__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
__email__ = "*****@*****.**"
__status__ = "Development"
import sys
import os
import moose
import moose.utils as mu
print('Using moose form %s' % moose.__file__)
print('\t Moose version %s' % moose.version())
# the model lives in the same directory as the test script
modeldir = os.path.dirname(os.path.realpath(__file__))
def main():
modelname = os.path.join(modeldir, './chem_models/00001-sbml-l3v1.xml')
model = moose.mooseReadSBML(modelname, '/sbml')
c = moose.element('/clock')
moose.reinit()
moose.start(200)
check()
def check():
# -*- coding: utf-8 -*-
# Test moose.Function with namedvar and without wrapper.
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2019-, Dilawar Singh"
__maintainer__ = "Dilawar Singh"
__email__ = "*****@*****.**"
import numpy as np
import moose
print("[INFO ] Using moose %s form %s" % (moose.version(), moose.__file__))
def create_func(funcname, expr):
f = moose.Function(funcname)
f.expr = expr
t = moose.Table(funcname + 'tab')
t.connect('requestOut', f, 'getValue')
moose.setClock(f.tick, 0.1)
moose.setClock(t.tick, 0.1)
return f, t
def test_var_order():
nsteps = 5
simtime = nsteps
dt = 1.0
fn1 = moose.Function('/fn1')
fn1.expr = 'B+A+y0+y1'
inputs = np.arange(0, nsteps + 1, 1.0)
x0 = moose.StimulusTable('/x0')
## COMPT: s ----> / s :ENDO
## s =chan= s
## \
##
## This becomes:
## \
## COMPT: s ----> s_xfer_endo / s :ENDO
## s =chan= s
## \
##
#########################################################################
import math
import numpy as np
import moose
print( '[INFO ] Using moose from %s, %s' % (moose.__file__, moose.version()) )
import moose.fixXreacs as fixXreacs
def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral( '/model' )
compartment = moose.CylMesh( '/model/compartment' )
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
s = moose.Pool( '/model/compartment/s' )
rXfer = moose.Reac( '/model/compartment/rXfer' )
#####################################################################
# Put in endo compartment. Add molecule s
endo = moose.EndoMesh( '/model/endo' )
# -*- coding: utf-8 -*-
"""test_docs.py:
Test if moose.doc is working.
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2017-, Dilawar Singh"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
__email__ = "*****@*****.**"
__status__ = "Development"
import sys
import os
import moose
print( '[INFO] Using moose from %s' % moose.__file__ )
print( '[INFO] Version : %s' % moose.version( ) )
def test_doc( ):
moose.doc( 'Compartment' )
def main():
test_doc()
if __name__ == '__main__':
main()
## \
##
## This becomes:
## \
## COMPT: s ----> s_xfer_endo / s :ENDO
## s =chan= s
## \
##
#########################################################################
import math
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import moose
print('[INFO ] Using moose from %s, %s' % (moose.__file__, moose.version()))
import moose.fixXreacs as fixXreacs
def makeModel():
# create container for model
num = 1 # number of compartments
model = moose.Neutral('/model')
compartment = moose.CylMesh('/model/compartment')
compartment.x1 = 1.0e-6 # Set it to a 1 micron single-voxel cylinder
# create molecules and reactions
s = moose.Pool('/model/compartment/s')
rXfer = moose.Reac('/model/compartment/rXfer')
#####################################################################
# Put in endo compartment. Add molecule s
# This example demonstrates insertion of endo-compartments into the
# dendrite. Here endo_compartments are used for the endoplasmic reticulum
# (ER) in a model of Calcium Induced Calcium Release through the
# IP3 receptor. It generates a series of propagating waves of calcium.
# Note that units of permeability in the ConcChan are 1/(millimolar.sec)
#
# Copyright (C) Upinder S. Bhalla NCBS 2018
# Released under the terms of the GNU Public License V3.
# Converted to a test by Dilawar Singh, 2020
import matplotlib as mpl
mpl.use('Agg')
import os
import moose
print("[INFO ] Using moose from %s (%s)" % (moose.__file__, moose.version()))
import numpy as np
import rdesigneur as rd
np.set_printoptions(precision=3)
sdir_ = os.path.dirname(os.path.realpath(__file__))
E = (np.array([1.09014453e-07, 7.28082797e-13, 2.75389935e-08, 4.09373273e-01,
5.13839676e-04, 5.04392239e-04, 5.18535951e-04, 5.20332653e-04,
5.20319412e-04, 5.20315927e-04, 5.20315785e-04, 5.20315780e-04,
5.20315780e-04, 5.20315780e-04, 5.13839676e-04, 5.04392239e-04,
5.18535951e-04, 5.20332653e-04, 5.20319412e-04, 5.20315927e-04,
5.20315785e-04, 5.20315780e-04, 5.20315780e-04, 5.20315780e-04,
4.03334121e-01, 4.04616316e-01, 4.03839819e-01, 4.03873596e-01,
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
__email__ = "*****@*****.**"
__status__ = "Development"
import sys
import os
import moose
import moose.utils as mu
print( 'Using moose form %s' % moose.__file__ )
print( '\t Moose version %s' % moose.version( ) )
# the model lives in the same directory as the test script
modeldir = os.path.dirname( os.path.realpath( __file__ ) )
def main():
modelname = os.path.join(modeldir, './chem_models/00001-sbml-l3v1.xml' )
model = moose.mooseReadSBML( modelname, '/sbml' )
c = moose.element('/clock')
moose.reinit()
moose.start(200)
check( )
def check( ):
# TODO: Add more tests here.
p = moose.wildcardFind( '/sbml/##' )
"""
__author__ = "Dilawar Singh, HarshaRani"
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
__email__ = "*****@*****.**"
__status__ = "Development"
import os
import moose
print("Using moose form %s" % moose.__file__)
print("\t Moose version %s" % moose.version())
# the model lives in the same directory as the test script
sdir_ = os.path.dirname(os.path.realpath(__file__))
def test_sbml():
modelname = os.path.join(sdir_, "..", "data", "00001-sbml-l3v1.xml")
model = moose.readSBML(modelname, "/sbml")
if not model:
print("Most likely python-libsbml is not installed.")
return 0
moose.reinit()
moose.start(200)
# TODO: Add more tests here.
p = moose.wildcardFind("/sbml/##")
import matplotlib as mpl
mpl.use('Agg')
import numpy as np
import matplotlib.pyplot as plt
import moose
print("[INFO ] MOOSE version=%s, loc=%s" % (moose.version(), moose.__file__))
import rdesigneur as rd
expected = (-0.051693861353435865, 0.004062563722923687,
np.array([7, 8, 11, 17, 34, 1852, 49, 31, 34, 958]),
np.array([
-0.065, -0.06309117, -0.06118235, -0.05927352, -0.05736469,
-0.05545587, -0.05354704, -0.05163822, -0.04972939,
-0.04782056, -0.04591174
]))
def test_msgs():
if moose.exists('/model'):
moose.delete('/model')
rdes = rd.rdesigneur(
stimList=[['soma', '1', '.', 'inject', '(t>0.1 && t<0.2) * 2e-8']],
plotList=[['soma', '1', '.', 'Vm', 'Soma membrane potential']])
rdes.buildModel()
msgs = moose.listmsg(rdes.soma)
assert len(msgs) == 3, msgs
def test_current_pulse():
"""Test current pulse.
"""
