llandsmeer

import numpy as np
import matplotlib.pyplot as plt
import numba
import time

NUM_STATE_VARS = 14

def main():
    n = 5
    s = make_initial_neuron_state(n ** 3, V_soma=None, V_axon=None)

llandsmeer

import sys
sys.path.insert(0, '/home/llandsmeer/repos/llandsmeer/arbor/build-debug/prefix/lib/python3.10/site-packages')
sys.path.append('/home/llandsmeer/repos/llandsmeer/nmlcc-cat')

import arbor
import matplotlib.pyplot as plt

import nmlcat

cat = nmlcat.Catalogue.make()

llandsmeer

# docker build -t arbor-gui . && docker run -it -p 5999:5999 arbor-gui
# then visit http://localhost:5999/vnc.html?host=localhost&port=5999&autoconnect=true

FROM ubuntu:latest
EXPOSE 5999

ENV DEBIAN_FRONTEND=noninteractive
RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections
ENV TZ=Europe/Amsterdam
RUN apt-get update && apt-get install -y xvfb x11vnc wget novnc git wmctrl

llandsmeer

# git clone --depth 1 --recursive --branch=SDE 'https://github.com/boeschf/arbor'
# cd arbor ; mkdir build ; cd build
# cmake -DCMAKE_INSTALL_PREFIX=$(realpath prefix) -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_PYTHON=ON ..
# make -j 12 && make install

import sys
import importlib.util
import os.path

#### IF INSTALLED USING PIP:

llandsmeer

import os.path
import numpy as np
import re
import subprocess
import tempfile
import arbor
from math import sqrt
import matplotlib.pyplot as plt

ARBOR_BUILD_CATALOGUE = 'arbor-build-catalogue'

llandsmeer

import sympy as sm
import lark

parser = lark.Lark(r'''
%import common.SIGNED_NUMBER    -> NUMBER
%import common.WS
%ignore WS
%ignore /\?.*\n/
%ignore /:.*\n/

llandsmeer

import os
import time
import json
import requests
import rtmidi

# pip install python-rtmidi
midi = rtmidi.MidiIn()

ports = midi.get_ports()

llandsmeer

import sys
import pyte
import struct
import select
import time
import fcntl
import os
import pty
import subprocess
import termios

llandsmeer

import sys
import numpy as np
from PyQt5 import QtGui, QtWidgets, QtCore

class MainWindow(QtWidgets.QMainWindow):
    def __init__(self):
        super().__init__()
        self.imshow = Grayscale()
        self.setCentralWidget(self.imshow)
        self.update_timer = QtCore.QTimer()

llandsmeer

import matplotlib.pyplot as plt
import numba
import numpy as np

@numba.jit(fastmath=True, cache=True, nopython=True)
def simulate(skip_initial_transient_seconds=0, sim_seconds=10, delta=0.005, record_every=20,
    # Parameters
    g_int           =   0.13,    # Cell internal conductance  -- now a parameter (0.13)
    p1              =   0.25,    # Cell surface ratio soma/dendrite
    p2              =   0.15,    # Cell surface ratio axon(hillock)/soma