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Lennart Landsmeer llandsmeer

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llandsmeer / ledfxmidi.py
Created September 23, 2022 22:37
Control LedFX using midi controller
import os
import time
import json
import requests
import rtmidi
# pip install python-rtmidi
midi = rtmidi.MidiIn()
ports = midi.get_ports()
@llandsmeer
llandsmeer / arbor_nmodl_to_sympy_v1.py
Created September 27, 2022 06:27
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
llandsmeer / single_file_custom_catalogue_arbor.py
Created September 28, 2022 08:06
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
llandsmeer / arbor_test_sde.py
Last active September 28, 2022 09:48
# 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
llandsmeer / Dockerfile
Created October 17, 2022 14:48
Arbor GUI in the browser via noVNC
# 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
llandsmeer / main.py
Last active November 16, 2022 23:53
Class-based custom mechanisms for arbor in python and C++ (DONT TRY THIS AT HOME!)
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
llandsmeer / npio.py
Created November 28, 2022 13:40
Single file numpy implementation of IO network
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
llandsmeer / arbor_as_ode_solver_lorenz.py
Last active November 30, 2022 14:33
Arbor as an arbitrary ODE solver
import arbor
import re
import subprocess
import tempfile
import pathlib
import matplotlib.pyplot as plt
nmodl = '''
NEURON {
SUFFIX node
@llandsmeer
llandsmeer / plot_benchmark_runtimes.py
Created December 2, 2022 11:44
iotf single benchmark plotter
import collections
import pandas as pd
import matplotlib.pyplot as plt
logfile = '<path to benchmark output.dat>'
tables = collections.defaultdict(list)
def tryfloat(x):
# the argument can be a float or
@llandsmeer
llandsmeer / Cell_type_0_code.gen.c
Created December 16, 2022 11:30
EDEN output for L5PC
// Generated code block BEGIN
#define M_PI 3.14159265358979323846
#include <math.h>
typedef float * __restrict__ __attribute__((align_value (32))) Table_F32;
typedef long long * __restrict__ __attribute__((align_value (32))) Table_I64;
typedef union { int i32; float f32; } TypePun_I32F32; typedef char static_assert[ sizeof(int) == sizeof(float) ];
static float EncodeI32ToF32( int i ){ TypePun_I32F32 cast; cast.i32 = i; return cast.f32;}
static int EncodeF32ToI32( float f ){ TypePun_I32F32 cast; cast.f32 = f; return cast.i32;}
static float stepf( float x ){ if( x < 0 ) return 0; else return 1; }