chemodiversity/app/Main.hs

{-# LANGUAGE BangPatterns #-}
{-# LANGUAGE OverloadedStrings #-}
module Main where

import Text.Printf
import Control.Monad.Reader
import qualified Numeric.LinearAlgebra as LA
import Data.List
import System.Random
import Control.Concurrent
import Control.Parallel.Strategies
import Control.Monad.Writer (tell)
import qualified Debug.Trace as Debug
import qualified Control.Foldl as F
import System.IO
import System.Environment
import Data.Aeson
import qualified Data.ByteString as BS
import qualified Data.ByteString.Lazy as LBS
import Options.Applicative
import Data.Semigroup ((<>))

import ArbitraryEnzymeTree
import Environment
import Evaluation

-- Example definitions
-- -------------------

-- Enzymes

-- pps :: Enzyme -- uses Phosphor from Substrate to produce PP
-- pps = Enzyme "PPS" [(Substrate Phosphor,1)] ((Substrate Phosphor,-1),(Produced PP,1)) Nothing
--
-- fpps :: Enzyme -- PP -> FPP
-- fpps = makeSimpleEnzyme (Produced PP) (Produced FPP)

-- Environment

exampleEnvironment :: Int -> [Enzyme] -> [(Predator,Probability)] -> [(Compound,Amount)] -> Environment
exampleEnvironment addedC es pred tox =
  Environment
    { soil = [ (PPM, 10)
             ]
    , predators = pred -- [ (greenfly, 0.1) ]
    , metabolismIteration = 100
    , maxCompound = maxCompoundWithoutGeneric + addedC
    , toxicCompounds = tox --[(Produced FPP,0.1)] ++ tox
    , possibleEnzymes = es -- [pps,fpps] ++ es
    , settings = Settings { automimicry = False
                          , predatorBehaviour = AttackInterval 10
                          , numPlants = 50
                          , logEveryNIterations = 10
                          , mutationRate = 0.01
                          , deletionDuplicationRate = 0.05
                          , geneAddRate = 0.005
                          , activationNoiseIntensity = 0.01
                          , staticEnzymeCost = 0.01
                          , nutrientImpact = 0.01
                          }
    }

-- Plants

-- examplePlants :: [Plant]
-- examplePlants = (\g -> Plant g defaultAbsorption) <$> genomes
--  where
--    enzymes = [pps, fpps]
--    quantity = [1,2] :: [Quantity]
--    activation = [0.7, 0.9, 1]
--
--    genomes = do
--      e <- permutations enzymes
--      e' <- subsequences e
--      q <- quantity
--      a <- activation
--      return $ (,,) <$> e' <*> [q] <*> [a]
--
--    defaultAbsorption = fmap ( limit Phosphor 2
--                             . limit Nitrate 1
--                             . limit Sulfur 0
--                             ) <$> fromEnv soil
--    -- custom absorbtion with helper-function:
--    limit :: Nutrient -> Amount -> (Nutrient, Amount) -> (Nutrient, Amount)
--    limit n a (n', a')
--      | n == n'   = (n, min a a') -- if we should limit, then we do ;)
--      | otherwise = (n', a')

-- Running the simulation
-- ----------------------

loop :: Int -> [Plant] -> Simulation -> CLIOptions -> IO ()
loop loopAmount ps env opts = loop' loopAmount 0 ps env

  where
    -- cache enzyme colorful-strings
    stringe :: [(Enzyme, String)]
    stringe = (\e -> case Data.List.find (\(t,_) -> (t==) . fst . snd . synthesis $ e) toxins of
               Just (_,toxicity) -> (e,"\ESC[38;5;" ++ show (16 + 36*5 + 6*floor (5*(1-toxicity)) + 0) ++ "m" -- yellow -> red rainbow for tocixity 0 -> 1
                                       ++ padded 50 (show (enzymeName e)) ++ "\ESC[0m")
               Nothing           -> (e, padded 50 (show (enzymeName e)))
             ) <$> possibleEnzymes (snd env)
    toxins :: [(Compound, Amount)]
    toxins = toxicCompounds (snd env)
    printEverything = verbose opts
    padded i str = take i $ str ++ repeat ' '
    printEvery = 10
    loop' :: Int -> Int -> [Plant] -> Simulation -> IO ()
    loop' loopAmount curLoop plants s = unless (loopAmount+1 == curLoop) $ do
      when (printEverything && curLoop `mod` printEvery == 0) $ do
        putStr "\ESC[2J\ESC[H"
        printEnvironment (snd env)
        putStrLn ""
        putStrLn $ "Generation " ++ show curLoop ++ " of " ++ show loopAmount ++ ":"
      newPlants <- simulate s $ do
          when (curLoop == 0) $ do
            preds <- length <$> fromEnv predators
                --- generates "pred1,pred2,pred3,.....predN"
            let additionalHeader = intercalate "," $ ("pred"++).show <$> [1..preds]
            tell $  "num_iter"
                 ++ ",c_sum_mu,c_sum_sigma"
                 ++ ",c_d_mu,c_d_sigma"
                 ++ ",e_d_mu,e_d_sigma"
                 ++ ",fitness_mean,fitness_sigma"
                 ++ ",percent_toxic_mean,percent_toxic_sigma"
                 ++ "," ++ additionalHeader
          logIter <- fromEnv $ logEveryNIterations . settings
          (!fs,cs) <- unzip <$> fitness curLoop plants
          txns <- fmap (fromEnum . fst) <$> fromEnv toxicCompounds -- [Int] of id's of toxic compounds
          let fps = zip plants fs -- gives us plants & their fitness in a tuple
              sumFitness = sum fs
              es = genomeToEnzymeAmount . genome <$> plants
              genomeToEnzymeAmount :: Genome -> LA.Vector Double
              genomeToEnzymeAmount g = LA.accum (LA.konst 0 (maxCompound . snd $ env)) (+) $ (\(e,q,a) -> ((fromEnum . fst . snd . synthesis $ e)-1,fromIntegral q*a)) <$> g
              -- $C_{\Sigma,mu}$: Durchschnittliche Menge an produzierten Stoffen
              -- $C_{\Sigma,sigma}$: Durchschnittliche Varianz an produzierten Stoffen
              (c_sum_mu, c_sum_sigma) = meanAndVar `from` sumProducedCompounds $ cs
              -- - $C_{i,\mu}$: Durchschnittliche Anzahl produzierter Komponenten
              -- - $C_{i,\sigma}$: Zusätzlich: Betrachtung der Varianz dieser Komponenten innerhalb der Population  
              --   (Z.B. Stoff A wird immer mit $0.5$ produziert, hat also keine Varianz,
              --   wogegen Stoff B *im Schnitt* mit $0.5$ produziert wird, aber dies eine extreme
              --   Varianz auslöst)
              (c_i_mu,c_i_sigma) = unzip $ meanAndVar `from` id <$> byProducts cs
              -- - $C_{\sigma,\{\mu/\sigma\}}$: Mittelwert/Varianz von $\C_{i,\sigma}$
              (c_sigma_mu, c_sigma_sigma) = meanAndVar `from` id $ c_i_sigma
              -- - $C_d$: Durchschnittliche Anzahl distinkter Produzierter Stoffe (sprich
              --   nicht-endemisch, $#i | C_{i,\mu} < \epsilon$ )
              isNotEndemicCompound :: LA.Vector Bool
              isNotEndemicCompound = LA.fromList $ (< 0.1) <$> c_i_mu
              (c_d_mu, c_d_sigma) = meanAndVar `from` countWith isNotEndemicCompound (>0.1) $ cs
              -- - $E_{i,\mu}$: Durchschnittliche Anzahl produzierbarer Komponenten (falls ausgangsstoff verfügbar)
              -- - $E_{i,\sigma}$: Zusätzlich: Betrachtung der Varianz dieser Komponenten innerhalb der Population
              -- analog zu $C_{i,\mu/\sigma}$
              (e_i_mu,e_i_sigma) = unzip $ meanAndVar `from` id <$> byCompound es
              -- - $E_d$: Durchschnittliche Anzahl distinkter Produzierter Stoffe (sprich
              --   nicht-endemisch, $#i | E_{i,\mu} < \epsilon$ )
              isNotEndemicEnzyme :: LA.Vector Bool
              isNotEndemicEnzyme = LA.fromList $ (< 0.5) <$> e_i_mu
              (e_d_mu, e_d_sigma) = meanAndVar `from` countWith isNotEndemicEnzyme (>0.5) $ es
              -- - $\mathbf{E}[C_{\Sigma,plant} - C_{\Sigma,mu}]$: Durchschnittliche Abweichung der produzierten
              --   Stoffe gegenüber dem Schnitt der Gesamtpopulation
              e_hash_plant = F.mean `from` numDistinctCompounds $ cs
              -- mean and variance of fitness
              fns = meanAndVar `from` id $ fs
              -- - $P_\{\mu,\sigma\}$ Mittelwert/Varianz der Anteile der Stoffe in Pflanze i, die giftig sind
              toxs = meanAndVar `from` percentagePoisonous txns $ cs
          when (printEverything && curLoop `mod` printEvery == 0) $ liftIO $ do
            printPopulation isNotEndemicEnzyme stringe (zip3 plants fs cs)
            putStrLn $ "Population statistics           (mean,variance):"
            putStrLn $ "Amount of Components produced = " ++ show (c_sum_mu,c_sum_sigma)
            putStrLn $ "Number of distinct Components = " ++ show (c_d_mu, c_d_sigma)
            putStrLn $ "Number of distinct Enzymes    = " ++ show (e_d_mu, e_d_sigma)
            putStrLn $ "Fitness                       = " ++ show fns
            putStrLn $ "Percentage of toxins in Cmpnds= " ++ show toxs
            hFlush stdout
            threadDelay $ 10*1000 -- sleep x*1000ns (=x ~ ms)
          when (curLoop `mod` logIter == 0) $ do
            preds <- fmap fst <$> fromEnv predators
            let numPlantsCanRepel = (\ir -> sum $ (\p -> if sum ((p LA.!) <$> ir) > 0 then 1 else 0) <$> cs) . fmap fromEnum . irresistance <$> preds
                addedData = intercalate "," $ show <$> numPlantsCanRepel
            tell $            show curLoop
                 ++  ","  ++  show c_sum_mu    ++  ","  ++  show c_sum_sigma
                 ++  ","  ++  show c_d_mu      ++  ","  ++  show c_d_sigma
                 ++  ","  ++  show e_d_mu      ++  ","  ++  show e_d_sigma
                 ++  ","  ++  show (fst fns)   ++  ","  ++  show (snd fns)
                 ++  ","  ++  show (fst toxs)  ++  ","  ++  show (snd toxs)
                 ++  ","  ++  addedData
          -- generate x new plants.
          np <- fromEnv (numPlants . settings)
          sequence . flip fmap [1..np] $ \_ -> do
                parent' <- liftIO $ randomRIO (0,sumFitness)
                let
                    -- if we only have one parent in our list, take it.
                    findParent :: Double -> [(Plant,Double)] -> Plant
                    findParent _ [(last,_)] = last
                    -- otherwise count down x to find the parent in the list
                    findParent x ((p,f):ps)
                      | x < f     = p
                      | otherwise = findParent (x-f) ps
                    parent = findParent parent' fps
                haploMate parent
      loop' loopAmount (curLoop+1) newPlants s

data CLIOptions = CLIOptions
    { environment     :: Maybe FilePath
    , logfile         :: FilePath
    , verbose         :: Bool
    , dumpEnvironment :: Bool
    }

cliOptParser :: Parser CLIOptions
cliOptParser = CLIOptions
    <$> optional (strOption
        (long "environment"
        <> short 'e'
        <> metavar "ENV"
        <> help "Environment to load"
        ))
    <*> option str
        (long "logfile"
        <> short 'l'
        <> metavar "LOG"
        <> showDefault
        <> value "simulation.log"
        <> help "Name for the logfile"
        )
    <*> switch
        (long "verbose"
        <> short 'v'
        <> help "show 'gui' during process"
        )
    <*> switch
        (long "write-environment"
        <> short 'w'
        <> help "write environment used to $PWD/environment.json"
        )

cliopts = info (cliOptParser <**> helper)
                (fullDesc
                <> progDesc "Simulation of Biological Systems"
                <> header "Chemodiversity made easy ;)"
                )


main :: IO ()
main = do
  opts <- execParser cliopts
  hSetBuffering stdin NoBuffering
  hSetBuffering stdout NoBuffering
  randomCompounds <- makeHead (Substrate PPM) <$> generateTreeFromList 30 (toEnum <$> [(maxCompoundWithoutGeneric+1)..] :: [Compound]) -- generate roughly x compounds
  ds <- randoms <$> newStdGen
  probs <- randomRs (0.2,0.7) <$> newStdGen
  let poisonedTree     = poisonTree ds randomCompounds
      poisonCompounds  = foldMap (\(a,b) -> [(b,a) | a > 0]) poisonedTree
  predators <- generatePredators 0.0 poisonedTree
  let poisonCompounds' = pruneCompounds poisonCompounds predators
      pruneCompounds cs ps = filter ((`elem` usedPoisons) . fst) cs
        where usedPoisons = concat $ irresistance <$> ps
  (Just env) <- case environment opts of
                  Nothing   -> return . Just $ exampleEnvironment (getTreeSize randomCompounds) (generateEnzymeFromTree randomCompounds) (zip predators probs) poisonCompounds'
                  Just file -> do
                    putStrLn $ "reading environment: " ++ file
                    decodeStrict' <$> BS.readFile file
  let emptyPlants      = replicate (numPlants . settings $ env) emptyPlant
      printEverything  = verbose opts
  enzs <- randomRs (0,length (possibleEnzymes env) - 1) <$> newStdGen
  let startPlants      = randomGenome 2 enzs (possibleEnzymes env) emptyPlants
  --writeFile "poison.twopi" $ generateDotFromPoisonTree "poison" 0.5 poisonedTree
  when (dumpEnvironment opts) $ LBS.writeFile "environment.json" . encode $ env
  when printEverything $ putStr "\ESC[?1049h"
  loghandle <- openFile (logfile opts) WriteMode
  putStrLn $ "logging to: " ++ logfile opts
  loop 2000 startPlants (loghandle,env) opts
  hClose loghandle
  when printEverything $ do
    putStrLn "Simulation ended. Press key to exit."
    _ <- getChar
    putStr "\ESC[?1049l"

randomGenome :: Int -> [Int] -> [Enzyme] -> [Plant] -> [Plant]
randomGenome num inds enzs []     = []
randomGenome num inds enzs (p:ps) = p { genome = genes} : randomGenome num r enzs ps
  where
    i' = take num inds
    r  = drop num inds
    enzymes = (enzs!!) <$> i'
    genes = (\e -> (e,1,0.5)) <$> enzymes


generatePredators :: Double -> EnzymeTree s (Double,Compound) -> IO [Predator]
generatePredators threshold t = do
    ps <- mapM generatePredators' $ getSubTrees t
    return $ filter ((/= []) . irresistance) $ concat ps -- filter out predators that are resistant to everything because this does not make sense in our model.
  where
      generatePredators' :: EnzymeTree s (Double, Compound) -> IO [Predator]
      generatePredators' t = do -- not fully resistant to t, but fully resistant to everything in ts
          let comps = foldMap (\(a,b) -> [(a,b) | a > threshold]) t
          amount <- randomRIO (0,length comps + 1) :: IO Int
          forM [1..amount] $ \_ -> do
              impact <- randomRIO (0.2,0.7)
              rands <- randoms <$> newStdGen
              let unresists = foldMap (\((a,b),r) -> [b | r*2 < a]) $ zip comps rands
              return $ Predator unresists impact 1

printEnvironment :: Environment -> IO ()
printEnvironment (Environment soil pred metaIter maxComp toxic possEnz settings) =
  do
    putStrLn "Environment:"
    putStrLn $ "Soil:      " ++ show soil
    putStrLn $ "Predators: " ++ show pred
    putStrLn $ "PSM Iters: " ++ show metaIter
    putStrLn $ "Compounds: " ++ show ((toEnum <$> [0..maxComp]) :: [Compound])
    putStrLn $ "Toxic:     " ++ show toxic
    putStrLn $ "Settings:  " ++ show settings

printPopulation :: LA.Vector Bool -> [(Enzyme,String)] -> [(Plant,Double,LA.Vector Amount)] -> IO ()
printPopulation endemic es ps = do
  let padded i str = take i $ str ++ repeat ' '
      n = length ps
      fitnesses = (\(_,f,_) -> f) <$> ps
      meanFitness = sum fitnesses / fromIntegral n
      maxFitness = maximum fitnesses
  putStr $ padded 50 (" Population: (fitness: mean " ++ padded 5 (show meanFitness) ++ ", max: " ++ padded 5 (show maxFitness) ++ ")")
  forM_ ps $ \(_,f,_) -> putStr (printColor (f/maxFitness) '█')
  putStrLn colorOff
  forM_ es $ \(e,s) -> do
    let enzymeProductNum = fromEnum . fst . snd . synthesis $ e
    if LA.toList endemic !! (enzymeProductNum - 1) then putStr ">" else putStr " "
    putStr s
    forM_ ps $ \(Plant g _,_,cs) -> do
      let curE = sum $ map (\(_,q,a) -> fromIntegral q*a)
                     . filter (\(e',_,_) -> e == e')
                     $ g
          plot x
           | x > 2     = 'O'
           | x > 1     = '+'
           | x > 0.7   = 'ö'
           | x > 0.5   = 'o'
           | x > 0     = '.'
           | otherwise = '_'
          amount = min 2 $ cs LA.! fromEnum (fst . snd . synthesis $ e)
      putStr $ printColor (amount/2) (plot curE)
    putStrLn colorOff

printColor :: Double -> Char -> String
printColor x c
  | x > 1 = "Error: " ++ show x
  | x*x < 0.5 = "\ESC[38;5;" ++ show (16 + 36*5 + 6*floor (5*2*x') + 0) ++ "m" ++ [c] ++ ""
  | otherwise = "\ESC[38;5;" ++ show (16 + 36*floor (5*2*(1-x')) + 6*5 + 0) ++ "m" ++ [c] ++ ""
  -- 32 bit
  -- | x*x < 0.5 = "\ESC[38;2;255;" ++ (show . floor $ 255*2*x') ++ ";0m" ++ [c] ++ ""
  -- | otherwise = "\ESC[38;2;" ++ (show . floor $ 255*2*(1-x')) ++ ";255;0m" ++ [c] ++ ""
   where x' = x*x

colorOff :: String
colorOff = "\ESC[0m"

generateEnzymeFromTree :: EnzymeTree s Compound -> [Enzyme]
generateEnzymeFromTree t = (makeSimpleEnzyme c . getElement <$> sts)
                           ++ concatMap generateEnzymeFromTree sts
  where
    c   = getElement t
    sts = getSubTrees t


stepDebug a = liftIO $ print a >> void getChar