bsb-nest 4.3.0__tar.gz → 4.3.2__tar.gz

{bsb_nest-4.3.0 → bsb_nest-4.3.2}/PKG-INFO

@@ -1,11 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: bsb-nest
-Version: 4.3.0
+Version: 4.3.2
 Summary: NEST simulation adapter for the BSB framework.
 Author-email: Robin De Schepper <robingilbert.deschepper@unipv.it>
 Description-Content-Type: text/markdown
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-Requires-Dist: bsb-core~=4.1
+Requires-Dist: bsb-core~=5.0
 Requires-Dist: bsb-nest[test] ; extra == "dev"
 Requires-Dist: build~=1.0 ; extra == "dev"
 Requires-Dist: twine~=4.0 ; extra == "dev"
@@ -17,7 +17,7 @@ Requires-Dist: bump-my-version~=0.24 ; extra == "dev"
 Requires-Dist: bsb-core[parallel] ; extra == "parallel"
 Requires-Dist: bsb-core[parallel] ; extra == "test"
 Requires-Dist: bsb-test~=4.0 ; extra == "test"
-Requires-Dist: bsb-hdf5~=4.0 ; extra == "test"
+Requires-Dist: bsb-hdf5~=5.0 ; extra == "test"
 Requires-Dist: bsb-arbor~=4.0 ; extra == "test"
 Requires-Dist: coverage~=7.0 ; extra == "test"
 Provides-Extra: dev
@@ -29,7 +29,7 @@ Provides-Extra: test
 
 # bsb-nest
 
-bsb-nest is a pluggin of [BSB](https://github.com/dbbs-lab/bsb) (see also 
+bsb-nest is a plugin of the [BSB](https://github.com/dbbs-lab/bsb) (see also 
 [bsb-core](https://github.com/dbbs-lab/bsb-core)). 
 It contains the interfaces and tools to simulate BSB circuit with the 
 [NEST simulator](https://www.nest-simulator.org/).

{bsb_nest-4.3.0 → bsb_nest-4.3.2}/README.md

@@ -3,7 +3,7 @@
 
 # bsb-nest
 
-bsb-nest is a pluggin of [BSB](https://github.com/dbbs-lab/bsb) (see also 
+bsb-nest is a plugin of the [BSB](https://github.com/dbbs-lab/bsb) (see also 
 [bsb-core](https://github.com/dbbs-lab/bsb-core)). 
 It contains the interfaces and tools to simulate BSB circuit with the 
 [NEST simulator](https://www.nest-simulator.org/).

{bsb_nest-4.3.0 → bsb_nest-4.3.2}/bsb_nest/__init__.py

@@ -9,4 +9,4 @@ from .adapter import NestAdapter
 from .simulation import NestSimulation
 
 __plugin__ = SimulationBackendPlugin(Simulation=NestSimulation, Adapter=NestAdapter)
-__version__ = "4.3.0"
+__version__ = "4.3.2"

{bsb_nest-4.3.0 → bsb_nest-4.3.2}/bsb_nest/device.py

@@ -1,7 +1,12 @@
+import typing
 import warnings
 
 import nest
-from bsb import DeviceModel, Targetting, config, refs, types
+from bsb import DeviceModel, SimulationData, Targetting, config, refs, types
+
+if typing.TYPE_CHECKING:
+    from .adapter import NestAdapter
+    from .simulation import NestSimulation
 
 
 @config.node
@@ -24,18 +29,56 @@ class NestDevice(DeviceModel):
     receptor_type = config.attr(type=int, required=False, default=0)
     """Integer ID of the postsynaptic target receptor"""
 
-    def get_target_nodes(self, adapter, simulation, simdata):
+    def get_dict_targets(
+        self,
+        adapter: "NestAdapter",
+        simulation: "NestSimulation",
+        simdata: "SimulationData",
+    ) -> dict:
+        """
+        Get a dictionary from a target group to its NEST Collection
+        for each target group of the device.
+
+        :param bsb_nest.NestAdapter adapter:
+        :param bsb_nest.NestSimulation simulation: Nest simulation instance
+        :param bsb.SimulationData simdata: Simulation data instance
+        :return: dictionary of device target group to NEST Collection
+        :rtype: dict
+        """
         if isinstance(self.targetting, Targetting):
-            node_collector = self.targetting.get_targets(
-                adapter, simulation, simdata
-            ).values()
+            node_collector = self.targetting.get_targets(adapter, simulation, simdata)
         else:
-            node_collector = (
-                simdata.populations[model][targets]
+            node_collector = {
+                model: simdata.populations[model][targets]
                 for model, targets in simdata.populations.items()
                 if not self.targetting.cell_models or model in self.targetting.cell_models
-            )
-        return sum(node_collector, start=nest.NodeCollection())
+            }
+        return node_collector
+
+    @staticmethod
+    def _flatten_nodes_ids(dict_targets):
+        return sum(dict_targets.values(), start=nest.NodeCollection())
+
+    @staticmethod
+    def _invert_targets_dict(dict_targets):
+        return {elem: k.name for k, v in dict_targets.items() for elem in v.tolist()}
+
+    def get_target_nodes(
+        self,
+        adapter: "NestAdapter",
+        simulation: "NestSimulation",
+        simdata: "SimulationData",
+    ):
+        """
+        Get the NEST Collection of the targets of the device.
+
+        :param bsb_nest.NestAdapter adapter:
+        :param bsb_nest.NestSimulation simulation: Nest simulation instance
+        :param bsb.SimulationData simdata: Simulation data instance
+        :return: Flattened NEST collection with all the targets of the device
+        """
+        targets_dict = self.get_dict_targets(adapter, simulation, simdata)
+        return self._flatten_nodes_ids(targets_dict)
 
     def connect_to_nodes(self, device, nodes):
         if len(nodes) == 0:
@@ -75,5 +118,5 @@ class ExtNestDevice(NestDevice, classmap_entry="external"):
         simdata.devices[self] = device = nest.Create(
             self.nest_model, params=self.constants
         )
-        nodes = self.get_target_nodes(adapter, simdata)
+        nodes = self.get_target_nodes(adapter, simulation, simdata)
         self.connect_to_nodes(device, nodes)

{bsb_nest-4.3.0 → bsb_nest-4.3.2}/bsb_nest/devices/multimeter.py

@@ -1,4 +1,5 @@
 import nest
+import numpy as np
 import quantities as pq
 from bsb import ConfigurationError, _util, config, types
 from neo import AnalogSignal
@@ -24,7 +25,9 @@ class Multimeter(NestDevice, classmap_entry="multimeter"):
 
     def implement(self, adapter, simulation, simdata):
 
-        nodes = self.get_target_nodes(adapter, simulation, simdata)
+        targets_dict = self.get_dict_targets(adapter, simulation, simdata)
+        nodes = self._flatten_nodes_ids(targets_dict)
+        inv_targets = self._invert_targets_dict(targets_dict)
         device = self.register_device(
             simdata,
             nest.Create(
@@ -38,15 +41,20 @@ class Multimeter(NestDevice, classmap_entry="multimeter"):
         self.connect_to_nodes(device, nodes)
 
         def recorder(segment):
-            for prop, unit in zip(self.properties, self.units):
-                segment.analogsignals.append(
-                    AnalogSignal(
-                        device.events[prop],
-                        units=pq.units.__dict__[unit],
-                        sampling_period=self.simulation.resolution * pq.ms,
-                        name=self.name,
-                        senders=device.events["senders"],
+            senders = device.events["senders"]
+            for sender in np.unique(senders):
+                sender_filter = senders == sender
+                for prop, unit in zip(self.properties, self.units):
+                    segment.analogsignals.append(
+                        AnalogSignal(
+                            device.events[prop][sender_filter],
+                            units=pq.units.__dict__[unit],
+                            sampling_period=self.simulation.resolution * pq.ms,
+                            name=self.name,
+                            cell_type=inv_targets[sender],
+                            cell_id=sender,
+                            prop_recorded=prop,
+                        )
                     )
-                )
 
         simdata.result.create_recorder(recorder)

{bsb_nest-4.3.0 → bsb_nest-4.3.2}/bsb_nest/devices/poisson_generator.py

@@ -35,6 +35,7 @@ class PoissonGenerator(NestDevice, classmap_entry="poisson_generator"):
                     senders=sr.events["senders"],
                     t_stop=simulation.duration,
                     device=self.name,
+                    pop_size=len(nodes),
                 )
             )
 

{bsb_nest-4.3.0 → bsb_nest-4.3.2}/bsb_nest/devices/sinusoidal_poisson_generator.py

@@ -1,5 +1,5 @@
 import nest
-from bsb import config
+from bsb import ConfigurationError, config
 from neo import SpikeTrain
 
 from ..device import NestDevice
@@ -56,6 +56,7 @@ class SinusoidalPoissonGenerator(
                     senders=sr.events["senders"],
                     t_stop=simulation.duration,
                     device=self.name,
+                    pop_size=len(nodes),
                 )
             )
 

{bsb_nest-4.3.0 → bsb_nest-4.3.2}/pyproject.toml

@@ -9,7 +9,7 @@ readme = "README.md"
 license = {file = "LICENSE"}
 classifiers = ["License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)"]
 dynamic = ["version", "description"]
-dependencies = ["bsb-core~=4.1"]
+dependencies = ["bsb-core~=5.0"]
 
 [tool.flit.module]
 name = "bsb_nest"
@@ -22,7 +22,7 @@ parallel = ["bsb-core[parallel]"]
 test = [
     "bsb-core[parallel]",
     "bsb-test~=4.0",
-    "bsb-hdf5~=4.0",
+    "bsb-hdf5~=5.0",
     # Required to load the Brunel config file
     "bsb-arbor~=4.0",
     "coverage~=7.0"
@@ -46,7 +46,7 @@ profile = "black"
 known_third_party = ["nest"]
 
 [tool.bumpversion]
-current_version = "4.3.0"
+current_version = "4.3.2"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"