src/Gargantext/Viz/Phylo/LevelMaker.hs

   1 {-|
   2 Module      : Gargantext.Viz.Phylo.Tools
   3 Description : Phylomemy Tools to build/manage it
   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
  13 {-# LANGUAGE NoImplicitPrelude    #-}
  14 {-# LANGUAGE FlexibleContexts     #-}
  15 {-# LANGUAGE OverloadedStrings    #-}
  16 {-# LANGUAGE TypeSynonymInstances #-}
  17 {-# LANGUAGE FlexibleInstances    #-}
  18
  19 module Gargantext.Viz.Phylo.LevelMaker
  20   where
  21
  22 import Control.Lens                 hiding (both, Level)
  23 import Data.List                    ((++), sort, concat, nub, zip, last)
  24 import Data.Map                     (Map, (!), empty, restrictKeys, filterWithKey, singleton, union)
  25 import Data.Text (Text)
  26 import Data.Tuple.Extra
  27 import Data.Vector                  (Vector)
  28 import Gargantext.Prelude
  29 import Gargantext.Viz.Phylo
  30 import Gargantext.Viz.Phylo.Aggregates.Cluster
  31 import Gargantext.Viz.Phylo.Aggregates.Cooc
  32 import Gargantext.Viz.Phylo.Aggregates.Document
  33 import Gargantext.Viz.Phylo.Aggregates.Fis
  34 import Gargantext.Viz.Phylo.BranchMaker
  35 import Gargantext.Viz.Phylo.LinkMaker
  36 import Gargantext.Viz.Phylo.Tools
  37 import qualified Data.Set    as Set
  38
  39
  40 -- | A typeClass for polymorphic PhyloLevel functions
  41 class PhyloLevelMaker aggregate
  42     where
  43         -- | To add a new Level of PhyloGroups to a Phylo based on a list of Aggregates
  44         addPhyloLevel :: Level -> Map (Date,Date) [aggregate] -> Phylo -> Phylo
  45         -- | To create a list of PhyloGroups based on a list of aggregates a
  46         toPhyloGroups :: Level -> (Date,Date)  -> [aggregate] -> Map (Date,Date) [aggregate] -> Phylo -> [PhyloGroup]
  47
  48
  49 instance PhyloLevelMaker PhyloCluster
  50   where
  51     --------------------------------------
  52     -- | Level -> Map (Date,Date) [Cluster] -> Phylo -> Phylo
  53     addPhyloLevel lvl m p
  54       | lvl > 1   = toPhyloLevel lvl m p
  55       | otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Clusters at level < 2")
  56     --------------------------------------
  57     -- | Level -> (Date,Date) -> [Cluster] -> Map (Date,Date) [Cluster] -> Phylo -> [PhyloGroup]
  58     toPhyloGroups lvl (d,d') l m p = map (\(idx,cluster) -> clusterToGroup (d,d') lvl idx "" cluster m p) $ zip [1..] l
  59     --------------------------------------
  60
  61
  62 instance PhyloLevelMaker PhyloFis
  63   where
  64     --------------------------------------
  65     -- | Level -> Map (Date,Date) [Fis] -> Phylo -> Phylo
  66     addPhyloLevel lvl m p
  67       | lvl == 1  = toPhyloLevel lvl m p
  68       | otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Fis at level <> 1")
  69     --------------------------------------
  70     -- | Level -> (Date,Date) -> [Fis] -> Map (Date,Date) [Fis] -> Phylo -> [PhyloGroup]
  71     toPhyloGroups lvl (d,d') l m p = map (\(idx,fis) -> cliqueToGroup (d,d') lvl idx "" fis m p) $ zip [1..] l
  72     --------------------------------------
  73
  74
  75 instance PhyloLevelMaker Document
  76   where
  77     --------------------------------------
  78     -- | Level -> Map (Date,Date) [Document] -> Phylo -> Phylo
  79     addPhyloLevel lvl m p
  80       | lvl == 0  = toPhyloLevel lvl m p
  81       | otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Documents at level <> 0")
  82     --------------------------------------
  83     -- | Level -> (Date,Date) -> [Document] -> Map (Date,Date) [Fis] -> Phylo -> [PhyloGroup]
  84     toPhyloGroups lvl (d,d') l _m p = map (\(idx,ngram) -> ngramsToGroup (d,d') lvl idx ngram [ngram] p)
  85                                           $ zip [1..]
  86                                           $ (nub . concat)
  87                                           $ map text l
  88     --------------------------------------
  89
  90
  91 -- | To transform a Cluster into a Phylogroup
  92 clusterToGroup :: PhyloPeriodId -> Level -> Int -> Text -> PhyloCluster -> Map (Date,Date) [PhyloCluster] -> Phylo -> PhyloGroup
  93 clusterToGroup prd lvl idx lbl groups _m p =
  94     PhyloGroup ((prd, lvl), idx) lbl ngrams empty cooc Nothing [] [] [] (map (\g -> (getGroupId g, 1)) groups)
  95       where
  96         --------------------------------------
  97         ngrams :: [Int]
  98         ngrams = (sort . nub . concat) $ map getGroupNgrams groups
  99         --------------------------------------
 100         cooc :: Map (Int, Int) Double
 101         cooc = filterWithKey (\k _ -> elem (fst k) ngrams && elem (snd k) ngrams)
 102               $ foldl union empty
 103               $ map getGroupCooc
 104               $ getGroupsWithFilters 1 prd p
 105         --------------------------------------
 106
 107
 108 -- | To transform a Clique into a PhyloGroup
 109 cliqueToGroup :: PhyloPeriodId -> Level -> Int -> Text -> PhyloFis -> Map (Date, Date) [PhyloFis] -> Phylo -> PhyloGroup
 110 cliqueToGroup prd lvl idx lbl fis m p =
 111     PhyloGroup ((prd, lvl), idx) lbl ngrams (singleton "support" (fromIntegral $ getSupport fis)) cooc Nothing [] [] [] []
 112       where
 113         --------------------------------------
 114         ngrams :: [Int]
 115         ngrams = sort $ map (\x -> getIdxInPeaks x p)
 116                       $ Set.toList
 117                       $ getClique fis
 118         --------------------------------------
 119         cooc :: Map (Int, Int) Double
 120         cooc =  filterWithKey (\k _ -> elem (fst k) ngrams && elem (snd k) ngrams)
 121                                      $ fisToCooc (restrictKeys m $ Set.fromList [prd]) p
 122         --------------------------------------
 123
 124
 125 -- | To transform a list of Ngrams into a PhyloGroup
 126 ngramsToGroup ::  PhyloPeriodId -> Level -> Int -> Text -> [Ngrams] -> Phylo -> PhyloGroup
 127 ngramsToGroup prd lvl idx lbl ngrams p =
 128     PhyloGroup ((prd, lvl), idx) lbl (sort $ map (\x -> getIdxInPeaks x p) ngrams) empty empty Nothing [] [] [] []
 129
 130
 131 -- | To traverse a Phylo and add a new PhyloLevel linked to a new list of PhyloGroups
 132 toPhyloLevel :: PhyloLevelMaker a => Level -> Map (Date, Date) [a] -> Phylo -> Phylo
 133 toPhyloLevel lvl m p = alterPhyloPeriods
 134                         (\period -> let pId = _phylo_periodId period
 135                                     in  over (phylo_periodLevels)
 136                                         (\phyloLevels ->
 137                                           let groups = toPhyloGroups lvl pId (m ! pId) m p
 138                                           in  phyloLevels ++ [PhyloLevel (pId, lvl) groups]
 139                                         ) period) p
 140
 141
 142 -- | To incrementally add new Levels to a Phylo by making all the linking and aggregation tasks
 143 toNthLevel :: Level -> Proximity -> Cluster -> Phylo -> Phylo
 144 toNthLevel lvlMax prox clus p
 145   | lvl >= lvlMax = p
 146   | otherwise     = toNthLevel lvlMax prox clus
 147                   $ setPhyloBranches (lvl + 1)
 148                   $ interTempoMatching Descendant (lvl + 1) prox
 149                   $ interTempoMatching Ascendant  (lvl + 1) prox
 150                   $ setLevelLinks (lvl, lvl + 1)
 151                   $ addPhyloLevel (lvl + 1)
 152                     (phyloToClusters lvl (getProximity clus) clus p) p
 153   where
 154     --------------------------------------
 155     lvl :: Level
 156     lvl = getLastLevel p
 157     --------------------------------------
 158
 159
 160 -- | To reconstruct the Level 1 of a Phylo based on a Clustering Method
 161 toPhylo1 :: Cluster -> Proximity -> [Metric] -> [Filter] -> Map (Date, Date) [Document] -> Phylo -> Phylo
 162 toPhylo1 clus prox metrics filters d p = case clus of
 163   Fis (FisParams k s) -> setPhyloBranches 1
 164                        $ interTempoMatching Descendant 1 prox
 165                        $ interTempoMatching Ascendant  1 prox
 166                        $ setLevelLinks (0,1)
 167                        $ setLevelLinks (1,0)
 168                        $ addPhyloLevel 1 phyloFis p
 169     where
 170       --------------------------------------
 171       phyloFis :: Map (Date, Date) [PhyloFis]
 172       phyloFis = toPhyloFis d k s metrics filters
 173       --------------------------------------
 174
 175   _   -> panic "[ERR][Viz.Phylo.LevelMaker.toPhylo1] fst clustering not recognized"
 176
 177
 178 -- | To reconstruct the Level 0 of a Phylo
 179 toPhylo0 :: Map (Date, Date) [Document] -> Phylo -> Phylo
 180 toPhylo0 d p = addPhyloLevel 0 d p
 181
 182
 183 -- | To reconstruct the Base of a Phylo
 184 toPhyloBase :: PhyloQueryBuild -> PhyloParam -> [(Date, Text)] -> [Ngrams] -> [Tree Ngrams] -> Phylo
 185 toPhyloBase q p c a ts = initPhyloBase periods foundations peaks p
 186   where
 187     --------------------------------------
 188     peaks :: PhyloPeaks
 189     peaks = initPeaks (map (\t -> alterLabels phyloAnalyzer t) ts) foundations
 190     --------------------------------------
 191     periods :: [(Date,Date)]
 192     periods = initPeriods (getPeriodGrain q) (getPeriodSteps q)
 193             $ both fst (head' "LevelMaker" c,last c)
 194     --------------------------------------
 195     foundations :: Vector Ngrams
 196     foundations = initFoundations a
 197     --------------------------------------
 198
 199
 200 -- | To reconstruct a Phylomemy from a PhyloQueryBuild, a Corpus and a list of actants
 201 toPhylo :: PhyloQueryBuild -> [(Date, Text)] -> [Ngrams] -> [Tree Ngrams] -> Phylo
 202 toPhylo q c a ts = toNthLevel (getNthLevel q) (getInterTemporalMatching q) (getNthCluster q) phylo1
 203   where
 204     --------------------------------------
 205     phylo1 :: Phylo
 206     phylo1 = toPhylo1 (getContextualUnit q) (getInterTemporalMatching q) (getContextualUnitMetrics q) (getContextualUnitFilters q) phyloDocs phylo0
 207     --------------------------------------
 208     phylo0 :: Phylo
 209     phylo0 = toPhylo0 phyloDocs phyloBase
 210     --------------------------------------
 211     phyloDocs :: Map (Date, Date) [Document]
 212     phyloDocs = corpusToDocs c phyloBase
 213     --------------------------------------
 214     phyloBase :: Phylo
 215     phyloBase = toPhyloBase q (initPhyloParam (Just defaultPhyloVersion) (Just defaultSoftware) (Just q)) c a ts
 216     --------------------------------------