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# https://chat.openai.com/c/cff8e0fc-20df-4425-9e2b-7aa8228ab7a1

## Install ffmpeg on RHEL8: https://www.benholcomb.com/ffmpeg-on-rhel8/
## After that
# sudo yum install python3-devel

## Create virtual environment
# python3 -m venv path/to/venv
# cd path/to/venv
# bin/activate

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Dialog.create("pTIRF movie creator");
Dialog.addNumber("Time interval between frames", 500, 0, 6, "ms");
Dialog.addNumber("Brightness/contrast: black level", 400, 0, 6, "counts");
Dialog.addNumber("Brightness/contrast: white level", 1000, 0, 6, "counts");
Dialog.addNumber("Time point of injection", 10, 1, 6, "s");
Dialog.show();

exp_time = Dialog.getNumber() / 1000.0;
low = Dialog.getNumber();
high = Dialog.getNumber();

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#!/usr/bin/env python
# Implementation of algorithm from http://stackoverflow.com/a/22640362/6029703
import numpy as np
import pylab

def thresholding_algo(y, lag, threshold, influence):
    signals = np.zeros(len(y))
    filteredY = np.array(y)
    avgFilter = [0]*len(y)
    stdFilter = [0]*len(y)

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#!/usr/bin/env python
# coding: utf-8

import skimage.io as skio
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from os.path import basename, splitext, exists
from time import sleep
from os import listdir

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function [ax,AxisPos] = subplotTight(nRow, nCol, varargin)
% subplotTight  faster version of subplot with tight plot spacing
%

% https://www.mathworks.com/matlabcentral/answers/16458-making-less-space-between-figures-in-subplot


%% Process input arguments
narginchk(2,Inf);
nargoutchk(0,1);

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#!/bin/bash

# Adapted from https://stackoverflow.com/a/52543399/6029703

if [ "$#" -gt 2  -o  "$#" -lt 1 ]; then
    echo "********************************************************************"
    echo "*                        Knitter version 1.1                       *"
    echo "********************************************************************"
    echo -e "This script converts Rmd files into HTML (default) or PDFs. \n"
    echo -e "usage: knitter file.Rmd [output_format] \n"

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// This creates an external pulse source for an Arduino board - useful for timer debugging!

/* python

from time import sleep
from serial import Serial
from ctypes import c_uint32
from avrpy.mega328P import Mega328P

avr = Mega328P("COM6")

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#include <stdint.h>
#include <Arduino.h>
#ifndef _AVR_IOXXX_H_
#include <avr/iom328.h> // Arduino Uno uses AtMega328p microchip
#endif

uint32_t us2cts(uint32_t us)
{
    return us >> 2;
}

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#define uchar unsigned char

void setup_timer_counter_1(){
  /* TCCR1: Timer Counter Control Register */
  //                 bit 7      6      5      4      3     2    1     0
  uchar _TCCR1A = 0;  // COM1A1 COM1A0 COM1B1 COM1B0 -     -    WGM10 WGM11
  uchar _TCCR1B = 0;  // ICNC1  ICES1  -      WGM13  WGM12 CS12 CS11  CS10
  uchar _TCCR1C = 0;  // FOC1A  FOC1B  -      -      -     -    -     -

  // Set COM (Compare Output Mode) for pins OC1A (#9) and OC1B (#10)

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# Video encoding. Arguments to ffmpeg should be passed in quotes
# Example
#  ls *.avi | ff_avi2webm "-filter:v 'crop=in_w-100:in_h/2'"

ff_any2webm(){
  parallel ffmpeg -i {} $1 -c:v vp9 {.}.webm
}

ff_whatsapp(){
  # Convert specified videos to mp4 that are compatible with whatsapp