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

python/damask/_result.py

@@ -276,7 +276,7 @@ class Result:
             Increment number of all increments within the given bounds.
 
         """
-        s,e = map(lambda x: int(x[10:] if isinstance(x,str) and x.startswith(prefix_inc) else x),
+        s,e = map(lambda x: int(x.split(prefix_inc)[-1] if isinstance(x,str) and x.startswith(prefix_inc) else x),
                   (self.incs[ 0] if start is None else start,
                    self.incs[-1] if  end  is None else  end))
         return [i for i in self.incs if s <= i <= e]
@@ -1516,7 +1516,9 @@ class Result:
 
 
     def export_XDMF(self,
-                    output: Union[str, List[str]] = '*'):
+                    output: Union[str, List[str]] = '*',
+                    target_dir: Union[str, Path] = None,
+                    absolute_path: bool = False):
         """
         Write XDMF file to directly visualize data from DADF5 file.
 
@@ -1529,12 +1531,17 @@ class Result:
         output : (list of) str
             Names of the datasets included in the XDMF file.
             Defaults to '*', in which case all datasets are considered.
+        target_dir : str or pathlib.Path, optional
+            Directory to save XDMF file. Will be created if non-existent.
+        absolute_path : bool, optional
+            Store absolute (instead of relative) path to DADF5 file.
+            Defaults to False, i.e. the XDMF file expects the
+            DADF5 file at a stable relative path.
 
         """
         if self.N_constituents != 1 or len(self.phases) != 1 or not self.structured:
             raise TypeError('XDMF output requires structured grid with single phase and single constituent.')
 
-
         attribute_type_map = defaultdict(lambda:'Matrix', ( ((),'Scalar'), ((3,),'Vector'), ((3,3),'Tensor')) )
 
         def number_type_map(dtype):
@@ -1544,29 +1551,34 @@ class Result:
 
 
         xdmf = ET.Element('Xdmf')
-        xdmf.attrib={'Version':  '2.0',
+        xdmf.attrib = {'Version':  '2.0',
-                     'xmlns:xi': 'http://www.w3.org/2001/XInclude'}
+                       'xmlns:xi': 'http://www.w3.org/2001/XInclude'}
 
         domain = ET.SubElement(xdmf, 'Domain')
 
         collection = ET.SubElement(domain, 'Grid')
-        collection.attrib={'GridType':       'Collection',
+        collection.attrib = {'GridType':       'Collection',
-                           'CollectionType': 'Temporal',
+                             'CollectionType': 'Temporal',
-                           'Name':           'Increments'}
+                             'Name':           'Increments'}
 
         time = ET.SubElement(collection, 'Time')
-        time.attrib={'TimeType': 'List'}
+        time.attrib = {'TimeType': 'List'}
 
         time_data = ET.SubElement(time, 'DataItem')
         times = [self.times[self.increments.index(i)] for i in self.visible['increments']]
-        time_data.attrib={'Format':     'XML',
+        time_data.attrib = {'Format':     'XML',
-                          'NumberType': 'Float',
+                            'NumberType': 'Float',
-                          'Dimensions': f'{len(times)}'}
+                            'Dimensions': f'{len(times)}'}
         time_data.text = ' '.join(map(str,times))
 
         attributes = []
         data_items = []
 
+        hdf5_name = self.fname.name
+        hdf5_dir  = self.fname.parent
+        xdmf_dir  = Path.cwd() if target_dir is None else Path(target_dir)
+        hdf5_link = (hdf5_dir if absolute_path else Path(os.path.relpath(hdf5_dir,xdmf_dir.resolve())))/hdf5_name
+
         with h5py.File(self.fname,'r') as f:
             for inc in self.visible['increments']:
 
@@ -1601,8 +1613,7 @@ class Result:
                 data_items[-1].attrib = {'Format':     'HDF',
                                          'Precision':  '8',
                                          'Dimensions': '{} {} {} 3'.format(*(self.cells[::-1]+1))}
-                data_items[-1].text = f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n'
+                data_items[-1].text = f'{hdf5_link}:/{inc}/geometry/u_n'
-
                 for ty in ['phase','homogenization']:
                     for label in self.visible[ty+'s']:
                         for field in _match(self.visible['fields'],f['/'.join([inc,ty,label])].keys()):
@@ -1624,9 +1635,10 @@ class Result:
                                                          'Precision':  f'{dtype.itemsize}',
                                                          'Dimensions': '{} {} {} {}'.format(*self.cells[::-1],1 if shape == () else
                                                                                                         np.prod(shape))}
-                                data_items[-1].text = f'{os.path.split(self.fname)[1]}:{name}'
+                                data_items[-1].text = f'{hdf5_link}:{name}'
 
-        with util.open_text(self.fname.with_suffix('.xdmf').name,'w') as f:
+        xdmf_dir.mkdir(parents=True,exist_ok=True)
+        with util.open_text((xdmf_dir/hdf5_name).with_suffix('.xdmf'),'w') as f:
             f.write(xml.dom.minidom.parseString(ET.tostring(xdmf).decode()).toprettyxml())
 
 
@@ -1654,6 +1666,7 @@ class Result:
                    output: Union[str,list] = '*',
                    mode: str = 'cell',
                    constituents: IntSequence = None,
+                   target_dir: Union[str, Path] = None,
                    fill_float: float = np.nan,
                    fill_int: int = 0,
                    parallel: bool = True):
@@ -1676,6 +1689,8 @@ class Result:
         constituents : (list of) int, optional
             Constituents to consider.
             Defaults to None, in which case all constituents are considered.
+        target_dir : str or pathlib.Path, optional
+            Directory to save VTK files. Will be created if non-existent.
         fill_float : float
             Fill value for non-existent entries of floating point type.
             Defaults to NaN.
@@ -1706,6 +1721,9 @@ class Result:
 
         at_cell_ph,in_data_ph,at_cell_ho,in_data_ho = self._mappings()
 
+        vtk_dir = Path.cwd() if target_dir is None else Path(target_dir)
+        vtk_dir.mkdir(parents=True,exist_ok=True)
+
         with h5py.File(self.fname,'r') as f:
             if self.version_minor >= 13:
                 creator = f.attrs['creator'] if h5py3 else f.attrs['creator'].decode()
@@ -1744,8 +1762,9 @@ class Result:
                         for label,dataset in outs.items():
                             v = v.set(' / '.join(['/'.join([ty,field,label]),dataset.dtype.metadata['unit']]),dataset)
 
-                v.save(f'{self.fname.stem}_inc{inc[10:].zfill(N_digits)}',parallel=parallel)
 
+                v.save(vtk_dir/f'{self.fname.stem}_inc{inc.split(prefix_inc)[-1].zfill(N_digits)}',
+                       parallel=parallel)
 
     def get(self,
             output: Union[str, List[str]] = '*',
@@ -1890,7 +1909,9 @@ class Result:
 
     def export_setup(self,
                      output: Union[str, List[str]] = '*',
-                     overwrite: bool = False):
+                     target_dir: Union[str, Path] = None,
+                     overwrite: bool = False,
+                     ):
         """
         Export configuration files.
 
@@ -1899,21 +1920,35 @@ class Result:
         output : (list of) str, optional
             Names of the datasets to export to the file.
             Defaults to '*', in which case all datasets are exported.
+        target_dir : str or pathlib.Path, optional
+            Directory to save configuration files. Will be created if non-existent.
         overwrite : bool, optional
             Overwrite existing configuration files.
             Defaults to False.
 
         """
-        def export(name: str, obj: Union[h5py.Dataset,h5py.Group], output: Union[str,List[str]], overwrite: bool):
+        def export(name: str,
-            if type(obj) == h5py.Dataset and  _match(output,[name]):
+                   obj: Union[h5py.Dataset,h5py.Group],
-                d = obj.attrs['description'] if h5py3 else obj.attrs['description'].decode()
+                   output: Union[str,List[str]],
-                if not Path(name).exists() or overwrite:
+                   cfg_dir: Path,
-                    with util.open_text(name,'w') as f_out: f_out.write(obj[0].decode())
+                   overwrite: bool):
-                    print(f'Exported {d} to "{name}".')
-                else:
-                    print(f'"{name}" exists, {d} not exported.')
-            elif type(obj) == h5py.Group:
-                os.makedirs(name, exist_ok=True)
 
+            cfg = cfg_dir/name
+
+            if type(obj) == h5py.Dataset and _match(output,[name]):
+                d = obj.attrs['description'] if h5py3 else obj.attrs['description'].decode()
+                if overwrite or not cfg.exists():
+                    with util.open_text(cfg,'w') as f_out: f_out.write(obj[0].decode())
+                    print(f'Exported {d} to "{cfg}".')
+                else:
+                    print(f'"{cfg}" exists, {d} not exported.')
+            elif type(obj) == h5py.Group:
+                cfg.mkdir(parents=True,exist_ok=True)
+
+        cfg_dir = (Path.cwd() if target_dir is None else Path(target_dir))
+        cfg_dir.mkdir(parents=True,exist_ok=True)
         with h5py.File(self.fname,'r') as f_in:
-            f_in['setup'].visititems(partial(export,output=output,overwrite=overwrite))
+            f_in['setup'].visititems(partial(export,
+                                             output=output,
+                                             cfg_dir=cfg_dir,
+                                             overwrite=overwrite))

python/tests/test_Result.py

@@ -323,12 +323,9 @@ class TestResult:
         created_first = last.place('sigma').dtype.metadata['created']
         created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
 
-        if overwrite == 'on':
+        last = last.view(protected=overwrite != 'on')
-            last = last.view(protected=False)
-        else:
-            last = last.view(protected=True)
 
-        time.sleep(2.)
+        time.sleep(2)
         try:
             last.add_calculation('#sigma#*0.0+311.','sigma','not the Cauchy stress')
         except ValueError:
@@ -380,13 +377,12 @@ class TestResult:
     @pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<9, reason='missing "Direction" attribute')
     def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
         result = Result(ref_path/fname).view(increments=inc)
-        os.chdir(tmp_path)
+        result.export_VTK(output,target_dir=tmp_path,parallel=False)
-        result.export_VTK(output,parallel=False)
         fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vti'
         v = VTK.load(tmp_path/fname)
         v.comments = 'n/a'
         v.save(tmp_path/fname,parallel=False)
-        with open(fname) as f:
+        with open(tmp_path/fname) as f:
             cur = hashlib.md5(f.read().encode()).hexdigest()
         if update:
             with open((ref_path/'export_VTK'/request.node.name).with_suffix('.md5'),'w') as f:
@@ -416,34 +412,34 @@ class TestResult:
         with pytest.raises(ValueError):
             single_phase.export_VTK(mode='invalid')
 
+    def test_vtk_custom_path(self,tmp_path,single_phase):
+        export_dir = tmp_path/'export_dir'
+        single_phase.export_VTK(mode='point',target_dir=export_dir,parallel=False)
+        assert set(os.listdir(export_dir))==set([f'{single_phase.fname.stem}_inc{i:02}.vtp' for i in range(0,40+1,4)])
 
     def test_XDMF_datatypes(self,tmp_path,single_phase,update,ref_path):
-        for shape in [('scalar',()),('vector',(3,)),('tensor',(3,3)),('matrix',(12,))]:
+        for what,shape in {'scalar':(),'vector':(3,),'tensor':(3,3),'matrix':(12,)}.items():
             for dtype in ['f4','f8','i1','i2','i4','i8','u1','u2','u4','u8']:
-                single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape[1]},'{dtype}')",f'{shape[0]}_{dtype}')
+                single_phase.add_calculation(f"np.ones(np.shape(#F#)[0:1]+{shape},'{dtype}')",f'{what}_{dtype}')
-        fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'.xdmf'
+        xdmf_path = tmp_path/single_phase.fname.with_suffix('.xdmf').name
-        os.chdir(tmp_path)
+        single_phase.export_XDMF(target_dir=tmp_path)
-        single_phase.export_XDMF()
         if update:
-            shutil.copy(tmp_path/fname,ref_path/fname)
+            shutil.copy(xdmf_path,ref_path/xdmf_path.name)
-
+        assert sorted(open(xdmf_path).read()) == sorted(open(ref_path/xdmf_path.name).read())
-        assert sorted(open(tmp_path/fname).read()) == sorted(open(ref_path/fname).read())           # XML is not ordered
 
     @pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')),
                         reason='https://discourse.vtk.org/t/2450')
     def test_XDMF_shape(self,tmp_path,single_phase):
-        os.chdir(tmp_path)
+        single_phase.export_XDMF(target_dir=single_phase.fname.parent)
-
+        fname = single_phase.fname.with_suffix('.xdmf')
-        single_phase.export_XDMF()
-        fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'.xdmf'
         reader_xdmf = vtk.vtkXdmfReader()
         reader_xdmf.SetFileName(fname)
         reader_xdmf.Update()
         dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
         bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
 
-        single_phase.view(increments=0).export_VTK(parallel=False)
+        single_phase.view(increments=0).export_VTK(target_dir=single_phase.fname.parent,parallel=False)
-        fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
+        fname = single_phase.fname.with_name(single_phase.fname.stem+'_inc00.vti')
         reader_vti = vtk.vtkXMLImageDataReader()
         reader_vti.SetFileName(fname)
         reader_vti.Update()
@@ -455,6 +451,40 @@ class TestResult:
         with pytest.raises(TypeError):
             default.export_XDMF()
 
+    def test_XDMF_custom_path(self,single_phase,tmp_path):
+        os.chdir(tmp_path)
+        single_phase.export_XDMF()
+        assert single_phase.fname.with_suffix('.xdmf').name in os.listdir(tmp_path)
+        export_dir = tmp_path/'export_dir'
+        single_phase.export_XDMF(target_dir=export_dir)
+        assert single_phase.fname.with_suffix('.xdmf').name in os.listdir(export_dir)
+
+    @pytest.mark.skipif(not (hasattr(vtk,'vtkXdmfReader') and hasattr(vtk.vtkXdmfReader(),'GetOutput')),
+                        reason='https://discourse.vtk.org/t/2450')
+    def test_XDMF_relabs_path(self,single_phase,tmp_path):
+        def dims(xdmf):
+            reader_xdmf = vtk.vtkXdmfReader()
+            reader_xdmf.SetFileName(xdmf)
+            reader_xdmf.Update()
+            return reader_xdmf.GetOutput().GetDimensions()
+
+        single_phase.export_XDMF(target_dir=tmp_path)
+        xdmfname = single_phase.fname.with_suffix('.xdmf').name
+        ref_dims = dims(tmp_path/xdmfname)
+
+        for (d,info) in {
+             'A': dict(absolute_path=True,
+                       mv='..',
+                       ),
+             'B': dict(absolute_path=False,
+                       mv='../A',
+                       ),
+            }.items():
+            sub = tmp_path/d; sub.mkdir(exist_ok=True)
+            single_phase.export_XDMF(target_dir=sub,absolute_path=info['absolute_path'])
+            os.replace(sub/xdmfname,sub/info['mv']/xdmfname)
+            assert ref_dims == dims(sub/info['mv']/xdmfname)
+
     @pytest.mark.parametrize('view,output,flatten,prune',
             [({},['F','P','F','L_p','F_e','F_p'],True,True),
              ({'increments':3},'F',True,True),
@@ -511,7 +541,17 @@ class TestResult:
     @pytest.mark.parametrize('output',['material.yaml','*'])
     @pytest.mark.parametrize('overwrite',[True,False])
     def test_export_setup(self,ref_path,tmp_path,fname,output,overwrite):
-        os.chdir(tmp_path)
         r = Result(ref_path/fname)
-        r.export_setup(output,overwrite)
+        r.export_setup(output,target_dir=tmp_path,overwrite=overwrite)
-        r.export_setup(output,overwrite)
+
+    def test_export_setup_custom_path(self,ref_path,tmp_path):
+        src = ref_path/'4grains2x4x3_compressionY.hdf5'
+        subdir = 'export_dir'
+        absdir = tmp_path/subdir
+        absdir.mkdir()
+
+        r = Result(src)
+        for t,cwd in zip([absdir,subdir,None],[tmp_path,tmp_path,absdir]):
+            os.chdir(cwd)
+            r.export_setup('material.yaml',target_dir=t)
+            assert 'material.yaml' in os.listdir(absdir); (absdir/'material.yaml').unlink()