Merge pull request #1539 from zm711/slice-none

Add test that all rawios accept `slice(None)`
NeuralEnsemble · Aug 29, 2024 · f0f4cc6 · f0f4cc6
2 parents 3b5488c + e2c1cf8
commit f0f4cc6
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Showing 2 changed files with 35 additions and 3 deletions.
diff --git a/neo/rawio/medrawio.py b/neo/rawio/medrawio.py
@@ -240,9 +240,18 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, strea
             self.sess.set_channel_active(self._stream_info[stream_index]["raw_chans"])
             num_channels = len(self._stream_info[stream_index]["raw_chans"])
             self.sess.set_reference_channel(self._stream_info[stream_index]["raw_chans"][0])
+
+        # in the case we have a slice or we give an ArrayLike we need to iterate through the channels
+        # in order to activate them.
         else:
-            if any(channel_indexes < 0):
-                raise IndexError(f"Can not index negative channels: {channel_indexes}")
+            if isinstance(channel_indexes, slice):
+                start = channel_indexes.start or 0
+                stop = channel_indexes.stop or len(self._stream_info[stream_index]["raw_chans"])
+                step = channel_indexes.step or 1
+                channel_indexes = [ch for ch in range(start, stop, step)]
+            else:
+                if any(channel_indexes < 0):
+                    raise IndexError(f"Can not index negative channels: {channel_indexes}")
             # Set all channels to be inactive, then selectively set some of them to be active
             self.sess.set_channel_inactive("all")
             for i, channel_idx in enumerate(channel_indexes):

diff --git a/neo/test/rawiotest/rawio_compliance.py b/neo/test/rawiotest/rawio_compliance.py
@@ -172,7 +172,7 @@ def read_analogsignals(reader):
         channel_names = signal_channels["name"][mask]
         channel_ids = signal_channels["id"][mask]
 
-        # acces by channel inde/ids/names should give the same chunk
+        # acces by channel index/ids/names should give the same chunk
         channel_indexes2 = channel_indexes[::2]
         channel_names2 = channel_names[::2]
         channel_ids2 = channel_ids[::2]
@@ -214,6 +214,29 @@ def read_analogsignals(reader):
             )
             np.testing.assert_array_equal(raw_chunk0, raw_chunk1)
 
+        # test slice(None). This should return the same array as giving
+        # all channel indexes or using None as an argument in `get_analogsignal_chunk`
+        # see https://github.com/NeuralEnsemble/python-neo/issues/1533
+
+        raw_chunk_slice_none = reader.get_analogsignal_chunk(
+            block_index=block_index,
+            seg_index=seg_index,
+            i_start=i_start,
+            i_stop=i_stop,
+            stream_index=stream_index,
+            channel_indexes=slice(None)
+        )
+        raw_chunk_channel_indexes = reader.get_analogsignal_chunk(
+            block_index=block_index,
+            seg_index=seg_index,
+            i_start=i_start,
+            i_stop=i_stop,
+            stream_index=stream_index,
+            channel_indexes=channel_indexes
+        )
+
+        np.testing.assert_array_equal(raw_chunk_slice_none, raw_chunk_channel_indexes)
+
         # test prefer_slice=True/False
         if nb_chan >= 3:
             for prefer_slice in (True, False):