[WIP] Nest3io

neo/io/__init__.py

@@ -133,7 +133,11 @@
 
     .. autoattribute:: extensions
 
-.. autoclass:: neo.io.NestIO
+.. autoclass:: neo.io.Nest2IO
+
+    .. autoattribute:: extensions
+
+.. autoclass:: neo.io.Nest3IO
 
     .. autoattribute:: extensions
 
@@ -243,7 +247,8 @@
 from neo.io.micromedio import MicromedIO
 from neo.io.hdf5io import NeoHdf5IO
 from neo.io.neomatlabio import NeoMatlabIO
-from neo.io.nestio import NestIO
+from neo.io.nest2io import Nest2IO
+from neo.io.nest3io import Nest3IO
 from neo.io.neuralynxio import NeuralynxIO
 from neo.io.neuralynxio_v1 import NeuralynxIO as OldNeuralynxIO
 from neo.io.neuroexplorerio import NeuroExplorerIO
@@ -285,7 +290,8 @@
     NixIO,  # place NixIO before NeoHdf5IO to make it the default for .h5 files
     NeoHdf5IO,
     NeoMatlabIO,
-    NestIO,
+    Nest2IO,
+    Nest3IO,
     NeuralynxIO,
     NeuroExplorerIO,
     NeuroScopeIO,

neo/io/nestio.py → neo/io/nest2io.py

@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 """
 Class for reading output files from NEST simulations
+using NEST versions 2.x
 ( http://www.nest-simulator.org/ ).
 Tested with NEST2.10.0
 
@@ -30,7 +31,7 @@
                    'no type': pq.dimensionless}
 
 
-class NestIO(BaseIO):
+class Nest2IO(BaseIO):
     """
     Class for reading NEST output files. GDF files for the spike data and DAT
     files for analog signals are possible.

neo/io/nest3io.py

@@ -0,0 +1,31 @@
+# -*- coding: utf-8 -*-
+"""
+neo.io have been split in 2 level API:
+  * neo.io: this API give neo object
+  * neo.rawio: this API give raw data as they are in files.
+
+Developer are encourage to use neo.rawio.
+
+When this is done the neo.io is done automagically with
+this king of following code.
+
+Author: Johanna Senk, Julia Sprenger
+
+"""
+
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.nest3rawio import Nest3RawIO
+
+
+class Nest3IO(Nest3RawIO, BaseFromRaw):
+    name = 'Nest3IO'
+    description = "Fake IO"
+
+    # This is an important choice when there are several channels.
+    #   'split-all' :  1 AnalogSignal each 1 channel
+    #   'group-by-same-units' : one 2D AnalogSignal for each group of channel with same units
+    _prefered_signal_group_mode = 'group-by-same-units'
+
+    def __init__(self, filename=''):
+        Nest3RawIO.__init__(self, filename=filename)
+        BaseFromRaw.__init__(self, filename)

neo/rawio/__init__.py

@@ -121,6 +121,7 @@
 from neo.rawio.examplerawio import ExampleRawIO
 from neo.rawio.intanrawio import IntanRawIO
 from neo.rawio.micromedrawio import MicromedRawIO
+from neo.rawio.nest3rawio import Nest3RawIO
 from neo.rawio.neuralynxrawio import NeuralynxRawIO
 from neo.rawio.neuroexplorerrawio import NeuroExplorerRawIO
 from neo.rawio.neuroscoperawio import NeuroScopeRawIO
@@ -142,6 +143,7 @@
     ElanRawIO,
     IntanRawIO,
     MicromedRawIO,
+    Nest3RawIO,
     NeuralynxRawIO,
     NeuroExplorerRawIO,
     NeuroScopeRawIO,