Merge branch 'master' of https://github.com/NeuralEnsemble/python-neo …

…into npix-sync

.github/workflows/io-test.yml

@@ -103,6 +103,8 @@ jobs:
           sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
 
       - name: Test with pytest
+        env:
+          HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_local_plugin_path
         run: |
           # only neo.rawio and neo.io
           pytest --cov=neo neo/test/rawiotest

doc/source/governance.rst

@@ -37,6 +37,7 @@ The current maintainers are:
 - Samuel Garcia (`@samuelgarcia`_)
 - Julia Sprenger (`@JuliaSprenger`_)
 - Michael Denker (`@mdenker`_)
+- Alessio Buccino (`@alejoe91`_)
 
 
 .. _`Neo maintainers team`: https://github.com/orgs/NeuralEnsemble/teams/neo-maintainers
@@ -45,3 +46,4 @@ The current maintainers are:
 .. _`@samuelgarcia`: https://github.com/samuelgarcia
 .. _`@JuliaSprenger`: https://github.com/JuliaSprenger
 .. _`@mdenker`: https://github.com/mdenker
+.. _`@alejoe91`: https://github.com/alejoe91

neo/core/analogsignal.py

@@ -718,7 +718,7 @@ def concatenate(self, *signals, overwrite=False, padding=False):
         if padding is not False:
             logger.warning('Signals will be padded using {}.'.format(padding))
             if padding is True:
-                padding = np.NaN * units
+                padding = np.nan * units
             if isinstance(padding, pq.Quantity):
                 padding = padding.rescale(units).magnitude
             else:

neo/io/klustakwikio.py

@@ -13,6 +13,7 @@
 * Load features in addition to spiketimes.
 """
 
+import re
 import glob
 import logging
 from pathlib import Path
@@ -439,7 +440,7 @@ def read_filenames(self, typestring='fet'):
         for v in all_filenames:
             # Test whether matches format, ie ends with digits
             split_fn = v.name
-            m = glob.re.search((r'^(\w+)\.%s\.(\d+)$' % typestring), split_fn)
+            m = re.search(rf'^(.*)\.{typestring}\.(\d+)$', split_fn)
             if m is not None:
                 # get basename from first hit if not specified
                 if self.basename is None:

neo/rawio/__init__.py

@@ -246,8 +246,18 @@
     WinWcpRawIO,
 ]
 
-
 def get_rawio_class(filename_or_dirname):
+    """Legacy function for returning class guess from file extension
+    DEPRECATED
+    """
+
+    import warnings
+    warnings.warn('get_rawio_class is deprecated. In the future please use get_rawio')
+
+    return get_rawio(filename_or_dirname)
+
+
+def get_rawio(filename_or_dirname):
     """
     Return a neo.rawio class guess from file extension.
     """

neo/rawio/blackrockrawio.py

@@ -1163,7 +1163,7 @@ def __get_event_segment_ids(self, raw_event_data, masks, nev_data_masks):
                 raw_event_data['timestamp'][mask_handled][1:] < raw_event_data['timestamp'][mask_handled][:-1]
             )[0] + 1
             jump_ids = np.where(mask_handled)[0][jump_ids_handled]  # jump ids in full set of events (incl. unhandled)
-            overlap = np.in1d(jump_ids, reset_ev_ids)
+            overlap = np.isin(jump_ids, reset_ev_ids)
             if not all(overlap):
                 # additional resets occurred without a reset event being stored
                 additional_ids = jump_ids[np.invert(overlap)]
@@ -2002,7 +2002,7 @@ def __get_nonneural_evdicts_variant_b(self, data):
         a 2.3 nev file.
         """
         # digital events
-        if not np.all(np.in1d(data['packet_insertion_reason'], [1, 129])):
+        if not np.all(np.isin(data['packet_insertion_reason'], [1, 129])):
             # Blackrock spec gives reason==64 means PERIODIC, but never seen this live
             warnings.warn("Unknown event codes found", RuntimeWarning)
         event_types = {

neo/rawio/intanrawio.py

@@ -27,7 +27,24 @@
 
 class IntanRawIO(BaseRawIO):
     """
-
+    Intan reader can handle two file formats 'rhd' and 'rhs'. It will automatically
+    check for the file extension and will gather the header information based on the
+    extension. Additionally it functions with RHS v 1.0 and RHD 1.0, 1.1, 1.2, 1.3, 2.0,
+    3.0, and 3.1 files.
+    Intan files contain amplifier channels labeled 'A', 'B' 'C' or 'D'
+    depending on the port in which they were recorded along with the following
+    additional channels.
+    1: 'RHD2000 auxiliary input channel',
+    2: 'RHD2000 supply voltage channel',
+    3: 'USB board ADC input channel',
+    4: 'USB board digital input channel',
+    5: 'USB board digital output channel'
+    Due to the structure of the digital input and output channels these can be accessed
+    as one long vector, which must be post-processed.
+    Parameters
+    ----------
+    filename: str
+       name of the 'rhd' or 'rhs' data file
     """
     extensions = ['rhd', 'rhs']
     rawmode = 'one-file'
@@ -543,10 +560,17 @@ def read_rhd(filename):
     # 4: USB board digital input channel
     # 5: USB board digital output channel
     for sig_type in [4, 5]:
-        # at the moment theses channel are not in sig channel list
-        # but they are in the raw memamp
+        # Now these are included so that user can obtain the
+        # dig signals and process them at the same time
         if len(channels_by_type[sig_type]) > 0:
             name = {4: 'DIGITAL-IN', 5: 'DIGITAL-OUT'}[sig_type]
+            chan_info = channels_by_type[sig_type][0]
+            chan_info['native_channel_name'] = name  # overwite to allow memmap to work
+            chan_info['sampling_rate'] = sr
+            chan_info['units'] = 'TTL'  # arbitrary units so I did TTL for the logic
+            chan_info['gain'] = 1.0
+            chan_info['offset'] = 0.0
+            ordered_channels.append(chan_info)
             data_dtype += [(name, 'uint16', BLOCK_SIZE)]
 
     if bool(global_info['notch_filter_mode']) and version >= V('3.0'):

neo/rawio/spikegadgetsrawio.py

@@ -183,10 +183,10 @@ def _parse_header(self):
                 self.selected_streams = [self.selected_streams]
             assert isinstance(self.selected_streams, list)
 
-            keep = np.in1d(signal_streams['id'], self.selected_streams)
+            keep = np.isin(signal_streams['id'], self.selected_streams)
             signal_streams = signal_streams[keep]
 
-            keep = np.in1d(signal_channels['stream_id'], self.selected_streams)
+            keep = np.isin(signal_channels['stream_id'], self.selected_streams)
             signal_channels = signal_channels[keep]
 
         # No events channels

neo/test/coretest/test_analogsignal.py

@@ -1537,7 +1537,7 @@ def test_concatenate_padding_True(self):
 
         result = signal1.concatenate(signal2, overwrite=False, padding=True)
         assert_array_equal(
-            np.array([0, 1, 2, 3, np.NaN, np.NaN, np.NaN, 4, 5, 6]).reshape((-1, 1)),
+            np.array([0, 1, 2, 3, np.nan, np.nan, np.nan, 4, 5, 6]).reshape((-1, 1)),
             result.magnitude)
 
     def test_concatenate_padding_quantity(self):

neo/test/coretest/test_base.py

@@ -853,7 +853,7 @@ def test_numpy_array_uint64(self):
 
     def test_numpy_array_float(self):
         '''test to make sure float type numpy arrays are accepted'''
-        value = np.array([1, 2, 3, 4, 5], dtype=np.float_)
+        value = np.array([1, 2, 3, 4, 5], dtype=np.float64)
         self.base.annotate(data=value)
         result = {'data': value}
         self.assertDictEqual(result, self.base.annotations)
@@ -1041,7 +1041,7 @@ def test_numpy_scalar_uint64(self):
 
     def test_numpy_scalar_float(self):
         '''test to make sure float type numpy scalars are accepted'''
-        value = np.array(99, dtype=np.float_)
+        value = np.array(99, dtype=np.float64)
         self.base.annotate(data=value)
         result = {'data': value}
         self.assertDictEqual(result, self.base.annotations)

neo/test/coretest/test_spiketrain.py

@@ -580,8 +580,8 @@ def test_defaults(self):
         train2 = _new_spiketrain(SpikeTrain, [3, 4, 5], units='sec', t_stop=10.0)
         assert_neo_object_is_compliant(train1)
         assert_neo_object_is_compliant(train2)
-        self.assertEqual(train1.dtype, np.float_)
-        self.assertEqual(train2.dtype, np.float_)
+        self.assertEqual(train1.dtype, np.float64)
+        self.assertEqual(train2.dtype, np.float64)
         self.assertEqual(train1.sampling_rate, 1.0 * pq.Hz)
         self.assertEqual(train2.sampling_rate, 1.0 * pq.Hz)
         self.assertEqual(train1.waveforms, None)

neo/test/iotest/test_asciisignalio.py

@@ -55,7 +55,7 @@ def test_csv_expect_success(self):
             (-64.6, -64.2, -77.0, 0.7),
             (-64.3, -64.0, -99.9, 0.8)
         ]
-        with open(filename, 'w') as csvfile:
+        with open(filename, 'w', newline='') as csvfile:
             writer = csv.writer(csvfile, delimiter=',',
                                 quotechar='|', quoting=csv.QUOTE_MINIMAL)
             for row in sample_data:

neo/test/iotest/test_nestio.py

@@ -356,7 +356,7 @@ def test_read_float(self):
                              t_stop=500. * pq.ms,
                              lazy=False, id_column_gdf=0, time_column_gdf=1)
         sts = seg.spiketrains
-        self.assertTrue(all([s.magnitude.dtype == np.float_ for s in sts]))
+        self.assertTrue(all([s.magnitude.dtype == np.float64 for s in sts]))
 
     def test_values(self):
         """

neo/test/rawiotest/test_get_rawio.py

@@ -1,4 +1,4 @@
-from neo.rawio import get_rawio_class
+from neo.rawio import get_rawio
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
@@ -7,7 +7,7 @@ def test_get_rawio_class():
     # use plexon io suffix for testing here
     non_existant_file = Path('non_existant_folder/non_existant_file.plx')
     non_existant_file.unlink(missing_ok=True)
-    ios = get_rawio_class(non_existant_file)
+    ios = get_rawio(non_existant_file)
 
     assert ios
 
@@ -19,7 +19,7 @@ def test_get_rawio_class_nonsupported_rawio():
 
     non_existant_file = Path('non_existant_folder/non_existant_file.fake')
     non_existant_file.unlink(missing_ok=True)
-    ios = get_rawio_class(non_existant_file)
+    ios = get_rawio(non_existant_file)
 
     assert ios is None
 

neo/utils/misc.py

@@ -247,13 +247,13 @@ def _get_valid_ids(obj, annotation_key, annotation_value):
         # wrap annotation value to be list
         if not type(annotation_value) in [list, np.ndarray]:
             annotation_value = [annotation_value]
-        valid_mask = np.in1d(obj.labels, annotation_value)
+        valid_mask = np.isin(obj.labels, annotation_value)
 
     elif annotation_key in obj.array_annotations:
         # wrap annotation value to be list
         if not type(annotation_value) in [list, np.ndarray]:
             annotation_value = [annotation_value]
-        valid_mask = np.in1d(obj.array_annotations[annotation_key], annotation_value)
+        valid_mask = np.isin(obj.array_annotations[annotation_key], annotation_value)
 
     elif hasattr(obj, annotation_key) and getattr(obj, annotation_key) == annotation_value:
         valid_mask = np.ones(obj.shape)