{-| Module : Gargantext.Viz.Phylo.SynchronicClustering Description : Module dedicated to the adaptative synchronic clustering of a Phylo. Copyright : (c) CNRS, 2017-Present License : AGPL + CECILL v3 Maintainer : team@gargantext.org Stability : experimental Portability : POSIX -} {-# LANGUAGE NoImplicitPrelude #-} {-# LANGUAGE FlexibleContexts #-} {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE MultiParamTypeClasses #-} module Gargantext.Viz.Phylo.SynchronicClustering where import Gargantext.Prelude import Gargantext.Viz.AdaptativePhylo import Gargantext.Viz.Phylo.PhyloTools import Gargantext.Viz.Phylo.TemporalMatching (weightedLogJaccard', filterDiago, reduceDiagos) import Gargantext.Viz.Phylo.PhyloExport (processDynamics) import Data.List ((++), null, intersect, nub, concat, sort, sortOn, init, all, group, maximum, groupBy) import Data.Map (Map, fromList, fromListWith, foldlWithKey, (!), insert, empty, restrictKeys, elems, mapWithKey, member, singleton) import Control.Lens hiding (Level) import Control.Parallel.Strategies (parList, rdeepseq, using) -- import Debug.Trace (trace) import qualified Data.Map as Map import qualified Data.Set as Set ------------------------- -- | New Level Maker | -- ------------------------- mergeBranchIds :: [[Int]] -> [Int] mergeBranchIds ids = (head' "mergeBranchIds" . sort . mostFreq) ids where -- | 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 mostFreq :: [[Int]] -> [[Int]] mostFreq ids' = let groupIds = (map (\gIds -> (length gIds, head' "gIds" gIds)) . group . sort) ids' sup = (fst . maximum) groupIds in map snd $ filter (\gIds -> fst gIds == sup) groupIds groupsToBranches' :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]] groupsToBranches' groups = -- | 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 in map (\ids -> let groups' = elems $ restrictKeys groups (Set.fromList ids) bId = mergeBranchIds $ map (\g -> snd $ g ^. phylo_groupBranchId) groups' in map (\g -> g & phylo_groupBranchId %~ (\(lvl,_) -> (lvl + 1,bId))) groups') graph getLastThr :: [PhyloGroup] -> Double getLastThr childs = maximum $ concat $ map (\g -> (g ^. phylo_groupMeta) ! "thr") childs mergeGroups :: [Cooc] -> PhyloGroupId -> Map PhyloGroupId PhyloGroupId -> [PhyloGroup] -> PhyloGroup mergeGroups coocs id mapIds childs = let ngrams = (sort . nub . concat) $ map _phylo_groupNgrams childs in PhyloGroup (fst $ fst id) (snd $ fst id) (snd id) "" (sum $ map _phylo_groupSupport childs) ngrams (ngramsToCooc ngrams coocs) ((snd $ fst id),(mergeBranchIds $ map (\g -> snd $ g ^. phylo_groupBranchId) childs)) (singleton "thr" [getLastThr childs]) [] (map (\g -> (getGroupId g, 1)) childs) (updatePointers $ concat $ map _phylo_groupPeriodParents childs) (updatePointers $ concat $ map _phylo_groupPeriodChilds childs) where updatePointers :: [Pointer] -> [Pointer] updatePointers pointers = map (\(pId,w) -> (mapIds ! pId,w)) pointers addPhyloLevel :: Level -> Phylo -> Phylo addPhyloLevel lvl phylo = over ( phylo_periods . traverse ) (\phyloPrd -> phyloPrd & phylo_periodLevels %~ (insert (phyloPrd ^. phylo_periodPeriod, lvl) (PhyloLevel (phyloPrd ^. phylo_periodPeriod) lvl empty))) phylo toNextLevel' :: Phylo -> [PhyloGroup] -> Phylo toNextLevel' phylo groups = let curLvl = getLastLevel phylo oldGroups = fromList $ map (\g -> (getGroupId g, getLevelParentId g)) groups newGroups = concat $ groupsToBranches' $ fromList $ map (\g -> (getGroupId g, g)) $ foldlWithKey (\acc id groups' -> -- | 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 $ 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 . filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == (curLvl + 1))) -- | 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 $ addPhyloLevel (curLvl + 1) -- | 1) update the current groups (with level parent pointers) in the phylo $ updatePhyloGroups curLvl (fromList $ map (\g -> (getGroupId g, g)) groups) phylo -------------------- -- | Clustering | -- -------------------- toPairs :: SynchronyStrategy -> [PhyloGroup] -> [(PhyloGroup,PhyloGroup)] toPairs strategy groups = case strategy of MergeRegularGroups -> pairs $ filter (\g -> all (== 3) $ (g ^. phylo_groupMeta) ! "dynamics") groups MergeAllGroups -> pairs groups where pairs :: [PhyloGroup] -> [(PhyloGroup,PhyloGroup)] pairs gs = filter (\(g,g') -> (not . null) $ intersect (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams)) (listToCombi' gs) toDiamonds :: [PhyloGroup] -> [[PhyloGroup]] toDiamonds groups = foldl' (\acc groups' -> acc ++ ( elems $ Map.filter (\v -> length v > 1) $ fromListWith (++) $ foldl' (\acc' g -> acc' ++ (map (\(id,_) -> (id,[g]) ) $ g ^. phylo_groupPeriodChilds)) [] groups')) [] $ elems $ Map.filter (\v -> length v > 1) $ fromListWith (++) $ foldl' (\acc g -> acc ++ (map (\(id,_) -> (id,[g]) ) $ g ^. phylo_groupPeriodParents) ) [] groups groupsToEdges :: Proximity -> Synchrony -> Double -> Map Int Double -> [PhyloGroup] -> [((PhyloGroup,PhyloGroup),Double)] groupsToEdges prox sync nbDocs diago groups = case sync of ByProximityThreshold thr sens _ strat -> filter (\(_,w) -> w >= thr) $ toEdges sens $ toPairs strat groups ByProximityDistribution sens strat -> let diamonds = sortOn snd $ toEdges sens $ concat $ map (\gs -> toPairs strat gs) $ toDiamonds groups in take (div (length diamonds) 2) diamonds where toEdges :: Double -> [(PhyloGroup,PhyloGroup)] -> [((PhyloGroup,PhyloGroup),Double)] toEdges sens edges = case prox of WeightedLogJaccard _ _ _ -> map (\(g,g') -> ((g,g'), weightedLogJaccard' sens nbDocs diago (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams))) edges _ -> undefined toRelatedComponents :: [PhyloGroup] -> [((PhyloGroup,PhyloGroup),Double)] -> [[PhyloGroup]] toRelatedComponents nodes edges = let ref = fromList $ map (\g -> (getGroupId g, g)) nodes clusters = relatedComponents $ ((map (\((g,g'),_) -> [getGroupId g, getGroupId g']) edges) ++ (map (\g -> [getGroupId g]) nodes)) in map (\cluster -> map (\gId -> ref ! gId) cluster) clusters toParentId :: PhyloGroup -> PhyloGroupId toParentId child = ((child ^. phylo_groupPeriod, child ^. phylo_groupLevel + 1), child ^. phylo_groupIndex) 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 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 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 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 $ toRelatedComponents groups edges) periods getGroupRealBId :: Double -> PhyloGroup -> [Int] getGroupRealBId step g = let nb = round(getGroupThr g / step) + 2 in take nb (snd $ g ^. phylo_groupBranchId) adjustClustering :: Synchrony -> Double -> [[PhyloGroup]] -> [[PhyloGroup]] adjustClustering sync step branches = case sync of ByProximityThreshold _ _ scope _ -> case scope of SingleBranch -> branches SiblingBranches -> groupBy (\g g' -> (init $ getGroupRealBId step g) == (init $ getGroupRealBId step g')) $ sortOn _phylo_groupBranchId $ concat branches -- SiblingBranches -> elems $ fromListWith (++) $ map (\b -> ((init . snd . _phylo_groupBranchId) $ head' "adjustClustering" b,b)) branches AllBranches -> [concat branches] ByProximityDistribution _ _ -> branches synchronicClustering :: Phylo -> Phylo synchronicClustering phylo = let prox = phyloProximity $ getConfig phylo sync = phyloSynchrony $ getConfig phylo docs = phylo ^. phylo_timeDocs diagos = map coocToDiago $ phylo ^. phylo_timeCooc newBranches = map (\branch -> reduceGroups prox sync docs diagos branch) $ map processDynamics $ adjustClustering sync (getPhyloThresholdStep phylo) $ phyloToLastBranches $ traceSynchronyStart phylo newBranches' = newBranches `using` parList rdeepseq in toNextLevel' phylo $ concat newBranches' ---------------- -- | probes | -- ---------------- -- synchronicDistance :: Phylo -> Level -> String -- synchronicDistance phylo lvl = -- foldl' (\acc branch -> -- acc <> (foldl' (\acc' period -> -- acc' <> let prox = phyloProximity $ getConfig phylo -- sync = phyloSynchrony $ getConfig phylo -- docs = _phylo_timeDocs phylo -- prd = _phylo_groupPeriod $ head' "distance" period -- edges = groupsToEdges prox 0.1 (_bpt_sensibility sync) -- ((sum . elems) $ restrictKeys docs $ periodsToYears [_phylo_groupPeriod $ head' "distance" period]) period -- in foldl' (\mem (_,w) -> -- mem <> show (prd) -- <> "\t" -- <> show (w) -- <> "\n" -- ) "" edges -- ) "" $ elems $ groupByField _phylo_groupPeriod branch) -- ) "period\tdistance\n" $ elems $ groupByField _phylo_groupBranchId $ getGroupsFromLevel lvl phylo