// genesis (R.M. 12/12/95)

// Follows instructions of Gert Van Dijck

// Copied from Parallel_fiber.g on 29/12//2001
// Intended to model a 2D array of electrodes

// IMPORTANT
// Because the efield object is not yet supported by the hines solver,
// the elctrodes must be made, and connected, after the hines solver 
// has been installed for the compartments to which the electrodes 
// are to be connected.
// For this reason, the constants, makearray and setup of messages are
// collapsed in this single script.


// according to Hugo Cornelis, now supported by hines solver (9/12/2006)



echo making electrodes

// the constants

   	int nx = 10 // 1 // 8 // 1 // 10 // 9 // 3 // 1   // number of electrodes along X-axis
   	int ny = 5 // 1 // 8 // 1 // 10 // 9 // 3 // 1   // number of electrodes along Y-axis
   	int number_electrodes = {nx * ny}
   	float dx = 17.3e-6 // 40e-6 // 50e-6 // 0  // interelectrode spacing
   	float dy = 17.3e-6 // 40e-6 // 50e-6 // 0 

// electrode array now centered at excitatory neuron

//   	float ox = - {4 * {dx} + {dx / 2}} // 20e-6 // -140e-6 // 20e-6 // 0 // -225e-6 // -50e-6 // 20e-6 // 0 
   	float ox = - {4 * {dx} + {dx / 2}} - 0.00004 // 20e-6 // -140e-6 // 20e-6 // 0 // -225e-6 // -50e-6 // 20e-6 // 0 
   	float oy = - 2 * {dy} // 20e-6 // -140e-6 // 20e-6 // 0 // -225e-6 // -50e-6 // 20e-6 // 0

	int number_contact_points = 12 // 8 // 11 // 1 // 11
   	float contact_separation = 60e-6 // 0.1e-3 // 0.15e-3 // 0.6e-3
   	float depth = -0.15e-3 // -0.5e-3 // 0 // -0.5e-3 // -1e-3 // vertical position electrode tip (on z-axis)

// 13de rij electrodes toegevoegd op vraag van Gert, 26Feb09
   number_contact_points = 13
   depth = -0.21e-3 + 0.0002


   	int i //  j, index



// make  prototype electrode

function make_electrode_shaft (number_contact_points, contact_separation, depth)

	int number_contacts_points, i
   	float contact_separation, depth

   	create efield /library/contact
   	setfield ^ scale -1e-3

//   possibility to low-pass-filter the electrode signal, so that it
//   can be sampled at a lower clock rate

   	create RC /library/contact/RC 
   	setfield ^ V0 0 R 1 C 0.005  // should give same amplitude as input,
                                //  but low-pass-filtered with tau 1 ms

   	addmsg /library/contact /library/contact/RC INJECT field

   	if(!{exists /library/electrode})
        	create neutral /library/electrode 
   	end

	createmap /library/contact  /library/electrode 1 {number_contact_points} \ 
                        -delta 0 {contact_separation} -origin 0 {depth}

	for (i = 0; {i < number_contact_points}; i = i + 1)
       		setfield /library/electrode/contact[{i}] z {getfield /library/electrode/contact[{i}] y}
       		setfield /library/electrode/contact[{i}] y 0
   	end
 
end



// make array of electrodes

function make_electrode_array  (number_contact_points, contact_separation, depth, nx, ny, dx, dy, ox, oy)

   	int   length, number_contact_points, i
   	float depth, contact_separation 

   	int   nx, ny // n = number
   	float dx, dy, ox, oy // d = delta, o = origin

    str name

   	if(!{exists /library})
          	create neutral /library 
          	disable /library
   	end

   	make_electrode_shaft {number_contact_points} {contact_separation} {depth}

   	createmap /library/electrode /electrode_array  {nx} {ny} -delta {dx} {dy} -origin {ox} {oy}

// this is new for the IMEC electrode

    for (i = 0; i < {nx * ny}; i = {i + 2})

      		foreach name ({el /electrode_array/electrode[{i}]/##[][TYPE=efield]})
                setfield {name} z {{getfield {name} z} + 30e-6} 
      		end
    end

end



// make the array

   	create neutral /electrode_array
   	make_electrode_array {number_contact_points} {contact_separation} {depth} {nx} {ny} {dx} {dy} {ox} {oy}



// connect all electrodes to all compartments of the PC

echo making msgs to electrodes

// this makes the msgs using diffamps to fix the hinessolver bug
// include electrodes_try.g
// connections must now be made by function call



// connect the electrodes to an asc_file element

   	str electrodes_ascii_filename   // =  "electrodes" @ "label" & ".ascii"
   	str name2, pathname

   	for (i = 0; i < {number_electrodes}; i = i + 1)
 
      		pathname = "/output/electrode" @ {i}
      		electrodes_ascii_filename   =  {filename} @ "electrode" @ {i} @ "-" @ {label} @ ".ascii"

      		if (!({exists {pathname}}))
            		create asc_file {pathname}
      		end
//   setclock 7 20e-5
      		useclock {pathname} 1
      		enable /output
      		enable {pathname}
      		setfield {pathname} filename {electrodes_ascii_filename} \ 
               		initialize 1 leave_open 1  flush 1
echo Output to {electrodes_ascii_filename}

      		foreach name2 ({el /electrode_array/electrode[{i}]/##[][TYPE=efield]})
			addmsg {name2} {pathname} SAVE field
//          addmsg {name2}/RC  /output/electrodes SAVE state
      		end

	end


// this reset is needed to activate the connections to the asc_file object ? 

//   reset