bsb-nest 4.2.1__py2.py3-none-any.whl → 4.3.1__py2.py3-none-any.whl

bsb_nest/__init__.py

@@ -9,4 +9,4 @@ from .adapter import NestAdapter
 from .simulation import NestSimulation
 
 __plugin__ = SimulationBackendPlugin(Simulation=NestSimulation, Adapter=NestAdapter)
-__version__ = "4.2.1"
+__version__ = "4.3.1"

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
@@ -21,19 +26,59 @@ class NestDevice(DeviceModel):
         type=types.or_(Targetting, NestRule), default=dict, call_default=True
     )
     """Targets of the device, which should be either a population or a nest rule"""
+    receptor_type = config.attr(type=int, required=False, default=0)
+    """Integer ID of the postsynaptic target receptor"""
+
+    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.
 
-    def get_target_nodes(self, adapter, simulation, simdata):
+        :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:
@@ -43,8 +88,13 @@ class NestDevice(DeviceModel):
                 nest.Connect(
                     device,
                     nodes,
-                    syn_spec={"weight": self.weight, "delay": self.delay},
+                    syn_spec={
+                        "weight": self.weight,
+                        "delay": self.delay,
+                        "receptor_type": self.receptor_type,
+                    },
                 )
+
             except Exception as e:
                 if "does not send output" not in str(e):
                     raise
@@ -68,5 +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/devices/__init__.py

@@ -1,4 +1,5 @@
 from .dc_generator import DCGenerator
 from .multimeter import Multimeter
 from .poisson_generator import PoissonGenerator
+from .sinusoidal_poisson_generator import SinusoidalPoissonGenerator
 from .spike_recorder import SpikeRecorder

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/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/devices/sinusoidal_poisson_generator.py

@@ -0,0 +1,63 @@
+import nest
+from bsb import ConfigurationError, config
+from neo import SpikeTrain
+
+from ..device import NestDevice
+
+
+@config.node
+class SinusoidalPoissonGenerator(
+    NestDevice, classmap_entry="sinusoidal_poisson_generator"
+):
+    rate = config.attr(type=float, required=True)
+    """Rate of the poisson generator"""
+    amplitude = config.attr(type=float, required=True)
+    """Amplitude of the sinusoidal signal"""
+    frequency = config.attr(type=float, required=True)
+    """Frequency of the sinusoidal signal"""
+    phase = config.attr(type=float, required=False, default=0.0)
+    """Phase of the sinusoidal signal"""
+    start = config.attr(type=float, required=False, default=0.0)
+    """Activation time in ms"""
+    stop = config.attr(type=float, required=False, default=None)
+    """Deactivation time in ms. 
+        If not specified, generator will last until the end of the simulation."""
+
+    def boot(self):
+        if self.stop is not None:
+            if self.stop <= self.start:
+                raise ConfigurationError(
+                    f"Stop time (given: {self.stop}) must be greater than start time (given: {self.start})."
+                )
+
+    def implement(self, adapter, simulation, simdata):
+        nodes = self.get_target_nodes(adapter, simulation, simdata)
+        params = {
+            "rate": self.rate,
+            "start": self.start,
+            "amplitude": self.amplitude,
+            "frequency": self.frequency,
+            "phase": self.phase,
+        }
+        if self.stop is not None:
+            params["stop"] = self.stop
+        device = self.register_device(
+            simdata, nest.Create("sinusoidal_poisson_generator", params=params)
+        )
+        sr = nest.Create("spike_recorder")
+        nest.Connect(device, sr)
+        self.connect_to_nodes(device, nodes)
+
+        def recorder(segment):
+            segment.spiketrains.append(
+                SpikeTrain(
+                    sr.events["times"],
+                    units="ms",
+                    senders=sr.events["senders"],
+                    t_stop=simulation.duration,
+                    device=self.name,
+                    pop_size=len(nodes),
+                )
+            )
+
+        simdata.result.create_recorder(recorder)

{bsb_nest-4.2.1.dist-info → bsb_nest-4.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: bsb-nest
-Version: 4.2.1
+Version: 4.3.1
 Summary: NEST simulation adapter for the BSB framework.
 Author-email: Robin De Schepper <robingilbert.deschepper@unipv.it>
 Description-Content-Type: text/markdown
@@ -24,7 +24,7 @@ Provides-Extra: dev
 Provides-Extra: parallel
 Provides-Extra: test
 
-[![Build Status](https://github.com/dbbs-lab/bsb-nest/actions/workflows/build.yml/badge.svg)](https://github.com/dbbs-lab/bsb-nest/actions/workflows/build.yml)
+[![Build Status](https://github.com/dbbs-lab/bsb-nest/actions/workflows/main.yml/badge.svg)](https://github.com/dbbs-lab/bsb-nest/actions/workflows/main.yml)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 # bsb-nest

bsb_nest-4.3.1.dist-info/RECORD

@@ -0,0 +1,19 @@
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+bsb_nest/adapter.py,sha256=uwFdicGOx7mRyYlfRY89zw7re0dnv9qumli1llJ0Rok,6668
+bsb_nest/cell.py,sha256=AauERRJd5OkKVSIxbx6LO2D9L7LDA6iMFfYjxu59e4c,960
+bsb_nest/connection.py,sha256=KFMXRvSR-tN7E52Mpo7dgWjXVQQSOd1VdryRPx-NfHQ,5571
+bsb_nest/device.py,sha256=s-cIgR2-6J1k9WqhYdZv2FfMUVnnIdmCG-lXNNPgfj8,4388
+bsb_nest/distributions.py,sha256=qAYaHJkMwaCfbTh_efoJT1hMoDHWsfQo_3SNLoD8WeA,1950
+bsb_nest/exceptions.py,sha256=NX4oiGWIshrLG1DCak_nTfI8cQI7GTdewR71qNzsXGM,264
+bsb_nest/simulation.py,sha256=MCfEhwhbl_S1WNyY-EAzW8SmVKk-nLui71jK9M3lGKw,985
+bsb_nest/devices/__init__.py,sha256=AgiHteAtWd5jhl_xB_V60oeM31fGb-DGi3WjoLZLL_E,232
+bsb_nest/devices/dc_generator.py,sha256=g-jRZorCl2yYhr5bx2I00ZlxYrblDcqVbtk0XYZzmdI,953
+bsb_nest/devices/multimeter.py,sha256=pM35gSCbjuAMOtj9m4r4eGusc5tnLXA0k2ZKtJMiMOc,2240
+bsb_nest/devices/poisson_generator.py,sha256=7knwxFmJbV_RCg18H4wizot23fKUrvr6IhIye0BeOfA,1506
+bsb_nest/devices/sinusoidal_poisson_generator.py,sha256=MEV5yJ5laKYLIy8T1W9cDbnAhFB7OPZAfaqH8ffqDwc,2252
+bsb_nest/devices/spike_recorder.py,sha256=vJ9FQqmrcF0HdLl5Jy_bt_ABCUIgF-PLVI23E76JkhY,894
+bsb_nest-4.3.1.dist-info/entry_points.txt,sha256=uJlX9h2VeYfAumav18IM2PTJ3FssfwDUnUmfSFdR2SA,41
+bsb_nest-4.3.1.dist-info/LICENSE,sha256=ljOS4DjXvqEo5VzGfdaRwgRZPbNScGBmfwyC8PChvmQ,32422
+bsb_nest-4.3.1.dist-info/WHEEL,sha256=ssQ84EZ5gH1pCOujd3iW7HClo_O_aDaClUbX4B8bjKY,100
+bsb_nest-4.3.1.dist-info/METADATA,sha256=QfslnPnYKys8N2puto1YZcIBoMEkJILcHEabaWz4AVY,1600
+bsb_nest-4.3.1.dist-info/RECORD,,

{bsb_nest-4.2.1.dist-info → bsb_nest-4.3.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: flit 3.9.0
+Generator: flit 3.10.1
 Root-Is-Purelib: true
 Tag: py2-none-any
 Tag: py3-none-any

bsb_nest-4.2.1.dist-info/RECORD

@@ -1,18 +0,0 @@
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-bsb_nest/adapter.py,sha256=uwFdicGOx7mRyYlfRY89zw7re0dnv9qumli1llJ0Rok,6668
-bsb_nest/cell.py,sha256=AauERRJd5OkKVSIxbx6LO2D9L7LDA6iMFfYjxu59e4c,960
-bsb_nest/connection.py,sha256=KFMXRvSR-tN7E52Mpo7dgWjXVQQSOd1VdryRPx-NfHQ,5571
-bsb_nest/device.py,sha256=w6jeGSOzqd8iTtw6HxsWS0TuYTxf6iO9eqAseaFC3W8,2615
-bsb_nest/distributions.py,sha256=qAYaHJkMwaCfbTh_efoJT1hMoDHWsfQo_3SNLoD8WeA,1950
-bsb_nest/exceptions.py,sha256=NX4oiGWIshrLG1DCak_nTfI8cQI7GTdewR71qNzsXGM,264
-bsb_nest/simulation.py,sha256=MCfEhwhbl_S1WNyY-EAzW8SmVKk-nLui71jK9M3lGKw,985
-bsb_nest/devices/__init__.py,sha256=0-zwJ8jdvBdTFetU-q87OfyZYpKl_JVcVDrsLNn7yHQ,163
-bsb_nest/devices/dc_generator.py,sha256=g-jRZorCl2yYhr5bx2I00ZlxYrblDcqVbtk0XYZzmdI,953
-bsb_nest/devices/multimeter.py,sha256=dLBDNCJuFIgxOZ0ssEoir7d65EW7ORS1jFNsvmU2wJ0,1811
-bsb_nest/devices/poisson_generator.py,sha256=SGo4jhq_rbIoB38OM5FTTYlyShxGAwWqCqAncWVB3qg,1465
-bsb_nest/devices/spike_recorder.py,sha256=vJ9FQqmrcF0HdLl5Jy_bt_ABCUIgF-PLVI23E76JkhY,894
-bsb_nest-4.2.1.dist-info/entry_points.txt,sha256=uJlX9h2VeYfAumav18IM2PTJ3FssfwDUnUmfSFdR2SA,41
-bsb_nest-4.2.1.dist-info/LICENSE,sha256=ljOS4DjXvqEo5VzGfdaRwgRZPbNScGBmfwyC8PChvmQ,32422
-bsb_nest-4.2.1.dist-info/WHEEL,sha256=Sgu64hAMa6g5FdzHxXv9Xdse9yxpGGMeagVtPMWpJQY,99
-bsb_nest-4.2.1.dist-info/METADATA,sha256=gm8BOcXCq1xdqi6oFDS3bUynPxa4BdvNaq_tiN0qnvk,1602
-bsb_nest-4.2.1.dist-info/RECORD,,