Use np.fromstring instead of np.loadtxt

src/filter.py

@@ -367,8 +367,11 @@ class Filter(object):
                 extract = extractor(self.src.path, interval.start, interval.end)
                 old_array = np.array([])
                 for batched in batch(extract, rows):
-                    # Read in this batch of data
-                    new_array = np.loadtxt(batched)
+                    # Read in this batch of data.  This turns out to
+                    # be a very fast way to read and convert it (order
+                    # of magnitude faster than numpy.loadtxt)
+                    new_array = np.fromstring("".join(batched), sep=' ')
+                    new_array = new_array.reshape(-1, self.src.total_count)
 
                     # If we still had old data left, combine it
                     if old_array.shape[0] != 0: