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# Deleting a line in matplot lib
fig = figure()
ax = fig.add_subplot(111)
x = linspace(0,10)
plot(x, sin(x), label='sin')
plot(x, cos(x), label='cos')
# Deleting the last one
del ax.lines[1]
draw() # updating the fig
def create_new_dir(self, prefix="./", root="Sims"):
Create the directory where to put the simulation
self.dirRoot = os.path.join(prefix, root)
today =
free = False
index = 0
View saving_compressed_array. Maybe useful later on.
def save_node(self, h5file_holder, group_path, section_name, variables,
"""Save a node to the h5file.
h5file_holder: The holder of the h5file
group_path: Where in the hierarchy the leaf has to be saved
section_name: The name of the section which the variables belong to
variables: The dictionary of the variable
found = False
target_group = None
from import visual
def draw_cyl(coords):
x_ax = coords['x1'] -coords['x0']
y_ax = coords['y1'] -coords['y0']
z_ax = coords['z1'] -coords['z0']
cyl = visual.Cylinder(pos=(coords['x0'],coords['y0'],coords['z0']),
axis=(x_ax,y_ax,z_ax), radius=1, length=10)
mattions /
Created May 4, 2011
Using mlab to change a second scalar for the cilinders..
import numpy as np
from mayavi import mlab
class Animator(object):
def __init__(self):
self.scalar_active_attribute = None
def add_scalar_array(self, dataset, tube, scalar_data, scalar_data_name):
mattions / a.param
Created Jun 27, 2011
Easy way to get params from external file in the main script (and work with them)
View a.param
# Parameters file for simulation.
"dt" : 0.025, # integration dt [ms]
"dict_ampa_s1" :
{"t_stim" : 0.130, # t_stim [s]
"numbers" : 4, # number
"delay" : 0.1, # delay [s]
"type" : "ampa" # , type
"dict_ampa_s2" :
mattions /
Created Sep 12, 2011
Off screen rendering of a 3D window of Neuronvisio
import os
from shutil import copyfile
import numpy as np
# Getting the qt in before mayavi
from PyQt4 import QtGui
app = QtGui.QApplication.instance()
from enthought.mayavi import mlab
# Offscreen
mattions /
Created Sep 12, 2011
run a downloaded model in Neuronvisio
def run_model_in_neuronvisio(model_dir):
if os.path.exists(os.path.join (model_dir, 'mosinit.hoc')):
#TODO: We should check if the file is already compiled,
# and call the right executable according to the system.
from neuron import gui # to not freeze neuron gui
from neuron import h
from neuronvisio.controls import Controls
mattions /
Created Oct 2, 2011
importing the right Qstring for Python 3 on windows
This is a check to make sure the sip and the Qstrings play nicely in Windows,
where the PySide is using the new Python API (Python 3)
This could be easily removed when we move to Python 3
if == 'nt':
import sip
sip.setapi('QString', 2)
mattions / neuronvisio_dev_reqs.txt
Created Feb 8, 2012
Requirements for version 0.8.0 of neuronvisio
View neuronvisio_dev_reqs.txt
-e git+
-e git+