Temporary class to explore the use of the chunk index, and

eventually, hopefully, address both the needs of
pyactivestorage (which needs access to the b-tree
chunk index) and jjhelmus#6

pyfive/as_dataobjects.py

@@ -0,0 +1,67 @@
+from .dataobjects import DataObjects, DATA_STORAGE_MSG_TYPE
+from .datatype_msg import DatatypeMessage
+import numpy as np
+from .btree import BTreeV1RawDataChunks
+
+class ADataObjects(DataObjects):
+ """ 
+ Subclass of DataObjets which access the chunk addresses for a given slice of data
+ """
+ def __init__(self,*args,**kwargs):
+ """
+ Initialise via super class
+ """
+ super().__init__(*args,**kwargs)
+
+ # not yet sure we need our own copy
+ self._as_chunk_index=[]
+
+ def get_offset_addresses(self, args=None):
+ """ 
+ Get the offset addresses for the data requested
+ """
+
+ # offset and size from data storage message
+ msg = self.find_msg_type(DATA_STORAGE_MSG_TYPE)[0]
+ msg_offset = msg['offset_to_message']
+ version, dims, layout_class, property_offset = (
+ self._get_data_message_properties(msg_offset))
+
+ if layout_class == 0: # compact storage
+ raise NotImplementedError("Compact storage")
+ elif layout_class == 1: # contiguous storage
+ return NotImplementedError("Contiguous storage")
+ if layout_class == 2: # chunked storage
+ return self._as_get_chunk_addresses(args)
+
+
+ def _as_get_chunk_addresses(self, args):
+ """ 
+ Get the offset addresses associated with all the chunks 
+ known to the b-tree of this object
+ """
+ self._get_chunk_params()
+
+ if self._as_chunk_index == []:
+ chunk_btree = BTreeV1RawDataChunks(
+ self.fh, self._chunk_address, self._chunk_dims)
+
+ count = np.prod(self.shape)
+ itemsize = np.dtype(self.dtype).itemsize
+ chunk_buffer_size = count * itemsize
+
+ for node in chunk_btree.all_nodes[0]:
+ for node_key, addr in zip(node['keys'], node['addresses']):
+ size = chunk_buffer_size
+ if self.filter_pipeline:
+ size = node_key['chunk_size']
+ start = node_key['chunk_offset'][:-1]
+ region = [slice(i, i+j) for i, j in zip(start, self.shape)]
+ self._as_chunk_index.append([region, start, size])
+
+ if args is not None:
+ return NotImplementedError
+ return self._as_chunk_index
+
+
+