issue #5 fixed unreferenced variable exception

Author: Lee Kamentsky

bioformats/formatreader.py

@@ -659,8 +659,8 @@ def init_reader(self):
         mdoptions = metadatatools.get_metadata_options(metadatatools.ALL)
         self.rdr.setMetadataOptions(mdoptions)
         self.rdr.setGroupFiles(False)
-        metadata = metadatatools.createOMEXMLMetadata()
-        self.rdr.setMetadataStore(metadata)
+        self.metadata = metadatatools.createOMEXMLMetadata()
+        self.rdr.setMetadataStore(self.metadata)
         try:
             self.rdr.setId(self.path)
         except jutil.JavaException, e:
@@ -788,7 +788,7 @@ def read(self, c = None, z = 0, t = 0, series = None, index = None,
             image = np.dstack(images)
             image.shape = (height, width, self.rdr.getSizeC())
             if not channel_names is None:
-                metadata = metadatatools.MetadataRetrieve(metadata)
+                metadata = metadatatools.MetadataRetrieve(self.metadata)
                 for i in range(self.rdr.getSizeC()):
                     index = self.rdr.getIndex(z, 0, t)
                     channel_name = metadata.getChannelName(index, i)