Merge pull request #1948 from JamesBelanger/blackrock-nsx21-last-sample

BlackrockRawIO: read the last sample of NSx 2.1 files

Author: h-mayorquin

neo/rawio/blackrockrawio.py

@@ -1351,7 +1351,7 @@ def _parse_nsx_data_v21(self, nsx_nb):
             self._nsx_basic_header[nsx_nb].dtype.itemsize + self._nsx_ext_header[nsx_nb].dtype.itemsize * channels
         )
         filesize = self._get_file_size(filename)
-        num_samples = int((filesize - bytes_in_headers) / (2 * channels) - 1)
+        num_samples = (filesize - bytes_in_headers) // (2 * channels)
 
         return [
             {

neo/test/iotest/test_blackrockio.py

@@ -179,13 +179,13 @@ def test_load_muliple_nsx(self):
         reader = BlackrockIO(filename=filename, nsx_to_load=5)
         seg = reader.read_segment()
         self.assertEqual(len(seg.analogsignals), 1)
-        self.assertEqual(seg.analogsignals[0].shape, (109224, 96))
+        self.assertEqual(seg.analogsignals[0].shape, (109225, 96))
 
         # load only ns2
         reader = BlackrockIO(filename=filename, nsx_to_load=2)
         seg = reader.read_segment()
         self.assertEqual(len(seg.analogsignals), 1)
-        self.assertEqual(seg.analogsignals[0].shape, (3640, 6))
+        self.assertEqual(seg.analogsignals[0].shape, (3641, 6))
 
         # load only ns2
         reader = BlackrockIO(filename=filename, nsx_to_load=[2])
@@ -196,14 +196,14 @@ def test_load_muliple_nsx(self):
         reader = BlackrockIO(filename=filename, nsx_to_load=[2, 5])
         seg = reader.read_segment()
         self.assertEqual(len(seg.analogsignals), 2)
-        self.assertEqual(seg.analogsignals[0].shape, (3640, 6))
-        self.assertEqual(seg.analogsignals[1].shape, (109224, 96))
+        self.assertEqual(seg.analogsignals[0].shape, (3641, 6))
+        self.assertEqual(seg.analogsignals[1].shape, (109225, 96))
 
         # load only ns5
         reader = BlackrockIO(filename=filename, nsx_to_load="max")
         seg = reader.read_segment()
         self.assertEqual(len(seg.analogsignals), 1)
-        self.assertEqual(seg.analogsignals[0].shape, (109224, 96))
+        self.assertEqual(seg.analogsignals[0].shape, (109225, 96))
 
     @unittest.skipUnless(HAVE_SCIPY, "requires scipy")
     def test_compare_blackrockio_with_matlabloader_v21(self):

neo/test/rawiotest/test_blackrockrawio.py

@@ -151,7 +151,10 @@ def test_compare_blackrockio_with_matlabloader_v21(self):
             for c in range(0, param[2]):
                 raw_sigs = reader.get_analogsignal_chunk(channel_indexes=[c])
                 raw_sigs = raw_sigs.flatten()
-                assert_equal(raw_sigs[:], lfp_ml[c, :])
+                # The Matlab export stops one sample before the end of the file
+                # (see test_nsx21_reads_the_last_sample)
+                self.assertEqual(raw_sigs.size, lfp_ml.shape[1] + 1)
+                assert_equal(raw_sigs[: lfp_ml.shape[1]], lfp_ml[c, :])
 
             # Check if spikes in channels are equal
             nb_unit = reader.spike_channels_count()
@@ -187,6 +190,21 @@ def test_compare_blackrockio_with_matlabloader_v21(self):
                         matlab_digievents = mts_ml[mid_ml == int(label)]
                         assert_equal(python_digievents, matlab_digievents)
 
+    def test_nsx21_reads_the_last_sample(self):
+        filename = self.get_local_path("blackrock/version_2_1/spikes/offline_sorted_units/online_sorted_units")
+
+        reader = BlackrockRawIO(filename=filename, nsx_to_load=2)
+        reader.parse_header()
+        number_of_samples = reader.get_signal_size(block_index=0, seg_index=0, stream_index=0)
+        expected_number_of_samples = 300  # 0.3 s at 1 kHz
+        self.assertEqual(number_of_samples, expected_number_of_samples)
+
+        reader = BlackrockRawIO(filename=filename, nsx_to_load=5)
+        reader.parse_header()
+        number_of_samples = reader.get_signal_size(block_index=0, seg_index=0, stream_index=0)
+        expected_number_of_samples = 9000  # 0.3 s at 30 kHz
+        self.assertEqual(number_of_samples, expected_number_of_samples)
+
     def test_blackrockrawio_ptp_timestamps(self):
         dirname = self.get_local_path("blackrock/blackrock_3_0_ptp/20231027-125608-001")
         reader = BlackrockRawIO(filename=dirname)