Merge branch 'result-export-DADF5' into 'development'

export to new DADF5 file

See merge request damask/DAMASK!644

python/damask/_result.py

@@ -283,16 +283,16 @@ class Result:
 
     def times_in_range(self,
                        start: float = None,
-                       end: float = None) -> Sequence[int]:
+                       end: float = None) -> Sequence[float]:
         """
-        Get all increments within a given time range.
+        Get times of all increments within a given time range.
 
         Parameters
         ----------
         start : float, optional
-            Time of start increment. Defaults to first.
+            Time of start increment. Defaults to time of first.
         end : float, optional
-            Time of end increment. Defaults to last.
+            Time of end increment. Defaults to time of last.
 
         Returns
         -------
@@ -817,7 +817,7 @@ class Result:
         ----------
         T_sym : str
             Name of symmetric tensor dataset.
-        eigenvalue : {'max', 'mid', 'min'}
+        eigenvalue : {'max', 'mid', 'min'}, optional
             Eigenvalue. Defaults to 'max'.
 
         Examples
@@ -863,7 +863,7 @@ class Result:
         ----------
         T_sym : str
             Name of symmetric tensor dataset.
-        eigenvalue : {'max', 'mid', 'min'}
+        eigenvalue : {'max', 'mid', 'min'}, optional
             Eigenvalue to which the eigenvector corresponds.
             Defaults to 'max'.
 
@@ -897,7 +897,7 @@ class Result:
         ----------
         l : numpy.array of shape (3)
             Lab frame direction for inverse pole figure.
-        q : str
+        q : str, optional
             Name of the dataset containing the crystallographic orientation as quaternions.
             Defaults to 'O'.
 
@@ -1104,7 +1104,7 @@ class Result:
 
         Parameters
         ----------
-        q : str
+        q : str, optional
             Name of the dataset containing the crystallographic orientation as quaternions.
             Defaults to 'O'.
         uvw|hkl : numpy.ndarray of shape (3)
@@ -1528,7 +1528,7 @@ class Result:
 
         Parameters
         ----------
-        output : (list of) str
+        output : (list of) str, optional
             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
@@ -1663,7 +1663,7 @@ class Result:
 
 
     def export_VTK(self,
-                   output: Union[str,list] = '*',
+                   output: Union[str,List[str]] = '*',
                    mode: str = 'cell',
                    constituents: IntSequence = None,
                    target_dir: Union[str, Path] = None,
@@ -1683,7 +1683,7 @@ class Result:
         output : (list of) str, optional
             Names of the datasets to export to the VTK file.
             Defaults to '*', in which case all datasets are exported.
-        mode : {'cell', 'point'}
+        mode : {'cell', 'point'}, optional
             Export in cell format or point format.
             Defaults to 'cell'.
         constituents : (list of) int, optional
@@ -1691,13 +1691,13 @@ class Result:
             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_float : float, optional
             Fill value for non-existent entries of floating point type.
             Defaults to NaN.
-        fill_int : int
+        fill_int : int, optional
             Fill value for non-existent entries of integer type.
             Defaults to 0.
-        parallel : bool
+        parallel : bool, optional
             Write VTK files in parallel in a separate background process.
             Defaults to True.
 
@@ -1775,14 +1775,14 @@ class Result:
 
         Parameters
         ----------
-        output : (list of) str
+        output : (list of) str, optional
             Names of the datasets to read.
             Defaults to '*', in which case all datasets are read.
-        flatten : bool
+        flatten : bool, optional
             Remove singular levels of the folder hierarchy.
             This might be beneficial in case of single increment,
             phase/homogenization, or field. Defaults to True.
-        prune : bool
+        prune : bool, optional
             Remove branches with no data. Defaults to True.
 
         Returns
@@ -1814,6 +1814,50 @@ class Result:
         return None if (type(r) == dict and r == {}) else r
 
 
+    def export_DADF5(self,
+                     fname,
+                     output: Union[str, List[str]] = '*'):
+        """
+        Export visible components into a new DADF5 file.
+
+        A DADF5 (DAMASK HDF5) file contains DAMASK results.
+        Its group/folder structure reflects the layout in material.yaml.
+
+        Parameters
+        ----------
+        fname : str or pathlib.Path
+            Name of the DADF5 file to be created.
+        output : (list of) str, optional
+            Names of the datasets to export.
+            Defaults to '*', in which case all visible datasets are exported.
+
+        """
+        if Path(fname).expanduser().absolute() == self.fname:
+            raise PermissionError(f'cannot overwrite {self.fname}')
+        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.create(k,v)
+            for g in ['setup','geometry','cell_to']:
+                f_in.copy(g,f_out)
+
+            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()):
+                    f_in[inc]['geometry'].copy(out,f_out[inc]['geometry'])
+
+                for label in self.homogenizations:
+                    f_in[inc]['homogenization'].copy(label,f_out[inc]['homogenization'],shallow=True)
+                for label in self.phases:
+                    f_in[inc]['phase'].copy(label,f_out[inc]['phase'],shallow=True)
+
+                for ty in ['phase','homogenization']:
+                    for label in self.visible[ty+'s']:
+                        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])
+
+
     def place(self,
               output: Union[str, List[str]] = '*',
               flatten: bool = True,
@@ -1836,19 +1880,19 @@ class Result:
         output : (list of) str, optional
             Names of the datasets to read.
             Defaults to '*', in which case all datasets are placed.
-        flatten : bool
+        flatten : bool, optional
             Remove singular levels of the folder hierarchy.
             This might be beneficial in case of single increment or field.
             Defaults to True.
-        prune : bool
+        prune : bool, optional
             Remove branches with no data. Defaults to True.
         constituents : (list of) int, optional
             Constituents to consider.
             Defaults to None, in which case all constituents are considered.
-        fill_float : float
+        fill_float : float, optional
             Fill value for non-existent entries of floating point type.
             Defaults to NaN.
-        fill_int : int
+        fill_int : int, optional
             Fill value for non-existent entries of integer type.
             Defaults to 0.
 

python/tests/test_Result.py

@@ -5,10 +5,13 @@ import shutil
 import os
 import sys
 import hashlib
+import fnmatch
+import random
 from datetime import datetime
 
 import pytest
 import vtk
+import h5py
 import numpy as np
 
 from damask import Result
@@ -542,6 +545,11 @@ class TestResult:
     @pytest.mark.parametrize('overwrite',[True,False])
     def test_export_setup(self,ref_path,tmp_path,fname,output,overwrite):
         r = Result(ref_path/fname)
+        r.export_setup(output,target_dir=tmp_path)
+        with h5py.File(ref_path/fname,'r') as f_hdf5:
+            for file in fnmatch.filter(f_hdf5['setup'].keys(),output):
+                with open(tmp_path/file) as f:
+                    assert f_hdf5[f'setup/{file}'][()][0].decode() == f.read()
         r.export_setup(output,target_dir=tmp_path,overwrite=overwrite)
 
     def test_export_setup_custom_path(self,ref_path,tmp_path):
@@ -555,3 +563,21 @@ class TestResult:
             os.chdir(cwd)
             r.export_setup('material.yaml',target_dir=t)
             assert 'material.yaml' in os.listdir(absdir); (absdir/'material.yaml').unlink()
+
+    @pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5',
+                                      '6grains6x7x8_single_phase_tensionY.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.export_DADF5(tmp_path/fname)
+        r_exp = Result(tmp_path/fname)
+        assert str(r.get()) == str(r_exp.get())
+        assert str(r.place()) == str(r_exp.place())
+
+    @pytest.mark.parametrize('fname',['4grains2x4x3_compressionY.hdf5',
+                                      '6grains6x7x8_single_phase_tensionY.hdf5'])
+    def test_export_DADF5_name_clash(self,ref_path,tmp_path,fname):
+        r = Result(ref_path/fname)
+        with pytest.raises(PermissionError):
+            r.export_DADF5(r.fname)