Merge pull request #395 from arnaudon/trunk_location

location along trunk

Author: wvangeit

bluepyopt/ephys/locations.py

@@ -25,6 +25,7 @@
 
 from bluepyopt.ephys.base import BaseEPhys
 from bluepyopt.ephys.serializer import DictMixin
+import numpy as np
 
 
 class Location(BaseEPhys):
@@ -354,7 +355,7 @@ def __init__(
             name,
             soma_distance=soma_distance,
             seclist_name=sec_name,
-            comment=''
+            comment=comment,
         )
         self.sec_index = sec_index
 
@@ -392,6 +393,74 @@ def instantiate(self, sim=None, icell=None):
         return self.find_icomp(sim, branches)
 
 
+class NrnTrunkSomaDistanceCompLocation(NrnSecSomaDistanceCompLocation):
+    """Location at a distance from soma along a main direction.
+
+    We search for the section that is the furthest away from some along
+    a direction, and pick a location at a given distance from soma along
+    the path to that section.
+
+    If direction == 'radial', the largest radial direction is used.
+
+    This is most useful to follow the trunk of an apical dendrite
+    without knowing the apical point, but only that apical trunk goes along y.
+    """
+
+    def __init__(
+        self,
+        name,
+        soma_distance=None,
+        sec_index=None,
+        sec_name=None,
+        direction=None,
+        comment=""
+    ):
+        """Constructor
+
+        Args:
+            name (str): name of this object
+            soma_distance (float): distance from soma to this compartment
+            sec_index (int): index of the section  to consider
+            sec_name (str): name of Neuron sections (ex: 'apic')
+            direction (list of 3 elements): 3d vector representing direction,
+                if None, default is [0, 1, 0]
+        """
+        super(NrnTrunkSomaDistanceCompLocation, self).__init__(
+            name,
+            soma_distance=soma_distance,
+            sec_index=sec_index,
+            sec_name=sec_name,
+            comment=comment
+        )
+
+        if direction is None:
+            direction = [0.0, 1.0, 0.0]
+        self.direction = direction
+
+    def set_sec_index(self, icell=None):
+        """Search for the point furthest away along given direction."""
+        points = np.array(
+            [
+                [
+                    section.x3d(section.n3d() - 1),
+                    section.y3d(section.n3d() - 1),
+                    section.z3d(section.n3d() - 1),
+                ]
+                for section in getattr(icell, self.seclist_name)
+            ]
+        )
+        if self.direction == 'radial':
+            self.sec_index = int(np.argmax(np.linalg.norm(points, axis=1)))
+        else:
+            self.sec_index = int(np.argmax(points.dot(self.direction)))
+
+    def instantiate(self, sim=None, icell=None):
+        """ """
+        if self.sec_index is None:
+            self.set_sec_index(icell=icell)
+        return super().instantiate(sim=sim, icell=icell)
+
+
 class EPhysLocInstantiateException(Exception):
 
     """All exception generated by location instantiation"""

bluepyopt/tests/test_ephys/test_locations.py

@@ -21,7 +21,7 @@
 
 # pylint:disable=W0612, W0201
 import json
-
+import numpy as np
 
 import pytest
 
@@ -272,6 +272,75 @@ class Cell(object):
         assert comp == dend4(0.5)
 
 
+@pytest.mark.unit
+class TestNrnTrunkSomaDistanceCompLocation(object):
+
+    """Test class for NrnTrunkSomaDistanceCompLocation"""
+
+    def setup(self):
+        """Setup"""
+        self.loc = ephys.locations.NrnTrunkSomaDistanceCompLocation(
+            'test',
+            soma_distance=150,
+            sec_name='testdend')
+        self.loc_other = ephys.locations.NrnTrunkSomaDistanceCompLocation(
+            'test',
+            soma_distance=350,
+            sec_name='testdend')
+
+        assert self.loc.name == 'test'
+        self.sim = ephys.simulators.NrnSimulator()
+
+    def test_instantiate(self):
+        """ephys.locations.NrnSomaDistanceCompLocation: test instantiate"""
+
+        # Create a little test class with a soma and two dendritic sections
+        class Cell(object):
+
+            """Cell class"""
+            pass
+        cell = Cell()
+        soma = self.sim.neuron.h.Section(name="soma[0]")
+        cell.soma = [soma]
+        cell.testdend = self.sim.neuron.h.SectionList()
+        dend1 = self.sim.neuron.h.Section(name='dend[0]')
+        dend2 = self.sim.neuron.h.Section(name='dend[1]')
+        dend3 = self.sim.neuron.h.Section(name='dend[2]')
+        dend4 = self.sim.neuron.h.Section(name='dend[3]')
+        dend5 = self.sim.neuron.h.Section(name='dend[4]')
+
+        cell.testdend.append(sec=dend1)
+        cell.testdend.append(sec=dend2)
+        cell.testdend.append(sec=dend3)
+        cell.testdend.append(sec=dend4)
+        cell.testdend.append(sec=dend5)
+
+        x0 = self.sim.neuron.h.Vector([0] * 10)
+        d = self.sim.neuron.h.Vector([1] * 10)
+
+        x1 = self.sim.neuron.h.Vector(np.linspace(0, 100, 10))
+        self.sim.neuron.h.pt3dadd(x0, x1, x0, d, sec=dend1)
+        x2 = self.sim.neuron.h.Vector(np.linspace(100, 200, 10))
+        self.sim.neuron.h.pt3dadd(x0, x2, x0, d, sec=dend2)
+        x3 = self.sim.neuron.h.Vector(np.linspace(200, 300, 10))
+        self.sim.neuron.h.pt3dadd(x0, x3, x0, d, sec=dend3)
+        x4 = self.sim.neuron.h.Vector(np.linspace(300, 400, 10))
+        self.sim.neuron.h.pt3dadd(x0, x4, x0, d, sec=dend4)
+        x5 = self.sim.neuron.h.Vector(np.linspace(400, 500, 10))
+        self.sim.neuron.h.pt3dadd(x0, x5, x0, d, sec=dend5)
+
+        dend1.connect(soma(0.5), 0.0)
+        dend2.connect(dend1(1.0), 0.0)
+        dend3.connect(dend1(1.0), 0.0)
+        dend4.connect(dend3(1.0), 0.0)
+        dend5.connect(dend4(1.0), 0.0)
+
+        comp = self.loc.instantiate(sim=self.sim, icell=cell)
+        assert comp == dend3(0.5)
+        comp = self.loc_other.instantiate(sim=self.sim, icell=cell)
+        assert comp == dend5(0.5)
+
+
 @pytest.mark.unit
 def test_serialize():
     """ephys.locations: Test serialize functionality"""