def distribute_spines(self, spine_dist, big_spine):
"""Attach spines to the dendrites"""
self.spines = {}
if spine_dist == 'zero':
pass
elif spine_dist == 'two':
## Trying some spines only for test
spine_positions = [0.3, 0.5]
self.populate_dend(spine_positions,
[h.MSP_Cell[0].dend3_1[1]],
big_spine)
elif spine_dist == 'onebranch' :
# This one populate one branch only for testing purpose
l = Loader()
if big_spine:
# Mid:
spines_pos_mid = l.load('branch_dist/mid_spines_per_branch.pickle')
first_half = [h.MSP_Cell[0].dend3_1[0]]
self.populate_dend(spines_pos_mid[0],
first_half,
big_spine)
# Distal:
spines_pos_dist = l.load('branch_dist/dist_spines_per_branch.pickle')
first_dist = [h.MSP_Cell[0].dend3_1[1]]
self.populate_dend(spines_pos_dist[0], first_dist, big_spine)
else:
s = "Small spine not yet implemented for spine_dist: %s" %spine_dist
raise NotImplementedError(s)
elif spine_dist == 'all':
l = Loader()
if big_spine:
# Mid:
spines_pos_mid = l.load('branch_dist/mid_spines_per_branch.pickle')
first_half = [h.MSP_Cell[0].dend1_1[0], h.MSP_Cell[0].dend2_1[0], h.MSP_Cell[0].dend3_1[0],
h.MSP_Cell[0].dend4_1[0]]
self.populate_dend(spines_pos_mid[0], first_half, big_spine)
second_half = [h.MSP_Cell[0].dend1_2[0], h.MSP_Cell[0].dend2_2[0], h.MSP_Cell[0].dend3_2[0],
h.MSP_Cell[0].dend4_2[0]]
self.populate_dend(spines_pos_mid[1], second_half, big_spine)
# Distal:
spines_pos_dist = l.load('branch_dist/dist_spines_per_branch.pickle')
first_dist = [h.MSP_Cell[0].dend1_1[1], h.MSP_Cell[0].dend2_1[1],
h.MSP_Cell[0].dend3_1[1], h.MSP_Cell[0].dend4_1[1]]
self.populate_dend(spines_pos_dist[0], first_dist, big_spine)
second_dist = [h.MSP_Cell[0].dend1_1[2], h.MSP_Cell[0].dend2_2[2],
h.MSP_Cell[0].dend3_2[2], h.MSP_Cell[0].dend4_2[2]]
self.populate_dend(spines_pos_dist[1], second_dist, big_spine)
third_dist = [h.MSP_Cell[0].dend1_2[1], h.MSP_Cell[0].dend2_2[1],
h.MSP_Cell[0].dend3_2[1], h.MSP_Cell[0].dend4_2[1]]
self.populate_dend(spines_pos_dist[2], third_dist, big_spine)
fourth_dist = [h.MSP_Cell[0].dend1_2[2], h.MSP_Cell[0].dend2_1[2],
h.MSP_Cell[0].dend3_1[2], h.MSP_Cell[0].dend4_1[2]]
self.populate_dend(spines_pos_dist[3], fourth_dist, big_spine)
else:
s = "Small spine not yet implemented for spine_dist: %s" %spine_dist
raise NotImplementedError(s)
else:
print "Value for the spine not understood"
sys.exit()
label="bio calcium")
plt.title("Total Calcium in the biochemical ")
plt.xlim(xlim)
plt.xlabel("Time [ms]")
plt.ylabel("Concentration [uM]")
plt.legend()
plt.ylim(-0.1, 5)
if dir is not None:
for format in [".png", ".pdf"]:
filename = spine + "_biochemical_free_and_buffered_calcium_subtracted" + format
plt.savefig(os.path.join(dir, filename))
if __name__ == "__main__":
if len(sys.argv) == 2:
filename = sys.argv[1]
l = Loader()
ecp = EcellPlotter()
timecourses = l.load(filename)
ecp.plot_timeCourses(timecourses, name='test_spine')
print "Time courses loaded in 'timecourses' object. Easy plotting \n\
with 'ecp' object. Have fun."
plt.show()
else:
print "Tell me which file with ecell Timeseries to load."
print "visualizatorBiochemical.py path/to/timecourses\n"
calcium_bio_and_calcium_calmodulin_buffered_subtracted = ((conc_tot_calcium_bound_to_cam - conc_tot_calcium_bound_to_cam[489]) + ca_conc.read()) * 1e6
plt.plot(t_bio_ms, calcium_bio_and_calcium_calmodulin_buffered_subtracted,
label="bio calcium")
plt.title("Total Calcium in the biochemical ")
plt.xlim(xlim)
plt.xlabel("Time [ms]")
plt.ylabel("Concentration [uM]")
plt.legend()
plt.ylim(-0.1, 5)
if dir is not None:
for format in [".png", ".pdf"]:
filename = spine + "_biochemical_free_and_buffered_calcium_subtracted" + format
plt.savefig(os.path.join(dir, filename))
if __name__ == "__main__":
if len(sys.argv) == 2:
filename = sys.argv[1]
l = Loader()
ecp = EcellPlotter()
timecourses = l.load(filename)
ecp.plot_timeCourses(timecourses, name='test_spine')
print "Time courses loaded in 'timecourses' object. Easy plotting \n\
with 'ecp' object. Have fun."
plt.show()
else:
print "Tell me which file with ecell Timeseries to load."
print "visualizatorBiochemical.py path/to/timecourses\n"
shortest.append(x)
# Insert the spines in perc
def calc_perc_pos(self, start, end, value):
"""Calc the percentual of the spine in the dends
lenght : 1 = value : x
x = value/lenght
"""
real_value = value - start
length = end -start
x = real_value/length
return x
if __name__ == "__main__":
l = Loader()
spines_pos = l.load('spines_pos.pickle')
plt.hist(spines_pos, bins=30, label='normal')
spinePer = spinePercentual()
spines_pos = spinePer.reduce_noise(spines_pos)
plt.hist(spines_pos, bins=30, label='noise red')
plt.legend()
print "Calculating the spines pos normalized to 1"
spinePer.convert_to_perc(spines_pos)
l.save(spinePer.mids, '.', 'mid_spines_per_branch.pickle')
l.save(spinePer.dists, '.', 'dist_spines_per_branch.pickle')
plt.show()