def __init__(self, morphology=None, area=None, segmenter=None, initial_voltage=None, cell_tags=None, cell_type=None, **kwargs):
if area is not None:
assert morphology is None
morphology = MorphologyBuilder.get_single_section_soma(area=area)
if cell_tags == None:
cell_tags = []
from morphforge.simulation.base.segmentation.cellsegmenter import CellSegmenter_MaxCompartmentLength
super(Cell, self).__init__(**kwargs)
self.morphology = morphology
self._cell_type = cell_type
self.cell_segmenter = (segmenter if segmenter else CellSegmenter_MaxCompartmentLength())
self.cell_segmenter.connect_to_cell(self)
self.biophysics = CellBiophysics(self)
self.initial_voltage = initial_voltage or unit('-51:mV')
self.cell_tags = cell_tags
if self.name:
self.cell_tags = self.cell_tags + [self.name]
self.population = None
def __init__(self, morphology=None, area=None, segmenter=None, initial_voltage=None, cell_tags=None, cell_type=None, **kwargs):
if area is not None:
assert morphology is None
morphology = MorphologyBuilder.get_single_section_soma(area=area)
if cell_tags == None:
cell_tags = []
from morphforge.simulation.base.segmentation.cellsegmenter import CellSegmenter_MaxCompartmentLength
super(Cell, self).__init__(**kwargs)
self.morphology = morphology
self._cell_type = cell_type
self.cell_segmenter = (segmenter if segmenter else CellSegmenter_MaxCompartmentLength())
#self.cell_segmenter.connect_to_cell(self)
self.biophysics = CellBiophysics(self)
self.initial_voltage = initial_voltage or qty('-51:mV')
self.cell_tags = cell_tags
if self.name:
self.cell_tags = self.cell_tags + [self.name]
self.population = None
class Cell(NamedSimulationObject):
class Recordables(object):
MembraneVoltage = StandardTags.Voltage
@property
def cell_type(self):
return self._cell_type
@property
def cell_type_str(self):
return (self._cell_type if self._cell_type else '<?>')
def __init__(self, morphology=None, area=None, segmenter=None, initial_voltage=None, cell_tags=None, cell_type=None, **kwargs):
if area is not None:
assert morphology is None
morphology = MorphologyBuilder.get_single_section_soma(area=area)
if cell_tags == None:
cell_tags = []
from morphforge.simulation.base.segmentation.cellsegmenter import CellSegmenter_MaxCompartmentLength
super(Cell, self).__init__(**kwargs)
self.morphology = morphology
self._cell_type = cell_type
self.cell_segmenter = (segmenter if segmenter else CellSegmenter_MaxCompartmentLength())
#self.cell_segmenter.connect_to_cell(self)
self.biophysics = CellBiophysics(self)
self.initial_voltage = initial_voltage or qty('-51:mV')
self.cell_tags = cell_tags
if self.name:
self.cell_tags = self.cell_tags + [self.name]
self.population = None
@property
def index_in_pop(self):
assert self.population is not None
return self.population.index(self)
def get_location(self, idtag, sectionpos=0.5):
return CellLocation(cell=self,
section=self.morphology.get_section(idtag=idtag),
sectionpos=sectionpos)
def get_region(self, region_name):
return self.morphology.get_region(region_name)
def get_regions(self):
return self.morphology.get_regions()
def get_biophysics(self):
return self.biophysics
def get_segmenter(self):
return self.cell_segmenter
# Make the object a bit more pythonic:
@property
def segmenter(self):
return self.cell_segmenter
@property
def presynaptic_connections(self):
return [synapse for synapse in self.simulation.synapses
if synapse.get_presynaptic_cell() == self]
@property
def postsynaptic_connections(self):
return [synapse for synapse in self.simulation.synapses
if synapse.get_postsynaptic_cell() == self]
@property
def electrical_connections(self):
return [gap_junction for gap_junction in self.simulation.gapjunctions if self
in gap_junction.connected_cells]
# Commonly used helper methods:
@property
def soma(self):
return self.get_location('soma')
@property
def is_single_compartment(self):
return len( self.morphology ) == 1 and \
self.segmenter.get_num_segments(self.soma.section) == 1
# Simple forwarding method to biophysics, (syntactic sugar)
def apply_channel(self, *args, **kwargs) :
self.biophysics.apply_channel(*args, **kwargs)
def set_passive(self, *args, **kwargs) :
self.biophysics.set_passive(*args, **kwargs)
class Cell(NamedSimulationObject):
class Recordables(object):
MembraneVoltage = StandardTags.Voltage
@property
def cell_type(self):
return self._cell_type
@property
def cell_type_str(self):
return (self._cell_type if self._cell_type else '<?>')
def __init__(self, morphology=None, area=None, segmenter=None, initial_voltage=None, cell_tags=None, cell_type=None, **kwargs):
if area is not None:
assert morphology is None
morphology = MorphologyBuilder.get_single_section_soma(area=area)
if cell_tags == None:
cell_tags = []
from morphforge.simulation.base.segmentation.cellsegmenter import CellSegmenter_MaxCompartmentLength
super(Cell, self).__init__(**kwargs)
self.morphology = morphology
self._cell_type = cell_type
self.cell_segmenter = (segmenter if segmenter else CellSegmenter_MaxCompartmentLength())
self.cell_segmenter.connect_to_cell(self)
self.biophysics = CellBiophysics(self)
self.initial_voltage = initial_voltage or unit('-51:mV')
self.cell_tags = cell_tags
if self.name:
self.cell_tags = self.cell_tags + [self.name]
self.population = None
@property
def index_in_pop(self):
assert self.population is not None
return self.population.index(self)
def get_location(self, idtag, sectionpos=0.5):
return CellLocation(cell=self,
section=self.morphology.get_section(idtag=idtag),
sectionpos=sectionpos)
def get_region(self, region_name):
return self.morphology.get_region(region_name)
def get_regions(self):
return self.morphology.get_regions()
def get_biophysics(self):
return self.biophysics
def get_segmenter(self):
return self.cell_segmenter
# Make the object a bit more pythonic:
@property
def segmenter(self):
return self.cell_segmenter
@property
def presynaptic_connections(self):
return [synapse for synapse in self.simulation.synapses
if synapse.get_presynaptic_cell() == self]
@property
def postsynaptic_connections(self):
return [synapse for synapse in self.simulation.synapses
if synapse.get_postsynaptic_cell() == self]
@property
def electrical_connections(self):
return [gap_junction for gap_junction in self.simulation.gapjunctions if self
in gap_junction.connected_cells]
# Commonly used helper methods:
@property
def soma(self):
return self.get_location('soma')
@property
def is_single_compartment(self):
return len( self.morphology ) == 1 and \
self.segmenter.get_num_segments(self.soma.section) == 1
# Simple forwarding method to biophysics, (syntactic sugar)
def apply_channel(self, *args, **kwargs) :
self.biophysics.apply_channel(*args, **kwargs)
def set_passive(self, *args, **kwargs) :
self.biophysics.set_passive(*args, **kwargs)
