def _showSimple():
max_interpol_pts = 10
def interpolate_section(section):
sec_start = section.get_distal_npa4()
sec_end = section.get_proximal_npa4()
length = section.get_length()
rad = min(section.d_r, section.p_r)
n = min(max(int(lToRRatio * length / rad), 1), max_interpol_pts)
j_vec_steps = (sec_end - sec_start) / n
int_pts = [sec_start + k * j_vec_steps for k in range(0, n)]
return int_pts
lbs = []
for morph in self.morphs:
lb = SeqUtils.flatten(ListBuilderSectionVisitor(functor=interpolate_section, morph=morph) ())
lbs.extend(lb)
pts = numpy.array(lbs)
x = pts[:, 0]
y = pts[:, 1]
z = pts[:, 2]
s = pts[:, 3]
mlab.points3d(x, y, z, s, colormap=self.colormap, scale_factor=self.scale_factor)
mlab.outline()
def check_tree(self):
if not self.morph.is_dummy_section_set():
return
dummy_section = self.morph.get_dummy_section()
self.check_dummy_section(dummy_section)
# Check nothing changed in the tree:
morphmd5 = _get_md5_of_morphology(self.morph)
if self.morphmd5cache:
if morphmd5 != self.morphmd5cache:
raise Exception('MD5 of tree has changed!')
else:
return
self.morphmd5cache = morphmd5
# Check the tree is sensible:
self.check_section(self.morph._dummysection, self.morph, dummysection=True, recurse=True)
# Check that there are not duplications of idTags in the tree:
idtags = SeqUtils.flatten([section.idtag for section in self.morph if section.idtag])
#print idtags
assert len(idtags) == len(list(set(idtags)))
# Check the regions
for rgn in self.morph.get_regions():
self.check_region(rgn, self.morph)
def get_region(self, name):
""" Returns a Region object relevant to this tree, given a filename"""
assert self.ensure_consistency()
return SeqUtils.filter_expect_single(self.get_regions(),
lambda r: r.name == name)
def check_tree(self):
if not self.morph.is_dummy_section_set():
return
dummy_section = self.morph.get_dummy_section()
self.check_dummy_section(dummy_section)
# Check nothing changed in the tree:
morphmd5 = _get_md5_of_morphology(self.morph)
if self.morphmd5cache:
if morphmd5 != self.morphmd5cache:
raise Exception('MD5 of tree has changed!')
else:
return
self.morphmd5cache = morphmd5
# Check the tree is sensible:
self.check_section(self.morph._dummysection,
self.morph,
dummysection=True,
recurse=True)
# Check that there are not duplications of idTags in the tree:
idtags = SeqUtils.flatten(
[section.idtag for section in self.morph if section.idtag])
#print idtags
assert len(idtags) == len(list(set(idtags)))
# Check the regions
for rgn in self.morph.get_regions():
self.check_region(rgn, self.morph)
def get_channel(self, name):
try:
return SeqUtils.filter_expect_single(
self.get_all_mechanisms_applied_to_cell(),
lambda chl: chl.name == name)
except:
print 'Options: ', [
chl.name for chl in self.get_all_mechanisms_applied_to_cell()
]
raise
def get_passives_for_section(self, section):
sectionptas = [pta for pta in self.appliedpassives
if pta.targetter.does_target_section(section)]
passivemechs = {}
for passiveproperty in PassiveProperty.all:
section_property_ptas = [spta for spta in sectionptas if spta.passiveproperty == passiveproperty]
highest_prority_mech = SeqUtils.max_with_unique_check(section_property_ptas, key=lambda pta: pta.targetter.get_priority())
passivemechs[passiveproperty] = highest_prority_mech
return passivemechs
def check_region(self, region, morph):
check_cstyle_varname(region.name)
# Check no-other region has this name:
# print "Checking region:", region.name
# print "All Regions:", ",".join([r.name for r in self.morph.get_regions()])
assert SeqUtils.filter_expect_single(self.morph.get_regions(),
lambda rgn: rgn.name == region.name) == region
assert region.morph == morph
for section in region.sections:
assert region == section.region
def __call__(self, morph=None):
self.morph = SeqUtils.filter_expect_single(
[morph, self.morph], lambda s: s is not None)
if not self.alreadycalled:
self.pretraversefunctor()
self.visit_section_internal(self.morph.get_dummy_section())
self.posttraversefunctor()
self.alreadycalled = True
return self.returnfunctor()
def check_region(self, region, morph):
check_cstyle_varname(region.name)
# Check no-other region has this name:
# print "Checking region:", region.name
# print "All Regions:", ",".join([r.name for r in self.morph.get_regions()])
assert SeqUtils.filter_expect_single(
self.morph.get_regions(),
lambda rgn: rgn.name == region.name) == region
assert region.morph == morph
for section in region.sections:
assert region == section.region
def get_resolved_mtas_for_section(self, section):
# TODO: Some basic error checking here: we should ensure that if we specialise a region/section, then we also
# cover the Everywhere. This should help us catch errors in ehich the user creates 2 mechanisms of the same thing, and
# and so applies the same channel twice accidentally.
# All the mechanisms targetting a certain region:
mtas_targetting_section = [mta for mta in self.appliedmechanisms if mta.targetter.does_target_section(section)]
mechs_targetting_section = set([ mta.mechanism for mta in self.appliedmechanisms])
resolved_mechs = []
for mech in mechs_targetting_section:
mtas_with_mech = [mta for mta in mtas_targetting_section if mta.mechanism is mech]
highest_prority_mech = SeqUtils.max_with_unique_check(mtas_with_mech, key=lambda pta: pta.targetter.get_priority())
resolved_mechs.append(highest_prority_mech)
return resolved_mechs
def get_passives_for_section(self, section):
sectionptas = [
pta for pta in self.appliedpassives
if pta.targetter.does_target_section(section)
]
passivemechs = {}
for passiveproperty in PassiveProperty.all:
section_property_ptas = [
spta for spta in sectionptas
if spta.passiveproperty == passiveproperty
]
highest_prority_mech = SeqUtils.max_with_unique_check(
section_property_ptas,
key=lambda pta: pta.targetter.get_priority())
passivemechs[passiveproperty] = highest_prority_mech
return passivemechs
def get_resolved_mtas_for_section(self, section):
# TODO: Some basic error checking here: we should ensure that if we specialise a region/section, then we also
# cover the Everywhere. This should help us catch errors in ehich the user creates 2 mechanisms of the same thing, and
# and so applies the same channel twice accidentally.
# All the mechanisms targetting a certain region:
mtas_targetting_section = [
mta for mta in self.appliedmechanisms
if mta.targetter.does_target_section(section)
]
mechs_targetting_section = set(
[mta.mechanism for mta in self.appliedmechanisms])
resolved_mechs = []
for mech in mechs_targetting_section:
mtas_with_mech = [
mta for mta in mtas_targetting_section if mta.mechanism is mech
]
highest_prority_mech = SeqUtils.max_with_unique_check(
mtas_with_mech, key=lambda pta: pta.targetter.get_priority())
resolved_mechs.append(highest_prority_mech)
return resolved_mechs
def _showSimple():
max_interpol_pts = 10
def interpolate_section(section):
sec_start = section.get_distal_npa4()
sec_end = section.get_proximal_npa4()
length = section.get_length()
rad = min(section.d_r, section.p_r)
n = min(max(int(lToRRatio * length / rad), 1),
max_interpol_pts)
j_vec_steps = (sec_end - sec_start) / n
int_pts = [sec_start + k * j_vec_steps for k in range(0, n)]
return int_pts
lbs = []
for morph in self.morphs:
lb = SeqUtils.flatten(
ListBuilderSectionVisitor(functor=interpolate_section,
morph=morph)())
lbs.extend(lb)
pts = numpy.array(lbs)
x = pts[:, 0]
y = pts[:, 1]
z = pts[:, 2]
s = pts[:, 3]
mlab.points3d(x,
y,
z,
s,
colormap=self.colormap,
scale_factor=self.scale_factor)
mlab.outline()
def get_channel(self, name):
try:
return SeqUtils.filter_expect_single(self.get_all_mechanisms_applied_to_cell(), lambda chl: chl.name==name)
except:
print 'Options: ', [ chl.name for chl in self.get_all_mechanisms_applied_to_cell() ]
raise
def get_section(self, idtag):
""" Returns a Section object with a given id"""
#assert self.ensure_consistency()
return SeqUtils.filter_expect_single(self, lambda s: s.idtag == idtag)
def get_region(self, name):
""" Returns a Region object relevant to this tree, given a filename"""
assert self.ensure_consistency()
return SeqUtils.filter_expect_single(self.get_regions(), lambda r: r.name == name)
def get_section(self, idtag):
""" Returns a Section object with a given id"""
#assert self.ensure_consistency()
return SeqUtils.filter_expect_single(self, lambda s: s.idtag == idtag)
def get_location_at_distance_away_from_dummy(cls, cell, distance, section_predicate=None):
"""Utility Function"""
return SeqUtils.expect_single(cls.get_locations_at_distance_away_from_dummy(cell=cell, distance=distance, section_predicate=section_predicate))
