runme.py

# linux only movie generation of a firing dentate gyrus granule cell

try:
    from neuron import h, gui
except:
    print 'This simulation requires NEURON with Python support.'
    print 'See: http://neuron.yale.edu'
    import sys
    sys.exit()

# setup directories
import os
try:
    os.makedirs('images')
except:
    os.system('rm -fr images')
    os.makedirs('images')

# load the morphology
h.load_file('n275.hoc')

# setup the discretization
for sec in h.allsec():
    sec.nseg = 21

# add ion channels
for sec in h.allsec():
    if 'dend' not in sec.name():
        sec.insert('hh')


# setup graphics
ps = h.PlotShape(0)
ps.size(-416.826, 396.319, -486.465, 472.666)
ps.variable('v')
ps.view(-416.826, -486.465, 813.145, 959.13, 151, 52, 559.68, 660.16)
h.fast_flush_list.append(ps)
ps.exec_menu('Shape Plot')
h.graphList[0].append(ps)

# initialize simulation
h.finitialize()

# setup current pulses to trigger APs
fire_times = [5, 25, 45, 60, 75]
iclamps = []
for time in fire_times:
    iclamp = h.IClamp(0.5, sec=h.soma[0])
    iclamp.delay = time
    iclamp.amp = 2
    iclamp.dur = 0.5
    iclamps.append(iclamp)

image_count = 0
save_every = 10

def savefig():
    global image_count
    filename = 'images/%04.2f.ps' % h.t
    ps.printfile(filename)
    # fatten the lines in the image to make it easier to see
    lines = []
    with open(filename) as f:
        for line in f:
            line = line.strip()
            if line == '0 setlinewidth':
                line = '5 setlinewidth'
            lines.append(line)
    # now rewrite the file with the thicker linewidth
    with open(filename, 'w') as f:
        for line in lines:
            f.write(line + '\n')
    # now convert it to a png
    png_filename = 'images/image%04d.png' % image_count
    image_count += 1
    os.system('convert %s -crop 558x660+0+0 %s' % (filename, png_filename))

# stop time
stop_time = 100

advance_count = 0
while h.t < stop_time:
    h.fadvance()
    h.doNotify()
    if advance_count % save_every == 0:
        savefig()
    advance_count += 1
    print h.t

# convert the pictures to a video
os.system('rm -f movie.mp4')
os.system('avconv -qscale 5 -r 20 -b 9600 -i images/image%04d.png movie.mp4')