def __init__(self,
t_trial,
n_trials,
seed,
path,
dt=0.05,
do_parallel=False):
Simulation.__init__(self, dt, t_trial, n_trials, seed)
global _loaded
if not _loaded:
h.nrn_load_dll(path + "/x86_64/.libs/libnrnmech.so")
h.load_file("stdrun.hoc")
_loaded = True
self.do_parallel = do_parallel
if do_parallel:
self.pc = h.ParallelContext()
self.id = int(self.pc.id())
self.nhost = int(self.pc.nhost())
else:
self.id = 0
self.nhost = 1
print("I am {} of {}".format(self.id, self.nhost))
h.celsius = 34
h.dt = self.dt
h.steps_per_ms = 1.0 / self.dt
self._gif_fun = dict()
self._inner_current = dict()
self._connections = []
self.synapses = dict()
self.randoms = [seed]
self.spikes = dict()
def load_hoc_model(self, model_dir, hoc_file):
"""Load an hoc files. It compiles the mod
before loading the hoc."""
try:
os.path.isfile(os.path.join (model_dir, hoc_file))
except IOError:
logger.error("Not existing file: %s" %e.value)
old_dir = os.path.abspath(os.getcwd())
logger.info("Path changed to %s" %(os.path.abspath(model_dir)))
if model_dir != '' :
os.chdir(model_dir)
try:
# Add all mod files into current directory
self.find_mod_files()
# If windows
if os.name == 'nt':
self.windows_compile_mod_files('.')
from neuron import h
h.nrn_load_dll('./nrnmech.dll')
else: # Anything else.
call(['nrnivmodl'])
import neuron
neuron.load_mechanisms('.') # Auto loading. Not needed anymore.
from neuron import gui # to not freeze neuron gui
from neuron import h
logger.info("Loading model in %s from %s"%(model_dir, hoc_file))
h.load_file(hoc_file)
except Exception as e:
logger.warning("Error running model: " + e.message)
logger.info("Path changed back to %s" %old_dir)
os.chdir(old_dir)
return True
def run_extracted_model(self, mod):
model_dir = mod.get_dir()
if os.path.exists(os.path.join (model_dir, 'mosinit.hoc')):
old_dir = os.path.abspath(os.getcwd())
logger.info("Path changed to %s" %(os.path.abspath(model_dir)))
os.chdir(model_dir)
try:
# If windows
if os.name == 'nt':
self.windows_compile_mod_files('.')
from neuron import h
h.nrn_load_dll('./nrnmech.dll')
else: # Anything else.
call(['nrnivmodl'])
import neuron
neuron.load_mechanisms('./')
from neuron import gui # to not freeze neuron gui
from neuron import h
logger.info("Loading model in %s" %model_dir)
h.load_file('mosinit.hoc')
except Exception as e:
logger.warning("Error running model: "+e.message)
logger.info("Path changed back to %s" %old_dir)
os.chdir(old_dir)
else:
response = """We didn't find any mosinit.hoc . Unfortunately we can't
automatically run the model. Check the README, maybe there is an
hint."""
logging.warning(response)
path_info = "You can find the extracted model in %s" %model_dir
mod.browse()
logging.info(path_info)
def load_mechanisms(path):
"""
Search for and load NMODL mechanisms from the path given.
This a stricter version of NEURON's own load_mechanisms function, which will
raise an IOError if no mechanisms are found at the given path. This function
will not load a mechanism path twice.
The path should specify the directory in which nrnivmodl was run, and in
which the directory 'i686' (or 'x86_64' or 'powerpc' depending on your
platform) was created.
"""
import platform
global nrn_dll_loaded
if path in nrn_dll_loaded:
logger.warning("Mechanisms already loaded from path: %s" % path)
return
# in case NEURON is assuming a different architecture to Python,
# we try multiple possibilities
arch_list = [platform.machine(), 'i686', 'x86_64', 'powerpc', 'umac']
for arch in arch_list:
lib_path = os.path.join(path, arch, '.libs', 'libnrnmech.so')
if os.path.exists(lib_path):
h.nrn_load_dll(lib_path)
nrn_dll_loaded.append(path)
return
raise IOError("NEURON mechanisms not found in %s. You may need to run 'nrnivmodl' in this directory." % path)
def load_hoc_model(self, model_dir, hoc_file):
"""Load an hoc files. It compiles the mod
before loading the hoc."""
try:
os.path.isfile(os.path.join(model_dir, hoc_file))
except IOError:
logger.error("Not existing file: %s" % e.value)
old_dir = os.path.abspath(os.getcwd())
logger.info("Path changed to %s" % (os.path.abspath(model_dir)))
if model_dir != '':
os.chdir(model_dir)
try:
# Add all mod files into current directory
self.find_mod_files()
# If windows
if os.name == 'nt':
self.windows_compile_mod_files('.')
from neuron import h
h.nrn_load_dll('./nrnmech.dll')
else: # Anything else.
call(['nrnivmodl'])
import neuron
neuron.load_mechanisms(
'.') # Auto loading. Not needed anymore.
from neuron import gui # to not freeze neuron gui
from neuron import h
logger.info("Loading model in %s from %s" % (model_dir, hoc_file))
h.load_file(hoc_file)
except Exception as e:
logger.warning("Error running model: " + e.message)
logger.info("Path changed back to %s" % old_dir)
os.chdir(old_dir)
return True
def load_mechanisms(path):
"""
Search for and load NMODL mechanisms from the path given.
This a stricter version of NEURON's own load_mechanisms function, which will
raise an IOError if no mechanisms are found at the given path. This function
will not load a mechanism path twice.
The path should specify the directory in which nrnivmodl was run, and in
which the directory 'i686' (or 'x86_64' or 'powerpc' depending on your
platform) was created.
"""
import platform
global nrn_dll_loaded
if path in nrn_dll_loaded:
logger.warning("Mechanisms already loaded from path: %s" % path)
return
# in case NEURON is assuming a different architecture to Python,
# we try multiple possibilities
arch_list = [platform.machine(), 'i686', 'x86_64', 'powerpc', 'umac']
for arch in arch_list:
lib_path = os.path.join(path, arch, '.libs', 'libnrnmech.so')
if os.path.exists(lib_path):
h.nrn_load_dll(lib_path)
nrn_dll_loaded.append(path)
return
raise IOError(
"NEURON mechanisms not found in %s. You may need to run 'nrnivmodl' in this directory."
% path)
def load_mod_files(self):
os.chdir(self.base_path)
libpath = "x86_64/.libs/libnrnmech.so.0"
os.system("nrnivmodl mechanisms") # do nrnivmodl in mechanisms directory
if not os.path.isfile(os.path.join(self.base_path, libpath)):
raise IOError("Error in compiling mod files!")
h.nrn_load_dll(str(libpath))
os.chdir(self.owd)
def load_custom_mechanisms():
if platform.system() == 'Windows':
mech_fname = op.join(op.dirname(__file__), '..', 'mod', 'nrnmech.dll')
else:
mech_fname = op.join(op.dirname(__file__), '..', 'mod', 'x86_64',
'.libs', 'libnrnmech.so')
h.nrn_load_dll(mech_fname)
print('Loading custom mechanism files from %s' % mech_fname)
def load_mod():
import fnmatch, os, platform
from neuron import h
# Mod files might have already been loaded, loading them again crashes NEURON
# Need to test if they've been loaded already
# I cannot find a NEURON function that lists loaded mechanisms, but...
# Trying to access them directly in Python results in an error - if the mechanism has been loaded
# The strategy here is to check if tryting to access those mod files throws that error
mod_files = [
file.replace('.mod', '') for file in os.listdir('.')
if file.endswith('.mod')
]
mod_loaded = False
for mod in mod_files:
try:
getattr(
h, mod
) # Results in TypeError if mod file has been loaded, else AttributeError
except AttributeError:
pass
except TypeError:
mod_loaded = True
break
# If none of the mod files have been loaded, load them
if not mod_loaded:
# First figure out where the compiled mod binaries are (platform dependent)
dll_path = None
target = "nrnmech.dll" if platform.system(
) == "Windows" else "libnrnmech.so"
try:
for root, dirnames, filenames in os.walk('.'):
for filename in fnmatch.filter(filenames, target):
dll_path = os.path.join(root, filename)
raise StopIteration() # Stop looking once found
except StopIteration:
pass
if dll_path is None:
raise Exception(
"Could not find compiled NEURON .mod files. Their compilation failed or they "
"are located somewhere else. Looked for " + target +
" here (inc. sub-dirs): " + os.getcwd())
# Load the mod files from the binary
from neuron import h
h.nrn_load_dll(dll_path)
def __init__(self, name="Golding"):
""" Constructor. """
modelpath = "./hippounit/models/hoc_models/Golding_dichotomy/fig08/"
libpath = "x86_64/.libs/libnrnmech.so.0"
if os.path.isfile(modelpath + libpath) is False:
os.system("cd " + modelpath + "; nrnivmodl")
h.nrn_load_dll(modelpath + libpath)
#self.dendA5_01111111100 = h.Section(name='foo', cell=self)
self.dendrite = None
self.name = "Golding"
self.threshold = -40
self.stim = None
self.soma = "somaA"
sciunit.Model.__init__(self, name=name)
self.c_step_start = 0.00004
self.c_step_stop = 0.000004
self.c_minmax = numpy.array([0.00004, 0.004])
self.dend_loc = [["dendA5_00", 0.275], ["dendA5_00", 0.925],
["dendA5_01100", 0.15], ["dendA5_01100", 0.76],
["dendA5_0111100", 0.115], ["dendA5_0111100", 0.96],
["dendA5_01111100", 0.38], ["dendA5_01111100", 0.98],
["dendA5_0111101", 0.06], ["dendA5_0111101", 0.937]]
self.trunk_dend_loc_distr = [["dendA5_01111111111111", 0.68],
["dendA5_01111111111111", 0.136],
["dendA5_01111111111111", 0.864],
["dendA5_011111111111111", 0.5],
["dendA5_0111111111111111", 0.5],
["dendA5_0111111111111", 0.786],
["dendA5_0111111111111", 0.5]]
self.trunk_dend_loc_clust = ["dendA5_01111111111111", 0.68]
self.AMPA_tau1 = 0.1
self.AMPA_tau2 = 2
self.start = 150
self.ns = None
self.ampa = None
self.nmda = None
self.ampa_nc = None
self.nmda_nc = None
self.ndend = None
self.xloc = None
def load_mechanisms(path=pyNN_path[0]):
# this now exists in the NEURON distribution, so could probably be removed
global nrn_dll_loaded
if path not in nrn_dll_loaded:
arch_list = [platform.machine(), 'i686', 'x86_64', 'powerpc']
# in case NEURON is assuming a different architecture to Python, we try multiple possibilities
for arch in arch_list:
lib_path = os.path.join(path, 'hoc', arch, '.libs',
'libnrnmech.so')
if os.path.exists(lib_path):
h.nrn_load_dll(lib_path)
nrn_dll_loaded.append(path)
return
raise Exception("NEURON mechanisms not found in %s." %
os.path.join(path, 'hoc'))
def __init__(self, hoc_model, path_mods, setting):
"""
Parameters
----------
hoc_model : str
the path to model in .hoc
path_mods : str
the path to the directory containing the .mod files
setting : dict
the dictionary containing setting
"""
self.setting = setting
h.nrn_load_dll(path_mods + 'nrnmech.dll')
h.xopen(hoc_model)
self.CA1 = h.CA1_PC_Tomko()
self.soma = self.CA1.soma[0]
self.all = list(self.CA1.all)
self.apical = list(self.CA1.apical)
self.basal = list(self.CA1.basal)
self.v_vec = h.Vector().record(self.soma(0.5)._ref_v)
self.t_vec = h.Vector().record(h._ref_t)
self.t_rs_vec = h.Vector().record(
h._ref_t, self.setting['simulation']['RECORDING_STEP'])
self.cai_vecs = {}
self.cal2_ica_vecs = {}
self.dend_vecs = {}
self.ina_vecs = {}
self.nmda_ica_vecs = {}
self.apc = None
self.apc_vec = h.Vector()
self.bcm = None
self.alpha_scout_vec = h.Vector()
self.d_vec = h.Vector()
self.p_vec = h.Vector()
self.syn_AMPA_count = 0
self.syn_NMDA_count = 0
self.synapses = {}
self.net_cons = []
self.net_stims = []
self.vBoxShape = None
self.shplot = None
def INIT_NEURON(reinit=False):
""" Initialise NEURON
- Compile mod files in `settings.MOD_PATH`. Files are recompiled if there are changes or
`settings.NEURON_RECOMPILE` is True.
- Load mod files into neuron
:param reinit:
:type reinit:
:return:
:rtype:
"""
global initialised, t_vec, __KWARGS__
if initialised and not reinit:
return True
else:
initialised = True
# compile mod files
if __mod_files_changed(settings.MOD_PATH) or settings.NEURON_RECOMPILE:
from src.utils.compile_mod import compile_mod
output = compile_mod(path=settings.MOD_PATH, mod=True)
if "Error" in str(output):
raise Exception("MOD FILES not compiled successfully")
# load mod files
h.nrn_load_dll(settings.NRNMECH_PATH)
# load hoc files including usefulFns.hoc
for hoc_file in glob.glob(settings.HOC_PATH + "/*.hoc"):
h.load_file(hoc_file.replace("\\", "/"))
# show GUI
if settings.NEURON_GUI:
# noinspection PyUnresolvedReferences
from neuron import gui
h.showRunControl()
# general properties
h.celsius = 37
h.v_init = -65
h.random_stream_offset_ = settings.RANDOM_STREAM_OFFSET
logger.info("celsius={} and v_init={}".format(h.celsius, h.v_init))
t_vec = h.Vector()
np.random.seed(settings.RANDOM_SEED)
# reset __KWARGS__
__KWARGS__ = {}
env_var(celsius=h.celsius, v_init=h.v_init)
def __init__(self):
#
self.model_scale = "cells"
self.model_name = "PC2015Masoli"
# check that the NEURON model is compiled if not compile
model_mod_path, model_lib_path = \
gmlp( model_scale = self.model_scale,
model_name = self.model_name )
ccm(model_mod_path, model_lib_path)
#print(model_mod_path, model_lib_path, os.getcwd())
#
# load NEURON model library
h.nrn_load_dll(model_lib_path)
#
# fixed time-step only
Fixed_step = h.CVode()
Fixed_step.active(0) #model doesn't work with variable time-step
#
# instantiate cell template
#cwd = os.getcwd()
#os.chdir(cwd + os.sep + "models" + os.sep + "cells" \
# + os.sep + "PC2015Masoli"
self.cell = Purkinje()
#os.chdir(cwd) # reset to original directory
#
# discover no.cores in 1CPU & activate multisplit to use all cores
dcam(h)
#
# =========attributed inherited from sciunit.Model===============
# pc.name defaults to class name, i.e, PurkinjeCell
self.name = "Masoli et al. 2015 model of PurkinjeCell"
self.description = "Masoli et al. 2015 model of PurkinjeCell (PC) and published in 10.3389/fncel.2015.00047 This is general PC model unlike special Z+ or Z- models. The model is based on adult (P90 or 3 months) Guinea pig. PC in younger ones are not mature and they grow until P90. This model is the SciUnit wrapped version of the NEURON model in modelDB accession # 229585."
#
# =========model predictions attached to the model object========
# Note: this is not part of inherited attributes from sciuni.Model
self.predictions = {} # added 21 Sept 2017
# =====save the predictions in model-predictions subfolders======
self.prediction_dir_path = cmdir( "model-predictions",
self.model_scale,
self.model_name )
# =====specify cell_regions from which you want predictions======
# created 22 Sept 2017
self.cell_regions = {"vm_soma": 0.0, "vm_NOR3": 0.0}
def load_custom_mechanisms():
import platform
import os.path as op
if _is_loaded_mechanisms():
return
if platform.system() == 'Windows':
mech_fname = op.join(op.dirname(__file__), 'mod', 'nrnmech.dll')
else:
mech_fname = op.join(op.dirname(__file__), 'mod', 'x86_64', '.libs',
'libnrnmech.so')
if not op.exists(mech_fname):
raise FileNotFoundError(f'The file {mech_fname} could not be found')
h.nrn_load_dll(mech_fname)
print('Loading custom mechanism files from %s' % mech_fname)
if not _is_loaded_mechanisms():
raise ValueError('The custom mechanisms could not be loaded')
def __init__(self, name="4 Compartments", model_dir="."):
sciunit.Model.__init__(self, name=name)
base_dir = os.path.abspath(model_dir)
mod_path = os.path.join(base_dir, "x86_64/.libs/libnrnmech.so.0")
hoc_path = os.path.join(base_dir, "mosinit.hoc")
if not os.path.isfile(mod_path):
os.system("cd " + base_dir + "; nrnivmodl NMODL")
sleep(2) # 2 seconds
while (not os.path.isfile(mod_path)):
# wait for nmodl compilation
sleep(1) # 1 second
# to supress hoc output from Jupyter notebook
save_stdout = sys.stdout
sys.stdout = open('/dev/stdout', 'w')
h.nrn_load_dll(mod_path)
h.load_file(hoc_path)
sys.stdout = save_stdout #setting output back to before
def load_mechanisms(path, mechname=None):
''' Rewrite of NEURON's native load_mechanisms method to ensure Windows and Linux compatibility.
:param path: full path to directory containing the MOD files of the mechanisms to load.
:param mechname (optional): name of specific mechanism to check for untracked changes
in source file.
'''
# Get OS
OS = platform.system()
# If Darwin, call native NEURON function and return
if OS == 'Darwin':
return load_mechanisms_native(path)
# Otherwise, get platform-dependent path to compiled library file
if OS == 'Windows':
lib_path = os.path.join(path, 'nrnmech.dll')
elif OS == 'Linux':
lib_path = os.path.join(path, platform.machine(), '.libs', 'libnrnmech.so')
else:
raise OSError('Mechanisms loading on "{}" currently not handled.'.format(platform.system()))
if not os.path.isfile(lib_path):
raise RuntimeError('Compiled library file not found for mechanisms in "{}"'.format(path))
# If mechanisms of input path are already loaded, return silently
global nrn_dll_loaded
if path in nrn_dll_loaded:
return
# If mechanism name is provided, check for untracked changes in source file
if mechname is not None:
mod_path = os.path.join(path, '{}.mod'.format(mechname))
if not os.path.isfile(mod_path):
raise RuntimeError('"{}.mod" not found in "{}"'.format(mechname, path))
if os.path.getmtime(mod_path) > os.path.getmtime(lib_path):
raise UserWarning('"{}.mod" more recent than compiled library'.format(mechname))
# Load library file and add directory to list of loaded libraries
h.nrn_load_dll(lib_path)
nrn_dll_loaded.append(path)
def __init__(self, name="Bianchi"):
""" Constructor. """
modelpath = "./hippounit/models/hoc_models/Ca1_Bianchi/experiment/"
libpath = "x86_64/.libs/libnrnmech.so.0"
if os.path.isfile(modelpath + libpath) is False:
os.system("cd " + modelpath + "; nrnivmodl")
h.nrn_load_dll(modelpath + libpath)
self.name = "Bianchi"
self.threshold = -20
self.stim = None
self.soma = "soma[0]"
sciunit.Model.__init__(self, name=name)
self.c_step_start = 0.00004
self.c_step_stop = 0.000004
self.c_minmax = numpy.array([0.00004, 0.004])
self.dend_loc = [[112, 0.375], [112, 0.875], [118, 0.167], [118, 0.99],
[30, 0.167], [30, 0.83], [107, 0.25], [107, 0.75],
[114, 0.01], [114, 0.75]]
self.trunk_dend_loc_distr = [[65, 0.5], [69, 0.5], [71,
0.5], [64, 0.5],
[62, 0.5], [60, 0.5], [81, 0.5]]
self.trunk_dend_loc_clust = [65, 0.5]
self.AMPA_tau1 = 0.1
self.AMPA_tau2 = 2
self.start = 150
self.ns = None
self.ampa = None
self.nmda = None
self.ampa_nc = None
self.nmda_nc = None
self.ndend = None
self.xloc = None
def __init__(self, name="Migliore"):
""" Constructor. """
modelpath = "./hippounit/models/hoc_models/Migliore_Schizophr/"
libpath = "x86_64/.libs/libnrnmech.so.0"
if os.path.isfile(modelpath + libpath) is False:
os.system("cd " + modelpath + "; nrnivmodl")
h.nrn_load_dll(modelpath + libpath)
self.name = "Migliore"
self.threshold = -20
self.stim = None
self.soma = "soma[0]"
sciunit.Model.__init__(self, name=name)
self.c_step_start = 0.00004
self.c_step_stop = 0.000004
self.c_minmax = numpy.array([0.00004, 0.004])
self.dend_loc = [[17, 0.3], [17, 0.9], [24, 0.3], [24, 0.7], [22, 0.3],
[22, 0.7], [25, 0.2], [25, 0.5], [30, 0.1], [30, 0.5]]
self.trunk_dend_loc_distr = [[10, 0.167], [10, 0.5], [10, 0.83],
[11, 0.5], [9, 0.5], [8, 0.5], [7, 0.5]]
self.trunk_dend_loc_clust = [10, 0.167]
self.AMPA_tau1 = 0.1
self.AMPA_tau2 = 2
self.start = 150
self.ns = None
self.ampa = None
self.nmda = None
self.ampa_nc = None
self.nmda_nc = None
self.ndend = None
self.xloc = None
def __init__(self, name="Kali"):
""" Constructor. """
modelpath = "./hippounit/models/hoc_models/Kali_Freund_modell/scppinput/"
libpath = "x86_64/.libs/libnrnmech.so.0"
if os.path.isfile(modelpath + libpath) is False:
os.system("cd " + modelpath + "; nrnivmodl")
h.nrn_load_dll(modelpath + libpath)
self.name = name
self.threshold = -20
self.stim = None
self.soma = "soma"
sciunit.Model.__init__(self, name=name)
self.c_step_start = 0.00004
self.c_step_stop = 0.000004
self.c_minmax = numpy.array([0.00004, 0.004])
self.dend_loc = [[80, 0.27], [80, 0.83], [54, 0.16], [54, 0.95],
[52, 0.38], [52, 0.83], [53, 0.17], [53, 0.7],
[28, 0.35], [28, 0.78]]
self.AMPA_tau1 = 0.1
self.AMPA_tau2 = 2
self.start = 150
self.ns = None
self.ampa = None
self.nmda = None
self.ampa_nc = None
self.nmda_nc = None
self.ndend = None
self.xloc = None
def load_compiled_mechanisms(path='precompiled'):
"""Loads precompiled mechanisms in pyDentate unless
path defines the full path to a compiled mechanism file."""
if path != 'precompiled':
h.nrn_load_dll(path)
else:
if platform.system() == 'Windows':
h.nrn_load_dll(windows_precompiled)
else:
h.nrn_load_dll(linux_precompiled)
import os
import numpy as np
from nrn_wrapper import Cell
from optimization.simulate import currents_given_v
from optimization.problems import CellFitProblem, get_channel_list, get_ionlist, convert_units
from optimization.linear_regression import linear_regression, plot_fit
__author__ = 'caro'
# TODO
from neuron import h
from optimization.problems import complete_mechanismdir
m_dir = '../../../model/channels/icgenealogy/Kchannels'
h.nrn_load_dll(complete_mechanismdir(m_dir))
m_dir = '../../../model/channels/icgenealogy/Nachannels'
h.nrn_load_dll(complete_mechanismdir(m_dir))
# parameter
save_dir = '../../../results/linear_regression/dapmodelnaka/'
n_trials = 1
params = {
'name': 'CellFitProblem',
'maximize': False,
'normalize': True,
'model_dir': '../../../model/cells/dapmodelnaka.json',
'mechanism_dir': '../../../model/channels/schmidthieber',
'variables': [],
'data_dir': '../../../data/2015_08_11d/merged/step_dap_zap.csv',
import os
import posix
import copy
import numpy as np
from ....trees.morphtree import MorphLoc
from ....trees.phystree import PhysTree, PhysNode
import neuron
from neuron import h
h.load_file("stdlib.hoc") # contains the lambda rule
h.nrn_load_dll(
os.path.join(os.path.dirname(__file__),
'x86_64/.libs/libnrnmech.so')) # load all mechanisms
# neuron.load_mechanisms(os.path.join(os.path.dirname(__file__),
# 'x86_64/.libs/libnrnmech.so')) # load all mechanisms
# mechanism_name_translation NEURON
class MechName(object):
def __init__(self):
self.names = {'L': 'pas', 'ca': 'CaDyn'}
def __getitem__(self, key):
if key in self.names:
return self.names[key]
else:
return 'I' + key
# 'TestChannel': 'ITestChannel', 'TestChannel2': 'ITestChannel2',
# 'h': 'Ih', 'h_HAY': 'Ih_HAY',
import sys
import h5py
import numpy as np
from matplotlib import pyplot as plt
from mpi4py import MPI
comm = MPI.COMM_WORLD
from neuron import h
from neuron import gui
pc = h.ParallelContext()
rank = int(pc.id())
size = int(pc.nhost())
h.nrn_load_dll('$i386/')
soma = h.Section()
soma.diam = 10
soma.L = 100 / (3.14 * soma.diam)
soma.insert('hh')
soma2 = h.Section()
soma2.diam = 10
soma2.L = 100 / (3.14 * soma2.diam)
soma2.insert('hh')
if (rank == 0):
stim = h.IClamp(.5)
stim.amp = 0.5
stim.dur = 0.1
def load_mod_files(self):
h.nrn_load_dll(self.modelpath + 'nrnmech.dll')
import sys, os
# Try standard locations to find neuron library
for nrnpath in ['/usr/local/nrn/lib/python']:
if os.path.isdir(nrnpath):
sys.path.append(nrnpath)
from neuron import h
import neuron
# try to load extra mechanisms
for name in ('i386', 'x86_64'):
mechlib = os.path.join(os.path.dirname(__file__),
name + '/.libs/libnrnmech.so')
print "NEURON load:", mechlib
if os.path.isfile(mechlib):
h.nrn_load_dll(mechlib)
h.celsius = 22
soma = h.Section()
soma.insert('hh')
soma.insert('pas')
#soma.insert('hcno')
soma.L = 20
soma.diam = 20
soma(0.5).pas.g = 2e-5
#soma(0.5).hcno.gbar = 15e-4
ic = h.IClamp(soma(0.5))
ic.dur = 1e9
ic.delay = 0
format='%(asctime)s %(funcName)s: %(message)s',
filemode='w')
logger = logging.getLogger('mb_model')
if sys.platform == 'win32':
os.environ['NEURONHOME'] = 'c:\\nrn'
sys.path += [
'c:\\nrn\\lib\\python', 'd:\\subhasis_ggn\\model\\common',
'd:\\subhasis_ggn\\model\\morphutils',
'd:\\subhasis_ggn\\model\\mb\\network'
]
# The mod files are in the directory `mod` and nrnmech.dll is created there
dll = os.path.join(os.path.dirname(__file__), 'mod', 'nrnmech.dll')
print('nrnmech', dll)
h.nrn_load_dll(dll)
else:
# os.environ['NEURONHOME'] = '/usr/local/apps/neuron/nrn-7.4/'
sys.path += [
'/home/rays3/projects/ggn/mb', '/home/rays3/projects/ggn/common',
'/home/rays3/projects/ggn/morphutils', '/home/rays3/projects/ggn/nrn',
'/home/rays3/projects/ggn/mb/network'
]
logger.info('sys.path={}'.format(str(sys.path)))
h.load_file('stdrun.hoc')
from pint import UnitRegistry
ur = UnitRegistry()
Q_ = ur.Quantity
def test_workflow(self):
#with self.subTest(stage="create"):
# run_cli_command("create test-project --overwrite")
if True:
network_path = "test-project"
if os.path.exists(network_path):
import shutil
shutil.rmtree(network_path)
os.mkdir(network_path)
os.chdir(network_path)
with self.subTest(stage="setup-parallel"):
os.environ["IPYTHONDIR"] = os.path.join(
os.path.abspath(os.getcwd()), ".ipython")
os.environ["IPYTHON_PROFILE"] = "Snudda_local"
os.system(
"ipcluster start -n 4 --profile=$IPYTHON_PROFILE --ip=127.0.0.1&"
)
time.sleep(10)
# with self.subTest(stage="init-parallel-BIG"):
# run_cli_command("init tiny_parallel --size 1000000 --overwrite")
# with self.subTest(stage="place-parallel-BIG"):
# run_cli_command("place tiny_parallel --parallel")
with self.subTest(stage="init-parallel"):
run_cli_command("init tiny_parallel --size 100 --overwrite")
# Lets reinit but a smaller network that contains all types of cells, to speed things up
with self.subTest(stage="small-reinit-1"):
config_name = os.path.join("tiny_parallel", "network-config.json")
cnc = SnuddaInit(struct_def={},
config_file=config_name,
random_seed=123456)
cnc.define_striatum(num_dSPN=4,
num_iSPN=4,
num_FS=2,
num_LTS=2,
num_ChIN=2,
volume_type="cube")
cnc.write_json(config_name)
with self.subTest(stage="place-parallel"):
run_cli_command("place tiny_parallel --parallel --raytraceBorders")
with self.subTest(stage="detect-parallel"):
run_cli_command("detect tiny_parallel --parallel")
with self.subTest(stage="prune-parallel"):
run_cli_command("prune tiny_parallel --parallel")
from shutil import copyfile
print(f"listdir: {os.listdir()}")
print(f"parent listdir: {os.listdir('..')}")
input_file = os.path.join(os.path.dirname(__file__), os.path.pardir,
"snudda", "data", "input_config",
"input-v10-scaled.json")
copyfile(input_file, os.path.join("tiny_parallel", "input.json"))
with self.subTest(stage="input"):
run_cli_command(
"input tiny_parallel --input tiny_parallel/input.json --parallel"
)
# with self.subTest(stage="init-parallel-full"):
# run_cli_command("init large_parallel --size 1670000 --overwrite")
# with self.subTest(stage="place-parallel-full"):
# run_cli_command("place large_parallel --parallel")
with self.subTest(stage="parallel-stop"):
os.system("ipcluster stop")
# Only serial tests below this line, we stopped ipcluster.
with self.subTest(stage="simulate"):
print("Running nrnivmodl:")
mech_dir = os.path.join(os.path.dirname(__file__), os.path.pardir,
"snudda", "data", "neurons", "mechanisms")
if not os.path.exists("mechanisms"):
print("----> Copying mechanisms")
# os.symlink(mech_dir, "mechanisms")
from distutils.dir_util import copy_tree
copy_tree(mech_dir, "mechanisms")
else:
print("-------------> !!! mechanisms already exists")
eval_str = f"nrnivmodl mechanisms" # f"nrnivmodl {mech_dir}
print(f"Running: {eval_str}")
os.system(eval_str)
# print("---> Testing to run simulate using os.system instead")
# os.system("snudda simulate tiny_parallel --time 0.1 --voltOut default")
# For the unittest we for some reason need to load mechansism
# separately
from mpi4py import MPI # This must be imported before neuron, to run parallel
from neuron import h # , gui
import neuron
# For some reason we need to import modules manually
# when running the unit test.
if os.path.exists("x86_64/.libs/libnrnmech.so"):
print("!!! Manually loading libraries")
try:
h.nrn_load_dll("x86_64/.libs/libnrnmech.so")
except:
import traceback
tstr = traceback.format_exc()
print(tstr)
if False:
try:
from snudda.simulate.simulate import SnuddaSimulate
ss = SnuddaSimulate(network_path="tiny_parallel")
ss.run(100)
ss.write_spikes()
except:
import traceback
tstr = traceback.format_exc()
print(tstr)
import pdb
pdb.set_trace()
print("Time to run simulation...")
run_cli_command(
"simulate tiny_parallel --time 0.1 --voltOut default")
os.environ["SLURM_JOBID"] = "1234"
with self.subTest(stage="init-serial"):
# Remove the old folder if it exists
if os.path.exists("tiny_serial"):
import shutil
shutil.rmtree("tiny_serial")
run_cli_command("init tiny_serial --size 100 --profile")
with self.subTest(stage="init-overwrite-fail"):
# Should not allow overwriting of existing folder if --overwrite is not specified
self.assertRaises(AssertionError, run_cli_command,
"init tiny_serial --size 100")
# Again, let us reinit to a smaller network to speed things up
with self.subTest(stage="small-reinit-2"):
config_name = os.path.join("tiny_serial", "network-config.json")
cnc = SnuddaInit(struct_def={},
config_file=config_name,
random_seed=1234)
cnc.define_striatum(num_dSPN=3,
num_iSPN=3,
num_FS=2,
num_LTS=2,
num_ChIN=2,
volume_type="cube")
cnc.write_json(config_name)
with self.subTest(stage="place-serial"):
run_cli_command("place tiny_serial --h5legacy")
with self.subTest(stage="detect-serial"):
run_cli_command(
"detect tiny_serial --volumeID Striatum --hvsize 120 --randomseed 123 --verbose --h5legacy"
)
with self.subTest(stage="detect-serial-cont"):
run_cli_command(
"detect tiny_serial --volumeID Striatum --hvsize 120 --cont --h5legacy"
)
with self.subTest(stage="prune-serial"):
run_cli_command("prune tiny_serial --h5legacy")
input_file = os.path.join(os.path.dirname(__file__), os.path.pardir,
"snudda", "data", "input_config",
"input-v10-scaled.json")
copyfile(input_file, "tiny_serial/input.json")
with self.subTest(stage="input"):
run_cli_command(
"input tiny_serial --time 1.0 --inputFile tiny_serial/input-spikes.hdf5"
)
def compile_load_mod_files(self):
if not os.path.isfile(self.lib_path):
os.system("cd " + self.mod_files_path + "; nrnivmodl")
h.nrn_load_dll(str(self.lib_path))
from neuron import h
h.nrn_load_dll("E:\\Google Drive\\Github\\Spinal-Cord-Modeling\\nrnmech.dll")
import helper_functions as hf
from Ia_template import Ia
from Mn_template import Mn
class Ia_network:
def __init__(self, N = 2, syn_w = 0.15, syn_delay = 1):
self._N = N;
self.cells = [] # Cells in the net
self.nclist = [] # NetCon list
self.syn_w = syn_w # Synaptic weight
self.syn_delay = syn_delay # Synaptic delay
self.t_vec = h.Vector() # Spike time of all cells
self.id_vec = h.Vector() # Ids of spike times
self.set_numcells(N) # Actually build the net.
#
def set_numcells(self, N):
"""Create, layout, and connect N cells."""
self._N = N
self.create_cells(N)
self.connect_cells()
#
def create_cells(self, N):
"""Create and layout N cells in the network."""
self.cells = []
r = 50 # Radius of cell locations from origin (0,0,0) in microns
N = self._N
position_factor = 5e3;
sim_params = hf.get_net_params(hf.get_tempdata_address())
from neuron import h
h.nrn_load_dll("E:\\Google Drive\\Github\\Spinal-Cord-Modeling\\nrnmech.dll")
import helper_functions as hf
from Ia_template import Ia
from Mn_template import Mn
class Ia_network:
def __init__(self, N=2, syn_w=0.15, syn_delay=1):
self._N = N
self.cells = [] # Cells in the net
self.nclist = [] # NetCon list
self.syn_w = syn_w # Synaptic weight
self.syn_delay = syn_delay # Synaptic delay
self.t_vec = h.Vector() # Spike time of all cells
self.id_vec = h.Vector() # Ids of spike times
self.set_numcells(N) # Actually build the net.
#
def set_numcells(self, N):
"""Create, layout, and connect N cells."""
self._N = N
self.create_cells(N)
self.connect_cells()
#
def create_cells(self, N):
"""Create and layout N cells in the network."""
self.cells = []
r = 50 # Radius of cell locations from origin (0,0,0) in microns
N = self._N
def load_mechanism_dir(mechanism_dir):
h.nrn_load_dll(complete_mechanismdir(str(mechanism_dir)))
"dentategyrusnet2005\\nrnmech.dll"),
"C:\\Users\\daniel\\Repos\\nrnmech.dll",
("C:\\Users\\Holger\\danielm\\models_dentate\\"
"dentate_gyrus_Santhakumar2005_and_Yim_patterns\\"
"dentategyrusnet2005\\nrnmech.dll"),
("C:\\Users\\Daniel\\repos\\"
"dentate_gyrus_Santhakumar2005_and_Yim_patterns\\"
"dentategyrusnet2005\\nrnmech.dll"),
("/home/daniel/repos/pyDentate/mechs_7-6_linux/"
"x86_64/.libs/libnrnmech.so")]
for x in dll_files:
if os.path.isfile(x):
dll_dir = x
print("DLL loaded from: " + dll_dir)
h.nrn_load_dll(dll_dir)
# Seed the numpy random number generator for replication
np.random.seed(seed)
# Randomly choose target cells for the PP lines
gauss_gc = stats.norm(loc=1000, scale=input_scale)
gauss_bc = stats.norm(loc=12, scale=(input_scale / 2000.0) * 24)
pdf_gc = gauss_gc.pdf(np.arange(2000))
pdf_gc = pdf_gc / pdf_gc.sum()
pdf_bc = gauss_bc.pdf(np.arange(24))
pdf_bc = pdf_bc / pdf_bc.sum()
GC_indices = np.arange(2000)
start_idc = np.random.randint(0, 1999, size=400)
PP_to_GCs = []
## So now we take the TEP model from first_tep.py where we really jsut used the defautl model times 3
# and we add predictions. we ant to see what happens when a tap comes in at certain delays after the pulse
#-------------------------------------
#Init
#-------------------------------------
from neuron import h
h.nrn_load_dll('C:\\Users\\ckohl\\Miniconda3\\Lib\\site-packages\\hnn_core\\nrnmech.dll')
import os.path as op
from hnn_core import simulate_dipole, Params, Network, read_params
import json
import numpy as np
import matplotlib.pyplot as plt
import sys
sys.path.append('C:\\Users\\ckohl\\Desktop\\Current\\TMS\\git-TEP_Analysis\\hnn_core_for_TEP')
import my_hnn_core_functions as m
from pptx import Presentation #https://python-pptx.readthedocs.io/en/latest/user/quickstart.html
from pptx.util import Inches
saving_dpl=False
my_param_out_dir='C:\\Users\\ckohl\\hnn_out\\'
dump_dir="C:\\Users\\ckohl\\Desktop\\Current\\TMS\\Core output"
#-------------------------------------
#PPT init
#-------------------------------------
left = 0
top=Inches(0.25)
# -*- coding: utf-8 -*-
"""
Created on Thu Jan 04 15:26:50 2018
@author: DanielM
"""
from neuron import h, gui
import numpy as np
import matplotlib.pyplot as plt
from pyDentate.mossycell_cat import MossyCell
from pyDentate.basketcell import BasketCell
h.nrn_load_dll("C:\\Users\\DanielM\\Repos\\models_dentate\\dentate_gyrus_Santhakumar2005_and_Yim_patterns\\dentategyrusnet2005\\nrnmech.dll")
stim_periods = [1000, 100, 33, 20]
for period in stim_periods:
"""Setup stimulation pattern"""
t_pattern = np.arange(100, 100+10*period, period)
vecstim = h.VecStim()
pattern_vec = h.Vector(t_pattern)
vecstim.play(pattern_vec)
"""Setup tmgsyn"""
mc_tmgsyn = MossyCell()
mc_tmgsyn_syn = h.tmgsyn(mc_tmgsyn.all_secs[1](0.5))
mc_tmgsyn_syn.e = 0
mc_tmgsyn_syn.tau_facil = 0 # This parameter gives the frequency dependence of facilitation
mc_tmgsyn_syn.tau_1 = 6.2
