1. Creating morphologies from python dictionaries

Creating morphologies from python dictionaries. In this example, we create 2 MorphologyTree objects from python dictionaries, and then demonstrate iterating over the sections

Code

from morphforge.morphology import MorphologyTree


# Build a morphology consisting of a single-section:
morphDict1 = {'root': {'length': 20, 'diam': 20} }
m1 = MorphologyTree.fromDictionary(morphDict1, name="SimpleMorphology1")
print "M1:"
for section in m1:
    print section


# Build a morphology consisting of a 2 compartments:
morphDict2 = {'root': {'length': 20, 'diam': 20, 'sections': [{'length': 300, 'diam': 2}]  } }
m2 = MorphologyTree.fromDictionary(morphDict2, name="SimpleMorphology2")
print "M2:"
for section in m2:
    print "Section:"
    print " - Proximal:", section.p_x, section.p_y, section.p_z, section.p_r
    print " - Distal:  ", section.d_x, section.d_y, section.d_z, section.d_r

Output

    Openning ScriptFlags
M1:
<SectionObject: [0.000000, 0.000000, 0.000000, r=10.000000] -> [20.000000, 0.000000, 0.000000, r=10.000000], Length: 20.00, Region:NoRegionGiven, >
M2:
Section:
 - Proximal: 0.0 0.0 0.0 10.0
 - Distal:   20.0 0.0 0.0 10.0
Section:
 - Proximal: 20.0 0.0 0.0 10.0
 - Distal:   320.0 0.0 0.0 1.0