Merge pull request #945 from samuelgarcia/openephys_binary

Start again openephys binary rawio.

Author: JuliaSprenger

neo/io/__init__.py

@@ -42,6 +42,7 @@
 * :attr:`NeuroshareIO`
 * :attr:`NixIO`
 * :attr:`OpenEphysIO`
+* :attr:`OpenEphysBinaryIO`
 * :attr:`PhyIO`
 * :attr:`PickleIO`
 * :attr:`PlexonIO`
@@ -172,6 +173,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.io.OpenEphysBinaryIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.io.PhyIO
 
     .. autoattribute:: extensions
@@ -270,6 +275,7 @@
 from neo.io.nixio import NixIO
 from neo.io.nixio_fr import NixIO as NixIOFr
 from neo.io.openephysio import OpenEphysIO
+from neo.io.openephysbinaryio import OpenEphysBinaryIO
 from neo.io.phyio import PhyIO
 from neo.io.pickleio import PickleIO
 from neo.io.plexonio import PlexonIO
@@ -314,6 +320,7 @@
     NeuroScopeIO,
     NeuroshareIO,
     OpenEphysIO,
+    OpenEphysBinaryIO,
     PhyIO,
     PickleIO,
     PlexonIO,

neo/io/openephysbinaryio.py

@@ -0,0 +1,11 @@
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.openephysbinaryrawio import OpenEphysBinaryRawIO
+
+
+class OpenEphysBinaryIO(OpenEphysBinaryRawIO, BaseFromRaw):
+    _prefered_signal_group_mode = 'group-by-same-units'
+    mode = 'dir'
+
+    def __init__(self, dirname):
+        OpenEphysBinaryRawIO.__init__(self, dirname=dirname)
+        BaseFromRaw.__init__(self, dirname)

neo/io/proxyobjects.py

@@ -33,10 +33,19 @@ def __init__(self, array_annotations=None, **annotations):
             # used to be str so raw bytes
             annotations['file_origin'] = str(self._rawio.source_name())
 
-        # this mock the array annotaions to avoid inherits DataObject
+        if array_annotations is None:
+            array_annotations = {}
+        for k, v in array_annotations.items():
+            array_annotations[k] = np.asarray(v)
+
+        # clean array annotations that are not 1D
+        # TODO remove this once multi-dimensional array_annotations are possible
+        array_annotations = {k: v for k, v in array_annotations.items()
+                             if v.ndim == 1}
+
+        # this mock the array annotations to avoid inherits DataObject
         self.array_annotations = ArrayDict(self.shape[-1])
-        if array_annotations is not None:
-            self.array_annotations.update(array_annotations)
+        self.array_annotations.update(array_annotations)
 
         BaseNeo.__init__(self, **annotations)
 

neo/rawio/__init__.py

@@ -25,6 +25,7 @@
 * :attr:`NeuroScopeRawIO`
 * :attr:`NIXRawIO`
 * :attr:`OpenEphysRawIO`
+* :attr:`OpenEphysBinaryRawIO`
 * :attr:'PhyRawIO'
 * :attr:`PlexonRawIO`
 * :attr:`RawBinarySignalRawIO`
@@ -88,6 +89,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.rawio.OpenEphysBinaryRawIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.rawio.PhyRawIO
 
     .. autoattribute:: extensions
@@ -141,6 +146,7 @@
 from neo.rawio.neuroscoperawio import NeuroScopeRawIO
 from neo.rawio.nixrawio import NIXRawIO
 from neo.rawio.openephysrawio import OpenEphysRawIO
+from neo.rawio.openephysbinaryrawio import OpenEphysBinaryRawIO
 from neo.rawio.phyrawio import PhyRawIO
 from neo.rawio.plexonrawio import PlexonRawIO
 from neo.rawio.rawbinarysignalrawio import RawBinarySignalRawIO
@@ -165,6 +171,7 @@
     NeuroScopeRawIO,
     NIXRawIO,
     OpenEphysRawIO,
+    OpenEphysBinaryRawIO,
     PhyRawIO,
     PlexonRawIO,
     RawBinarySignalRawIO,