Merge pull request #1258 from h-mayorquin/improve_mearec

Add option to `MEArecRawIO` for loading only recordings or only sorting data

Author: samuelgarcia

neo/io/mearecio.py

@@ -6,6 +6,10 @@ class MEArecIO(MEArecRawIO, BaseFromRaw):
     __doc__ = MEArecRawIO.__doc__
     mode = 'file'
 
-    def __init__(self, filename):
-        MEArecRawIO.__init__(self, filename=filename)
+    def __init__(self, filename, load_spiketrains=True, load_analogsignal=True):
+        MEArecRawIO.__init__(self, 
+                            filename=filename, 
+                            load_spiketrains=load_spiketrains, 
+                            load_analogsignal=load_analogsignal
+                            )
         BaseFromRaw.__init__(self, filename)

neo/rawio/baserawio.py

@@ -550,6 +550,18 @@ def get_analogsignal_chunk(self, block_index=0, seg_index=0, i_start=None, i_sto
                               np.ndarray and are contiguous
         :return: array with raw signal samples
         """
+        
+        signal_streams = self.header['signal_streams']
+        signal_channels = self.header['signal_channels']
+        no_signal_streams = signal_streams.size == 0
+        no_channels = signal_channels.size == 0
+        if no_signal_streams or no_channels:
+            error_message = (
+                "get_analogsignal_chunk can't be called on a file with no signal streams or channels."
+                "Double check that your file contains signal streams and channels."
+            )
+            raise AttributeError(error_message)
+                
         stream_index = self._get_stream_index_from_arg(stream_index)
         channel_indexes = self._get_channel_indexes(stream_index, channel_indexes,
                                                     channel_names, channel_ids)
@@ -579,7 +591,7 @@ def rescale_signal_raw_to_float(self, raw_signal, dtype='float32', stream_index=
                                     channel_indexes=None, channel_names=None, channel_ids=None):
         """
         Rescale a chunk of raw signals which are provided as a Numpy array. These are normally
-        returned by a call to get_analog_signal_chunk. The channels are specified either by
+        returned by a call to get_analogsignal_chunk. The channels are specified either by
         channel_names, if provided, otherwise by channel_ids, if provided, otherwise by
         channel_indexes, if provided, otherwise all channels are selected.
 

neo/rawio/mearecrawio.py

@@ -20,6 +20,18 @@ class MEArecRawIO(BaseRawIO):
     """
     Class for "reading" fake data from a MEArec file.
 
+    This class provides a convenient way to read data from a MEArec file.
+
+    Parameters
+    ----------
+    filename : str
+        The filename of the MEArec file to read.
+    load_spiketrains : bool, optional
+        Whether or not to load spike train data. Defaults to `True`.
+    load_analogsignal : bool, optional
+        Whether or not to load continuous recording data. Defaults to `True`.
+
+
     Usage:
         >>> import neo.rawio
         >>> r = neo.rawio.MEArecRawIO(filename='mearec.h5')
@@ -36,52 +48,75 @@ class MEArecRawIO(BaseRawIO):
     extensions = ['h5']
     rawmode = 'one-file'
 
-    def __init__(self, filename=''):
+    def __init__(self, filename='', load_spiketrains=True, load_analogsignal=True):
         BaseRawIO.__init__(self)
         self.filename = filename
-
+        self.load_spiketrains = load_spiketrains
+        self.load_analogsignal = load_analogsignal
+        
     def _source_name(self):
         return self.filename
 
     def _parse_header(self):
+        load = ["channel_positions"] 
+        if self.load_analogsignal:
+            load.append("recordings")
+        if self.load_spiketrains:
+            load.append("spiketrains")
+        
         import MEArec as mr
         self._recgen = mr.load_recordings(recordings=self.filename, return_h5_objects=True,
                                           check_suffix=False,
-                                          load=['recordings', 'spiketrains', 'channel_positions'],
+                                          load=load,
                                           load_waveforms=False)
-        self._sampling_rate = self._recgen.info['recordings']['fs']
-        self._recordings = self._recgen.recordings
-        self._num_frames, self._num_channels = self._recordings.shape
-
-        signal_streams = np.array([('Signals', '0')], dtype=_signal_stream_dtype)
 
+        self.info_dict = deepcopy(self._recgen.info)
+        self.channel_positions = self._recgen.channel_positions
+        if self.load_analogsignal:
+            self._recordings = self._recgen.recordings
+        if self.load_spiketrains:
+            self._spiketrains = self._recgen.spiketrains
+
+        self._sampling_rate = self.info_dict['recordings']['fs']
+        self.duration_seconds = self.info_dict["recordings"]["duration"]
+        self._num_frames = int(self._sampling_rate * self.duration_seconds)
+        self._num_channels = self.channel_positions.shape[0]
+        self._dtype = self.info_dict["recordings"]["dtype"]
+        
+        signals = [('Signals', '0')] if self.load_analogsignal else []
+        signal_streams = np.array(signals, dtype=_signal_stream_dtype)
+
+        
         sig_channels = []
-        for c in range(self._num_channels):
-            ch_name = 'ch{}'.format(c)
-            chan_id = str(c + 1)
-            sr = self._sampling_rate  # Hz
-            dtype = self._recordings.dtype
-            units = 'uV'
-            gain = 1.
-            offset = 0.
-            stream_id = '0'
-            sig_channels.append((ch_name, chan_id, sr, dtype, units, gain, offset, stream_id))
+        if self.load_analogsignal:
+            for c in range(self._num_channels):
+                ch_name = 'ch{}'.format(c)
+                chan_id = str(c + 1)
+                sr = self._sampling_rate  # Hz
+                dtype = self._dtype
+                units = 'uV'
+                gain = 1.
+                offset = 0.
+                stream_id = '0'
+                sig_channels.append((ch_name, chan_id, sr, dtype, units, gain, offset, stream_id))
+    
         sig_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
 
         # creating units channels
         spike_channels = []
-        self._spiketrains = self._recgen.spiketrains
-        for c in range(len(self._spiketrains)):
-            unit_name = 'unit{}'.format(c)
-            unit_id = '#{}'.format(c)
-            # if spiketrains[c].waveforms is not None:
-            wf_units = ''
-            wf_gain = 1.
-            wf_offset = 0.
-            wf_left_sweep = 0
-            wf_sampling_rate = self._sampling_rate
-            spike_channels.append((unit_name, unit_id, wf_units, wf_gain,
-                                  wf_offset, wf_left_sweep, wf_sampling_rate))
+        if self.load_spiketrains:
+            for c in range(len(self._spiketrains)):
+                unit_name = 'unit{}'.format(c)
+                unit_id = '#{}'.format(c)
+                # if spiketrains[c].waveforms is not None:
+                wf_units = ''
+                wf_gain = 1.
+                wf_offset = 0.
+                wf_left_sweep = 0
+                wf_sampling_rate = self._sampling_rate
+                spike_channels.append((unit_name, unit_id, wf_units, wf_gain,
+                                    wf_offset, wf_left_sweep, wf_sampling_rate))
+        
         spike_channels = np.array(spike_channels, dtype=_spike_channel_dtype)
 
         event_channels = []
@@ -98,7 +133,7 @@ def _parse_header(self):
         self._generate_minimal_annotations()
         for block_index in range(1):
             bl_ann = self.raw_annotations['blocks'][block_index]
-            bl_ann['mearec_info'] = deepcopy(self._recgen.info)
+            bl_ann['mearec_info'] = self.info_dict
 
     def _segment_t_start(self, block_index, seg_index):
         all_starts = [[0.]]
@@ -119,6 +154,10 @@ def _get_signal_t_start(self, block_index, seg_index, stream_index):
 
     def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop,
                                 stream_index, channel_indexes):
+        
+        if not self.load_analogsignal:
+            raise AttributeError("Recordings not loaded. Set load_analogsignal=True in MEArecRawIO constructor")
+        
         if i_start is None:
             i_start = 0
         if i_stop is None:
@@ -127,23 +166,25 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop,
         if channel_indexes is None:
             channel_indexes = slice(self._num_channels)
         if isinstance(channel_indexes, slice):
-            raw_signals = self._recgen.recordings[i_start:i_stop, channel_indexes]
+            raw_signals = self._recordings[i_start:i_stop, channel_indexes]
         else:
             # sort channels because h5py neeeds sorted indexes
             if np.any(np.diff(channel_indexes) < 0):
                 sorted_channel_indexes = np.sort(channel_indexes)
                 sorted_idx = np.array([list(sorted_channel_indexes).index(ch)
                                        for ch in channel_indexes])
-                raw_signals = self._recgen.recordings[i_start:i_stop, sorted_channel_indexes]
+                raw_signals = self._recordings[i_start:i_stop, sorted_channel_indexes]
                 raw_signals = raw_signals[:, sorted_idx]
             else:
-                raw_signals = self._recgen.recordings[i_start:i_stop, channel_indexes]
+                raw_signals = self._recordings[i_start:i_stop, channel_indexes]
         return raw_signals
 
     def _spike_count(self, block_index, seg_index, unit_index):
+        
         return len(self._spiketrains[unit_index])
 
     def _get_spike_timestamps(self, block_index, seg_index, unit_index, t_start, t_stop):
+        
         spike_timestamps = self._spiketrains[unit_index].times.magnitude
         if t_start is None:
             t_start = self._segment_t_start(block_index, seg_index)

neo/test/rawiotest/test_mearecrawio.py

@@ -27,6 +27,40 @@ class TestMEArecRawIO(BaseTestRawIO, unittest.TestCase, ):
         'mearec/mearec_test_10s.h5'
     ]
 
+    def test_not_loading_recordings(self):
+        
+        filename = self.entities_to_test[0]
+        filename = self.get_local_path(filename)
+        rawio = self.rawioclass(filename=filename, load_analogsignal=False)
+        rawio.parse_header()
+        
+        # Test that rawio does not have a _recordings attribute
+        self.assertFalse(hasattr(rawio, '_recordings'))
+        
+        # Test that calling get_spike_timestamps works 
+        rawio.get_spike_timestamps()
+
+        # Test that caling anlogsignal chunk raises the right error
+        with self.assertRaises(AttributeError):
+            rawio.get_analogsignal_chunk()
+
+
+    def test_not_loading_spiketrain(self):
+        
+        filename = self.entities_to_test[0]
+        filename = self.get_local_path(filename)
+        rawio = self.rawioclass(filename=filename, load_spiketrains=False)
+        rawio.parse_header()
+        
+        # Test that rawio does not have a _spiketrains attribute
+        self.assertFalse(hasattr(rawio, '_spiketrains'))
+        
+        # Test that calling analogsignal chunk works
+        rawio.get_analogsignal_chunk()
+
+        # Test that calling get_spike_timestamps raises an the right error
+        with self.assertRaises(AttributeError):
+            rawio.get_spike_timestamps()
 
 if __name__ == "__main__":
     unittest.main()