Merge pull request #462 from achilleas-k/file-references

File references

Author: jgrewe

nixio/block.py

@@ -38,8 +38,9 @@
 
 class Block(Entity):
 
-    def __init__(self, nixparent, h5group, compression=Compression.Auto):
-        super(Block, self).__init__(nixparent, h5group)
+    def __init__(self, nixfile, nixparent, h5group,
+                 compression=Compression.Auto):
+        super(Block, self).__init__(nixfile, nixparent, h5group)
         self._groups = None
         self._data_arrays = None
         self._tags = None
@@ -49,9 +50,10 @@ def __init__(self, nixparent, h5group, compression=Compression.Auto):
         self._data_frames = None
 
     @classmethod
-    def _create_new(cls, nixparent, h5parent, name, type_, compression):
-        newentity = super(Block, cls)._create_new(nixparent, h5parent,
-                                                  name, type_)
+    def create_new(cls, nixparent, h5parent, name, type_, compression):
+        nixfile = nixparent  # file is parent
+        newentity = super(Block, cls).create_new(nixfile, nixparent, h5parent,
+                                                 name, type_)
         newentity._compr = compression
         return newentity
 
@@ -101,8 +103,8 @@ def create_multi_tag(self, name="", type_="", positions=None,
                                                  "{}-extents".format(type_),
                                                  data=extents)
                 extcreated = True
-            mtag = MultiTag._create_new(self, multi_tags,
-                                        name, type_, positions)
+            mtag = MultiTag.create_new(self.file, self, multi_tags,
+                                       name, type_, positions)
         except Exception as e:
             msg = "MultiTag Creation Failed"
             if poscreated:
@@ -150,7 +152,7 @@ def create_tag(self, name="", type_="", position=0,
         tags = self._h5group.open_group("tags")
         if name in tags:
             raise exceptions.DuplicateName("create_tag")
-        tag = Tag._create_new(self, tags, name, type_, position)
+        tag = Tag.create_new(self.file, self, tags, name, type_, position)
         return tag
 
     # Source
@@ -170,7 +172,7 @@ def create_source(self, name, type_):
         sources = self._h5group.open_group("sources")
         if name in sources:
             raise exceptions.DuplicateName("create_source")
-        src = Source._create_new(self, sources, name, type_)
+        src = Source.create_new(self.file, self, sources, name, type_)
         return src
 
     # Group
@@ -190,7 +192,7 @@ def create_group(self, name, type_):
         groups = self._h5group.open_group("groups")
         if name in groups:
             raise exceptions.DuplicateName("open_group")
-        grp = Group._create_new(self, groups, name, type_)
+        grp = Group.create_new(self.file, self, groups, name, type_)
         return grp
 
     def create_data_array(self, name="", array_type="", dtype=None, shape=None,
@@ -250,8 +252,8 @@ def create_data_array(self, name="", array_type="", dtype=None, shape=None,
             raise exceptions.DuplicateName("create_data_array")
         if compression == Compression.Auto:
             compression = self._compr
-        da = DataArray._create_new(self, data_arrays, name, array_type,
-                                   dtype, shape, compression)
+        da = DataArray.create_new(self.file, self, data_arrays, name, array_type,
+                                  dtype, shape, compression)
         if data is not None:
             da.write_direct(data)
         return da
@@ -328,7 +330,7 @@ def create_data_frame(self, name="", type_="", col_dict=None,
                     )
                 else:  # col_dtypes is None and data is None
                     raise ValueError(
-                           "The data type of each column have to be specified"
+                        "The data type of each column have to be specified"
                     )
                 if len(col_names) != len(col_dict):
                     raise exceptions.DuplicateColumnName
@@ -348,7 +350,7 @@ def create_data_frame(self, name="", type_="", col_dict=None,
                     # data is None or type(data[0]) != np.void
                     # data_type doesnt matter
                     raise ValueError(
-                           "No information about column names is provided!"
+                        "No information about column names is provided!"
                     )
 
         if col_dict is not None:
@@ -362,8 +364,8 @@ def create_data_frame(self, name="", type_="", col_dict=None,
             dt_arr = list(col_dict.items())
             col_dtype = np.dtype(dt_arr)
 
-        df = DataFrame._create_new(self, data_frames, name,
-                                   type_, shape, col_dtype, compression)
+        df = DataFrame.create_new(self.file, self, data_frames, name,
+                                  type_, shape, col_dtype, compression)
 
         if data is not None:
             if type(data[0]) == np.void:
@@ -510,7 +512,7 @@ def sources(self):
         This is a read only attribute.
         """
         if self._sources is None:
-            self._sources = SourceContainer("sources", self, Source)
+            self._sources = SourceContainer("sources", self.file, self, Source)
         return self._sources
 
     @property
@@ -522,7 +524,8 @@ def multi_tags(self):
         This is a read only attribute.
         """
         if self._multi_tags is None:
-            self._multi_tags = Container("multi_tags", self, MultiTag)
+            self._multi_tags = Container("multi_tags", self.file,
+                                         self, MultiTag)
         return self._multi_tags
 
     @property
@@ -534,7 +537,7 @@ def tags(self):
         This is a read only attribute.
         """
         if self._tags is None:
-            self._tags = Container("tags", self, Tag)
+            self._tags = Container("tags", self.file, self, Tag)
         return self._tags
 
     @property
@@ -547,13 +550,15 @@ def data_arrays(self):
         This is a read only attribute.
         """
         if self._data_arrays is None:
-            self._data_arrays = Container("data_arrays", self, DataArray)
+            self._data_arrays = Container("data_arrays", self.file,
+                                          self, DataArray)
         return self._data_arrays
 
     @property
     def data_frames(self):
         if self._data_frames is None:
-            self._data_frames = Container("data_frames", self, DataFrame)
+            self._data_frames = Container("data_frames", self.file,
+                                          self, DataFrame)
         return self._data_frames
 
     @property
@@ -565,7 +570,7 @@ def groups(self):
         This is a read only attribute.
         """
         if self._groups is None:
-            self._groups = Container("groups", self, Group)
+            self._groups = Container("groups", self.file, self, Group)
         return self._groups
 
     # metadata
@@ -579,7 +584,8 @@ def metadata(self):
         :type: Section
         """
         if "metadata" in self._h5group:
-            return Section(None, self._h5group.open_group("metadata"))
+            return Section(self.file, None,
+                           self._h5group.open_group("metadata"))
         else:
             return None
 

nixio/container.py

@@ -23,14 +23,15 @@ class Container(object):
     checking and instantiations)
     """
 
-    def __init__(self, name, parent, itemclass):
+    def __init__(self, name, nixfile, parent, itemclass):
         self._backend = parent._h5group.open_group(name)
         self._itemclass = itemclass
+        self._file = nixfile
         self._parent = parent
         self._name = name
 
     def _inst_item(self, item):
-        return self._itemclass(self._parent, item)
+        return self._itemclass(self._file, self._parent, item)
 
     def __len__(self):
         return len(self._backend)
@@ -56,10 +57,7 @@ def __delitem__(self, item):
                     self._itemclass.__name__)
             )
 
-        root = self._backend.h5root
-        if not root:
-            root = self._parent._h5group
-        root.delete_all([item.id])
+        self._file._h5group.delete_all([item.id])
 
     def __iter__(self):
         for group in self._backend:
@@ -121,8 +119,7 @@ def __delitem__(self, item):
         # the root block
         secids = [s.id for s in item.find_sections()]
 
-        root = self._backend.file
-        root.delete_all(secids)
+        self._file._h5group.delete_all(secids)
 
 
 class SourceContainer(Container):
@@ -145,9 +142,7 @@ def __delitem__(self, item):
         # the root block
         srcids = [s.id for s in item.find_sources()]
         srcids.append(item.id)
-
-        root = self._backend.h5root
-        root.delete_all(srcids)
+        self._file._h5group.delete_all(srcids)
 
 
 class LinkContainer(Container):
@@ -180,7 +175,8 @@ class LinkContainer(Container):
     """
 
     def __init__(self, name, parent, itemclass, itemstore):
-        super(LinkContainer, self).__init__(name, parent, itemclass)
+        super(LinkContainer, self).__init__(name, parent.file,
+                                            parent, itemclass)
         self._itemstore = itemstore
 
     def __delitem__(self, item):
@@ -249,7 +245,7 @@ def __contains__(self, item):
         return False
 
     def _inst_item(self, item):
-        return self._itemclass(self._itemstore._parent, item)
+        return self._itemclass(self._file, self._itemstore._parent, item)
 
     @staticmethod
     def _item_key(item):