Skeleton for spikegadgets implementation.

Author: samuelgarcia

neo/io/__init__.py

@@ -49,6 +49,7 @@
 * :attr:`RawBinarySignalIO`
 * :attr:`RawMCSIO`
 * :attr:`Spike2IO`
+* :attr:`SpikeGadgetsIO`
 * :attr:`SpikeGLXIO`
 * :attr:`StimfitIO`
 * :attr:`TdtIO`
@@ -201,6 +202,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: SpikeGadgetsIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: SpikeGLXIO
 
     .. autoattribute:: extensions
@@ -284,6 +289,7 @@
 from neo.io.rawbinarysignalio import RawBinarySignalIO
 from neo.io.rawmcsio import RawMCSIO
 from neo.io.spike2io import Spike2IO
+from neo.io.spikegadgetsio import SpikeGadgetsIO
 from neo.io.spikeglxio import SpikeGLXIO
 from neo.io.stimfitio import StimfitIO
 from neo.io.tdtio import TdtIO
@@ -329,6 +335,7 @@
     RawBinarySignalIO,
     RawMCSIO,
     Spike2IO,
+    SpikeGadgetsIO,
     SpikeGLXIO,
     StimfitIO,
     TdtIO,

neo/io/spikegadgetsio.py

@@ -0,0 +1,10 @@
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.spikegadgetsrawio import SpikeGadgetsRawIO
+
+
+class SpikeGadgetsIO(SpikeGadgetsRawIO, BaseFromRaw):
+    """
+    """
+    def __init__(self, filename):
+        SpikeGadgetsRawIO.__init__(self, filename=filename)
+        BaseFromRaw.__init__(self, filename)

neo/rawio/__init__.py

@@ -29,6 +29,7 @@
 * :attr:`RawBinarySignalRawIO`
 * :attr:`RawMCSRawIO`
 * :attr:`Spike2RawIO`
+* :attr:`SpikeGadgetsRawIO`
 * :attr:`SpikeGLXRawIO`
 * :attr:`TdtRawIO`
 * :attr:`WinEdrRawIO`
@@ -103,6 +104,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.rawio.SpikeGadgetsRawIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.rawio.SpikeGLXRawIO
 
     .. autoattribute:: extensions
@@ -140,6 +145,7 @@
 from neo.rawio.rawbinarysignalrawio import RawBinarySignalRawIO
 from neo.rawio.rawmcsrawio import RawMCSRawIO
 from neo.rawio.spike2rawio import Spike2RawIO
+from neo.rawio.spikegadgetsrawio import SpikeGadgetsRawIO
 from neo.rawio.spikeglxrawio import SpikeGLXRawIO
 from neo.rawio.tdtrawio import TdtRawIO
 from neo.rawio.winedrrawio import WinEdrRawIO
@@ -163,6 +169,7 @@
     RawBinarySignalRawIO,
     RawMCSRawIO,
     Spike2RawIO,
+    SpikeGadgetsRawIO,
     SpikeGLXRawIO,
     TdtRawIO,
     WinEdrRawIO,

neo/rawio/spikegadgetsrawio.py

@@ -0,0 +1,65 @@
+"""
+Class for reading  spikegadgets file.
+Only signals ability at the moment.
+
+https://spikegadgets.com/spike-products/
+
+Author: Samuel Garcia
+"""
+from .baserawio import (BaseRawIO, _signal_channel_dtype, _unit_channel_dtype,
+                        _event_channel_dtype)
+
+import numpy as np
+
+
+class SpikeGadgetsRawIO(BaseRawIO):
+    extensions = ['rec']
+    rawmode = 'one-file'
+
+    def __init__(self, filename=''):
+        BaseRawIO.__init__(self)
+        self.filename = filename
+
+    def _source_name(self):
+        return self.filename
+
+    def _parse_header(self):
+        
+        signal_channels = []
+        signal_channels = np.array(sig_channels, dtype=_signal_channel_dtype)
+
+        # No events
+        event_channels = []
+        event_channels = np.array(event_channels, dtype=_event_channel_dtype)
+
+        # No spikes
+        unit_channels = []
+        unit_channels = np.array(unit_channels, dtype=_unit_channel_dtype)
+
+        # fille into header dict
+        self.header = {}
+        self.header['nb_block'] = 1
+        self.header['nb_segment'] = [nb_segment]
+        self.header['signal_channels'] = sig_channels
+        self.header['unit_channels'] = unit_channels
+        self.header['event_channels'] = event_channels
+
+        self._generate_minimal_annotations()
+
+    def _segment_t_start(self, block_index, seg_index):
+        return 0.
+
+    def _segment_t_stop(self, block_index, seg_index):
+        return t_stop
+
+    def _get_signal_size(self, block_index, seg_index, channel_indexes):
+        sie = 0
+        return size
+
+    def _get_signal_t_start(self, block_index, seg_index, channel_indexes):
+        return 0.
+
+    def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, channel_indexes):
+        raw_signals = None
+        return raw_signals
+

neo/test/iotest/test_spikegadgetsio.py

@@ -0,0 +1,14 @@
+import unittest
+
+from neo.io import SpikeGadgetsIO
+from neo.test.iotest.common_io_test import BaseTestIO
+
+
+class TestSpikeGadgetsIO(BaseTestIO, unittest.TestCase, ):
+    ioclass = SpikeGadgetsIO
+    files_to_test =  ['20210225_em8_minirec2_ac.rec']
+    files_to_download = files_to_test
+
+
+if __name__ == "__main__":
+    unittest.main()

neo/test/rawiotest/test_spikegadgetsrawio.py

@@ -0,0 +1,14 @@
+import unittest
+
+from neo.rawio.spikegadgetsrawio import SpikeGadgetsRawIO
+from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
+
+
+class TestSpikeGadgetsRawIO(BaseTestRawIO, unittest.TestCase, ):
+    rawioclass = SpikeGadgetsRawIO
+    entities_to_test = ['20210225_em8_minirec2_ac.rec']
+    files_to_download = entities_to_test
+
+
+if __name__ == "__main__":
+    unittest.main()