Merge branch 'NeuralEnsemble:master' into enh/array_anno_types

ocefpaf · May 23, 2023 · 8d2ac21 · 8d2ac21
2 parents 95d6ad2 + 29d73f6
commit 8d2ac21
Show file tree

Hide file tree

Showing 54 changed files with 595 additions and 343 deletions.
diff --git a/codemeta.json b/codemeta.json
@@ -0,0 +1,113 @@
+{
+  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+  "@type": "SoftwareSourceCode",
+  "license": "https://spdx.org/licenses/BSD-3-Clause",
+  "codeRepository": "https://github.com/NeuralEnsemble/python-neo",
+  "contIntegration": "https://github.com/NeuralEnsemble/python-neo/actions",
+  "dateModified": "2023-04-04",
+  "downloadUrl": "https://files.pythonhosted.org/packages/4d/95/e79e05c9bc8ef61d89a8a6b949db03adb2046b9fca38422d570c7add543d/neo-0.12.0.tar.gz",
+  "issueTracker": "https://github.com/NeuralEnsemble/python-neo/issues",
+  "name": "Neo",
+  "version": "0.12.0",
+  "identifier": "RRID:SCR_000634",
+  "description": "Neo is a Python package for working with electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5.\n\nThe goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization.\n\nNeo is used by a number of other software tools, including SpykeViewer (data analysis and visualization), Elephant (data analysis), the G-node suite (databasing), PyNN (simulations), tridesclous_ (spike sorting) and ephyviewer (data visualization).\n\nNeo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.",
+  "applicationCategory": "neuroscience",
+  "releaseNotes": "https://neo.readthedocs.io/en/stable/releases/0.12.0.html",
+  "funding": "https://cordis.europa.eu/project/id/945539",
+  "developmentStatus": "active",
+  "referencePublication": "https://doi.org/10.3389/fninf.2014.00010",
+  "funder": {
+    "@type": "Organization",
+    "name": "European Commission"
+  },
+  "programmingLanguage": ["Python"],
+  "operatingSystem": ["Linux", "Windows", "macOS"],
+  "softwareRequirements": [
+    "Python (version 3.8+)",
+    "see https://github.com/NeuralEnsemble/python-neo/blob/master/pyproject.toml"
+  ],
+  "relatedLink": [
+    "https://neo.readthedocs.io",
+    "https://neuralensemble.org/community"
+  ],
+  "author": [
+    { "@type": "Person", "givenName": "Samuel", "familyName": "Garcia" },
+    {
+      "@type": "Person",
+      "@id": "http://orcid.org/0000-0002-4793-7541",
+      "givenName": "Andrew P.",
+      "familyName": "Davison"
+    },
+    { "@type": "Person", "givenName": "Chris", "familyName": "Rodgers" },
+    { "@type": "Person", "givenName": "Pierre", "familyName": "Yger" },
+    { "@type": "Person", "givenName": "Yann", "familyName": "Mahnoun" },
+    { "@type": "Person", "givenName": "Luc", "familyName": "Estabanez" },
+    { "@type": "Person", "givenName": "Andrey", "familyName": "Sobolev" },
+    { "@type": "Person", "givenName": "Thierry", "familyName": "Brizzi" },
+    { "@type": "Person", "givenName": "Florent", "familyName": "Jaillet" },
+    { "@type": "Person", "givenName": "Philipp", "familyName": "Rautenberg" },
+    { "@type": "Person", "givenName": "Thomas", "familyName": "Wachtler" },
+    { "@type": "Person", "givenName": "Cyril", "familyName": "Dejean" },
+    { "@type": "Person", "givenName": "Robert", "familyName": "Pröpper" },
+    { "@type": "Person", "givenName": "Domenico", "familyName": "Guarino" },
+    { "@type": "Person", "givenName": "Achilleas", "familyName": "Koutsou" },
+    { "@type": "Person", "givenName": "Erik", "familyName": "Li" },
+    { "@type": "Person", "givenName": "Georg", "familyName": "Raiser" },
+    { "@type": "Person", "givenName": "Joffrey", "familyName": "Gonin" },
+    { "@type": "Person", "givenName": "Kyler", "familyName": "Brown" },
+    { "@type": "Person", "givenName": "Mikkel Elle", "familyName": "Lepperød" },
+    { "@type": "Person", "givenName": "C Daniel", "familyName": "Meliza" },
+    { "@type": "Person", "givenName": "Julia", "familyName": "Sprenger" },
+    { "@type": "Person", "givenName": "Maximilian", "familyName": "Schmidt" },
+    { "@type": "Person", "givenName": "Johanna", "familyName": "Senk" },
+    { "@type": "Person", "givenName": "Carlos", "familyName": "Canova" },
+    { "@type": "Person", "givenName": "Hélissande", "familyName": "Fragnaud" },
+    { "@type": "Person", "givenName": "Mark", "familyName": "Hollenbeck" },
+    { "@type": "Person", "givenName": "Mieszko", "familyName": "Grodzicki" },
+    { "@type": "Person", "givenName": "Rick", "familyName": "Gerkin" },
+    { "@type": "Person", "givenName": "Matthieu", "familyName": "Sénoville" },
+    { "@type": "Person", "givenName": "Chadwick", "familyName": "Boulay" },
+    { "@type": "Person", "givenName": "Björn", "familyName": "Müller" },
+    { "@type": "Person", "givenName": "William", "familyName": "Hart" },
+    { "@type": "Person", "alternateName": "erikli(github)" },
+    { "@type": "Person", "givenName": "Jeffrey", "familyName": "Gill" },
+    {
+      "@type": "Person",
+      "givenName": "Lucas",
+      "alternateName": "lkoelman@github"
+    },
+    { "@type": "Person", "givenName": "Mark", "familyName": "Histed" },
+    { "@type": "Person", "givenName": "Mike", "familyName": "Sintsov" },
+    { "@type": "Person", "givenName": "Scott W", "familyName": "Harden" },
+    {
+      "@type": "Person",
+      "givenName": "Chek Yin",
+      "familyName": "Choi",
+      "alternateName": "hkchekc@github"
+    },
+    { "@type": "Person", "givenName": "Corentin", "familyName": "Fragnaud" },
+    {
+      "@type": "Person",
+      "givenName": "Alexander",
+      "familyName": "Kleinjohann"
+    },
+    { "@type": "Person", "givenName": "Christian", "familyName": "Kothe" },
+    { "@type": "Person", "alternateName": "rishidhingra@github" },
+    { "@type": "Person", "givenName": "Hugo", "familyName": "van Kemenade" },
+    {
+      "@type": "Person",
+      "givenName": "Aitor",
+      "familyName": "Morales-Gregorio"
+    },
+    { "@type": "Person", "givenName": "Peter N", "familyName": "Steinmetz" },
+    { "@type": "Person", "givenName": "Shashwat", "familyName": "Sridhar" },
+    { "@type": "Person", "givenName": "Alessio", "familyName": "Buccino" },
+    { "@type": "Person", "givenName": "Regimantas", "familyName": "Jurkus" },
+    { "@type": "Person", "givenName": "Steffen", "familyName": "Buergers" },
+    { "@type": "Person", "givenName": "Etienne", "familyName": "Combrisson" },
+    { "@type": "Person", "givenName": "Ben", "familyName": "Dichter" },
+    { "@type": "Person", "givenName": "Elodie", "familyName": "Legouée" },
+    { "@type": "Person", "givenName": "Heberto", "familyName": "Mayorquin" },
+    { "@type": "Person", "givenName": "Thomas", "familyName": "Perret" }
+  ]
+}
diff --git a/doc/old_stuffs/grouping.rst b/doc/old_stuffs/grouping.rst
@@ -34,7 +34,6 @@ Using :class:`ChannelIndex`::
 
     block = Block()
     segment = Segment()
-    segment.block = block
     block.segments.append(segment)
 
     for i in (0, 1):
@@ -55,7 +54,6 @@ Using array annotations, we annotate the channels of the :class:`AnalogSignal` d
 
     block = Block()
     segment = Segment()
-    segment.block = block
     block.segments.append(segment)
 
     for i in (0, 1):
@@ -77,7 +75,6 @@ Each :class:`ChannelIndex` also contains the list of channels on which that neur
 
     block = Block(name="probe data")
     segment = Segment()
-    segment.block = block
     block.segments.append(segment)
 
     # create 4-channel AnalogSignal with dummy data
@@ -119,7 +116,6 @@ Using :class:`ChannelView` and :class:`Group`::
 
     block = Block(name="probe data")
     segment = Segment()
-    segment.block = block
     block.segments.append(segment)
 
     # create 4-channel AnalogSignal with dummy data

diff --git a/doc/old_stuffs/io_developers_guide.rst b/doc/old_stuffs/io_developers_guide.rst
@@ -38,7 +38,6 @@ Miscellaneous
 =============
 
     * If your IO supports several versions of a format (like ABF1, ABF2), upload to the gin.g-node.org test file repository all file versions possible. (for test coverage).
-    * :py:func:`neo.core.Block.create_many_to_one_relationship` offers a utility to complete the hierarchy when all one-to-many relationships have been created.
     * In the docstring, explain where you obtained the file format specification if it is a closed one.
     * If your IO is based on a database mapper, keep in mind that the returned object MUST be detached,
       because this object can be written to another url for copying.

diff --git a/doc/source/images/generate_diagram.py b/doc/source/images/generate_diagram.py
@@ -28,7 +28,6 @@ def get_rect_height(name, obj):
     nlines = 1.5
     nlines += len(getattr(obj, '_all_attrs', []))
     nlines += len(getattr(obj, '_single_child_objects', []))
-    nlines += len(getattr(obj, '_multi_child_objects', []))
     return nlines * line_heigth
 
 
@@ -74,9 +73,7 @@ def generate_diagram(rect_pos, rect_width, figsize):
     alpha = [1., 1., 0.3]
     for name, pos in rect_pos.items():
         obj = objs[name]
-        relationships = [getattr(obj, '_single_child_objects', []),
-                         getattr(obj, '_multi_child_objects', []),
-                         getattr(obj, '_child_properties', [])]
+        relationships = [getattr(obj, '_single_child_objects', [])]
 
         for r in range(3):
             for ch_name in relationships[r]:
@@ -122,16 +119,6 @@ def generate_diagram(rect_pos, rect_width, figsize):
                          facecolor='c', edgecolor='k', alpha=.5)
         ax.add_patch(rect)
 
-        # multi relationship
-        relationship = list(getattr(obj, '_multi_child_objects', []))
-        pos2 = (pos[1] + htotal - line_heigth * (1.5 + len(relationship))
-                - rect_height)
-        rect_height = len(relationship) * line_heigth
-
-        rect = Rectangle((pos[0], pos2), rect_width, rect_height,
-                         facecolor='m', edgecolor='k', alpha=.5)
-        ax.add_patch(rect)
-
         # necessary attr
         pos2 = (pos[1] + htotal
                 - line_heigth * (1.5 + len(allrelationship) + len(obj._necessary_attrs)))

diff --git a/doc/source/scripts/multi_tetrode_example.py b/doc/source/scripts/multi_tetrode_example.py
@@ -35,7 +35,6 @@
 
 # Create dummy data, one segment at a time
 for segment in block.segments:
-    segment.block = block
 
     # create two 4-channel AnalogSignals with dummy data
     signals = {
@@ -46,8 +45,6 @@
     }
     if store_signals:
         segment.analogsignals.extend(signals.values())
-        for signal in signals:
-            signal.segment = segment
 
     # create spike trains with dummy data
     # we will pretend the spikes have been extracted from the dummy signal
@@ -56,7 +53,6 @@
             spiketrain = SpikeTrain(np.random.uniform(0, 100, size=30) * ms, t_stop=100 * ms)
             # assign each spiketrain to the appropriate segment
             segment.spiketrains.append(spiketrain)
-            spiketrain.segment = segment
             # assign each spiketrain to a given neuron
             current_group = next(iter_group)
             current_group.add(spiketrain)

diff --git a/examples/generated_data.py b/examples/generated_data.py
@@ -58,7 +58,6 @@ def generate_block(n_segments=3, n_channels=4, n_units=3,
                 seg.spiketrains.append(train)
                 u.spiketrains.append(train)
 
-    block.create_many_to_one_relationship()
     return block
 
 

diff --git a/neo/core/block.py b/neo/core/block.py
@@ -10,6 +10,10 @@
 from datetime import datetime
 
 from neo.core.container import Container, unique_objs
+from neo.core.group import Group
+from neo.core.objectlist import ObjectList
+from neo.core.regionofinterest import RegionOfInterest
+from neo.core.segment import Segment
 
 
 class Block(Container):
@@ -64,7 +68,6 @@ class Block(Container):
     '''
 
     _container_child_objects = ('Segment', 'Group')
-    _child_properties = ()
     _recommended_attrs = ((('file_datetime', datetime),
                            ('rec_datetime', datetime),
                            ('index', int)) +
@@ -86,9 +89,27 @@ def __init__(self, name=None, description=None, file_origin=None,
         self.file_datetime = file_datetime
         self.rec_datetime = rec_datetime
         self.index = index
-        self.regionsofinterest = []   # temporary workaround.
-        # the goal is to store all sub-classes of RegionOfInterest in a single list
-        # but this will need substantial changes to container handling
+        self._segments = ObjectList(Segment, parent=self)
+        self._groups = ObjectList(Group, parent=self)
+        self._regionsofinterest = ObjectList(RegionOfInterest, parent=self)
+
+    segments = property(
+        fget=lambda self: self._get_object_list("_segments"),
+        fset=lambda self, value: self._set_object_list("_segments", value),
+        doc="list of Segments contained in this block"
+    )
+
+    groups = property(
+        fget=lambda self: self._get_object_list("_groups"),
+        fset=lambda self, value: self._set_object_list("_groups", value),
+        doc="list of Groups contained in this block"
+    )
+
+    regionsofinterest = property(
+        fget=lambda self: self._get_object_list("_regionsofinterest"),
+        fset=lambda self, value: self._set_object_list("_regionsofinterest", value),
+        doc="list of RegionOfInterest objects contained in this block"
+    )
 
     @property
     def data_children_recur(self):