src/Gargantext/Core/Viz/Phylo/SynchronicClustering.hs

   1 {-|
   2 Module      : Gargantext.Core.Viz.Phylo.SynchronicClustering
   3 Description : Module dedicated to the adaptative synchronic clustering of a Phylo.
   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 module Gargantext.Core.Viz.Phylo.SynchronicClustering where
  13
  14 import Gargantext.Prelude
  15 import Gargantext.Core.Viz.AdaptativePhylo
  16 import Gargantext.Core.Viz.Phylo.PhyloTools
  17 import Gargantext.Core.Viz.Phylo.TemporalMatching (weightedLogJaccard', filterDiago, reduceDiagos)
  18 import Gargantext.Core.Viz.Phylo.PhyloExport (processDynamics)
  19
  20 import Data.List ((++), null, intersect, nub, concat, sort, sortOn, groupBy)
  21 import Data.Map  (Map, fromList, fromListWith, foldlWithKey, (!), insert, empty, restrictKeys, elems, mapWithKey, member)
  22
  23 import Control.Lens hiding (Level)
  24 import Control.Parallel.Strategies (parList, rdeepseq, using)
  25 -- import Debug.Trace (trace)
  26
  27 import qualified Data.Map as Map
  28
  29
  30 -------------------------
  31 -- | New Level Maker | --
  32 -------------------------
  33
  34
  35 mergeGroups :: [Cooc] -> PhyloGroupId -> Map PhyloGroupId PhyloGroupId -> [PhyloGroup] -> PhyloGroup
  36 mergeGroups coocs id mapIds childs =
  37     let ngrams = (sort . nub . concat) $ map _phylo_groupNgrams childs
  38     in PhyloGroup (fst $ fst id) (snd $ fst id) (snd id)  ""
  39                   (sum $ map _phylo_groupSupport childs)  ngrams
  40                   (ngramsToCooc ngrams coocs)
  41                   ((snd $ fst id),bId)
  42                   (mergeMeta bId childs) [] (map (\g -> (getGroupId g, 1)) childs)
  43                   (updatePointers $ concat $ map _phylo_groupPeriodParents childs)
  44                   (updatePointers $ concat $ map _phylo_groupPeriodChilds  childs)
  45                   (mergeAncestors $ concat $ map _phylo_groupAncestors childs)
  46     where
  47         --------------------
  48         bId :: [Int]
  49         bId = mergeBranchIds $ map (\g -> snd $ g ^. phylo_groupBranchId) childs
  50         --------------------
  51         updatePointers :: [Pointer] -> [Pointer]
  52         updatePointers pointers = map (\(pId,w) -> (mapIds ! pId,w)) pointers
  53         --------------------
  54         mergeAncestors :: [Pointer] -> [Pointer]
  55         mergeAncestors pointers = Map.toList $ fromListWith max pointers
  56
  57
  58 addPhyloLevel :: Level -> Phylo -> Phylo
  59 addPhyloLevel lvl phylo =
  60   over ( phylo_periods .  traverse )
  61        (\phyloPrd -> phyloPrd & phylo_periodLevels
  62                         %~ (insert (phyloPrd ^. phylo_periodPeriod, lvl) (PhyloLevel (phyloPrd ^. phylo_periodPeriod) lvl empty))) phylo
  63
  64
  65 toNextLevel' :: Phylo -> [PhyloGroup] -> Phylo
  66 toNextLevel' phylo groups =
  67     let curLvl = getLastLevel phylo
  68         oldGroups = fromList $ map (\g -> (getGroupId g, getLevelParentId g)) groups
  69         newGroups = concat $ groupsToBranches
  70                   $ fromList $ map (\g -> (getGroupId g, g))
  71                   $ foldlWithKey (\acc id groups' ->
  72                         --  4) create the parent group
  73                         let parent = mergeGroups (elems $ restrictKeys (phylo ^. phylo_timeCooc) $ periodsToYears [(fst . fst) id]) id oldGroups groups'
  74                         in  acc ++ [parent]) []
  75                   --  3) group the current groups by parentId
  76                   $ fromListWith (++) $ map (\g -> (getLevelParentId g, [g])) groups
  77
  78         newPeriods = fromListWith (++) $ map (\g -> (g ^. phylo_groupPeriod, [g])) newGroups
  79     in  traceSynchronyEnd
  80       $ over ( phylo_periods . traverse . phylo_periodLevels . traverse
  81              --  6) update each period at curLvl + 1
  82              . filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == (curLvl + 1)))
  83              --  7) by adding the parents
  84              (\phyloLvl ->
  85                 if member (phyloLvl ^. phylo_levelPeriod) newPeriods
  86                     then phyloLvl & phylo_levelGroups
  87                             .~ fromList (map (\g -> (getGroupId g, g)) $ newPeriods ! (phyloLvl ^. phylo_levelPeriod))
  88                     else phyloLvl)
  89       --  2) add the curLvl + 1 phyloLevel to the phylo
  90       $ addPhyloLevel (curLvl + 1)
  91       --  1) update the current groups (with level parent pointers) in the phylo
  92       $ updatePhyloGroups curLvl (fromList $ map (\g -> (getGroupId g, g)) groups) phylo
  93
  94 --------------------
  95 -- | Clustering | --
  96 --------------------
  97
  98 toPairs :: SynchronyStrategy -> [PhyloGroup] -> [(PhyloGroup,PhyloGroup)]
  99 toPairs strategy groups = case strategy of
 100   MergeRegularGroups -> pairs
 101                       $ filter (\g -> all (== 3) $ (g ^. phylo_groupMeta) ! "dynamics") groups
 102   MergeAllGroups -> pairs groups
 103   where
 104     pairs :: [PhyloGroup] -> [(PhyloGroup,PhyloGroup)]
 105     pairs gs = filter (\(g,g') -> (not . null) $ intersect (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams)) (listToCombi' gs)
 106
 107
 108 toDiamonds :: [PhyloGroup] -> [[PhyloGroup]]
 109 toDiamonds groups = foldl' (\acc groups' ->
 110                         acc ++ ( elems
 111                                $ Map.filter (\v -> length v > 1)
 112                                $ fromListWith (++)
 113                                $ foldl' (\acc' g ->
 114                                     acc' ++ (map (\(id,_) -> (id,[g]) ) $ g ^. phylo_groupPeriodChilds)) [] groups')) []
 115                   $ elems
 116                   $ Map.filter (\v -> length v > 1)
 117                   $ fromListWith (++)
 118                   $ foldl' (\acc g -> acc ++ (map (\(id,_) -> (id,[g]) ) $ g ^. phylo_groupPeriodParents)  ) [] groups
 119
 120
 121 groupsToEdges :: Proximity -> Synchrony -> Double -> Map Int Double -> [PhyloGroup] -> [((PhyloGroup,PhyloGroup),Double)]
 122 groupsToEdges prox sync nbDocs diago groups =
 123     case sync of
 124         ByProximityThreshold  thr sens _ strat ->
 125             filter (\(_,w) -> w >= thr)
 126           $ toEdges sens
 127           $ toPairs strat groups
 128         ByProximityDistribution sens strat ->
 129             let diamonds = sortOn snd
 130                          $ toEdges sens $ concat
 131                          $ map (\gs -> toPairs strat gs) $ toDiamonds groups
 132              in take (div (length diamonds) 2) diamonds
 133     where
 134         toEdges :: Double -> [(PhyloGroup,PhyloGroup)] -> [((PhyloGroup,PhyloGroup),Double)]
 135         toEdges sens edges =
 136             case prox of
 137                 WeightedLogJaccard _ -> map (\(g,g') ->
 138                                                      ((g,g'), weightedLogJaccard' (1 / sens) nbDocs diago
 139                                                                   (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams))) edges
 140                 _ -> undefined
 141
 142 toParentId :: PhyloGroup -> PhyloGroupId
 143 toParentId child = ((child ^. phylo_groupPeriod, child ^. phylo_groupLevel + 1), child ^. phylo_groupIndex)
 144
 145
 146 reduceGroups :: Proximity -> Synchrony -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
 147 reduceGroups prox sync docs diagos branch =
 148     --  1) reduce a branch as a set of periods & groups
 149     let periods = fromListWith (++)
 150                  $ map (\g -> (g ^. phylo_groupPeriod,[g])) branch
 151     in  (concat . concat . elems)
 152       $ mapWithKey (\prd groups ->
 153             --  2) for each period, transform the groups as a proximity graph filtered by a threshold
 154             let diago = reduceDiagos $ filterDiago diagos [prd]
 155                 edges = groupsToEdges prox sync ((sum . elems) $ restrictKeys docs $ periodsToYears [prd]) diago groups
 156              in map (\comp ->
 157                     --  4) add to each groups their futur level parent group
 158                     let parentId = toParentId (head' "parentId" comp)
 159                     in  map (\g -> g & phylo_groupLevelParents %~ (++ [(parentId,1)]) ) comp )
 160                 -- 3) reduce the graph a a set of related components
 161               $ toRelatedComponents groups edges) periods
 162
 163
 164 adjustClustering :: Synchrony -> [[PhyloGroup]] -> [[PhyloGroup]]
 165 adjustClustering sync branches = case sync of
 166   ByProximityThreshold _ _ scope _ -> case scope of
 167       SingleBranch -> branches
 168       SiblingBranches -> groupBy (\g g' -> (last' "adjustClustering" $ (g  ^. phylo_groupMeta) ! "breaks")
 169                                         == (last' "adjustClustering" $ (g' ^. phylo_groupMeta) ! "breaks"))
 170                        $ sortOn _phylo_groupBranchId $ concat branches
 171       AllBranches -> [concat branches]
 172   ByProximityDistribution _ _ -> branches
 173
 174
 175 levelUpAncestors :: [PhyloGroup] -> [PhyloGroup]
 176 levelUpAncestors groups =
 177   -- 1) create an associative map of (old,new) ids
 178   let ids' = fromList $ map (\g -> (getGroupId g, fst $ head' "levelUpAncestors" ( g ^. phylo_groupLevelParents))) groups
 179    in map (\g ->
 180         let id' = ids' ! (getGroupId g)
 181             ancestors  = g ^. phylo_groupAncestors
 182             -- 2) level up the ancestors ids and filter the ones that will be merged
 183             ancestors' = filter (\(id,_) -> id /= id') $ map (\(id,w) -> (ids' ! id,w)) ancestors
 184          in g & phylo_groupAncestors .~ ancestors'
 185       ) groups
 186
 187 synchronicClustering :: Phylo -> Phylo
 188 synchronicClustering phylo =
 189     let prox = phyloProximity $ getConfig phylo
 190         sync = phyloSynchrony $ getConfig phylo
 191         docs = phylo ^. phylo_timeDocs
 192         diagos = map coocToDiago $ phylo ^. phylo_timeCooc
 193         newBranches  = map (\branch -> levelUpAncestors $ reduceGroups prox sync docs diagos branch)
 194                      $ map processDynamics
 195                      $ adjustClustering sync
 196                      $ phyloToLastBranches
 197                      $ traceSynchronyStart phylo
 198         newBranches' = newBranches `using` parList rdeepseq
 199      in toNextLevel' phylo $ concat newBranches'
 200
 201
 202 -- synchronicDistance :: Phylo -> Level -> String
 203 -- synchronicDistance phylo lvl =
 204 --     foldl' (\acc branch ->
 205 --              acc <> (foldl' (\acc' period ->
 206 --                               acc' <> let prox  = phyloProximity $ getConfig phylo
 207 --                                           sync  = phyloSynchrony $ getConfig phylo
 208 --                                           docs  = _phylo_timeDocs phylo
 209 --                                           prd   = _phylo_groupPeriod $ head' "distance" period
 210 --                                           edges = groupsToEdges prox 0.1 (_bpt_sensibility sync)
 211 --                                                   ((sum . elems) $ restrictKeys docs $ periodsToYears [_phylo_groupPeriod $ head' "distance" period]) period
 212 --                                       in foldl' (\mem (_,w) ->
 213 --                                           mem <> show (prd)
 214 --                                               <> "\t"
 215 --                                               <> show (w)
 216 --                                               <> "\n"
 217 --                                         ) "" edges
 218 --                      ) ""  $ elems $ groupByField _phylo_groupPeriod branch)
 219 --     ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo