new functions (takeover from old branch)
This commit is contained in:
Martin Diehl
parent
e46395be41
commit
5822ad8b05
|
|
@ -16,23 +16,23 @@ from . import mechanics
|
|||
class DADF5():
|
||||
"""
|
||||
Read and write to DADF5 files.
|
||||
|
||||
|
||||
DADF5 files contain DAMASK results.
|
||||
"""
|
||||
|
||||
|
||||
# ------------------------------------------------------------------
|
||||
def __init__(self,fname):
|
||||
"""
|
||||
Opens an existing DADF5 file.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str
|
||||
name of the DADF5 file to be openend.
|
||||
|
||||
|
||||
"""
|
||||
with h5py.File(fname,'r') as f:
|
||||
|
||||
|
||||
try:
|
||||
self.version_major = f.attrs['DADF5_version_major']
|
||||
self.version_minor = f.attrs['DADF5_version_minor']
|
||||
|
|
@ -43,16 +43,16 @@ class DADF5():
|
|||
if self.version_major != 0 or not 2 <= self.version_minor <= 6:
|
||||
raise TypeError('Unsupported DADF5 version {}.{} '.format(f.attrs['DADF5_version_major'],
|
||||
f.attrs['DADF5_version_minor']))
|
||||
|
||||
|
||||
self.structured = 'grid' in f['geometry'].attrs.keys()
|
||||
|
||||
|
||||
if self.structured:
|
||||
self.grid = f['geometry'].attrs['grid']
|
||||
self.size = f['geometry'].attrs['size']
|
||||
if self.version_major == 0 and self.version_minor >= 5:
|
||||
self.origin = f['geometry'].attrs['origin']
|
||||
|
||||
|
||||
|
||||
r=re.compile('inc[0-9]+')
|
||||
increments_unsorted = {int(i[3:]):i for i in f.keys() if r.match(i)}
|
||||
self.increments = [increments_unsorted[i] for i in sorted(increments_unsorted)]
|
||||
|
|
@ -78,23 +78,23 @@ class DADF5():
|
|||
'constituent': range(self.Nconstituents), # ToDo: stupid naming
|
||||
'con_physics': self.con_physics,
|
||||
'mat_physics': self.mat_physics}
|
||||
|
||||
|
||||
self.fname = fname
|
||||
|
||||
|
||||
def __manage_visible(self,datasets,what,action):
|
||||
"""
|
||||
Manages the visibility of the groups.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
datasets : list of str or Boolean
|
||||
name of datasets as list, supports ? and * wildcards.
|
||||
True is equivalent to [*], False is equivalent to []
|
||||
what : str
|
||||
attribute to change (must be in self.visible)
|
||||
attribute to change (must be in self.visible)
|
||||
action : str
|
||||
select from 'set', 'add', and 'del'
|
||||
select from 'set', 'add', and 'del'
|
||||
|
||||
"""
|
||||
# allow True/False and string arguments
|
||||
|
|
@ -103,7 +103,7 @@ class DADF5():
|
|||
elif datasets is False:
|
||||
datasets = []
|
||||
choice = [datasets] if isinstance(datasets,str) else datasets
|
||||
|
||||
|
||||
valid = [e for e_ in [glob.fnmatch.filter(getattr(self,what),s) for s in choice] for e in e_]
|
||||
existing = set(self.visible[what])
|
||||
|
||||
|
|
@ -113,8 +113,8 @@ class DADF5():
|
|||
self.visible[what] = list(existing.union(valid))
|
||||
elif action == 'del':
|
||||
self.visible[what] = list(existing.difference_update(valid))
|
||||
|
||||
|
||||
|
||||
|
||||
def __time_to_inc(self,start,end):
|
||||
selected = []
|
||||
for i,time in enumerate(self.times):
|
||||
|
|
@ -166,8 +166,8 @@ class DADF5():
|
|||
|
||||
"""
|
||||
self.__manage_visible(self.__time_to_inc(start,end),'increments','del')
|
||||
|
||||
|
||||
|
||||
|
||||
def set_by_increment(self,start,end):
|
||||
"""
|
||||
Set active time increments based on start and end increment.
|
||||
|
|
@ -229,7 +229,7 @@ class DADF5():
|
|||
Parameters
|
||||
----------
|
||||
what : str
|
||||
attribute to change (must be in self.visible)
|
||||
attribute to change (must be in self.visible)
|
||||
|
||||
"""
|
||||
datasets = self.visible[what]
|
||||
|
|
@ -242,19 +242,19 @@ class DADF5():
|
|||
last_datasets = self.visible[what]
|
||||
yield dataset
|
||||
self.__manage_visible(datasets,what,'set')
|
||||
|
||||
|
||||
|
||||
|
||||
def set_visible(self,what,datasets):
|
||||
"""
|
||||
Set active groups.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
datasets : list of str or Boolean
|
||||
name of datasets as list, supports ? and * wildcards.
|
||||
True is equivalent to [*], False is equivalent to []
|
||||
what : str
|
||||
attribute to change (must be in self.visible)
|
||||
attribute to change (must be in self.visible)
|
||||
|
||||
"""
|
||||
self.__manage_visible(datasets,what,'set')
|
||||
|
|
@ -263,14 +263,14 @@ class DADF5():
|
|||
def add_visible(self,what,datasets):
|
||||
"""
|
||||
Add to active groups.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
datasets : list of str or Boolean
|
||||
name of datasets as list, supports ? and * wildcards.
|
||||
True is equivalent to [*], False is equivalent to []
|
||||
what : str
|
||||
attribute to change (must be in self.visible)
|
||||
attribute to change (must be in self.visible)
|
||||
|
||||
"""
|
||||
self.__manage_visible(datasets,what,'add')
|
||||
|
|
@ -279,14 +279,14 @@ class DADF5():
|
|||
def del_visible(self,what,datasets):
|
||||
"""
|
||||
Delete from active groupse.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
datasets : list of str or Boolean
|
||||
name of datasets as list, supports ? and * wildcards.
|
||||
True is equivalent to [*], False is equivalent to []
|
||||
what : str
|
||||
attribute to change (must be in self.visible)
|
||||
attribute to change (must be in self.visible)
|
||||
|
||||
"""
|
||||
self.__manage_visible(datasets,what,'del')
|
||||
|
|
@ -295,17 +295,17 @@ class DADF5():
|
|||
def groups_with_datasets(self,datasets):
|
||||
"""
|
||||
Get groups that contain all requested datasets.
|
||||
|
||||
Only groups within inc?????/constituent/*_*/* inc?????/materialpoint/*_*/*
|
||||
|
||||
Only groups within inc?????/constituent/*_*/* inc?????/materialpoint/*_*/*
|
||||
are considered as they contain the data.
|
||||
Single strings will be treated as list with one entry.
|
||||
|
||||
|
||||
Wild card matching is allowed, but the number of arguments need to fit.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
datasets : iterable or str or boolean
|
||||
|
||||
|
||||
Examples
|
||||
--------
|
||||
datasets = False matches no group
|
||||
|
|
@ -315,13 +315,13 @@ class DADF5():
|
|||
datasets = ['*'] does not match a group with ['F','P','sigma']
|
||||
datasets = ['*','*'] does not match a group with ['F','P','sigma']
|
||||
datasets = ['*','*','*'] matches a group with ['F','P','sigma']
|
||||
|
||||
|
||||
"""
|
||||
if datasets is False: return []
|
||||
sets = [datasets] if isinstance(datasets,str) else datasets
|
||||
|
||||
groups = []
|
||||
|
||||
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
for i in self.iter_visible('increments'):
|
||||
for o,p in zip(['constituents','materialpoints'],['con_physics','mat_physics']):
|
||||
|
|
@ -378,8 +378,8 @@ class DADF5():
|
|||
except KeyError as e:
|
||||
pass
|
||||
return path
|
||||
|
||||
|
||||
|
||||
|
||||
def get_constituent_ID(self,c=0):
|
||||
"""Pointwise constituent ID."""
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
|
|
@ -396,7 +396,7 @@ class DADF5():
|
|||
def read_dataset(self,path,c=0,plain=False):
|
||||
"""
|
||||
Dataset for all points/cells.
|
||||
|
||||
|
||||
If more than one path is given, the dataset is composed of the individual contributions.
|
||||
"""
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
|
|
@ -405,11 +405,11 @@ class DADF5():
|
|||
dataset = np.full(shape,np.nan,dtype=np.dtype(f[path[0]]))
|
||||
for pa in path:
|
||||
label = pa.split('/')[2]
|
||||
|
||||
|
||||
if (pa.split('/')[1] == 'geometry'):
|
||||
dataset = np.array(f[pa])
|
||||
continue
|
||||
|
||||
|
||||
p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label))[0]
|
||||
if len(p)>0:
|
||||
u = (f['mapping/cellResults/constituent']['Position'][p,c])
|
||||
|
|
@ -425,7 +425,7 @@ class DADF5():
|
|||
if len(a.shape) == 1:
|
||||
a=a.reshape([a.shape[0],1])
|
||||
dataset[p,:] = a[u,:]
|
||||
|
||||
|
||||
if plain and dataset.dtype.names is not None:
|
||||
return dataset.view(('float64',len(dataset.dtype.names)))
|
||||
else:
|
||||
|
|
@ -444,8 +444,8 @@ class DADF5():
|
|||
else:
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
return f['geometry/x_c'][()]
|
||||
|
||||
|
||||
|
||||
|
||||
def add_absolute(self,x):
|
||||
"""
|
||||
Add absolute value.
|
||||
|
|
@ -469,14 +469,14 @@ class DADF5():
|
|||
}
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
|
||||
self.__add_generic_pointwise(__add_absolute,requested)
|
||||
|
||||
|
||||
|
||||
def add_calculation(self,formula,label,unit='n/a',description=None,vectorized=True):
|
||||
"""
|
||||
Add result of a general formula.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
formula : str
|
||||
|
|
@ -493,15 +493,15 @@ class DADF5():
|
|||
"""
|
||||
if vectorized is False:
|
||||
raise NotImplementedError
|
||||
|
||||
|
||||
def __add_calculation(**kwargs):
|
||||
|
||||
|
||||
formula = kwargs['formula']
|
||||
for d in re.findall(r'#(.*?)#',formula):
|
||||
formula = formula.replace('#{}#'.format(d),"kwargs['{}']['data']".format(d))
|
||||
|
||||
|
||||
return {
|
||||
'data': eval(formula),
|
||||
'data': eval(formula),
|
||||
'label': kwargs['label'],
|
||||
'meta': {
|
||||
'Unit': kwargs['unit'],
|
||||
|
|
@ -509,17 +509,17 @@ class DADF5():
|
|||
'Creator': 'dadf5.py:add_calculation v{}'.format(version)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
requested = [{'label':d,'arg':d} for d in set(re.findall(r'#(.*?)#',formula))] # datasets used in the formula
|
||||
pass_through = {'formula':formula,'label':label,'unit':unit,'description':description}
|
||||
|
||||
pass_through = {'formula':formula,'label':label,'unit':unit,'description':description}
|
||||
|
||||
self.__add_generic_pointwise(__add_calculation,requested,pass_through)
|
||||
|
||||
|
||||
def add_Cauchy(self,P='P',F='F'):
|
||||
"""
|
||||
Add Cauchy stress calculated from 1. Piola-Kirchhoff stress and deformation gradient.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
P : str, optional
|
||||
|
|
@ -535,15 +535,17 @@ class DADF5():
|
|||
'label': 'sigma',
|
||||
'meta': {
|
||||
'Unit': P['meta']['Unit'],
|
||||
'Description': 'Cauchy stress calculated from {} ({}) '.format(P['label'],P['meta']['Description'])+\
|
||||
'and deformation gradient {} ({})'.format(F['label'],F['meta']['Description']),
|
||||
'Description': 'Cauchy stress calculated from {} ({}) '.format(P['label'],
|
||||
P['meta']['Description'])+\
|
||||
'and deformation gradient {} ({})'.format(F['label'],
|
||||
F['meta']['Description']),
|
||||
'Creator': 'dadf5.py:add_Cauchy v{}'.format(version)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
requested = [{'label':F,'arg':'F'},
|
||||
{'label':P,'arg':'P'} ]
|
||||
|
||||
|
||||
self.__add_generic_pointwise(__add_Cauchy,requested)
|
||||
|
||||
|
||||
|
|
@ -558,7 +560,7 @@ class DADF5():
|
|||
|
||||
"""
|
||||
def __add_determinant(x):
|
||||
|
||||
|
||||
return {
|
||||
'data': np.linalg.det(x['data']),
|
||||
'label': 'det({})'.format(x['label']),
|
||||
|
|
@ -568,9 +570,9 @@ class DADF5():
|
|||
'Creator': 'dadf5.py:add_determinant v{}'.format(version)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
|
||||
self.__add_generic_pointwise(__add_determinant,requested)
|
||||
|
||||
|
||||
|
|
@ -585,10 +587,10 @@ class DADF5():
|
|||
|
||||
"""
|
||||
def __add_deviator(x):
|
||||
|
||||
|
||||
if not np.all(np.array(x['data'].shape[1:]) == np.array([3,3])):
|
||||
raise ValueError
|
||||
|
||||
|
||||
return {
|
||||
'data': mechanics.deviatoric_part(x['data']),
|
||||
'label': 's_{}'.format(x['label']),
|
||||
|
|
@ -598,16 +600,106 @@ class DADF5():
|
|||
'Creator': 'dadf5.py:add_deviator v{}'.format(version)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
|
||||
self.__add_generic_pointwise(__add_deviator,requested)
|
||||
|
||||
|
||||
|
||||
|
||||
def add_eigenvalues(self,x):
|
||||
"""
|
||||
Add eigenvalues of symmetric tensor.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
x : str
|
||||
Label of the dataset containing a symmetric tensor.
|
||||
|
||||
"""
|
||||
def __add_eigenvalue(x):
|
||||
|
||||
return {
|
||||
'data': mechanics.eigenvalues(x['data']),
|
||||
'label': 'lambda({})'.format(x['label']),
|
||||
'meta' : {
|
||||
'Unit': x['meta']['Unit'],
|
||||
'Description': 'Eigenvalues of {} ({})'.format(x['label'],x['meta']['Description']),
|
||||
'Creator': 'dadf5.py:add_eigenvalues v{}'.format(version)
|
||||
}
|
||||
}
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
self.__add_generic_pointwise(__add_eigenvalue,requested)
|
||||
|
||||
|
||||
def add_eigenvectors(self,x):
|
||||
"""
|
||||
Add eigenvectors of symmetric tensor.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
x : str
|
||||
Label of the dataset containing a symmetric tensor.
|
||||
|
||||
"""
|
||||
def __add_eigenvector(x):
|
||||
|
||||
return {
|
||||
'data': mechanics.eigenvectors(x['data']),
|
||||
'label': 'v({})'.format(x['label']),
|
||||
'meta' : {
|
||||
'Unit': '1',
|
||||
'Description': 'Eigenvectors of {} ({})'.format(x['label'],x['meta']['Description']),
|
||||
'Creator': 'dadf5.py:add_eigenvectors v{}'.format(version)
|
||||
}
|
||||
}
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
self.__add_generic_pointwise(__add_eigenvector,requested)
|
||||
|
||||
|
||||
def add_IPFcolor(self,q,p):
|
||||
"""
|
||||
Add RGB color tuple of inverse pole figure (IPF) color.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
orientation : str
|
||||
Label of the dataset containing the orientation data as quaternions.
|
||||
pole : list of int
|
||||
Pole direction as Miller indices. Default value is [0, 0, 1].
|
||||
|
||||
"""
|
||||
def __add_IPFcolor(orientation,pole):
|
||||
|
||||
lattice = orientation['meta']['Lattice']
|
||||
unit_pole = pole/np.linalg.norm(pole)
|
||||
colors = np.empty((len(orientation['data']),3),np.uint8)
|
||||
|
||||
for i,q in enumerate(orientation['data']):
|
||||
rot = Rotation(np.array([q['w'],q['x'],q['y'],q['z']]))
|
||||
orientation = Orientation(rot,lattice = lattice).reduced()
|
||||
colors[i] = np.uint8(orientation.IPFcolor(unit_pole)*255)
|
||||
return {
|
||||
'data': colors,
|
||||
'label': 'IPFcolor_[{} {} {}]'.format(*pole),
|
||||
'meta' : {
|
||||
'Unit': 'RGB (8bit)',
|
||||
'Lattice': lattice,
|
||||
'Description': 'Inverse Pole Figure colors',
|
||||
'Creator': 'dadf5.py:addIPFcolor v{}'.format(version)
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':'orientation','arg':'orientation'}]
|
||||
|
||||
self.__add_generic_pointwise(__add_IPFcolor,requested,{'pole':pole})
|
||||
|
||||
|
||||
def add_maximum_shear(self,x):
|
||||
"""
|
||||
Add maximum shear components of symmetric tensor.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
x : str
|
||||
|
|
@ -634,7 +726,7 @@ class DADF5():
|
|||
def add_Mises(self,x):
|
||||
"""
|
||||
Add the equivalent Mises stress or strain of a symmetric tensor.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
x : str
|
||||
|
|
@ -654,16 +746,94 @@ class DADF5():
|
|||
'Creator': 'dadf5.py:add_Mises v{}'.format(version)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
|
||||
self.__add_generic_pointwise(__add_Mises,requested)
|
||||
|
||||
|
||||
def add_PK2(self,F='F',P='P'):
|
||||
"""
|
||||
Add 2. Piola-Kirchhoff calculated from 1. Piola-Kirchhoff stress and deformation gradient.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
P : str, optional
|
||||
Label of the dataset containing the 1. Piola-Kirchhoff stress. Default value is ‘P’.
|
||||
F : str, optional
|
||||
Label of the dataset containing the deformation gradient. Default value is ‘F’.
|
||||
|
||||
"""
|
||||
def __add_PK2(F,P):
|
||||
|
||||
return {
|
||||
'data': mechanics.PK2(F['data'],P['data']),
|
||||
'label': 'S',
|
||||
'meta': {
|
||||
'Unit': P['meta']['Unit'],
|
||||
'Description': '2. Kirchhoff stress calculated from {} ({}) '.format(P['label'],
|
||||
P['meta']['Description'])+\
|
||||
'and deformation gradient {} ({})'.format(F['label'],
|
||||
F['meta']['Description']),
|
||||
'Creator': 'dadf5.py:add_PK2 v{}'.format(version)
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':F,'arg':'F'},
|
||||
{'label':P,'arg':'P'},]
|
||||
|
||||
self.__add_generic_pointwise(__add_PK2,requested)
|
||||
|
||||
|
||||
def addPole(self,q,p,polar=False):
|
||||
"""
|
||||
Add coordinates of stereographic projection of given direction (pole) in crystal frame.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
q : str
|
||||
Label of the dataset containing the crystallographic orientation as a quaternion.
|
||||
p : numpy.array of shape (3)
|
||||
Pole (direction) in crystal frame.
|
||||
polar : bool, optional
|
||||
Give pole in polar coordinates. Default is false.
|
||||
|
||||
"""
|
||||
def __addPole(orientation,pole):
|
||||
|
||||
pole = np.array(pole)
|
||||
unit_pole /= np.linalg.norm(pole)
|
||||
coords = np.empty((len(orientation['data']),2))
|
||||
|
||||
for i,q in enumerate(orientation['data']):
|
||||
o = Rotation(np.array([q['w'],q['x'],q['y'],q['z']]))
|
||||
rotatedPole = o*pole # rotate pole according to crystal orientation
|
||||
(x,y) = rotatedPole[0:2]/(1.+abs(pole[2])) # stereographic projection
|
||||
|
||||
if polar is True:
|
||||
coords[i] = [np.sqrt(x*x+y*y),np.arctan2(y,x)]
|
||||
else:
|
||||
coords[i] = [x,y]
|
||||
|
||||
return {
|
||||
'data': coords,
|
||||
'label': 'Pole',
|
||||
'meta' : {
|
||||
'Unit': '1',
|
||||
'Description': 'Coordinates of stereographic projection of given direction (pole) in crystal frame',
|
||||
'Creator' : 'dadf5.py:addPole v{}'.format(version)
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':'orientation','arg':'orientation'}]
|
||||
|
||||
self.__add_generic_pointwise(__addPole,requested,{'pole':pole})
|
||||
|
||||
|
||||
def add_norm(self,x,ord=None):
|
||||
"""
|
||||
Add the norm of vector or tensor.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
x : str
|
||||
|
|
@ -699,14 +869,14 @@ class DADF5():
|
|||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
self.__add_generic_pointwise(__add_norm,requested,{'ord':ord})
|
||||
|
||||
|
||||
|
||||
|
||||
def add_principal_components(self,x):
|
||||
"""
|
||||
Add principal components of symmetric tensor.
|
||||
|
||||
|
||||
The principal components are sorted in descending order, each repeated according to its multiplicity.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
x : str
|
||||
|
|
@ -741,7 +911,7 @@ class DADF5():
|
|||
|
||||
"""
|
||||
def __add_spherical(x):
|
||||
|
||||
|
||||
if not np.all(np.array(x['data'].shape[1:]) == np.array([3,3])):
|
||||
raise ValueError
|
||||
|
||||
|
|
@ -756,16 +926,16 @@ class DADF5():
|
|||
}
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
|
||||
self.__add_generic_pointwise(__add_spherical,requested)
|
||||
|
||||
|
||||
def add_strain_tensor(self,F='F',t='U',m=0):
|
||||
"""
|
||||
Add strain tensor calculated from a deformation gradient.
|
||||
|
||||
|
||||
For details refer to damask.mechanics.strain_tensor
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
F : str, optional
|
||||
|
|
@ -778,9 +948,9 @@ class DADF5():
|
|||
|
||||
"""
|
||||
def __add_strain_tensor(F,t,m):
|
||||
|
||||
|
||||
return {
|
||||
'data': mechanics.strain_tensor(F['data'],t,m),
|
||||
'data': mechanics.strain_tensor(F['data'],t,m),
|
||||
'label': 'epsilon_{}^{}({})'.format(t,m,F['label']),
|
||||
'meta': {
|
||||
'Unit': F['meta']['Unit'],
|
||||
|
|
@ -790,14 +960,14 @@ class DADF5():
|
|||
}
|
||||
|
||||
requested = [{'label':F,'arg':'F'}]
|
||||
|
||||
|
||||
self.__add_generic_pointwise(__add_strain_tensor,requested,{'t':t,'m':m})
|
||||
|
||||
|
||||
def __add_generic_pointwise(self,func,datasets_requested,extra_args={}):
|
||||
"""
|
||||
General function to add pointwise data.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
func : function
|
||||
|
|
@ -811,14 +981,14 @@ class DADF5():
|
|||
def job(args):
|
||||
"""Call function with input data + extra arguments, returns results + group."""
|
||||
args['results'].put({**args['func'](**args['in']),'group':args['group']})
|
||||
|
||||
|
||||
|
||||
N_threads = 1 # ToDo: should be a parameter
|
||||
|
||||
results = Queue(N_threads)
|
||||
pool = util.ThreadPool(N_threads)
|
||||
N_added = N_threads + 1
|
||||
|
||||
|
||||
todo = []
|
||||
# ToDo: It would be more memory efficient to read only from file when required, i.e. do to it in pool.add_task
|
||||
for group in self.groups_with_datasets([d['label'] for d in datasets_requested]):
|
||||
|
|
@ -831,18 +1001,18 @@ class DADF5():
|
|||
datasets_in[d['arg']] = {'data': data, 'meta' : meta, 'label' : d['label']}
|
||||
|
||||
todo.append({'in':{**datasets_in,**extra_args},'func':func,'group':group,'results':results})
|
||||
|
||||
|
||||
pool.map(job, todo[:N_added]) # initialize
|
||||
|
||||
N_not_calculated = len(todo)
|
||||
while N_not_calculated > 0:
|
||||
while N_not_calculated > 0:
|
||||
result = results.get()
|
||||
with h5py.File(self.fname,'a') as f: # write to file
|
||||
dataset_out = f[result['group']].create_dataset(result['label'],data=result['data'])
|
||||
for k in result['meta'].keys():
|
||||
dataset_out.attrs[k] = result['meta'][k].encode()
|
||||
N_not_calculated-=1
|
||||
|
||||
|
||||
if N_added < len(todo): # add more jobs
|
||||
pool.add_task(job,todo[N_added])
|
||||
N_added +=1
|
||||
|
|
@ -853,7 +1023,7 @@ class DADF5():
|
|||
def to_vtk(self,labels,mode='Cell'):
|
||||
"""
|
||||
Export to vtk cell/point data.
|
||||
|
||||
|
||||
Parameters
|
||||
----------
|
||||
labels : str or list of
|
||||
|
|
@ -866,24 +1036,24 @@ class DADF5():
|
|||
if mode=='Cell':
|
||||
|
||||
if self.structured:
|
||||
|
||||
|
||||
coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
|
||||
for dim in [0,1,2]:
|
||||
for c in np.linspace(0,self.size[dim],1+self.grid[dim]):
|
||||
coordArray[dim].InsertNextValue(c)
|
||||
|
||||
|
||||
vtk_geom = vtk.vtkRectilinearGrid()
|
||||
vtk_geom.SetDimensions(*(self.grid+1))
|
||||
vtk_geom.SetXCoordinates(coordArray[0])
|
||||
vtk_geom.SetYCoordinates(coordArray[1])
|
||||
vtk_geom.SetZCoordinates(coordArray[2])
|
||||
|
||||
|
||||
else:
|
||||
|
||||
|
||||
nodes = vtk.vtkPoints()
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
nodes.SetData(numpy_support.numpy_to_vtk(f['/geometry/x_n'][()],deep=True))
|
||||
|
||||
|
||||
vtk_geom = vtk.vtkUnstructuredGrid()
|
||||
vtk_geom.SetPoints(nodes)
|
||||
vtk_geom.Allocate(f['/geometry/T_c'].shape[0])
|
||||
|
|
@ -910,22 +1080,22 @@ class DADF5():
|
|||
|
||||
elif mode == 'Point':
|
||||
Points = vtk.vtkPoints()
|
||||
Vertices = vtk.vtkCellArray()
|
||||
Vertices = vtk.vtkCellArray()
|
||||
for c in self.cell_coordinates():
|
||||
pointID = Points.InsertNextPoint(c)
|
||||
Vertices.InsertNextCell(1)
|
||||
Vertices.InsertCellPoint(pointID)
|
||||
|
||||
|
||||
vtk_geom = vtk.vtkPolyData()
|
||||
vtk_geom.SetPoints(Points)
|
||||
vtk_geom.SetVerts(Vertices)
|
||||
vtk_geom.Modified()
|
||||
|
||||
|
||||
N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1
|
||||
|
||||
|
||||
for i,inc in enumerate(self.iter_visible('increments')):
|
||||
vtk_data = []
|
||||
|
||||
|
||||
materialpoints_backup = self.visible['materialpoints'].copy()
|
||||
self.set_visible('materialpoints',False)
|
||||
for label in (labels if isinstance(labels,list) else [labels]):
|
||||
|
|
@ -983,8 +1153,8 @@ class DADF5():
|
|||
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
|
||||
vtk_geom.GetCellData().AddArray(vtk_data[-1])
|
||||
self.set_visible('constituents',constituents_backup)
|
||||
|
||||
if mode=='Cell':
|
||||
|
||||
if mode=='Cell':
|
||||
writer = vtk.vtkXMLRectilinearGridWriter() if self.structured else \
|
||||
vtk.vtkXMLUnstructuredGridWriter()
|
||||
x = self.get_dataset_location('u_n')
|
||||
|
|
@ -995,11 +1165,11 @@ class DADF5():
|
|||
elif mode == 'Point':
|
||||
writer = vtk.vtkXMLPolyDataWriter()
|
||||
|
||||
|
||||
|
||||
file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
|
||||
inc[3:].zfill(N_digits),
|
||||
writer.GetDefaultFileExtension())
|
||||
|
||||
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetFileName(file_out)
|
||||
|
|
|
|||
Loading…
Reference in New Issue