don't support old file formats
This commit is contained in:
Martin Diehl
parent
285889b48e
commit
190ddafa44
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@ -79,34 +79,25 @@ class Result:
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self.version_major = f.attrs['DADF5_version_major']
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self.version_minor = f.attrs['DADF5_version_minor']
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if self.version_major != 0 or not 7 <= self.version_minor <= 12:
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if self.version_major != 0 or not 12 <= self.version_minor <= 12:
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raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}')
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self.structured = 'grid' in f['geometry'].attrs.keys() or \
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'cells' in f['geometry'].attrs.keys()
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self.structured = 'cells' in f['geometry'].attrs.keys()
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if self.structured:
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try:
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self.cells = f['geometry'].attrs['cells']
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except KeyError:
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self.cells = f['geometry'].attrs['grid']
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self.cells = f['geometry'].attrs['cells']
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self.size = f['geometry'].attrs['size']
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self.origin = f['geometry'].attrs['origin']
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r=re.compile('inc[0-9]+' if self.version_minor < 12 else 'increment_[0-9]+')
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r=re.compile('increment_[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 = [round(f[i].attrs['time/s' if self.version_minor < 12 else
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't/s'],12) for i in self.increments]
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self.times = [round(f[i].attrs['t/s'],12) for i in self.increments]
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grp = 'mapping' if self.version_minor < 12 else 'cell_to'
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self.N_materialpoints, self.N_constituents = np.shape(f[f'cell_to/phase'])
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self.N_materialpoints, self.N_constituents = np.shape(f[f'{grp}/phase'])
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self.homogenizations = [m.decode() for m in np.unique(f[f'{grp}/homogenization']
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['Name' if self.version_minor < 12 else 'label'])]
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self.homogenizations = [m.decode() for m in np.unique(f[f'cell_to/homogenization']['label'])]
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self.homogenizations = sorted(self.homogenizations,key=util.natural_sort)
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self.phases = [c.decode() for c in np.unique(f[f'{grp}/phase']
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['Name' if self.version_minor < 12 else 'label'])]
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self.phases = [c.decode() for c in np.unique(f[f'cell_to/phase']['label'])]
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self.phases = sorted(self.phases,key=util.natural_sort)
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self.fields = []
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@ -172,10 +163,9 @@ class Result:
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choice = list(datasets).copy() if hasattr(datasets,'__iter__') and not isinstance(datasets,str) else \
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[datasets]
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inc = 'inc' if self.version_minor < 12 else 'increment_' # compatibility hack
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if what == 'increments':
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choice = [c if isinstance(c,str) and c.startswith(inc) else
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f'{inc}{c}' for c in choice]
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choice = [c if isinstance(c,str) and c.startswith('increment_') else
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f'increment_{c}' for c in choice]
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elif what == 'times':
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what = 'increments'
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if choice == ['*']:
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@ -233,11 +223,9 @@ class Result:
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End increment.
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"""
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# compatibility hack
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ln = 3 if self.version_minor < 12 else 10
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selected = []
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for i,inc in enumerate([int(i[ln:]) for i in self.increments]):
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s,e = map(lambda x: int(x[ln:] if isinstance(x,str) and x.startswith('inc') else x), (start,end))
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for i,inc in enumerate([int(i[10:]) for i in self.increments]):
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s,e = map(lambda x: int(x[10:] if isinstance(x,str) and x.startswith('inc') else x), (start,end))
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if s <= inc <= e:
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selected.append(self.increments[i])
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return selected
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@ -341,9 +329,6 @@ class Result:
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def list_data(self):
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"""Return information on all active datasets in the file."""
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# compatibility hack
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de = 'Description' if self.version_minor < 12 else 'description'
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un = 'Unit' if self.version_minor < 12 else 'unit'
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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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@ -356,10 +341,10 @@ class Result:
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msg = ' '.join([msg,f'{field}\n'])
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for d in f['/'.join([inc,ty,label,field])].keys():
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dataset = f['/'.join([inc,ty,label,field,d])]
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unit = f' / {dataset.attrs[un]}' if h5py3 else \
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f' / {dataset.attrs[un].decode()}'
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description = dataset.attrs[de] if h5py3 else \
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dataset.attrs[de].decode()
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unit = f' / {dataset.attrs["unit"]}' if h5py3 else \
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f' / {dataset.attrs["unit"].decode()}'
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description = dataset.attrs['description'] if h5py3 else \
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dataset.attrs['description'].decode()
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msg = ' '.join([msg,f'{d}{unit}: {description}\n'])
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return msg
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@ -1023,7 +1008,6 @@ class Result:
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Defaults to '*', in which case all datasets are considered.
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"""
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u = 'Unit' if self.version_minor < 12 else 'unit' # compatibility hack
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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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@ -1104,7 +1088,8 @@ class Result:
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shape = f[name].shape[1:]
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dtype = f[name].dtype
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unit = f[name].attrs[u] if h5py3 else f[name].attrs[u].decode()
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unit = f[name].attrs['unit'] if h5py3 else \
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f[name].attrs['unit'].decode()
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attributes.append(ET.SubElement(grid, 'Attribute'))
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attributes[-1].attrib = {'Name': '/'.join([ty,field,out])+f' / {unit}',
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@ -1123,23 +1108,20 @@ class Result:
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def _mappings(self):
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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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"""Mappings to place data spatially."""
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with h5py.File(self.fname,'r') as f:
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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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at_cell_ph.append({label: np.where(f['/'.join(['cell_to','phase'])][:,c]['label'] == 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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in_data_ph.append({label: f['/'.join(['cell_to','phase'])]['entry'][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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at_cell_ho = {label: np.where(f['/'.join(['cell_to','homogenization'])][:]['label'] == 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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in_data_ho = {label: f['/'.join(['cell_to','homogenization'])]['entry'][at_cell_ho[label]] \
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for label in self.visible['homogenizations']}
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return at_cell_ph,in_data_ph,at_cell_ho,in_data_ho
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@ -1176,8 +1158,7 @@ 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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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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N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][10:])))))+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])
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@ -1221,7 +1202,7 @@ class Result:
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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)}',parallel=parallel)
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v.save(f'{self.fname.stem}_inc{inc[10:].zfill(N_digits)}',parallel=parallel)
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def get(self,output='*',flatten=True,prune=True):
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