#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# - Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# - Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in
# the documentation and/or other materials provided with the
# distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ----------------------------------------------------------------------
from morphforge.units import qty
from morphforge.constants import StandardTags
from morphforge.morphology.core import MorphPath
from morphforge.simulation.base.base_classes import NamedSimulationObject
[docs]class Stimulation(NamedSimulationObject):
[docs] def __init__(self, cell_location, **kwargs):
super(Stimulation, self).__init__(**kwargs)
self.cell_location = cell_location
[docs] def get_summary_description(self):
raise NotImplementedError()
# Helper methods:
@property
def cell(self):
return self.cell_location.cell
@property
def distance_to_soma(self):
morphology_path = MorphPath(self.cell.soma, self.cell_location.morphlocation)
return morphology_path.get_length()
@property
def location_summary_str(self):
return '%s (%0.0fum from soma)' % (self.cell.name, self.distance_to_soma),
@property
def location_summary_dot_str(self):
# Minimal description for single compartments:
if self.cell.is_single_compartment:
return ''
# Are we in the soma:
if self.cell_location.section.idtag:
return '%s' % self.cell_location.section.idtag
#== 'soma':
#loc = 'soma'
return '%s - %0.0fum from soma' % (self.cell.name, self.distance_to_soma),
[docs]class CurrentClamp(Stimulation):
[docs] class Recordables(object):
Current = StandardTags.Current
[docs] def get_summary_description(self):
raise NotImplementedError()
[docs]class VoltageClamp(Stimulation):
[docs] class Recordables(object):
Current = StandardTags.Current
[docs] def get_summary_description(self):
raise NotImplementedError()
[docs]class CurrentClampStepChange(CurrentClamp):
[docs] def __init__(self, amp, dur, delay, **kwargs):
super(CurrentClampStepChange, self).__init__(**kwargs)
self.amp = qty(amp)
self.dur = qty(dur)
self.delay = qty(delay)
[docs] def get_summary_description(self):
return 'Step-Change: amp=%s dur=%s delay=%s' % (self.amp, self.dur, self.delay)
[docs]class VoltageClampStepChange(VoltageClamp):
[docs] def __init__(
self,
dur1,
amp1,
dur2='0:ms',
dur3='0:ms',
amp2='0:mV',
amp3='0:mV',
rs='0.01:MOhm',
**kwargs
):
super(VoltageClampStepChange, self).__init__(**kwargs)
self.dur1 = qty(dur1)
self.dur2 = qty(dur2)
self.dur3 = qty(dur3)
self.amp1 = qty(amp1)
self.amp2 = qty(amp2)
self.amp3 = qty(amp3)
self.rs = qty(rs)
[docs] def get_summary_description(self):
return 'Step-Change: amp1=%s dur1=%s amp2=%s dur2=%s amp3=%s dur3=%s' % \
(self.amp1, self.dur1,
self.amp2, self.dur2,
self.amp3, self.dur3)
__all__ = ['CurrentClamp', 'VoltageClamp', 'CurrentClampStepChange',
'VoltageClampStepChange', 'Stimulation']