Merge branch 'master' into remove-copy

Author: zm711

neo/io/__init__.py

@@ -45,6 +45,7 @@
 * :attr:`NestIO`
 * :attr:`NeuralynxIO`
 * :attr:`NeuroExplorerIO`
+* :attr:`NeuroNexusIO
 * :attr:`NeuroScopeIO`
 * :attr:`NeuroshareIO`
 * :attr:`NixIO`
@@ -191,6 +192,9 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.io.NeuroNexusIO
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.io.NeuroScopeIO
 
     .. autoattribute:: extensions
@@ -326,6 +330,7 @@
 from neo.io.nestio import NestIO
 from neo.io.neuralynxio import NeuralynxIO
 from neo.io.neuroexplorerio import NeuroExplorerIO
+from neo.io.neuronexusio import NeuroNexusIO
 from neo.io.neuroscopeio import NeuroScopeIO
 from neo.io.nixio import NixIO
 from neo.io.nixio_fr import NixIO as NixIOFr
@@ -382,6 +387,7 @@
     NestIO,
     NeuralynxIO,
     NeuroExplorerIO,
+    NeuroNexusIO,
     NeuroScopeIO,
     NeuroshareIO,
     NWBIO,

neo/io/neuronexusio.py

@@ -0,0 +1,11 @@
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.neuronexusrawio import NeuroNexusRawIO
+
+
+class NeuroNexusIO(NeuroNexusRawIO, BaseFromRaw):
+    __doc__ = NeuroNexusRawIO.__doc__
+    _prefered_signal_group_mode = "group-by-same-units"
+
+    def __init__(self, filename):
+        NeuroNexusRawIO.__init__(self, filename=filename)
+        BaseFromRaw.__init__(self, filename)

neo/rawio/__init__.py

@@ -29,6 +29,7 @@
 * :attr:`MicromedRawIO`
 * :attr:`NeuralynxRawIO`
 * :attr:`NeuroExplorerRawIO`
+* :attr:`NeuroNexusRawIO
 * :attr:`NeuroScopeRawIO`
 * :attr:`NIXRawIO`
 * :attr:`OpenEphysRawIO`
@@ -114,6 +115,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.rawio.NeuroNexusRawIO
+
+    .. autoattributes:: extensions
+
 .. autoclass:: neo.rawio.NeuroScopeRawIO
 
     .. autoattribute:: extensions
@@ -197,6 +202,7 @@
 from neo.rawio.micromedrawio import MicromedRawIO
 from neo.rawio.neuralynxrawio import NeuralynxRawIO
 from neo.rawio.neuroexplorerrawio import NeuroExplorerRawIO
+from neo.rawio.neuronexusrawio import NeuroNexusRawIO
 from neo.rawio.neuroscoperawio import NeuroScopeRawIO
 from neo.rawio.nixrawio import NIXRawIO
 from neo.rawio.openephysrawio import OpenEphysRawIO
@@ -231,6 +237,7 @@
     MedRawIO,
     NeuralynxRawIO,
     NeuroExplorerRawIO,
+    NeuroNexusRawIO,
     NeuroScopeRawIO,
     NIXRawIO,
     OpenEphysRawIO,

neo/rawio/intanrawio.py

@@ -179,6 +179,7 @@ def _parse_header(self):
             self._raw_data = np.memmap(self.filename, dtype=memmap_data_dtype, mode="r", offset=header_size)
 
         # for 'one-file-per-signal' we have one memory map / neo stream
+        # based on https://github.com/NeuralEnsemble/python-neo/issues/1556 bug in versions 0.13.1, .2, .3
         elif self.file_format == "one-file-per-signal":
             self._raw_data = {}
             for stream_index, (stream_index_key, stream_datatype) in enumerate(memmap_data_dtype.items()):
@@ -188,8 +189,8 @@ def _parse_header(self):
                 dtype_size = np.dtype(stream_datatype).itemsize
                 n_samples = size_in_bytes // (dtype_size * num_channels)
                 signal_stream_memmap = np.memmap(
-                    file_path, dtype=stream_datatype, mode="r", shape=(num_channels, n_samples)
-                ).T
+                    file_path, dtype=stream_datatype, mode="r", shape=(n_samples, num_channels), order='C',
+                )
                 self._raw_data[stream_index] = signal_stream_memmap
 
         # for one-file-per-channel we have one memory map / channel stored as a list / neo stream