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DAMASK_EICMD
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out of place behavior

This commit is contained in:
Martin Diehl 2021-04-05 07:53:19 +02:00
parent fc409fcf08
commit 62c85db745
2 changed files with 84 additions and 182 deletions
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192
python/damask/_result.py
View File

@ -2,6 +2,7 @@ import multiprocessing as mp
import re import re
import fnmatch import fnmatch
import os import os
import copy
import datetime import datetime
import xml.etree.ElementTree as ET import xml.etree.ElementTree as ET
import xml.dom.minidom import xml.dom.minidom
@ -27,11 +28,13 @@ h5py3 = h5py.__version__[0] == '3'
def _read(dataset): def _read(dataset):
"""Read a dataset and its metadata into a numpy.ndarray."""
metadata = {k:(v if h5py3 else v.decode()) for k,v in dataset.attrs.items()} metadata = {k:(v if h5py3 else v.decode()) for k,v in dataset.attrs.items()}
dtype = np.dtype(dataset.dtype,metadata=metadata) dtype = np.dtype(dataset.dtype,metadata=metadata)
return np.array(dataset,dtype=dtype) return np.array(dataset,dtype=dtype)
def _match(requested,existing): def _match(requested,existing):
"""Find matches among two sets of labels"""
def flatten_list(list_of_lists): def flatten_list(list_of_lists):
return [e for e_ in list_of_lists for e in e_] return [e for e_ in list_of_lists for e in e_]
@ -47,6 +50,7 @@ def _match(requested,existing):
key=util.natural_sort) key=util.natural_sort)
def _empty(dataset,N_materialpoints,fill_float,fill_int): def _empty(dataset,N_materialpoints,fill_float,fill_int):
"""Create empty numpy.ma.MaskedArray."""
return ma.array(np.empty((N_materialpoints,)+dataset.shape[1:],dataset.dtype), 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, fill_value = fill_float if dataset.dtype in np.sctypes['float'] else fill_int,
mask = True) mask = True)
@ -123,17 +127,21 @@ class Result:
self._allow_modification = False self._allow_modification = False
def __copy__(self):
"""Create deep copy."""
return copy.deepcopy(self)
copy = __copy__
def __repr__(self): def __repr__(self):
"""Show summary of file content.""" """Show summary of file content."""
visible_increments = self.visible['increments'] visible_increments = self.visible['increments']
self.view('increments',visible_increments[0:1]) first = self.view('increments',visible_increments[0:1]).list_data()
first = self.list_data()
self.view('increments',visible_increments[-1:]) last = '' if len(visible_increments) < 2 else \
last = '' if len(visible_increments) < 2 else self.list_data() self.view('increments',visible_increments[-1:]).list_data()
self.view('increments',visible_increments)
in_between = '' if len(visible_increments) < 3 else \ in_between = '' if len(visible_increments) < 3 else \
''.join([f'\n{inc}\n ...\n' for inc in visible_increments[1:-1]]) ''.join([f'\n{inc}\n ...\n' for inc in visible_increments[1:-1]])
@ -186,24 +194,31 @@ class Result:
valid = _match(choice,getattr(self,what)) valid = _match(choice,getattr(self,what))
existing = set(self.visible[what]) existing = set(self.visible[what])
dup = self.copy()
if action == 'set': if action == 'set':
self.visible[what] = sorted(set(valid), key=util.natural_sort) dup.visible[what] = sorted(set(valid), key=util.natural_sort)
elif action == 'add': elif action == 'add':
add = existing.union(valid) add = existing.union(valid)
self.visible[what] = sorted(add, key=util.natural_sort) dup.visible[what] = sorted(add, key=util.natural_sort)
elif action == 'del': elif action == 'del':
diff = existing.difference(valid) diff = existing.difference(valid)
self.visible[what] = sorted(diff, key=util.natural_sort) dup.visible[what] = sorted(diff, key=util.natural_sort)
return dup
def allow_modification(self): def allow_modification(self):
"""Allow to overwrite existing data.""" """Allow to overwrite existing data."""
print(util.warn('Warning: Modification of existing datasets allowed!')) print(util.warn('Warning: Modification of existing datasets allowed!'))
self._allow_modification = True dup = self.copy()
dup._allow_modification = True
return dup
def disallow_modification(self): def disallow_modification(self):
"""Disallow to overwrite existing data (default case).""" """Disallow to overwrite existing data (default case)."""
self._allow_modification = False dup = self.copy()
dup._allow_modification = False
return dup
def increments_in_range(self,start,end): def increments_in_range(self,start,end):
@ -247,28 +262,6 @@ class Result:
return selected return selected
def iterate(self,what):
"""
Iterate over visible items and view them independently.
Parameters
----------
what : str
Attribute to change (must be from self.visible).
"""
datasets = self.visible[what]
last_view = datasets.copy()
for dataset in datasets:
if last_view != self.visible[what]:
self._manage_view('set',what,datasets)
raise Exception
self._manage_view('set',what,dataset)
last_view = self.visible[what]
yield dataset
self._manage_view('set',what,datasets)
def view(self,what,datasets): def view(self,what,datasets):
""" """
Set view. Set view.
@ -279,10 +272,10 @@ class Result:
Attribute to change (must be from self.visible). Attribute to change (must be from self.visible).
datasets : list of str or bool datasets : list of str or bool
Name of datasets as list; supports ? and * wildcards. Name of datasets as list; supports ? and * wildcards.
True is equivalent to [*], False is equivalent to []. True is equivalent to *, False is equivalent to [].
""" """
self._manage_view('set',what,datasets) return self._manage_view('set',what,datasets)
def view_more(self,what,datasets): def view_more(self,what,datasets):
@ -295,10 +288,10 @@ class Result:
Attribute to change (must be from self.visible). Attribute to change (must be from self.visible).
datasets : list of str or bool datasets : list of str or bool
Name of datasets as list; supports ? and * wildcards. Name of datasets as list; supports ? and * wildcards.
True is equivalent to [*], False is equivalent to []. True is equivalent to *, False is equivalent to [].
""" """
self._manage_view('add',what,datasets) return self._manage_view('add',what,datasets)
def view_less(self,what,datasets): def view_less(self,what,datasets):
@ -311,10 +304,10 @@ class Result:
Attribute to change (must be from self.visible). Attribute to change (must be from self.visible).
datasets : list of str or bool datasets : list of str or bool
Name of datasets as list; supports ? and * wildcards. Name of datasets as list; supports ? and * wildcards.
True is equivalent to [*], False is equivalent to []. True is equivalent to *, False is equivalent to [].
""" """
self._manage_view('del',what,datasets) return self._manage_view('del',what,datasets)
def rename(self,name_old,name_new): def rename(self,name_old,name_new):
@ -334,11 +327,11 @@ class Result:
with h5py.File(self.fname,'a') as f: with h5py.File(self.fname,'a') as f:
for inc in self.visible['increments']: for inc in self.visible['increments']:
for ty in ['phases','homogenizations']: for ty in ['phase','homogenization']:
for label in self.visible[ty]: for label in self.visible[ty+'s']:
for field in self.visible['fields']: for field in self.visible['fields']:
path_old = '/'.join([inc,ty[:-1],label,field,name_old]) path_old = '/'.join([inc,ty,label,field,name_old])
path_new = '/'.join([inc,ty[:-1],label,field,name_new]) path_new = '/'.join([inc,ty,label,field,name_new])
if path_old in f.keys(): if path_old in f.keys():
f[path_new] = f[path_old] f[path_new] = f[path_old]
f[path_new].attrs['renamed'] = f'original name: {name_old}' if h5py3 else \ f[path_new].attrs['renamed'] = f'original name: {name_old}' if h5py3 else \
@ -351,48 +344,25 @@ class Result:
# compatibility hack # compatibility hack
de = 'Description' if self.version_minor < 12 else 'description' de = 'Description' if self.version_minor < 12 else 'description'
un = 'Unit' if self.version_minor < 12 else 'unit' un = 'Unit' if self.version_minor < 12 else 'unit'
message = '' msg = ''
with h5py.File(self.fname,'r') as f: with h5py.File(self.fname,'r') as f:
for inc in self.visible['increments']: for inc in self.visible['increments']:
''.join([message,f'\n{inc} ({self.times[self.increments.index(inc)]}s)\n']) msg = ''.join([msg,f'\n{inc} ({self.times[self.increments.index(inc)]}s)\n'])
for ty in ['phases','homogenizations']: for ty in ['phase','homogenization']:
' '.join([message,f'{ty[:-1]}\n']) msg = ' '.join([msg,f'{ty}\n'])
for label in self.visible[ty]: for label in self.visible[ty+'s']:
' '.join([message,f'{label}\n']) msg = ' '.join([msg,f'{label}\n'])
for field in self.visible['fields']: for field in self.visible['fields']:
' '.join([message,f'{field}\n']) msg = ' '.join([msg,f'{field}\n'])
for d in f['/'.join([inc,ty[:-1],label,field])].keys(): for d in f['/'.join([inc,ty,label,field])].keys():
dataset = f['/'.join([inc,ty[:-1],label,field,d])] dataset = f['/'.join([inc,ty,label,field,d])]
unit = f' / {dataset.attrs[un]}' if h5py3 else \ unit = f' / {dataset.attrs[un]}' if h5py3 else \
f' / {dataset.attrs[un].decode()}' f' / {dataset.attrs[un].decode()}'
description = dataset.attrs[de] if h5py3 else \ description = dataset.attrs[de] if h5py3 else \
dataset.attrs[de].decode() dataset.attrs[de].decode()
' '.join([message,f'{d}{unit}: {description}\n']) msg = ' '.join([msg,f'{d}{unit}: {description}\n'])
return message return msg
def get_dataset_location(self,label):
"""Return the location of all active datasets with given label."""
path = []
with h5py.File(self.fname,'r') as f:
for i in self.visible['increments']:
k = '/'.join([i,'geometry',label])
try:
f[k]
path.append(k)
except KeyError:
pass
for o,p in zip(['phases','homogenizations'],['fields','fields']):
for oo in self.visible[o]:
for pp in self.visible[p]:
k = '/'.join([i,o[:-1],oo,pp,label])
try:
f[k]
path.append(k)
except KeyError:
pass
return path
def enable_user_function(self,func): def enable_user_function(self,func):
@ -400,60 +370,6 @@ class Result:
print(f'Function {func.__name__} enabled in add_calculation.') print(f'Function {func.__name__} enabled in add_calculation.')
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.
Parameters
----------
path : list of strings
The name of the datasets to consider.
c : int, optional
The constituent to consider. Defaults to 0.
plain: boolean, optional
Convert into plain numpy datatype.
Only relevant for compound datatype, e.g. the orientation.
Defaults to False.
"""
# compatibility hack
name = 'Name' if self.version_minor < 12 else 'label'
member = 'Position' if self.version_minor < 12 else 'entry'
grp = 'mapping' if self.version_minor < 12 else 'cell_to'
with h5py.File(self.fname,'r') as f:
shape = (self.N_materialpoints,) + np.shape(f[path[0]])[1:]
if len(shape) == 1: shape = shape +(1,)
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[f'{grp}/phase'][:,c][name] == str.encode(label))[0]
if len(p)>0:
u = (f[f'{grp}/phase'][member][p,c])
a = np.array(f[pa])
if len(a.shape) == 1:
a=a.reshape([a.shape[0],1])
dataset[p,:] = a[u,:]
p = np.where(f[f'{grp}/homogenization'][name] == str.encode(label))[0]
if len(p)>0:
u = (f[f'{grp}/homogenization'][member][p.tolist()])
a = np.array(f[pa])
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:
return dataset
@property @property
def coordinates0_point(self): def coordinates0_point(self):
"""Return initial coordinates of the cell centers.""" """Return initial coordinates of the cell centers."""
@ -1044,10 +960,10 @@ class Result:
groups = [] groups = []
with h5py.File(self.fname,'r') as f: with h5py.File(self.fname,'r') as f:
for inc in self.visible['increments']: for inc in self.visible['increments']:
for ty in ['phases','homogenizations']: for ty in ['phase','homogenization']:
for label in self.visible[ty]: for label in self.visible[ty+'s']:
for field in self.visible['fields']: for field in self.visible['fields']:
group = '/'.join([inc,ty[:-1],label,field]) group = '/'.join([inc,ty,label,field])
if set(datasets.values()).issubset(f[group].keys()): groups.append(group) if set(datasets.values()).issubset(f[group].keys()): groups.append(group)
if len(groups) == 0: if len(groups) == 0:
@ -1176,11 +1092,11 @@ class Result:
'Dimensions': '{} {} {} 3'.format(*(self.cells+1))} 'Dimensions': '{} {} {} 3'.format(*(self.cells+1))}
data_items[-1].text=f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n' data_items[-1].text=f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n'
for ty in ['phases','homogenizations']: for ty in ['phase','homogenization']:
for label in self.visible[ty]: for label in self.visible[ty+'s']:
for field in self.visible['fields']: for field in self.visible['fields']:
for out in _match(output,f['/'.join((inc,ty[:-1],label,field))].keys()): for out in _match(output,f['/'.join((inc,ty,label,field))].keys()):
name = '/'.join([inc,ty[:-1],label,field,out]) name = '/'.join([inc,ty,label,field,out])
shape = f[name].shape[1:] shape = f[name].shape[1:]
dtype = f[name].dtype dtype = f[name].dtype

74
python/tests/test_Result.py
View File

@ -24,8 +24,7 @@ def default(tmp_path,ref_path):
fname = '12grains6x7x8_tensionY.hdf5' fname = '12grains6x7x8_tensionY.hdf5'
shutil.copy(ref_path/fname,tmp_path) shutil.copy(ref_path/fname,tmp_path)
f = Result(tmp_path/fname) f = Result(tmp_path/fname)
f.view('times',20.0) return f.view('times',20.0)
return f
@pytest.fixture @pytest.fixture
def single_phase(tmp_path,ref_path): def single_phase(tmp_path,ref_path):
@ -58,49 +57,37 @@ class TestResult:
def test_view_all(self,default): def test_view_all(self,default):
default.view('increments',True) a = default.view('increments',True).read('F')
a = default.read('F')
default.view('increments','*') assert dict_equal(a,default.view('increments','*').read('F'))
assert dict_equal(a,default.read('F')) assert dict_equal(a,default.view('increments',default.increments_in_range(0,np.iinfo(int).max)).read('F'))
default.view('increments',default.increments_in_range(0,np.iinfo(int).max))
assert dict_equal(a,default.read('F'))
default.view('times',True) assert dict_equal(a,default.view('times',True).read('F'))
assert dict_equal(a,default.read('F')) assert dict_equal(a,default.view('times','*').read('F'))
default.view('times','*') assert dict_equal(a,default.view('times',default.times_in_range(0.0,np.inf)).read('F'))
assert dict_equal(a,default.read('F'))
default.view('times',default.times_in_range(0.0,np.inf))
assert dict_equal(a,default.read('F'))
@pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations @pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations
def test_view_none(self,default,what): def test_view_none(self,default,what):
default.view(what,False) a = default.view(what,False).read('F')
a = default.read('F') b = default.view(what,[]).read('F')
default.view(what,[])
b = default.read('F')
assert a == b == {} assert a == b == {}
@pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations @pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations
def test_view_more(self,default,what): def test_view_more(self,default,what):
default.view(what,False) empty = default.view(what,False)
default.view_more(what,'*')
a = default.read('F')
default.view(what,True) a = empty.view_more(what,'*').read('F')
b = default.read('F') b = empty.view_more(what,True).read('F')
assert dict_equal(a,b) assert dict_equal(a,b)
@pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations @pytest.mark.parametrize('what',['increments','times','phases']) # ToDo: discuss homogenizations
def test_view_less(self,default,what): def test_view_less(self,default,what):
default.view(what,True) full = default.view(what,True)
default.view_less(what,'*')
a = default.read('F')
default.view(what,False) a = full.view_less(what,'*').read('F')
b = default.read('F') b = full.view_less(what,True).read('F')
assert a == b == {} assert a == b == {}
@ -279,41 +266,41 @@ class TestResult:
@pytest.mark.parametrize('overwrite',['off','on']) @pytest.mark.parametrize('overwrite',['off','on'])
def test_add_overwrite(self,default,overwrite): def test_add_overwrite(self,default,overwrite):
default.view('times',default.times_in_range(0,np.inf)[-1]) last = default.view('times',default.times_in_range(0,np.inf)[-1])
default.add_stress_Cauchy() last.add_stress_Cauchy()
with h5py.File(default.fname,'r') as f: with h5py.File(last.fname,'r') as f:
created_first = default.place('sigma').dtype.metadata['created'] created_first = default.place('sigma').dtype.metadata['created']
created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z') created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
if overwrite == 'on': if overwrite == 'on':
default.allow_modification() last = last.allow_modification()
else: else:
default.disallow_modification() last = last.disallow_modification()
time.sleep(2.) time.sleep(2.)
try: try:
default.add_calculation('sigma','#sigma#*0.0+311.','not the Cauchy stress') last.add_calculation('sigma','#sigma#*0.0+311.','not the Cauchy stress')
except ValueError: except ValueError:
pass pass
with h5py.File(default.fname,'r') as f: with h5py.File(last.fname,'r') as f:
created_second = default.place('sigma').dtype.metadata['created'] created_second = last.place('sigma').dtype.metadata['created']
created_second = datetime.strptime(created_second,'%Y-%m-%d %H:%M:%S%z') created_second = datetime.strptime(created_second,'%Y-%m-%d %H:%M:%S%z')
if overwrite == 'on': if overwrite == 'on':
assert created_first < created_second and np.allclose(default.place('sigma'),311.) assert created_first < created_second and np.allclose(last.place('sigma'),311.)
else: else:
assert created_first == created_second and not np.allclose(default.place('sigma'),311.) assert created_first == created_second and not np.allclose(last.place('sigma'),311.)
@pytest.mark.parametrize('allowed',['off','on']) @pytest.mark.parametrize('allowed',['off','on'])
def test_rename(self,default,allowed): def test_rename(self,default,allowed):
if allowed == 'on': if allowed == 'on':
F = default.place('F') F = default.place('F')
default.allow_modification() default = default.allow_modification()
default.rename('F','new_name') default.rename('F','new_name')
assert np.all(F == default.place('new_name')) assert np.all(F == default.place('new_name'))
default.disallow_modification() default = default.disallow_modification()
with pytest.raises(PermissionError): with pytest.raises(PermissionError):
default.rename('P','another_new_name') default.rename('P','another_new_name')
@ -333,8 +320,7 @@ class TestResult:
@pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1)) @pytest.mark.parametrize('fname',['12grains6x7x8_tensionY.hdf5'],ids=range(1))
@pytest.mark.parametrize('inc',[4,0],ids=range(2)) @pytest.mark.parametrize('inc',[4,0],ids=range(2))
def test_vtk(self,request,tmp_path,ref_path,update,output,fname,inc): def test_vtk(self,request,tmp_path,ref_path,update,output,fname,inc):
result = Result(ref_path/fname) result = Result(ref_path/fname).view('increments',inc)
result.view('increments',inc)
os.chdir(tmp_path) os.chdir(tmp_path)
result.save_VTK(output) result.save_VTK(output)
fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vtr' fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vtr'
@ -387,7 +373,7 @@ class TestResult:
def test_read(self,update,request,ref_path,view,output,compress,strip): def test_read(self,update,request,ref_path,view,output,compress,strip):
result = Result(ref_path/'4grains2x4x3_compressionY.hdf5') result = Result(ref_path/'4grains2x4x3_compressionY.hdf5')
for key,value in view.items(): for key,value in view.items():
result.view(key,value) result = result.view(key,value)
fname = request.node.name fname = request.node.name
cur = result.read(output,compress,strip) cur = result.read(output,compress,strip)
@ -412,7 +398,7 @@ class TestResult:
def test_place(self,update,request,ref_path,view,output,compress,strip,constituents): def test_place(self,update,request,ref_path,view,output,compress,strip,constituents):
result = Result(ref_path/'4grains2x4x3_compressionY.hdf5') result = Result(ref_path/'4grains2x4x3_compressionY.hdf5')
for key,value in view.items(): for key,value in view.items():
result.view(key,value) result = result.view(key,value)
fname = request.node.name fname = request.node.name
cur = result.place(output,compress,strip,constituents) cur = result.place(output,compress,strip,constituents)