russelljjarvis

FROM jupyter/base-notebook
USER root
RUN apt update
RUN apt install -y git
USER jovyan
WORKDIR $HOME
RUN conda install -c conda-forge micromamba
RUN conda install poetry matplotlib pandas jupyterlab
RUN git clone https://github.com/lava-nc/lava.git
WORKDIR lava

russelljjarvis

#!/usr/bin/env python
# coding: utf-8
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from tqdm.notebook import tqdm
import navis
import pickle
import os
import navis

russelljjarvis

##
# Install from:
# https://geomdata.gitlab.io/hiveplotlib/basic_usage.html
##

from hiveplotlib import hive_plot_n_axes
from hiveplotlib.converters import networkx_to_nodes_edges
from hiveplotlib.viz import hive_plot_viz_mpl
from matplotlib.lines import Line2D
import networkx as nx

russelljjarvis

using SpikingNN
using Distributions
using Distributions: sample


"""

This model/code works with the standard Pkg.add("SpikingNN.jl") it does not work with the other git branches such as refactor/kd which 
may have more recent code added)

russelljjarvis

ENV["PYTHON"] = "/opt/conda/bin/python"

using Conda
using ModernGL
using PyCall;

pushfirst!(PyVector(pyimport("sys")["path"]),"")
pushfirst!(PyVector(pyimport("sys")["path"]),"/opt/conda/bin/python")
pushfirst!(PyVector(pyimport("sys")["path"]),"/home/jovyan/neuronunit")

russelljjarvis

from deap import tools
def _get_offspring_time_diminishing_eta(parents, toolbox, cxpb, mutpb,gen, ngen):
	'''return the offspring, use toolbox.variate if possible'''


	BOUND_LOW = []
	BOUND_UP = []
	NDIM = len(parents[0])
	fit_dim = len(parents[0].fitness.values)
	for x in range(0,len(parents[0])):

russelljjarvis

from typing import Any, Dict, List, Optional, Tuple, Type, Union, Text

import pickle
import seaborn as sns
import os
import copy
import numpy as np
from collections.abc import Iterable
import pandas as pd
import quantities as pq

russelljjarvis

if (localStorage.getItem("localnet") === null) {
    network = drawGraph();
    localStorage.setItem('localnet', JSON.stringify(network));

}else{
    network = localStorage.getItem('localnet')

russelljjarvis

'''
Author information. This is an extension to the Utils class from Allen Brain API. 
The parallel wiring related functions are written by Russell Jarvis [email protected]
'''


from allensdk.model.biophys_sim.neuron.hoc_utils import HocUtils
import logging
import glob
from mpi4py import MPI

russelljjarvis

import numpy as np
import matplotlib.pyplot as plt
import scipy.stats as scs

def z_val(sig_level=0.05, two_tailed=True):
    """Returns the z value for a given significance level"""
    z_dist = scs.norm()
    if two_tailed:
        sig_level = sig_level/2
        area = 1 - sig_level