Merge branch 'regrid-result' into 'development'

regrid/map when exporting DADF5

See merge request damask/DAMASK!748

python/damask/_result.py

@@ -1927,7 +1927,8 @@ class Result:
 
     def export_DADF5(self,
                      fname,
-                     output: Union[str, List[str]] = '*'):
+                     output: Union[str, List[str]] = '*',
+                     mapping = None):
         """
         Export visible components into a new DADF5 file.
 
@@ -1941,20 +1942,61 @@ class Result:
         output : (list of) str, optional
             Names of the datasets to export.
             Defaults to '*', in which case all visible datasets are exported.
+        mapping : numpy.ndarray of int, shape (:,:,:), optional
+            Indices for regridding.
 
         """
         if Path(fname).expanduser().absolute() == self.fname:
             raise PermissionError(f'cannot overwrite {self.fname}')
+
+        def cp(path_in,path_out,label,mapping):
+            if mapping is None:
+                path_in.copy(label,path_out)
+            else:
+                path_out.create_dataset(label,data=path_in[label][()][mapping])
+                path_out[label].attrs.update(path_in[label].attrs)
+
+
         with h5py.File(self.fname,'r') as f_in, h5py.File(fname,'w') as f_out:
-            for k,v in f_in.attrs.items():
+            f_out.attrs.update(f_in.attrs)
-                f_out.attrs.create(k,v)
+            for g in ['setup','geometry'] + (['cell_to'] if mapping is None else []):
-            for g in ['setup','geometry','cell_to']:
                 f_in.copy(g,f_out)
 
+            if mapping is not None:
+                cells = mapping.shape
+                mapping_flat = mapping.flatten(order='F')
+                f_out['geometry'].attrs['cells'] = cells
+                f_out.create_group('cell_to')                                                       # ToDo: attribute missing
+                mappings = {'phase':{},'homogenization':{}}                                         # type: ignore
+
+                mapping_phase = f_in['cell_to']['phase'][()][mapping_flat]
+                for p in np.unique(mapping_phase['label']):
+                    m = mapping_phase['label'] == p
+                    mappings['phase'][p] = mapping_phase[m]['entry']
+                    c = np.count_nonzero(m)
+                    mapping_phase[m] = list(zip((p,)*c,tuple(np.arange(c))))
+                f_out['cell_to'].create_dataset('phase',data=mapping_phase.reshape(np.prod(mapping_flat.shape),-1))
+
+                mapping_homog = f_in['cell_to']['homogenization'][()][mapping]
+                for h in np.unique(mapping_homog['label']):
+                    m = mapping_homog['label'] == h
+                    mappings['homogenization'][h] = mapping_homog[m]['entry']
+                    c = np.count_nonzero(m)
+                    mapping_homog[mapping_homog['label'] == h] = list(zip((h,)*c,tuple(np.arange(c))))
+                f_out['cell_to'].create_dataset('homogenization',data=mapping_homog.flatten())
+
+
             for inc in util.show_progress(self.visible['increments']):
                 f_in.copy(inc,f_out,shallow=True)
-                for out in _match(output,f_in['/'.join([inc,'geometry'])].keys()):
+                if mapping is None:
-                    f_in[inc]['geometry'].copy(out,f_out[inc]['geometry'])
+                    for label in ['u_p','u_n']:
+                        f_in[inc]['geometry'].copy(label,f_out[inc]['geometry'])
+                else:
+                    u_p = f_in[inc]['geometry']['u_p'][()][mapping_flat]
+                    f_out[inc]['geometry'].create_dataset('u_p',data=u_p)
+                    u_n = np.zeros((len(mapping_flat),3))                                           # ToDo: needs implementation
+                    f_out[inc]['geometry'].create_dataset('u_n',data=u_n)
+
 
                 for label in self.homogenizations:
                     f_in[inc]['homogenization'].copy(label,f_out[inc]['homogenization'],shallow=True)
@@ -1966,7 +2008,7 @@ class Result:
                         for field in _match(self.visible['fields'],f_in['/'.join([inc,ty,label])].keys()):
                             p = '/'.join([inc,ty,label,field])
                             for out in _match(output,f_in[p].keys()):
-                                f_in[p].copy(out,f_out[p])
+                                cp(f_in[p],f_out[p],out,None if mapping is None else mappings[ty][label.encode()])
 
 
     def export_simulation_setup(self,

python/tests/test_Result.py

@@ -603,11 +603,13 @@ class TestResult:
             assert 'material.yaml' in os.listdir(absdir); (absdir/'material.yaml').unlink()
 
     @pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5',
-                                      '6grains6x7x8_single_phase_tensionY.hdf5'])
+                                      '6grains6x7x8_single_phase_tensionY.hdf5',
+                                      '12grains6x7x8_tensionY.hdf5',
+                                      'check_compile_job1.hdf5',])
     def test_export_DADF5(self,ref_path,tmp_path,fname):
         r = Result(ref_path/fname)
         r = r.view(phases = random.sample(r.phases,1))
-        r = r.view(increments = random.sample(r.increments,np.random.randint(2,len(r.increments))))
+        r = r.view(increments = random.sample(r.increments,np.random.randint(1,len(r.increments))))
         r.export_DADF5(tmp_path/fname)
         r_exp = Result(tmp_path/fname)
         assert str(r.get()) == str(r_exp.get())
@@ -619,3 +621,12 @@ class TestResult:
         r = Result(ref_path/fname)
         with pytest.raises(PermissionError):
             r.export_DADF5(r.fname)
+
+    @pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5',
+                                      '6grains6x7x8_single_phase_tensionY.hdf5',
+                                      '12grains6x7x8_tensionY.hdf5'])
+    def test_export_DADF5_regrid(self,ref_path,tmp_path,fname):
+        r = Result(ref_path/fname)
+        m = grid_filters.regrid(r.size,np.broadcast_to(np.eye(3),tuple(r.cells)+(3,3)),r.cells*2)
+        r.export_DADF5(tmp_path/'regridded.hdf5',mapping=m)
+        assert np.all(Result(tmp_path/'regridded.hdf5').cells == r.cells*2)