Example 9. Hodgkin-Huxley ‘52 neuron simulation with automatic summary pdf generation
Hodgkin-Huxley ‘52 neuron simulation with automatic summary pdf generation.
The same simulation of the HodgkinHuxley52 neuron as before, but by adding a single line, we can generate a pdf output of the simulation! (You can do this on any simulation.)
SimulationSummariser(simulationresult=results, filename="SimulationOutput.pdf", make_graphs=True)
TODO: THIS IS NOT WORKING - DISABLED TO ALLOW runnnign during pdf gen refactor
Code
from morphforge.stdimports import *
from morphforgecontrib.stdimports import StdChlLeak, StdChlAlphaBeta
# Create the environment:
env = NEURONEnvironment()
# Create the simulation:
sim = env.Simulation()
# Create a cell:
morphDict1 = {'root': {'length': 20, 'diam': 20, 'id':'soma'} }
m1 = MorphologyTree.fromDictionary(morphDict1)
cell = sim.create_cell(name="Cell1", morphology=m1)
lk_chl = env.Channel(
StdChlLeak,
name="LkChl",
conductance=qty("0.3:mS/cm2"),
reversalpotential=qty("-54.3:mV"),
)
na_state_vars = { "m": {
"alpha":[-4.00,-0.10,-1.00,40.00,-10.00],
"beta": [4.00, 0.00, 0.00,65.00, 18.00]},
"h": {
"alpha":[0.07,0.00,0.00,65.00,20.00] ,
"beta": [1.00,0.00,1.00,35.00,-10.00]}
}
na_chl = env.Channel(
StdChlAlphaBeta,
name="NaChl", ion="na",
equation="m*m*m*h",
conductance=qty("120:mS/cm2"),
reversalpotential=qty("50:mV"),
statevars=na_state_vars,
)
k_state_vars = { "n": {
"alpha":[-0.55,-0.01,-1.0,55.0,-10.0],
"beta": [0.125,0,0,65,80]},
}
k_chl = env.Channel(
StdChlAlphaBeta,
name="KChl", ion="k",
equation="n*n*n*n",
conductance=qty("36:mS/cm2"),
reversalpotential=qty("-77:mV"),
statevars=k_state_vars,
)
# Apply the channels uniformly over the cell
cell.apply_channel( lk_chl)
cell.apply_channel( na_chl)
cell.apply_channel( k_chl)
cell.set_passive( PassiveProperty.SpecificCapacitance, qty('1.0:uF/cm2'))
# Create the stimulus and record the injected current:
cc = sim.create_currentclamp(name="Stim1", amp=qty("250:pA"), dur=qty("100:ms"), delay=qty("100:ms"), cell_location=cell.soma)
sim.record(cc, what=StandardTags.Current)
# Define what to record:
sim.record(cell, what=StandardTags.Voltage, name="SomaVoltage", cell_location = cell.soma)
# run the simulation
results = sim.run()
# Create an output .pdf
SimulationMRedoc.build( sim ).to_pdf(__file__ + '.pdf')
# Display the results:
TagViewer([results], timerange=(50, 250)*units.ms, show=True)
Output
No handlers could be found for logger "neurounits"
2013-12-01 17:10:35,102 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:10:35,102 - DISABLEDLOGGING - INFO - _run_spawn() [Pickling Sim]
No handlers could be found for logger "neurounits"
2013-12-01 17:10:37,250 - morphforge.core.logmgr - INFO - Logger Started OK
2013-12-01 17:10:37,250 - DISABLEDLOGGING - INFO - Ensuring Modfile is built
NEURON -- Release 7.3 (869:0141cf0aff14) 2013-05-10
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits
['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', 'LD_LIBRARY_PATH', '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']
Loading Bundle from: /mnt/scratch/tmp/morphforge/tmp/simulationresults/26/2607e3e2726bea30b32ea1330fbe6aa2.bundle (11k) : 0.831 seconds
set(['conductance', 'reversalpotential'])
__dict__ {'mm_neuronNumber': None, 'cachedNeuronSuffix': None, 'reversalpotential': array(-54.3) * mV, '_name': 'LkChl', '_simulation': None, 'conductance': array(3.0) * s**3*A**2/(kg*m**4)}
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_af84455a7bd10be7408061ecd02b589b.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_fb18cab9ab8db5d2c968f5e6fba6a942.so
loading membrane mechanisms from /mnt/scratch/tmp/morphforge/tmp/modout/mod_e1d9b15c15cf730d6ad5de223a1b3007.so
Running Hoc File: /mnt/scratch/tmp/morphforge/tmp/tmp_f9eabaec748627fc36116940a8512cba.hoc
1
1
0.01
0
1
50000
1
50000
1
Running Simulation
Time for Extracting Data: (2 records) 0.00352597236633
Running simulation : 0.449 seconds
Size of results file: 0.1 (MB)
Post-processing : 0.011 seconds
Entire load-run-save time : 1.291 seconds
Suceeded
/usr/bin/pdflatex
['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']
_run_spawn() [Loading results from /mnt/scratch/tmp/morphforge/tmp/simulationresults/26//2607e3e2726bea30b32ea1330fbe6aa2.neuronsim.results.pickle ]
Warning: node 'Cell1', graph 'graphname' size too small for label
Warning: node 'Stim1', graph 'graphname' size too small for label
[(100.0, array([ 1., 0., 0.])), (0.0, array([ 0., 1., 0.])), (0.0, array([ 0., 0., 1.]))]
Saving figure /home/michael/.mredoc/build/figs/opfile0002
Saving figure /home/michael/.mredoc/build/figs/opfile0003
Saving figure /home/michael/.mredoc/build/figs/opfile0004
Tex File: /home/michael/.mredoc/build/pdflatex/eqnset.tex
Successfully written PDF to: /mnt/scratch/tmp/morphforge/tmp/mf_doc_build/singlecell_simulation030.py.pdf
PlotManger saving: _output/figures/singlecell_simulation030/{png,svg}/fig000_Autosave_figure_1.{png,svg}
PlotManger saving: _output/figures/singlecell_simulation030/{png,svg}/fig001_Autosave_figure_2.{png,svg}
PlotManger saving: _output/figures/singlecell_simulation030/{png,svg}/fig002_Autosave_figure_3.{png,svg}
PlotManger saving: _output/figures/singlecell_simulation030/{png,svg}/fig003_Autosave_figure_4.{png,svg}