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Commit e76327dc authored by Tim De Coster's avatar Tim De Coster
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started commenting APqr8

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APqr7/APqr7.cpp
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View file @ e76327dc
......@@ -229,6 +229,7 @@ void gAPqr7::execute(void)
// 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
}
......
APqr8/APqr8.cpp
+ 189
− 18
View file @ e76327dc
......@@ -25,11 +25,63 @@
#include <math.h>
#include <vector>
/*
*********
* APqr8 *
*********
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 gAPqr8();
}
/*
vars[]
----
This is not a function, but rather the construction of a list. This list contains
all the variables that are visible and/or modifiable in the GUI of the software
module. There is the choice between INPUT, OUTPUT, PARAMETER and STATE.
INPUT: connected to the input port
OUTPUT: connected to the output port
PARAMETER: modifiable variable in the code
STATE: non-modifiable variable in the code
*/
static DefaultGUIModel::variable_t vars[] = {
{ "Vm (mV)", "Membrane potential (mV)", DefaultGUIModel::INPUT, },
{ "Iout (pA)", "Output current (pA)", DefaultGUIModel::OUTPUT, },
......@@ -68,8 +120,25 @@ static DefaultGUIModel::variable_t vars[] = {
{ "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);
/*
gAPqr8
------
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
*/
gAPqr8::gAPqr8(void) : DefaultGUIModel("APqr8", ::vars, ::num_vars)
{
setWhatsThis(
......@@ -81,54 +150,128 @@ gAPqr8::gAPqr8(void) : DefaultGUIModel("APqr8", ::vars, ::num_vars)
resizeMe();
}
gAPqr8::~gAPqr8(void)
{
}
gAPqr8::~gAPqr8(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 gAPqr8::cleanup()
{
for(i=0;i<10000;i++){
Vm_log[i]=0;
Vm_diff_log[i]=0;
ideal_AP[i]=0;
}
}
/*
execute
-------
This is the main funtcion of the code that is looped through real-time.
It contains the four main parts of the algorithm:
1) Recording the ideal AP
2) Detecting AP upstrokes
3) Computing AP correction and outputting this
4) Updating the necessary variables
IN:
*) None
OUT:
*) Vout voltage that is used to inject the calculated amount
of current into the excitable system
*/
void gAPqr8::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.
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;
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)
{
BCL = (APs==-1? 0: (BCL*APs + count2)/(APs+1));
log_ideal_on = 1;
count2 = 0;
enter = 1;
APs++;
// 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)
{
enter = 0;
// 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)
{
ideal_AP[count2] = (ideal_AP[count2]*APs + Vm)/(APs+1);
count2++;
// 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)
{
count = 0;
act = 1;
// 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
}
// *************************************************
// *************************************************
// ** Computing AP correction and outputting this **
// *************************************************
// *************************************************
if (act == 1)
{
Iout = Cm * (1/Rm) * (Vm - ideal_AP[count]);
......@@ -168,6 +311,23 @@ void gAPqr8::execute(void)
}
/*
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 gAPqr8::update(DefaultGUIModel::update_flags_t flag)
{
switch (flag)
......@@ -234,6 +394,17 @@ void gAPqr8::update(DefaultGUIModel::update_flags_t flag)
}
}
/*
initParameters
--------------
This function sets all values to their defaults when no external parameters are provided
through the GUI interface.
IN:
*) None
OUT:
*) None
*/
void gAPqr8::initParameters()
{
Vm = -80; // mV
......
APqr8/APqr8.h
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View file @ e76327dc
......@@ -21,6 +21,7 @@
#include <string>
#include <vector>
// All parameters and functions related to the gAPqr8 class.
class gAPqr8 : public DefaultGUIModel
{
......
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