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 _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 _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()
