make sure vectorattributes definitions are stored and copied

fixes amusecode#856

src/amuse/datamodel/particles.py

@@ -386,6 +386,7 @@ def copy(self, memento = None, keep_structure = False, filter_attributes = lambd
                 converted.append(x)
         result.add_particles_to_store(keys, attributes, converted)
 
+        object.__setattr__(result, "_derived_attributes", CompositeDictionary(self._derived_attributes))
         result._private.collection_attributes = self._private.collection_attributes._copy_for_collection(result)
 
         return result
@@ -425,6 +426,7 @@ def copy_to_new_particles(self, keys = None, keys_generator = None, memento = No
 
         result.add_particles_to_store(particle_keys, attributes, converted)
 
+        object.__setattr__(result, "_derived_attributes", CompositeDictionary(self._derived_attributes))
         result._private.collection_attributes = self._private.collection_attributes._copy_for_collection(result)
 
         return result

src/amuse/io/store_v2.py

@@ -23,6 +23,8 @@
 from amuse.datamodel import Grid
 from amuse.datamodel import GridPoint
 from amuse.datamodel import AbstractSet
+from amuse.datamodel.base import VectorAttribute
+
 
 from amuse.io import store_v1
 
@@ -847,6 +849,7 @@ def store_particles(self, particles, extra_attributes = {}, parent=None, mapping
         self.hdf5file.flush()
         self.store_collection_attributes(particles, group, extra_attributes, links)
         self.store_values(particles, group, links)
+        self.store_selected_derived_attributes(particles,group)    
 
         mapping_from_setid_to_group[id(particles)] = group
 
@@ -868,6 +871,7 @@ def store_grid(self, grid, extra_attributes = {}, parent=None, mapping_from_seti
             compression_opts=self.compression_opts,
         )
 
+        self.store_selected_derived_attributes(grid, group)
         self.store_collection_attributes(grid, group, extra_attributes, links)
         self.store_values(grid, group, links)
 
@@ -924,8 +928,15 @@ def store_values(self, container, group, links = []):
                     )
                     dataset.attrs["units"] = "none".encode('ascii')
 
+    def store_selected_derived_attributes(self, container, group):
+        saving=dict()
+        for key in container._derived_attributes.keys():
+            attr=container._derived_attributes[key]
+            if key not in container.GLOBAL_DERIVED_ATTRIBUTES and isinstance(attr, VectorAttribute):
+                saving[key]=attr
+        if len(saving): 
+            group.attrs["extra_vector_attributes"]=pickle_to_string(saving)
 
-
     def store_linked_array(self, attribute, attributes_group, quantity, group, links):
         subgroup = attributes_group.create_group(attribute)
         shape = quantity.shape
@@ -1127,8 +1138,9 @@ def load_particles_from_group(self, group):
 
             self.mapping_from_groupid_to_set[group.id] = particles
             self.load_collection_attributes(particles, group)
-
-
+        if "extra_vector_attributes" in group.attrs.keys():
+            self.load_extra_derived_attributes(particles, group)
+
         return particles
 
     def load_grid_from_group(self, group):
@@ -1143,9 +1155,16 @@ def load_grid_from_group(self, group):
         container._private.attribute_storage = HDF5GridAttributeStorage(shape, group, self)
         self.mapping_from_groupid_to_set[group.id] = container
         self.load_collection_attributes(container, group)
+        if "extra_vector_attributes" in group.attrs.keys():
+            self.load_extra_derived_attributes(container, group)
 
         return container
 
+    def load_extra_derived_attributes(self, container, group):
+        attrs=unpickle_from_string(group.attrs["extra_vector_attributes"])
+        for key, attr in attrs.items():
+            container._derived_attributes[key]=attr
+
     def load_from_group(self, group):
         container_type = group.attrs['type'] if isinstance(group.attrs['type'], str) else group.attrs['type'].decode('ascii') 
 

src/amuse/test/suite/ticket_tests/test_github856.py

@@ -0,0 +1,32 @@
+import os
+from amuse.test import amusetest
+
+from amuse.datamodel import new_cartesian_grid, Particles
+
+from amuse.io import read_set_from_file, write_set_to_file
+
+class test_github856(amusetest.TestCase):
+    def test1(self):
+        filename=os.path.join(self.get_path_to_results(),"github856.amuse")
+
+        g1=new_cartesian_grid((5,5), 1)
+        write_set_to_file(g1,filename,"amuse")
+        del g1
+        g2=read_set_from_file(filename,"amuse")
+        self.assertEquals(g2.get_axes_names(),"xy")
+
+    def test2(self):      
+        g1=Particles(lon=[1,2], lat=[3,4])
+        g1.add_vector_attribute("lonlat",["lon","lat"])
+        g2=g1.copy()
+        self.assertEquals(g2.lonlat,[[1,3],[2,4]])
+
+    def test3(self):
+        filename=os.path.join(self.get_path_to_results(),"github856_2.amuse")
+
+        g1=Particles(lon=[1,2], lat=[3,4])
+        g1.add_vector_attribute("lonlat",["lon","lat"])
+        write_set_to_file(g1,filename,"amuse")
+        del g1
+        g2=read_set_from_file(filename,"amuse")
+        self.assertEquals(g2.lonlat,[[1,3],[2,4]])