write statserver without closing h5py.File

statserver.py

@@ -423,57 +423,62 @@ class StatServer:
         stop[numpy.isnan(self.stop.astype('float'))] = -1
         stop = stop.astype('int8', copy=False)
 
-        with h5py.File(output_file_name, mode) as f:
+        if isinstnace(output_file_name, h5py._hl.files.File):
+            f = output_file_name
+        else;
+            f = h5py.File(output_file_name, mode)
 
             # If the file doesn't exist before, create it
-            if mode == "w" or not file_already_exist:
-
-                f.create_dataset(prefix+"modelset", data=self.modelset.astype('S'),
+        if mode == "w" or not file_already_exist:
+
+            f.create_dataset(prefix+"modelset", data=self.modelset.astype('S'),
+                             maxshape=(None,),
+                             compression="gzip",
+                             fletcher32=True)
+            f.create_dataset(prefix+"segset", data=self.segset.astype('S'),
+                             maxshape=(None,),
+                             compression="gzip",
+                             fletcher32=True)
+            f.create_dataset(prefix+"stat0", data=self.stat0.astype(numpy.float32),
+                             maxshape=(None, self.stat0.shape[1]),
+                             compression="gzip",
+                             fletcher32=True)
+            f.create_dataset(prefix+"stat1", data=self.stat1.astype(numpy.float32),
+                             maxshape=(None, self.stat1.shape[1]),
+                             compression="gzip",
+                             fletcher32=True)
+            f.create_dataset(prefix+"start", data=start,
+                             maxshape=(None,),
+                             compression="gzip",
+                             fletcher32=True)
+            f.create_dataset(prefix+"stop", data=stop,
                                  maxshape=(None,),
                                  compression="gzip",
                                  fletcher32=True)
-                f.create_dataset(prefix+"segset", data=self.segset.astype('S'),
-                                 maxshape=(None,),
-                                 compression="gzip",
-                                 fletcher32=True)
-                f.create_dataset(prefix+"stat0", data=self.stat0.astype(numpy.float32),
-                                 maxshape=(None, self.stat0.shape[1]),
-                                 compression="gzip",
-                                 fletcher32=True)
-                f.create_dataset(prefix+"stat1", data=self.stat1.astype(numpy.float32),
-                                 maxshape=(None, self.stat1.shape[1]),
-                                 compression="gzip",
-                                 fletcher32=True)
 
-                f.create_dataset(prefix+"start", data=start,
-                                 maxshape=(None,),
-                                 compression="gzip",
-                                 fletcher32=True)
-                f.create_dataset(prefix+"stop", data=stop,
-                                 maxshape=(None,),
-                                 compression="gzip",
-                                 fletcher32=True)
-
-            # If the file already exist, we extend all datasets and add the new data
-            else:
+        # If the file already exist, we extend all datasets and add the new data
+        else:
 
-                previous_size = f[prefix+"modelset"].shape[0]
-
-                # Extend the size of each dataset
-                f[prefix+"modelset"].resize((previous_size + self.modelset.shape[0],))
-                f[prefix+"segset"].resize((previous_size + self.segset.shape[0],))
-                f[prefix+"start"].resize((previous_size + start.shape[0],))
-                f[prefix+"stop"].resize((previous_size + stop.shape[0],))
-                f[prefix+"stat0"].resize((previous_size + self.stat0.shape[0], self.stat0.shape[1]))
-                f[prefix+"stat1"].resize((previous_size + self.stat1.shape[0], self.stat1.shape[1]))
-
-                # add the new data; WARNING: no check is done on the new data, beware of duplicated entries
-                f[prefix+"modelset"][previous_size:] = self.modelset.astype('S')
-                f[prefix+"segset"][previous_size:] = self.segset.astype('S')
-                f[prefix+"start"][previous_size:] = start
-                f[prefix+"stop"][previous_size:] = stop
-                f[prefix+"stat0"][previous_size:, :] = self.stat0.astype(STAT_TYPE)
-                f[prefix+"stat1"][previous_size:, :] = self.stat1.astype(STAT_TYPE)
+            previous_size = f[prefix+"modelset"].shape[0]
+
+            # Extend the size of each dataset
+            f[prefix+"modelset"].resize((previous_size + self.modelset.shape[0],))
+            f[prefix+"segset"].resize((previous_size + self.segset.shape[0],))
+            f[prefix+"start"].resize((previous_size + start.shape[0],))
+            f[prefix+"stop"].resize((previous_size + stop.shape[0],))
+            f[prefix+"stat0"].resize((previous_size + self.stat0.shape[0], self.stat0.shape[1]))
+            f[prefix+"stat1"].resize((previous_size + self.stat1.shape[0], self.stat1.shape[1]))
+
+            # add the new data; WARNING: no check is done on the new data, beware of duplicated entries
+            f[prefix+"modelset"][previous_size:] = self.modelset.astype('S')
+            f[prefix+"segset"][previous_size:] = self.segset.astype('S')
+            f[prefix+"start"][previous_size:] = start
+            f[prefix+"stop"][previous_size:] = stop
+            f[prefix+"stat0"][previous_size:, :] = self.stat0.astype(STAT_TYPE)
+            f[prefix+"stat1"][previous_size:, :] = self.stat1.astype(STAT_TYPE)
+
+        if not isinstnace(output_file_name, h5py._hl.files.File):
+            f.close()
 
     def get_model_stat0(self, mod_id):
         """Return zero-order statistics of a given model