Merge branch 'user_defined_add_calculation' into 'development'

User defined add calculation

See merge request damask/DAMASK!195

python/damask/_result.py

@@ -466,6 +466,11 @@ class Result:
             return f[self.get_dataset_location('orientation')[0]].attrs['Lattice'].astype('str')    # np.bytes_ to string
 
 
+    def enable_user_function(self,func):
+        globals()[func.__name__]=func
+        print(f'Function {func.__name__} enabled in add_calculation.')
+
+
     def read_dataset(self,path,c=0,plain=False):
         """
         Dataset for all points/cells.
@@ -504,7 +509,7 @@ class Result:
         else:
             return dataset
 
-
+    @property
     def cell_coordinates(self):
         """Return initial coordinates of the cell centers."""
         if self.structured:
@@ -513,6 +518,7 @@ class Result:
             with h5py.File(self.fname,'r') as f:
                 return f['geometry/x_c'][()]
 
+    @property
     def node_coordinates(self):
         """Return initial coordinates of the cell centers."""
         if self.structured:
@@ -561,7 +567,7 @@ class Result:
                           'Creator':     inspect.stack()[0][3][1:]
                           }
                  }
-    def add_calculation(self,label,formula,unit='n/a',description=None,vectorized=True):
+    def add_calculation(self,label,formula,unit='n/a',description=None):
         """
         Add result of a general formula.
 
@@ -575,13 +581,8 @@ class Result:
             Physical unit of the result.
         description : str, optional
             Human-readable description of the result.
-        vectorized : bool, optional
-            Indicate whether the formula can be used in vectorized form. Defaults to ‘True’.
 
         """
-        if not vectorized:
-            raise NotImplementedError
-
         dataset_mapping  = {d:d for d in set(re.findall(r'#(.*?)#',formula))}                       # datasets used in the formula
         args             = {'formula':formula,'label':label,'unit':unit,'description':description}
         self._add_generic_pointwise(self._add_calculation,dataset_mapping,args)

python/tests/test_Geom.py

@@ -1,5 +1,4 @@
 import copy
-import os
 
 import pytest
 import numpy as np
@@ -26,7 +25,7 @@ def default():
 @pytest.fixture
 def reference_dir(reference_dir_base):
     """Directory containing reference results."""
-    return os.path.join(reference_dir_base,'Geom')
+    return reference_dir_base/'Geom'
 
 
 class TestGeom:
@@ -87,7 +86,7 @@ class TestGeom:
         modified = copy.deepcopy(default)
         modified.mirror(directions,reflect)
         tag = f'directions={"-".join(directions)}_reflect={reflect}'
-        reference = os.path.join(reference_dir,f'mirror_{tag}.geom')
+        reference = reference_dir/f'mirror_{tag}.geom'
         if update: modified.to_file(reference)
         assert geom_equal(modified,Geom.from_file(reference))
 
@@ -96,7 +95,7 @@ class TestGeom:
         modified = copy.deepcopy(default)
         modified.clean(stencil)
         tag = f'stencil={stencil}'
-        reference = os.path.join(reference_dir,f'clean_{tag}.geom')
+        reference = reference_dir/f'clean_{tag}.geom'
         if update: modified.to_file(reference)
         assert geom_equal(modified,Geom.from_file(reference))
 
@@ -113,7 +112,7 @@ class TestGeom:
         modified = copy.deepcopy(default)
         modified.scale(grid)
         tag = f'grid={util.srepr(grid,"-")}'
-        reference = os.path.join(reference_dir,f'scale_{tag}.geom')
+        reference = reference_dir/f'scale_{tag}.geom'
         if update: modified.to_file(reference)
         assert geom_equal(modified,Geom.from_file(reference))
 
@@ -152,7 +151,7 @@ class TestGeom:
         modified = copy.deepcopy(default)
         modified.rotate(Rotation.from_Eulers(Eulers,degrees=True))
         tag = f'Eulers={util.srepr(Eulers,"-")}'
-        reference = os.path.join(reference_dir,f'rotate_{tag}.geom')
+        reference = reference_dir/f'rotate_{tag}.geom'
         if update: modified.to_file(reference)
         assert geom_equal(modified,Geom.from_file(reference))
 

python/tests/test_Orientation.py

@@ -33,7 +33,7 @@ def inverse_pole(orientation,axis,proper=False,SST=True):
 @pytest.fixture
 def reference_dir(reference_dir_base):
     """Directory containing reference results."""
-    return os.path.join(reference_dir_base,'Rotation')
+    return reference_dir_base/'Rotation'
 
 
 class TestOrientation:

python/tests/test_Result.py

@@ -1,6 +1,7 @@
 import time
 import shutil
 import os
+import sys
 from datetime import datetime
 
 import pytest
@@ -10,13 +11,14 @@ import h5py
 import damask
 from damask import Result
 from damask import mechanics
+from damask import grid_filters
 
 @pytest.fixture
 def default(tmp_path,reference_dir):
     """Small Result file in temp location for modification."""
     fname = '12grains6x7x8_tensionY.hdf5'
-    shutil.copy(os.path.join(reference_dir,fname),tmp_path)
+    shutil.copy(reference_dir/fname,tmp_path)
-    f = Result(os.path.join(tmp_path,fname))
+    f = Result(tmp_path/fname)
     f.pick('times',20.0)
     return f
 
@@ -24,13 +26,13 @@ def default(tmp_path,reference_dir):
 def single_phase(tmp_path,reference_dir):
     """Single phase Result file in temp location for modification."""
     fname = '6grains6x7x8_single_phase_tensionY.hdf5'
-    shutil.copy(os.path.join(reference_dir,fname),tmp_path)
+    shutil.copy(reference_dir/fname,tmp_path)
-    return Result(os.path.join(tmp_path,fname))
+    return Result(tmp_path/fname)
 
 @pytest.fixture
 def reference_dir(reference_dir_base):
     """Directory containing reference results."""
-    return os.path.join(reference_dir_base,'Result')
+    return reference_dir_base/'Result'
 
 
 class TestResult:
@@ -98,8 +100,19 @@ class TestResult:
         in_file   = default.read_dataset(loc['|Fe|'],0)
         assert np.allclose(in_memory,in_file)
 
-    def test_add_calculation(self,default):
+    @pytest.mark.parametrize('mode',['direct','function'])
-        default.add_calculation('x','2.0*np.abs(#F#)-1.0','-','my notes')
+    def test_add_calculation(self,default,tmp_path,mode):
+
+        if mode == 'direct':
+            default.add_calculation('x','2.0*np.abs(#F#)-1.0','-','my notes')
+        else:
+            with open(tmp_path/'f.py','w') as f:
+                f.write("import numpy as np\ndef my_func(field):\n  return 2.0*np.abs(field)-1.0\n")
+            sys.path.insert(0,str(tmp_path))
+            import f
+            default.enable_user_function(f.my_func)
+            default.add_calculation('x','my_func(#F#)','-','my notes')
+
         loc = {'F':    default.get_dataset_location('F'),
                'x':    default.get_dataset_location('x')}
         in_memory = 2.0*np.abs(default.read_dataset(loc['F'],0))-1.0
@@ -312,6 +325,16 @@ class TestResult:
         with pytest.raises(PermissionError):
             default.rename('P','another_new_name')
 
+    @pytest.mark.parametrize('mode',['cell','node'])
+    def test_coordinates(self,default,mode):
+         if   mode == 'cell':
+             a = grid_filters.cell_coord0(default.grid,default.size,default.origin)
+             b = default.cell_coordinates.reshape(tuple(default.grid)+(3,),order='F')
+         elif mode == 'node':
+             a = grid_filters.node_coord0(default.grid,default.size,default.origin)
+             b = default.node_coordinates.reshape(tuple(default.grid+1)+(3,),order='F')
+         assert np.allclose(a,b)
+
     @pytest.mark.parametrize('output',['F',[],['F','P']])
     def test_vtk(self,tmp_path,default,output):
         os.chdir(tmp_path)

python/tests/test_Rotation.py

@@ -6,7 +6,7 @@ import numpy as np
 from damask import Rotation
 from damask import _rotation
 
-n = 1100
+n = 1000
 atol=1.e-4
 
 @pytest.fixture

python/tests/test_Table.py

@@ -1,5 +1,3 @@
-import os
-
 import pytest
 import numpy as np
 
@@ -15,7 +13,7 @@ def default():
 @pytest.fixture
 def reference_dir(reference_dir_base):
     """Directory containing reference results."""
-    return os.path.join(reference_dir_base,'Table')
+    return reference_dir_base/'Table'
 
 class TestTable:
 
@@ -35,9 +33,13 @@ class TestTable:
         d = default.get('5_F')
         assert np.allclose(d,1.0) and d.shape[1:] == (1,)
 
-    def test_write_read_str(self,default,tmpdir):
+    @pytest.mark.parametrize('mode',['str','path'])
-        default.to_ASCII(str(tmpdir.join('default.txt')))
+    def test_write_read(self,default,tmpdir,mode):
-        new = Table.from_ASCII(str(tmpdir.join('default.txt')))
+        default.to_ASCII(tmpdir/'default.txt')
+        if   mode == 'path':
+            new = Table.from_ASCII(tmpdir/'default.txt')
+        elif mode == 'str':
+            new = Table.from_ASCII(str(tmpdir/'default.txt'))
         assert all(default.data==new.data) and default.shapes == new.shapes
 
     def test_write_read_file(self,default,tmpdir):
@@ -54,20 +56,25 @@ class TestTable:
             new = Table.from_ASCII(f)
         assert all(default.data==new.data) and default.shapes == new.shapes
 
-    def test_read_ang_str(self,reference_dir):
+
-        new = Table.from_ang(os.path.join(reference_dir,'simple.ang'))
+    @pytest.mark.parametrize('mode',['str','path'])
+    def test_read_ang(self,reference_dir,mode):
+        if   mode == 'path':
+            new = Table.from_ang(reference_dir/'simple.ang')
+        elif mode == 'str':
+            new = Table.from_ang(str(reference_dir/'simple.ang'))
         assert new.data.shape == (4,10) and \
                new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
 
     def test_read_ang_file(self,reference_dir):
-        f = open(os.path.join(reference_dir,'simple.ang'))
+        f = open(reference_dir/'simple.ang')
         new = Table.from_ang(f)
         assert new.data.shape == (4,10) and \
                new.labels == ['eu', 'pos', 'IQ', 'CI', 'ID', 'intensity', 'fit']
 
     @pytest.mark.parametrize('fname',['datatype-mix.txt','whitespace-mix.txt'])
     def test_read_strange(self,reference_dir,fname):
-        with open(os.path.join(reference_dir,fname)) as f:
+        with open(reference_dir/fname) as f:
             Table.from_ASCII(f)
 
     def test_set(self,default):