src/Gargantext/Prelude.hs

   1 {-|
   2 Module      : Gargantext.Prelude
   3 Description : Specific Prelude of the project
   4 Copyright   : (c) CNRS, 2017-Present
   5 License     : AGPL + CECILL v3
   6 Maintainer  : team@gargantext.org
   7 Stability   : experimental
   8 Portability : POSIX
   9
  10 -}
  11
  12 {-# OPTIONS_GHC -fno-warn-name-shadowing #-}
  13 {-# OPTIONS_GHC -fno-warn-type-defaults  #-}
  14
  15 {-# LANGUAGE     FlexibleContexts        #-}
  16 {-# LANGUAGE     NoImplicitPrelude       #-}
  17 {-# LANGUAGE     OverloadedStrings       #-}
  18 {-# LANGUAGE     RankNTypes              #-}
  19
  20 module Gargantext.Prelude
  21   ( module Gargantext.Prelude
  22   , module Protolude
  23   , headMay, lastMay
  24   , module GHC.Err.Located
  25   , module Text.Show
  26   , module Text.Read
  27   , cs
  28   , module Data.Maybe
  29   , round
  30   , sortWith
  31   , module Prelude
  32   , MonadBase(..)
  33   )
  34   where
  35
  36 import Control.Monad.Base (MonadBase(..))
  37 import GHC.Exts (sortWith)
  38 import GHC.Err.Located (undefined)
  39 import GHC.Real (round)
  40 import Data.Maybe (isJust, fromJust, maybe)
  41 import Data.Text (Text)
  42 import Protolude ( Bool(True, False), Int, Int64, Double, Integer
  43                  , Fractional, Num, Maybe(Just,Nothing)
  44                  , Enum, Bounded, Float
  45                  , Floating, Char, IO
  46                  , pure, (>>=), (=<<), (<*>), (<$>), (>>)
  47                  , head, flip
  48                  , Ord, Integral, Foldable, RealFrac, Monad, filter
  49                  , reverse, map, mapM, zip, drop, take, zipWith
  50                  , sum, fromIntegral, length, fmap, foldl, foldl'
  51                  , takeWhile, sqrt, identity
  52                  , abs, min, max, maximum, minimum, return, snd, truncate
  53                  , (+), (*), (/), (-), (.), ($), (&), (**), (^), (<), (>), log
  54                  , Eq, (==), (>=), (<=), (<>), (/=)
  55                  , (&&), (||), not, any, all
  56                  , fst, snd, toS
  57                  , elem, die, mod, div, const, either
  58                  , curry, uncurry, repeat
  59                  , otherwise, when
  60                  , IO()
  61                  , compare
  62                  , on
  63                  , panic
  64                  )
  65
  66 import Prelude (Enum, Bounded, minBound, maxBound, putStrLn)
  67 -- TODO import functions optimized in Utils.Count
  68 -- import Protolude hiding (head, last, all, any, sum, product, length)
  69 -- import Gargantext.Utils.Count
  70 import qualified Data.List     as L hiding (head, sum)
  71 import qualified Control.Monad as M
  72
  73 import Data.Map (Map)
  74 import qualified Data.Map as M
  75
  76 import Data.Map.Strict (insertWith)
  77 import qualified Data.Vector as V
  78 import Safe (headMay, lastMay, initMay, tailMay)
  79 import Text.Show (Show(), show)
  80 import Text.Read (Read())
  81 import Data.String.Conversions (cs)
  82
  83
  84 printDebug :: (Show a, MonadBase IO m) => [Char] -> a -> m ()
  85 printDebug msg x = liftBase . putStrLn $ msg <> " " <> show x
  86 -- printDebug _ _ = pure ()
  87
  88
  89 -- | splitEvery n == chunkAlong n n
  90 splitEvery :: Int -> [a] -> [[a]]
  91 splitEvery _ [] = []
  92 splitEvery n xs =
  93   let (h,t) = L.splitAt n xs
  94   in  h : splitEvery n t
  95
  96 type Grain = Int
  97 type Step  = Int
  98
  99 -- | Function to split a range into chunks
 100 -- if   step == grain then linearity (splitEvery)
 101 -- elif step < grain then overlapping
 102 -- else dotted with holes
 103 -- TODO FIX BUG if Steps*Grain /= length l
 104 -- chunkAlong 10 10 [1..15] == [1..10]
 105 -- BUG: what about the rest of (divMod 15 10)?
 106 -- TODO: chunkAlongNoRest or chunkAlongWithRest
 107 -- default behavior: NoRest
 108
 109 chunkAlong :: Eq a => Grain -> Step -> [a] -> [[a]]
 110 chunkAlong a b l = case a >= length l of
 111   True  -> [l]
 112   False -> chunkAlong' a b l
 113
 114 chunkAlong' :: Eq a => Grain -> Step -> [a] -> [[a]]
 115 chunkAlong' a b l = case a > 0 && b > 0 of
 116   True  -> chunkAlong'' a b l
 117   False -> panic "ChunkAlong: Parameters should be > 0 and Grain > Step"
 118
 119 chunkAlong'' :: Eq a => Int -> Int -> [a] -> [[a]]
 120 chunkAlong'' a b l = filter (/= []) $ only (while dropAlong)
 121   where
 122     only      = map       (take a)
 123     while     = takeWhile (\x -> length x >= a)
 124     dropAlong = L.scanl   (\x _y -> drop b x) l ([1..] :: [Integer])
 125
 126 -- | Optimized version (Vector)
 127 chunkAlongV :: Int -> Int -> V.Vector a -> V.Vector (V.Vector a)
 128 chunkAlongV a b l = only (while  dropAlong)
 129   where
 130     only      = V.map       (V.take a)
 131     while     = V.takeWhile (\x -> V.length x >= a)
 132     dropAlong = V.scanl     (\x _y -> V.drop b x) l (V.fromList [1..])
 133
 134 -- | TODO Inverse of chunk ? unchunkAlong ?
 135 -- unchunkAlong :: Int -> Int -> [[a]] -> [a]
 136 -- unchunkAlong = undefined
 137
 138
 139 -- splitAlong [2,3,4] ("helloworld" :: [Char]) == ["he", "llo", "worl", "d"]
 140 splitAlong :: [Int] -> [Char] -> [[Char]]
 141 splitAlong _ [] = [] -- No list? done
 142 splitAlong [] xs = [xs] -- No place to split at? Return the remainder
 143 splitAlong (x:xs) ys = take x ys : splitAlong xs (drop x ys)
 144 -- take until our split spot, recurse with next split spot and list remainder
 145
 146 takeWhileM :: (Monad m) => (a -> Bool) -> [m a] -> m [a]
 147 takeWhileM _ [] = return []
 148 takeWhileM p (a:as) = do
 149     v <- a
 150     if p v
 151         then do
 152             vs <- takeWhileM p as
 153             return (v:vs)
 154         else return []
 155
 156 -- SUMS
 157 -- To select the right algorithme according to the type:
 158 -- https://github.com/mikeizbicki/ifcxt
 159
 160 sumSimple :: Num a => [a] -> a
 161 sumSimple = L.foldl' (+) 0
 162
 163 -- | https://en.wikipedia.org/wiki/Kahan_summation_algorithm
 164 sumKahan :: Num a => [a] -> a
 165 sumKahan = snd . L.foldl' go (0,0)
 166     where
 167         go (c,t) i = ((t'-t)-y,t')
 168             where
 169                 y  = i-c
 170                 t' = t+y
 171
 172 -- | compute part of the dict
 173 count2map :: (Ord k, Foldable t) => t k -> Map k Double
 174 count2map xs = M.map (/ (fromIntegral (length xs))) (count2map' xs)
 175
 176 -- | insert in a dict
 177 count2map' :: (Ord k, Foldable t) => t k -> Map k Double
 178 count2map' xs = L.foldl' (\x y -> insertWith (+) y 1 x) M.empty xs
 179
 180 trunc :: (RealFrac a, Integral c, Integral b) => b -> a -> c
 181 trunc n = truncate . (* 10^n)
 182
 183 trunc' :: Int -> Double -> Double
 184 trunc' n x = fromIntegral $ truncate $ (x * 10^n)
 185
 186 ------------------------------------------------------------------------
 187 bool2num :: Num a => Bool -> a
 188 bool2num True  = 1
 189 bool2num False = 0
 190
 191 bool2double :: Bool -> Double
 192 bool2double = bool2num
 193
 194 bool2int :: Bool -> Int
 195 bool2int = bool2num
 196 ------------------------------------------------------------------------
 197
 198 -- Normalizing && scaling data
 199 scale :: [Double] -> [Double]
 200 scale = scaleMinMax
 201
 202 scaleMinMax :: [Double] -> [Double]
 203 scaleMinMax xs = map (\x -> (x - mi / (ma - mi + 1) )) xs'
 204     where
 205         ma  = maximum xs'
 206         mi  = minimum xs'
 207         xs' = map abs xs
 208
 209 scaleNormalize :: [Double] -> [Double]
 210 scaleNormalize xs = map (\x -> (x - v / (m + 1))) xs'
 211     where
 212         v   = variance  xs'
 213         m   = mean      xs'
 214         xs' = map abs   xs
 215
 216 normalize :: [Double] -> [Double]
 217 normalize as = normalizeWith identity as
 218
 219 normalizeWith :: Fractional b => (a -> b) -> [a] -> [b]
 220 normalizeWith extract bs = map (\x -> x/(sum bs')) bs'
 221     where
 222         bs' = map extract bs
 223
 224 -- Zip functions to add
 225 zipFst :: ([b] -> [a]) -> [b] -> [(a, b)]
 226 zipFst  f xs = zip (f xs) xs
 227
 228 zipSnd :: ([a] -> [b]) -> [a] -> [(a, b)]
 229 zipSnd f xs = zip xs (f xs)
 230
 231 -- | maximumWith
 232 maximumWith :: (Ord a1, Foldable t) => (a2 -> a1) -> t a2 -> a2
 233 maximumWith f = L.maximumBy (compare `on` f)
 234
 235 -- | To get all combinations of a list with no
 236 -- repetition and apply a function to the resulting list of pairs
 237 listToCombi :: forall a b. (a -> b) -> [a] -> [(b,b)]
 238 listToCombi f l = [ (f x, f y) | (x:rest) <- L.tails l,  y <- rest ]
 239
 240 ------------------------------------------------------------------------
 241 -- Empty List Sugar Error Handling
 242 -- TODO add Garg Monad Errors
 243
 244 listSafe1 :: Text -> ([a] -> Maybe a)
 245           -> Text -> [a] -> a
 246 listSafe1 s f e xs = maybe (panic $ h <> e) identity (f xs)
 247   where
 248     h = "[ERR][Gargantext] Empty list for " <> s <> " in "
 249
 250 head' :: Text -> [a] -> a
 251 head' = listSafe1 "head" headMay
 252
 253 last' :: Text -> [a] -> a
 254 last' = listSafe1 "last" lastMay
 255
 256 ------------------------------------------------------------------------
 257
 258 listSafeN :: Text -> ([a] -> Maybe [a])
 259           -> Text -> [a] -> [a]
 260 listSafeN s f e xs = maybe (panic $ h <> e) identity (f xs)
 261   where
 262     h = "[ERR][Gargantext] Empty list for " <> s <> " in "
 263
 264 tail' :: Text -> [a] -> [a]
 265 tail' = listSafeN "tail" tailMay
 266
 267 init' :: Text -> [a] -> [a]
 268 init' = listSafeN "init" initMay
 269
 270 ------------------------------------------------------------------------
 271 --- Some Statistics sugar functions
 272 -- Exponential Average
 273 eavg :: [Double] -> Double
 274 eavg (x:xs) = a*x + (1-a)*(eavg xs)
 275   where a = 0.70
 276 eavg [] = 0
 277
 278 -- Simple Average
 279 mean :: Fractional a => [a] -> a
 280 mean xs = sum xs / fromIntegral (length xs)
 281
 282 sumMaybe :: Num a => [Maybe a] -> Maybe a
 283 sumMaybe = fmap sum . M.sequence
 284
 285 variance :: Floating a => [a] -> a
 286 variance xs = sum ys  / (fromIntegral (length xs) - 1)
 287   where
 288     m = mean xs
 289     ys = map (\x -> (x - m) ** 2) xs
 290
 291 deviation :: Floating a => [a] -> a
 292 deviation = sqrt . variance
 293
 294 movingAverage :: (Eq b, Fractional b) => Int -> [b] -> [b]
 295 movingAverage steps xs = map mean $ chunkAlong steps 1 xs
 296
 297 ma :: [Double] -> [Double]
 298 ma = movingAverage 3
 299
 300
 301 -----------------------------------------------------------------------
 302 fib :: Int -> Int
 303 fib 0 = 0
 304 fib 1 = 1
 305 fib n = fib (n-1) + fib (n-2)
 306
 307
 308
 309 -----------------------------------------------------------------------
 310 -- Memory Optimization
 311
 312 inMVarIO :: MonadIO m => m b -> m b
 313 inMVarIO f = do
 314   mVar <- liftIO newEmptyMVar
 315   zVar <- f
 316   _ <- liftIO $ forkIO $ putMVar mVar zVar
 317   liftIO $ takeMVar mVar
 318
 319 inMVar :: b -> IO b
 320 inMVar f = do
 321   mVar <- newEmptyMVar
 322   let zVar = f
 323   _ <- liftIO $ forkIO $ putMVar mVar zVar
 324   liftIO $ takeMVar mVar
 325