bsb-nest 4.0.0__py2.py3-none-any.whl → 4.1.0__py2.py3-none-any.whl

bsb_nest/devices/spike_recorder.py

@@ -1,30 +1,30 @@
-import nest
-from bsb import config
-from neo import SpikeTrain
-
-from ..device import NestDevice
-
-
-@config.node
-class SpikeRecorder(NestDevice, classmap_entry="spike_recorder"):
-    weight = config.provide(1)
-
-    def implement(self, adapter, simulation, simdata):
-
-        nodes = self.get_target_nodes(adapter, simulation, simdata)
-        device = self.register_device(simdata, nest.Create("spike_recorder"))
-        self.connect_to_nodes(device, nodes)
-
-        def recorder(segment):
-            segment.spiketrains.append(
-                SpikeTrain(
-                    device.events["times"],
-                    units="ms",
-                    senders=device.events["senders"],
-                    t_stop=simulation.duration,
-                    device=self.name,
-                    pop_size=len(nodes),
-                )
-            )
-
-        simdata.result.create_recorder(recorder)
+import nest
+from bsb import config
+from neo import SpikeTrain
+
+from ..device import NestDevice
+
+
+@config.node
+class SpikeRecorder(NestDevice, classmap_entry="spike_recorder"):
+    weight = config.provide(1)
+
+    def implement(self, adapter, simulation, simdata):
+
+        nodes = self.get_target_nodes(adapter, simulation, simdata)
+        device = self.register_device(simdata, nest.Create("spike_recorder"))
+        self.connect_to_nodes(device, nodes)
+
+        def recorder(segment):
+            segment.spiketrains.append(
+                SpikeTrain(
+                    device.events["times"],
+                    units="ms",
+                    senders=device.events["senders"],
+                    t_stop=simulation.duration,
+                    device=self.name,
+                    pop_size=len(nodes),
+                )
+            )
+
+        simdata.result.create_recorder(recorder)

bsb_nest/distributions.py

@@ -0,0 +1,62 @@
+import builtins
+import typing
+
+import errr
+import nest.random.hl_api_random as _distributions
+from bsb import DistributionCastError, TypeHandler, config, types
+
+if typing.TYPE_CHECKING:
+    from bsb import Scaffold
+
+_available_distributions = [d for d in _distributions.__all__]
+
+
+@config.node
+class NestRandomDistribution:
+    """
+    Class to handle NEST random distributions.
+    """
+
+    scaffold: "Scaffold"
+    distribution: str = config.attr(
+        type=types.in_(_available_distributions), required=True
+    )
+    """Distribution name. Should correspond to a function of nest.random.hl_api_random"""
+    parameters: dict[str, typing.Any] = config.catch_all(type=types.any_())
+    """Dictionary of parameters to assign to the distribution. Should correspond to NEST's"""
+
+    def __init__(self, **kwargs):
+        try:
+            self._distr = getattr(_distributions, self.distribution)(**self.parameters)
+        except Exception as e:
+            errr.wrap(
+                DistributionCastError, e, prepend=f"Can't cast to '{self.distribution}': "
+            )
+
+    def __call__(self):
+        return self._distr
+
+    def __getattr__(self, attr):
+        # hasattr does not work here. So we use __dict__
+        if "_distr" not in self.__dict__:
+            raise AttributeError("No underlying _distr found for distribution node.")
+        return getattr(self._distr, attr)
+
+
+class nest_parameter(TypeHandler):
+    """
+    Type validator. Type casts the value or node to a Nest parameter, that can be either a value or
+    a NestRandomDistribution.
+    """
+
+    def __call__(self, value, _key=None, _parent=None):
+        if isinstance(value, builtins.dict) and "distribution" in value.keys():
+            return NestRandomDistribution(**value, _key=_key, _parent=_parent)
+        return value
+
+    @property
+    def __name__(self):  # pragma: nocover
+        return "nest parameter"
+
+    def __inv__(self, value):
+        return value

bsb_nest/exceptions.py

@@ -1,22 +1,22 @@
-class KernelWarning(Warning):
-    pass
-
-
-class NestError(Exception):
-    pass
-
-
-class NestKernelError(NestError):
-    pass
-
-
-class NestModuleError(NestKernelError):
-    pass
-
-
-class NestModelError(NestError):
-    pass
-
-
-class NestConnectError(NestError):
-    pass
+class KernelWarning(Warning):
+    pass
+
+
+class NestError(Exception):
+    pass
+
+
+class NestKernelError(NestError):
+    pass
+
+
+class NestModuleError(NestKernelError):
+    pass
+
+
+class NestModelError(NestError):
+    pass
+
+
+class NestConnectError(NestError):
+    pass

bsb_nest/simulation.py

@@ -1,21 +1,27 @@
-from bsb import Simulation, config, types
-
-from .cell import NestCell
-from .connection import NestConnection
-from .device import NestDevice
-
-
-@config.node
-class NestSimulation(Simulation):
-    """
-    Interface between the scaffold model and the NEST simulator.
-    """
-
-    modules = config.list(type=str)
-    threads = config.attr(type=types.int(min=1), default=1)
-    resolution = config.attr(type=types.float(min=0.0), required=True)
-    verbosity = config.attr(type=str, default="M_ERROR")
-
-    cell_models = config.dict(type=NestCell, required=True)
-    connection_models = config.dict(type=NestConnection, required=True)
-    devices = config.dict(type=NestDevice, required=True)
+from bsb import Simulation, config, types
+
+from .cell import NestCell
+from .connection import NestConnection
+from .device import NestDevice
+
+
+@config.node
+class NestSimulation(Simulation):
+    """
+    Interface between the scaffold model and the NEST simulator.
+    """
+
+    modules = config.list(type=str)
+    """List of NEST modules to load at the beginning of the simulation"""
+    threads = config.attr(type=types.int(min=1), default=1)
+    """Number of threads to use during simulation"""
+    resolution = config.attr(type=types.float(min=0.0), required=True)
+    """Simulation time step size in milliseconds"""
+    verbosity = config.attr(type=str, default="M_ERROR")
+    """NEST verbosity level"""
+    seed = config.attr(type=int, default=None)
+    """Random seed for the simulations"""
+
+    cell_models = config.dict(type=NestCell, required=True)
+    connection_models = config.dict(type=NestConnection, required=True)
+    devices = config.dict(type=NestDevice, required=True)