out of place behavior for VTK
This commit is contained in:
Martin Diehl
parent
c975a5b437
commit
e8a4f06634
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@ -644,8 +644,8 @@ class Grid:
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Compress with zlib algorithm. Defaults to True.
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"""
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v = VTK.from_image_data(self.cells,self.size,self.origin)
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v.add(self.material.flatten(order='F'),'material')
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v = VTK.from_image_data(self.cells,self.size,self.origin)\
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.add(self.material.flatten(order='F'),'material')
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v.comments += self.comments
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v.save(fname,parallel=False,compress=compress)
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@ -693,8 +693,8 @@ class Grid:
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Colors used to map material IDs.
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"""
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v = VTK.from_image_data(self.cells,self.size,self.origin)
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v.add(self.material.flatten(),'material')
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v = VTK.from_image_data(self.cells,self.size,self.origin) \
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.add(self.material.flatten(),'material')
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v.show('material',colormap)
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@ -1656,7 +1656,7 @@ class Result:
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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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v = 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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@ -1683,7 +1683,7 @@ class Result:
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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 = v.add(dataset,' / '.join(['/'.join([ty,field,label]),dataset.dtype.metadata['unit']]))
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v.save(f'{self.fname.stem}_inc{inc[10:].zfill(N_digits)}',parallel=parallel)
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@ -589,7 +589,7 @@ class Table:
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labels += [f'{util.srepr(self.shapes[l],"x")}:{i+1}_{l}' \
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for i in range(np.prod(self.shapes[l]))]
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f = open(fname,'w',newline='\n') if isinstance(fname, (str, Path)) else fname
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f = open(Path(fname).expanduser(),'w',newline='\n') if isinstance(fname, (str, Path)) else fname
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f.write('\n'.join([f'# {c}' for c in self.comments] + [' '.join(labels)])+'\n')
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self.data.to_csv(f,sep=' ',na_rep='nan',index=False,header=False)
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@ -42,11 +42,11 @@ class VTK:
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if isinstance(self.vtk_data,vtk.vtkImageData):
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dup = vtk.vtkImageData()
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elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid):
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dup = vtk.vtkUnstructuredGrid
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dup = vtk.vtkUnstructuredGrid()
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elif isinstance(self.vtk_data,vtk.vtkPolyData):
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dup = vtk.vtkPolyData
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dup = vtk.vtkPolyData()
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elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
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dup = vtk.vtkRectilinearGrid
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dup = vtk.vtkRectilinearGrid()
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else:
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raise TypeError
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@ -222,7 +222,7 @@ class VTK:
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VTK-based geometry from file.
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"""
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if not os.path.isfile(os.path.expanduser(fname)): # vtk has a strange error handling
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if not Path(fname).expanduser().is_file(): # vtk has a strange error handling
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raise FileNotFoundError(f'No such file: {fname}')
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if (ext := Path(fname).suffix) == '.vtk' or dataset_type is not None:
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reader = vtk.vtkGenericDataObjectReader()
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@ -315,7 +315,6 @@ class VTK:
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# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
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# Needs support for damask.Table
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def add(self,
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data: Union[np.ndarray, np.ma.MaskedArray, 'Table'],
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label: str = None):
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@ -332,7 +331,7 @@ class VTK:
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"""
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def _add_array(self,
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def _add_array(vtk_data,
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data: np.ndarray,
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label: str):
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@ -350,27 +349,29 @@ class VTK:
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d.SetName(label)
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if N_data == self.N_points:
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self.vtk_data.GetPointData().AddArray(d)
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elif N_data == self.N_cells:
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self.vtk_data.GetCellData().AddArray(d)
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if N_data == vtk_data.GetNumberOfPoints():
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vtk_data.GetPointData().AddArray(d)
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elif N_data == vtk_data.GetNumberOfCells():
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vtk_data.GetCellData().AddArray(d)
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else:
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raise ValueError(f'Data count mismatch ({N_data} ≠ {self.N_points} & {self.N_cells})')
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dup = self.copy()
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if isinstance(data,np.ndarray):
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if label is not None:
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_add_array(self,
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_add_array(dup.vtk_data,
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np.where(data.mask,data.fill_value,data) if isinstance(data,np.ma.MaskedArray) else data,
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label)
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else:
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raise ValueError('No label defined for numpy.ndarray')
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elif isinstance(data,Table):
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for l in data.labels:
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_add_array(self,data.get(l),l)
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_add_array(dup.vtk_data,data.get(l),l)
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else:
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raise TypeError
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return dup
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def get(self,
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label: str) -> np.ndarray:
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@ -147,8 +147,8 @@ class TestVTK:
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@pytest.mark.parametrize('N_values',[5*6*7,6*7*8])
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def test_add_get(self,default,data_type,shape,N_values):
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data = np.squeeze(np.random.randint(0,100,(N_values,)+shape)).astype(data_type)
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default.add(data,'data')
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assert (np.squeeze(data.reshape(N_values,-1)) == default.get('data')).all()
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new = default.add(data,'data')
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assert (np.squeeze(data.reshape(N_values,-1)) == new.get('data')).all()
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@pytest.mark.parametrize('shapes',[{'scalar':(1,),'vector':(3,),'tensor':(3,3)},
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@ -160,18 +160,17 @@ class TestVTK:
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for k,s in shapes.items():
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d[k] = dict(shape = s,
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data = np.random.random(N*np.prod(s)).reshape((N,-1)))
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default.add(Table(np.column_stack([d[k]['data'] for k in shapes.keys()]),shapes))
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new = default.add(Table(np.column_stack([d[k]['data'] for k in shapes.keys()]),shapes))
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for k,s in shapes.items():
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assert np.allclose(np.squeeze(d[k]['data']),default.get(k),rtol=1e-7)
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assert np.allclose(np.squeeze(d[k]['data']),new.get(k),rtol=1e-7)
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def test_add_masked(self,default):
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data = np.random.rand(5*6*7,3)
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masked = ma.MaskedArray(data,mask=data<.4,fill_value=42.)
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default.add(masked,'D')
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result_masked = str(default)
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default.add(np.where(masked.mask,masked.fill_value,masked),'D')
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assert result_masked == str(default)
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mask_auto = default.add(masked,'D')
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mask_manual = default.add(np.where(masked.mask,masked.fill_value,masked),'D')
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assert str(mask_manual) == str(mask_auto)
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def test_comments(self,tmp_path,default):
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@ -183,8 +182,7 @@ class TestVTK:
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@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')
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def test_compare_reference_polyData(self,update,ref_path,tmp_path):
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points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
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polyData = VTK.from_poly_data(points)
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polyData.add(points,'coordinates')
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polyData = VTK.from_poly_data(points).add(points,'coordinates')
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if update:
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polyData.save(ref_path/'polyData')
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else:
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@ -197,12 +195,12 @@ class TestVTK:
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grid = [np.arange(4)**2.,
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np.arange(5)**2.,
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np.arange(6)**2.] # ParaView renders tetrahedral meshing unless using float coordinates!
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rectilinearGrid = VTK.from_rectilinear_grid(grid)
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coords = np.stack(np.meshgrid(*grid,indexing='ij'),axis=-1)
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c = coords[:-1,:-1,:-1,:].reshape(-1,3,order='F')
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n = coords[:,:,:,:].reshape(-1,3,order='F')
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rectilinearGrid.add(np.ascontiguousarray(c),'cell')
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rectilinearGrid.add(np.ascontiguousarray(n),'node')
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rectilinearGrid = VTK.from_rectilinear_grid(grid) \
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.add(np.ascontiguousarray(c),'cell') \
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.add(np.ascontiguousarray(n),'node')
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if update:
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rectilinearGrid.save(ref_path/'rectilinearGrid')
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else:
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