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# 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

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# 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:

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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'

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import sympy as sm
import lark

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

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import os
import time
import json
import requests
import rtmidi

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

ports = midi.get_ports()

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

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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()

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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

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• Shape(ptr)
• array_polar(shape, n, center=(0, 0))

  Iterates a shape about an optional center position

• array_polar_z(shape, n, center=(0, 0))

  Iterates a shape about an optional center position

• array_x(shape, nx, dx)

  Iterates a part in a 1D array

• array_xy(shape, nx, ny, delta)

  Iterates a part in a 2D array

• array_xyz(shape, nx, ny, nz, delta)

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# Adapted from https://hodgkin-huxley-tutorial.readthedocs.io/en/latest/_static/Hodgkin%20Huxley.html

%matplotlib inline

import numpy as np
import matplotlib.pyplot as plt
from scipy.integrate import solve_ivp

C_m  =   1.0
g_Na = 120.0