bluepyopt/ephys/locations.py
"""Location classes"""
"""
Copyright (c) 2016-2020, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as published
by the Free Software Foundation.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
"""
# pylint: disable=W0511
import itertools
from bluepyopt.ephys.base import BaseEPhys
from bluepyopt.ephys.serializer import DictMixin
from bluepyopt.ephys.parameterscalers import format_float
from bluepyopt.ephys.acc import ArbLabel
from bluepyopt.ephys.morphologies import ArbFileMorphology
import numpy as np
import logging
logger = logging.getLogger(__name__)
class Location(BaseEPhys):
"""Location"""
pass
# TODO make all these locations accept a cell name
# TODO instantiate should get the entire simulation environment
# TODO find better/more general name for this
# TODO specify in document abrevation comp=compartment, sec=section, ...
def _nth_isectionlist(isectionlist, index):
"""Get nth element of isectionlist
Sectionlists don't support direct indexing
"""
isection = next(
itertools.islice(
isectionlist,
index,
index + 1))
return isection
class NrnSeclistCompLocation(Location, DictMixin):
"""Compartment in a sectionlist"""
SERIALIZED_FIELDS = (
'name',
'comment',
'seclist_name',
'sec_index',
'comp_x',
)
def __init__(
self,
name,
seclist_name=None,
sec_index=None,
comp_x=None,
comment=''):
"""Constructor
Args:
name (str): name of the object
seclist_name (str): name of Neuron section list (ex: 'somatic')
sec_index (int): index of the section in the section list
comp_x (float): segx (0..1) of segment inside section
"""
super(NrnSeclistCompLocation, self).__init__(name, comment)
self.seclist_name = seclist_name
self.sec_index = sec_index
self.comp_x = comp_x
def instantiate(self, sim=None, icell=None): # pylint: disable=W0613
"""Find the instantiate compartment"""
iseclist = getattr(icell, self.seclist_name)
iseclist_size = len([x for x in iseclist])
if self.sec_index >= iseclist_size:
raise Exception(
'NrnSeclistCompLocation: section index %d falls out of '
'SectionList size of %d' %
(self.sec_index, iseclist_size))
isection = _nth_isectionlist(iseclist, self.sec_index)
icomp = isection(self.comp_x)
# The code above seems to add put a section on the stack
# TODO remove line below once we figure out where the section is pushed
sim.neuron.h.pop_section()
return icomp
def acc_label(self):
"""Arbor label"""
raise EPhysLocAccException(
'%s not supported in Arbor' % type(self).__name__ +
' (uses branches instead of NEURON sections).'
' Use ArbBranchRelLocation/ArbSegmentRelLocation/'
'ArbLocsetLocation instead (consider using the'
' Arbor GUI to identify the precise branch/segment index'
' and relative position).')
def __str__(self):
"""String representation"""
return '%s[%s](%s)' % (self.seclist_name, self.sec_index, self.comp_x)
class NrnSectionCompLocation(Location, DictMixin):
"""Compartment in a section"""
SERIALIZED_FIELDS = (
'name',
'comment',
'seclist_name',
'sec_index',
'comp_x',
)
def __init__(
self,
name,
sec_name=None,
comp_x=None,
comment=''):
"""Constructor
Args:
name (str): name of the object
sec_name (str): name of Neuron section (ex: 'soma[0]')
comp_x (float): segx (0..1) of segment inside section
"""
super(NrnSectionCompLocation, self).__init__(name, comment)
self.sec_name = sec_name
self.comp_x = comp_x
def instantiate(self, sim=None, icell=None): # pylint: disable=W0613
"""Find the instantiate compartment"""
# Dont see any other way but to use eval, apart from parsing the
# sec_name string which can be complicated
isection = eval('icell.%s' % self.sec_name) # pylint: disable=W0123
icomp = isection(self.comp_x)
return icomp
def acc_label(self):
"""Arbor label"""
raise EPhysLocAccException(
'%s not supported in Arbor' % type(self).__name__ +
' (uses branches instead of NEURON sections).'
' Use ArbBranchRelLocation/ArbSegmentRelLocation/'
'ArbLocsetLocation instead (consider using the'
' Arbor GUI to identify the precise branch/segment index'
' and relative position).')
def __str__(self):
return '%s(%s)' % (self.sec_name, self.comp_x)
class NrnPointProcessLocation(Location):
"""Point process location"""
def __init__(
self,
name,
pprocess_mech,
comment=''):
"""Constructor
Args:
name (str): name of the object
pprocess_mech (str): point process mechanism
"""
super(NrnPointProcessLocation, self).__init__(name, comment)
self.pprocess_mech = pprocess_mech
def instantiate(self, sim=None, icell=None): # pylint: disable=W0613
"""Find the instantiated point processes"""
return self.pprocess_mech.pprocesses
def acc_label(self):
"""Arbor label"""
return [loc.acc_label() for loc in self.pprocess_mech.locations]
def __str__(self):
"""String representation"""
return '%s' % (self.pprocess_mech.name)
class NrnSeclistLocation(Location, DictMixin):
"""Section in a sectionlist"""
SERIALIZED_FIELDS = ('name', 'comment', 'seclist_name', )
def __init__(
self,
name,
seclist_name=None,
comment=''):
"""Constructor
Args:
name (str): name of the object
seclist_name (str): name of NEURON section list (ex: 'somatic')
"""
super(NrnSeclistLocation, self).__init__(name, comment)
self.seclist_name = seclist_name
def instantiate(self, sim=None, icell=None): # pylint: disable=W0613
"""Find the instantiate compartment"""
isectionlist = getattr(icell, self.seclist_name)
return (isection for isection in isectionlist)
def acc_label(self):
"""Arbor label"""
return ArbFileMorphology.region_labels[self.seclist_name]
def __str__(self):
"""String representation"""
return '%s' % (self.seclist_name)
class NrnSeclistSecLocation(Location, DictMixin):
"""Section in a sectionlist"""
SERIALIZED_FIELDS = ('name', 'comment', 'seclist_name', 'sec_index', )
def __init__(
self,
name,
seclist_name=None,
sec_index=None,
comment=''):
"""Constructor
Args:
name (str): name of this object
seclist_name (str): name of Neuron section list (ex: 'somatic')
sec_index (int): index of the section
"""
super(NrnSeclistSecLocation, self).__init__(name, comment)
self.seclist_name = seclist_name
self.sec_index = sec_index
def instantiate(self, sim=None, icell=None): # pylint: disable=W0613
"""Find the instantiate compartment"""
isectionlist = getattr(icell, self.seclist_name)
isection = _nth_isectionlist(isectionlist, self.sec_index)
return isection
def acc_label(self):
"""Arbor label"""
raise EPhysLocAccException(
'%s not supported in Arbor' % type(self).__name__ +
' (uses branches instead of NEURON sections).'
' Use ArbBranchLocation/ArbSegmentLocation/ArbRegionLocation'
' instead (consider using the Arbor GUI to identify the'
' precise branch/segment index).')
def __str__(self):
"""String representation"""
return '%s[%s]' % (self.seclist_name, self.sec_index)
class NrnSomaDistanceCompLocation(Location, DictMixin):
"""Compartment at distance from soma"""
SERIALIZED_FIELDS = ('name', 'comment', 'soma_distance', 'seclist_name', )
def __init__(
self,
name,
soma_distance=None,
seclist_name=None,
comment=''):
"""Constructor
Args:
name (str): name of this object
soma_distance (float): distance from soma to this compartment
seclist_name (str): name of Neuron section list (ex: 'apical')
"""
super(NrnSomaDistanceCompLocation, self).__init__(name, comment)
self.soma_distance = soma_distance
self.seclist_name = seclist_name
# TODO this definitely has to be unit-tested
# TODO add ability to specify origin
def find_icomp(self, sim, iseclist):
"""Find the index of the compartment based on a list of isec
and a distance"""
icomp = None
for isec in iseclist:
start_distance = sim.neuron.h.distance(1, 0.0, sec=isec)
end_distance = sim.neuron.h.distance(1, 1.0, sec=isec)
min_distance = min(start_distance, end_distance)
max_distance = max(start_distance, end_distance)
if min_distance <= self.soma_distance <= max_distance:
comp_x = float(self.soma_distance - min_distance) / \
(max_distance - min_distance)
comp_diam = isec(comp_x).diam
if comp_diam > 0.0:
icomp = isec(comp_x)
if icomp is None:
raise EPhysLocInstantiateException(
'No comp found at %s distance from soma' %
self.soma_distance)
return icomp
def instantiate(self, sim=None, icell=None):
"""Find the instantiate compartment"""
soma = icell.soma[0]
sim.neuron.h.distance(0, 0.5, sec=soma)
iseclist = getattr(icell, self.seclist_name)
return self.find_icomp(sim, iseclist)
def acc_label(self):
"""Arbor label"""
# Potentially non-unique location - in that case to be refined in the
# Arbor GUI (create ArbLocsetLocation directly).
# Alternatives to (on-components 0.5 (region "soma")) are
# - '(segment <id>)'
# - '(proximal (region %s)))' % self.seclist_name
# If outer restrict results in non-unique location (cf. GUI) use
# specific branch or similar instead of seclist_name, e.g.
# - (proximal-interval (distal (branch <id>)))
# for a branch distally from the desired location
acc_label = ArbLabel(
'locset', self.name,
'(restrict (distal-translate (on-components 0.5 %s) %s) %s)' %
(ArbFileMorphology.region_labels['somatic'].ref,
format_float(self.soma_distance),
ArbFileMorphology.region_labels[self.seclist_name].ref))
logger.warning(
'Make sure that ACC label %s' % acc_label.loc +
' for NrnSomaDistanceCompLocation (%s) ' % str(self) +
' instantiates to a unique location on the morphology.'
' Use the Arbor GUI to validate/refine the location expression.')
return acc_label
def __str__(self):
"""String representation"""
return '%f micron from soma in %s' % (
self.soma_distance, self.seclist_name)
class NrnSecSomaDistanceCompLocation(NrnSomaDistanceCompLocation):
"""Compartment on a section defined both by a section index and distance
from the soma """
SERIALIZED_FIELDS = ('name', 'comment', 'soma_distance', 'seclist_name',
'sec_index', )
def __init__(
self,
name,
soma_distance=None,
sec_index=None,
seclist_name=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
seclist_name (str): name of Neuron sections (ex: 'apic')
"""
super(NrnSecSomaDistanceCompLocation, self).__init__(
name,
soma_distance=soma_distance,
seclist_name=seclist_name,
comment=comment,
)
self.sec_index = sec_index
def instantiate(self, sim=None, icell=None):
"""Find the instantiate compartment"""
if self.sec_index is None:
raise EPhysLocInstantiateException(
"No apical point was given")
sections = getattr(icell, self.seclist_name)
section = _nth_isectionlist(sections, self.sec_index)
branches = []
while True:
name = str(section.name()).split(".")[-1]
if name == "soma[0]":
break
branches.append(section)
if sim.neuron.h.SectionRef(sec=section).has_parent():
section = sim.neuron.h.SectionRef(sec=section).parent
else:
raise EPhysLocInstantiateException(
"soma[0] was not reached from isec point "
"%f" % self.sec_index
)
soma = icell.soma[0]
sim.neuron.h.distance(0, 0.5, sec=soma)
return self.find_icomp(sim, branches)
def acc_label(self):
"""Arbor label"""
raise EPhysLocAccException('%s not supported in Arbor.' %
type(self).__name__)
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,
seclist_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,
seclist_name=seclist_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 len(points) > 0:
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)))
else:
raise EPhysLocInstantiateException(
"Empty seclist: %s" % self.seclist_name
)
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)
def acc_label(self):
"""Arbor label"""
raise EPhysLocAccException('%s not supported in Arbor.' %
type(self).__name__)
class ArbLocation(Location):
"""Arbor Location"""
def instantiate(self, sim=None, icell=None): # pylint: disable=W0613
"""Find the instantiate compartment (default implementation)"""
raise EPhysLocInstantiateException(
'%s not supported in NEURON.' % type(self).__name__)
def __str__(self):
"""String representation"""
return '%s \'%s\'' % (type(self).__name__, self.acc_label().defn)
class ArbSegmentLocation(ArbLocation):
"""Segment in an Arbor morphology.
"""
def __init__(self, name, segment, comment=''):
super().__init__(name, comment)
self.segment = segment
def acc_label(self):
"""Arbor label"""
return ArbLabel('region', self.name, '(segment %s)' % (self.segment))
class ArbBranchLocation(ArbLocation):
"""Branch in an Arbor morphology.
Arbor's counterpart of NrnSeclistSecLocation.
"""
def __init__(self, name, branch, comment=''):
super().__init__(name, comment)
self.branch = branch
def acc_label(self):
"""Arbor label"""
return ArbLabel('region', self.name, '(branch %s)' % (self.branch))
class ArbSegmentRelLocation(ArbLocation):
"""Relative position on a segment in an Arbor morphology.
"""
def __init__(self, name, segment, pos, comment=''):
super().__init__(name, comment)
self.segment = segment
self.pos = pos
def acc_label(self):
"""Arbor label"""
return ArbLabel('locset', self.name,
'(on-components %s (segment %s))' %
(format_float(self.pos), self.segment))
class ArbBranchRelLocation(ArbLocation):
"""Relative position on a branch in an Arbor morphology.
Arbor's counterpart of NrnSeclistCompLocation.
"""
def __init__(self, name, branch, pos, comment=''):
super().__init__(name, comment)
self.branch = branch
self.pos = pos
def acc_label(self):
"""Arbor label"""
return ArbLabel('locset', self.name,
'(location %s %s)' %
(self.branch, format_float(self.pos)))
class ArbLocsetLocation(ArbLocation):
"""Arbor location set defined by a user-supplied string (S-expression).
"""
def __init__(self, name, locset, comment=''):
super().__init__(name, comment)
self.locset = locset
def acc_label(self):
"""Arbor label"""
return ArbLabel('locset', self.name, self.locset)
class ArbRegionLocation(ArbLocation):
"""Arbor region defined by a user-supplied string (S-expression).
"""
def __init__(self, name, region, comment=''):
super().__init__(name, comment)
self.region = region
def acc_label(self):
"""Arbor label"""
return ArbLabel('region', self.name, self.region)
class EPhysLocInstantiateException(Exception):
"""All exceptions generated by location instantiation"""
def __init__(self, message):
"""Constructor"""
super(EPhysLocInstantiateException, self).__init__(message)
class EPhysLocAccException(Exception):
"""All exceptions generated by ACC label creation"""
def __init__(self, message):
"""Constructor"""
super(EPhysLocAccException, self).__init__(message)