])]))
if ty == 'phase':
if out+suffixes[0] not in r[inc][ty][field].keys():
for c,suffix in zip(constituents_,suffixes):
r[inc][ty][field][out+suffix] = \
_empty_like(data,self.N_materialpoints,fill_float,fill_int)
for c,suffix in zip(constituents_,suffixes):
r[inc][ty][field][out+suffix][at_cell_ph[c][label]] = data[in_data_ph[c][label]]
if ty == 'homogenization':
if out not in r[inc][ty][field].keys():
r[inc][ty][field][out] = \
_empty_like(data,self.N_materialpoints,fill_float,fill_int)
r[inc][ty][field][out][at_cell_ho[label]] = data[in_data_ho[label]]
if prune: r = util.dict_prune(r)
if flatten: r = util.dict_flatten(r)
return None if (type(r) == dict and r == {}) else r