using new logic
This commit is contained in:
Martin Diehl
parent
e8ff509502
commit
20d0242d59
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@ -1246,17 +1246,27 @@ class Result:
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f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
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def save_VTK(self,labels=[],mode='cell'):
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def save_VTK(self,output='*',mode='cell',constituents=None,fill_float=np.nan,fill_int=0):
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"""
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Export to vtk cell/point data.
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Parameters
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----------
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labels : str or list of, optional
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Labels of the datasets to be exported.
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output : str or list of, optional
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Labels of the datasets to place. Defaults to '*', in which
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case all datasets are exported.
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mode : str, either 'cell' or 'point'
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Export in cell format or point format.
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Defaults to 'cell'.
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constituents : int or list of, optional
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Constituents to consider. Defaults to 'None', in which case
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all constituents are considered.
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fill_float : float
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Fill value for non-existent entries of floating point type.
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Defaults to 0.0.
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fill_int : int
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Fill value for non-existent entries of integer type.
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Defaults to 0.
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"""
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if mode.lower()=='cell':
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@ -1272,53 +1282,76 @@ class Result:
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elif mode.lower()=='point':
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v = VTK.from_poly_data(self.coordinates0_point)
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# compatibility hack
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ln = 3 if self.version_minor < 12 else 10
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ln = 3 if self.version_minor < 12 else 10 # compatibility hack
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N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][ln:])))))+1
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for inc in util.show_progress(self.iterate('increments'),len(self.visible['increments'])):
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output_ = set([output] if isinstance(output,str) else output)
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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])
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viewed_backup_ho = self.visible['homogenizations'].copy()
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self.view('homogenizations',False)
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for label in (labels if isinstance(labels,list) else [labels]):
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for o in self.iterate('fields'):
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for c in range(self.N_constituents):
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prefix = '' if self.N_constituents == 1 else f'constituent{c}/'
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if o not in ['mechanics', 'mechanical']: # compatibility hack
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for _ in self.iterate('phases'):
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path = self.get_dataset_location(label)
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if len(path) == 0:
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continue
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array = self.read_dataset(path,c)
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v.add(array,prefix+path[0].split('/',1)[1]+f' / {self._get_attribute(path[0],"unit")}')
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else:
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paths = self.get_dataset_location(label)
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if len(paths) == 0:
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continue
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array = self.read_dataset(paths,c)
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if self.version_minor < 12:
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ph_name = re.compile(r'(?<=(phase\/))(.*?)(?=(mechanics))') # identify phase name
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else:
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ph_name = re.compile(r'(?<=(phase\/))(.*?)(?=(mechanical))') # identify phase name
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dset_name = prefix+re.sub(ph_name,r'',paths[0].split('/',1)[1]) # remove phase name
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v.add(array,dset_name+f' / {self._get_attribute(paths[0],"unit")}')
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self.view('homogenizations',viewed_backup_ho)
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suffixes = [''] if self.N_constituents == 1 or isinstance(constituents,int) else \
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[f'#{c}' for c in constituents_]
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viewed_backup_ph = self.visible['phases'].copy()
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self.view('phases',False)
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for label in (labels if isinstance(labels,list) else [labels]):
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for _ in self.iterate('fields'):
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paths = self.get_dataset_location(label)
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if len(paths) == 0:
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continue
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array = self.read_dataset(paths)
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v.add(array,paths[0].split('/',1)[1]+f' / {self._get_attribute(paths[0],"unit")}')
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self.view('phases',viewed_backup_ph)
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grp = 'mapping' if self.version_minor < 12 else 'cell_to' # compatibility hack
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name = 'Name' if self.version_minor < 12 else 'label' # compatibility hack
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member = 'member' if self.version_minor < 12 else 'entry' # compatibility hack
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u = self.read_dataset(self.get_dataset_location('u_n' if mode.lower() == 'cell' else 'u_p'))
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v.add(u,'u')
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with h5py.File(self.fname,'r') as f:
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v.save(f'{self.fname.stem}_inc{inc[ln:].zfill(N_digits)}')
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at_cell_ph = []
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in_data_ph = []
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for c in range(self.N_constituents):
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at_cell_ph.append({label: np.where(f['/'.join((grp,'phase'))][:,c][name] == label.encode())[0] \
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for label in self.visible['phases']})
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in_data_ph.append({label: f['/'.join((grp,'phase'))][member][at_cell_ph[c][label]][:,c] \
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for label in self.visible['phases']})
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at_cell_ho = {label: np.where(f['/'.join((grp,'homogenization'))][:][name] == label.encode())[0] \
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for label in self.visible['homogenizations']}
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in_data_ho = {label: f['/'.join((grp,'homogenization'))][member][at_cell_ho[label]] \
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for label in self.visible['homogenizations']}
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for inc in util.show_progress(self.visible['increments']):
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u = _read(f['/'.join((inc,'geometry','u_n' if mode.lower() == 'cell' else 'u_p'))])
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v.add(u,'u')
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for ty in ['phase','homogenization']:
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for field in self.visible['fields']:
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for label in self.visible[ty+'s']:
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if field not in f['/'.join((inc,ty,label))].keys(): continue
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outs = {}
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for out in f['/'.join((inc,ty,label,field))].keys() if '*' in output_ else \
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output_.intersection(f['/'.join((inc,ty,label,field))].keys()):
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data = ma.array(_read(f['/'.join((inc,ty,label,field,out))]))
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if ty == 'phase':
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if out+suffixes[0] not in outs.keys():
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container = np.empty((self.N_materialpoints,)+data.shape[1:],data.dtype)
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fill_value = fill_float if data.dtype in np.sctypes['float'] else \
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fill_int
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for c,suffix in zip(constituents_,suffixes):
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outs[out+suffix] = \
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ma.array(container,fill_value=fill_value,mask=True)
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for c,suffix in zip(constituents_,suffixes):
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outs[out+suffix][at_cell_ph[c][label]] = data[in_data_ph[c][label]]
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if ty == 'homogenization':
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if out not in outs.keys():
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container = np.empty((self.N_materialpoints,)+data.shape[1:],data.dtype)
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fill_value = fill_float if data.dtype in np.sctypes['float'] else \
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fill_int
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outs[out] = \
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ma.array(container,fill_value=fill_value,mask=True)
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outs[out][at_cell_ho[label]] = data[in_data_ho[label]]
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for label,dataset in outs.items():
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v.add(dataset,' / '.join(('/'.join((ty,field,label)),dataset.dtype.metadata['unit'])))
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v.save(f'{self.fname.stem}_inc{inc[ln:].zfill(N_digits)}')
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def read(self,output='*',flatten=True,prune=True):
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@ -1375,7 +1408,8 @@ class Result:
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in the DADF5 file.
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Multi-phase data is fused into a single output.
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`place` is equivalent to `read` if only one phase and one constituent is present.
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`place` is equivalent to `read` if only one phase/homogenization
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and one constituent is present.
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Parameters
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----------
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@ -1408,9 +1442,9 @@ class Result:
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suffixes = [''] if self.N_constituents == 1 or isinstance(constituents,int) else \
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[f'#{c}' for c in constituents_]
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grp = 'mapping' if self.version_minor < 12 else 'cell_to'
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name = 'Name' if self.version_minor < 12 else 'label'
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member = 'member' if self.version_minor < 12 else 'entry'
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grp = 'mapping' if self.version_minor < 12 else 'cell_to' # compatibility hack
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name = 'Name' if self.version_minor < 12 else 'label' # compatibility hack
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member = 'member' if self.version_minor < 12 else 'entry' # compatibility hack
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with h5py.File(self.fname,'r') as f:
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@ -376,7 +376,7 @@ class TestResult:
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b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F')
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assert np.allclose(a,b)
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@pytest.mark.parametrize('output',['F',[],['F','P']])
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@pytest.mark.parametrize('output',['F','*',['F','P']])
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def test_vtk(self,tmp_path,default,output):
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os.chdir(tmp_path)
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default.save_VTK(output)
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