__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. """