--LuigI/O v3.0, a neuroevolutionary AI designed to teach itself how to beat Super Mario Bros and Lost Levels

--Based on MarI/O created by Sethbling
--LuigI/O versions 1, 2, and many minor adjustments and bugfixes made by Akisame
--LuigI/O version 3 made by Electra & Akisame
--Thanks to LuigI/O testers Akisame, Electra, Jonathan, AlejoGDOfficial, and Niko.

--V3 changelog: https://pastebin.com/KxtgyRe6

-- Pressing N will show the Neural net, pressing M will show the mutation rates, pressing L will load the last saved generation, pressing B will display the genome with the top fitness.

-- To use this script you will need to download FCEUX and create a savestate in state 1 as as player 1 (mario) for smb or as either player in Lost Levels.
-- If you are playing Lost Levels, set this variable to 1:
LostLevels = 0
-- If you want to play as Luigi in SMB1, set this variable to 2:
player = 2
-- To set the game in turbo, do NES -> Emulation Speed -> Turbo, also make sure to set priority to realtime in Task Manager
-- If you want it to go as fast as possible turn off the neural net win N, it doubles the speed basically

-- Click file -> lua -> 'new lua script window' and load the script.
-- Have fun!

-- Keep in mind that this code is provided for Non-Commercial usage and it is not permitted to request financial compensation (either by means of ads, donations, subscriptions or other means) for selling, streaming or otherwise previewing this code or its execution.

--FCEUX doesn't allow for user string input but if you press 'L' on your keyboard it should load the latest generation that was saved
--for loading specific generations replace nil with the filename as shown in the example below
savedpool = nil --"backups/backup.666.SMB8-3.state.pool"
--savedpool = "backup.71.SMB2-4.state.pool"
--savedpool = "backups/backup.118.SMB2-1.state.pool"

-- HUD options. These can be changed on the fly by pressing 'M' for the mutation rates and 'N' for the network
mutation_rates_disp = false
neural_net_disp = true

--set to false if you want warning popups before loading anything that might cause you to lose your current progress
nopopup = true

savestate_slot = 1 -- Load the level from FCEUX savestate slot. Set to 3 if you are loading a level that mario has reached by completing another level

--SAVE_LOAD_FILE = "test.pool" --filename to be used
SAVE_LOAD_FILE = nil --auto generate appropriate name from level values in ram (might not completely match with actual level)

AllowAutoTurbo = true --Automatic turbo
AllowSlowdownNearMax = false --This is slow down the turbo when it nears to furthest it has currently gotten
FirstGenSpeedup = false --This will speed up the first generation
BottleneckTurbo = false --Activate turbo on bottleneck detection
TurboGenBottleneck = 20 --will start the turbo when it is in a bottleneck for 20 generations. Please adjust to match your taste

World43SavestateSlot = 2

activateNicknames = true --allows you to give species nicknames
displayBasicInfo = true --writes basic info about a species to a file so you can show it in a stream

os.execute("mkdir backups") --create the folder to save the pools in
os.execute("mkdir v3wins") --create a folder for the v3 winning genomes
os.execute("mkdir v2wins") --create a folder for the v2 winning genomes


SavestateObj = savestate.object(savestate_slot)

    ButtonNames = {
        "A",
        "B",
        "up",
        "down",
        "left",
        "right",
    }


BoxRadius = 6
InputSize = (BoxRadius*2+1)*(BoxRadius*2+1)

switchtime = {10,12,18}
switchtimer = {}
initialswitchvalue = {}
for i=1,#switchtime do
    switchtimer[i] = switchtime[i]
    initialswitchvalue[i] = 1
end

Inputs = InputSize+1+#initialswitchvalue+2
Outputs = #ButtonNames

Population = 1000
DeltaDisjoint = 2.0
DeltaWeights = 0.4
DeltaThreshold = 1.0

keyflag = false --used for keyboard input
endlevel = false --flag to detect a level finish
preparenext = false --flag for preparing for the next level
secondbest = 0 --second best fitness
maxright = 0 --Highest fitness without speed compensation
restoreturbo = false --flag for temporary turning off turbo
rerunning = false --flag for requiring rerunning the level if it finished with turbo enabled
killcounter = 0 --number of deaths

StaleSpecies = 25 --increased slightly to allow for longer evolution
mariohole = false --flag for mario falling into a hole
mariopipe = false --flag for mario exiting a pipe
marioPipeEnter = false --new flag for entering a pipe
offset = 0 --offset value for when mario exits a pipe
timebonus = 0 --timebonus to prevent the hard drops in fitness when exiting a pipe
maxcounter = 0 --species that reach the max fitness
currentTracker = 0 --tracks location on screen
loop = false --flag for when a loop is detected
previousmaxfitness = 0 --memory slot for the previous max fitness. used to check if it increased more than a set amount
bottleneckcounter = 0 --amount of generations since last "real" breakthrough

MutateConnectionsChance = 0.25
PerturbChance = 0.90
CrossoverChance = 0.75
LinkMutationChance = 2.0
NodeMutationChance = 0.50
BiasMutationChance = 0.40
SpeedMutationChance = 0.075
StepSize = 0.1
DisableMutationChance = 0.4
EnableMutationChance = 0.2
oscillationmutationchance = 0.2
interbreedchance = 0.03
networkswitchmutationchance = 0.01

nswitch = 1
ntrigger = true

ncount = 0

TimeoutConstant = 120 --set to a higher value but see for yourself what is acceptable

MaxNodes = 1000000

MaxNetworks = 95 --Max networks it is able to have, 95 is basically no limit but you can set it lower
speciesToAutoNetworkSwitch = 10 --Number of gens after each bottleneck loop where network chance is increased
increasedNetworkChance = 0.02 --Increased network chance
rsncChanceDecrease = 0.1 --Multiplier to the rsnc chance of adding new network rather than replacing, applied a number of times equal to the number of new networks
replaceSecondNetworkChance = 0.02 --Chance of rsnc by default
minBnLoopsBeforeNew = 1 --Number of bottleneck loops before the first network switch (increases by 1 per network switch)

gensBetweenPopOscil = 6 --generations after a breakthrough where the population decreases before starting a population oscillation
popOscilMultiplier = 1 --Multiplier on the base length for an oscillation (default is about 20 for the first, 30 for the second, etc)

networkPenaltyInner = 0.7
networkPenaltyOuter = 0.87
-- Multiplies average by (Inner * Outer^networks)^networks to encourage new networks to not take over population until sure they are needed
maxIncreaseWithoutBnReset = 30 --Number the max fitness can increase by before triggering bottleneck reset

hbValue = 60

function getPositions()
        marioX = memory.readbyte(0x6D) * 0x100 + memory.readbyte(0x86)
        marioY = memory.readbyte(0x03B8)+16
        mariostate = memory.readbyte(0x0E) --get mario's state. (entering exiting pipes, dying, picking up a mushroom etc etc)
        yspeed = memory.readbyte(0x009F) --y velocity 1-5 are falling and 250-255 is jumping
        xspeed = memory.readbyte(0x0057) --x position ranging from -48 to 48
        if yspeed >1 and yspeed <10 then
            falling = true
        else
            falling = false
        end

        currentscreen = memory.readbyte(0x071A) --finds current screen for loop detection
        nextscreen = memory.readbyte(0x071B) --finds next screen

        CurrentWorld = memory.readbyte(0x075F) --finds the current world (value + 1 is world)
        CurrentLevel = memory.readbyte(0x0760) --finds the current level (0=1 2=2 3=3 4=4)
        demoruncheck = memory.readbyte(0x0770) --equals 0 for demo and 1 for normal run
        statuscheck = memory.readbyte(0x0772) -- 3= playing 1 = loading

        screenX = memory.readbyte(0x03AD)
        screenY = memory.readbyte(0x03B8)
end

hiddenblocks = {}
hitblocks = 0

function getTile(dx, dy)
        local x = marioX + dx + 8
        local y = marioY + dy - 16
        local page = math.floor(x/256)%2

        local subx = math.floor((x%256)/16)
        local suby = math.floor((y - 32)/16)
        local addr = 0x500 + page*13*16+suby*16+subx

	local tilex = math.floor(x/16)
	local tiley = math.floor(y/16)

	local hbid = 95 - LostLevels
	if (memory.readbyte(addr) == hbid) then
	    local dupe = false
	    for b=1,#hiddenblocks do
		if hiddenblocks[b][1] == tilex and hiddenblocks[b][2] == tiley then
		    dupe = true
		    break
		end
	    end
	    if not dupe and tiley > -1 then
	        table.insert(hiddenblocks,{tilex,tiley})
	    end
	end

	for b=1,#hiddenblocks do
	    if hiddenblocks[b][1] == tilex and hiddenblocks[b][2] == tiley then
                if memory.readbyte(addr) ~= hbid then
	             table.remove(hiddenblocks,b)
		     hitblocks = hitblocks + 1
		     break
		end
	    end
	end

        if suby >= 13 or suby < 0 then
            return 0
        end

        if memory.readbyte(addr) ~= 0 then
            return 1
        else
            return 0
        end
end

function getSprites()
        local sprites = {}
        for slot=0,4 do
            local enemy = memory.readbyte(0xF+slot)
            if enemy ~= 0 then
                local ex = memory.readbyte(0x6E + slot)*0x100 + memory.readbyte(0x87+slot)
                local ey = memory.readbyte(0xCF + slot)+36 --changed this to stop sprites from floating in mid air on the neural network
                sprites[#sprites+1] = {["x"]=ex,["y"]=ey}
            end
        end

        return sprites
end

function getInputs()
    getPositions()

    sprites = getSprites()

    local inputs = {}

    for dy=-BoxRadius*16,BoxRadius*16,16 do
        for dx=-BoxRadius*16,BoxRadius*16,16 do
            inputs[#inputs+1] = 0

            tile = getTile(dx, dy)
            if tile == 1 and marioY+dy < 0x1B0 then
                inputs[#inputs] = 1
            end

            for i = 1,#sprites do
                distx = math.abs(sprites[i]["x"] - (marioX+dx))
                disty = math.abs(sprites[i]["y"] - (marioY+dy+16))
                if distx <= 8 and disty <= 8 then
                    inputs[#inputs] = -1
                end
            end
        end
    end

    --mariovx = memory.read_s8(0x7B)
    --mariovy = memory.read_s8(0x7D)

    return inputs
end

function sigmoid(x)
    return 2/(1+math.exp(-4.9*x))-1
end

function newInnovation()
    pool.innovation = pool.innovation + 1
    return pool.innovation
end

function newGSID()
    pool.gsid = pool.gsid + 1
    return pool.gsid
end

function newPool()
    local pool = {}
    pool.species = {}
    pool.generation = 0
    pool.innovation = Outputs
    pool.currentSpecies = 1
    pool.currentGenome = 1
    pool.currentFrame = 0
	pool.measured = 0
	pool.total = 0
    hitblocks = 0
    hiddenblocks = {}
    pool.maxFitness = 0
    pool.maxcounter = 0  --counter for %max species reached
    pool.gsid = -1
    return pool
end

function newSpecies()
    local species = {}
    species.topFitness = 0
    species.staleness = 0
    species.genomes = {}
    species.averageFitness = 0
    species.nickname = 'none'
	species.turbo = 'on'
    species.gsid = newGSID()
    species.topright = 0
    return species
end

function getCurrentGenome()
    local species = pool.species[pool.currentSpecies]
    return species.genomes[pool.currentGenome]
end

function toRGBA(ARGB)
    return bit.lshift(ARGB, 8) + bit.rshift(ARGB, 24)
end


function newGenome()
    local genome = {}
	genome.old = 0
    genome.genes = {}
    genome.genes[1] = {}
    genome.fitness = 0
    genome.adjustedFitness = 0
    genome.network = {}
    genome.network[1] = {}
    genome.maxneuron = 0
    genome.globalRank = 0
    genome.oscillations = {{}}
    genome.networkswitch = {}
    for i=1,#switchtime do
        genome.oscillations[1][i] = switchtime[i]
    end
    genome.mutationRates = {}
    genome.mutationRates["connections"] = MutateConnectionsChance
    genome.mutationRates["link"] = LinkMutationChance
    genome.mutationRates["bias"] = BiasMutationChance
    genome.mutationRates["node"] = NodeMutationChance
    genome.mutationRates["enable"] = EnableMutationChance
    genome.mutationRates["disable"] = DisableMutationChance
    genome.mutationRates["step"] = StepSize
    genome.mutationRates["oscillation"] = oscillationmutationchance
    genome.mutationRates["networkswitch"] = networkswitchmutationchance

    return genome
end

function copyGenome(genome)
    local genome2 = newGenome()
	genome2.old = genome.old
    for n=1,#genome.genes do
        if n > 1 then
            table.insert(genome2.genes, {})
            table.insert(genome2.oscillations, {})
        end
        for g=1,#genome.genes[n] do
            table.insert(genome2.genes[n], copyGene(genome.genes[n][g]))
        end

        for i=1,#genome.oscillations[n] do
            genome2.oscillations[n][i] = genome.oscillations[n][i]
        end
    end
    for n=1,#genome.networkswitch do
        table.insert(genome2.networkswitch, genome.networkswitch[n])
    end
    genome2.maxneuron = genome.maxneuron
    genome2.mutationRates["connections"] = genome.mutationRates["connections"]
    genome2.mutationRates["link"] = genome.mutationRates["link"]
    genome2.mutationRates["bias"] = genome.mutationRates["bias"]
    genome2.mutationRates["node"] = genome.mutationRates["node"]
    genome2.mutationRates["enable"] = genome.mutationRates["enable"]
    genome2.mutationRates["disable"] = genome.mutationRates["disable"]
    genome2.mutationRates["oscillation"] = genome.mutationRates["oscillation"]
    genome2.mutationRates["networkswitch"] = genome.mutationRates["networkswitch"]

    return genome2
end

function basicGenome()
    local genome = newGenome()
    local innovation = 1

    genome.maxneuron = Inputs
    mutate(genome, 1)

    return genome
end

function newGene()
    local gene = {}
    gene.into = 0
    gene.out = 0
    gene.weight = 0.0
    gene.enabled = true
    gene.innovation = 0

    return gene
end

function copyGene(gene)
    local gene2 = newGene()
    gene2.into = gene.into
    gene2.out = gene.out
    gene2.weight = gene.weight
    gene2.enabled = gene.enabled
    gene2.innovation = gene.innovation

    return gene2
end

function copyGeneOld(gene)
    local gene2 = newGene()
    gene2.into = gene.into
    gene2.out = gene.out
	if gene2.into > Inputs-2 and gene2.into <= MaxNodes then gene2.into = gene2.into + 2 end
	if gene2.out > Inputs-2 and gene2.out <= MaxNodes then gene2.out = gene2.out + 2 end
		
    gene2.weight = gene.weight
    gene2.enabled = gene.enabled
    gene2.innovation = gene.innovation

    return gene2
end

function newNeuron()
    local neuron = {}
    neuron.incoming = {}
    neuron.value = 0.0
    neuron.switcher = false
    neuron.timer = 60
    neuron.multiplier = 1

    return neuron
end

function generateNetwork(genome,printing)
    for n=1,#genome.genes do
        local network = {}
        network.neurons = {}

        for i=1,Inputs do
            network.neurons[i] = newNeuron()
        end

        for o=1,Outputs do
            network.neurons[MaxNodes+o] = newNeuron()
        end

        table.sort(genome.genes[n], function (a,b)
            return (a.out < b.out)
        end)
        for i=1,#genome.genes[n] do
            local gene = genome.genes[n][i]
            if gene.enabled then
                if network.neurons[gene.out] == nil then
                    network.neurons[gene.out] = newNeuron()
                end
                local neuron = network.neurons[gene.out]
                table.insert(neuron.incoming, gene)
                if network.neurons[gene.into] == nil then
                    network.neurons[gene.into] = newNeuron()
                end
			end
        end

        genome.network[n] = network
    end
end

function evaluateNetwork(n, inputs, genome)
    local network = genome.network[n]
	local Inputs = Inputs
	if genome.old >= nswitch then
		Inputs = Inputs -2
	end
    table.insert(inputs, 1) -- bias input node
    for i = 1,#initialswitchvalue do
        if genome.oscillations[n][i] > 0 then --oscillating nodes
            if switchtimer[i] > 0 then
                switchtimer[i] = switchtimer[i] -1
            else
                switchtimer[i] = genome.oscillations[n][i]
                initialswitchvalue[i] = initialswitchvalue[i]*-1
            end
        end
        table.insert(inputs, initialswitchvalue[i])
    end
	if not (genome.old >= nswitch) then --speed nodes
		if (xspeed < 100) then
			table.insert(inputs,xspeed / 48)
		else
			table.insert(inputs,(xspeed - 256) / 48)
		end
		if (yspeed < 10) then
			table.insert(inputs,yspeed / 5)
		else
			table.insert(inputs,(yspeed - 256) / 5)
		end

		if #inputs ~= Inputs then
			return {}
		end
	end
    for i=1,Inputs do
        network.neurons[i].value = inputs[i]
    end
	for _,neuron in pairs(network.neurons) do
        local sum = 0
        for j = 1,#neuron.incoming do
            local incoming = neuron.incoming[j]
            local other = network.neurons[incoming.into]
            sum = sum + incoming.weight * other.value
        end
       
        if #neuron.incoming > 0 then
			if neuron.switcher and sigmoid(sum)>0 then
				neuron.timer = neuron.timer - 1
			elseif neuron.switcher then
				neuron.timer = 120
				neuron.multiplier = 1
			end
			
			if neuron.switcher and neuron.timer < 0 then
				neuron.multiplier = -neuron.multiplier
				neuron.timer = 10
			end
			neuron.value = sigmoid(sum) * neuron.multiplier
			
        end
    end
   
    local outputs = {}
    for o=1,Outputs do
        local button = ButtonNames[o]
        if network.neurons[MaxNodes+o].value > 0 then
            outputs[button] = true
        else
            outputs[button] = false
        end
    end
   
	--emu.print(outputs)
	--emu.print(pool.currentFrame/5)
	--emu.print(network.neurons)
    return outputs
end

function crossover(g1, g2)
    if g2.fitness > g1.fitness then
        tempg = g1
        g1 = g2
        g2 = tempg
    end
    local child = newGenome()
    for n=1,#g1.networkswitch do
        table.insert(child.networkswitch, g1.networkswitch[n])
    end
	child.old = math.min(g1.old,g2.old)
    for n=1,#g1.genes do
        local innovations2 = {}
		local g1old = g1.old >= n
		local g2old = g2.old >= n
        if n > 1 then
            table.insert(child.genes,{})
            table.insert(child.oscillations,{})
        end
        if #g2.genes >= n then
            for i=1,#g2.genes[n] do
                local gene = g2.genes[n][i]
                innovations2[gene.innovation] = gene
            end
            for i=1,#g1.oscillations[n] do
                child.oscillations[n][i] = g1.oscillations[n][i]
            end
        else
            for i=1,#g1.oscillations[n] do
                child.oscillations[n][i] = switchtime[i]
            end
        end
        for i=1,#g1.genes[n] do
            local gene1 = g1.genes[n][i]
            local gene2 = innovations2[gene1.innovation]
			if (g1old and not g2old) then
				if gene2 ~= nil and math.random(1,2) == 1 and gene2.enabled then
					table.insert(child.genes[n], copyGene(gene2))
				else
					table.insert(child.genes[n], copyGeneOld(gene1))
				end
			elseif (g2old and not g1old) then
				if gene2 ~= nil and math.random(1,2) == 1 and gene2.enabled then
					table.insert(child.genes[n], copyGeneOld(gene2))
				else
					table.insert(child.genes[n], copyGene(gene1))
				end
			else
				if gene2 ~= nil and math.random(1,2) == 1 and gene2.enabled then
					table.insert(child.genes[n], copyGene(gene2))
				else
					table.insert(child.genes[n], copyGene(gene1))
				end
			end
        end
    end

    child.maxneuron = math.max(g1.maxneuron,g2.maxneuron)

    for mutation,rate in pairs(g1.mutationRates) do
        child.mutationRates[mutation] = rate
    end

    return child
end

function randomNeuron(genes, nonInput)
    local neurons = {}
    if not nonInput then
        for i=1,Inputs do
            neurons[i] = true
        end
    end
    for o=1,Outputs do
        neurons[MaxNodes+o] = true
    end
    for i=1,#genes do
        if (not nonInput) or genes[i].into > Inputs then
            neurons[genes[i].into] = true
        end
        if (not nonInput) or genes[i].out > Inputs then
            neurons[genes[i].out] = true
        end
    end
    local count = 0
    for _,_ in pairs(neurons) do
        count = count + 1
    end
    local n = math.random(1, count)
    for k,v in pairs(neurons) do
        n = n-1
        if n == 0 then
            return k
        end
    end

    return 0
end

function containsLink(genes, link)
    for i=1,#genes do
        local gene = genes[i]
        if gene.into == link.into and gene.out == link.out then
            return true
        end
    end
end

function pointMutate(genome, which)
    local step = genome.mutationRates["step"]
    local gene = {}
    for i=1,#genome.genes[which] do
        gene = genome.genes[which][i]
        if math.random() < PerturbChance then
            gene.weight = gene.weight + math.random() * step*2 - step
        else
            gene.weight = math.random()*4-2
        end
    end
end

function linkMutate(genome, forceBias, forceSpeed, which)
    local neuron1 = randomNeuron(genome.genes[which], false)
    local neuron2 = randomNeuron(genome.genes[which], true)

    local newLink = newGene()
    if neuron1 <= Inputs and neuron2 <= Inputs then
        --Both input nodes
        return
    end

    if neuron2 <= Inputs then
        -- Swap output and input
        local temp = neuron1
        neuron1 = neuron2
        neuron2 = temp
    end

    newLink.into = neuron1
    newLink.out = neuron2
    if forceBias then
        local adjustment = math.random(0,#initialswitchvalue)
        newLink.into = Inputs - adjustment - 2
    end
    if forceSpeed then
        local adjustment = math.random(0,1)
        newLink.into = Inputs - adjustment
    end
    if containsLink(genome.genes[which], newLink) then
        return
    end
    newLink.innovation = newInnovation()
    newLink.weight = math.random()*4-2
    table.insert(genome.genes[which], newLink)
end

function nodeMutate(genome, which)
    if #genome.genes[which] == 0 then
        return
    end

    genome.maxneuron = genome.maxneuron + 1
    local gene = {}
    gene = genome.genes[which][math.random(1,#genome.genes[which])]
    if not gene.enabled then
        return
    end
    gene.enabled = false

    local gene1 = copyGene(gene)
    gene1.out = genome.maxneuron
    gene1.weight = 1.0
    gene1.innovation = newInnovation()
    gene1.enabled = true
    table.insert(genome.genes[which], gene1)

    local gene2 = copyGene(gene)
    gene2.into = genome.maxneuron
    gene2.innovation = newInnovation()
    gene2.enabled = true
    table.insert(genome.genes[which], gene2)
end

function enableDisableMutate(genome, enable, which)
    local candidates = {}
    for _,gene in pairs(genome.genes[which]) do
        if gene.enabled == not enable then
            table.insert(candidates, gene)
        end
    end

    if #candidates == 0 then
        return
    end

    local gene = candidates[math.random(1,#candidates)]
    gene.enabled = not gene.enabled
end

function oscillationMutate(genome, which)
    mutationpoint = math.random(1,#genome.oscillations[which])
    if genome.oscillations[which][mutationpoint]>0 then
        if math.random(1,2) == 1 then
            genome.oscillations[which][mutationpoint] = genome.oscillations[which][mutationpoint] + 1
        else
            genome.oscillations[which][mutationpoint] = genome.oscillations[which][mutationpoint] - 1
        end
    end
    if genome.oscillations[which][mutationpoint]<0 then
        genome.oscillations[which][mutationpoint] = 0
    end
end

function NswitchMutate(genome)
    which = #genome.networkswitch
    if math.random() < 0.25 then
        which = math.random(1,#genome.networkswitch)
    end
    genome.networkswitch[which] = genome.networkswitch[which] + math.random()-0.5
    if genome.networkswitch[which] < 0 then
        genome.networkswitch[which] = math.random(0,12)
    end
    if genome.networkswitch[which] > 12 then
        genome.networkswitch[which] = math.random(0,12)
    end
    table.sort(genome.networkswitch, function(a,b)
        return (a < b)
    end)
end

function mutate(genome, which)
    for mutation,rate in pairs(genome.mutationRates) do
        if math.random(1,2) == 1 then
            genome.mutationRates[mutation] = 0.95*rate
        else
            genome.mutationRates[mutation] = 1.05263*rate
        end
    end
    if math.random() < genome.mutationRates["connections"] then
        pointMutate(genome, which)
    end

    local p = genome.mutationRates["link"]
    while p > 0 do
        if math.random() < p then
            linkMutate(genome, false, false, which)
        end
        p = p - 1
    end

    p = genome.mutationRates["bias"]
    while p > 0 do
        if math.random() < p then
            linkMutate(genome, true, false, which)
        end
        p = p - 1
    end
    
    p = SpeedMutationChance
	if math.random() < p and genome.old >= which then
		linkMutate(genome, false, true, which)
	end
    p = p - 1

    p = genome.mutationRates["node"]
    while p > 0 do
        if math.random() < p then
            nodeMutate(genome, which)
        end
        p = p - 1
    end

    p = genome.mutationRates["enable"]
    while p > 0 do
        if math.random() < p then
            enableDisableMutate(genome, true, which)
        end
        p = p - 1
    end

    p = genome.mutationRates["disable"]
    while p > 0 do
        if math.random() < p then
            enableDisableMutate(genome, false, which)
        end
        p = p - 1
    end

    p = genome.mutationRates["oscillation"]
    while p > 0 do
        if math.random() < p then
            oscillationMutate(genome, which)
        end
        p = p - 1
    end

    if #genome.networkswitch > 0 then
        p = genome.mutationRates["networkswitch"]
        while p > 0 do
            if math.random() < p then
                NswitchMutate(genome)
            end
            p = p - 1
        end
    end
end

function disjoint(genes1, genes2)
    local i1 = {}
    for i = 1,#genes1 do
        local gene = genes1[i]
        i1[gene.innovation] = true
    end

    local i2 = {}
    for i = 1,#genes2 do
        local gene = genes2[i]
        i2[gene.innovation] = true
    end

    local disjointGenes = 0
    for i = 1,#genes1 do
        local gene = genes1[i]
        if not i2[gene.innovation] then
            disjointGenes = disjointGenes+1
        end
    end

    for i = 1,#genes2 do
        local gene = genes2[i]
        if not i1[gene.innovation] then
            disjointGenes = disjointGenes+1
        end
    end

    local n = math.max(#genes1, #genes2)

    return disjointGenes / n
end

function weights(genes1, genes2)
    local i2 = {}
    for i = 1,#genes2 do
        local gene = genes2[i]
        i2[gene.innovation] = gene
    end

    local sum = 0
    local coincident = 0
    for i = 1,#genes1 do
        local gene = genes1[i]
        if i2[gene.innovation] ~= nil then
            local gene2 = i2[gene.innovation]
            sum = sum + math.abs(gene.weight - gene2.weight)
            coincident = coincident + 1
        end
    end
    if coincident == 0 then
        return 10
    end
    return sum / coincident
end

function sameSpecies(genome1, genome2)
    if #genome1.networkswitch ~= #genome2.networkswitch then
        return false
    end
    for n=1,#genome1.networkswitch do
        if math.abs(genome1.networkswitch[n] - genome2.networkswitch[n]) > 0.6 then
            return false
        end
    end
    for n=1,#genome1.genes do
        --if genome2.genes[n] == nil then
            --emu.print(genome1.genes)
            --emu.print(genome1.networkswitch)
            --emu.print(genome2.genes)
            --emu.print(genome2.networkswitch)
        --end
        dd = DeltaDisjoint*disjoint(genome1.genes[n],genome2.genes[n])
        dw = DeltaWeights*weights(genome1.genes[n],genome2.genes[n])
        if dd + dw > DeltaThreshold then
            return false
        end
    end
    return true
end

function rankGlobally()
    local global = {}
    for s = 1,#pool.species do
        local species = pool.species[s]
        for g = 1,#species.genomes do
            table.insert(global, species.genomes[g])
        end
    end
    table.sort(global, function (a,b)
        return (a.fitness < b.fitness)
    end)

    for g=1,#global do
        global[g].globalRank = g
    end
end

function calculateAverageFitness(species)
    local total = 0

    for g=1,#species.genomes do
        local genome = species.genomes[g]
        total = total + genome.globalRank
    end
        if species.topFitness < pool.averagemaxfitness - (pool.standardDeviationMaxFitness *2) then
            species.averageFitness = (total / #species.genomes) / 4
        elseif species.topFitness < pool.averagemaxfitness - pool.standardDeviationMaxFitness then
            species.averageFitness = (total / #species.genomes) / 2.5
        elseif species.topFitness > pool.averagemaxfitness + (pool.standardDeviationMaxFitness *3) then
            species.averageFitness = (total / #species.genomes) * 2
        elseif species.topFitness > pool.averagemaxfitness + (pool.standardDeviationMaxFitness *2) then
            species.averageFitness = (total / #species.genomes) * 1.5
        else
            species.averageFitness = total / #species.genomes
        end
        species.averageFitness = species.averageFitness * math.pow(networkPenaltyOuter*math.pow(networkPenaltyInner,#species.genomes[1].networkswitch),#species.genomes[1].networkswitch)
end

function calculateStandardDeviationMax()
    local deviationtotal = 0
    for s=1,#pool.species do
        deviationtotal = deviationtotal + math.abs(pool.species[s].topFitness - pool.averagemaxfitness)
    end
    pool.standardDeviationMaxFitness = deviationtotal / #pool.species
end

function AverageMaxFitness()
    local total = 0
    for s = 1,#pool.species do
        local species = pool.species[s]
        total = total + species.topFitness
    end

    pool.averagemaxfitness = total / #pool.species
end

function totalAverageFitness()
    local total = 0
    for s = 1,#pool.species do
        local species = pool.species[s]
        total = total + species.averageFitness
    end

    return total
end

function cullSpecies(cutToOne)
    for s = 1,#pool.species do
        local species = pool.species[s]

        table.sort(species.genomes, function (a,b)
            return (a.fitness > b.fitness)
        end)

        local percent = 0.5
        --if species.staleness > 10 then
            --percent = math.pow(0.5,(species.staleness+5)/15)
        --end
        local remaining = math.ceil(#species.genomes*percent)
        if cutToOne then
            remaining = 1
        end
        while #species.genomes > remaining do
            table.remove(species.genomes)
        end
    end
end

function breedChild(species)
    local child = {}
    if math.random() < CrossoverChance then
        g1 = species.genomes[math.random(1, #species.genomes)]
        g2 = species.genomes[math.random(1, #species.genomes)]
        child = crossover(g1, g2)
    else
        g = species.genomes[math.random(1, #species.genomes)]
        child = copyGenome(g)
    end

    local which = #child.genes
    if which > 1 and species.topright > 0 then
		emu.print(child.networkswitch[#child.networkswitch])
        local mutatePrevNetworkChance = 0.5 + (child.networkswitch[#child.networkswitch]-species.topright/500)/2
        if math.random() < mutatePrevNetworkChance then
            which = #child.genes - 1
        end
    end
    
    mutate(child,which)

    return child
end

function secondbestspecies() --added this to help prevent the formation of monospecies when LuigI/O encounters a major bottleneck
    local bestfitness = 0
    local secondbestfitness = 0
    for s = 1,#pool.species do
        local species = pool.species[s]

        if species.topFitness > bestfitness then
            secondbestfitness = bestfitness
            bestfitness = species.topFitness
        elseif species.topFitness > secondbestfitness then
            secondbestfitness = species.topFitness
        end
    end
    return secondbestfitness
end


function removeStaleSpecies()
    local survived = {}
    --emu.print("Max Fitness: ".. pool.maxFitness ..". second best: ".. secondbest)
    for s = 1,#pool.species do
        local species = pool.species[s]

        table.sort(species.genomes, function (a,b)
            return (a.fitness > b.fitness)
        end)

        if species.genomes[1].fitness > species.topFitness then
            species.topFitness = species.genomes[1].fitness
            species.staleness = 0
        else
            species.staleness = species.staleness + 1
        end
    end
    secondbest = secondbestspecies()

    for s = 1,#pool.species do
        local species = pool.species[s]
        if species.staleness < StaleSpecies or species.topFitness >= secondbest then --originally species.topFitness >= pool.maxFitness
            table.insert(survived, species)
        end
    end

    pool.species = survived
end

function removeWeakSpecies()
    local survived = {}
	local breed
    local sum = totalAverageFitness()
    for s = 1,#pool.species do
        local species = pool.species[s]
        breed = math.floor(species.averageFitness / sum * Population)
        if breed >= 1 then
            table.insert(survived, species)
        end
    end

    pool.species = survived
end


function addToSpecies(child)
    local foundSpecies = false
    for s=1,#pool.species do
        local species = pool.species[s]
        if not foundSpecies and sameSpecies(child, species.genomes[1]) then
            table.insert(species.genomes, child)
            foundSpecies = true
        end
    end

    if not foundSpecies then
        local childSpecies = newSpecies()
        table.insert(childSpecies.genomes, child)
        table.insert(pool.species, childSpecies)
    end
end

function replaceSecondNetwork(g1,g2,tr)
    local genome2 = newGenome()
	
	for n=1,#g1.genes do
        if n > 1 then
            table.insert(genome2.genes,{})
            table.insert(genome2.oscillations,{})
        end
		if g1.old >= n then
			for g=1,#g1.genes[n] do
				table.insert(genome2.genes[n], copyGeneOld(g1.genes[n][g]))
			end
		else
			for g=1,#g1.genes[n] do
				table.insert(genome2.genes[n], copyGene(g1.genes[n][g]))
			end
		end
        for i=1,#g1.oscillations[n] do
            genome2.oscillations[n][i] = g1.oscillations[n][i]
        end
    end
    for n=1,#g1.networkswitch do
        genome2.networkswitch[n] = g1.networkswitch[n]
    end
    genome2.maxneuron = g1.maxneuron
    genome2.mutationRates["connections"] = g1.mutationRates["connections"]
    genome2.mutationRates["link"] = g1.mutationRates["link"]
    genome2.mutationRates["bias"] = g1.mutationRates["bias"]
    genome2.mutationRates["node"] = g1.mutationRates["node"]
    genome2.mutationRates["enable"] = g1.mutationRates["enable"]
    genome2.mutationRates["disable"] = g1.mutationRates["disable"]
    genome2.mutationRates["oscillation"] = g1.mutationRates["oscillation"]
    genome2.mutationRates["networkswitch"] = g1.mutationRates["networkswitch"]

    if g1.fitness + 300 <= pool.maxFitness or math.random() > math.pow(rsncChanceDecrease,#genome2.networkswitch) or #genome2.genes >= MaxNetworks or bnLoops < #genome2.genes then
        
		genome2.genes[#genome2.genes] = {}
        which = math.random(1,#g2.genes)
		if g2.old >= which then
			for g=1,#g2.genes[which] do
				table.insert(genome2.genes[#genome2.genes], copyGeneOld(g2.genes[which][g]))
			end
		else
			for g=1,#g2.genes[which] do
				table.insert(genome2.genes[#genome2.genes], copyGene(g2.genes[which][g]))
			end
		end
    else
        table.insert(genome2.genes,{})
        which = math.random(1,#g2.genes)
		if g2.old >= which then
			for g=1,#g2.genes[which] do
				table.insert(genome2.genes[#genome2.genes], copyGeneOld(g2.genes[which][g]))
			end
		else
			for g=1,#g2.genes[which] do
				table.insert(genome2.genes[#genome2.genes], copyGene(g2.genes[which][g]))
			end
		end
        table.insert(genome2.oscillations,{switchtime[1],switchtime[2],switchtime[3]})
        table.insert(genome2.networkswitch,tr/500 - 0.2-0.1*math.random())
    end
    table.sort(genome2.networkswitch, function(a,b)
        return (a < b)
    end)
    return genome2
end

function FileExists(name)
	local file = io.open(name,"r")
	if file~=nil then io.close(file) return true else return false end
end

bnLoops = 0
function newGeneration()
    writeFile("backups/backup3." .. pool.generation .. "." .. SAVE_LOAD_FILE)
	if originalmaxfitness == nil or originalmaxfitness > previousmaxfitness then
		originalmaxfitness = previousmaxfitness
	end
	local population = Population
    if pool.maxFitness-maxIncreaseWithoutBnReset > previousmaxfitness then
        previousmaxfitness = pool.maxFitness
		originalmaxfitness = pool.maxFitness
        bottleneckcounter = 0
        if AllowAutoTurbo then
            emu.speedmode("normal")
            turbo = false
        end
        bnLoops = 0
	elseif pool.maxFitness - (4*maxIncreaseWithoutBnReset) > originalmaxfitness then
		previousmaxfitness = pool.maxFitness
		originalmaxfitness = pool.maxFitness
        bottleneckcounter = 0
        if AllowAutoTurbo then
            emu.speedmode("normal")
            turbo = false
        end
        bnLoops = 0
    else
        bottleneckcounter = bottleneckcounter + 1
		previousmaxfitness = pool.maxFitness
    end
	local bottleneckc = bottleneckcounter
	local GBPO = gensBetweenPopOscil
    local targetPop = math.min(900,500 + 100*bnLoops)
    local length= math.min(12*popOscilMultiplier,(5 + 2*bnLoops)*popOscilMultiplier)
    local targetPopLower = math.min(300,600 - targetPop/2)
    local currentPopLower = math.min(300,targetPopLower+50)

    if bottleneckc <= GBPO then
	if population > 300 then
            population = math.floor(population * 0.905 * 0.905)
            if population < 300 then population = 300 end
        end
    end
    if bottleneckc > GBPO then
        if bottleneckc < GBPO + length then
            population = currentPopLower + math.floor((targetPop - currentPopLower)/length*(bottleneckc-GBPO))
        elseif bottleneckc == GBPO + length then
            population = targetPop
        elseif bottleneckc <= GBPO + length*3 then
            population = targetPopLower + math.floor((targetPop - targetPopLower)/length/2*(GBPO+length*3-bottleneckc))
        end
        if bottleneckc == GBPO + length*3 then
            bottleneckcounter = 0
            bnLoops = bnLoops + 1
        end
    end
    if bottleneckcounter > TurboGenBottleneck and AllowAutoTurbo and BottleneckTurbo then
        emu.speedmode("turbo")
        turbo = true
    end
	
	Population = population


    cullSpecies(false) -- Cull the bottom half of each species
    rankGlobally()
    removeStaleSpecies()
    AverageMaxFitness()
    calculateStandardDeviationMax()
    rankGlobally()
	local numSpecies = #pool.species
    for s = 1,numSpecies do
        local species = pool.species[s]
        calculateAverageFitness(species)
    end
    removeWeakSpecies()
    local sum = totalAverageFitness()
    local children = {}
	local breed
    for s = 1,#pool.species do
        local species = pool.species[s]
        breed = math.floor(species.averageFitness / sum * population) - 1
        if breed > 10 then
            breed = math.ceil(breed * math.sqrt(species.topFitness / pool.maxFitness))
        end
        if breed > population/4 then
            breed = math.floor(Population/4)
        end
        for i=1,breed do
            table.insert(children, breedChild(species))
        end
    end
    cullSpecies(true) -- Cull all but the top member of each species
    if #pool.species < 30 then
        interbreedchance = 0.2
    else
        interbreedchance = 0.03
    end
    for i=1,#pool.species do
        if math.random() < interbreedchance then
            local counterbreed = math.random(1, #pool.species)
            if counterbreed ~= i then
                table.insert(children, crossover(pool.species[i].genomes[1], pool.species[counterbreed].genomes[1]))

            end
        end
            if pool.species[i].topFitness + 300 > pool.maxFitness and (math.random() < increasedNetworkChance*(bnLoops - #pool.species[i].genomes[1].networkswitch) or #pool.species <= speciesToAutoNetworkSwitch) and #pool.species[i].genomes[1].genes < MaxNetworks then
                local tfit = pool.species[i].topFitness
                child = copyGenome(pool.species[i].genomes[1])
                switchlocation = pool.species[i].topright/500 - 0.2 - 0.1*math.random()
                table.insert(child.networkswitch,switchlocation)
                table.insert(child.oscillations,{switchtime[1],switchtime[2],switchtime[3]})
                table.insert(child.genes,{})
                table.insert(children, child)
                table.sort(child.networkswitch, function(a,b)
                    return (a < b)
    		end)
				emu.print(pool.species[i].genomes[1].fitness)
				emu.print(switchlocation)
            end
        if math.random() < replaceSecondNetworkChance and pool.species[i].topFitness > 500 then
            if #pool.species[i].genomes[1].networkswitch > 0 then
                if math.random() < 0.5 then
                    local donornetwork = math.random(1, #pool.species)
                    if donornetwork ~= i then
                        table.insert(children, replaceSecondNetwork(pool.species[i].genomes[1], pool.species[donornetwork].genomes[1],pool.species[i].topright))
                    end
                end
            else
                local donornetwork = math.random(1, #pool.species)
                if donornetwork ~= i then
                    table.insert(children, replaceSecondNetwork(pool.species[i].genomes[1], pool.species[donornetwork].genomes[1],pool.species[i].topright))
                end
            end
        end
    end
    while #children + #pool.species < Population do
        local species = pool.species[math.random(1, #pool.species)]
        table.insert(children, breedChild(species))
    end
    for c=1,#children do
        local child = children[c]
        addToSpecies(child)
    end
    local children = {}
    local replace = 0
    for s=1,#pool.species do
        local species = pool.species[s]
        if species.topFitness < secondbest and #species.genomes > Population/12 then
            while #species.genomes > Population/12 do
                table.remove(species.genomes)
                replace = replace + 1
            end
        elseif species.topFitness >= secondbest and #species.genomes>Population/7 then
            while #species.genomes > Population/7 do
                table.remove(species.genomes)
                replace = replace + 1
            end
        end
    end
    for r=1,replace do
        local species = pool.species[math.random(1, #pool.species)]
        table.insert(children, breedChild(species))
    end
    for c=1,#children do
        local child = children[c]
        addToSpecies(child)
    end
    count = 0
    for s=1,#pool.species do
        local species = pool.species[s]
        if species.topFitness < secondbest and #species.genomes > Population/12 then
            while #species.genomes > Population/12 do
                table.remove(species.genomes)
            end
        elseif species.topFitness >= secondbest and #species.genomes>Population/7 then
            while #species.genomes > Population/7 do
                table.remove(species.genomes)
            end
        end
        count = count + #species.genomes
    end

    --emu.print("Count: " .. count)
	secondbest = secondbestspecies()
    pool.generation = pool.generation + 1
    pool.maxcounter = 0 --reset max fitness counter

    --gsidFile("backups/gsid." .. pool.generation .. "." .. SAVE_LOAD_FILE)
    writeFile("backups/backup3." .. SAVE_LOAD_FILE)
    writelatestgen() --tracker for the latest generation
end

function initializePool()
    pool = newPool()
	added = LoadPreviousV2Win()
	added = added + LoadPreviousV3Win(added)
	local basic
    for i=1,Population-added do
        basic = basicGenome()
        addToSpecies(basic)
    end

    initializeRun()
end

function clearJoypad()
    controller = {}
    for b = 1,#ButtonNames do
        controller[ButtonNames[b]] = false
    end
    joypad.set(player, controller)
end

function LoadPreviousV3Win(start)
	if FileExists('v3wins.txt') then
		local file = io.open('v3wins.txt', "r")
		local line = file:read("*line")
		local count = 0
		while line ~= nil do
			PlaceV3Genome(line)
			count = count + 1
			line = file:read("*line")
		end
		file:close()
		
		local file = io.open('v3nicks.txt', "r")
		local line = file:read("*line")
		local count2 = start
		while line ~= nil do
			count2 = count2 + 1
			pool.species[count2].nickname = line
			line = file:read("*line")
		end
		file:close()
		return count
	else
		return 0
	end
end

function LoadPreviousV2Win()
	if FileExists('v2wins.txt') then
		local file = io.open('v2wins.txt', "r")
		local line = file:read("*line")
		local count = 0
		while line ~= nil do
			PlaceGenome(line)
			count = count + 1
			line = file:read("*line")
		end
		file:close()
		local file = io.open('v2nicks.txt', "r")
		local line = file:read("*line")
		local count2 = 0
		while line ~= nil do
			count2 = count2 + 1
			pool.species[count2].nickname = line
			line = file:read("*line")
		end
		file:close()
		return count
	else
		return 0
	end
end

function PlaceV3Genome(filename)
	if FileExists(filename) then
		local file = io.open(filename, "r")
		local genome = newGenome()
		local innov = pool.innovation
		genome.fitness = 0
		genome.old = 0
		genome.maxneuron = file:read("*number")
		local line = file:read("*line")
		while line ~= "done" do
			genome.mutationRates[line] = file:read("*number")
			line = file:read("*line")
		end
		local splits = file:read("*number")
		
		local highinnov = 0
		print(splits)
		for s=1,splits do
			local numGenes = file:read("*number")
			for n=1,numGenes do
				local gene = newGene()
				table.insert(genome.genes[s], gene)
				local enabled
				gene.into, gene.out, gene.weight, gene.innovation, enabled = file:read("*number", "*number", "*number", "*number", "*number")
				if gene.innovation > highinnov then highinnov = gene.innovation end
				gene.innovation = gene.innovation + innov
				-- if gene.into > Inputs-2 and gene.into <= Inputs then gene.into = gene.into + 2 end
				-- if gene.out > Inputs-2 and gene.out <= Inputs then gene.out = gene.out + 2 end
				--gene.into = gene.into+2
				--gene.out = gene.out+2
				if enabled == 0 then
					gene.enabled = false
				else
					gene.enabled = true
				end
			end
			if s < splits then
				table.insert(genome.genes,{})
				table.insert(genome.oscillations,{})
			end
		end
		for n=1,splits-1 do
			genome.networkswitch[n] = file:read("*number")
		end
		local numosci = 3
		for n=1,splits do

			for o=1,numosci do
				genome.oscillations[n][o] = file:read("*number")
			end
		end
		pool.innovation = pool.innovation + highinnov
		addToSpecies(genome)
		file:close()
	end
end

function PlaceGenome(filename)
	filename = filename .. ".txt"
	if FileExists(filename) then
		emu.print("loading in genome at location " .. filename)
		
		local file = io.open(filename, "r")
		local genome = newGenome()
		local innov = pool.innovation
		genome.fitness = 0
		genome.old = 1
		genome.maxneuron = file:read("*number")
		local line = file:read("*line")
		while line ~= "done" do
			genome.mutationRates[line] = file:read("*number")
			line = file:read("*line")
		end
		local numGenes = file:read("*number")
		local highinnov = 0
		for n=1,numGenes do
			local gene = newGene()
			table.insert(genome.genes[1], gene)
			local enabled
			gene.into, gene.out, gene.weight, gene.innovation, enabled = file:read("*number", "*number", "*number", "*number", "*number")
			if gene.innovation > highinnov then highinnov = gene.innovation end
			gene.innovation = gene.innovation + innov
			-- if gene.into > Inputs-2 and gene.into <= Inputs then gene.into = gene.into + 2 end
			-- if gene.out > Inputs-2 and gene.out <= Inputs then gene.out = gene.out + 2 end
			--gene.into = gene.into+2
			--gene.out = gene.out+2
			if enabled == 0 then
				gene.enabled = false
			else
				gene.enabled = true
			end
		end
		--table.insert(genome.genes,{})
		table.insert(genome.oscillations,{})
		local numGenes2 = file:read("*number")
		genes2 = {}
		for n=1,numGenes2 do
			local gene2 = newGene()
			table.insert(genes2, gene2)
			local enabled
			--I am able to revert back to the original loading script with FCEUX
			gene2.into, gene2.out, gene2.weight, gene2.innovation, enabled = file:read("*number", "*number", "*number", "*number", "*number")
			if gene2.innovation > highinnov then highinnov = gene2.innovation end
			gene2.innovation = gene2.innovation + innov
			-- if gene2.into > Inputs-2 and gene2.into <= Inputs then gene2.into = gene2.into + 2 end
			-- if gene2.out > Inputs-2 and gene2.out <= Inputs then gene2.out = gene2.out + 2 end
			
			if enabled == 0 then
				gene2.enabled = false
			else
				gene2.enabled = true
			end
		end
		pool.innovation = pool.innovation + highinnov
		local ns = file:read("*number")
		local numosci = file:read("*number")
		for i=1,numosci do
			genome.oscillations[1][i] = file:read("*number")
		end
		if (ns > 0) then
			genome.old = 2
			genome.genes[2] = genes2
			for i=1,numosci do
				genome.oscillations[2][i] = genome.oscillations[1][i]
			end
			table.insert(genome.networkswitch,ns)
		end
		
		
		addToSpecies(genome)
		file:close()
	end
end

function initializeRun()

    savestate.load(SavestateObj);
    rightmost = 0
    pool.currentFrame = 0
    hitblocks = 0
	timebonus = 0
    hiddenblocks = {}
    timeout = TimeoutConstant
    clearJoypad()
    currentTracker = memory.readbyte(0x071A) --sets the current tracker to the current screen
	local measured = 0
	local total = 0
	for _,species in pairs(pool.species) do
		for _,genome in pairs(species.genomes) do
			total = total + 1
			if genome.fitness ~= 0 then
				measured = measured + 1
			end
		end
	end
	pool.measured = measured
	pool.total = total
    local species = pool.species[pool.currentSpecies]
    local genome = species.genomes[pool.currentGenome]
    for i=1,#genome.oscillations[1] do
        switchtimer[i] = genome.oscillations[1][i]
        initialswitchvalue[i] = 1
    end
    generateNetwork(genome,true)
    evaluateCurrent()
end

function reRun()
    savestate.load(savestate.object(previous_savestate));
    rightmost = 0
    pool.currentFrame = 0
    hitblocks = 0
    hiddenblocks = {}
    timeout = TimeoutConstant
    clearJoypad()
    currentTracker = memory.readbyte(0x071A) --sets the current tracker to the current screen
    offset = 0 --offset in x coordinates for pipe
    timebonus = 0 --used to freeze fitness
    mariohole = false --reset the fallen into hole variable
    mariopipe = false --is mario exiting a pipe or just teleporting
    loop = false --is this a loop?
    marioPipeEnter = false --has mario entered a pipe
    currentTracker = 1 --tracker for the loop
    killtrigger = false
    ntrigger = true
    nswitch = 1
    local species = pool.species[pool.currentSpecies]
    local genome = species.genomes[pool.currentGenome]
    for i=1,#genome.oscillations[1] do
        switchtimer[i] = genome.oscillations[1][i]
        initialswitchvalue[i] = 1
    end
    generateNetwork(genome,true)
    evaluateCurrent()
end

function evaluateCurrent()
    local species = pool.species[pool.currentSpecies]
    local genome = species.genomes[pool.currentGenome]

	--emu.print(nswitch)
    inputs = getInputs()
    controller = evaluateNetwork(nswitch, inputs, genome)

    if controller["left"] and controller["right"] then
        controller["left"] = false
        controller["right"] = false
    end
    if controller["up"] and controller["down"] then
        controller["up"] = false
        controller["down"] = false
    end

    joypad.set(player, controller)
end

if pool == nil then
    initializePool() --------------------------------------------------------------------------------------------------------------------------------------------------------
end


function nextGenome()
    pool.currentGenome = pool.currentGenome + 1
    if pool.currentGenome > #pool.species[pool.currentSpecies].genomes then
        pool.currentGenome = 1
        pool.currentSpecies = pool.currentSpecies+1
        if pool.currentSpecies > #pool.species then
            newGeneration()
            pool.currentSpecies = 1
        end
    end
end

function fitnessAlreadyMeasured()
    local species = pool.species[pool.currentSpecies]
    local genome = species.genomes[pool.currentGenome]
	--return false
    return genome.fitness ~= 0
end

function exportGenome(genome, nickname)
	local filename = "v3wins/v3-" .. CurrentWorld+1 .."-".. CurrentLevel .. "-H.txt"
	local file2 = io.open("v3wins.txt", "a")
	file2:write(filename .. "\n")
	file2:close()
	local file3 = io.open("v3nicks.txt", "a")
	if nickname == "none" then
		file3:write("nameless winner" .. "\n")
	else
		file3:write(nickname .. "\n")
	end
	file3:close()
    local file = io.open(filename, "w")
	file:write(genome.maxneuron .. "\n")
	for mutation,rate in pairs(genome.mutationRates) do
		file:write(mutation .. "\n")
		file:write(rate .. "\n")
	end
	file:write("done\n")
	file:write(#genome.genes .. "\n")
	for k,network in pairs(genome.genes) do
		file:write(#network .. "\n")
		for l,gene in pairs(network) do
			file:write(gene.into .. " ")
			file:write(gene.out .. " ")
			file:write(gene.weight .. " ")
			file:write(gene.innovation .. " ")
			if(gene.enabled) then
				file:write("1\n")
			else
				file:write("0\n")
			end
		end
		--emu.print(#network)
	end
	--emu.print(#genome.genes)
	for i,ns in pairs(genome.networkswitch) do
		file:write(ns .. "\n")
	end
	--emu.print(genome.oscillations)
	for i,osc in pairs(genome.oscillations) do
		file:write(#osc .. "\n")
		for i,oscn in pairs(osc) do
			file:write(oscn .. "\n")
		end
	end
	file:write(genome.old)
    file:close()
end

function GenerateNewKeepBest(genome, nickname)
    Population = 1000
    previousbest = copyGenome(genome)
	exportGenome(previousbest, nickname) --saves the winning genome
    previousmaxfitness = 1
	originalmaxfitness = 1
    maxright = 1
    offset = 0 --offset in x coordinates for pipe
    timebonus = 0 --used to freeze fitness
    timeout = TimeoutConstant
    mariohole = false --reset the fallen into hole variable
    mariopipe = false --is mario exiting a pipe or just teleporting
    loop = false --is this a loop?
    marioPipeEnter = false --has mario entered a pipe
    currentTracker = 1 --tracker for the loop
    pool = newPool()
	added = LoadPreviousV2Win()
	added = added + LoadPreviousV3Win(added)
    --addToSpecies(previousbest)
    for i=1,Population-added do
        basic = basicGenome()
        addToSpecies(basic)
    end
    initializeRun()
end

function displayGenome(genome)
    gui.opacity(0.53)
	local Inputs = Inputs
	local nswitch = nswitch
	local BoxRadius = BoxRadius
	if genome.old >= nswitch then
		Inputs = Inputs -2
	end
    if not genome then return end
    local network = {}
    network = genome.network[nswitch]
    local cells = {}
    local i = 1
    local cell = {}
    for dy=-BoxRadius,BoxRadius do
        for dx=-BoxRadius,BoxRadius do
            cell = {}
            cell.x = 50+5*dx
            cell.y = 70+5*dy
            cell.value = network.neurons[i].value
            cells[i] = cell
            i = i + 1
        end
    end
    local biasCell = {}
    biasCell.x = 80
    biasCell.y = 110
	local switchCell = {}
	local speedCell = {}
	if genome.old >= nswitch then
		biasCell.value = network.neurons[Inputs-#initialswitchvalue].value
		cells[Inputs-#initialswitchvalue] = biasCell
		for i=0,#initialswitchvalue-1 do
			switchCell = {}
			switchCell.x = 80-10*#initialswitchvalue+10*i
			switchCell.y = 110
			switchCell.value = network.neurons[Inputs-i].value
			cells[Inputs-i] = switchCell
		end
	else
		biasCell.value = network.neurons[Inputs-#initialswitchvalue-2].value
		cells[Inputs-#initialswitchvalue-2] = biasCell
		for i=0,#initialswitchvalue-1 do
			switchCell = {}
			switchCell.x = 80-10*#initialswitchvalue+10*i
			switchCell.y = 110
			switchCell.value = network.neurons[Inputs-i-2].value
			cells[Inputs-i-2] = switchCell
		end
		for i=0,1 do
			speedCell = {}
			speedCell.x = 80 - 10*(6)+10*i
			speedCell.y = 110
			speedCell.value = network.neurons[Inputs-i].value
			cells[Inputs-i] = speedCell
		end
	end

    gui.drawbox(215,32,245,82,toRGBA(0x80808080),toRGBA(0x00000000))
	local color
    gui.opacity(0.85)
    for o = 1,Outputs do
        cell = {}
        cell.x = 220
        cell.y = 30 + 8 * o
        cell.value = network.neurons[MaxNodes + o].value
        cells[MaxNodes+o] = cell
        
        if cell.value > 0 then
            color = 0xFF0000FF
        else
            color = 0xFF777777-- original color = 0xFF000000
        end
        gui.drawtext(225, 26+8*o, ButtonNames[o], toRGBA(color), 0x0) --moved slightly for better alignment
    end
    for n,neuron in pairs(network.neurons) do
        cell = {}
        if n > Inputs and n <= MaxNodes then
            cell.x = 140
            cell.y = 40
            cell.value = neuron.value
            -- if neuron.value >0 then
                -- neuron.switcher = true
            -- end
            cells[n] = cell
        end
    end
    local genes = {}
    genes = genome.genes[nswitch]
    for n=1,4 do
        for _,gene in pairs(genes) do
            if gene.enabled then
                local c1 = cells[gene.into]
                local c2 = cells[gene.out]
                if gene.into > Inputs and gene.into <= MaxNodes then
                    c1.x = 0.75*c1.x + 0.25*c2.x
                    if c1.x >= c2.x then
                        c1.x = c1.x - 40
                    end
                    if c1.x < 90 then
                        c1.x = 90
                    end

                    if c1.x > 220 then
                        c1.x = 220
                    end
                    c1.y = 0.75*c1.y + 0.25*c2.y

                end
                if gene.out > Inputs and gene.out <= MaxNodes then
                    c2.x = 0.25*c1.x + 0.75*c2.x
                    if c1.x >= c2.x then
                        c2.x = c2.x + 40
                    end
                    if c2.x < 90 then
                        c2.x = 90
                    end
                    if c2.x > 220 then
                        c2.x = 220
                    end
                    c2.y = 0.25*c1.y + 0.75*c2.y
                end
            end
        end
    end

    gui.drawbox(50-BoxRadius*5-3,70-BoxRadius*5-3,50+BoxRadius*5+2,70+BoxRadius*5+2, toRGBA(0x80808080), toRGBA(0xFF000000))
    for n,cell in pairs(cells) do
        if n > Inputs or cell.value ~= 0 then
            color = math.floor((cell.value+1)/2*256)
            if color > 255 then color = 255 end
            if color < 0 then color = 0 end
            local opacity = 0xFF000000
            if cell.value == 0 then
                opacity = 0x50000000
            end
            inversecolor = (color - 255) * (-1)
            bordercolor = 0x50000000 + inversecolor*0x10000 + inversecolor*0x100 + inversecolor
            color = opacity + color*0x10000 + color*0x100 + color
            gui.drawbox(cell.x-2,cell.y-2,cell.x+2,cell.y+2,toRGBA(color), toRGBA(bordercolor))
        end
    end
    for _,gene in pairs(genes) do
        if gene.enabled then
            local c1 = cells[gene.into]
            local c2 = cells[gene.out]
            local opacity = 0xF0000000
            if pool.generation > 50 then
                    opacity = 0x80000000
                end
            if c1.value == 0 then
                if pool.generation <10 then --slowly reducing the visibility of non active connections
                    opacity = 0x80000000
                elseif pool.generation < 15 then
                    opacity = 0x60000000
                elseif pool.generation < 25 then
                    opacity = 0x40000000
                end
            end
            local color = 0x80-math.floor(math.abs(sigmoid(gene.weight))*0x80)
            if gene.weight > 0 then
                color = opacity + 0x8000 + 0x10000*color
            else
                color = opacity + 0x800000 + 0x100*color
            end
            if c1.value ~= 0 or pool.generation < 5 then -- remove non active connections from generation 50 onwards
                gui.drawline(c1.x+1, c1.y, c2.x-3, c2.y, toRGBA(color))
            end
        end
    end

    gui.drawbox(49,71,51,78,toRGBA(0x80FF0000),toRGBA(0x00000000))
    if mutation_rates_disp then
        local pos = 120
        for mutation,rate in pairs(genome.mutationRates) do
            gui.drawtext(16, pos, mutation .. ": " .. rate, toRGBA(0xFF000000), 0x0)
            pos = pos + 8
        end
    end
end

function toBase95(num,places)
    local str = ""
    for p=1,places do
        local numPlace = math.floor(num / math.pow(95,p-1))
        str = str .. string.char((numPlace % 95) + 32)
    end
    return str
end

function fromBase95(str,places)
    local num = 0
    for p=1,string.len(str) do
        local numPlace = string.byte(string.sub(str,p,p))-32
        num = num + numPlace * math.pow(95,p-1)
    end
    return num
end

function gsidFile(filename)
    local file = io.open(filename, "w")
    file:write("G")
    for n,species in pairs(pool.species) do
        file:write(toBase95(species.gsid,3))
    end
    file:close()
end

function writeFile(filename)
    local file = io.open(filename, "w")
    file:write("B" .. "\n")
    file:write(pool.generation .. "\n")
    file:write(math.floor(pool.maxFitness*10)/10 .. "\n")
    file:write(Population .. "\n")
	file:write(bnLoops .. "\n")
    file:write(bottleneckcounter .. "\n")
    file:write(pool.innovation .. "\n")
    file:write(pool.gsid .. "\n")
    file:write(#pool.species .. "\n")
    for n,species in pairs(pool.species) do
        file:write(math.floor(species.topFitness*10)/10 .. "\n")
        file:write(species.staleness .. "\n")
        file:write(species.gsid .. "\n")
        file:write(#species.genomes .. "\n")
        for m,genome in pairs(species.genomes) do
            file:write(math.floor(genome.fitness*10)/10 .. "\n")
            file:write(genome.maxneuron .. "\n")
            for i,rate in pairs(genome.mutationRates) do
				file:write(i .. "\n")
                file:write(math.floor(rate*10000)/10000 .. "\n")
            end
			file:write("done" .. "\n")
            file:write(#genome.genes .. "\n")
            for k,network in pairs(genome.genes) do
                file:write(#network .. "\n")
                for l,gene in pairs(network) do
					local enabledChar
                    if(gene.enabled) then
                        enabledChar = "1"
                    else
                        enabledChar = "0"
                    end
                    file:write(gene.into .. " " .. gene.out .. " " .. math.floor(gene.weight*10000000)/10000000 .. " " .. gene.innovation .. " " .. enabledChar .. "\n")
                end
                --emu.print(#network)
            end
            --emu.print(#genome.genes)
            for i,ns in pairs(genome.networkswitch) do
                file:write(math.floor(ns*500)/500 .. "\n")
            end
            --emu.print(genome.oscillations)
            for i,osc in pairs(genome.oscillations) do
                for i,oscn in pairs(osc) do
                    file:write(oscn .. "\n")
                end
            end
			file:write(genome.old .. "\n")
        end
    end
    file:close()
end

function savePool() --used to save when a new max fitness is reached
    local filename = "backups/backup3." .. pool.generation .. "." .. SAVE_LOAD_FILE
    writeFile(filename)
    emu.print("saved pool due to new max fitness")  --suggestion by DeltaLeeds
end

function loadFile(filename)
	emu.print(filename)
    local file = io.open(filename, "r")
    fileString = file:read("*line")
    file:close()
    if string.sub(fileString,1,1) == "B" then
		local file = io.open(filename, "r")
		file:read("*line")
        pool = newPool()
        pool.species = {}
        pool.generation = file:read("*number")
        pool.maxFitness = file:read("*number")
		pool.maxFitness = 0
		previousmaxfitness = pool.maxFitness
        Population = file:read("*number")
		bnLoops = file:read("*number")
        bottleneckcounter = file:read("*number")
        pool.innovation = file:read("*number")
        local gsidMax = file:read("*number")
        local numSpecies = file:read("*number")
        for s=1,numSpecies do
            local species = newSpecies()
            species.genomes = {}
            species.topFitness = file:read("*number")
			species.topFitness = 0
            species.staleness = file:read("*number")
            species.gsid = file:read("*number")
            local numGenomes = file:read("*number")
            for g=1,numGenomes do
                local genome = newGenome()
                genome.fitness = file:read("*number")
				genome.fitness = 0
                --emu.print(genome.fitness)
                genome.maxneuron = file:read("*number")
                local line = file:read("*line")
                while line ~= "done" do
					if line == "oscilation" then line = "oscillation" end
                    genome.mutationRates[line] = file:read("*number")
                    line = file:read("*line")
                end
                local numNetworks = file:read("*number")
                for n=1,numNetworks do
                    if n > 1 then
                        table.insert(genome.genes,{})
                        table.insert(genome.oscillations,{})
                    end
                    local numGenes = file:read("*number")
                    for gn=1,numGenes do
                        local gene = newGene()
						local enabled
						gene.into, gene.out, gene.weight, gene.innovation, enabled = file:read("*number", "*number", "*number", "*number", "*number")
						if enabled == 0 then
							gene.enabled = false
						else
							gene.enabled = true
						end
                        table.insert(genome.genes[n],gene)
                    end
                    --emu.print("gn" .. #genome.genes[n])
                end
                --emu.print("N" .. numNetworks)
                for n=1,numNetworks-1 do
                    table.insert(genome.networkswitch,file:read("*number"))
                end

                --emu.print(genome.networkswitch)
                for n=1,numNetworks do
                    genome.oscillations[n][1]=file:read("*number")
					genome.oscillations[n][2]=file:read("*number")
					genome.oscillations[n][3]=file:read("*number")
                end
                --emu.print(genome.oscillations)
                table.insert(species.genomes,genome)
                --emu.print(genome.oscillations)
				genome.old = file:read("*number")
            end
            table.insert(pool.species,species)
        end
        pool.gsid = gsidMax
    elseif string.sub(fileString,1,1) == "A" then
        local i = 1
        pool = newPool()
        pool.species = {}
        pool.generation = fromBase95(string.sub(fileString,i+1,i+2))
        pool.maxFitness = 0--fromBase95(string.sub(fileString,i+3,i+5))/10
        if pool.maxFitness > 80000 then
          pool.maxFitness = pool.maxFitness - 85737.5
        end
		previousmaxfitness = pool.maxFitness
        Population = fromBase95(string.sub(fileString,i+6,i+7))
		bnLoops = fromBase95(string.sub(fileString,i+8,i+8))
        bottleneckcounter = fromBase95(string.sub(fileString,i+9,i+9))
        pool.innovation = fromBase95(string.sub(fileString,i+10,i+13))
        local gsidMax = fromBase95(string.sub(fileString,i+14,i+16))
        local numSpecies = fromBase95(string.sub(fileString,i+17,i+18))
        i = i + 18
        for s=1,numSpecies do
            local species = newSpecies()
            species.genomes = {}
            species.topFitness = 0--fromBase95(string.sub(fileString,i+1,i+3))/10
            if species.topFitness > 80000 then
              species.topFitness = species.topFitness - 85737.5
            end
            species.staleness = fromBase95(string.sub(fileString,i+4,i+4))
            species.gsid = fromBase95(string.sub(fileString,i+5,i+7))
            local numGenomes = fromBase95(string.sub(fileString,i+8,i+9))
            i = i + 9
            for g=1,numGenomes do
                local genome = newGenome()
                genome.fitness = 0--fromBase95(string.sub(fileString,i+1,i+3))/10

                if genome.fitness > 80000 then
                  genome.fitness = genome.fitness - 85737.5
                end
				genome.fitness = 0
                --emu.print(genome.fitness)
                genome.maxneuron = fromBase95(string.sub(fileString,i+4,i+5))
                genome.mutationRates["connections"] = fromBase95(string.sub(fileString,i+6,i+8))/10000
                genome.mutationRates["oscillation"] = fromBase95(string.sub(fileString,i+9,i+11))/10000
                genome.mutationRates["link"] = fromBase95(string.sub(fileString,i+12,i+14))/10000
                genome.mutationRates["enable"] = fromBase95(string.sub(fileString,i+15,i+17))/10000
                genome.mutationRates["step"] = fromBase95(string.sub(fileString,i+18,i+20))/10000
                genome.mutationRates["networkswitch"] = fromBase95(string.sub(fileString,i+21,i+23))/10000
                genome.mutationRates["bias"] = fromBase95(string.sub(fileString,i+24,i+26))/10000
                genome.mutationRates["node"] = fromBase95(string.sub(fileString,i+27,i+29))/10000
                genome.mutationRates["disable"] = fromBase95(string.sub(fileString,i+30,i+32))/10000
                local numNetworks = fromBase95(string.sub(fileString,i+33,i+33))
                i = i + 33
                for n=1,numNetworks do
                    if n > 1 then
                        table.insert(genome.genes,{})
                        table.insert(genome.oscillations,{})
                    end
                    local numGenes = fromBase95(string.sub(fileString,i+1,i+2))
                    i = i + 2
                    for gn=1,numGenes do
                        local gene = newGene()
                        gene.into = fromBase95(string.sub(fileString,i+1,i+2))
                        gene.out = fromBase95(string.sub(fileString,i+3,i+4))
                        gene.weight = (fromBase95(string.sub(fileString,i+5,i+8))/10000000)-4
                        gene.innovation = fromBase95(string.sub(fileString,i+9,i+12))
                        gene.enabled = (string.sub(fileString,i+13,i+13) == "1")
                        table.insert(genome.genes[n],gene)
                        i = i + 13
						if gene.into > 9000 then gene.into = gene.into + 991000 end
						if gene.out > 9000 then gene.out = gene.out + 991000 end
                    end
                    --emu.print("gn" .. #genome.genes[n])
                end
                --emu.print("N" .. numNetworks)
                for n=1,numNetworks-1 do
                    table.insert(genome.networkswitch,fromBase95(string.sub(fileString,i+1,i+2))/500)
                    i = i + 2
                end

                --emu.print(genome.networkswitch)
                for n=1,numNetworks do
                    genome.oscillations[n][1]=fromBase95(string.sub(fileString,i+1,i+1))
                    genome.oscillations[n][2]=fromBase95(string.sub(fileString,i+2,i+2))
                    genome.oscillations[n][3]=fromBase95(string.sub(fileString,i+3,i+3))
                    i = i + 3
                end
                --emu.print(genome.oscillations)
                table.insert(species.genomes,genome)
                --emu.print(genome.oscillations)
            end
            table.insert(pool.species,species)
        end
        pool.gsid = gsidMax
    else
        local file = io.open(filename, "r")
        pool = newPool()
        pool.generation = file:read("*number")
        pool.maxFitness = file:read("*number")
		previousmaxfitness = pool.maxFitness
        Population = file:read("*number")
        pool.innovation = file:read("*number")
        bottleneckcounter = file:read("*number")
        local numSpecies = file:read("*number")
		pool.gsid = numSpecies - 1
		maxstale = 0
        for s=1,numSpecies do
            local species = newSpecies()
            table.insert(pool.species, species)
            species.topFitness = file:read("*number")
            species.staleness = file:read("*number")
			if species.staleness > maxstale then maxstale = species.staleness end
            species.gsid = s - 1
            local numGenomes = file:read("*number")
            for g=1,numGenomes do
                local genome = newGenome()
                table.insert(species.genomes, genome)
                genome.fitness = file:read("*number")
                genome.maxneuron = file:read("*number")
				genome.fitness = 0
                local line = file:read("*line")
                while line ~= "done" do
					if line == "oscilation" then line = "oscillation" end
                    genome.mutationRates[line] = file:read("*number")
                    line = file:read("*line")
                end
                local numGenes = file:read("*number")
                genes1 = {}
				genes1Legacy = {}
                for n=1,numGenes do
                    local gene = newGene()
					table.insert(genes1Legacy, gene)
                    local enabled
                    --I am able to revert back to the original loading script with FCEUX
                    gene.into, gene.out, gene.weight, gene.innovation, enabled = file:read("*number", "*number", "*number", "*number", "*number")
                    if enabled == 0 then
                        gene.enabled = false
                    else
                        gene.enabled = true
                    end
                end
				
				local genomeLegacy = newGenome()
				genomeLegacy.genes = {genes1Legacy}
				MaxNodes = 1000000
				generateNetwork(genomeLegacy,false)
				--MaxNodes = 9000
				local net = genomeLegacy.network[1]
				local mapping = {}
				local numMappedNodes = 0
				for nid, neuron in pairs(net.neurons) do
					numMappedNodes = numMappedNodes + 1
					if numMappedNodes == 174 then numMappedNodes = 176 end
					mapping[nid+0.5] = numMappedNodes
					--emu.print(mapping)
				end
				for nid, neuron in pairs(net.neurons) do
					for inc=1,#neuron.incoming do
						local geneWrong = neuron.incoming[inc]
						local geneRight = newGene()
						geneRight.weight = geneWrong.weight
						geneRight.enabled = geneWrong.enabled
						geneRight.innovation = geneWrong.innovation
						geneRight.out = mapping[nid+0.5]
						if mapping[geneWrong.into+0.5] ~= nil then
							geneRight.into = mapping[geneWrong.into+0.5]
							table.insert(genes1,geneRight)
							if geneRight.enabled and s == 1 and g == 2 then
								--emu.print("ACCEPTED " .. geneWrong.into .. " " .. geneWrong.out .. " " .. geneRight.out .. " " .. geneRight.into)
							end
						elseif s == 1 and g == 2 then
							emu.print("REJECTED " .. geneWrong.into .. " " .. geneWrong.out .. " " .. geneRight.out)
						end
					end
					
					--emu.print(nid)
				end
				
				for outputid=1,6 do
					local geneRight = newGene()
					geneRight.weight = 1.0
					geneRight.enabled = true
					geneRight.innovation = newInnovation()
					geneRight.into = mapping[outputid+1000000.5]
					geneRight.out = 9000+outputid
					table.insert(genes1,geneRight)
				end
				
				
                local numGenes2 = file:read("*number")
                genes2 = {}
				genes2Legacy = {}
                for n=1,numGenes2 do
                    local gene2 = newGene()
					table.insert(genes2Legacy, gene2)
                    local enabled
                    --I am able to revert back to the original loading script with FCEUX
                    gene2.into, gene2.out, gene2.weight, gene2.innovation, enabled = file:read("*number", "*number", "*number", "*number", "*number")
                    if enabled == 0 then
                        gene2.enabled = false
                    else
                        gene2.enabled = true
                    end

                end
				
				local genome2Legacy = newGenome()
				genome2Legacy.genes = {genes2Legacy}
				MaxNodes = 1000000
				generateNetwork(genome2Legacy,false)
				MaxNodes = 9000
				net = genome2Legacy.network[1]
				mapping = {}
				numMappedNodes = 0
				for nid, neuron in pairs(net.neurons) do
					numMappedNodes = numMappedNodes + 1
					if numMappedNodes == 174 then numMappedNodes = 176 end
					mapping[nid+0.5] = numMappedNodes
					--emu.print(mapping)
				end
				for nid, neuron in pairs(net.neurons) do
					for inc=1,#neuron.incoming do
						local geneWrong = neuron.incoming[inc]
						local geneRight = newGene()
						geneRight.weight = geneWrong.weight
						geneRight.enabled = geneWrong.enabled
						geneRight.innovation = geneWrong.innovation
						geneRight.out = mapping[nid+0.5]
						if mapping[geneWrong.into+0.5] ~= nil then
							geneRight.into = mapping[geneWrong.into+0.5]
							table.insert(genes2,geneRight)
							if geneRight.enabled and s == 1 and g == 2 then
								--emu.print("ACCEPTED " .. geneWrong.into .. " " .. geneWrong.out .. " " .. geneRight.out .. " " .. geneRight.into)
							end
						elseif s == 1 and g == 2 then
							emu.print("REJECTED " .. geneWrong.into .. " " .. geneWrong.out .. " " .. geneRight.out)
						end
					end
					
					--emu.print(nid)
				end
				
				for outputid=1,6 do
					local geneRight = newGene()
					geneRight.weight = 1.0
					geneRight.enabled = true
					geneRight.innovation = newInnovation()
					geneRight.into = mapping[outputid+1000000.5]
					geneRight.out = 9000+outputid
					table.insert(genes2,geneRight)
				end
				
				
				
                ns = file:read("*number")
                if ns == 0 then
                    genome.networkswitch = {}
                    genome.oscillations = {{}}
                    genome.genes = {genes1}
                else
                    genome.networkswitch = {ns}
                    genome.genes = {genes1,genes2}
                    genome.oscillations = {{},{}}
                end
                local numosci = file:read("*number")
                for i=1,numosci do
                    genome.oscillations[1][i] = file:read("*number")
                    if ns > 0 then
                        genome.oscillations[2][i] = genome.oscillations[1][i]
                    end
                end
				if g == 1 then
					genomeCopy = copyGenome(genome)
					table.insert(species.genomes,genomeCopy)
				end
            end
			if s == 1 then
				--emu.print(species.genomes[2].genes[1])
				--emu.print("*3")
			end
			bnLoops = 0
			bottleneck = 0
			for i=1,maxstale do
				bottleneck = bottleneck + 1
				length= math.min(12*popOscilMultiplier,(5 + 2*bnLoops)*popOscilMultiplier)
				if bottleneckcounter == GBPO + length*3 then
					bottleneckcounter = 0
					bnLoops = bnLoops + 1
				end
			end
        end
        file:close()
    end

    --while fitnessAlreadyMeasured() do
    --    nextGenome()
    --end
    initializeRun()
    pool.currentFrame = pool.currentFrame + 1
end


function playTop()
    local maxfitness = 0
    local maxs, maxg
    rightmost = 0
    pool.currentFrame = 0
    hitblocks = 0
    hiddenblocks = {}
    offset = 0 --offset in x coordinates for pipe
    timebonus = 0 --used to freeze fitness
    mariohole = false --reset the fallen into hole variable
    mariopipe = false --is mario exiting a pipe or just teleporting
    loop = false --is this a loop?
    marioPipeEnter = false --has mario entered a pipe
    currentTracker = 1 --tracker for the loop
    killtrigger = false
    ntrigger = true
    nswitch = 1
    for s,species in pairs(pool.species) do
        for g,genome in pairs(species.genomes) do
            if genome.fitness > maxfitness then
                maxfitness = genome.fitness
                maxs = s
                maxg = g
            end
        end
    end

    pool.currentSpecies = maxs
    pool.currentGenome = maxg
    pool.maxFitness = maxfitness
    initializeRun()
    pool.currentFrame = pool.currentFrame + 1
    return
end

function fitnesstracker()
	if pool.maxFitness > 0 then
		local file = io.open('fitnesstracker.txt', "a")
		file:write("Gen: " .. pool.generation .. " Species: " .. pool.currentSpecies .. " Genome: " .. pool.currentGenome .. " Fitness: ".. pool.maxFitness .. "\n")
		file:close()
	end
end

function writelatestgen() --used to write the generation tracker to a file
    local file = io.open('backups/latestgen', "w")
    file:write(SAVE_LOAD_FILE .. "\n")
    file:write(savestate_slot .. "\n")
    file:write(pool.generation)
    file:close()
end

function readlatestgen() --used to retrieve the latest generation from a file
	if FileExists('backups/latestgen') then
		local file = io.open('backups/latestgen', "r")
		SAVE_LOAD_FILE = file:read("*line")
		savestate_slot = file:read("*number")
		SavestateObj = savestate.object(savestate_slot)
		local latestgen = file:read("*number")-1
		file:close()
		local name = 'backups/backup3.' .. SAVE_LOAD_FILE
		print('loaded: '.. name)
		return name
	else
		print('Please first run the AI normally before trying to fast load the latest generation')
	end
end

function keyboardinput()
    local keyboard = input.get()
    if keyboard['N'] and keyflag == false then
        if neural_net_disp then
            neural_net_disp = false
        else
            neural_net_disp = true
        end
        keyflag = true
    end
    if keyboard['M'] and keyflag == false then
        if mutation_rates_disp then
            mutation_rates_disp = false
        else
            mutation_rates_disp = true
        end
        keyflag = true
    end
    if keyboard['L'] and keyflag == false then
        if not nopopup then
            local loadyn = input.popup('Are you sure you want to load the last saved generation?')
        end
        if loadyn == 'yes' or nopopup then
            name = readlatestgen()
            loadFile(name)
        end
        keyflag = true
    end
    if keyboard['B'] and keyflag == false then
        if not nopopup then
            local loadyn = input.popup('Are you sure you want to show the topFitness genome?')
        end
        if loadyn == 'yes' or nopopup then
            playTop()
        end
    end


    if keyboard['S'] and keyflag == false then
        savePool()
        keyflag = true
    end
    if not (keyboard['N'] or keyboard['L'] or keyboard['M'] or keyboard['T'] or keyboard['B'] or keyboard['S']) and keyflag == true then
        keyflag = false
    end
    if keyboard['T'] and keyflag == false then
        if turbo then
            emu.speedmode("normal")
            turbo = false
            print('stop turbo')
        elseif not turbo and not restoreturbo then
            emu.speedmode("turbo")
            turbo = true
        elseif restoreturbo then
            restoreturbo = false
        end
        keyflag = true
    end
end


writeFile("temp.pool")
requiredFitness = 0
minFitness = 0
if SAVE_LOAD_FILE == nil then
    if LostLevels == 1 then
        SAVE_LOAD_FILE = "SMBLL".. CurrentWorld+1 .."-".. CurrentLevel ..".state.pool"
    else
        SAVE_LOAD_FILE = "SMB".. CurrentWorld+1 .."-".. CurrentLevel ..".state.pool"
    end
end

if savedpool then
    loadFile(savedpool)
end


while true do
    keyboardinput()
    local backgroundColor = toRGBA(0xD0FFFFFF)
        gui.drawbox(0, 0, 260, 30, backgroundColor, backgroundColor)

    if pool.maxcounter == nil then
        pool.maxcounter = 0
        --emu.print("caught missing variable")
    end

    local species = pool.species[pool.currentSpecies]
    local genome = species.genomes[pool.currentGenome]

    if neural_net_disp then
        displayGenome(genome)
    end
    if pool.generation == 0 and pool.currentSpecies ~= 1 and not turbo and AllowAutoTurbo and FirstGenSpeedup then
        emu.speedmode("turbo")
        turbo = true
    -- elseif pool.generation == 2 and turbo and AllowAutoTurbo and FirstGenSpeedup then
        -- emu.speedmode("turbo")
        -- turbo = false
    end

    local nscompare = rightmost / 500.0
    local nsw = 1
    for n=1,#genome.networkswitch do
        if nscompare > genome.networkswitch[n] then
            nsw = n+1
        end
    end
	nswitch = nsw

    if pool.currentFrame%5 == 0 then
        evaluateCurrent()
    end

    joypad.set(player, controller)

    getPositions()
	local mariostate = mariostate
	local adjustfitness
	local CurrentWorld = CurrentWorld
	local CurrentLevel = CurrentLevel
	local marioX = marioX
	local marioY = marioY
    if mariostate == 2 or mariostate == 3 then --detects when mario enters a pipe
        marioPipeEnter = true
        if mariostate == 2 then
            adjustfitness = true
        else
            adjustfitness = false
        end
    end
    if (CurrentWorld == 3 and CurrentLevel == 4) or (CurrentWorld == 6 and CurrentLevel == 4) or (CurrentWorld == 7 and CurrentLevel == 3) then
        if currentTracker == currentscreen or currentTracker == nextscreen and not mariopipe then --follows the progress of mario
            currentTracker = nextscreen
        elseif currentTracker > nextscreen and not mariopipe and not marioPipeEnter and mariostate ~= 7 then --if mario suddenly goes back trigger loop detection
            loop = true
        elseif currentscreen == 0 and nextscreen == 0 and mariopipe and mariostate ~= 7 then -- if mario enters a piperoom negate loop detection
            loop = false
            currentTracker = nextscreen
        elseif nextscreen >= (currentTracker - 1) and mariopipe and mariostate ~= 7 then -- if mario goes forward in the level by entering a pipe negate loop detection
            loop = false
            currentTracker = nextscreen
            pipeexit = true
        else --if nothing is true then we are in a loop
            if not pipeexit then --prevents the extra one frame flicker of the tracker
            loop = true
            else
            pipeexit = false
            end
        end
    end
    if marioPipeEnter == true and mariostate == 7 then --set mariopipe when exiting the pipe
        mariopipe = true
    end
    if adjustfitness then
        if mariopipe == true and mariostate ~= 7 and rightmost > marioX and not mariohole then --calculate offset
            offset = rightmost - marioX
            mariopipe = false
            marioPipeEnter = false
        elseif mariopipe == true and mariostate ~= 7 and rightmost <= marioX and not mariohole then --if the exit coordinates are higher than rightmost after exiting a pipe set offset to 0
            offset = 0
            mariopipe = false
            marioPipeEnter = false
        end
    else
        if mariopipe == true and mariostate ~= 7 and not mariohole then --calculate offset --and rightmost > marioX
            offset = rightmost - marioX
            mariopipe = false
            marioPipeEnter = false
        end
    end
--Custom Fix: Springs
	--emu.print(marioY + memory.readbyte(0xB5)*255)
    if (marioY + memory.readbyte(0xB5)*255 > 512)then --added the fallen into a hole variable that will activate when LuigI/O goes below screen 
        if marioY + memory.readbyte(0xB5)*255 > 768 and not mariohole then -- Added this bit to prevent LuigI/O from being treated as fallen when he goes too high on the screen due to Lost Level springs. 
        TimeoutConstant = 800 -- Increase the TimeoutConstant so that the game won't timeout when LuigI/O uses the spring.
        else
        mariohole = true
		
        end
    else -- If LuigI/O's marioY + 0xB5 byte * 255 is less than 512, he is visible on the screen
        TimeoutConstant = 120 --Reset TimeoutConstant back to normal when visible on screen.
    end
    local dis = false
	local specialy = false
    if marioX > 2370 and marioX < 2460 and (LostLevels == 0 and CurrentWorld == 7 and CurrentLevel == 3) then
	specialy = true
    end
    if marioX > 2460 and marioX < 3000 and (LostLevels == 0 and CurrentWorld == 7 and CurrentLevel == 3) then
	dis = true
    end
    if marioX > 3000 and marioX < 3160 and marioY < 192 and marioY > 64 and (LostLevels == 1 and CurrentWorld == 1 and CurrentLevel == 1) then
	dis = true
    end

    if marioX > 496 and marioX < 928 and marioY < 128 and (LostLevels == 1 and CurrentWorld == 2 and CurrentLevel == 4) then
	dis = true
    end
    if marioX > 928 and marioX < 1264 and marioY < 160 and (LostLevels == 1 and CurrentWorld == 2 and CurrentLevel == 4) then
	dis = true
    end
    if marioX > 1632 and marioX < 2384 and (marioY > 80 or hitblocks == 0) and (LostLevels == 1 and CurrentWorld == 2 and CurrentLevel == 4) then
	dis = true
    end
	
	local ymulti = 0.2
	if (LostLevels == 0 and CurrentWorld == 3 and CurrentLevel > 2) then ymulti = 1 end
	
	local newright = marioX + offset - (marioY - 192)*ymulti + (50 *memory.readbyte(0x06D9))
	if specialy then
		newright = 2370 + offset - marioY + 192 + (50 *memory.readbyte(0x06D9))
	end
	
	if LostLevels == 0 and CurrentWorld == 3 and CurrentLevel == 4 then
		if marioX > 1680 and marioX < 2288 and marioY <= 144 then
			dis = true
		end
		if marioX > 300 and marioX < 1200 and marioY > 80 then
			dis = true
		end
		if marioX > 1512 and marioX < 1680 then
			if marioY <= 80 then
				newright = marioX + offset + 112 + (50 *memory.readbyte(0x06D9))
			elseif marioY <= 144 then
				newright = 3360 - marioX + offset + 176 + (50 *memory.readbyte(0x06D9))
			else
				newright = 352 + marioX + offset + 224 + (50 *memory.readbyte(0x06D9))
			end
		elseif marioX > 1680 then
			newright = 352 + marioX + offset + 224 + 192 - marioY + (50 *memory.readbyte(0x06D9))
		end
	end
	
	
	if newright > rightmost and not mariohole and not loop and not marioPipeEnter and not killtrigger and not falling and not dis then
		rightmost = newright
		if rightmost > species.topright then
			species.topright = rightmost
		end
		timebonus = timebonus + (TimeoutConstant - timeout) * 11/20
		timeout = TimeoutConstant
	end

    if marioPipeEnter == true then --freeze fitness and timer when mario enters a pipe
        timeout = timeout + 1
        timebonus = timebonus + 2/3
    end

--Custom Fix: Changes made for Lost Levels 3-1 so that going in the subworld trap pipe won't increase fitness and for the last part "(marioX > 2900 and memory.readbyte(0xB5)*255 > 768)", when LuigI/O goes over the flagpole thanks to the spring (yes, it can happen, I tested), fitness will not increase as well.
	if(CurrentWorld == 2 and CurrentLevel == 0 and LostLevels == 1) then
		if (mariopipe and ((marioX > 500 and marioX < 572) or (marioX > 1244 and marioX < 1396) or (marioX > 3558 and marioX < 3708))) or (marioX > 2900 and memory.readbyte(0xB5)*255 > 768)  then
			loop = true
		end
    end

    if (mariostate == 4 or (memory.readbyte(0x000C) == 1 and statuscheck == 0) or ((memory.readbyte(0x06D6) ~= 0 and memory.readbyte(0x06D6) ~= 1) and marioPipeEnter)) or endlevel then --and statuscheck == 0
        timeout = timeout +1
        timebonus = timebonus + 2/3
        endlevel = true
    end


    if endlevel and mariostate == 8 and demoruncheck == 1 and statuscheck == 3 + LostLevels then
		local timeoutBonus = pool.currentFrame / 4
		local fitness = rightmost - pool.currentFrame / 2 +40 + timebonus
		genome.fitness = fitness
		pool.maxFitness = fitness
		fitnesstracker()
		savePool()
        if not rerunning then
            if LostLevels==1 then
                SAVE_LOAD_FILE = "SMBLL".. CurrentWorld+1 .."-".. CurrentLevel ..".state.pool"
            else
                SAVE_LOAD_FILE = "SMB".. CurrentWorld+1 .."-".. CurrentLevel ..".state.pool"
            end
            previous_savestate = savestate_slot
            savestate_slot = savestate_slot + 1
            if savestate_slot == 10 then
                savestate_slot = 1
            end

            Savestatebackup = savestate.object(savestate_slot)
            savestate.save(Savestatebackup)
            savestate.persist(Savestatebackup)
            savestate.save(SavestateObj)

        end
        SavestateObj = savestate.object(savestate_slot)
        endlevel = false
        if (turbo or restoreturbo) and not rerunning then
            rerunning = true
            requiredFitness = 0
			minFitness = 0
            emu.speedmode("normal")
            turbo = false
            restoreturbo = false
            reRun()
        else
            rerunning = false
            preparenext = true
        end
    end

    if CurrentWorld == 0 and CurrentLevel == 0 and demoruncheck == 0 then
        savestate.load(SavestateObj)
    end

    timeout = timeout - 1
    if preparenext then
        rerunning = false
        preparenext = false
        GenerateNewKeepBest(genome, species.nickname)
    end
    if rightmost > maxright then
        maxright = rightmost
    end
    if rightmost > maxright*0.85 and AllowSlowdownNearMax then
        if turbo and maxright > 200 and AllowSlowdownNearMax and not restoreturbo then
            emu.speedmode("normal")
            turbo = false
            restoreturbo = true
        end
    elseif restoreturbo and not (requiredFitness > 10) then
        emu.speedmode("turbo")
        turbo = true
        restoreturbo = false
    end
    --emu.print(marioX .. " " .. marioY)
    local timeoutBonus = pool.currentFrame / 4
    if (mariostate == 11 or mariohole or math.floor(rightmost - (pool.currentFrame) / 2 + - (timeout + timeoutBonus)*2/3 +40 + timebonus) < -50 ) and timeout > 40-timeoutBonus then
        local temptimeout = timeout
        timeout = 30 - timeoutBonus
        local difference = temptimeout - timeout
        pool.currentFrame = pool.currentFrame + difference
        killtrigger = true
    end
    local timeoutBonus = pool.currentFrame / 4
    if timeout + timeoutBonus <= 0 then
        local fitness = rightmost - pool.currentFrame / 2 +40 + timebonus + hitblocks * hbValue
        if fitness == 0 then
            fitness = -1
        end

            genome.fitness = fitness

		if species.topFitness < secondbest and fitness > secondbest and fitness < pool.maxFitness then --system for automatically updating the second best value
			secondbest = fitness
		elseif species.topFitness < pool.maxFitness and fitness > pool.maxFitness then
			secondbest = pool.maxFitness
		elseif species.topFitness == secondbest and fitness > secondbest and fitness < pool.maxFitness then
			secondbest = fitness
		elseif species.topFitness == secondbest and fitness > pool.maxFitness then
			secondbest = pool.maxFitness
		end
		
        if fitness > pool.maxFitness then
            pool.maxFitness = fitness
			fitnesstracker()
            savePool()
        end

        if fitness > pool.maxFitness - 30 then
            pool.maxcounter = pool.maxcounter + 1
        end

        emu.print("Gen " .. pool.generation .. " species " .. pool.currentSpecies .. " genome " .. pool.currentGenome .. " fitness: " .. fitness)
        pool.currentSpecies = 1
        pool.currentGenome = 1
        while fitnessAlreadyMeasured() do
            offset = 0 --offset in x coordinates for pipe
            timebonus = 0 --used to freeze fitness
            mariohole = false --reset the fallen into hole variable
            mariopipe = false --is mario exiting a pipe or just teleporting
            loop = false --is this a loop?
            marioPipeEnter = false --has mario entered a pipe
            currentTracker = 1 --tracker for the loop
            killtrigger = false
            ntrigger = true
            nswitch = 1
            if rerunning then
                rerunning = false
                preparenext = true
            end
            nextGenome()
        end
        

        initializeRun()
    end

    
        gui.opacity(1) --made the top banner opaque. you can change this if you want a slightly transparent banner
        if turbo then
            gui.drawtext(250, 11, "T", toRGBA(0xFFFF0000), 0x0)
        end
        gui.drawtext(5, 11, "Gen " .. pool.generation .. " species " .. pool.currentSpecies .. " genome " .. pool.currentGenome .. " (" .. math.floor(pool.measured/pool.total*100) .. "%) ".. "Pop: ".. Population, toRGBA(0xFF000000), 0x0)
        gui.drawtext(5, 20, "Fitness: " .. math.floor(hitblocks * hbValue + rightmost - (pool.currentFrame) / 2 + - (timeout + timeoutBonus)*2/3 +40 + timebonus) , toRGBA(0xFF000000), 0x0) --the (timeout + timeoutBonus)*2/3 makes sure that the displayed fitness remains stable for the viewers pleasure
        gui.drawtext(80, 20, "Max Fitness:" .. math.floor(pool.maxFitness) .. " (".. math.floor(secondbest) .. ")".. " ".. "(" .. pool.maxcounter .. "x)", toRGBA(0xFF000000), 0x0)

    pool.currentFrame = pool.currentFrame + 1

    emu.frameadvance();
end