{-# LANGUAGE Strict #-}

module Currycarbon.Calibration.Calibration
    ( -- * Calibration functions
      --
      -- $calibration
      --
      -- This module provides an interface to the calibration logic
        getRelevantCalCurveSegment
      , prepareCalCurveSegment
      , makeCalCurveMatrix
      , uncalToPDF
      , calibrateDates
      , refineCalDates
      , refineCalDate
      , CalibrateDatesConf (..)
      , defaultCalConf
    ) where

import Currycarbon.Calibration.Utils
import Currycarbon.Calibration.Bchron
import Currycarbon.Calibration.MatrixMult
import Currycarbon.Types
import Currycarbon.Utils

import Data.List (sort, sortBy, groupBy)
import qualified Data.Vector.Unboxed as VU

-- | A data type to cover the configuration options of the calibrateDates function
data CalibrateDatesConf = CalibrateDatesConf {
      -- | The calibration algorithm that should be used  
        CalibrateDatesConf -> CalibrationMethod
_calConfMethod :: CalibrationMethod
      -- | Allow calibration to run outside of the range of the calibration curve
      , CalibrateDatesConf -> Bool
_calConfAllowOutside :: Bool
      -- | Interpolate the calibration curve before calibration.
      -- This is a simple linear interpolation only to increase the output
      -- resolution for earlier time periods, where the typical calibration
      -- curves are less dense by default. With the interpolation, the output
      -- will be a per-year density. The mechanism is inspired by the 
      -- [implementation in the Bchron R package](https://github.com/andrewcparnell/Bchron/blob/b202d18550319b488e676a8b542aba55853f6fa3/R/BchronCalibrate.R#L118-L119)
      , CalibrateDatesConf -> Bool
_calConfInterpolateCalCurve :: Bool 
    } deriving (Int -> CalibrateDatesConf -> ShowS
[CalibrateDatesConf] -> ShowS
CalibrateDatesConf -> String
(Int -> CalibrateDatesConf -> ShowS)
-> (CalibrateDatesConf -> String)
-> ([CalibrateDatesConf] -> ShowS)
-> Show CalibrateDatesConf
forall a.
(Int -> a -> ShowS) -> (a -> String) -> ([a] -> ShowS) -> Show a
showList :: [CalibrateDatesConf] -> ShowS
$cshowList :: [CalibrateDatesConf] -> ShowS
show :: CalibrateDatesConf -> String
$cshow :: CalibrateDatesConf -> String
showsPrec :: Int -> CalibrateDatesConf -> ShowS
$cshowsPrec :: Int -> CalibrateDatesConf -> ShowS
Show, CalibrateDatesConf -> CalibrateDatesConf -> Bool
(CalibrateDatesConf -> CalibrateDatesConf -> Bool)
-> (CalibrateDatesConf -> CalibrateDatesConf -> Bool)
-> Eq CalibrateDatesConf
forall a. (a -> a -> Bool) -> (a -> a -> Bool) -> Eq a
/= :: CalibrateDatesConf -> CalibrateDatesConf -> Bool
$c/= :: CalibrateDatesConf -> CalibrateDatesConf -> Bool
== :: CalibrateDatesConf -> CalibrateDatesConf -> Bool
$c== :: CalibrateDatesConf -> CalibrateDatesConf -> Bool
Eq)

-- | A default configuration that should yield almost identical calibration results 
-- to the [Bchron R package](https://github.com/andrewcparnell/Bchron)
--
-- >>> defaultCalConf
-- CalibrateDatesConf {_calConfMethod = Bchron {distribution = StudentTDist {ndf = 100.0}}, _calConfAllowOutside = False, _calConfInterpolateCalCurve = True}
defaultCalConf :: CalibrateDatesConf
defaultCalConf :: CalibrateDatesConf
defaultCalConf = CalibrateDatesConf :: CalibrationMethod -> Bool -> Bool -> CalibrateDatesConf
CalibrateDatesConf {
        _calConfMethod :: CalibrationMethod
_calConfMethod = Bchron :: CalibrationDistribution -> CalibrationMethod
Bchron { distribution :: CalibrationDistribution
distribution = Double -> CalibrationDistribution
StudentTDist Double
100 }
      , _calConfAllowOutside :: Bool
_calConfAllowOutside = Bool
False 
      , _calConfInterpolateCalCurve :: Bool
_calConfInterpolateCalCurve = Bool
True
    }

-- | Calibrates a list of dates with the provided calibration curve
calibrateDates :: CalibrateDatesConf -- ^ Configuration options to consider
                  -> CalCurveBP -- ^ A calibration curve
                  -> [UncalC14] -- ^ A list of uncalibrated radiocarbon dates  
                  -> [Either CurrycarbonException CalPDF] -- ^ The function returns a list for each input date, with
                                                          -- either an exception if the calibration failed for some
                                                          -- reason, or a 'CalPDF'
calibrateDates :: CalibrateDatesConf
-> CalCurveBP -> [UncalC14] -> [Either CurrycarbonException CalPDF]
calibrateDates CalibrateDatesConf
_ CalCurveBP
_ [] = []
calibrateDates (CalibrateDatesConf CalibrationMethod
MatrixMultiplication Bool
allowOutside Bool
interpolate) CalCurveBP
calCurve [UncalC14]
uncalDates =
    (UncalC14 -> Either CurrycarbonException CalPDF)
-> [UncalC14] -> [Either CurrycarbonException CalPDF]
forall a b. (a -> b) -> [a] -> [b]
map (Bool
-> Bool
-> CalCurveBP
-> UncalC14
-> Either CurrycarbonException CalPDF
calibrateDateMatrixMult Bool
allowOutside Bool
interpolate CalCurveBP
calCurve) [UncalC14]
uncalDates
calibrateDates (CalibrateDatesConf Bchron{distribution :: CalibrationMethod -> CalibrationDistribution
distribution=CalibrationDistribution
distr} Bool
allowOutside Bool
interpolate) CalCurveBP
calCurve [UncalC14]
uncalDates =
    (UncalC14 -> Either CurrycarbonException CalPDF)
-> [UncalC14] -> [Either CurrycarbonException CalPDF]
forall a b. (a -> b) -> [a] -> [b]
map (CalibrationDistribution
-> Bool
-> Bool
-> CalCurveBP
-> UncalC14
-> Either CurrycarbonException CalPDF
calibrateDateBchron CalibrationDistribution
distr Bool
allowOutside Bool
interpolate CalCurveBP
calCurve) [UncalC14]
uncalDates

-- | Transforms the raw, calibrated probability density table to a meaningful representation of a
-- calibrated radiocarbon date
-- 
-- >>> :{
--   let years = VU.fromList [-3000,-2900,-2800,-2700,-2600]
--       densities = VU.fromList [0.1,0.2,0.3,0.2,0.1]
--   in refineCalDates [CalPDF {_calPDFid = "", _calPDFCals = years, _calPDFDens = densities}]
-- :}
-- [CalC14 {_calC14id = "", _calC14HDROneSigma = [HDR {_hdrstart = -2800, _hdrstop = -2900}], _calC14HDRTwoSigma = [HDR {_hdrstart = -2600, _hdrstop = -3000}]}]
refineCalDates :: [CalPDF] -> [CalC14]
refineCalDates :: [CalPDF] -> [CalC14]
refineCalDates = (CalPDF -> CalC14) -> [CalPDF] -> [CalC14]
forall a b. (a -> b) -> [a] -> [b]
map CalPDF -> CalC14
refineCalDate

refineCalDate :: CalPDF -> CalC14
refineCalDate :: CalPDF -> CalC14
refineCalDate (CalPDF String
name Vector Int
cals Vector Float
dens) =
    let sortedDensities :: [(Int, Float)]
sortedDensities = ((Int, Float) -> (Int, Float) -> Ordering)
-> [(Int, Float)] -> [(Int, Float)]
forall a. (a -> a -> Ordering) -> [a] -> [a]
sortBy (((Int, Float) -> (Int, Float) -> Ordering)
-> (Int, Float) -> (Int, Float) -> Ordering
forall a b c. (a -> b -> c) -> b -> a -> c
flip (\ (Int
_, Float
dens1) (Int
_, Float
dens2) -> Float -> Float -> Ordering
forall a. Ord a => a -> a -> Ordering
compare Float
dens1 Float
dens2)) (Vector (Int, Float) -> [(Int, Float)]
forall a. Unbox a => Vector a -> [a]
VU.toList (Vector (Int, Float) -> [(Int, Float)])
-> Vector (Int, Float) -> [(Int, Float)]
forall a b. (a -> b) -> a -> b
$ Vector Int -> Vector Float -> Vector (Int, Float)
forall a b.
(Unbox a, Unbox b) =>
Vector a -> Vector b -> Vector (a, b)
VU.zip Vector Int
cals Vector Float
dens)
        cumsumDensities :: [Float]
cumsumDensities = (Float -> Float -> Float) -> [Float] -> [Float]
forall a. (a -> a -> a) -> [a] -> [a]
scanl1 Float -> Float -> Float
forall a. Num a => a -> a -> a
(+) ([Float] -> [Float]) -> [Float] -> [Float]
forall a b. (a -> b) -> a -> b
$ ((Int, Float) -> Float) -> [(Int, Float)] -> [Float]
forall a b. (a -> b) -> [a] -> [b]
map (Int, Float) -> Float
forall a b. (a, b) -> b
snd [(Int, Float)]
sortedDensities
        isIn68 :: [Bool]
isIn68 = (Float -> Bool) -> [Float] -> [Bool]
forall a b. (a -> b) -> [a] -> [b]
map (Float -> Float -> Bool
forall a. Ord a => a -> a -> Bool
< Float
0.683) [Float]
cumsumDensities
        isIn95 :: [Bool]
isIn95 = (Float -> Bool) -> [Float] -> [Bool]
forall a b. (a -> b) -> [a] -> [b]
map (Float -> Float -> Bool
forall a. Ord a => a -> a -> Bool
< Float
0.954) [Float]
cumsumDensities
        contextualizedDensities :: [(Int, Float, Bool, Bool)]
contextualizedDensities = [(Int, Float, Bool, Bool)] -> [(Int, Float, Bool, Bool)]
forall a. [a] -> [a]
reverse ([(Int, Float, Bool, Bool)] -> [(Int, Float, Bool, Bool)])
-> [(Int, Float, Bool, Bool)] -> [(Int, Float, Bool, Bool)]
forall a b. (a -> b) -> a -> b
$ [(Int, Float, Bool, Bool)] -> [(Int, Float, Bool, Bool)]
forall a. Ord a => [a] -> [a]
sort ([(Int, Float, Bool, Bool)] -> [(Int, Float, Bool, Bool)])
-> [(Int, Float, Bool, Bool)] -> [(Int, Float, Bool, Bool)]
forall a b. (a -> b) -> a -> b
$ ((Int, Float) -> Bool -> Bool -> (Int, Float, Bool, Bool))
-> [(Int, Float)] -> [Bool] -> [Bool] -> [(Int, Float, Bool, Bool)]
forall a b c d. (a -> b -> c -> d) -> [a] -> [b] -> [c] -> [d]
zipWith3 (\(Int
y,Float
d) Bool
in68 Bool
in95 -> (Int
y,Float
d,Bool
in68,Bool
in95)) [(Int, Float)]
sortedDensities [Bool]
isIn68 [Bool]
isIn95
    in String -> [HDR] -> [HDR] -> CalC14
CalC14 String
name ([(Int, Float, Bool, Bool)] -> [HDR]
densities2HDR68 [(Int, Float, Bool, Bool)]
contextualizedDensities) ([(Int, Float, Bool, Bool)] -> [HDR]
densities2HDR95 [(Int, Float, Bool, Bool)]
contextualizedDensities)
    where
        densities2HDR68 :: [(Int, Float, Bool, Bool)] -> [HDR]
        densities2HDR68 :: [(Int, Float, Bool, Bool)] -> [HDR]
densities2HDR68 [(Int, Float, Bool, Bool)]
cDensities = 
            let highDensityGroups :: [[(Int, Float, Bool, Bool)]]
highDensityGroups = ((Int, Float, Bool, Bool) -> (Int, Float, Bool, Bool) -> Bool)
-> [(Int, Float, Bool, Bool)] -> [[(Int, Float, Bool, Bool)]]
forall a. (a -> a -> Bool) -> [a] -> [[a]]
groupBy (\(Int
_,Float
_,Bool
in681,Bool
_) (Int
_,Float
_,Bool
in682,Bool
_) -> Bool
in681 Bool -> Bool -> Bool
forall a. Eq a => a -> a -> Bool
== Bool
in682) [(Int, Float, Bool, Bool)]
cDensities
                filteredDensityGroups :: [[(Int, Float, Bool, Bool)]]
filteredDensityGroups = ([(Int, Float, Bool, Bool)] -> Bool)
-> [[(Int, Float, Bool, Bool)]] -> [[(Int, Float, Bool, Bool)]]
forall a. (a -> Bool) -> [a] -> [a]
filter (((Int, Float, Bool, Bool) -> Bool)
-> [(Int, Float, Bool, Bool)] -> Bool
forall (t :: * -> *) a. Foldable t => (a -> Bool) -> t a -> Bool
all (Int, Float, Bool, Bool) -> Bool
getIn68) [[(Int, Float, Bool, Bool)]]
highDensityGroups
            in ([(Int, Float, Bool, Bool)] -> HDR)
-> [[(Int, Float, Bool, Bool)]] -> [HDR]
forall a b. (a -> b) -> [a] -> [b]
map (\[(Int, Float, Bool, Bool)]
xs -> let yearRange :: [Int]
yearRange = ((Int, Float, Bool, Bool) -> Int)
-> [(Int, Float, Bool, Bool)] -> [Int]
forall a b. (a -> b) -> [a] -> [b]
map (Int, Float, Bool, Bool) -> Int
getYear [(Int, Float, Bool, Bool)]
xs in Int -> Int -> HDR
HDR ([Int] -> Int
forall a. [a] -> a
head [Int]
yearRange) ([Int] -> Int
forall a. [a] -> a
last [Int]
yearRange)) [[(Int, Float, Bool, Bool)]]
filteredDensityGroups
        densities2HDR95 :: [(Int, Float, Bool, Bool)] -> [HDR]
        densities2HDR95 :: [(Int, Float, Bool, Bool)] -> [HDR]
densities2HDR95 [(Int, Float, Bool, Bool)]
cDensities = 
            let highDensityGroups :: [[(Int, Float, Bool, Bool)]]
highDensityGroups = ((Int, Float, Bool, Bool) -> (Int, Float, Bool, Bool) -> Bool)
-> [(Int, Float, Bool, Bool)] -> [[(Int, Float, Bool, Bool)]]
forall a. (a -> a -> Bool) -> [a] -> [[a]]
groupBy (\(Int
_,Float
_,Bool
_,Bool
in951) (Int
_,Float
_,Bool
_,Bool
in952) -> Bool
in951 Bool -> Bool -> Bool
forall a. Eq a => a -> a -> Bool
== Bool
in952) [(Int, Float, Bool, Bool)]
cDensities
                filteredDensityGroups :: [[(Int, Float, Bool, Bool)]]
filteredDensityGroups = ([(Int, Float, Bool, Bool)] -> Bool)
-> [[(Int, Float, Bool, Bool)]] -> [[(Int, Float, Bool, Bool)]]
forall a. (a -> Bool) -> [a] -> [a]
filter (((Int, Float, Bool, Bool) -> Bool)
-> [(Int, Float, Bool, Bool)] -> Bool
forall (t :: * -> *) a. Foldable t => (a -> Bool) -> t a -> Bool
all (Int, Float, Bool, Bool) -> Bool
getIn95) [[(Int, Float, Bool, Bool)]]
highDensityGroups
            in ([(Int, Float, Bool, Bool)] -> HDR)
-> [[(Int, Float, Bool, Bool)]] -> [HDR]
forall a b. (a -> b) -> [a] -> [b]
map (\[(Int, Float, Bool, Bool)]
xs -> let yearRange :: [Int]
yearRange = ((Int, Float, Bool, Bool) -> Int)
-> [(Int, Float, Bool, Bool)] -> [Int]
forall a b. (a -> b) -> [a] -> [b]
map (Int, Float, Bool, Bool) -> Int
getYear [(Int, Float, Bool, Bool)]
xs in Int -> Int -> HDR
HDR ([Int] -> Int
forall a. [a] -> a
head [Int]
yearRange) ([Int] -> Int
forall a. [a] -> a
last [Int]
yearRange)) [[(Int, Float, Bool, Bool)]]
filteredDensityGroups
        getIn68 :: (Int, Float, Bool, Bool) -> Bool
        getIn68 :: (Int, Float, Bool, Bool) -> Bool
getIn68 (Int
_,Float
_,Bool
x,Bool
_) = Bool
x
        getIn95 :: (Int, Float, Bool, Bool) -> Bool
        getIn95 :: (Int, Float, Bool, Bool) -> Bool
getIn95 (Int
_,Float
_,Bool
_,Bool
x) = Bool
x
        getYear :: (Int, Float, Bool, Bool) -> Int
        getYear :: (Int, Float, Bool, Bool) -> Int
getYear (Int
year,Float
_,Bool
_,Bool
_) = Int
year