Merge pull request #237 from simphony/feature-material

Feature material

doc/Makefile

@@ -181,4 +181,4 @@ uml:
 	java -jar plantuml.jar "source/uml/" "source/images"
 	mv source/uml/*.png source/images
 	@echo
-	@echo "Coversion finished the uml files are in source/images."
+	@echo "Conversion finished the uml files are in source/images."

doc/source/api/cuds.rst

@@ -56,6 +56,8 @@ Pure Python implementation
    ~mesh.Edge
    ~mesh.Face
    ~mesh.Cell
+   ~material.Material
+   ~materials.Materials
 
 .. rubric:: Functions
 
@@ -89,3 +91,11 @@ Pure Python implementation
 .. automodule:: simphony.cuds.particles
    :members:
    :undoc-members:
+
+.. automodule:: simphony.cuds.material
+   :members:
+   :undoc-members:
+
+.. automodule:: simphony.cuds.materials
+   :members:
+   :undoc-members:

doc/source/cuba.rst

@@ -71,4 +71,5 @@ PoissonRatio                Poisson Ratio
 LnOfRestitutionCoefficient  Natural Logarithm of the Restitution Coefficient                      ['DEM']                                            LN_OF_RESTITUTION_COEFFICIENT        65  [1]      double
 RollingFriction             Rolling Friction coefficient                                          ['DEM']                                            ROLLING_FRICTION                     66  [1]      double
 VolumeFraction              Volume fraction                                                       ['FEM', 'FVM']                                     VOLUME_FRACTION                      67  [1]      double
+Material                    Material                                                              ['ATM', 'DEM', 'FEM', 'FVM', 'LBM', 'SPH', 'VIS']  MATERIAL                             68  [1]      uuid
 ==========================  ====================================================================  =================================================  =============================  ========  =======  =======

doc/source/cuds_definition.rst

@@ -89,3 +89,14 @@ Core items
 The CUBA attribute container part of the SimPhoNy core. A dictionary
 like object maps :class:`~.CUBA` enum keys to they values. In its
 native python implementation it can support all CUBA attributes.
+
+Materials
+----------
+
+.. figure:: ./images/material_materials.png
+
+   **Figure 4:** UML diagram of Materials and Material.
+
+In the SimPhoNy modeling framework, :class:`~.Materials` and :class:`~.Material`
+are used to describe materials and to define common material properties. Each
+low-level object (e.g. Point, Particle) can be of a certain material.

doc/source/uml/engine.txt

@@ -3,6 +3,7 @@ abstract class ABCModelingEngine {
   BC : DataContainer
   CM : DataContainer
   SP : DataContainer
+  materials : Materials
   --
   {abstract} run()
   ..

doc/source/uml/material.txt

@@ -0,0 +1,9 @@
+@startuml
+class Material {
+   uid: uuid.UUID
+   data: DataContainer
+   description: str
+   -- classmethods --
+   from_material(material: Material): Material {copy}
+}
+@enduml

doc/source/uml/material_materials.txt

@@ -0,0 +1,4 @@
+@startuml
+!include materials.txt
+!include material.txt
+@enduml

doc/source/uml/materials.txt

@@ -0,0 +1,8 @@
+@startuml
+class Materials {
+  add_material(Material)
+  get_material(uid: uuid.UUID): Materials
+  update_material(material: Material)
+  iter_materials(uids: iterable of uuid.UUID {optional}): iterator of Materials {unordered}
+}
+@enduml

simphony/core/cuba.py

@@ -71,3 +71,4 @@ class CUBA(IntEnum):
     LN_OF_RESTITUTION_COEFFICIENT = 65
     ROLLING_FRICTION = 66
     VOLUME_FRACTION = 67
+    MATERIAL = 68

simphony/core/cuba.yml

@@ -473,4 +473,11 @@
   name: VolumeFraction
   number: 67
   shape: [1]
-  type: double
+  type: double
+- description: Material
+  domain: [ATM, DEM, FEM, FVM, LBM, SPH, VIS]
+  key: MATERIAL
+  name: Material
+  number: 68
+  shape: [1]
+  type: uuid

simphony/core/keywords.py

@@ -554,4 +554,12 @@
         number=67,
         shape=[1],
         dtype=numpy.float64),
+    'MATERIAL': Keyword(
+        name='Material',
+        description='Material',  # noqa
+        domain=['ATM', 'DEM', 'FEM', 'FVM', 'LBM', 'SPH', 'VIS'],
+        key='MATERIAL',
+        number=68,
+        shape=[1],
+        dtype='uuid'),
 }

simphony/cuds/abc_modeling_engine.py

@@ -16,6 +16,8 @@ class ABCModelingEngine(object):  # pragma: no cover
         container of attributes related to the computational method
     SP : DataContainer
         container of attributes related to the system parameters/conditions
+    materials : Materials
+        materials related to state data
 
     """
     __metaclass__ = ABCMeta

simphony/cuds/material.py

@@ -0,0 +1,31 @@
+import uuid
+
+from simphony.core.data_container import DataContainer
+
+
+class Material(object):
+    """A class that represents a material.
+
+    Class describes a material and its data.
+
+    Attributes
+    ----------
+    uid : uuid.UUID
+        the id of the material. If None, then it is generated
+    data : DataContainer
+        data associated with this material
+    description : str
+        textual description of the material
+
+    """
+    def __init__(self, uid=None, data=None, description=""):
+        self.data = data if data else DataContainer()
+        self.uid = uid if uid else uuid.uuid4()
+        self.description = description
+
+    @classmethod
+    def from_material(cls, material):
+        return cls(
+            uid=material.uid,
+            description=material.description,
+            data=DataContainer(material.data))

simphony/cuds/materials.py

@@ -0,0 +1,99 @@
+from simphony.cuds.material import Material
+
+
+class Materials(object):
+    """A class that contains materials.
+
+    Class manages the materials.
+
+    """
+    def __init__(self):
+        self._materials = {}
+
+    def add_material(self, material):
+        """Add a material
+
+        Parameters
+        ----------
+        material : Material
+            the material to be added.
+
+        Raises
+        ------
+        ValueError:
+            If a material with the same uid already exists
+
+        """
+        try:
+            self._materials[material.uid] = Material.from_material(material)
+        except KeyError:
+            raise ValueError
+
+    def remove_material(self, uid):
+        """ Remove a material
+
+        Parameters
+        ----------
+        uid: uuid.UUID
+            the id of the material to be deleted
+
+        Raises
+        ------
+        KeyError:
+            If there is no material with the given uid
+
+        """
+        del self._materials[uid]
+
+    def update_material(self, material):
+        """ Update a material
+
+        Parameters
+        ----------
+        material : Material
+            the material to be updated.
+
+        Raises
+        ------
+        ValueError:
+            If a material with this uid does not exist
+
+        """
+        self._materials[material.uid] = Material.from_material(material)
+
+    def get_material(self, uid):
+        """ Get the material
+
+        Parameters
+        ----------
+        uid: uuid.UUID
+            the id of the material to be retrieved.
+
+        Returns
+        -------
+        material
+
+        Raises
+        ------
+        KeyError:
+            If there is no material with the given uid
+
+        """
+        return Material.from_material(self._materials[uid])
+
+    def iter_materials(self, uids=None):
+        """ Returns an iterator over a subset or all of the materials.
+
+        Parameters
+        ----------
+        uids : sequence of uids, optional
+            uids of specific material to be iterated over. If uids is not
+            given, then all materials will be iterated over.
+
+        """
+        if uids is None:
+            for material in self._materials.itervalues():
+                yield material
+        else:
+            for uid in uids:
+                yield self.get_material(uid)

simphony/cuds/tests/test_materials.py

@@ -0,0 +1,66 @@
+import unittest
+import uuid
+from functools import partial
+
+from simphony.cuds.materials import Materials
+from simphony.cuds.material import Material
+from simphony.testing.utils import (compare_material,
+                                    create_data_container)
+
+
+class TestMaterials(unittest.TestCase):
+    """Test case for Materials class."""
+
+    def setUp(self):
+        self.addTypeEqualityFunc(Material,
+                                 partial(compare_material, testcase=self))
+        self.materials = Materials()
+        self.example_materials = []
+        for i in xrange(5):
+            self.example_materials.append(
+                Material(description="Material {}".format(i),
+                         data=create_data_container()))
+
+    def test_add_get_material(self):
+        self.materials.add_material(self.example_materials[0])
+        self.assertEqual(self.materials.get_material(
+            self.example_materials[0].uid),
+            self.example_materials[0])
+
+    def test_get_missing_material(self):
+        with self.assertRaises(KeyError):
+            self.materials.get_material(uuid.uuid4())
+
+    def test_remove_missing_material(self):
+        with self.assertRaises(KeyError):
+            self.materials.remove_material(uuid.uuid4())
+
+    def test_iter_materials_with_ids(self):
+        # given
+        material_subset = [material for material in self.example_materials[:2]]
+        subset_ids = [material.uid for material in material_subset]
+        for material in self.example_materials:
+            self.materials.add_material(material)
+
+        # when
+        iterated_with_id_materials = [
+            material for material in self.materials.iter_materials(
+                subset_ids)]
+
+        # then
+        for m, r in zip(iterated_with_id_materials, material_subset):
+            self.assertEqual(m, r)
+
+        # when
+        iterated_all_materials = {material.uid: material for material
+                                  in self.materials.iter_materials()}
+
+        # then
+        self.assertEqual(len(iterated_all_materials),
+                         len(self.example_materials))
+        for material in self.example_materials:
+            self.assertEqual(material, iterated_all_materials[material.uid])
+
+
+if __name__ == '__main__':
+    unittest.main()

simphony/io/data_container_description.py

@@ -70,16 +70,17 @@ class Data(tables.IsDescription):
     ln_of_restitution_coefficient = tables.Float64Col(pos=63)
     rolling_friction = tables.Float64Col(pos=64)
     volume_fraction = tables.Float64Col(pos=65)
+    material = tables.StringCol(pos=66, itemsize=32)
 
 
 class Record(tables.IsDescription):
 
     index = tables.StringCol(itemsize=32, pos=0)
     data = Data()
-    mask = tables.BoolCol(pos=1, shape=(66,))
+    mask = tables.BoolCol(pos=1, shape=(67,))
 
 
 class NoUIDRecord(tables.IsDescription):
 
     data = Data()
-    mask = tables.BoolCol(pos=1, shape=(66,))
+    mask = tables.BoolCol(pos=1, shape=(67,))

simphony/io/data_container_table.py

@@ -5,6 +5,8 @@
 import tables
 
 from simphony.io.data_container_description import Record
+from simphony.io.data_conversion import (convert_from_file_type,
+                                         convert_to_file_type)
 from simphony.core.cuba import CUBA
 from simphony.core.data_container import DataContainer
 
@@ -172,8 +174,9 @@ def _populate(self, row, value):
         data = list(row['data'])
         for key in value:
             if key in positions:
-                data[positions[key]] = value[key]
+                data[positions[key]] = convert_to_file_type(value[key], key)
                 mask[positions[key]] = True
+
         row['mask'] = mask
         row['data'] = tuple(data)
 
@@ -185,5 +188,5 @@ def _retrieve(self, row):
         mask = row['mask']
         data = row['data']
         return DataContainer({
-            cuba[index]: data[index]
+            cuba[index]: convert_from_file_type(data[index], cuba[index])
             for index, valid in enumerate(mask) if valid})