# Calculate the angle of the current section:
if parent_section:
joining_vec = new_section.get_distal_npa3(
) - parent_section.get_distal_npa3()
angle = math.radians(math.atan2(joining_vec[1],
joining_vec[0]))
section_angles_dict[new_section] = angle
#Save the section:
section_dict[yaml_id] = new_section
# # TODO: THIS IS A HACK! Ensure the dummy node has no attached regions:
# section_dict[None].regions = []
assert section_dict[0].region == None
if section_dict[0].children == []:
raise ValueError("No segments found")
morphs = MorphologyTree(name=name,
dummysection=section_dict[0],
metadata=metadata)
if len(morphs) < 1:
raise ValueError
return morphs
MorphologyImporter.register('fromDictionary',
DictionaryLoader.load,
allow_override=False,
as_type=MorphologyTree)
0].getAttribute("y"), pNode[0].getAttribute("z")
p_diamR = pNode[0].getAttribute("diameter")
# I do not understand MorphML to understand why these checks do not fail....
#print (p_xR, p_yR, p_zR)
#print (parent_Dist_Loc[0], parent_Dist_Loc[1], parent_Dist_Loc[2])
#assert (p_xR, p_yR, p_zR) == (parent_Dist_Loc[0], parent_Dist_Loc[1], parent_Dist_Loc[2])
# In this case, use the diameter just read:
p_x, p_y, p_z = p_xR, p_yR, p_zR
p_diam = p_diamR
else:
assert False
print id, name, cable, parent, (p_x, p_y, p_z,
p_diam), (d_x, d_y, d_z, d_diam)
infTuple = (id, name, cable, parent, (float(p_x), float(p_y),
float(p_z), float(p_diam)),
(float(d_x), float(d_y), float(d_z), float(d_diam)))
assert not id in segmentListInfo
segmentListInfo[id] = infTuple
# Now we have read the file and created the dictionaries:
return (cableIDToRegionName, segmentListInfo)
MorphologyImporter.register(method_name='fromMorphML',
import_functor=MorphMLLoader.load,
as_type=MorphologyTree)
lines = [line.strip() for line in src.readlines()]
lines = [line for line in lines if line and line[0] != '#']
# Break into sections where we get a new parent:
splits = [[]]
for line in lines:
if int(line.split()[-1]) == -1:
splits.append([])
splits[-1].append(line)
splits = splits[1:]
data_blocks = ['\n'.join(blk) for blk in splits]
file_objs = [StringIO(blk) for blk in data_blocks]
morphs = [cls.load_swc_single(src=fobj) for fobj in file_objs]
return morphs
# To Array:
MorphologyImporter.register('fromSWC', NewSWCLoader.load_swc_single, as_type=MorphologyArray)
# To Tree:
def _load_swc_single_tree(*args, **kwargs):
return NewSWCLoader.load_swc_single(*args, **kwargs).to_tree()
MorphologyImporter.register('fromSWC', _load_swc_single_tree, as_type=MorphologyTree)
# I do not understand MorphML to understand why these checks do not fail....
# print (p_xR, p_yR, p_zR)
# print (parent_Dist_Loc[0], parent_Dist_Loc[1], parent_Dist_Loc[2])
# assert (p_xR, p_yR, p_zR) == (parent_Dist_Loc[0], parent_Dist_Loc[1], parent_Dist_Loc[2])
# In this case, use the diameter just read:
p_x, p_y, p_z = p_xR, p_yR, p_zR
p_diam = p_diamR
else:
assert False
print id, name, cable, parent, (p_x, p_y, p_z, p_diam), (d_x, d_y, d_z, d_diam)
infTuple = (
id,
name,
cable,
parent,
(float(p_x), float(p_y), float(p_z), float(p_diam)),
(float(d_x), float(d_y), float(d_z), float(d_diam)),
)
assert not id in segmentListInfo
segmentListInfo[id] = infTuple
# Now we have read the file and created the dictionaries:
return (cableIDToRegionName, segmentListInfo)
MorphologyImporter.register(method_name="fromMorphML", import_functor=MorphMLLoader.load, as_type=MorphologyTree)
else:
newSection = Section(x=xyz[0], y=xyz[1], z=xyz[2], r=rad, region=None, idTag=sectionIdTag)
sectionDict[None] = newSection
# Calculate the angle of the current section:
if parentSection:
joiningVec = newSection.getDistalNPA3() - parentSection.getDistalNPA3()
angle = math.radians(math.atan2(joiningVec[1], joiningVec[0]))
sectionAnglesDict[newSection] = angle
#Save the section:
sectionDict[yamlID] = newSection
## TODO: THIS IS A HACK! Ensure the dummy node has no attached regions:
#sectionDict[None].regions = []
assert sectionDict[0].region == None
if sectionDict[0].children == []: raise ValueError("No segments found")
c = MorphologyTree(name=name, dummysection=sectionDict[0], metadata=metaData)
if len(c) < 1: raise ValueError
return c
MorphologyImporter.register("fromDictionary", DictionaryLoader.Load, allow_override=False, as_type=MorphologyTree)
