Merge branch 'timestamps_writing' into 'master'

Write timestamps to file as dataset attributes along with data

See merge request !19

bob/io/stream/stream.py

@@ -862,7 +862,16 @@ class StreamSave(StreamFilter):
             raise ValueError("Output file is not a valid StreamFile.")
 
     def put(self, data, timestamp=None):
-        self.file.put_frame(self.name, data)
+        """Pass data and timestamp to the :obj:`~bob.io.stream.StreamFile` to write to disk.
+
+        Parameters
+        ----------
+        data : :obj:`numpy.ndarray`
+            data to write to file.
+        timestamp : int or float
+            Timestamp of `data`, by default None.
+        """
+        self.file.put_frame(self.name, data, timestamp)
 
 
 ################################################################################

bob/io/stream/stream_file.py

@@ -200,7 +200,7 @@ class StreamFile:
         # TODO rotate if requested
         return data
 
-    def put_frame(self, name, data):
+    def put_frame(self, name, data, timestamp=None):
         """Appends `data` (a frame of a stream) to the hdf5 file.
 
         Parameters
@@ -211,3 +211,9 @@ class StreamFile:
             Data frame to append.
         """
         self.hdf5_file.append(name, data)
+        if timestamp is not None:
+            try:
+                previous_timestamps = self.hdf5_file.get_attribute("timestamps", name)
+            except RuntimeError:  # No previous timestamps
+                previous_timestamps = []
+            self.hdf5_file.set_attribute("timestamps", np.append(previous_timestamps, timestamp), name)

bob/io/stream/test/test.py

@@ -38,19 +38,30 @@ def test_stream_write():
         np.arange(12 * 52).astype(np.float64).reshape((12, 52)),
     ]
 
-    for a_test_data in test_data:
+    test_timestamps = [
+        np.linspace(0, 20*test_data[0].shape[0], test_data[0].shape[0]),
+        np.linspace(10, 10*test_data[1].shape[0], test_data[1].shape[0]),
+        np.linspace(100, 200*test_data[2].shape[0], test_data[2].shape[0]),
+        np.linspace(5, 6*test_data[3].shape[0], test_data[3].shape[0]),
+    ]
+
+    for a_test_data, a_test_timestamps in zip(test_data, test_timestamps):
         with StreamFile(resource_path("test/data/save_test.h5"), mode="w") as output_file:
             stream = Stream("test_data")
             save_filter = stream.save(output_file)
             for i in range(a_test_data.shape[0]):
-                stream.put(a_test_data[i])
+                stream.put(a_test_data[i], a_test_timestamps[i])
 
         with StreamFile(resource_path("test/data/save_test.h5"), mode="r") as input_file:
             stream = Stream("test_data", input_file)
             data = stream.load()
+            timestamps = input_file.get_stream_timestamps("test_data")
+            if np.isscalar(timestamps): # if there is only 1 frame, timestamps are returned as a scalar
+                timestamps = np.array([timestamps])
 
         assert np.array_equal(data, a_test_data)
         assert data.dtype == a_test_data.dtype
+        assert np.array_equal(timestamps, a_test_timestamps)
 
     os.remove(resource_path("test/data/save_test.h5"))