regrid/map when exporting DADF5
This commit is contained in:
Martin Diehl
parent
69e4d17be2
commit
d2e85ef15b
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@ -1044,7 +1044,7 @@ class Grid:
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Parameters
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----------
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idx : numpy.ndarray of int, shape (:,:,:) or (:,:,:,3)
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Grid of flat indices or coordinate indices.
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Grid of flat indices or coordinate indices.
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Returns
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-------
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@ -1927,7 +1927,8 @@ class Result:
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def export_DADF5(self,
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fname,
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output: Union[str, List[str]] = '*'):
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output: Union[str, List[str]] = '*',
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mapping = None):
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"""
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Export visible components into a new DADF5 file.
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@ -1941,20 +1942,61 @@ class Result:
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output : (list of) str, optional
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Names of the datasets to export.
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Defaults to '*', in which case all visible datasets are exported.
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mapping : numpy.ndarray of int, shape (:,:,:), optional
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Indices for regridding.
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"""
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if Path(fname).expanduser().absolute() == self.fname:
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raise PermissionError(f'cannot overwrite {self.fname}')
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def cp(path_in,path_out,label,mapping):
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if mapping is None:
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path_in.copy(label,path_out)
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else:
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path_out.create_dataset(label,data=path_in[label][()][mapping])
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path_out[label].attrs.update(path_in[label].attrs)
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with h5py.File(self.fname,'r') as f_in, h5py.File(fname,'w') as f_out:
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for k,v in f_in.attrs.items():
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f_out.attrs.create(k,v)
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for g in ['setup','geometry','cell_to']:
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f_out.attrs.update(f_in.attrs)
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for g in ['setup','geometry'] + (['cell_to'] if mapping is None else []):
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f_in.copy(g,f_out)
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if mapping is not None:
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cells = mapping.shape
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mapping_flat = mapping.flatten(order='F')
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f_out['geometry'].attrs['cells'] = cells
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f_out.create_group('cell_to') # ToDo: attribute missing
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mappings = {'phase':{},'homogenization':{}} # type: ignore
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mapping_phase = f_in['cell_to']['phase'][()][mapping_flat]
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for p in np.unique(mapping_phase['label']):
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m = mapping_phase['label'] == p
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mappings['phase'][p] = mapping_phase[m]['entry']
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c = np.count_nonzero(m)
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mapping_phase[m] = list(zip((p,)*c,tuple(np.arange(c))))
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f_out['cell_to'].create_dataset('phase',data=mapping_phase.reshape(np.prod(mapping_flat.shape),-1))
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mapping_homog = f_in['cell_to']['homogenization'][()][mapping]
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for h in np.unique(mapping_homog['label']):
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m = mapping_homog['label'] == h
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mappings['homogenization'][h] = mapping_homog[m]['entry']
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c = np.count_nonzero(m)
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mapping_homog[mapping_homog['label'] == h] = list(zip((h,)*c,tuple(np.arange(c))))
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f_out['cell_to'].create_dataset('homogenization',data=mapping_homog.flatten())
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for inc in util.show_progress(self.visible['increments']):
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f_in.copy(inc,f_out,shallow=True)
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for out in _match(output,f_in['/'.join([inc,'geometry'])].keys()):
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f_in[inc]['geometry'].copy(out,f_out[inc]['geometry'])
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if mapping is None:
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for label in ['u_p','u_n']:
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f_in[inc]['geometry'].copy(label,f_out[inc]['geometry'])
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else:
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u_p = f_in[inc]['geometry']['u_p'][()][mapping_flat]
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f_out[inc]['geometry'].create_dataset('u_p',data=u_p)
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u_n = np.zeros((len(mapping_flat),3)) # ToDo: needs implementation
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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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f_in[inc]['homogenization'].copy(label,f_out[inc]['homogenization'],shallow=True)
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@ -1966,7 +2008,7 @@ class Result:
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for field in _match(self.visible['fields'],f_in['/'.join([inc,ty,label])].keys()):
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p = '/'.join([inc,ty,label,field])
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for out in _match(output,f_in[p].keys()):
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f_in[p].copy(out,f_out[p])
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cp(f_in[p],f_out[p],out,None if mapping is None else mappings[ty][label.encode()])
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def export_simulation_setup(self,
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@ -603,11 +603,13 @@ class TestResult:
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assert 'material.yaml' in os.listdir(absdir); (absdir/'material.yaml').unlink()
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@pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5',
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'6grains6x7x8_single_phase_tensionY.hdf5'])
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'6grains6x7x8_single_phase_tensionY.hdf5',
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'12grains6x7x8_tensionY.hdf5',
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'check_compile_job1.hdf5',])
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def test_export_DADF5(self,ref_path,tmp_path,fname):
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r = Result(ref_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(2,len(r.increments))))
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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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@ -619,3 +621,12 @@ class TestResult:
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r = Result(ref_path/fname)
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with pytest.raises(PermissionError):
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r.export_DADF5(r.fname)
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@pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5',
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'6grains6x7x8_single_phase_tensionY.hdf5',
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'12grains6x7x8_tensionY.hdf5'])
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def test_export_DADF5_regrid(self,ref_path,tmp_path,fname):
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r = Result(ref_path/fname)
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m = grid_filters.regrid(r.size,np.broadcast_to(np.eye(3),tuple(r.cells)+(3,3)),r.cells*2)
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r.export_DADF5(tmp_path/'regridded.hdf5',mapping=m)
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assert np.all(Result(tmp_path/'regridded.hdf5').cells == r.cells*2)
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