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haskell-gargantext
haskell-gargantext
Commit 19071e4b authored by Przemyslaw Kaminski's avatar Przemyslaw Kaminski
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Merge branch 'dev' into dev-doc-table-optimization

parents 4caaf612 63e3a6fd
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    package.yaml
    View file @ 19071e4b
    ......@@ -6,15 +6,15 @@ category: Data
    author: Gargantext Team
    maintainer: team@gargantext.org
    copyright:
    - ! 'Copyright: (c) 2017-2018: see git logs and README'
    license: BSD3
    - ! 'Copyright: (c) 2017-Present: see git logs and README'
    license: AGPL-3
    homepage: https://gargantext.org
    ghc-options: -Wall
    extra-libraries:
    - gfortran
    - gfortran
    dependencies:
    - extra
    - text
    - extra
    - text
    default-extensions:
    - DataKinds
    - DeriveGeneric
    ......@@ -59,6 +59,7 @@ library:
    - Gargantext.Text
    - Gargantext.Text.Context
    - Gargantext.Text.Corpus.Parsers
    - Gargantext.Text.Corpus.Parsers.Date.Parsec
    - Gargantext.Text.Corpus.API
    - Gargantext.Text.Corpus.Parsers.CSV
    - Gargantext.Text.Examples
    ......@@ -364,36 +365,58 @@ executables:
    tests:
    # garg-test:
    # main: Main.hs
    # source-dirs: src-test
    # ghc-options:
    # - -threaded
    # - -rtsopts
    # - -with-rtsopts=-N
    # dependencies:
    # - base
    # - gargantext
    # - hspec
    # - QuickCheck
    # - quickcheck-instances
    # - time
    # - parsec
    # - duckling
    # - text
    garg-doctest:
    main: Main.hs
    source-dirs: src-doctest
    ghc-options:
    - -O2
    - -Wcompat
    - -Wmissing-signatures
    - -rtsopts
    - -threaded
    - -with-rtsopts=-N
    dependencies:
    - doctest
    - Glob
    - QuickCheck
    - base
    - gargantext
    garg-test:
    main: Main.hs
    source-dirs: src-test
    default-extensions:
    - DataKinds
    - DeriveGeneric
    - FlexibleContexts
    - FlexibleInstances
    - GeneralizedNewtypeDeriving
    - MultiParamTypeClasses
    - NoImplicitPrelude
    - OverloadedStrings
    - RankNTypes
    ghc-options:
    - -threaded
    - -rtsopts
    - -with-rtsopts=-N
    dependencies:
    - base
    - gargantext
    - hspec
    - QuickCheck
    - quickcheck-instances
    - time
    - parsec
    - duckling
    - text
    # garg-doctest:
    # main: Main.hs
    # source-dirs: src-doctest
    # ghc-options:
    # - -O2
    # - -Wcompat
    # - -Wmissing-signatures
    # - -rtsopts
    # - -threaded
    # - -with-rtsopts=-N
    # dependencies:
    # - doctest
    # - Glob
    # - QuickCheck
    # - base
    # - gargantext
    # default-extensions:
    # - DataKinds
    # - DeriveGeneric
    # - FlexibleContexts
    # - FlexibleInstances
    # - GeneralizedNewtypeDeriving
    # - MultiParamTypeClasses
    # - NoImplicitPrelude
    # - OverloadedStrings
    # - RankNTypes
    #
    src-doctest/Main.hs
    View file @ 19071e4b
    import System.FilePath.Glob
    import Test.DocTest
    import Gargantext.Prelude
    main :: IO ()
    main = glob "src/Gargantext/" >>= doctest
    ......
    src-test/Main.hs
    View file @ 19071e4b
    ......@@ -12,15 +12,17 @@ Portability : POSIX
    import Gargantext.Prelude
    import Gargantext.Core (Lang(..))
    --import qualified Ngrams.Lang.Fr as Fr
    import qualified Ngrams.Lang as Lang
    --import qualified Ngrams.Lang as Lang
    import qualified Ngrams.Lang.Occurrences as Occ
    import qualified Ngrams.Metrics as Metrics
    import qualified Parsers.Date as PD
    import qualified Graph.Distance as GD
    main :: IO ()
    main = do
    Occ.parsersTest
    Lang.ngramsExtractionTest FR
    Lang.ngramsExtractionTest EN
    Metrics.main
    -- Occ.parsersTest
    -- Lang.ngramsExtractionTest FR
    -- Lang.ngramsExtractionTest EN
    -- Metrics.main
    PD.testFromRFC3339
    GD.test
    src-test/Ngrams/Lang.hs
    View file @ 19071e4b
    ......@@ -15,6 +15,7 @@ commentary with @some markup@.
    module Ngrams.Lang where
    {-
    import Gargantext.Prelude (IO())
    import Gargantext.Core (Lang(..))
    ......@@ -24,4 +25,4 @@ import qualified Ngrams.Lang.En as En
    ngramsExtractionTest :: Lang -> IO ()
    ngramsExtractionTest FR = Fr.ngramsExtractionTest
    ngramsExtractionTest EN = En.ngramsExtractionTest
    -}
    src-test/Ngrams/Lang/En.hs
    View file @ 19071e4b
    ......@@ -15,6 +15,7 @@ commentary with @some markup@.
    module Ngrams.Lang.En where
    {-
    import Data.List ((!!))
    import Data.Text (Text)
    ......@@ -22,8 +23,11 @@ import Test.Hspec
    import Gargantext.Prelude
    import Gargantext.Core (Lang(..))
    import Gargantext.Text.Ngrams.PosTagging.Parser (extractNgrams, selectNgrams)
    -- TODO this import is not used anymore
    import Gargantext.Text.Ngrams.PosTagging.Parser (extractNgrams, selectNgrams)
    -- use instead
    -- import Gargantext.Text.Terms (extractNgramsT)
    ngramsExtractionTest :: IO ()
    ngramsExtractionTest = hspec $ do
    ......@@ -43,4 +47,4 @@ ngramsExtractionTest = hspec $ do
    t2 <- map (selectNgrams EN) <$> extractNgrams EN t
    t2 `shouldBe` [[("Donald Trump","NNP","PERSON"),("president of the United-States of America","NN","LOCATION")]]
    -}
    src-test/Ngrams/Lang/Fr.hs
    View file @ 19071e4b
    ......@@ -15,12 +15,15 @@ commentary with @some markup@.
    module Ngrams.Lang.Fr where
    {-
    import Test.Hspec
    import Gargantext.Prelude
    import Gargantext.Core (Lang(..))
    -- TODO this import is not used anymore
    import Gargantext.Text.Ngrams.PosTagging.Parser (extractNgrams, selectNgrams)
    -- use instead
    -
    ngramsExtractionTest :: IO ()
    ngramsExtractionTest = hspec $ do
    describe "Behavioral tests: ngrams extraction in French Language" $ do
    ......@@ -61,4 +64,4 @@ ngramsExtractionTest = hspec $ do
    let textFr1 = "L'heure d'arrivée des coureurs dépend de la météo du jour."
    testFr1 <- map (selectNgrams FR) <$> (extractNgrams FR) textFr1
    testFr1 `shouldBe` [[("heure d' arrivée des coureurs","NC","O"),("météo du jour","NC","O")]]
    -}
    src-test/Ngrams/Lang/Occurrences.hs
    View file @ 19071e4b
    ......@@ -15,6 +15,7 @@ commentary with @some markup@.
    module Ngrams.Lang.Occurrences where
    {-
    import Test.Hspec
    import Data.Either (Either(Right))
    ......@@ -59,4 +60,4 @@ parsersTest = hspec $ do
    -- describe "Parser for nodes" $ do
    -- it "returns the result of one parsing after space" $ do
    -- occOfCorpus 249509 "sciences" `shouldReturn` 7
    -}
    src-test/Ngrams/Metrics.hs
    View file @ 19071e4b
    ......@@ -15,8 +15,10 @@ commentary with @some markup@.
    {-# LANGUAGE CPP #-}
    module Ngrams.Metrics (main) where
    --module Ngrams.Metrics (main) where
    module Ngrams.Metrics where
    {-
    import Data.Text (Text)
    import qualified Data.Text as T
    import Data.Ratio
    ......@@ -139,3 +141,5 @@ testPair :: (Eq a, Show a)
    -> SpecWith ()
    testPair f a b r = it ("‘" <> T.unpack a <> "’ and ‘" <> T.unpack b <> "’") $
    f a b `shouldBe` r
    -}
    src-test/Parsers/Date.hs
    View file @ 19071e4b
    ......@@ -28,7 +28,7 @@ import Duckling.Time.Types (toRFC3339)
    -----------------------------------------------------------
    import Gargantext.Prelude
    import Gargantext.Text.Parsers.Date (fromRFC3339)
    import Gargantext.Text.Corpus.Parsers.Date.Parsec (fromRFC3339)
    import Parsers.Types
    -----------------------------------------------------------
    ......
    src/Gargantext/API/Admin/Orchestrator/Types.hs
    View file @ 19071e4b
    ......@@ -27,12 +27,12 @@ instance Arbitrary a => Arbitrary (JobOutput a) where
    arbitrary = JobOutput <$> arbitrary
    -- | Main Types
    -- TODO IsidoreAuth
    data ExternalAPIs = All
    | PubMed
    | HAL
    | IsTex
    | Isidore
    -- | IsidoreAuth
    deriving (Show, Eq, Enum, Bounded, Generic)
    ......
    src/Gargantext/API/Node/Update.hs
    View file @ 19071e4b
    ......@@ -81,7 +81,7 @@ updateNode uId nId (UpdateNodeParamsGraph metric) logStatus = do
    logStatus JobLog { _scst_succeeded = Just 1
    , _scst_failed = Just 0
    , _scst_remaining = Just 2
    , _scst_remaining = Just 1
    , _scst_events = Just []
    }
    ......
    src/Gargantext/Text/Terms.hs
    View file @ 19071e4b
    ......@@ -175,6 +175,6 @@ newTries n t = buildTries n (fmap toToken $ uniText t)
    uniText :: Text -> [[Text]]
    uniText = map (List.filter (not . isPunctuation))
    . map tokenize
    . sentences -- | TODO get sentences according to lang
    . sentences -- TODO get sentences according to lang
    . Text.toLower
    src/Gargantext/Text/Terms/Eleve.hs
    View file @ 19071e4b
    ......@@ -73,12 +73,12 @@ subst (src, dst) x | sim src x = dst
    | otherwise = x
    ------------------------------------------------------------------------
    -- | TODO: Show Instance only used for debugging
    type Entropy e =
    ( Fractional e
    , Floating e
    , P.RealFloat e
    , Show e
    -- ^ TODO: only used for debugging
    )
    ------------------------------------------------------------------------
    -- | Example and tests for development
    ......
    src/Gargantext/Viz/AdaptativePhylo.hs
    View file @ 19071e4b
    ......@@ -65,11 +65,13 @@ data SeaElevation =
    data Proximity =
    WeightedLogJaccard
    { _wlj_sensibility :: Double
    { _wlj_sensibility :: Double
    {-
    -- , _wlj_thresholdInit :: Double
    -- , _wlj_thresholdStep :: Double
    -- | max height for sea level in temporal matching
    -- , _wlj_elevation :: Double
    -}
    }
    | Hamming
    deriving (Show,Generic,Eq)
    ......
    src/Gargantext/Viz/Graph/API.hs
    View file @ 19071e4b
    ......@@ -147,8 +147,9 @@ computeGraph cId d nt repo = do
    lIds <- selectNodesWithUsername NodeList userMaster
    let ngs = filterListWithRoot MapTerm $ mapTermListRoot [lId] nt repo
    -- TODO split diagonal
    myCooc <- Map.filter (>1)
    <$> getCoocByNgrams (Diagonal True)
    <$> getCoocByNgrams (Diagonal False)
    <$> groupNodesByNgrams ngs
    <$> getNodesByNgramsOnlyUser cId (lIds <> [lId]) nt (Map.keys ngs)
    ......
    src/Gargantext/Viz/Graph/Distances.hs
    View file @ 19071e4b
    ......@@ -27,6 +27,7 @@ import Test.QuickCheck.Arbitrary
    ------------------------------------------------------------------------
    data Distance = Conditional | Distributional
    deriving (Show)
    measure :: Distance -> Matrix Int -> Matrix Double
    measure Conditional = measureConditional
    ......
    src/Gargantext/Viz/Graph/Distances/Distributional.hs
    View file @ 19071e4b
    ......@@ -18,18 +18,15 @@ module Gargantext.Viz.Graph.Distances.Distributional
    where
    import Data.Matrix hiding (identity)
    import qualified Data.Map as M
    import Data.Vector (Vector)
    import qualified Data.Vector as V
    import Gargantext.Prelude
    import Gargantext.Viz.Graph.Utils
    distributional :: (Floating a, Ord a) => Matrix a -> [((Int, Int), a)]
    distributional m = filter (\((x,y), d) -> foldl' (&&) True (conditions x y d) ) distriList
    distributional' :: (Floating a, Ord a) => Matrix a -> [((Int, Int), a)]
    distributional' m = filter (\((x,y), d) -> foldl' (&&) True (conditions x y d) ) distriList
    where
    conditions x y d = [ (x /= y)
    , (d > miniMax')
    ......@@ -51,7 +48,6 @@ ri m = matrix c r doRi
    $ V.zip (ax Col x y mi') (ax Row x y mi')
    (c,r) = (nOf Col m, nOf Row m)
    mi :: (Ord a, Floating a) => Matrix a -> Matrix a
    mi m = matrix c r createMat
    where
    ......
    src/Gargantext/Viz/Graph/Distances/Matrice.hs
    View file @ 19071e4b
    ......@@ -17,14 +17,6 @@ Implementation use Accelerate library which enables GPU and CPU computation:
    [Accelerating Haskell Array Codes with Multicore GPUs][CKLM+11].
    In _DAMP '11: Declarative Aspects of Multicore Programming_, ACM, 2011.
    * Trevor L. McDonell, Manuel M. T. Chakravarty, Gabriele Keller, and Ben Lippmeier.
    [Optimising Purely Functional GPU Programs][MCKL13].
    In _ICFP '13: The 18th ACM SIGPLAN International Conference on Functional Programming_, ACM, 2013.
    * Robert Clifton-Everest, Trevor L. McDonell, Manuel M. T. Chakravarty, and Gabriele Keller.
    [Embedding Foreign Code][CMCK14].
    In _PADL '14: The 16th International Symposium on Practical Aspects of Declarative Languages_, Springer-Verlag, LNCS, 2014.
    * Trevor L. McDonell, Manuel M. T. Chakravarty, Vinod Grover, and Ryan R. Newton.
    [Type-safe Runtime Code Generation: Accelerate to LLVM][MCGN15].
    In _Haskell '15: The 8th ACM SIGPLAN Symposium on Haskell_, ACM, 2015.
    ......@@ -34,13 +26,14 @@ Implementation use Accelerate library which enables GPU and CPU computation:
    {-# LANGUAGE TypeFamilies #-}
    {-# LANGUAGE TypeOperators #-}
    {-# LANGUAGE ScopedTypeVariables #-}
    {-# LANGUAGE ViewPatterns #-}
    module Gargantext.Viz.Graph.Distances.Matrice
    where
    import Debug.Trace (trace)
    import Data.Array.Accelerate
    import Data.Array.Accelerate.Interpreter (run)
    import qualified Gargantext.Prelude as P
    ......@@ -49,8 +42,8 @@ import qualified Gargantext.Prelude as P
    --
    -- >>> vector 3
    -- Vector (Z :. 3) [0,1,2]
    vector :: Int -> (Array (Z :. Int) Int)
    vector n = fromList (Z :. n) [0..n]
    vector :: Elt c => Int -> [c] -> (Array (Z :. Int) c)
    vector n l = fromList (Z :. n) l
    -- | Define a matrix
    --
    ......@@ -85,16 +78,26 @@ dim m = n
    -- indexTail (arrayShape m)
    -----------------------------------------------------------------------
    -- TODO move to Utils
    runExp :: Elt e => Exp e -> e
    runExp e = indexArray (run (unit e)) Z
    -----------------------------------------------------------------------
    -- | Sum of a Matrix by Column
    --
    -- >>> run $ matSum 3 (use $ matrix 3 [1..])
    -- >>> run $ matSumCol 3 (use $ matrix 3 [1..])
    -- Matrix (Z :. 3 :. 3)
    -- [ 12.0, 15.0, 18.0,
    -- 12.0, 15.0, 18.0,
    -- 12.0, 15.0, 18.0]
    matSum :: Dim -> Acc (Matrix Double) -> Acc (Matrix Double)
    matSum r mat = replicate (constant (Z :. (r :: Int) :. All)) $ sum $ transpose mat
    matSumCol :: Dim -> Acc (Matrix Double) -> Acc (Matrix Double)
    matSumCol r mat = replicate (constant (Z :. (r :: Int) :. All)) $ sum $ transpose mat
    matSumCol' :: Matrix Double -> Matrix Double
    matSumCol' m = run $ matSumCol n m'
    where
    n = dim m
    m' = use m
    -- | Proba computes de probability matrix: all cells divided by thee sum of its column
    ......@@ -106,14 +109,16 @@ matSum r mat = replicate (constant (Z :. (r :: Int) :. All)) $ sum $ transpose m
    -- 0.3333333333333333, 0.3333333333333333, 0.3333333333333333,
    -- 0.5833333333333334, 0.5333333333333333, 0.5]
    matProba :: Dim -> Acc (Matrix Double) -> Acc (Matrix Double)
    matProba r mat = zipWith (/) mat (matSum r mat)
    matProba r mat = zipWith (/) mat (matSumCol r mat)
    -- | Diagonal of the matrix
    --
    -- >>> run $ diag (use $ matrix 3 ([1..] :: [Int]))
    -- Vector (Z :. 3) [1,5,9]
    diag :: Elt e => Acc (Matrix e) -> Acc (Vector e)
    diag m = backpermute (indexTail (shape m)) (lift1 (\(Z :. x) -> (Z :. x :. (x :: Exp Int)))) m
    diag m = backpermute (indexTail (shape m))
    (lift1 (\(Z :. x) -> (Z :. x :. (x :: Exp Int))))
    m
    -- | Divide by the Diagonal of the matrix
    --
    ......@@ -145,8 +150,8 @@ matMiniMax m = map (\x -> ifThenElse (x > miniMax') x 0) (transpose m)
    -- [ 0.0, 0.0, 7.0,
    -- 0.0, 0.0, 8.0,
    -- 0.0, 6.0, 9.0]
    matFilter :: Double -> Acc (Matrix Double) -> Acc (Matrix Double)
    matFilter t m = map (\x -> ifThenElse (x > (constant t)) x 0) (transpose m)
    filter' :: Double -> Acc (Matrix Double) -> Acc (Matrix Double)
    filter' t m = map (\x -> ifThenElse (x > (constant t)) x 0) (transpose m)
    -----------------------------------------------------------------------
    -- * Measures of proximity
    ......@@ -164,7 +169,9 @@ matFilter t m = map (\x -> ifThenElse (x > (constant t)) x 0) (transpose m)
    -- interactions of 2 terms in the corpus.
    measureConditional :: Matrix Int -> Matrix Double
    --measureConditional m = run (matMiniMax $ matProba (dim m) $ map fromIntegral $ use m)
    measureConditional m = run (matProba (dim m) $ map fromIntegral $ use m)
    measureConditional m = run $ matProba (dim m)
    $ map fromIntegral
    $ use m
    -- *** Conditional distance (advanced)
    ......@@ -196,9 +203,9 @@ conditional' m = ( run $ ie $ map fromIntegral $ use m
    r = dim m
    xs :: Acc (Matrix Double) -> Acc (Matrix Double)
    xs mat = zipWith (-) (matSum r $ matProba r mat) (matProba r mat)
    xs mat = zipWith (-) (matSumCol r $ matProba r mat) (matProba r mat)
    ys :: Acc (Matrix Double) -> Acc (Matrix Double)
    ys mat = zipWith (-) (matSum r $ transpose $ matProba r mat) (matProba r mat)
    ys mat = zipWith (-) (matSumCol r $ transpose $ matProba r mat) (matProba r mat)
    -----------------------------------------------------------------------
    -- ** Distributional Distance
    ......@@ -206,11 +213,11 @@ conditional' m = ( run $ ie $ map fromIntegral $ use m
    -- | Distributional Distance Measure
    --
    -- Distributional measure is a relative measure which depends on the
    -- selected list, it represents structural equivalence.
    -- selected list, it represents structural equivalence of mutual information.
    --
    -- The distributional measure P(c) of @i@ and @j@ terms is: \[
    -- S_{MI} = \frac {\sum_{k \neq i,j ; MI_{ik} >0}^{} \min(MI_{ik},
    -- MI_{jk})}{\sum_{k \neq i,j ; MI_{ik}}^{}} \]
    -- MI_{jk})}{\sum_{k \neq i,j ; MI_{ik}>0}^{}} \]
    --
    -- Mutual information
    -- \[S_{MI}({i},{j}) = \log(\frac{C{ij}}{E{ij}})\]
    ......@@ -228,26 +235,120 @@ conditional' m = ( run $ ie $ map fromIntegral $ use m
    -- \[N_{m} = \sum_{i,i \neq i}^{m} \sum_{j, j \neq j}^{m} S_{ij}\]
    --
    distributional :: Matrix Int -> Matrix Double
    distributional m = run $ matMiniMax $ ri (map fromIntegral $ use m)
    distributional m = run {- -- $ matMiniMax
    -- $ ri
    -- $ myMin
    -}
    $ filter' 0
    $ s_mi
    $ map fromIntegral
    {- from Int to Double -}
    $ use m
    {- push matrix in Accelerate type -}
    where
    -- filter m = zipWith (\a b -> max a b) m (transpose m)
    ri mat = zipWith (/) mat1 mat2
    {-
    ri :: Acc (Matrix Double) -> Acc (Matrix Double)
    ri mat = mat1 -- zipWith (/) mat1 mat2
    where
    mat1 = matSum n $ zipWith min (s_mi mat) (s_mi $ transpose mat)
    mat2 = matSum n mat
    s_mi m' = zipWith (\a b -> log (a/b)) m'
    $ zipWith (/) (crossProduct m') (total m')
    mat1 = matSumCol n $ zipWith min' (myMin mat) (myMin $ transpose mat)
    mat2 = total mat
    myMin :: Acc (Matrix Double) -> Acc (Matrix Double)
    myMin = replicate (constant (Z :. n :. All)) . minimum
    -}
    -- TODO fix NaN
    -- Quali TEST: OK
    s_mi :: Acc (Matrix Double) -> Acc (Matrix Double)
    s_mi m' = zipWith (\x y -> log (x / y)) (diagNull n m')
    $ zipWith (/) (crossProduct n m') (total m')
    -- crossProduct n m'
    total m'' = replicate (constant (Z :. n :. n)) $ fold (+) 0 $ fold (+) 0 m''
    total :: Acc (Matrix Double) -> Acc (Matrix Double)
    total = replicate (constant (Z :. n :. n)) . sum . sum
    n :: Dim
    n = dim m
    crossProduct m''' = zipWith (*) (cross m''' ) (cross (transpose m'''))
    cross mat = zipWith (-) (matSum n mat) (mat)
    -- run $ (identityMatrix (DAA.constant (10::Int)) :: DAA.Acc (DAA.Matrix Int)) Matrix (Z :. 10 :. 10)
    identityMatrix :: Num a => Exp Int -> Acc (Matrix a)
    identityMatrix n =
    let zeros = fill (index2 n n) 0
    ones = fill (index1 n) 1
    in
    permute const zeros (\(unindex1 -> i) -> index2 i i) ones
    eyeMatrix :: Num a => Dim -> Acc (Matrix a) -> Acc (Matrix a)
    eyeMatrix n' _m =
    let ones = fill (index2 n n) 1
    zeros = fill (index1 n) 0
    n = constant n'
    in
    permute const ones (\(unindex1 -> i) -> index2 i i) zeros
    selfMatrix :: Num a => Dim -> Acc (Matrix a) -> Acc (Matrix a)
    selfMatrix n' _m =
    let zeros = fill (index2 n n) 0
    ones = fill (index2 n n) 1
    n = constant n'
    in
    permute const ones ( lift1 ( \(Z :. (i :: Exp Int) :. (_j:: Exp Int))
    -> -- ifThenElse (i /= j)
    -- (Z :. i :. j)
    (Z :. i :. i)
    )) zeros
    selfMatrix' :: (Elt a, P.Num (Exp a)) => Array DIM2 a -> Matrix a
    selfMatrix' m' = run $ selfMatrix n m
    where
    n = dim m'
    m = use m'
    -------------------------------------------------
    diagNull :: Num a => Dim -> Acc (Matrix a) -> Acc (Matrix a)
    diagNull n m = zipWith (*) m eye
    where
    eye = eyeMatrix n m
    -------------------------------------------------
    crossProduct :: Dim -> Acc (Matrix Double) -> Acc (Matrix Double)
    crossProduct n m = trace (P.show (run m',run m'')) $ zipWith (*) m' m''
    where
    m' = cross n m
    m'' = cross n (transpose m)
    crossT :: Matrix Double -> Matrix Double
    crossT = run . transpose . use
    crossProduct' :: Matrix Double -> Matrix Double
    crossProduct' m = run $ crossProduct n m'
    where
    n = dim m
    m' = use m
    runWith :: (Arrays c, Elt a1)
    => (Dim -> Acc (Matrix a1) -> a2 -> Acc c)
    -> Matrix a1
    -> a2
    -> c
    runWith f m = run . f (dim m) (use m)
    -- | cross
    cross :: Dim -> Acc (Matrix Double) -> Acc (Matrix Double)
    cross n mat = diagNull n (matSumCol n $ diagNull n mat)
    cross' :: Matrix Double -> Matrix Double
    cross' mat = run $ cross n mat'
    where
    mat' = use mat
    n = dim mat
    -----------------------------------------------------------------------
    -----------------------------------------------------------------------
    ......
    src/Gargantext/Viz/Graph/Tools.hs
    View file @ 19071e4b
    ......@@ -56,6 +56,7 @@ cooc2graph :: Distance
    -> (Map (Text, Text) Int)
    -> IO Graph
    cooc2graph distance threshold myCooc = do
    printDebug "cooc2graph" distance
    let
    (ti, _) = createIndices myCooc
    myCooc' = toIndex ti myCooc
    ......
    src/Gargantext/Viz/Phylo/LevelMaker.hs
    View file @ 19071e4b
    ......@@ -207,7 +207,7 @@ toNthLevel lvlMax prox clus p
    | otherwise = toNthLevel lvlMax prox clus
    $ traceBranches (lvl + 1)
    $ setPhyloBranches (lvl + 1)
    -- $ transposePeriodLinks (lvl + 1)
    -- \$ transposePeriodLinks (lvl + 1)
    $ traceTranspose (lvl + 1) Descendant
    $ transposeLinks (lvl + 1) Descendant
    $ traceTranspose (lvl + 1) Ascendant
    ......@@ -230,15 +230,15 @@ toNthLevel lvlMax prox clus p
    toPhylo1 :: Cluster -> Proximity -> Map (Date, Date) [Document] -> Phylo -> Phylo
    toPhylo1 clus prox d p = case clus of
    Fis (FisParams k s t) -> traceBranches 1
    -- $ reLinkPhyloBranches 1
    -- $ traceBranches 1
    -- \$ reLinkPhyloBranches 1
    -- \$ traceBranches 1
    $ setPhyloBranches 1
    $ traceTempoMatching Descendant 1
    $ interTempoMatching Descendant 1 prox
    $ traceTempoMatching Ascendant 1
    $ interTempoMatching Ascendant 1 prox
    $ tracePhyloN 1
    -- $ setLevelLinks (0,1)
    -- \$ setLevelLinks (0,1)
    $ addPhyloLevel 1 (getPhyloFis phyloFis)
    $ trace (show (size $ getPhyloFis phyloFis) <> " Fis created") $ phyloFis
    where
    ......
    src/Gargantext/Viz/Phylo/LinkMaker.hs
    View file @ 19071e4b
    ......@@ -126,15 +126,15 @@ phyloGroupMatching :: [PhyloPeriodId] -> PhyloGroup -> Phylo -> [Pointer]
    phyloGroupMatching periods g p = case pointers of
    Nothing -> []
    Just pts -> head' "phyloGroupMatching"
    -- | Keep only the best set of pointers grouped by proximity
    -- Keep only the best set of pointers grouped by proximity
    $ groupBy (\pt pt' -> snd pt == snd pt')
    $ reverse $ sortOn snd pts
    -- | Find the first time frame where at leats one pointer satisfies the proximity threshold
    -- Find the first time frame where at leats one pointer satisfies the proximity threshold
    where
    --------------------------------------
    pointers :: Maybe [Pointer]
    pointers = find (not . null)
    -- | For each time frame, process the Proximity on relevant pairs of targeted groups
    -- For each time frame, process the Proximity on relevant pairs of targeted groups
    $ scanl (\acc frame ->
    let pairs = makePairs frame g p
    in acc ++ ( filter (\(_,proxi) -> filterProximity proxi (getPhyloProximity p))
    ......@@ -145,7 +145,7 @@ phyloGroupMatching periods g p = case pointers of
    if (t == t')
    then [(getGroupId t,proxi)]
    else [(getGroupId t,proxi),(getGroupId t',proxi)] ) pairs ) ) []
    -- | [[1900],[1900,1901],[1900,1901,1902],...] | length max => + 5 years
    -- [[1900],[1900,1901],[1900,1901,1902],...] | length max => + 5 years
    $ inits periods
    --------------------------------------
    ......@@ -218,8 +218,6 @@ interTempoMatching fil lvl _ p = updateGroups fil lvl (Map.fromList pointers) p
    ------------------------------------------------------------------------
    -- | Make links from Period to Period after level 1
    listToTuple :: (a -> b) -> [a] -> [(b,a)]
    listToTuple f l = map (\x -> (f x, x)) l
    ......
    src/Gargantext/Viz/Phylo/Metrics.hs
    View file @ 19071e4b
    ......@@ -90,13 +90,13 @@ findDynamics n pv pn m =
    bid = fromJust $ (pn ^. pn_bid)
    end = last' "dynamics" (sort $ map snd $ elems m)
    in if (((snd prd) == (snd $ m ! n)) && (snd prd /= end))
    -- | emergence
    -- emergence
    then 2
    else if ((fst prd) == (fst $ m ! n))
    -- | recombination
    -- recombination
    then 0
    else if (not $ sharedWithParents (fst prd) bid n pv)
    -- | decrease
    -- decrease
    then 1
    else 3
    ......@@ -175,9 +175,3 @@ hamming f1 f2 = fromIntegral $ max ((size inter) - (size f1)) ((size inter) - (s
    inter :: Map (Int, Int) Double
    inter = intersection f1 f2
    --------------------------------------
    src/Gargantext/Viz/Phylo/PhyloExport.hs
    View file @ 19071e4b
    ......@@ -171,12 +171,12 @@ exportToDot phylo export =
    <> "##########################") $
    digraph ((Str . fromStrict) $ (phyloName $ getConfig phylo)) $ do
    -- | 1) init the dot graph
    {- 1) init the dot graph -}
    graphAttrs ( [ Label (toDotLabel $ (phyloName $ getConfig phylo))]
    <> [ FontSize 30, LabelLoc VTop, NodeSep 1, RankSep [1], Rank SameRank, Splines SplineEdges, Overlap ScaleOverlaps
    , Ratio FillRatio
    , Style [SItem Filled []],Color [toWColor White]]
    -- | home made attributes
    {-- home made attributes -}
    <> [(toAttr (fromStrict "phyloFoundations") $ pack $ show (length $ Vector.toList $ getRoots phylo))
    ,(toAttr (fromStrict "phyloTerms") $ pack $ show (length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) $ export ^. export_groups))
    ,(toAttr (fromStrict "phyloDocs") $ pack $ show (sum $ elems $ phylo ^. phylo_timeDocs))
    ......@@ -185,36 +185,36 @@ exportToDot phylo export =
    ,(toAttr (fromStrict "phyloGroups") $ pack $ show (length $ export ^. export_groups))
    ])
    {-
    -- toAttr (fromStrict k) $ (pack . unwords) $ map show v
    -- | 2) create a layer for the branches labels
    -- 2) create a layer for the branches labels -}
    subgraph (Str "Branches peaks") $ do
    graphAttrs [Rank SameRank]
    -- | 3) group the branches by hierarchy
    {-
    -- 3) group the branches by hierarchy
    -- mapM (\branches ->
    -- subgraph (Str "Branches clade") $ do
    -- graphAttrs [Rank SameRank]
    -- -- | 4) create a node for each branch
    -- -- 4) create a node for each branch
    -- mapM branchToDotNode branches
    -- ) $ elems $ fromListWith (++) $ map (\b -> ((init . snd) $ b ^. branch_id,[b])) $ export ^. export_branches
    -}
    mapM (\b -> branchToDotNode b (fromJust $ elemIndex b (export ^. export_branches))) $ export ^. export_branches
    -- | 5) create a layer for each period
    {-- 5) create a layer for each period -}
    _ <- mapM (\period ->
    subgraph ((Str . fromStrict . Text.pack) $ ("Period" <> show (fst period) <> show (snd period))) $ do
    graphAttrs [Rank SameRank]
    periodToDotNode period
    -- | 6) create a node for each group
    {-- 6) create a node for each group -}
    mapM (\g -> groupToDotNode (getRoots phylo) g (toBid g (export ^. export_branches))) (filter (\g -> g ^. phylo_groupPeriod == period) $ export ^. export_groups)
    ) $ getPeriodIds phylo
    -- | 7) create the edges between a branch and its first groups
    {-- 7) create the edges between a branch and its first groups -}
    _ <- mapM (\(bId,groups) ->
    mapM (\g -> toDotEdge (branchIdToDotId bId) (groupIdToDotId $ getGroupId g) "" BranchToGroup) groups
    )
    ......@@ -224,31 +224,29 @@ exportToDot phylo export =
    $ sortOn (fst . _phylo_groupPeriod) groups)
    $ fromListWith (++) $ map (\g -> (g ^. phylo_groupBranchId,[g])) $ export ^. export_groups
    -- | 8) create the edges between the groups
    {- 8) create the edges between the groups -}
    _ <- mapM (\((k,k'),_) ->
    toDotEdge (groupIdToDotId k) (groupIdToDotId k') "" GroupToGroup
    ) $ (toList . mergePointers) $ export ^. export_groups
    -- | 7) create the edges between the periods
    {- 7) create the edges between the periods -}
    _ <- mapM (\(prd,prd') ->
    toDotEdge (periodIdToDotId prd) (periodIdToDotId prd') "" PeriodToPeriod
    ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ getPeriodIds phylo
    -- | 8) create the edges between the branches
    {- 8) create the edges between the branches
    -- _ <- mapM (\(bId,bId') ->
    -- toDotEdge (branchIdToDotId bId) (branchIdToDotId bId')
    -- (Text.pack $ show(branchIdsToProximity bId bId'
    -- (getThresholdInit $ phyloProximity $ getConfig phylo)
    -- (getThresholdStep $ phyloProximity $ getConfig phylo))) BranchToBranch
    -- ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ map _branch_id $ export ^. export_branches
    -}
    graphAttrs [Rank SameRank]
    ----------------
    -- | Filter | --
    ----------------
    ......@@ -439,13 +437,13 @@ toDynamics n parents g m =
    let prd = g ^. phylo_groupPeriod
    end = last' "dynamics" (sort $ map snd $ elems m)
    in if (((snd prd) == (snd $ m ! n)) && (snd prd /= end))
    -- | decrease
    {- decrease -}
    then 2
    else if ((fst prd) == (fst $ m ! n))
    -- | recombination
    {- recombination -}
    then 0
    else if isNew
    -- | emergence
    {- emergence -}
    then 1
    else 3
    where
    ......
    src/Gargantext/Viz/Phylo/PhyloMaker.hs
    View file @ 19071e4b
    ......@@ -115,7 +115,7 @@ cliqueToGroup fis pId lvl idx fdt coocs =
    (fis ^. phyloClique_support)
    ngrams
    (ngramsToCooc ngrams coocs)
    (1,[0]) -- | branchid (lvl,[path in the branching tree])
    (1,[0]) -- branchid (lvl,[path in the branching tree])
    (fromList [("breaks",[0]),("seaLevels",[0])])
    [] [] [] []
    ......@@ -142,24 +142,24 @@ toPhylo1 docs phyloBase = case (getSeaElevation phyloBase) of
    ---------------------------
    -- | To apply a filter with the possibility of keeping some periods non empty (keep : True|False)
    -- To apply a filter with the possibility of keeping some periods non empty (keep : True|False)
    filterClique :: Bool -> Int -> (Int -> [PhyloClique] -> [PhyloClique]) -> Map (Date, Date) [PhyloClique] -> Map (Date, Date) [PhyloClique]
    filterClique keep thr f m = case keep of
    False -> map (\l -> f thr l) m
    True -> map (\l -> keepFilled (f) thr l) m
    -- | To filter Fis with small Support
    -- To filter Fis with small Support
    filterCliqueBySupport :: Int -> [PhyloClique] -> [PhyloClique]
    filterCliqueBySupport thr l = filter (\clq -> (clq ^. phyloClique_support) >= thr) l
    -- | To filter Fis with small Clique size
    -- To filter Fis with small Clique size
    filterCliqueBySize :: Int -> [PhyloClique] -> [PhyloClique]
    filterCliqueBySize thr l = filter (\clq -> (size $ clq ^. phyloClique_nodes) >= thr) l
    -- | To filter nested Fis
    -- To filter nested Fis
    filterCliqueByNested :: Map (Date, Date) [PhyloClique] -> Map (Date, Date) [PhyloClique]
    filterCliqueByNested m =
    let clq = map (\l ->
    ......@@ -173,16 +173,16 @@ filterCliqueByNested m =
    in fromList $ zip (keys m) clq'
    -- | To transform a time map of docs innto a time map of Fis with some filters
    -- To transform a time map of docs innto a time map of Fis with some filters
    toPhyloClique :: Phylo -> Map (Date, Date) [Document] -> Map (Date,Date) [PhyloClique]
    toPhyloClique phylo phyloDocs = case (clique $ getConfig phylo) of
    Fis s s' -> -- traceFis "Filtered Fis"
    filterCliqueByNested
    -- $ traceFis "Filtered by clique size"
    {- \$ traceFis "Filtered by clique size" -}
    $ filterClique True s' (filterCliqueBySize)
    -- $ traceFis "Filtered by support"
    {- \$ traceFis "Filtered by support" -}
    $ filterClique True s (filterCliqueBySupport)
    -- $ traceFis "Unfiltered Fis"
    {- \$ traceFis "Unfiltered Fis" -}
    phyloClique
    MaxClique _ -> undefined
    where
    ......@@ -204,7 +204,7 @@ toPhyloClique phylo phyloDocs = case (clique $ getConfig phylo) of
    --------------------
    -- | To transform the docs into a time map of coocurency matrix
    -- To transform the docs into a time map of coocurency matrix
    docsToTimeScaleCooc :: [Document] -> Vector Ngrams -> Map Date Cooc
    docsToTimeScaleCooc docs fdt =
    let mCooc = fromListWith sumCooc
    ......@@ -221,7 +221,7 @@ docsToTimeScaleCooc docs fdt =
    -- | to Phylo Base | --
    -----------------------
    -- | To group a list of Documents by fixed periods
    -- To group a list of Documents by fixed periods
    groupDocsByPeriod' :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc]
    groupDocsByPeriod' f pds docs =
    let docs' = groupBy (\d d' -> f d == f d') $ sortOn f docs
    ......@@ -237,7 +237,7 @@ groupDocsByPeriod' f pds docs =
    -- | To group a list of Documents by fixed periods
    -- To group a list of Documents by fixed periods
    groupDocsByPeriod :: (NFData doc, Ord date, Enum date) => (doc -> date) -> [(date,date)] -> [doc] -> Map (date, date) [doc]
    groupDocsByPeriod _ _ [] = panic "[ERR][Viz.Phylo.PhyloMaker] Empty [Documents] can not have any periods"
    groupDocsByPeriod f pds es =
    ......@@ -265,7 +265,7 @@ docsToTermFreq docs fdt =
    in map (/sumFreqs) freqs
    -- | To count the number of docs by unit of time
    -- To count the number of docs by unit of time
    docsToTimeScaleNb :: [Document] -> Map Date Double
    docsToTimeScaleNb docs =
    let docs' = fromListWith (+) $ map (\d -> (date d,1)) docs
    ......@@ -279,7 +279,7 @@ initPhyloLevels lvlMax pId =
    fromList $ map (\lvl -> ((pId,lvl),PhyloLevel pId lvl empty)) [1..lvlMax]
    -- | To init the basic elements of a Phylo
    -- To init the basic elements of a Phylo
    toPhyloBase :: [Document] -> TermList -> Config -> Phylo
    toPhyloBase docs lst conf =
    let foundations = PhyloFoundations (Vector.fromList $ nub $ concat $ map text docs) lst
    ......
    src/Gargantext/Viz/Phylo/SynchronicClustering.hs
    View file @ 19071e4b
    ......@@ -36,13 +36,13 @@ import qualified Data.Set as Set
    mergeBranchIds :: [[Int]] -> [Int]
    mergeBranchIds ids = (head' "mergeBranchIds" . sort . mostFreq') ids
    where
    -- | 2) find the most Up Left ids in the hierarchy of similarity
    -- 2) find the most Up Left ids in the hierarchy of similarity
    -- mostUpLeft :: [[Int]] -> [[Int]]
    -- mostUpLeft ids' =
    -- let groupIds = (map (\gIds -> (length $ head' "gIds" gIds, head' "gIds" gIds)) . groupBy (\id id' -> length id == length id') . sortOn length) ids'
    -- inf = (fst . minimum) groupIds
    -- in map snd $ filter (\gIds -> fst gIds == inf) groupIds
    -- | 1) find the most frequent ids
    -- 1) find the most frequent ids
    mostFreq' :: [[Int]] -> [[Int]]
    mostFreq' ids' =
    let groupIds = (map (\gIds -> (length gIds, head' "gIds" gIds)) . group . sort) ids'
    ......@@ -58,12 +58,12 @@ mergeMeta bId groups =
    groupsToBranches' :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]]
    groupsToBranches' groups =
    -- | run the related component algorithm
    -- run the related component algorithm
    let egos = map (\g -> [getGroupId g]
    ++ (map fst $ g ^. phylo_groupPeriodParents)
    ++ (map fst $ g ^. phylo_groupPeriodChilds) ) $ elems groups
    graph = relatedComponents egos
    -- | update each group's branch id
    -- update each group's branch id
    in map (\ids ->
    let groups' = elems $ restrictKeys groups (Set.fromList ids)
    bId = mergeBranchIds $ map (\g -> snd $ g ^. phylo_groupBranchId) groups'
    ......@@ -103,26 +103,26 @@ toNextLevel' phylo groups =
    newGroups = concat $ groupsToBranches'
    $ fromList $ map (\g -> (getGroupId g, g))
    $ foldlWithKey (\acc id groups' ->
    -- | 4) create the parent group
    -- 4) create the parent group
    let parent = mergeGroups (elems $ restrictKeys (phylo ^. phylo_timeCooc) $ periodsToYears [(fst . fst) id]) id oldGroups groups'
    in acc ++ [parent]) []
    -- | 3) group the current groups by parentId
    -- 3) group the current groups by parentId
    $ fromListWith (++) $ map (\g -> (getLevelParentId g, [g])) groups
    newPeriods = fromListWith (++) $ map (\g -> (g ^. phylo_groupPeriod, [g])) newGroups
    in traceSynchronyEnd
    $ over ( phylo_periods . traverse . phylo_periodLevels . traverse
    -- | 6) update each period at curLvl + 1
    -- 6) update each period at curLvl + 1
    . filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == (curLvl + 1)))
    -- | 7) by adding the parents
    -- 7) by adding the parents
    (\phyloLvl ->
    if member (phyloLvl ^. phylo_levelPeriod) newPeriods
    then phyloLvl & phylo_levelGroups
    .~ fromList (map (\g -> (getGroupId g, g)) $ newPeriods ! (phyloLvl ^. phylo_levelPeriod))
    else phyloLvl)
    -- | 2) add the curLvl + 1 phyloLevel to the phylo
    -- 2) add the curLvl + 1 phyloLevel to the phylo
    $ addPhyloLevel (curLvl + 1)
    -- | 1) update the current groups (with level parent pointers) in the phylo
    -- 1) update the current groups (with level parent pointers) in the phylo
    $ updatePhyloGroups curLvl (fromList $ map (\g -> (getGroupId g, g)) groups) phylo
    --------------------
    ......@@ -187,19 +187,19 @@ toParentId child = ((child ^. phylo_groupPeriod, child ^. phylo_groupLevel + 1),
    reduceGroups :: Proximity -> Synchrony -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
    reduceGroups prox sync docs diagos branch =
    -- | 1) reduce a branch as a set of periods & groups
    -- 1) reduce a branch as a set of periods & groups
    let periods = fromListWith (++)
    $ map (\g -> (g ^. phylo_groupPeriod,[g])) branch
    in (concat . concat . elems)
    $ mapWithKey (\prd groups ->
    -- | 2) for each period, transform the groups as a proximity graph filtered by a threshold
    -- 2) for each period, transform the groups as a proximity graph filtered by a threshold
    let diago = reduceDiagos $ filterDiago diagos [prd]
    edges = groupsToEdges prox sync ((sum . elems) $ restrictKeys docs $ periodsToYears [prd]) diago groups
    in map (\comp ->
    -- | 4) add to each groups their futur level parent group
    -- 4) add to each groups their futur level parent group
    let parentId = toParentId (head' "parentId" comp)
    in map (\g -> g & phylo_groupLevelParents %~ (++ [(parentId,1)]) ) comp )
    -- |3) reduce the graph a a set of related components
    -- 3) reduce the graph a a set of related components
    $ toRelatedComponents groups edges) periods
    ......@@ -251,4 +251,4 @@ synchronicClustering phylo =
    -- <> "\n"
    -- ) "" edges
    -- ) "" $ elems $ groupByField _phylo_groupPeriod branch)
    -- ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo
    \ No newline at end of file
    -- ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo
    src/Gargantext/Viz/Phylo/TemporalMatching.hs
    View file @ 19071e4b
    ......@@ -117,7 +117,7 @@ makePairs' (egoId, egoNgrams) candidates periods oldPointers fil thr prox docs d
    if (null periods)
    then []
    else removeOldPointers oldPointers fil thr prox lastPrd
    -- | at least on of the pair candidates should be from the last added period
    {- at least on of the pair candidates should be from the last added period -}
    $ filter (\((id,_),(id',_)) -> ((fst . fst) id == lastPrd) || ((fst . fst) id' == lastPrd))
    $ listToKeys
    $ filter (\(id,ngrams) ->
    ......@@ -143,36 +143,36 @@ phyloGroupMatching :: [[(PhyloGroupId,[Int])]] -> Filiation -> Proximity -> Map
    -> Double -> [Pointer] -> (PhyloGroupId,[Int]) -> [Pointer]
    phyloGroupMatching candidates fil proxi docs diagos thr oldPointers (id,ngrams) =
    if (null $ filterPointers proxi thr oldPointers)
    -- | let's find new pointers
    {- let's find new pointers -}
    then if null nextPointers
    then []
    else head' "phyloGroupMatching"
    -- | Keep only the best set of pointers grouped by proximity
    {- Keep only the best set of pointers grouped by proximity -}
    $ groupBy (\pt pt' -> snd pt == snd pt')
    $ reverse $ sortOn snd $ head' "pointers" nextPointers
    -- | Find the first time frame where at leats one pointer satisfies the proximity threshold
    {- Find the first time frame where at leats one pointer satisfies the proximity threshold -}
    else oldPointers
    where
    nextPointers :: [[Pointer]]
    nextPointers = take 1
    $ dropWhile (null)
    -- | for each time frame, process the proximity on relevant pairs of targeted groups
    {- for each time frame, process the proximity on relevant pairs of targeted groups -}
    $ scanl (\acc groups ->
    let periods = nub $ map (fst . fst . fst) $ concat groups
    nbdocs = sum $ elems $ (filterDocs docs ([(fst . fst) id] ++ periods))
    diago = reduceDiagos
    $ filterDiago diagos ([(fst . fst) id] ++ periods)
    -- | important resize nbdocs et diago dans le make pairs
    {- important resize nbdocs et diago dans le make pairs -}
    pairs = makePairs' (id,ngrams) (concat groups) periods oldPointers fil thr proxi docs diagos
    in acc ++ ( filterPointers proxi thr
    $ concat
    $ map (\(c,c') ->
    -- | process the proximity between the current group and a pair of candidates
    {- process the proximity between the current group and a pair of candidates -}
    let proximity = toProximity nbdocs diago proxi ngrams (snd c) (snd c')
    in if (c == c')
    then [(fst c,proximity)]
    else [(fst c,proximity),(fst c',proximity)] ) pairs )) []
    $ inits candidates -- | groups from [[1900],[1900,1901],[1900,1901,1902],...]
    $ inits candidates {- groups from [[1900],[1900,1901],[1900,1901,1902],...] -}
    filterDocs :: Map Date Double -> [PhyloPeriodId] -> Map Date Double
    ......@@ -205,19 +205,19 @@ matchGroupsToGroups :: Int -> [PhyloPeriodId] -> Proximity -> Double -> Map Date
    matchGroupsToGroups frame periods proximity thr docs coocs groups =
    let groups' = groupByField _phylo_groupPeriod groups
    in foldl' (\acc prd ->
    let -- | 1) find the parents/childs matching periods
    let -- 1) find the parents/childs matching periods
    periodsPar = getNextPeriods ToParents frame prd periods
    periodsChi = getNextPeriods ToChilds frame prd periods
    -- | 2) find the parents/childs matching candidates
    -- 2) find the parents/childs matching candidates
    candidatesPar = map (\prd' -> map (\g -> (getGroupId g, g ^. phylo_groupNgrams)) $ findWithDefault [] prd' groups') periodsPar
    candidatesChi = map (\prd' -> map (\g -> (getGroupId g, g ^. phylo_groupNgrams)) $ findWithDefault [] prd' groups') periodsChi
    -- | 3) find the parents/child number of docs by years
    -- 3) find the parents/child number of docs by years
    docsPar = filterDocs docs ([prd] ++ periodsPar)
    docsChi = filterDocs docs ([prd] ++ periodsChi)
    -- | 4) find the parents/child diago by years
    -- 4) find the parents/child diago by years
    diagoPar = filterDiago (map coocToDiago coocs) ([prd] ++ periodsPar)
    diagoChi = filterDiago (map coocToDiago coocs) ([prd] ++ periodsPar)
    -- | 5) match in parallel all the groups (egos) to their possible candidates
    -- 5) match in parallel all the groups (egos) to their possible candidates
    egos = map (\ego ->
    let pointersPar = phyloGroupMatching (getCandidates ego candidatesPar) ToParents proximity docsPar diagoPar
    thr (getPeriodPointers ToParents ego) (getGroupId ego, ego ^. phylo_groupNgrams)
    ......@@ -272,19 +272,19 @@ toPhyloQuality' beta freq branches =
    groupsToBranches :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]]
    groupsToBranches groups =
    -- | run the related component algorithm
    -- run the related component algorithm
    let egos = groupBy (\gs gs' -> (fst $ fst $ head' "egos" gs) == (fst $ fst $ head' "egos" gs'))
    $ sortOn (\gs -> fst $ fst $ head' "egos" gs)
    $ map (\group -> [getGroupId group]
    ++ (map fst $ group ^. phylo_groupPeriodParents)
    ++ (map fst $ group ^. phylo_groupPeriodChilds) ) $ elems groups
    -- | first find the related components by inside each ego's period
    -- | a supprimer
    -- first find the related components by inside each ego's period
    -- a supprimer
    graph' = map relatedComponents egos
    -- | then run it for the all the periods
    -- then run it for the all the periods
    graph = zip [1..]
    $ relatedComponents $ concat (graph' `using` parList rdeepseq)
    -- | update each group's branch id
    -- update each group's branch id
    in map (\(bId,ids) ->
    let groups' = map (\group -> group & phylo_groupBranchId %~ (\(lvl,lst) -> (lvl,lst ++ [bId])))
    $ elems $ restrictKeys groups (Set.fromList ids)
    ......@@ -300,14 +300,14 @@ updateThr thr branches = map (\b -> map (\g ->
    g & phylo_groupMeta .~ (singleton "seaLevels" (((g ^. phylo_groupMeta) ! "seaLevels") ++ [thr]))) b) branches
    -- | Sequentially break each branch of a phylo where
    -- Sequentially break each branch of a phylo where
    -- done = all the allready broken branches
    -- ego = the current branch we want to break
    -- rest = the branches we still have to break
    breakBranches :: Proximity -> Double -> Map Int Double -> Int -> Double -> Double -> Double
    -> Int -> Map Date Double -> Map Date Cooc -> [PhyloPeriodId] -> [([PhyloGroup],Bool)] -> ([PhyloGroup],Bool) -> [([PhyloGroup],Bool)] -> [([PhyloGroup],Bool)]
    breakBranches proximity beta frequency minBranch thr depth elevation frame docs coocs periods done ego rest =
    -- | 1) keep or not the new division of ego
    -- 1) keep or not the new division of ego
    let done' = done ++ (if snd ego
    then
    (if ((null (fst ego')) || (quality > quality'))
    ......@@ -325,7 +325,7 @@ breakBranches proximity beta frequency minBranch thr depth elevation frame docs
    ((map (\e -> (e,True)) (fst ego')) ++ (map (\e -> (e,False)) (snd ego'))))
    else [ego])
    in
    -- | 2) if there is no more branches in rest then return else continue
    -- 2) if there is no more branches in rest then return else continue
    if null rest
    then done'
    else breakBranches proximity beta frequency minBranch thr depth elevation frame docs coocs periods
    ......@@ -352,11 +352,11 @@ breakBranches proximity beta frequency minBranch thr depth elevation frame docs
    seaLevelMatching :: Proximity -> Double -> Int -> Map Int Double -> Double -> Double -> Double -> Double
    -> Int -> [PhyloPeriodId] -> Map Date Double -> Map Date Cooc -> [([PhyloGroup],Bool)] -> [([PhyloGroup],Bool)]
    seaLevelMatching proximity beta minBranch frequency thr step depth elevation frame periods docs coocs branches =
    -- | if there is no branch to break or if seaLvl level > 1 then end
    -- if there is no branch to break or if seaLvl level > 1 then end
    if (thr >= 1) || ((not . or) $ map snd branches)
    then branches
    else
    -- | break all the possible branches at the current seaLvl level
    -- break all the possible branches at the current seaLvl level
    let branches' = breakBranches proximity beta frequency minBranch thr depth elevation frame docs coocs periods
    [] (head' "seaLevelMatching" branches) (tail' "seaLevelMatching" branches)
    frequency' = reduceFrequency frequency (map fst branches')
    ......@@ -368,7 +368,7 @@ constanteTemporalMatching start step phylo = updatePhyloGroups 1
    (fromList $ map (\g -> (getGroupId g,g)) $ traceMatchEnd $ concat branches)
    phylo
    where
    -- | 2) process the temporal matching by elevating seaLvl level
    -- 2) process the temporal matching by elevating seaLvl level
    branches :: [[PhyloGroup]]
    branches = map fst
    $ seaLevelMatching (phyloProximity $ getConfig phylo)
    ......@@ -383,8 +383,8 @@ constanteTemporalMatching start step phylo = updatePhyloGroups 1
    (phylo ^. phylo_timeDocs)
    (phylo ^. phylo_timeCooc)
    groups
    -- | 1) for each group process an initial temporal Matching
    -- | here we suppose that all the groups of level 1 are part of the same big branch
    -- 1) for each group process an initial temporal Matching
    -- here we suppose that all the groups of level 1 are part of the same big branch
    groups :: [([PhyloGroup],Bool)]
    groups = map (\b -> (b,(length $ nub $ map _phylo_groupPeriod b) >= (_qua_minBranch $ phyloQuality $ getConfig phylo)))
    $ groupsToBranches $ fromList $ map (\g -> (getGroupId g, g))
    ......@@ -441,7 +441,7 @@ adaptativeBreakBranches :: Proximity -> Double -> Double -> Map (PhyloGroupId,Ph
    -> [PhyloPeriodId] -> [([PhyloGroup],(Bool,[Double]))] -> ([PhyloGroup],(Bool,[Double])) -> [([PhyloGroup],(Bool,[Double]))]
    -> [([PhyloGroup],(Bool,[Double]))]
    adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods done ego rest =
    -- | 1) keep or not the new division of ego
    -- 1) keep or not the new division of ego
    let done' = done ++ (if (fst . snd) ego
    then (if ((null (fst ego')) || (quality > quality'))
    then
    ......@@ -451,13 +451,13 @@ adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency min
    ++ (map (\e -> (e,(False, ((snd . snd) ego)))) (snd ego'))))
    else [(concat $ thrToMeta thr $ [fst ego], snd ego)])
    in
    -- | uncomment let .. in for debugging
    -- uncomment let .. in for debugging
    -- let part1 = partition (snd) done'
    -- part2 = partition (snd) rest
    -- in trace ( "[✓ " <> show(length $ fst part1) <> "(" <> show(length $ concat $ map (fst) $ fst part1) <> ")|✗ " <> show(length $ snd part1) <> "(" <> show(length $ concat $ map (fst) $ snd part1) <> ")] "
    -- <> "[✓ " <> show(length $ fst part2) <> "(" <> show(length $ concat $ map (fst) $ fst part2) <> ")|✗ " <> show(length $ snd part2) <> "(" <> show(length $ concat $ map (fst) $ snd part2) <> ")]"
    -- ) $
    -- | 2) if there is no more branches in rest then return else continue
    -- 2) if there is no more branches in rest then return else continue
    if null rest
    then done'
    else adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods
    ......@@ -489,11 +489,11 @@ adaptativeSeaLevelMatching :: Proximity -> Double -> Double -> Map (PhyloGroupId
    -> Int -> [PhyloPeriodId] -> Map Date Double -> Map Date Cooc
    -> [([PhyloGroup],(Bool,[Double]))] -> [([PhyloGroup],(Bool,[Double]))]
    adaptativeSeaLevelMatching proxiConf depth elevation groupsProxi beta minBranch frequency frame periods docs coocs branches =
    -- | if there is no branch to break or if seaLvl level >= depth then end
    -- if there is no branch to break or if seaLvl level >= depth then end
    if (Map.null groupsProxi) || (depth <= 0) || ((not . or) $ map (fst . snd) branches)
    then branches
    else
    -- | break all the possible branches at the current seaLvl level
    -- break all the possible branches at the current seaLvl level
    let branches' = adaptativeBreakBranches proxiConf depth elevation groupsProxi beta frequency minBranch frame docs coocs periods
    [] (head' "seaLevelMatching" branches) (tail' "seaLevelMatching" branches)
    frequency' = reduceFrequency frequency (map fst branches')
    ......@@ -511,7 +511,7 @@ adaptativeTemporalMatching elevation phylo = updatePhyloGroups 1
    (fromList $ map (\g -> (getGroupId g,g)) $ traceMatchEnd $ concat branches)
    phylo
    where
    -- | 2) process the temporal matching by elevating seaLvl level
    -- 2) process the temporal matching by elevating seaLvl level
    branches :: [[PhyloGroup]]
    branches = map fst
    $ adaptativeSeaLevelMatching (phyloProximity $ getConfig phylo)
    ......@@ -526,8 +526,8 @@ adaptativeTemporalMatching elevation phylo = updatePhyloGroups 1
    (phylo ^. phylo_timeDocs)
    (phylo ^. phylo_timeCooc)
    groups
    -- | 1) for each group process an initial temporal Matching
    -- | here we suppose that all the groups of level 1 are part of the same big branch
    -- 1) for each group process an initial temporal Matching
    -- here we suppose that all the groups of level 1 are part of the same big branch
    groups :: [([PhyloGroup],(Bool,[Double]))]
    groups = map (\b -> (b,((length $ nub $ map _phylo_groupPeriod b) >= (_qua_minBranch $ phyloQuality $ getConfig phylo),[thr])))
    $ groupsToBranches $ fromList $ map (\g -> (getGroupId g, g))
    ......
    stack.yaml
    View file @ 19071e4b
    ......@@ -58,7 +58,6 @@ extra-deps:
    commit: 308c74b71a1abb0a91546fa57d353131248e3a7f
    - Unique-0.4.7.6@sha256:a1ff411f4d68c756e01e8d532fbe8e57f1ac77f2cc0ee8a999770be2bca185c5,2723
    - KMP-0.1.0.2
    - accelerate-1.2.0.1
    - aeson-lens-0.5.0.0
    - deepseq-th-0.1.0.4
    - duckling-0.1.3.0
    ......@@ -84,3 +83,7 @@ extra-deps:
    - password-2.0.1.1
    - base64-0.4.2@sha256:e9523e18bdadc3cab9dc32dfe3ac09c718fe792076326d6d353437b8b255cb5b,2888
    - ghc-byteorder-4.11.0.0.10@sha256:5ee4a907279bfec27b0f9de7b8fba4cecfd34395a0235a7784494de70ad4e98f,1535
    # Matrix Computation
    - accelerate-1.2.0.1
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