Merge pull request #818 from apdavison/arbor-ci

Start testing pyNN.arbor

Author: apdavison

.github/workflows/full-test.yml

@@ -50,9 +50,13 @@ jobs:
         cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local -Dwith-mpi=ON ./nest-simulator-3.8
         make
         make install
+    - name: Install Arbor
+      if: startsWith(matrix.os, 'ubuntu')
+      run: |
+        python -m pip install arbor==0.9.0 libNeuroML
     - name: Install PyNN itself
       run: |
-        pip install -e ".[test]"
+        python -m pip install -e ".[test]"
     - name: Test installation has worked (Ubuntu)
       # this is needed because the PyNN tests are just skipped if the simulator
       # fails to install, so we need to catch import failures separately
@@ -61,6 +65,7 @@ jobs:
         python -c "import pyNN.nest"
         python -c "import pyNN.neuron"
         python -c "import pyNN.brian2"
+        python -c "import pyNN.arbor"
     - name: Test installation has worked (Windows)
       if: startsWith(matrix.os, 'windows')
       run: |

pyNN/arbor/cells.py

@@ -125,7 +125,9 @@ def _build_decor(self, i):
             location_generator = current_source["location_generator"]
             mechanism = getattr(arbor, current_source["model_name"])
             for locset, label in location_generator.generate_locations(morph, label=f"{current_source['model_name']}_label"):
-                decor.place(locset, mechanism(**current_source["parameters"].evaluate()), label)
+                params = current_source["parameters"].evaluate(simplify=True)
+                mech = mechanism(**params)
+                decor.place(locset, mech, label)
 
         # add spike source
         decor.place('"root"', arbor.threshold_detector(-10), "detector")

pyNN/arbor/populations.py

@@ -117,6 +117,8 @@ def _create_cells(self):
             [simulator.Cell(id) for id in id_range],
             dtype=simulator.Cell
         )
+        for obj in self.all_cells:
+            obj.parent = self
 
         # for i, cell in enumerate(self.all_cells):
         #     #for key, value in parameter_space.items():

pyNN/arbor/simulator.py

@@ -35,12 +35,17 @@ def build_mechanisms():
         return mech_path
 
 
-class Cell(int):
+class Cell(int, common.IDMixin):
+    local = True
 
     def __init__(self, n):
         """Create an ID object with numerical value `n`."""
-        self.gid = n
-        self.local = True
+        int.__init__(n)
+        common.IDMixin.__init__(self)
+
+    @property
+    def gid(self):
+        return int(self)
 
 
 class NetworkRecipe(arbor.recipe):

pyNN/arbor/standardmodels.py

@@ -8,6 +8,7 @@
 import logging
 from copy import deepcopy
 
+import numpy as np
 import arbor
 
 from ..standardmodels import cells, ion_channels, synapses, electrodes, receptors, build_translations
@@ -60,9 +61,15 @@ def inject_into(self, cells, location=None):  # rename to `locations` ?
         if hasattr(cells, "parent"):
             cell_descr = cells.parent._arbor_cell_description.base_value
             index = cells.parent.id_to_index(cells.all_cells.astype(int))
-        else:
+        elif hasattr(cells, "_arbor_cell_description"):
             cell_descr = cells._arbor_cell_description.base_value
             index = cells.id_to_index(cells.all_cells.astype(int))
+        else:
+            assert isinstance(cells, (list, tuple))
+            # we're assuming all cells have the same parent here
+            cell_descr = cells[0].parent._arbor_cell_description.base_value
+            index = np.array(cells, dtype=int)
+
         self.parameter_space.shape = (1,)
         if location is None:
             raise NotImplementedError

pyNN/common/populations.py

@@ -46,7 +46,7 @@ class IDMixin(object):
     where p is a Population object.
     """
     # Simulator ID classes should inherit both from the base type of the ID
-    # (e.g., int or long) and from IDMixin.
+    # (e.g., int) and from IDMixin.
 
     def __getattr__(self, name):
         if name == "parent":
@@ -128,9 +128,12 @@ def _get_position(self):
     def local(self):
         return self.parent.is_local(self)
 
-    def inject(self, current_source):
+    def inject(self, current_source, location=None):
         """Inject current from a current source object into the cell."""
-        current_source.inject_into([self])
+        if location is None:
+            current_source.inject_into([self])
+        else:
+            current_source.inject_into([self], location=location)
 
     def get_initial_value(self, variable):
         """Get the initial value of a state variable of the cell."""

pyNN/neuron/standardmodels/electrodes.py

@@ -147,7 +147,7 @@ def inject_into(self, cells, location=None):
                         pass
                     else:
                         raise TypeError("location must be a string or a LocationGenerator")
-                    morphology = cells.celltype.parameter_space["morphology"].base_value  # todo: evaluate lazyarray
+                    morphology = id.celltype.parameter_space["morphology"].base_value  # todo: evaluate lazyarray
                     locations = location.generate_locations(morphology, label_prefix="dc_current_source", cell=id._cell)
                     sections = []
                     for loc in locations:

test/system/scenarios/fixtures.py

@@ -21,6 +21,12 @@
 except ImportError:
     pass
 
+try:
+    import pyNN.arbor
+    available_modules["arbor"] = pyNN.arbor
+except ImportError:
+    pass
+
 
 class SimulatorNotAvailable:
 

test/system/scenarios/test_scenario5.py

@@ -0,0 +1,100 @@
+import sys
+import numpy as np
+
+try:
+    from neuroml import Morphology, Segment, Point3DWithDiam as P
+    have_neuroml = True
+except ImportError:
+    have_neuroml = False
+
+from pyNN.utility import init_logging
+from pyNN.morphology import NeuroMLMorphology
+from pyNN.parameters import IonicSpecies
+
+import pytest
+
+from .fixtures import run_with_simulators
+
+
+@run_with_simulators("arbor", "neuron")
+def test_scenario5(sim):
+    """
+    Array of multi-compartment neurons, each injected with a different current.
+    """
+    if not have_neuroml:
+        pytest.skip("libNeuroML not available")
+
+    init_logging(logfile=None, debug=True)
+
+    sim.setup(timestep=0.01)
+
+    soma = Segment(proximal=P(x=18.8, y=0, z=0, diameter=18.8),
+                distal=P(x=0, y=0, z=0, diameter=18.8),
+                name="soma", id=0)
+    dend = Segment(proximal=P(x=0, y=0, z=0, diameter=2),
+                distal=P(x=-500, y=0, z=0, diameter=2),
+                name="dendrite",
+                parent=soma, id=1)
+
+    cell_class = sim.MultiCompartmentNeuron
+    cell_class.label = "ExampleMultiCompartmentNeuron"
+    cell_class.ion_channels = {'pas': sim.PassiveLeak, 'na': sim.NaChannel, 'kdr': sim.KdrChannel}
+
+    cell_type = cell_class(
+        morphology=NeuroMLMorphology(Morphology(segments=(soma, dend))),
+        cm=1.0,    # mF / cm**2
+        Ra=500.0,  # ohm.cm
+        ionic_species={
+                "na": IonicSpecies("na", reversal_potential=50.0),
+                "k": IonicSpecies("k", reversal_potential=-77.0)
+        },
+        pas={"conductance_density": sim.morphology.uniform('all', 0.0003),
+             "e_rev":-54.3},
+        na={"conductance_density": sim.morphology.uniform('soma', 0.120)},
+        kdr={"conductance_density": sim.morphology.uniform('soma', 0.036)}
+    )
+
+    neurons = sim.Population(5, cell_type, initial_values={'v': -60.0})
+
+    I = (0.04, 0.11, 0.13, 0.15, 0.18)
+    currents = [sim.DCSource(start=50, stop=150, amplitude=amp)
+                for amp in I]
+    for j, (neuron, current) in enumerate(zip(neurons, currents)):
+        if j % 2 == 0:                              # these should
+            neuron.inject(current, location="soma") # be entirely
+        else:                                       # equivalent
+            current.inject_into([neuron], location="soma")
+
+    neurons.record('spikes')
+
+    sim.run(200.0)
+
+    spiketrains = neurons.get_data().segments[0].spiketrains
+    assert len(spiketrains) == 5
+    assert len(spiketrains[0]) == 0  # first cell does not fire
+    # expected values taken from the average of simulations with NEURON and Arbor
+    expected_spike_times = [
+        np.array([]),
+        np.array([52.41]),
+        np.array([52.15, 68.45, 84.73, 101.02, 117.31, 133.61, 149.9]),
+        np.array([51.96, 67.14, 82.13, 97.11, 112.08, 127.06, 142.04]),
+        np.array([51.75, 65.86, 79.7, 93.51, 107.33, 121.14, 134.96, 148.77])
+    ]
+    spike_times = [np.array(st) for st in spiketrains[1:]]
+    max_error = 0
+    for a, b in zip(spike_times, expected_spike_times[1:]):
+        if a.size == b.size:
+            max_error += abs((a - b) / b).max()
+        else:
+            max_error += 1
+    print("max error =", max_error)
+    assert max_error < 0.005, max_error
+    sim.end()
+    if "pytest" not in sys.modules:
+        return a, b, spike_times
+
+
+if __name__ == '__main__':
+    from pyNN.utility import get_simulator
+    sim, args = get_simulator()
+    test_scenario5(sim)