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, all, 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                   []
  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
  55 addPhyloLevel :: Level -> Phylo -> Phylo
  56 addPhyloLevel lvl phylo =
  57   over ( phylo_periods .  traverse )
  58        (\phyloPrd -> phyloPrd & phylo_periodLevels
  59                         %~ (insert (phyloPrd ^. phylo_periodPeriod, lvl) (PhyloLevel (phyloPrd ^. phylo_periodPeriod) lvl empty))) phylo
  60
  61
  62 toNextLevel' :: Phylo -> [PhyloGroup] -> Phylo
  63 toNextLevel' phylo groups =
  64     let curLvl = getLastLevel phylo
  65         oldGroups = fromList $ map (\g -> (getGroupId g, getLevelParentId g)) groups
  66         newGroups = concat $ groupsToBranches
  67                   $ fromList $ map (\g -> (getGroupId g, g))
  68                   $ foldlWithKey (\acc id groups' ->
  69                         --  4) create the parent group
  70                         let parent = mergeGroups (elems $ restrictKeys (phylo ^. phylo_timeCooc) $ periodsToYears [(fst . fst) id]) id oldGroups groups'
  71                         in  acc ++ [parent]) []
  72                   --  3) group the current groups by parentId
  73                   $ fromListWith (++) $ map (\g -> (getLevelParentId g, [g])) groups
  74
  75         newPeriods = fromListWith (++) $ map (\g -> (g ^. phylo_groupPeriod, [g])) newGroups
  76     in  traceSynchronyEnd
  77       $ over ( phylo_periods . traverse . phylo_periodLevels . traverse
  78              --  6) update each period at curLvl + 1
  79              . filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == (curLvl + 1)))
  80              --  7) by adding the parents
  81              (\phyloLvl ->
  82                 if member (phyloLvl ^. phylo_levelPeriod) newPeriods
  83                     then phyloLvl & phylo_levelGroups
  84                             .~ fromList (map (\g -> (getGroupId g, g)) $ newPeriods ! (phyloLvl ^. phylo_levelPeriod))
  85                     else phyloLvl)
  86       --  2) add the curLvl + 1 phyloLevel to the phylo
  87       $ addPhyloLevel (curLvl + 1)
  88       --  1) update the current groups (with level parent pointers) in the phylo
  89       $ updatePhyloGroups curLvl (fromList $ map (\g -> (getGroupId g, g)) groups) phylo
  90
  91 --------------------
  92 -- | Clustering | --
  93 --------------------
  94
  95 toPairs :: SynchronyStrategy -> [PhyloGroup] -> [(PhyloGroup,PhyloGroup)]
  96 toPairs strategy groups = case strategy of
  97   MergeRegularGroups -> pairs
  98                       $ filter (\g -> all (== 3) $ (g ^. phylo_groupMeta) ! "dynamics") groups
  99   MergeAllGroups -> pairs groups
 100   where
 101     pairs :: [PhyloGroup] -> [(PhyloGroup,PhyloGroup)]
 102     pairs gs = filter (\(g,g') -> (not . null) $ intersect (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams)) (listToCombi' gs)
 103
 104
 105 toDiamonds :: [PhyloGroup] -> [[PhyloGroup]]
 106 toDiamonds groups = foldl' (\acc groups' ->
 107                         acc ++ ( elems
 108                                $ Map.filter (\v -> length v > 1)
 109                                $ fromListWith (++)
 110                                $ foldl' (\acc' g ->
 111                                     acc' ++ (map (\(id,_) -> (id,[g]) ) $ g ^. phylo_groupPeriodChilds)) [] groups')) []
 112                   $ elems
 113                   $ Map.filter (\v -> length v > 1)
 114                   $ fromListWith (++)
 115                   $ foldl' (\acc g -> acc ++ (map (\(id,_) -> (id,[g]) ) $ g ^. phylo_groupPeriodParents)  ) [] groups
 116
 117
 118 groupsToEdges :: Proximity -> Synchrony -> Double -> Map Int Double -> [PhyloGroup] -> [((PhyloGroup,PhyloGroup),Double)]
 119 groupsToEdges prox sync nbDocs diago groups =
 120     case sync of
 121         ByProximityThreshold  thr sens _ strat ->
 122             filter (\(_,w) -> w >= thr)
 123           $ toEdges sens
 124           $ toPairs strat groups
 125         ByProximityDistribution sens strat ->
 126             let diamonds = sortOn snd
 127                          $ toEdges sens $ concat
 128                          $ map (\gs -> toPairs strat gs) $ toDiamonds groups
 129              in take (div (length diamonds) 2) diamonds
 130     where
 131         toEdges :: Double -> [(PhyloGroup,PhyloGroup)] -> [((PhyloGroup,PhyloGroup),Double)]
 132         toEdges sens edges =
 133             case prox of
 134                 WeightedLogJaccard _ -> map (\(g,g') ->
 135                                                      ((g,g'), weightedLogJaccard' sens nbDocs diago
 136                                                                   (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams))) edges
 137                 _ -> undefined
 138
 139 toParentId :: PhyloGroup -> PhyloGroupId
 140 toParentId child = ((child ^. phylo_groupPeriod, child ^. phylo_groupLevel + 1), child ^. phylo_groupIndex)
 141
 142
 143 reduceGroups :: Proximity -> Synchrony -> Map Date Double -> Map Date Cooc -> [PhyloGroup] -> [PhyloGroup]
 144 reduceGroups prox sync docs diagos branch =
 145     --  1) reduce a branch as a set of periods & groups
 146     let periods = fromListWith (++)
 147                  $ map (\g -> (g ^. phylo_groupPeriod,[g])) branch
 148     in  (concat . concat . elems)
 149       $ mapWithKey (\prd groups ->
 150             --  2) for each period, transform the groups as a proximity graph filtered by a threshold
 151             let diago = reduceDiagos $ filterDiago diagos [prd]
 152                 edges = groupsToEdges prox sync ((sum . elems) $ restrictKeys docs $ periodsToYears [prd]) diago groups
 153              in map (\comp ->
 154                     --  4) add to each groups their futur level parent group
 155                     let parentId = toParentId (head' "parentId" comp)
 156                     in  map (\g -> g & phylo_groupLevelParents %~ (++ [(parentId,1)]) ) comp )
 157                 -- 3) reduce the graph a a set of related components
 158               $ toRelatedComponents groups edges) periods
 159
 160
 161 adjustClustering :: Synchrony -> [[PhyloGroup]] -> [[PhyloGroup]]
 162 adjustClustering sync branches = case sync of
 163   ByProximityThreshold _ _ scope _ -> case scope of
 164       SingleBranch -> branches
 165       SiblingBranches -> groupBy (\g g' -> (last' "adjustClustering" $ (g  ^. phylo_groupMeta) ! "breaks")
 166                                         == (last' "adjustClustering" $ (g' ^. phylo_groupMeta) ! "breaks"))
 167                        $ sortOn _phylo_groupBranchId $ concat branches
 168       AllBranches -> [concat branches]
 169   ByProximityDistribution _ _ -> branches
 170
 171
 172
 173 synchronicClustering :: Phylo -> Phylo
 174 synchronicClustering phylo =
 175     let prox = phyloProximity $ getConfig phylo
 176         sync = phyloSynchrony $ getConfig phylo
 177         docs = phylo ^. phylo_timeDocs
 178         diagos = map coocToDiago $ phylo ^. phylo_timeCooc
 179         newBranches  = map (\branch -> reduceGroups prox sync docs diagos branch)
 180                      $ map processDynamics
 181                      $ adjustClustering sync
 182                      $ phyloToLastBranches
 183                      $ traceSynchronyStart phylo
 184         newBranches' = newBranches `using` parList rdeepseq
 185      in toNextLevel' phylo $ concat newBranches'
 186
 187
 188 -- synchronicDistance :: Phylo -> Level -> String
 189 -- synchronicDistance phylo lvl =
 190 --     foldl' (\acc branch ->
 191 --              acc <> (foldl' (\acc' period ->
 192 --                               acc' <> let prox  = phyloProximity $ getConfig phylo
 193 --                                           sync  = phyloSynchrony $ getConfig phylo
 194 --                                           docs  = _phylo_timeDocs phylo
 195 --                                           prd   = _phylo_groupPeriod $ head' "distance" period
 196 --                                           edges = groupsToEdges prox 0.1 (_bpt_sensibility sync)
 197 --                                                   ((sum . elems) $ restrictKeys docs $ periodsToYears [_phylo_groupPeriod $ head' "distance" period]) period
 198 --                                       in foldl' (\mem (_,w) ->
 199 --                                           mem <> show (prd)
 200 --                                               <> "\t"
 201 --                                               <> show (w)
 202 --                                               <> "\n"
 203 --                                         ) "" edges
 204 --                      ) ""  $ elems $ groupByField _phylo_groupPeriod branch)
 205 --     ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo