APqrPID3.cpp

/*
 Copyright (C) 2011 Georgia Institute of Technology

 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.

 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.

 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.

 */

/*
	In this version, output(0) is used to control a 470 nm LED to have depolarizing effect (e.g. by activating 
	Cheriff) and output(1) is used to control a 617 nm LED to have depolarizing effect (e.g. Jaws).
	This version makes use of a new concept, namely that of the PID-controller, where output is regulated based on
	present information (P), past infromation (I) and expected information (D)

	
 */

#include <APqrPID3.h>
#include <math.h>
#include <vector>

/*
 ************
 * APqrPID3 *
 ************

This software provides an Action Potential Cure (APqr) to correct divergent
membrane potentials in excitable biological systems. The first X action
potentials are logged when the software starts, after which AP correction
starts from the (X+1)-st AP onwards. This correction occurs with the use of
LED-controlled illumination on optogenetically modified cells.

IN:
	*) Cm				Capacitance of the cell
	*) V_cutoff			Threshold potential for the detection of the beginning
						of an AP
	*) Slope_tresh		Slope threshold that defines the beginning of the
						AP (mV/ms)
	*) BCL_cutoff		Threshold value for the end of an AP, given as a
						percentage of the total APD
	*) lognum			Number of APs that need to be logged as a reference
	*) Rm				Initial resistance
	*) Rm_corr_up		Factor to increase Rm with when necessary
	*) Rm_corr_down		Factor to decrease Rm with when necessary
	*) noise_tresh		The noise level that is allowed around the ideal value
						before correcting
OUT:
	*) Vout 			voltage that is used to inject the calculated amount
						of current into the excitable system
*/

/*
createRTXIPlugin
----------------
Creation of a new RTXI Plugin

IN:
	*) None
OUT:
	*) RTXIPlugin
*/
extern "C" Plugin::Object *createRTXIPlugin(void)
{
	return new gAPqrPID3();
}

static DefaultGUIModel::variable_t vars[] = {
	{ "Vm (mV)", "Membrane potential (mV)", DefaultGUIModel::INPUT, },
	{ "VLED1", "Output for LED driver", DefaultGUIModel::OUTPUT, },
	{ "VLED2", "Output for LED driver", DefaultGUIModel::OUTPUT, },	
	{ "iAP", "ideal AP", DefaultGUIModel::STATE, },
	{ "V_cutoff (mV)", "Threshold potential for the detection of the beginning of an AP, together with Slope_thresh", 
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "Slope_thresh (mV/ms)", "SLope threshold that defines the beginning of the AP (mV/ms)",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "BCL_cutoff (pct)", "Threshold value for the end of an AP, given as a percentage of the total APD",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "Rm_blue (MOhm)", "MOhm", DefaultGUIModel::PARAMETER
	| DefaultGUIModel::DOUBLE, },
	{ "Rm_red (MOhm)", "MOhm", DefaultGUIModel::PARAMETER
	| DefaultGUIModel::DOUBLE, },
	{ "lognum", "Number of APs that need to be logged as a reference", DefaultGUIModel::PARAMETER
	| DefaultGUIModel::DOUBLE, },
	{ "Correction start", "iAP count (index+1) when correction starts",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "Blue_Vrev", "Apparent reversal potential of the 'blue' ChR current",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "K_p", "Scale factor for the proportional part of the PID",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "K_i", "Scale factor for the integral part of the PID",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "K_d", "Scale factor for the derivative part of the PID",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "length", "Amount of points that need to be taken into account to find the derivative (slope of the linear trend line of these points)",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "PID_tresh", "treshold value under which the same output as before gets repeated",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "min_PID", "value under which the lights get switched off",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "reset_I_on", "value that indicates whetehr or not to reset I at RMP",
	DefaultGUIModel::PARAMETER | DefaultGUIModel::DOUBLE, },
	{ "Vm2 (mV)", "Membrane potential (mV)", DefaultGUIModel::STATE, },
	{ "P", "P term", DefaultGUIModel::STATE, },
	{ "I", "I term", DefaultGUIModel::STATE, },
	{ "D", "D term", DefaultGUIModel::STATE, },
	{ "PID", "PID term", DefaultGUIModel::STATE, },
	{ "Period (ms)", "Period (ms)", DefaultGUIModel::STATE, }, 
	{ "Time (ms)", "Time (ms)", DefaultGUIModel::STATE, },
	{ "APs2", "APs", DefaultGUIModel::STATE, },
	{ "log_ideal_on2", "log_ideal_on", DefaultGUIModel::STATE, },
	{ "BCL2", "BCL", DefaultGUIModel::STATE, },
	{ "enter2", "enter", DefaultGUIModel::STATE, },
	{ "act2", "0 or 1", DefaultGUIModel::STATE, },
	{ "count", "number", DefaultGUIModel::STATE, },
	{ "count2", "number", DefaultGUIModel::STATE, },
	{ "modulo_state", "number", DefaultGUIModel::STATE, },
};

/*
num_vars
--------
variable denoting the amount of variables that is displayed in the GUI
*/
static size_t num_vars = sizeof(vars) / sizeof(DefaultGUIModel::variable_t);

/*
gAPqrPID3
------
This function constructs the actual GUI by basing itself on the Default GUI Model.
It creates a module with a name, initializes the GUI, initializes the parameters,
adds a refresh, and allows you to resize.

IN:
	*) None
OUT:
	*) None
*/
gAPqrPID3::gAPqrPID3(void) : DefaultGUIModel("APqrPID3", ::vars, ::num_vars)
{
	setWhatsThis(
		"<p><b>APqr:</b><br>APqrPID3 </p>");
	DefaultGUIModel::createGUI(vars, num_vars);
	initParameters();
	update(INIT);
	refresh();
	resizeMe();
}

gAPqrPID3::~gAPqrPID3(void){}

/*
cleanup
-------
The APqr software makes use of three list structures which need cleaning after
a reset of parameters. The cleanup function takes care of this.

IN:
	*) None
OUT:
	*) None
*/
void gAPqrPID3::cleanup()
{
	for(i=0;i<10000;i++){
		Vm_log[i]=0;
		Vm_diff_log[i]=0;
		ideal_AP[i]=0;
	}
}

double gAPqrPID3::sumy(double arr[], int n, double length, double modulo)
{
    double sumy = 0; // initialize sum
 
    // Iterate through all elements
    // and add them to sum
    for (int i = n-length+1 ; i < n+1; i++)
    sumy += arr[i % (int)modulo];
 
    return sumy;
}

double gAPqrPID3::sumxy(double arr[], int n, double length, double period, double modulo)
{
    double sumxy = 0; // initialize sum
	int j = 0;

    // Iterate through all elements
    // and add them to sum
    for (int i = n-length+1 ; i < n+1; i++)
    {
		sumxy += arr[i % (int)modulo] * (j*period);
		j++;
	}
 
    return sumxy;
}

double gAPqrPID3::sumx(double period, double length)
{
	double sumx = 0;

	for (int i = 0; i<length; i++)
	sumx += i*period;

	return sumx;
}

double gAPqrPID3::sumx2(double period, double length)
{
	double sumx2 = 0;

	for (int i = 0; i<length; i++)
	sumx2 += i*period*i*period;

	return sumx2;
}

void gAPqrPID3::execute(void)
{
	systime = count * period;	// time in milli-seconds
	Vm = input(0) * 1e2;		// convert 10V to mV. Divided by 10 because
								// the amplifier produces 10-fold amplified
								// voltages. Multiplied by 1000 to convert
								// V to mV.

	Vm_log[count % (int)modulo] = Vm;	// Logging the measured Vm in a list
										// where the modulo component makes
										// sure you keep cycling when you have
										// reached the maximum number in the list.

	// ****************************
	// ****************************
	// ** Recording the ideal AP **
	// ****************************
	// ****************************
	if(count>(int)(1/period)-1 && (Vm - Vm_log[(count-(int)(1/period)) % (int)modulo]) >= slope_thresh && APs<lognum && enter == 0 && Vm > V_cutoff)
	{
		// This statement is entered whenever an upstroke is detected and the amount of
		// recorded APs is smaller than lognum.
		// The if conditions measure the following:
		// 1) Whether you are far enough in the recording such that you don't accidentaly
		//    start in an ongoing AP
		// 2) Whether two consecutive measuring points show a large enough slope that can
		//    be identified with an upstroke
		// 3) Whether less than lognum APs were recorded
		// 4) Whether you are currently not in an action potential
		// 5) Whether the mesured voltage is above a voltage treshold

		BCL = (APs==-1? 0: (BCL*APs + count2)/(APs+1)); // Rolling average of the basic cycle length
		log_ideal_on = 1; // Switches on logging the AP
		count2 = 0; // Resets the logging counter
		enter = 1; // Switches on the indicator that an AP has started
		APs++; // Counts the AP upstrokes that have passed
	}

	if((Vm - Vm_log[(count-(int)(1/period)) % (int)modulo]) < 0 && enter == 1)
	{
		// This statement is entered whenever the upstroke phase of an AP is over.
		// The if conditions measure the following:
		// 1) Whether two consecutive measuring points show a negative slope
		// 2) Whether you currently are in an ongoing AP

		enter = 0; // Switches off the indicator that an AP has started
	}

	if(APs<lognum && log_ideal_on == 1)
	{
		// This statement is entered whenever logging of the AP is on
		// The if conditions measure the following:
		// 1) Whether less than lognum APs were recorded
		// 2) Whether the AP should be logged

		ideal_AP[count2] = (ideal_AP[count2]*APs + Vm)/(APs+1); // Rolling average of the AP values
		count2++; // Increasing the logging counter
	}
	
	// ****************************
	// ****************************
	// ** Detecting AP upstrokes **
	// ****************************
	// ****************************
	if (act == 0 && (Vm - Vm_log[(count-(int)(1/period)) % (int)modulo]) >= slope_thresh && APs >= lognum && Vm > V_cutoff)
	{
		// This statement is entered whenever an upstroke is detected after the
		// ideal APs have been recorded.
		// The if conditions measure the following:
		// 1) Whether currently nothing is being done or corrected
		// 2) Whether two consecutive measuring points show a large enough slope that can
		//    be identified with an upstroke
		// 3) Whether lognum APs were already recorded before
		// 4) Whether the mesured voltage is above a voltage treshold

		count = 0; // Reset the correction counter
		act = 1; // Switch the correction on
	}

	// Part of the code that implements the PID
	if (act == 1)
	{
		iAP = ideal_AP[count];
		Vm_diff_log[count] = Vm - ideal_AP[count];
		if (VLED < 5 && (Vm < blue_Vrev || Vm_diff_log[count] > 0)) //this line was modified so that Int is only calculated when the output has not reached its maximum (5V) and either hyperpolarization is needed (red ch) or depolarization is needed (blue ch) and Vm is more negative than blue_Vrev.
			{Int = Int + Vm_diff_log[count];}
		num = length *(sumxy(Vm_diff_log, count, length, period, modulo)) - sumx(period, length)*sumy(Vm_diff_log, count, length, modulo);
		denom = length*sumx2(period, length) - sumx(period, length)*sumx(period, length);
		if (abs(denom) < 0.001)
			{slope = 10000;}
		else
			{slope = num/denom;} // Slope is measured in mV/ms

		P = K_p * Vm_diff_log[count]; // Term that is proportional to the instantaneous difference in voltage.
		I = K_i * Int; // Term that speeds up or slows down the rate of change based on the history of voltage differences.
		D = K_d * slope; // Term that predicts the behaviour that is about to happen and helps in stabilizing.

		PID_diff = PID;
		PID = P + I + D;
		PID_diff = PID_diff - PID;

		if (count >= corr_start-1 && abs(PID_diff) > PID_tresh){
			// PID_tresh gives a value that bounds the actions of the output (applies to PID_diff).
			// When smaller than this value, the previous light-ouput will be repeated.
			// This explains the lack of an else case.
			if (PID < 0 && abs(PID) > min_PID && Vm < blue_Vrev)
			{
				// min_PID gives a value where you don't consider it necessary to correct anything (applies to PID).
				// So when the absolute value is smaller than this value, the output will be set to 0.
				// This is the else case.
				VLED = -PID * (1/Rm_blue);			
				if (VLED > 5){VLED = 5;}
				output(0) = VLED;
				output(1) = 0;
			}
			else if (PID > 0 && abs(PID) > min_PID)
			{
				VLED = PID * (1/Rm_red);
				// Rm_red scales the amount of applied light for the red channel.
				// By lowering this value compared to Rm_blue, it is possible to counteract the smaller effect of repolarizing currents than depolarizing currents.
				if (VLED > 5){VLED = 5;}	
				output(1) = VLED;
				output(0) = 0;		
			}
			else
			{
				output(0) = 0;
				output(1) = 0;
			}			
		}
	}
	else
	{
		output(0) = 0;
		output(1) = 0;
	}

	// This part of the code resets the I and D terms when the measured AP is very close to resting membrane potential (This
	// is taken as the value close to the end of the ideal AP)
	if (reset_I_on && abs(Vm - ideal_AP[int(BCL_cutoff*BCL)]) < 0.005){
		idx_diff = count - prev_idx;
		prev_idx = count;
		if (idx_diff == 1){
			reset_I_counter +=1;
		}
		else{
			reset_I_counter = 0;
		}
		if (reset_I_counter == length){
			Int = 0;
			reset_I_counter = 0;
		}
	}

	// This part of the code makes sure no output is produced in the last part of the action potential to let the cell come to rest.
	if (count > BCL_cutoff*BCL){
		act = 0;
		output(0) = 0;
		output(1) = 0;
	}

	count++;

	count_r = (double)count/1000.0; // For display purposes
	count2_r = (double)count2/1000.0; // For display purposes

}

/*
Update
------
This function updates the parameters of the code depending on the flag that is 
given to it, where each flag is associated to a button.
INIT: associated to the loading of the module
MODIFY: associated to the Modify button
PERIOD: associated to the period linker with the "system control panel" module
PAUSE: associate to the pause button when pressing on it
UNPAUSE: associated to the pause button when unpressing it

IN:
	*) flag				Indicating the state of the update:
						INIT, MODIFY, PERIOD, PAUSE, UNPAUSE
OUT:
	*) None
*/
void gAPqrPID3::update(DefaultGUIModel::update_flags_t flag)
{
	switch (flag)
	{
	case INIT:
		setParameter("V_cutoff (mV)", V_cutoff);
		setParameter("Rm_blue (MOhm)", Rm_blue);
		setParameter("Rm_red (MOhm)", Rm_red);
		setParameter("lognum", lognum);
		setParameter("BCL_cutoff (pct)", BCL_cutoff);
		setParameter("Slope_thresh (mV/ms)", slope_thresh);
		setParameter("Correction start", corr_start);
		setParameter("Blue_Vrev", blue_Vrev);
		setParameter("K_p", K_p);
		setParameter("K_i", K_i);
		setParameter("K_d", K_d);
		setParameter("length", length);
		setParameter("PID_tresh", PID_tresh);
		setParameter("min_PID", min_PID);
		setParameter("reset_I_on", reset_I_on);
		setState("Vm2 (mV)", Vm);
		setState("Time (ms)", systime);
		setState("Period (ms)", period);
		setState("APs2", APs);
		setState("log_ideal_on2", log_ideal_on);
		setState("BCL2", BCL);
		setState("enter2", enter);
		setState("act2", act);
		setState("count", count_r);
		setState("count2", count2_r);
		setState("modulo_state", modulo);
		setState("iAP", iAP);
		setState("P", P);
		setState("I", I);
		setState("D", D);
		setState("PID", PID);
		break;
	case MODIFY:
		lognum = getParameter("lognum").toDouble();
		BCL_cutoff = getParameter("BCL_cutoff (pct)").toDouble();
		Rm_blue = getParameter("Rm_blue (MOhm)").toDouble();
		Rm_red = getParameter("Rm_red (MOhm)").toDouble();
		slope_thresh = getParameter("Slope_thresh (mV/ms)").toDouble();
		V_cutoff = getParameter("V_cutoff (mV)").toDouble();
		corr_start = getParameter("Correction start").toDouble();
		blue_Vrev = getParameter("Blue_Vrev").toDouble();
		K_p = getParameter("K_p").toDouble();
		K_i = getParameter("K_i").toDouble();
		K_d = getParameter("K_d").toDouble();
		length = getParameter("length").toDouble();
		PID_tresh = getParameter("PID_tresh").toDouble();
		min_PID = getParameter("min_PID").toDouble();
		reset_I_on = getParameter("reset_I_on").toDouble();
		systime = 0;
		count = 0;
		APs = -1;
		BCL = 0;
		log_ideal_on = 0;
		enter = 0;
		count2 = 0;
		PID = 0;
		PID_diff = 0;
		Int = 0;
		cleanup();
		break;
	case PERIOD:
		period = RT::System::getInstance()->getPeriod() * 1e-6; // time in milli-seconds
		modulo = (1.0/(RT::System::getInstance()->getPeriod() * 1e-6)) * 1000.0;
		break;
	case PAUSE:
		output(0) = 0.0;
		output(1) = 0.0;
		act = 0;
		systime = 0;
		break;
	case UNPAUSE:
		break;
	default:
		break;
	}
}

/*
initParameters
--------------
This function sets all values to their defaults when no external parameters are provided
through the GUI interface.

IN:
	*) None
OUT:
	*) None
*/
void gAPqrPID3::initParameters()
{
	Vm = -80; // mV
	Rm_blue = 150; // MOhm
	Rm_red = 50; // MOhm
	slope_thresh = 5.0; // mV
	corr_start = 0;
	blue_Vrev = -20;
	VLED = 0;
	output(0) = 0;
	output(1) = 0;
	period = RT::System::getInstance()->getPeriod() * 1e-6; // ms
	systime = 0;
	count = 0;
	idx_diff = 0;
	prev_idx = 0;
	reset_I_counter = 0;
	PID = 0;
	length = 10;
	act = 0;
	iAP=0;
	BCL = 0;
	count2 = 0;
	APs = -1;
	V_cutoff = -40;
	BCL_cutoff = 0.8;
	enter = 0;
	log_ideal_on = 0;
	lognum = 3;
	count_r = 0;
	count2_r = 0;
	modulo = (1.0/(RT::System::getInstance()->getPeriod() * 1e-6)) * 1000.0;
	Int = 0;
	num = 0;
	denom = 1;
	slope = 0;
	P = 0;
	I = 0;
	D = 0;
	K_p = 1;
	K_i = 0.1;
	K_d = 0.1;
	PID_diff = 0;
	PID = 0;
	PID_tresh = 0.1;
	min_PID = 0.2;
	reset_I_on = 0;
}