Example 2. Loading from SWC and rendering with Matplotlib

Loading from SWC and rendering with Matplotlib. This example shows loading in a morphology from an SWC file and then viewing it in matplotlib, using Principle Component Analysis (PCA) to align the features of the morphology to the plot window.

Code

from morphforge.core import LocMgr, Join
from morphforge.morphology.ui import MatPlotLibViewer
from morphforge.morphology.core import MorphologyTree

testSrcsPath = LocMgr().get_test_srcs_path()
srcSWCFile = Join(testSrcsPath, "swc_files/28o_spindle20aFI.CNG.swc")

m = MorphologyTree.fromSWC(src=open(srcSWCFile))
MatPlotLibViewer(m, use_pca=False)
MatPlotLibViewer(m, use_pca=True)

Figures

../_images/morphology020_out1.png

Download Figure

../_images/morphology020_out2.png

Download Figure

Output

    ['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']
[(18904.787115151994, array([ 0.17, -0.97,  0.15])), (560.28926277794278, array([-0.98, -0.18, -0.05])), (73.826665068840015, array([-0.08,  0.14,  0.99]))]