attributes should depend on view
hidden attributes contain the view-independent variables, getter for currently visible quantities
This commit is contained in:
Martin Diehl
parent
84af516cdb
commit
38f9c1977c
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit 29ef436acca5417aebc945b688642c34697af911
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Subproject commit 5a715996e6e8418a59fbcaf3715a2516ad05ed51
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@ -119,29 +119,29 @@ class Result:
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self.add_curl = self.add_divergence = self.add_gradient = None # type: ignore
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r = re.compile(rf'{prefix_inc}([0-9]+)')
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self.increments = sorted([i for i in f.keys() if r.match(i)],key=util.natural_sort)
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self.times = np.around([f[i].attrs['t/s'] for i in self.increments],12)
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if len(self.increments) == 0:
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self._increments = sorted([i for i in f.keys() if r.match(i)],key=util.natural_sort)
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self._times = np.around([f[i].attrs['t/s'] for i in self._increments],12)
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if len(self._increments) == 0:
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raise ValueError('incomplete DADF5 file')
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self.N_materialpoints, self.N_constituents = np.shape(f['cell_to/phase'])
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self.homogenization = f['cell_to/homogenization']['label'].astype('str')
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self.homogenizations = sorted(np.unique(self.homogenization),key=util.natural_sort)
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self.phase = f['cell_to/phase']['label'].astype('str')
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self.phases = sorted(np.unique(self.phase),key=util.natural_sort)
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self.homogenization = f['cell_to/homogenization']['label'].astype('str')
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self._homogenizations = sorted(np.unique(self.homogenization),key=util.natural_sort)
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self.phase = f['cell_to/phase']['label'].astype('str')
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self._phases = sorted(np.unique(self.phase),key=util.natural_sort)
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self.fields: List[str] = []
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for c in self.phases:
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self.fields += f['/'.join([self.increments[0],'phase',c])].keys()
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for m in self.homogenizations:
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self.fields += f['/'.join([self.increments[0],'homogenization',m])].keys()
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self.fields = sorted(set(self.fields),key=util.natural_sort) # make unique
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fields: List[str] = []
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for c in self._phases:
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fields += f['/'.join([self._increments[0],'phase',c])].keys()
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for m in self._homogenizations:
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fields += f['/'.join([self._increments[0],'homogenization',m])].keys()
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self._fields = sorted(set(fields),key=util.natural_sort) # make unique
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self.visible = {'increments': self.increments,
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'phases': self.phases,
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'homogenizations': self.homogenizations,
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'fields': self.fields,
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self.visible = {'increments': self._increments,
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'phases': self._phases,
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'homogenizations': self._homogenizations,
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'fields': self._fields,
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}
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self.fname = Path(fname).expanduser().absolute()
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@ -223,24 +223,24 @@ class Result:
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if what == 'increments':
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choice = [c if isinstance(c,str) and c.startswith(prefix_inc) else
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self.increments[c] if isinstance(c,int) and c<0 else
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self._increments[c] if isinstance(c,int) and c<0 else
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f'{prefix_inc}{c}' for c in choice]
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elif what == 'times':
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atol = 1e-2 * np.min(np.diff(self.times))
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atol = 1e-2 * np.min(np.diff(self._times))
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what = 'increments'
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if choice == ['*']:
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choice = self.increments
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choice = self._increments
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else:
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iterator = np.array(choice).astype(float)
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choice = []
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for c in iterator:
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idx = np.searchsorted(self.times,c,side='left')
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if idx<len(self.times) and np.isclose(c,self.times[idx],rtol=0,atol=atol):
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choice.append(self.increments[idx])
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elif idx>0 and np.isclose(c,self.times[idx-1],rtol=0,atol=atol):
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choice.append(self.increments[idx-1])
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idx = np.searchsorted(self._times,c,side='left')
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if idx<len(self._times) and np.isclose(c,self._times[idx],rtol=0,atol=atol):
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choice.append(self._increments[idx])
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elif idx>0 and np.isclose(c,self._times[idx-1],rtol=0,atol=atol):
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choice.append(self._increments[idx-1])
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valid = _match(choice,getattr(self,what))
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valid = _match(choice,getattr(self,'_'+what))
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existing = set(self.visible[what])
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if action == 'set':
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@ -273,9 +273,9 @@ class Result:
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"""
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s,e = map(lambda x: int(x.split(prefix_inc)[-1] if isinstance(x,str) and x.startswith(prefix_inc) else x),
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(self.incs[ 0] if start is None else start,
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self.incs[-1] if end is None else end))
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return [i for i in self.incs if s <= i <= e]
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(self._incs[ 0] if start is None else start,
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self._incs[-1] if end is None else end))
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return [i for i in self._incs if s <= i <= e]
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def times_in_range(self,
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start: Optional[float] = None,
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@ -296,9 +296,9 @@ class Result:
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Time of each increment within the given bounds.
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"""
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s,e = (self.times[ 0] if start is None else start,
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self.times[-1] if end is None else end)
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return [t for t in self.times if s <= t <= e]
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s,e = (self._times[ 0] if start is None else start,
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self._times[-1] if end is None else end)
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return [t for t in self._times if s <= t <= e]
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def view(self,*,
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@ -533,7 +533,7 @@ class Result:
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msg = []
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with h5py.File(self.fname,'r') as f:
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for inc in self.visible['increments']:
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msg += [f'\n{inc} ({self.times[self.increments.index(inc)]} s)']
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msg += [f'\n{inc} ({self._times[self._increments.index(inc)]} s)']
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for ty in ['phase','homogenization']:
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msg += [f' {ty}']
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for label in self.visible[ty+'s']:
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@ -566,8 +566,28 @@ class Result:
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return files
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@property
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def incs(self):
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return [int(i.split(prefix_inc)[-1]) for i in self.increments]
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def _incs(self):
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return [int(i.split(prefix_inc)[-1]) for i in self._increments]
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@property
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def increments(self):
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return [int(i.split(prefix_inc)[-1]) for i in self.visible['increments']]
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@property
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def times(self):
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return NotImplementedError
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@property
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def phases(self):
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return [copy.deepcopy(self.visible['phases'])]
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@property
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def homogenizations(self):
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return [copy.deepcopy(self.visible['homogenizations'])]
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@property
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def fields(self):
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return [copy.deepcopy(self.visible['fields'])]
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@property
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@ -1723,7 +1743,7 @@ class Result:
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DADF5 file at a stable relative path.
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"""
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if self.N_constituents != 1 or len(self.phases) != 1 or not self.structured:
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if self.N_constituents != 1 or len(self._phases) != 1 or not self.structured:
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raise TypeError('XDMF output requires structured grid with single phase and single constituent.')
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attribute_type_map = defaultdict(lambda:'Matrix', ( ((),'Scalar'), ((3,),'Vector'), ((3,3),'Tensor')) )
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@ -1749,7 +1769,7 @@ class Result:
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time.attrib = {'TimeType': 'List'}
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time_data = ET.SubElement(time, 'DataItem')
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times = [self.times[self.increments.index(i)] for i in self.visible['increments']]
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times = [self._times[self._increments.index(i)] for i in self.visible['increments']]
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time_data.attrib = {'Format': 'XML',
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'NumberType': 'Float',
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'Dimensions': f'{len(times)}'}
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@ -1876,7 +1896,7 @@ class Result:
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v.comments = [util.execution_stamp('Result','export_VTK')]
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N_digits = int(np.floor(np.log10(max(1,self.incs[-1]))))+1
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N_digits = int(np.floor(np.log10(max(1,self._incs[-1]))))+1
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constituents_ = constituents if isinstance(constituents,Iterable) else \
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(range(self.N_constituents) if constituents is None else [constituents]) # type: ignore
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@ -1966,7 +1986,7 @@ class Result:
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if self.N_constituents != 1 or not self.structured:
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raise TypeError('DREAM3D output requires structured grid with single constituent.')
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N_digits = int(np.floor(np.log10(max(1,self.incs[-1]))))+1
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N_digits = int(np.floor(np.log10(max(1,self._incs[-1]))))+1
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at_cell_ph,in_data_ph,_,_ = self._mappings()
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@ -2036,12 +2056,12 @@ class Result:
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cell_ensemble.create_dataset(name='PhaseName',data = phase_name, dtype=h5py.Datatype(tid))
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cell_ensemble.attrs['AttributeMatrixType'] = np.array([11],np.uint32)
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cell_ensemble.attrs['TupleDimensions'] = np.array([len(self.phases) + 1], np.uint64)
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cell_ensemble.attrs['TupleDimensions'] = np.array([len(self._phases) + 1], np.uint64)
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for group in ['CrystalStructures','PhaseTypes','PhaseName']:
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add_attribute(cell_ensemble[group], 'ComponentDimensions', np.array([1],np.uint64))
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add_attribute(cell_ensemble[group], 'Tuple Axis Dimensions', f'x={len(self.phases)+1}')
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add_attribute(cell_ensemble[group], 'Tuple Axis Dimensions', f'x={len(self._phases)+1}')
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add_attribute(cell_ensemble[group], 'DataArrayVersion', np.array([2],np.int32))
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add_attribute(cell_ensemble[group], 'TupleDimensions', np.array([len(self.phases) + 1],np.uint64))
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add_attribute(cell_ensemble[group], 'TupleDimensions', np.array([len(self._phases) + 1],np.uint64))
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for group in ['CrystalStructures','PhaseTypes']:
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add_attribute(cell_ensemble[group], 'ObjectType', 'DataArray<uint32_t>')
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add_attribute(cell_ensemble['PhaseName'], 'ObjectType', 'StringDataArray')
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@ -2129,9 +2149,9 @@ class Result:
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f_out[inc]['geometry'].create_dataset('u_n',data=u_n)
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for label in self.homogenizations:
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for label in self._homogenizations:
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f_in[inc]['homogenization'].copy(label,f_out[inc]['homogenization'],shallow=True)
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for label in self.phases:
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for label in self._phases:
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f_in[inc]['phase'].copy(label,f_out[inc]['phase'],shallow=True)
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for ty in ['phase','homogenization']:
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@ -126,7 +126,7 @@ class TestResult:
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@pytest.mark.parametrize('sign',[+1,-1])
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def test_view_approxtimes(self,default,inc,sign):
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eps = sign*1e-3
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assert [default.increments[inc]] == default.view(times=default.times[inc]+eps).visible['increments']
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assert [default._increments[inc]] == default.view(times=default._times[inc]+eps).visible['increments']
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def test_add_invalid(self,default):
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default.add_absolute('xxxx')
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@ -470,7 +470,7 @@ class TestResult:
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assert np.array_equal(dset,cur[path])
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else:
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c = [_.decode() for _ in cur[path]]
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r = ['Unknown Phase Type'] + result.phases
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r = ['Unknown Phase Type'] + result._phases
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assert c == r
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grp = os.path.split(path)[0]
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for attr in ref[grp].attrs:
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@ -650,8 +650,8 @@ class TestResult:
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'check_compile_job1.hdf5',])
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def test_export_DADF5(self,res_path,tmp_path,fname):
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r = Result(res_path/fname)
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r = r.view(phases = random.sample(r.phases,1))
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r = r.view(increments = random.sample(r.increments,np.random.randint(1,len(r.increments))))
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r = r.view(phases = random.sample(r._phases,1))
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r = r.view(increments = random.sample(r._increments,np.random.randint(1,len(r._increments))))
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r.export_DADF5(tmp_path/fname)
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r_exp = Result(tmp_path/fname)
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assert str(r.get()) == str(r_exp.get())
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