Merge branch 'development' into modularize-mech

VERSION

@@ -1 +1 @@
-v3.0.0-alpha-644-g063334fc1
+v3.0.0-alpha-658-g14209f3a1

python/damask/_asciitable.py

@@ -385,38 +385,3 @@ class ASCIItable():
     self.data = np.loadtxt(self.__IO__['in'],usecols=use,ndmin=2)
 
     return labels_missing
-
-# ------------------------------------------------------------------
-  def data_write(self):
-    """Write current data array and report alive output back."""
-    if len(self.data) == 0: return True
-
-    if isinstance(self.data[0],list):
-      return self.output_write(['\t'.join(map(self._quote,items)) for items in self.data])
-    else:
-      return self.output_write( '\t'.join(map(self._quote,self.data)))
-
-# ------------------------------------------------------------------
-  def data_writeArray(self):
-    """Write whole numpy array data."""
-    for row in self.data:
-      try:
-        output = list(map(repr,row))
-      except Exception:
-        output = [repr(row)]
-
-      try:
-        self.__IO__['out'].write('\t'.join(output) + '\n')
-      except Exception:
-        pass
-
-# ------------------------------------------------------------------
-  def data_append(self,
-                  what):
-    if isinstance(what, str):
-      self.data += [what]
-    else:
-      try:
-        for item in what: self.data_append(item)
-      except TypeError:
-        self.data += [str(what)]

python/damask/_geom.py

@@ -785,7 +785,7 @@ class Geom:
         """
         def mp(entry,mapper):
             return mapper[entry] if entry in mapper else entry
-       
+
         mp = np.vectorize(mp)
         mapper = dict(zip(from_material,to_material))
 
@@ -796,6 +796,20 @@ class Geom:
                    )
 
 
+    def sort(self):
+        """Sort material indices such that min(material) is located at (0,0,0)."""
+        a = self.material.flatten(order='F')
+        from_ma = pd.unique(a)
+        sort_idx = np.argsort(from_ma)
+        ma = np.unique(a)[sort_idx][np.searchsorted(from_ma,a,sorter = sort_idx)]
+
+        return Geom(material = ma.reshape(self.grid,order='F'),
+                    size     = self.size,
+                    origin   = self.origin,
+                    comments = self.comments+[util.execution_stamp('Geom','sort')],
+                   )
+
+
     def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
         """
         Offset material index of points in the vicinity of xxx.
@@ -822,15 +836,11 @@ class Geom:
         def tainted_neighborhood(stencil,trigger):
 
             me = stencil[stencil.shape[0]//2]
-            if len(trigger) == 0:
+            return np.any(stencil != me
-                return np.any(stencil != me)
+                          if len(trigger) == 0 else
-            if me in trigger:
+                          np.in1d(stencil,np.array(list(set(trigger) - {me}))))
-                trigger = set(trigger)
-                trigger.remove(me)
-                trigger = list(trigger)
-            return np.any(np.in1d(stencil,np.array(trigger)))
 
-        offset_ = np.nanmax(self.material) if offset is None else offset
+        offset_ = np.nanmax(self.material)+1 if offset is None else offset
         mask = ndimage.filters.generic_filter(self.material,
                                               tainted_neighborhood,
                                               size=1+2*vicinity,

python/damask/_test.py

@@ -316,12 +316,6 @@ class Test:
     return self.compare_Array(refName,curName)
 
 
-  def compare_ArrayCurCur(self,cur0,cur1):
-
-    cur0Name = self.fileInCurrent(cur0)
-    cur1Name = self.fileInCurrent(cur1)
-    return self.compare_Array(cur0Name,cur1Name)
-
   def compare_Table(self,headings0,file0,
                          headings1,file1,
                          normHeadings='',normType=None,

python/tests/test_Geom.py

@@ -6,6 +6,7 @@ from damask import Geom
 from damask import Table
 from damask import Rotation
 from damask import util
+from damask import seeds
 from damask import grid_filters
 
 
@@ -204,6 +205,11 @@ class TestGeom:
         assert np.array_equiv(t,f) or (not geom_equal(modified,default))
         assert geom_equal(default, modified.substitute(t,f))
 
+    def test_sort(self):
+        grid = np.random.randint(5,20,3)
+        m = Geom(np.random.randint(1,20,grid)*3,np.ones(3)).sort().material.flatten(order='F')
+        for i,v in enumerate(m):
+            assert i==0 or v > m[:i].max() or v in m[:i]
 
     @pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
                                            np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
@@ -384,3 +390,13 @@ class TestGeom:
         t = Table(np.column_stack((coords,z)),{'coords':3,'z':1})
         g = Geom.from_table(t,'coords',['1_coords','z'])
         assert g.N_materials == g.grid[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == grid[0]).all()
+
+
+    def test_from_table_recover(self,tmp_path):
+        grid = np.random.randint(60,100,3)
+        size = np.ones(3)+np.random.rand(3)
+        s = seeds.from_random(size,np.random.randint(60,100))
+        geom = Geom.from_Voronoi_tessellation(grid,size,s)
+        coords = grid_filters.cell_coord0(grid,size)
+        t = Table(np.column_stack((coords.reshape(-1,3,order='F'),geom.material.flatten(order='F'))),{'c':3,'m':1})
+        assert geom_equal(geom.sort().renumber(),Geom.from_table(t,'c',['m']))