Merge branch 'NeuralEnsemble:master' into feature/newFilter

Author: Moritz-Alexander-Kern

.github/workflows/core-test.yml

@@ -7,6 +7,7 @@ on:
     paths:
       - 'neo/core/**'
       - 'pyproject.toml'
+      - '.github/workflows/*.yml'
 
   # run checks on any change of master, including merge of PRs
   push:
@@ -26,14 +27,12 @@ jobs:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
         python-version: ['3.8', '3.9', '3.10', '3.11']
-        numpy-version: ['1.19.5', '1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1']
+        numpy-version: ['1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1', '1.25.1']
         exclude:
-           - python-version: '3.10'
-             numpy-version: '1.19.5'
+           - python-version: '3.8'
+             numpy-version: '1.25.1'
            - python-version: '3.10'
              numpy-version: '1.20.3'
-           - python-version: '3.11'
-             numpy-version: '1.19.5'
            - python-version: '3.11'
              numpy-version: '1.20.3'
            - python-version: '3.11'

doc/source/authors.rst

@@ -63,6 +63,7 @@ and may not be the current affiliation of a contributor.
 * Oliver Kloss [13]
 * Heberto Mayorquin [24]
 * Thomas Perret [25]
+* Kyle Johnsen [26, 27]
 
 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
@@ -89,6 +90,8 @@ and may not be the current affiliation of a contributor.
 23. Bio Engineering Laboratory, DBSSE, ETH, Basel, Switzerland
 24. CatalystNeuro
 25. Institut des Sciences Cognitives Marc Jeannerod, CNRS UMR5229, Lyon, France
+26. Georgia Institute of Technology
+27. Emory University
 
 If we've somehow missed you off the list we're very sorry - please let us know.
 

neo/core/container.py

@@ -333,6 +333,39 @@ def size(self):
         return {name: len(getattr(self, name))
                     for name in self._child_containers}
 
+    @property
+    def _container_lookup(self):
+        return {
+            cls_name: getattr(self, container_name)
+            for cls_name, container_name in zip(self._child_objects, self._child_containers)
+        }
+
+    def _get_container(self, cls):
+        if hasattr(cls, "proxy_for"):
+            cls = cls.proxy_for
+        return self._container_lookup[cls.__name__]
+
+    def add(self, *objects):
+        """Add a new Neo object to the Container"""
+        for obj in objects:
+            if (
+                obj.__class__.__name__ in self._child_objects
+                or (
+                    hasattr(obj, "proxy_for")
+                    and obj.proxy_for.__name__ in self._child_objects
+                )
+            ):
+                container = self._get_container(obj.__class__)
+                container.append(obj)
+            else:
+                raise TypeError(
+                    f"Cannot add object of type {obj.__class__.__name__} "
+                    f"to a {self.__class__.__name__}, can only add objects of the "
+                    f"following types: {self._child_objects}"
+                )
+
+
+
     def filter(self, targdict=None, data=True, container=False, recursive=True,
                objects=None, **kwargs):
         """

neo/core/group.py

@@ -76,6 +76,9 @@ def __init__(self, objects=None, name=None, description=None, file_origin=None,
             self.allowed_types = None
         else:
             self.allowed_types = tuple(allowed_types)
+            for type_ in self.allowed_types:
+                if type_.__name__ not in self._child_objects:
+                    raise TypeError(f"Groups can not contain objects of type {type_.__name__}")
 
         if objects:
             self.add(*objects)
@@ -134,26 +137,13 @@ def __init__(self, objects=None, name=None, description=None, file_origin=None,
         doc="list of Groups contained in this group"
     )
 
-    @property
-    def _container_lookup(self):
-        return {
-            cls_name: getattr(self, container_name)
-            for cls_name, container_name in zip(self._child_objects, self._child_containers)
-        }
-
-    def _get_container(self, cls):
-        if hasattr(cls, "proxy_for"):
-            cls = cls.proxy_for
-        return self._container_lookup[cls.__name__]
-
     def add(self, *objects):
         """Add a new Neo object to the Group"""
         for obj in objects:
             if self.allowed_types and not isinstance(obj, self.allowed_types):
                 raise TypeError("This Group can only contain {}, but not {}"
                                 "".format(self.allowed_types, type(obj)))
-            container = self._get_container(obj.__class__)
-            container.append(obj)
+        super().add(*objects)
 
     def walk(self):
         """

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,

neo/rawio/maxwellrawio.py

@@ -183,9 +183,10 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop,
             if np.array(channel_indexes).size > 1 and np.any(np.diff(channel_indexes) < 0):
                 # get around h5py constraint that it does not allow datasets
                 # to be indexed out of order
-                sorted_channel_indexes = np.sort(channel_indexes)
-                resorted_indexes = np.array(
-                    [list(channel_indexes).index(ch) for ch in sorted_channel_indexes])
+                order_f = np.argsort(channel_indexes) 
+                sorted_channel_indexes = channel_indexes[order_f] 
+                # use argsort again on order_f to obtain resorted_indexes 
+                resorted_indexes = np.argsort(order_f)
 
         try:
             if resorted_indexes is None: