Merge branch 'result_custom_path_export' into 'development'
added custom path export option to Result.export_* functions Closes #172 See merge request damask/DAMASK!599
This commit is contained in:
Philip Eisenlohr
commit
1fae90b9b5
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@ -276,7 +276,7 @@ class Result:
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Increment number of all increments within the given bounds.
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"""
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s,e = map(lambda x: int(x[10:] if isinstance(x,str) and x.startswith(prefix_inc) else x),
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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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@ -1516,7 +1516,9 @@ class Result:
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def export_XDMF(self,
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output: Union[str, List[str]] = '*'):
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output: Union[str, List[str]] = '*',
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target_dir: Union[str, Path] = None,
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absolute_path: bool = False):
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"""
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Write XDMF file to directly visualize data from DADF5 file.
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@ -1529,12 +1531,17 @@ class Result:
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output : (list of) str
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Names of the datasets included in the XDMF file.
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Defaults to '*', in which case all datasets are considered.
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target_dir : str or pathlib.Path, optional
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Directory to save XDMF file. Will be created if non-existent.
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absolute_path : bool, optional
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Store absolute (instead of relative) path to DADF5 file.
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Defaults to False, i.e. the XDMF file expects the
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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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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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def number_type_map(dtype):
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@ -1544,29 +1551,34 @@ class Result:
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xdmf = ET.Element('Xdmf')
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xdmf.attrib={'Version': '2.0',
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'xmlns:xi': 'http://www.w3.org/2001/XInclude'}
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xdmf.attrib = {'Version': '2.0',
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'xmlns:xi': 'http://www.w3.org/2001/XInclude'}
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domain = ET.SubElement(xdmf, 'Domain')
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collection = ET.SubElement(domain, 'Grid')
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collection.attrib={'GridType': 'Collection',
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'CollectionType': 'Temporal',
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'Name': 'Increments'}
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collection.attrib = {'GridType': 'Collection',
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'CollectionType': 'Temporal',
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'Name': 'Increments'}
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time = ET.SubElement(collection, 'Time')
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time.attrib={'TimeType': 'List'}
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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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time_data.attrib={'Format': 'XML',
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'NumberType': 'Float',
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'Dimensions': f'{len(times)}'}
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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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time_data.text = ' '.join(map(str,times))
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attributes = []
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data_items = []
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hdf5_name = self.fname.name
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hdf5_dir = self.fname.parent
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xdmf_dir = Path.cwd() if target_dir is None else Path(target_dir)
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hdf5_link = (hdf5_dir if absolute_path else Path(os.path.relpath(hdf5_dir,xdmf_dir.resolve())))/hdf5_name
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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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@ -1601,8 +1613,7 @@ class Result:
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data_items[-1].attrib = {'Format': 'HDF',
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'Precision': '8',
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'Dimensions': '{} {} {} 3'.format(*(self.cells[::-1]+1))}
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data_items[-1].text = f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n'
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data_items[-1].text = f'{hdf5_link}:/{inc}/geometry/u_n'
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for ty in ['phase','homogenization']:
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for label in self.visible[ty+'s']:
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for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
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@ -1624,9 +1635,10 @@ class Result:
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'Precision': f'{dtype.itemsize}',
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'Dimensions': '{} {} {} {}'.format(*self.cells[::-1],1 if shape == () else
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np.prod(shape))}
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data_items[-1].text = f'{os.path.split(self.fname)[1]}:{name}'
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data_items[-1].text = f'{hdf5_link}:{name}'
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with util.open_text(self.fname.with_suffix('.xdmf').name,'w') as f:
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xdmf_dir.mkdir(parents=True,exist_ok=True)
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with util.open_text((xdmf_dir/hdf5_name).with_suffix('.xdmf'),'w') as f:
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f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
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@ -1654,6 +1666,7 @@ class Result:
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output: Union[str,list] = '*',
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mode: str = 'cell',
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constituents: IntSequence = None,
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target_dir: Union[str, Path] = None,
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fill_float: float = np.nan,
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fill_int: int = 0,
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parallel: bool = True):
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@ -1676,6 +1689,8 @@ class Result:
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constituents : (list of) int, optional
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Constituents to consider.
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Defaults to None, in which case all constituents are considered.
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target_dir : str or pathlib.Path, optional
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Directory to save VTK files. Will be created if non-existent.
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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 NaN.
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@ -1706,6 +1721,9 @@ class Result:
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at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings()
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vtk_dir = Path.cwd() if target_dir is None else Path(target_dir)
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vtk_dir.mkdir(parents=True,exist_ok=True)
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with h5py.File(self.fname,'r') as f:
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if self.version_minor >= 13:
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creator = f.attrs['creator'] if h5py3 else f.attrs['creator'].decode()
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@ -1744,8 +1762,9 @@ class Result:
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for label,dataset in outs.items():
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v = v.set(' / '.join(['/'.join([ty,field,label]),dataset.dtype.metadata['unit']]),dataset)
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v.save(f'{self.fname.stem}_inc{inc[10:].zfill(N_digits)}',parallel=parallel)
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v.save(vtk_dir/f'{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}',
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parallel=parallel)
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def get(self,
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output: Union[str, List[str]] = '*',
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@ -1890,7 +1909,9 @@ class Result:
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def export_setup(self,
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output: Union[str, List[str]] = '*',
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overwrite: bool = False):
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target_dir: Union[str, Path] = None,
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overwrite: bool = False,
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):
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"""
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Export configuration files.
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@ -1899,21 +1920,35 @@ class Result:
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output : (list of) str, optional
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Names of the datasets to export to the file.
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Defaults to '*', in which case all datasets are exported.
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target_dir : str or pathlib.Path, optional
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Directory to save configuration files. Will be created if non-existent.
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overwrite : bool, optional
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Overwrite existing configuration files.
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Defaults to False.
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"""
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def export(name: str, obj: Union[h5py.Dataset,h5py.Group], output: Union[str,List[str]], overwrite: bool):
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if type(obj) == h5py.Dataset and _match(output,[name]):
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d = obj.attrs['description'] if h5py3 else obj.attrs['description'].decode()
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if not Path(name).exists() or overwrite:
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with util.open_text(name,'w') as f_out: f_out.write(obj[0].decode())
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print(f'Exported {d} to "{name}".')
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else:
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print(f'"{name}" exists, {d} not exported.')
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elif type(obj) == h5py.Group:
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os.makedirs(name, exist_ok=True)
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def export(name: str,
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obj: Union[h5py.Dataset,h5py.Group],
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output: Union[str,List[str]],
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cfg_dir: Path,
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overwrite: bool):
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cfg = cfg_dir/name
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if type(obj) == h5py.Dataset and _match(output,[name]):
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d = obj.attrs['description'] if h5py3 else obj.attrs['description'].decode()
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if overwrite or not cfg.exists():
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with util.open_text(cfg,'w') as f_out: f_out.write(obj[0].decode())
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print(f'Exported {d} to "{cfg}".')
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else:
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print(f'"{cfg}" exists, {d} not exported.')
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elif type(obj) == h5py.Group:
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cfg.mkdir(parents=True,exist_ok=True)
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cfg_dir = (Path.cwd() if target_dir is None else Path(target_dir))
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cfg_dir.mkdir(parents=True,exist_ok=True)
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with h5py.File(self.fname,'r') as f_in:
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f_in['setup'].visititems(partial(export,output=output,overwrite=overwrite))
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f_in['setup'].visititems(partial(export,
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output=output,
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cfg_dir=cfg_dir,
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overwrite=overwrite))
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File diff suppressed because it is too large
Load Diff
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@ -323,12 +323,9 @@ class TestResult:
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created_first = last.place('sigma').dtype.metadata['created']
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created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
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if overwrite == 'on':
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last = last.view(protected=False)
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else:
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last = last.view(protected=True)
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last = last.view(protected=overwrite != 'on')
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time.sleep(2.)
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time.sleep(2)
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try:
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last.add_calculation('#sigma#*0.0+311.','sigma','not the Cauchy stress')
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except ValueError:
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@ -380,13 +377,12 @@ class TestResult:
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@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<9, reason='missing "Direction" attribute')
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def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
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result = Result(ref_path/fname).view(increments=inc)
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os.chdir(tmp_path)
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result.export_VTK(output,parallel=False)
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result.export_VTK(output,target_dir=tmp_path,parallel=False)
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fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vti'
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v = VTK.load(tmp_path/fname)
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v.comments = 'n/a'
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v.save(tmp_path/fname,parallel=False)
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with open(fname) as f:
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with open(tmp_path/fname) as f:
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cur = hashlib.md5(f.read().encode()).hexdigest()
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if update:
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with open((ref_path/'export_VTK'/request.node.name).with_suffix('.md5'),'w') as f:
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@ -416,34 +412,34 @@ class TestResult:
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with pytest.raises(ValueError):
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single_phase.export_VTK(mode='invalid')
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def test_vtk_custom_path(self,tmp_path,single_phase):
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export_dir = tmp_path/'export_dir'
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single_phase.export_VTK(mode='point',target_dir=export_dir,parallel=False)
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assert set(os.listdir(export_dir))==set([f'{single_phase.fname.stem}_inc{i:02}.vtp' for i in range(0,40+1,4)])
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def test_XDMF_datatypes(self,tmp_path,single_phase,update,ref_path):
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for shape in [('scalar',()),('vector',(3,)),('tensor',(3,3)),('matrix',(12,))]:
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for what,shape in {'scalar':(),'vector':(3,),'tensor':(3,3),'matrix':(12,)}.items():
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for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']:
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single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')",f'{shape[0]}_{dtype}')
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fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'.xdmf'
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os.chdir(tmp_path)
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single_phase.export_XDMF()
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single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape},'{dtype}')",f'{what}_{dtype}')
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xdmf_path = tmp_path/single_phase.fname.with_suffix('.xdmf').name
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single_phase.export_XDMF(target_dir=tmp_path)
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if update:
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shutil.copy(tmp_path/fname,ref_path/fname)
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assert sorted(open(tmp_path/fname).read()) == sorted(open(ref_path/fname).read()) # XML is not ordered
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shutil.copy(xdmf_path,ref_path/xdmf_path.name)
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assert sorted(open(xdmf_path).read()) == sorted(open(ref_path/xdmf_path.name).read())
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@pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')),
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reason='https://discourse.vtk.org/t/2450')
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def test_XDMF_shape(self,tmp_path,single_phase):
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os.chdir(tmp_path)
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single_phase.export_XDMF()
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fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'.xdmf'
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single_phase.export_XDMF(target_dir=single_phase.fname.parent)
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fname = single_phase.fname.with_suffix('.xdmf')
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reader_xdmf = vtk.vtkXdmfReader()
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reader_xdmf.SetFileName(fname)
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reader_xdmf.Update()
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dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
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bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
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single_phase.view(increments=0).export_VTK(parallel=False)
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fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
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single_phase.view(increments=0).export_VTK(target_dir=single_phase.fname.parent,parallel=False)
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fname = single_phase.fname.with_name(single_phase.fname.stem+'_inc00.vti')
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reader_vti = vtk.vtkXMLImageDataReader()
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reader_vti.SetFileName(fname)
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reader_vti.Update()
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@ -455,6 +451,40 @@ class TestResult:
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with pytest.raises(TypeError):
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default.export_XDMF()
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def test_XDMF_custom_path(self,single_phase,tmp_path):
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os.chdir(tmp_path)
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single_phase.export_XDMF()
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assert single_phase.fname.with_suffix('.xdmf').name in os.listdir(tmp_path)
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export_dir = tmp_path/'export_dir'
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single_phase.export_XDMF(target_dir=export_dir)
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assert single_phase.fname.with_suffix('.xdmf').name in os.listdir(export_dir)
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@pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')),
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reason='https://discourse.vtk.org/t/2450')
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def test_XDMF_relabs_path(self,single_phase,tmp_path):
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def dims(xdmf):
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reader_xdmf = vtk.vtkXdmfReader()
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reader_xdmf.SetFileName(xdmf)
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reader_xdmf.Update()
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return reader_xdmf.GetOutput().GetDimensions()
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single_phase.export_XDMF(target_dir=tmp_path)
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xdmfname = single_phase.fname.with_suffix('.xdmf').name
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ref_dims = dims(tmp_path/xdmfname)
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for (d,info) in {
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'A': dict(absolute_path=True,
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mv='..',
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),
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'B': dict(absolute_path=False,
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mv='../A',
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),
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}.items():
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sub = tmp_path/d; sub.mkdir(exist_ok=True)
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single_phase.export_XDMF(target_dir=sub,absolute_path=info['absolute_path'])
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os.replace(sub/xdmfname,sub/info['mv']/xdmfname)
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assert ref_dims == dims(sub/info['mv']/xdmfname)
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@pytest.mark.parametrize('view,output,flatten,prune',
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[({},['F','P','F','L_p','F_e','F_p'],True,True),
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({'increments':3},'F',True,True),
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@ -511,7 +541,17 @@ class TestResult:
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@pytest.mark.parametrize('output',['material.yaml','*'])
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@pytest.mark.parametrize('overwrite',[True,False])
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def test_export_setup(self,ref_path,tmp_path,fname,output,overwrite):
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os.chdir(tmp_path)
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r = Result(ref_path/fname)
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r.export_setup(output,overwrite)
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r.export_setup(output,overwrite)
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r.export_setup(output,target_dir=tmp_path,overwrite=overwrite)
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def test_export_setup_custom_path(self,ref_path,tmp_path):
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src = ref_path/'4grains2x4x3_compressionY.hdf5'
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subdir = 'export_dir'
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absdir = tmp_path/subdir
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absdir.mkdir()
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r = Result(src)
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for t,cwd in zip([absdir,subdir,None],[tmp_path,tmp_path,absdir]):
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os.chdir(cwd)
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r.export_setup('material.yaml',target_dir=t)
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assert 'material.yaml' in os.listdir(absdir); (absdir/'material.yaml').unlink()
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