Light to Brain Model

; creating all variables used other than sliders that are present on interface
globals[
  StepSize ; how far photon moves with each tick
  rods-stimulated ; how many rods were stimulated by a burst of photons
  ystart ; starting y coordinate of yellow photons at the lefthand side of the screen
  ycell ; default y coordinate for retinal cells in zoomed in window
  yline ; starting y coordinate of green photons along white line
  cycles ; one cycle is one run of the simulation (i.e. one burst)
  number_photons ; the number of photons sent out per burst
  decays ; number of photons that have been absorbed in a cycle (gets updated continuously)
  CorneaDecay ; absorption value for cornea per pixel
  AqueousHumourDecay ; absorption value for aqueous humour per pixel
  VitreousHumourDecay ; absorption value for vitreous humour per pixel
  LensDecay ; absorption value for lens per pixel
  RetinaDecay ; absorption value for lens per pixel
  nwater ; absorption value for water per pixel with respect to depth
  irisMin ; magnitude of y coordinate of inside of iris (radius of pupil)
  bkgdcolor ; a number is assigned to represent a given background colour
  beamradius ; variable to convert beamwidth slider value (in mm) to pixels
  photoncount ; a list of the number of photons at each tick from 0 to 600
  currentphotons ; variable used to create blue line on the photon vs time graph
  ; it is the average of the number of photons at a given tick value over the cycles that have occurred
  gphotons ; the number of green photons that have appeared in the zoomed in retinal panel on the right side of interface
]

breed [photons photon] ; breed for turtles that act as photons to allow for easier
breed [bolts bolt] ; breed for turtles shaped like lightning bolts that represent the signal that is sent when enough rods are stimulated

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;;;;;;;;;;;;; setup procedures ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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; regular simulation setup procedure. must be activated after sliders are changed and before any other button

to setup
  clear-all
  ; set up standard background colour by filling entire interface with grey
  ask patches
  [
    if pxcor <= max-pxcor
    [
      set pcolor grey
    ]
  ]

  ; create white line to split interface
  ask patches with  [pxcor = 100]
  [
    set pcolor white
  ]

  ; the number of pixels a photon will move by on each tick
  set StepSize 1

  ; set variables/lists to 0 and will later be given values
  set bkgdcolor 0 ; variable to check background colour: 0 if grey, 1 if blue
  set cycles 0
  set gphotons 0
  set decays 0
  set rods-stimulated 0
  set photoncount (n-values 601 [0]) ; set up list to have 601 entries of zero so they can be identified and replaced later

  ; set decay/absorption rates to match literature values (references outlined in info tab)
  set CorneaDecay 0.0084929
  set AqueousHumourDecay 0.0013648
  set VitreousHumourDecay 0.00050404
  set LensDecay 0.0010123
  set RetinaDecay 0.001358
  set nwater 0.002

  ; call set scale procedure that creates the scale bars
  setscale

  ; call procedures that draw the parts of the eye
  ; size and distances are scaled version of actual eye layer dimensions
  sclera
  VitreousHumour
  aqueoushumour
  lens
  cornea
  irisStructure
  retina

  ; add labels for temporal and nasal sides of the eye
  ask patch (-60) (175) [set plabel-color 9.9 set plabel "Temporal"]
  ask patch (-60) (-175) [set plabel-color 9.9 set plabel "Nasal"]

  ; write "loading ..." in output on interface which will later announce if a visual response has occurred
  output-write "Loading ..."

  reset-ticks
  ; call procedure that makes photons so there are photons when the simulation starts
  make-photons
end 

; procedure to create scale bars

to setscale
  ; scale bar for left side of interface
  ; this scale was calculated to be 12 pixels/mm
  ask patches with [pxcor >= -290 and pxcor < (-290 + 120) and -180 >= pycor and pycor >= -190] [set pcolor 0] ; draw a 10 mm-long scale bar in the lower left corner
  ask patch (-215) (-170) [set plabel-color 0 set plabel "10 mm"]  ; add the label for the scale bar

  ; scale bar for right side of interface (zoomed in retinal window)
  ; this scale was calculated to be 1 pixels/μm
  ask patches with [pxcor >= 288 and pxcor < (298) and (-190 + 40) >= pycor and pycor >= -190] [set pcolor 0] ; draw a 40 μm-long scale bar in the lower right corner
  ask patch (298) (-130) [set plabel-color 0 set plabel "40"]  ; add the label for the scale bar
  ask patch (298) (-140) [set plabel-color 0 set plabel "μm"]
end 

; experimental setup procedure which is the same as standard setup but without calling "clear-all" first as that would clear all plot data on the interface

to setupexp
  ; the following clear procedures are still necessary to reset the interface and variables for each run
  clear-drawing
  clear-turtles

  ; set up standard background colour by filling entire interface with grey
  ask patches
  [
    if pxcor <= max-pxcor
    [
      set pcolor grey
    ]
  ]

  ; create white line to split interface
  ask patches with  [pxcor = 100]
  [
    set pcolor white
  ]

  ; the number of pixels a photon will move by on each tick
  set StepSize 1

  ; set variables/lists to 0 and will later be given values
  set bkgdcolor 0 ; variable to check background colour: 0 if grey, 1 if blue
  set cycles 0
  set gphotons 0
  set decays 0
  set rods-stimulated 0
  set photoncount (n-values 601 [0]) ; set up list to have 601 entries of zero so they can be identified and replaced later

  ; set decay/absorption rates to match literature values (references outlined in info tab)
  set CorneaDecay 0.0084929
  set AqueousHumourDecay 0.0013648
  set VitreousHumourDecay 0.00050404
  set LensDecay 0.0010123
  set RetinaDecay 0.001358
  set nwater 0.002

  ; call set scale procedure that creates the scale bars
  setscale

  ; call procedures that draw the parts of the eye. size and distances are scaled version of actual eye layer dimensions
  sclera
  VitreousHumour
  aqueoushumour
  lens
  cornea
  irisStructure
  retina

  ; add labels for temporal and nasal sides of the eye
  ask patch (-60) (175) [set plabel-color 9.9 set plabel "Temporal"]
  ask patch (-60) (-175) [set plabel-color 9.9 set plabel "Nasal"]

  ; write "loading ..." in output on interface which will later announce if a visual response has occurred
  output-write "Loading ..."

  reset-ticks
  ; call procedure that makes photons so there are photons when the simulation starts
  make-photons
end 

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;;;;;;;;;;;;; draw eye layers & cells ;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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; procedure to draw cornea

to Cornea
  ; draw cornea by filling in the region between a circle and ellipse
  ; the outer circle has the same radius of curvature as the cornea
  ; the inner ellipse is placed at the literature distance from the outer layer
  ask patches with [(pxcor + 144) ^ 2 + (pycor) ^ 2 < 8761 and (pxcor + 140 ) ^ 2 + (pycor / 1.05) ^ 2 > 8661]
  [
    set pcolor pink
  ]
end 

; procedure to draw sclera

to Sclera
  ; fill in region between concentric circles
  ; circle size was determined so that the distance between the cornea and the back of the sclera would be equivalent to 24 mm
  ask patches with [(pxcor + 80 ) ^ 2 + (pycor) ^ 2 < 20000 and (pxcor + 80 ) ^ 2 + (pycor) ^ 2 > 19000]
  [
    set pcolor red
  ]
  ; call procedures to replace region of sclera with the retinal test patch
  RetinaPatch
end 

; procedure to create test patch region on retina

to RetinaPatch
  ; fills in a region of the retina 2 pixels out from either side of a line that passes from the centre of the light beam through the centre of the lens (line of no refraction for photons)
  ; this region is the smaller depiction of the zoomed in window on the right-side of interface in which the number of rods stimulated will be recorded
  ask patches
  [
    if pcolor = red and (((47 / 130)* pxcor + (31)) >= pycor and pycor >= ((47 / 130)* pxcor + 27) and pxcor >= 0)
    [set pcolor 94]
  ]
end 

; procedure to draw aqueous humour

to AqueousHumour
  ; fill in region between cornea and lens with white (representing the humour)
  ask patches with [(pxcor + 140) ^ 2 + (pycor) ^ 2 < 8761 and -200 >= pxcor]
  [
    set pcolor white
  ]
end 

; procedure to draw lens

to Lens
  ; lens drawn as region contained by two circles with radii equivalent to the anterior and posterior radii of curvature of the lens
  ask patches with [(pxcor + 79) ^ 2 + (pycor) ^ 2 < 14400 and (pxcor + 211) ^ 2 + (pycor) ^ 2 < 5184]
  [
    set pcolor 88
  ]
end 

; procedure to draw vitreous humour

to VitreousHumour
  ; fill in any grey region within the sclera with white (representing humour)
  ask patches with [(pxcor + 80 ) ^ 2 + (pycor) ^ 2 < 20000 and pcolor = grey]
  [
    set pcolor white
  ]
end 

; procedure to draw iris and pupil structure

to irisStructure
  ; first relate pupil slider to size of iris
  ; set the magnitude for the inner y coordinate of the iris to be the radius of the pupil in pixels
  set irisMin ((12 * (Pupil / 2)))
  ; create top half of iris
  ask patches with [(72 >= pycor and pycor >= irisMin and -200 >= pxcor and pxcor >= -203)]
    [
      set pcolor 34
  ]
  ; create bottom half of iris
  ask patches with [((- irisMin) >= pycor and pycor >= -72 and -200 >= pxcor and pxcor >= -203)]
  [
    set pcolor 34
  ]
end 

; procedure to draw retinal cells using rectangles

to retina
  ; set default y coordinates for retinal cells
  set ycell 195
  ask patches [
    if ycell >= pycor and pycor >= -195 [
      ; create retinal ganglion cells which are the lightest blue ones furthest to left
      ask patches with [190 >= pxcor and pxcor >= 175 and ycell >= pycor and pycor >= (ycell - 2)] [
        set pcolor 98
      ]
      ; create bipolar cells wihch are the next cells to the right of the retinal ganglion cells
      ask patches with [210 >= pxcor and pxcor >= 195 and ycell >= pycor and pycor >= (ycell - 2)] [
        set pcolor 97
      ]
      ; create rods which are the longer cells to the right of the bipolar cells
      ask patches with [265 >= pxcor and pxcor >= 215 and ycell >= pycor and pycor >= (ycell - 2)] [
        set pcolor 96
      ]
      ; create retinal pigment epithelium cells
      ; goes all the way across since they're densely packed and are the last layer which then absorbs scattered light
      ask patches with [280 >= pxcor and pxcor >= 270 and 200 >= pycor and pycor >= -200] [
        set pcolor 95
      ]
      ; decrease y values of the retinal ganglion cells, bipolar cells, and rods by 5 on each loop to create evenly spaced cells
      set ycell (ycell - 5)
    ]
  ]
end 

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;;;;;;;;;;;;; underwater setup ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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; underwater setup procedure that alters the started setup

to underwater
  clear-turtles
  clear-drawing
  set bkgdcolor 1 ; set this variable to 1 to indicate that the background is now blue
  set avgphotons 1000 ; assuming that 1000 photons are entering the water at sea level

  ; set background colour to be blue to represent water
  ask patches with [pcolor = grey and 100 > pxcor] [
    set pcolor 105
  ]

  ; call goggle procedures
  goggles

  ; reset the iris region to be white so it can be replaced by the appropriate pupil size
  ; for the given depth chosen on the slider prior to pressing the underwater button
  ask patches with [ 72 >= pycor and pycor >= -72 and -200 >= pxcor and pxcor >= -203]
  [
    set pcolor white
  ]

  ; set pupil size to increase with depth (based on what is selected on slider)
  ; nwater values are also set according to literature values with respect to depth to simulate
  ; the decrease in light intensity as depth increases
  ; the size of the pupil increases with depth
  if 0 >= depth and depth > -2
  [
    set nwater 0 ; absorption values are based on the shallowest depth, in this case 0 m from sea level
    set pupil 2
    irisStructure
  ]
  if -2 >= depth and depth > -4
  [
    set nwater 0.008355
    set pupil 3
    irisStructure

  ]
  if -4 >= depth and depth > -6
  [
    set nwater 0.01585
    set pupil 4
    irisStructure
  ]
  if -6 >= depth and depth > -8
  [
    set nwater 0.02332
    set pupil 5
    irisStructure
  ]
  if -8 >= depth and depth > -10
  [
    set nwater 0.0303
    set pupil 6
    irisStructure
  ]
  if -10 >= depth and depth > -12 [
    set nwater 0.0394
    set pupil 7
    irisStructure
  ]
  if -12 >= depth and depth >= -14 [
    set nwater 0.0461
    set pupil 8 ; assuming the maximum dilation of the eye occurs at a depth between -12 m and -14 m
    irisStructure
  ]
  if -14 >= depth and depth >= -16 [
    set nwater 0.0506
    set pupil 8
    irisStructure
  ]
  if -16 >= depth and depth >= -18 [
    set nwater 0.6060
    set pupil 8
    irisStructure
  ]

  make-photons
end 

; draw goggles around eye

to goggles
  ; create air pocket between goggle lens and eye
  ask patches with [ pcolor = 105 and 100 >= pxcor and pxcor >= -269 and 145 >= pycor and pycor >= -145]
    [
      set pcolor grey
  ]
  ; lens of goggles
  ask patches with [ -267 >= pxcor and pxcor >= -271 and 145 >= pycor and pycor >= -145]
  [
    set pcolor 89
  ]
end 

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;;;;;;;;;;;;; make-photons ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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; procedure to make intial photons

to make-photons
  ; set the number of photons per burst with a Poisson distribution centred at the average photons chosen on the slider
  set number_photons (random-poisson avgphotons)
  create-photons Number_Photons
  [
    ; translate mm to pixels and diameter of beam to radius
    set beamradius (0.5 * 12 * beamwidth)
    ; centre light beam around (-300, -564/23) which is the point on the line though the centre of the mens and to the retinal patch when x = -300
    set ystart ((-564 / 23) - beamradius + random(2 * beamradius))
    set shape "Arrow"
    set color 66 ; starting photons are green
    ; the starting y coordinate for the inital photons can be -564/23 +/- the beam radius
    setxy -300 ystart

    ; set up angle of beam (from up as 0°)
    if(bkgdcolor = 0) ; grey background (air)
    [
      set heading 78 ; angle that causes centre of beam to pass through centre of lens and reach retina with no refraction
    ]
    if(bkgdcolor = 1) ; blue background (water)
    [
      set heading 46 ; angle calculated using Snell's Law for refraction that occurs when light moves from air to water
    ]
    set size 15
    pen-down
  ]
  reset-ticks
end 


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;;;;;;;;;;;;; go procedures ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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to burst
  ask photons
  [

    forward StepSize ; the photons move forward 1 pixel/tick

     ;;;;;;;; specifying the absorption values for each layer of the eye ;;;;;;;;;

    ; absorption and refraction at cornea
    if pcolor = pink [
      facexy 55 48 ; focal point is just beyond retina
      absorbcornea
    ]

    ; absorption in humours
    if pcolor = white [absorbhumour]

    ; absorption and refraction at lens
    if pcolor = 88
    [
      ; call absorption
      absorblens

      ; if photons reach center of lens, refract
      if pxcor = -180
      [
        facexy 50 47 ; bend to focus light on retinal patch (correct cornea refraction)
      ]
    ]

    ; the iris is the structure that preventing photons from passing, except if they are within the pupil
    if pcolor = 34
    [
      set decays decays + 1
      die ; when the photons hit the iris they die
    ]

    ; underwater media absorption for when underwater procedure activated by button
    if pcolor = 105 [waterabsorb]

    ; refraction at goggles
    if pcolor = 89
    [
      set heading 78 ; based on refraction values in air
    ]

    ;;;;;;;; absorption within right panel of the interface  ;;;;;;;;;;;;;;;;;;;;;;;;

    ; absorption of photons by rods
    if 270 >= xcor and xcor >= 175 ; contains the entire area of the retina on the right panel of the interface
    [
      absorbretina
    ]

    ;; if incident photon hits retinal test patch, moves to random y-coordinate at x = 105 in the retina
    if pcolor = 94 ; the colour of the retinal test patch
    [
      set yline random-ycor ; provides variation along the y-axis of the retina
      pen-up
      set color 67 ; changes the photons to the colour green
      set size 10
      set shape "circle"
      setxy 105 yline
      facexy 300 yline
      wait 0.03 ; create time delay between photon hitting patch and appearing in window, for cosmetic purposes
      pen-down
    ]

    if pcolor = 95 [die] ; absorbed by retinal epithelium layer
    if pcolor = red [die] ; absorbed by the sclera
    if pxcor = 100 [die] ; for initial photons that pass the eye, ensures they don't enter the retina

  ]

  ; if one of the patches changes to the yellow colour, all remaining blue rod pixels change to yellow
  ask patches
  [
    if pcolor = 46
    [
      ask neighbors
      [
        if pcolor = 96
        [
          set pcolor 46 ; changes final colour to yellow
        ]
      ]
    ]
  ]

  ; the following steps are called if the number of rods stimulated is at least equal to the number of photons needed to be
  ; absorbed by rods to elicit a visual response as chosen in the n slider
  if rods-stimulated >= n
  [
  create-bolts 1 ; the presence of a bolt is a visual depiction of a light signal being sent to the brain
    [
      set shape "lightning"
      set color 46
      set size 75
      setxy 140 0 ; the bolt forms to the left of the cells of the retina
    ]
  ]

  ; after all photons have died
  if any? photons = false
  [
    ifelse rods-stimulated >= n
    [
      ; if enough rods have been stimulated for a given burst, "visual response" is shown in the output monitor on interface
      clear-output
      output-write "Visual Response"
    ]
    [
     ; if not enough rods have been stimulated for a given burst, "no visual response" is shown in the output monitor on interface
      clear-output
      output-write "No Visual Response"
    ]
  ]

  ; data for 'average' line of cycles in photons vs time graph

  ; photoncount updates the index with the current photons, in addition value of the array at that tick from past cycles
  ; photoncount is an array that indicates the total number of photons for a given time (tick) value
  set photoncount (replace-item ticks photoncount ((item ticks photoncount) + (count photons)))

  ; currentphotons is a running average of the photons at a given time (tick), across cycles
  set currentphotons ((item ticks photoncount) / (cycles + 1))

  tick

  ; once the green photons enter the zoomed in retina window, but before the retina, gphotons is updated
  ; gphotons is used to calculate the number of photons that successfully entered the retinal patch
  if ticks = 390
  [
    set gphotons (count photons)
  ]

  if ticks = 600 [stop] ; a full cycles has been completed after 600 ticks
end 

to rerun

  burst ; call the single go procedure (burst)

  ; allows 10x cycles each with 600 ticks to be run
  if ticks = 600
  [
    set cycles (cycles + 1)
    reset-ticks
    set gphotons 0
    set decays 0
    resetYellow ; reset the color and state of rods
    clear-drawing
    make-photons
    clear-output
    output-write "Loading ..."
  ]

  if cycles = 10 [stop]
end 

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;;;;;;;;;;;;; absorb ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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; when within the pink-coloured cornea region, probabilistic absorption photons occurs

to absorbcornea
  if random-float 1 < CorneaDecay ; calculated absorption/pixel for the cornea
      [
        set decays decays + 1 ; allows for the number of absorbed ('decayed') photons to measured
        die ; these photons do not proceed towards the retina
    ]
end 

; when within the white-coloured aqueous and vitreous humour region, probabilistic absorption occurs

to absorbhumour
  if -180 >= pxcor
  [
    if random-float 1 < AqueousHumourDecay ; calculated absorption/pixel for aqueous humour
        [
          set decays decays + 1
          die
    ]
  ]
  if pxcor >= -180
  [
    if random-float 1 < VitreousHumourDecay ; calculated absorption/pixel for vitreous humour
        [
          set decays decays + 1
          die
    ]
  ]
end 

; when within the lens region, probabilistic absorption occurs

to absorblens
  if random-float 1 < LensDecay ; calculated absorption/pixel for lens
        [
          set decays decays + 1
          die
  ]
end 

; account for the refractive index of water that surrounds the eye when underwater

to waterabsorb
  if random-float 1 < nwater ; nwater changes based on depth, in "underwater setup"
      [
        set decays decays + 1
        die
  ]
end 

; when within the retina region, probabilistic absorption occurs

to absorbretina
  if random-float 1 < RetinaDecay ; calculated absorption/pixel for the retina
  [

    ; if in the blue rods, visually show activated rods with yellow
    ifelse pcolor = 96
    [
      set rods-stimulated (rods-stimulated + 1) ; shows that the rods have been stimulated
      if [pcolor] of patch-ahead 1 != 46 ; change pcolour, as long as the patch 1 ahead is not already yellow (activated)
      [
        set pcolor 46 ; change pcolour to yellow to show activation
      ]
      die
    ]

    ; if not in the retina region, the same retina absorption rate will apply
    [
      set decays decays + 1
      die
    ]

  ]
end 

; used after each cycle to reset the patch colour and remove the lightning bolt

to resetYellow
  ask patches
  [
    if pcolor = 46
    [
      set pcolor 96
      set rods-stimulated 0
    ]
    ask bolts with [color = 46] [die]
  ]
end 

; ISCI 2A18 Enrichment Project 2023
; More detailed information about model in the "Info" tab
; Authors: Jeremy Dykstra and Naya Davidson-Lindfors
; Supervisor: Dr. Cecile Fradin