Parser adaption

input

@@ -1,4 +1,11 @@
-0.01 2.46 0.88 2.33 2.28 2.24 2.21 2.17 2.14 2.11 2.08 2.03 2.02 2.04 1.99 1.95 1.91 1.87
-0.02 4.98 1.73 4.6 4.45 4.31 4.15 4.07 3.97 3.86 3.78 3.7 3.62 3.5 3.39 3.29 3.2 3.13
-0.03 7.45 2.49 6.84 6.47 6.2 5.97 5.76 5.56 5.41 5.27 5.13 5 4.81 4.65 4.5 4.37 4.27
-0.04 9.99 3.26 8.88 8.32 7.9 7.53 7.23 6.97 6.75 6.55 6.36 6.21 5.95 5.73 5.55 5.42 5.29
+t     10.0  20.0  30.0  40.0  50.0  60.0  70.0  80.0  90.0  100.0 110.0 120.0
+0.01  0.05  0.06  0.06  0.15  0.17  0.23  0.54  1.23  5.32  4.23  5.02  7.03 kappa0=15.0 kappaInf=14.0
+0.02  0.05  0.06  0.06  0.15  0.17  0.23  0.54  1.23  5.32  4.23  5.02  7.03 kappa0=15.0 kappaInf=14.0
+0.03  0.05  0.06  0.06  0.15  0.17  0.23  0.54  1.23  5.32  4.23  5.02  7.03 kappa0=15.0 kappaInf=14.0
+0.04  0.05  0.06  0.06  0.15  0.17  0.23  0.54  1.23  5.32  4.23  5.02  7.03 kappa0=15.0 kappaInf=14.0
+
+t     10.0  20.0  30.0  40.0  50.0  60.0  70.0  80.0  90.0  100.0 110.0 120.0
+0.01  0.05  0.06  0.06  0.15  0.17  0.23  0.54  1.23  5.32  4.23  5.02  7.03 kappa0=15.0 kappaInf=14.0
+0.02  0.05  0.06  0.06  0.15  0.17  0.23  0.54  1.23  5.32  4.23  5.02  7.03 kappa0=15.0 kappaInf=14.0
+0.03  0.05  0.06  0.06  0.15  0.17  0.23  0.54  1.23  5.32  4.23  5.02  7.03 kappa0=15.0 kappaInf=14.0
+0.04  0.05  0.06  0.06  0.15  0.17  0.23  0.54  1.23  5.32  4.23  5.02  7.03 kappa0=15.0 kappaInf=14.0

linreg.cabal

@@ -0,0 +1,57 @@
+cabal-version: 1.12
+
+-- This file has been generated from package.yaml by hpack version 0.31.1.
+--
+-- see: https://github.com/sol/hpack
+--
+-- hash: fa0bf8bdd10e604d4f1906b3674014839def0801ad2d850159658cec73d30778
+
+name:           linreg
+version:        0.1.0.0
+description:    Fitting ester hydrolysis kinetics correctly
+homepage:       https://github.com/ptrab/linreg#readme
+bug-reports:    https://github.com/ptrab/linreg/issues
+author:         Philipp Traber
+maintainer:     phillip.traber@uni-jena.de
+copyright:      2019 Philipp Traber
+license:        GPL-3
+license-file:   LICENSE
+build-type:     Simple
+extra-source-files:
+    LICENSE
+
+source-repository head
+  type: git
+  location: https://github.com/ptrab/linreg
+
+library
+  exposed-modules:
+      Linreg.Numeric
+      Linreg.Parser
+      Linreg.Types
+  other-modules:
+      Paths_linreg
+  hs-source-dirs:
+      src/lib
+  ghc-options: -optP-Wno-nonportable-include-path -O2 -Wall -Wno-unused-top-binds -Wno-unused-local-binds -Wno-type-defaults
+  build-depends:
+      attoparsec >=0.13.2.2
+    , base >=4.7 && <5
+    , text >=1.2.3.1
+    , time >=1.8.0.2
+  default-language: Haskell2010
+
+executable exckel
+  main-is: linreg.hs
+  other-modules:
+      Paths_linreg
+  hs-source-dirs:
+      src/app
+  ghc-options: -threaded -rtsopts -with-rtsopts=-N -optP-Wno-nonportable-include-path -O2 -Wall -Wno-unused-top-binds -Wno-unused-local-binds -Wno-type-defaults
+  build-depends:
+      attoparsec >=0.13.2.2
+    , base >=4.7 && <5
+    , linreg
+    , text >=1.2.3.1
+    , time >=1.8.0.2
+  default-language: Haskell2010

package.yaml

@@ -0,0 +1,62 @@
+name:                linreg
+version:             0.1.0.0
+github:              "ptrab/linreg"
+license:             GPL-3
+author:              "Philipp Traber"
+maintainer:          "phillip.traber@uni-jena.de"
+copyright:           "2019 Philipp Traber"
+
+extra-source-files:
+  - LICENSE
+
+# Metadata used when publishing your package
+# synopsis:            Short description of your package
+# category:            Web
+
+# To avoid duplicated efforts in documentation and dealing with the
+# complications of embedding Haddock markup inside cabal files, it is
+# common to point users to the README.md file.
+description: Fitting ester hydrolysis kinetics correctly
+
+dependencies:
+  - base >= 4.7 && < 5
+  - text >= 1.2.3.1
+  - attoparsec >= 0.13.2.2
+  - time >= 1.8.0.2
+
+library:
+  source-dirs: src/lib
+  ghc-options:
+    - -optP-Wno-nonportable-include-path
+    - -O2
+    - -Wall
+    - -Wno-unused-top-binds
+    - -Wno-unused-local-binds
+    - -Wno-type-defaults
+    # - -static
+    # - -fPIC
+    # - -optl-static
+    # - -optl-pthread
+    #- -optc-static
+
+executables:
+  exckel:
+    main: linreg.hs
+    source-dirs: src/app
+    ghc-options:
+      - -threaded
+      - -rtsopts
+      - -with-rtsopts=-N
+      - -optP-Wno-nonportable-include-path
+      - -O2
+      - -Wall
+      - -Wno-unused-top-binds
+      - -Wno-unused-local-binds
+      - -Wno-type-defaults
+      # - -static
+      # - -fPIC
+      # - -optl-static
+      # - -optl-pthread
+      #- -optc-static
+    dependencies:
+      - linreg

src/app/HReg.hs → src/app/linreg.hs

@@ -1,14 +1,14 @@
 import           Data.Attoparsec.Text.Lazy
 import qualified Data.Text.IO              as T
-import           HReg.Numeric
-import           HReg.Parser
+import           Linreg.Numeric
+import           Linreg.Parser
 import           System.Environment
 
 main :: IO ()
 main = do
   inputFilePath <- head <$> getArgs
   rawVals <- T.readFile inputFilePath
-  let vals = parseOnly (many1 parse_LinRegValues) rawVals
+  let vals = concat <$> parseOnly (many1 linRegValues) rawVals
       results = regression <$> vals
   case results of
     Right (Just x) -> putStr $ show x

src/lib/HReg/Numeric.hs → src/lib/Linreg/Numeric.hs

@@ -1,10 +1,9 @@
-module HReg.Numeric
+module Linreg.Numeric
 ( regression
 ) where
 import           Data.List
-import           Data.Maybe
 import           Data.Time
-import           HReg.Types
+import           Linreg.Types
 
 --------------------------------------------------------------------------------
 -- helper functions
@@ -31,7 +30,7 @@ genT i
 -- regression logic
 --------------------------------------------------------------------------------
 -- | calculate c0/c = (kappa0 - kappaInf) / (kappaT - kappaInf)
-c0pc :: LinRegValues -> [(Maybe DiffTime, Double)]
+c0pc :: LinRegValues -> [(DiffTime, Double)]
 c0pc vals =
   [ (fst i, (kappa0' - kappaInf') / (snd i - kappaInf'))
   | i <- kappaT'
@@ -49,17 +48,17 @@ sumY y = sum . concat $ y
 -- | Calculates the sum over the c*x products
 -- |   sum_i^n sum_j^m c_j x_i
 sumCX :: (Num a) => [a] -> [a] -> a
-sumCX c x = sum $ (*) <$> c <*> x
+sumCX c' x = sum $ (*) <$> c' <*> x
 
 -- | Sum of all squared c and x values
 -- |   sum_i^n sum_j^m c_j^2 x_i^2
 sumC2X2 :: (Num a) => [a] -> [a] -> a
-sumC2X2 c x = sum $ (*) <$> map (^2) c <*> map (^2) x
+sumC2X2 c' x = sum $ (*) <$> map (^2) c' <*> map (^2) x
 
 -- | Zipping products
 -- |   sum_i^n sum_j^m c_j x_i y_ij
 sumCXY :: (Num a) => [a] -> [a] -> [[a]] -> a
-sumCXY c x y = sum $ zipWith (*) ((*) <$> c <*> x) (concat y)
+sumCXY c' x y = sum $ zipWith (*) ((*) <$> c' <*> x) (concat y)
 
 -- | Mean of a list
 -- |   sum_i^n x_i / n
@@ -103,14 +102,10 @@ regression vals
     --
     c' = map c vals
     mVals = map c0pc vals
-    t' = nub . map (map $ fmap ((/10^12) . fromIntegral . diffTimeToPicoseconds) . fst) $ mVals
+    t' = nub . map (map $ (/10^12) . fromIntegral . diffTimeToPicoseconds . fst) $ mVals
     timesAllTheSame = length t' == 1
     t'' = head t'
-    t''' =
-      [ fromMaybe (genT i) (t'' !! i)
-      | i <- [0 .. length t'' - 1]
-      ]
-    x' = t'''
+    x' = t''
     y' = map (map snd) mVals
     sCX = sumCX c' x'
     sCXY = sumCXY c' x' y'

src/lib/Linreg/Parser.hs

@@ -0,0 +1,54 @@
+{-# LANGUAGE OverloadedStrings #-}
+module Linreg.Parser
+( linRegValues
+) where
+import           Data.Attoparsec.Text.Lazy
+import           Data.Time
+import           Linreg.Types
+import Prelude hiding (takeWhile)
+
+-- | Parsing a single block with same "t" as shown in this repository (see "input" file).
+linRegValues :: Parser [LinRegValues]
+linRegValues = do
+  -- Parse first line of a block, starting with a "t", followed by many times in seconds
+  timeSeries <- do
+    skipSpace
+    _ <- string "t"
+    _ <- takeWhile isHorizontalSpace
+    times <- many1 $ do
+      time <- double
+      _ <- takeWhile isHorizontalSpace
+      return time
+    endOfLine
+    return times
+  -- Parse multiple lines of concentration series. First number is c0, then followed by
+  -- (length times) concentrations corresponding to the times and then kappa0 and kappaInf
+  linregSeries <- many1 $ do
+    _ <- takeWhile isHorizontalSpace
+    c' <- double
+    _ <- takeWhile isHorizontalSpace
+    kappaT' <- count (length timeSeries) $ do
+      cAtTime <- double
+      _ <- takeWhile isHorizontalSpace
+      return cAtTime
+    _ <- takeWhile isHorizontalSpace
+    _ <- string "kappa0"
+    _ <- takeWhile isHorizontalSpace
+    _ <- string "="
+    _ <- takeWhile isHorizontalSpace
+    kappa0' <- double
+    _ <- takeWhile isHorizontalSpace
+    _ <- string "kappaInf"
+    _ <- takeWhile isHorizontalSpace
+    _ <- string "="
+    _ <- takeWhile isHorizontalSpace
+    kappaInf' <- double
+    _ <- takeWhile isHorizontalSpace
+    endOfLine
+    return LinRegValues
+      { c        = c'
+      , kappa0   = kappa0'
+      , kappaInf = kappaInf'
+      , kappaT   = zip (map (picosecondsToDiffTime . (* 10^12) . round) $ timeSeries) kappaT'
+      }
+  return linregSeries

src/lib/HReg/Types.hs → src/lib/Linreg/Types.hs

@@ -1,18 +1,16 @@
-module HReg.Types
+module Linreg.Types
 ( LinRegValues(..)
 , RegressionResult(..)
 ) where
 import           Data.Time
-import           Data.Text
 import           Text.Printf
 
 -- | what we get from the measurements
 data LinRegValues = LinRegValues
   { c        :: Double                     -- concentration of this series
   , kappa0   :: Double
   , kappaInf :: Double
-  , kappaT   :: [(Maybe DiffTime, Double)] -- the optional time and corresping
-                                           --   kappa_t
+  , kappaT   :: [(DiffTime, Double)]       -- the  time and corresping kappa_t
   }
 
 -- | what we calculate by regression from the measurements

stack.yaml

@@ -18,7 +18,7 @@
 #
 # resolver: ./custom-snapshot.yaml
 # resolver: https://example.com/snapshots/2018-01-01.yaml
-resolver: lts-12.1
+resolver: lts-13.14
 
 # User packages to be built.
 # Various formats can be used as shown in the example below.