Merge pull request #1288 from dancrepeau/master

Add MED wrapper

Author: JuliaSprenger

neo/io/__init__.py

@@ -39,6 +39,7 @@
 * :attr:`KlustaKwikIO`
 * :attr:`KwikIO`
 * :attr:`MaxwellIO`
+* :attr:`MedIO`
 * :attr:`MicromedIO`
 * :attr:`NeoMatlabIO`
 * :attr:`NestIO`
@@ -165,6 +166,10 @@
 .. autoclass:: neo.io.MaxwellIO
 
     .. autoattribute:: extensions
+    
+.. autoclass:: neo.io.MedIO
+
+    .. autoattribute:: extensions
 
 .. autoclass:: neo.io.MicromedIO
 
@@ -313,6 +318,7 @@
 from neo.io.kwikio import KwikIO
 from neo.io.mearecio import MEArecIO
 from neo.io.maxwellio import MaxwellIO
+from neo.io.medio import MedIO
 from neo.io.micromedio import MicromedIO
 from neo.io.neomatlabio import NeoMatlabIO
 from neo.io.nestio import NestIO
@@ -366,6 +372,7 @@
     KwikIO,
     MEArecIO,
     MaxwellIO,
+    MedIO,
     MicromedIO,
     NixIO,
     NixIOFr,

neo/io/medio.py

@@ -0,0 +1,52 @@
+"""
+IO for reading MED datasets using dhn-med-py library.
+
+dhn-med-py
+https://medformat.org
+https://pypi.org/project/dhn-med-py/
+
+MED Format Specifications: https://medformat.org
+
+Author: Dan Crepeau, Matt Stead
+"""
+
+from neo.io.basefromrawio import BaseFromRaw
+from neo.rawio.medrawio import MedRawIO
+
+
+class MedIO(MedRawIO, BaseFromRaw):
+    """
+    IO for reading MED datasets.
+    """
+    name = 'MED IO'
+    description = "IO for reading MED datasets"
+    
+    _prefered_signal_group_mode = 'group-by-same-units'
+    mode = 'dir'
+
+    def __init__(self, dirname=None, password=None, keep_original_times=False):
+        MedRawIO.__init__(self, dirname=dirname, password=password,
+            keep_original_times=keep_original_times)
+        """
+        Initialise IO instance
+
+        Parameters
+        ----------
+        dirname : str
+            Directory containing data files
+        password : str
+            MED sessions can be optionally encrypted with a password.
+            Default: None
+        keep_original_times : bool
+            Preserve original time stamps as in data files. By default datasets are
+            shifted to begin at t_start = 0.  When set to True, timestamps will be
+            returned as UTC (seconds since midnight 1 Jan 1970).
+            Default: False
+        """
+        BaseFromRaw.__init__(self, dirname)
+        
+    def close(self):
+        MedRawIO.close(self)
+        
+    def __del__(self):
+        MedRawIO.__del__(self)

neo/rawio/__init__.py

@@ -24,6 +24,7 @@
 * :attr:`ElanRawIO`
 * :attr:`IntanRawIO`
 * :attr:`MaxwellRawIO`
+* :attr:`MedRawIO`
 * :attr:`MEArecRawIO`
 * :attr:`MicromedRawIO`
 * :attr:`NeuralynxRawIO`
@@ -93,6 +94,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.rawio.MedRawIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.rawio.MEArecRawIO
 
     .. autoattribute:: extensions
@@ -186,6 +191,7 @@
 from neo.rawio.intanrawio import IntanRawIO
 from neo.rawio.maxwellrawio import MaxwellRawIO
 from neo.rawio.mearecrawio import MEArecRawIO
+from neo.rawio.medrawio import MedRawIO
 from neo.rawio.micromedrawio import MicromedRawIO
 from neo.rawio.neuralynxrawio import NeuralynxRawIO
 from neo.rawio.neuroexplorerrawio import NeuroExplorerRawIO
@@ -220,6 +226,7 @@
     MicromedRawIO,
     MaxwellRawIO,
     MEArecRawIO,
+    MedRawIO,
     NeuralynxRawIO,
     NeuroExplorerRawIO,
     NeuroScopeRawIO,