Merge pull request #987 from samuelgarcia/ced_sonpy_implementation

Ced sonpy implementation

neo/io/__init__.py

@@ -28,6 +28,7 @@
 * :attr:`BrainwareDamIO`
 * :attr:`BrainwareF32IO`
 * :attr:`BrainwareSrcIO`
+* :attr:`CedIO`
 * :attr:`ElanIO`
 * :attr:`IgorIO`
 * :attr:`IntanIO`
@@ -114,6 +115,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.io.CedIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.io.ElanIO
 
     .. autoattribute:: extensions
@@ -264,6 +269,7 @@
 from neo.io.brainwaredamio import BrainwareDamIO
 from neo.io.brainwaref32io import BrainwareF32IO
 from neo.io.brainwaresrcio import BrainwareSrcIO
+from neo.io.cedio import CedIO
 from neo.io.elanio import ElanIO
 # from neo.io.elphyio import ElphyIO
 from neo.io.exampleio import ExampleIO
@@ -310,6 +316,7 @@
     BrainwareDamIO,
     BrainwareF32IO,
     BrainwareSrcIO,
+    CedIO,
     ElanIO,
     # ElphyIO,
     ExampleIO,

neo/io/cedio.py

@@ -0,0 +1,10 @@
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.cedrawio import CedRawIO
+
+
+class CedIO(CedRawIO, BaseFromRaw):
+    __doc__ = CedRawIO.__doc__
+
+    def __init__(self, filename, entfile=None, posfile=None):
+        CedRawIO.__init__(self, filename=filename)
+        BaseFromRaw.__init__(self, filename)

neo/rawio/__init__.py

@@ -17,6 +17,7 @@
 * :attr:`AxonRawIO`
 * :attr:`BlackrockRawIO`
 * :attr:`BrainVisionRawIO`
+* :attr:`CedRawIO`
 * :attr:`ElanRawIO`
 * :attr:`IntanRawIO`
 * :attr:`MEArecRawIO`
@@ -58,6 +59,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.rawio.CedRawIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.rawio.ElanRawIO
 
     .. autoattribute:: extensions
@@ -142,6 +147,7 @@
 from neo.rawio.axonrawio import AxonRawIO
 from neo.rawio.blackrockrawio import BlackrockRawIO
 from neo.rawio.brainvisionrawio import BrainVisionRawIO
+from neo.rawio.cedrawio import CedRawIO
 from neo.rawio.elanrawio import ElanRawIO
 from neo.rawio.examplerawio import ExampleRawIO
 from neo.rawio.intanrawio import IntanRawIO
@@ -169,6 +175,7 @@
     AxonRawIO,
     BlackrockRawIO,
     BrainVisionRawIO,
+    CedRawIO,
     ElanRawIO,
     IntanRawIO,
     MicromedRawIO,

neo/rawio/cedrawio.py

@@ -0,0 +1,177 @@
+"""
+Class for reading data from CED (Cambridge Electronic Design)
+http://ced.co.uk/
+
+This read *.smrx (and *.smr) from spike2 and signal software.
+
+Note Spike2RawIO/Spike2IO is the old implementation in neo.
+It still works without any dependency and should be faster.
+Spike2IO only works for smr (32 bit) and not for smrx (64 bit) files.
+
+This implementation depends on the SONPY package:
+https://pypi.org/project/sonpy/
+
+Please note that the SONPY package:
+  * is NOT open source
+  * internally uses a list instead of numpy.ndarray, potentially causing slow data reading
+  *  is maintained by CED
+
+
+Author : Samuel Garcia
+"""
+
+from .baserawio import (BaseRawIO, _signal_channel_dtype, _signal_stream_dtype,
+                _spike_channel_dtype, _event_channel_dtype)
+
+import numpy as np
+from copy import deepcopy
+
+try:
+    import sonpy
+    HAVE_SONPY = True
+except ImportError:
+    HAVE_SONPY = False
+
+
+class CedRawIO(BaseRawIO):
+    """
+    Class for reading data from CED (Cambridge Electronic Design) spike2.
+    This internally uses the sonpy package which is closed source.
+
+    This IO reads smr and smrx files
+    """
+    extensions = ['smr', 'smrx']
+    rawmode = 'one-file'
+
+    def __init__(self, filename='', take_ideal_sampling_rate=False, ):
+        BaseRawIO.__init__(self)
+        self.filename = filename
+
+        self.take_ideal_sampling_rate = take_ideal_sampling_rate
+
+    def _source_name(self):
+        return self.filename
+
+    def _parse_header(self):
+        assert HAVE_SONPY, 'sonpy must be installed'
+
+        self.smrx_file = sonpy.lib.SonFile(sName=str(self.filename), bReadOnly=True)
+        smrx = self.smrx_file
+
+        channel_infos = []
+        signal_channels = []
+        for chan_ind in range(smrx.MaxChannels()):
+            chan_type = smrx.ChannelType(chan_ind)
+            if chan_type == sonpy.lib.DataType.Adc:
+                physical_chan = smrx.PhysicalChannel(chan_ind)
+                divide = smrx.ChannelDivide(chan_ind)
+                if self.take_ideal_sampling_rate:
+                    sr = smrx.GetIdealRate(chan_ind)
+                else:
+                    sr = 1. / (smrx.GetTimeBase() * divide)
+                max_time = smrx.ChannelMaxTime(chan_ind)
+                first_time = smrx.FirstTime(chan_ind, 0, max_time)
+                # max_times is included so +1
+                time_size = (max_time - first_time) / divide + 1
+                channel_infos.append((first_time, max_time, divide, time_size, sr))
+                gain = smrx.GetChannelScale(chan_ind) / 6553.6
+                offset = smrx.GetChannelOffset(chan_ind)
+                units = smrx.GetChannelUnits(chan_ind)
+                ch_name = smrx.GetChannelTitle(chan_ind)
+                chan_id = str(chan_ind)
+                dtype = 'int16'
+                # set later after grouping
+                stream_id = '0'
+                signal_channels.append((ch_name, chan_id, sr, dtype,
+                                        units, gain, offset, stream_id))
+
+        signal_channels = np.array(signal_channels, dtype=_signal_channel_dtype)
+
+        # channels are grouped into stream if they have a common start, stop, size, divide and sampling_rate
+        channel_infos = np.array(channel_infos,
+                    dtype=[('first_time', 'i8'), ('max_time', 'i8'),
+                           ('divide', 'i8'), ('size', 'i8'), ('sampling_rate', 'f8')])
+        unique_info = np.unique(channel_infos)
+        self.stream_info = unique_info
+        signal_streams = []
+        for i, info in enumerate(unique_info):
+            stream_id = str(i)
+            mask = channel_infos == info
+            signal_channels['stream_id'][mask] = stream_id
+            num_chans = np.sum(mask)
+            stream_name = f'{stream_id} {num_chans}chans'
+            signal_streams.append((stream_name, stream_id))
+        signal_streams = np.array(signal_streams, dtype=_signal_stream_dtype)
+
+        # spike channels not handled
+        spike_channels = []
+        spike_channels = np.array([], dtype=_spike_channel_dtype)
+
+        # event channels not handled
+        event_channels = []
+        event_channels = np.array(event_channels, dtype=_event_channel_dtype)
+
+        self._seg_t_start = np.inf
+        self._seg_t_stop = -np.inf
+        for info in self.stream_info:
+            self._seg_t_start = min(self._seg_t_start,
+                                    info['first_time'] / info['sampling_rate'])
+            self._seg_t_stop = max(self._seg_t_stop,
+                                   info['max_time'] / info['sampling_rate'])
+
+        self.header = {}
+        self.header['nb_block'] = 1
+        self.header['nb_segment'] = [1]
+        self.header['signal_streams'] = signal_streams
+        self.header['signal_channels'] = signal_channels
+        self.header['spike_channels'] = spike_channels
+        self.header['event_channels'] = event_channels
+
+        self._generate_minimal_annotations()
+
+    def _segment_t_start(self, block_index, seg_index):
+        return self._seg_t_start
+
+    def _segment_t_stop(self, block_index, seg_index):
+        return self._seg_t_stop
+
+    def _get_signal_size(self, block_index, seg_index, stream_index):
+        size = self.stream_info[stream_index]['size']
+        return size
+
+    def _get_signal_t_start(self, block_index, seg_index, stream_index):
+        info = self.stream_info[stream_index]
+        t_start = info['first_time'] / info['sampling_rate']
+        return t_start
+
+    def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop,
+                                stream_index, channel_indexes):
+
+        if i_start is None:
+            i_start = 0
+        if i_stop is None:
+            i_stop = self.stream_info[stream_index]['size']
+
+        stream_id = self.header['signal_streams']['id'][stream_index]
+        signal_channels = self.header['signal_channels']
+        mask = signal_channels['stream_id'] == stream_id
+        signal_channels = signal_channels[mask]
+        if channel_indexes is not None:
+            signal_channels = signal_channels[channel_indexes]
+
+        num_chans = len(signal_channels)
+
+        size = i_stop - i_start
+        sigs = np.zeros((size, num_chans), dtype='int16')
+
+        info = self.stream_info[stream_index]
+        t_from = info['first_time'] + info['divide'] * i_start
+        t_upto = info['first_time'] + info['divide'] * i_stop
+
+        for i, chan_id in enumerate(signal_channels['id']):
+            chan_ind = int(chan_id)
+            sig = self.smrx_file.ReadInts(chan=chan_ind,
+                    nMax=size, tFrom=t_from, tUpto=t_upto)
+            sigs[:, i] = sig
+
+        return sigs

neo/rawio/spike2rawio.py

@@ -27,7 +27,8 @@
 
 class Spike2RawIO(BaseRawIO):
     """
-
+    This implementation in neo read only old smr files.
+    For smrx files you need to use CedRawIO which is based on sonpy.
     """
     extensions = ['smr']
     rawmode = 'one-file'

neo/test/iotest/test_cedio.py

@@ -0,0 +1,20 @@
+import unittest
+
+from neo.io import CedIO
+from neo.test.iotest.common_io_test import BaseTestIO
+
+
+class TestCedIO(BaseTestIO, unittest.TestCase, ):
+    ioclass = CedIO
+    entities_to_test = [
+        'spike2/m365_1sec.smrx',
+        'spike2/File_spike2_1.smr',
+        'spike2/Two-mice-bigfile-test000.smr'
+    ]
+    entities_to_download = [
+        'spike2'
+    ]
+
+
+if __name__ == "__main__":
+    unittest.main()

neo/test/rawiotest/test_cedrawio.py

@@ -0,0 +1,21 @@
+import unittest
+
+from neo.rawio.cedrawio import CedRawIO
+
+from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
+
+
+class TestCedRawIO(BaseTestRawIO, unittest.TestCase, ):
+    rawioclass = CedRawIO
+    entities_to_test = [
+        'spike2/m365_1sec.smrx',
+        'spike2/File_spike2_1.smr',
+        'spike2/Two-mice-bigfile-test000.smr'
+    ]
+    entities_to_download = [
+        'spike2'
+    ]
+
+
+if __name__ == "__main__":
+    unittest.main()

requirements_testing.txt

@@ -12,3 +12,4 @@ ipython
 coverage
 coveralls
 pillow
+sonpy