Example 5. Load morphologies from MorphML, and plot using MayaVI
Load morphologies from MorphML, and plot using MayaVI
Code
import morphforge.stdimports as mf
import morphforgecontrib.morphology.importers.import_tree_morphml
import pylab
testSrcsPath = mf.LocMgr().get_test_srcs_path()
srcMorphMLFile = mf.Join(testSrcsPath, "neuroml/morphml/CablesIncluded.xml")
m = mf.MorphologyTree.fromMorphML(src=open(srcMorphMLFile) )
#mf.MayaViRenderer(m).show_as_points_interpolated()
## TODO - SPEAK TO PADRAIG:
#raise NotImplementedError()
#srcMorphMLFile = mf.Join(testSrcsPath, "neuroml/morphml/L23PyrFRB.morph.xml",)
#m = mf.MorphologyTree.fromMorphML(
# src=open(srcMorphMLFile),
# regions={
# 'all':'Rgn1',
# 'ModelViewParmSubset_1':'Rgn2',
# 'ModelViewParmSubset_3':'Rgn2',
# 'ModelViewParmSubset_8':'Rgn2',
# 'OneSecGrp_SectionRef_1':'Rgn1',
# }
#)
#mf.MayaViRenderer(m).show_as_points_interpolated()
Output
No handlers could be found for logger "neurounits"
/home/michael/hw_to_come/morphforge/src/morphforgecontrib/morphology/importers/import_tree_morphml.py:34: UserWarning: MorphML code in development
warnings.warn('MorphML code in development')
['DBUS_SESSION_BUS_ADDRESS', 'DEFAULTS_PATH', 'DESKTOP_SESSION', 'DESKTOP_STARTUP_ID', 'DISPLAY', 'GDMSESSION', 'GNOME_KEYRING_CONTROL', 'GNOME_KEYRING_PID', 'GREP_COLOR', 'GREP_OPTIONS', 'GRIN_ARGS', 'GTK_MODULES', 'HOME', 'INFANDANGO_CONFIGFILE', 'INFANDANGO_ROOT', 'LANG', 'LANGUAGE', 'LC_CTYPE', 'LESS', 'LOGNAME', 'LSCOLORS', 'MANDATORY_PATH', 'MREORG_CONFIG', 'OLDPWD', 'PAGER', 'PATH', 'PWD', 'PYTHONPATH', 'SHELL', 'SHLVL', 'SSH_AGENT_PID', 'SSH_AUTH_SOCK', 'TERM', 'TEXTDOMAIN', 'TEXTDOMAINDIR', 'UBUNTU_MENUPROXY', 'USER', 'WINDOWID', 'XAUTHORITY', 'XDG_CONFIG_DIRS', 'XDG_DATA_DIRS', 'XDG_RUNTIME_DIR', 'XDG_SEAT_PATH', 'XDG_SESSION_COOKIE', 'XDG_SESSION_PATH', 'XTERM_LOCALE', 'XTERM_SHELL', 'XTERM_VERSION', '_', '_JAVA_AWT_WM_NONREPARENTING']
CellName: CellWithCables
Loaded Cable: 0 SomaSec
Loaded Cable: 1 DendSec1
Loaded Cable: 2 DendSec2
Segment
0 SomaSeg 0 (u'0', u'0', u'0', u'10') (u'10', u'0', u'0', u'10')
Segment
1 DendSeg1 1 0 (u'5', u'0', u'0', u'5') (u'5', u'10', u'0', u'5')
Segment
2 DendSeg2 1 1 (5.0, 10.0, 0.0, 5.0) (u'5', u'20', u'0', u'5')
Segment
3 DendSeg3 1 2 (5.0, 20.0, 0.0, 5.0) (u'5', u'30', u'0', u'5')
Segment
4 DendSeg4 2 0 (u'10', u'0', u'0', u'3') (u'10', u'0', u'10', u'3')
Segment
5 DendSeg5 2 4 (10.0, 0.0, 10.0, 3.0) (u'10', u'0', u'20', u'3')
RegionNames: [u'soma_group', u'dendrite_group']