module Gargantext.Viz.Phylo.PhyloMaker where
-
-import Data.Map (Map, fromListWith, keys, unionWith, fromList)
+import Data.List (concat, nub, partition, sort, (++), group, intersect, null, sortOn, groupBy)
+import Data.Map (Map, fromListWith, keys, unionWith, fromList, empty, toList, elems, (!), restrictKeys, foldlWithKey)
+import Data.Set (size)
+import Data.Vector (Vector)
import Gargantext.Prelude
import Gargantext.Viz.AdaptativePhylo
import Gargantext.Viz.Phylo.PhyloTools
+import Gargantext.Viz.Phylo.TemporalMatching (adaptativeTemporalMatching, constanteTemporalMatching, getNextPeriods, filterDocs, filterDiago, reduceDiagos, toProximity)
+import Gargantext.Viz.Phylo.SynchronicClustering (synchronicClustering)
+import Gargantext.Text.Context (TermList)
+import Gargantext.Text.Metrics.FrequentItemSet (fisWithSizePolyMap, Size(..))
+
+import Control.DeepSeq (NFData)
+import Control.Parallel.Strategies (parList, rdeepseq, using)
+import Debug.Trace (trace)
+import Control.Lens hiding (Level)
+
+import qualified Data.Vector as Vector
+import qualified Data.Set as Set
+
+
+------------------
+-- | To Phylo | --
+------------------
+
+
+toPhylo :: [Document] -> TermList -> Config -> Phylo
+toPhylo docs lst conf = trace ("# phylo1 groups " <> show(length $ getGroupsFromLevel 1 phylo1))
+ $ traceToPhylo (phyloLevel conf) $
+ if (phyloLevel conf) > 1
+ then foldl' (\phylo' _ -> synchronicClustering phylo') phylo1 [2..(phyloLevel conf)]
+ else phylo1
+ where
+ --------------------------------------
+ phylo1 :: Phylo
+ phylo1 = toPhylo1 docs phyloBase
+ --------------------------------------
+ phyloBase :: Phylo
+ phyloBase = toPhyloBase docs lst conf
+ --------------------------------------
+
--------------------
--- | to Phylo 0 | --
+-- | To Phylo 1 | --
--------------------
-nbDocsByTime :: [Document] -> Int -> Map Date Double
-nbDocsByTime docs step =
+toGroupsProxi :: Level -> Phylo -> Phylo
+toGroupsProxi lvl phylo =
+ let proximity = phyloProximity $ getConfig phylo
+ groupsProxi = foldlWithKey (\acc pId pds ->
+ -- 1) process period by period
+ let egos = map (\g -> (getGroupId g, g ^. phylo_groupNgrams))
+ $ elems
+ $ view ( phylo_periodLevels
+ . traverse . filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == lvl)
+ . phylo_levelGroups ) pds
+ next = getNextPeriods ToParents (getTimeFrame $ timeUnit $ getConfig phylo) pId (keys $ phylo ^. phylo_periods)
+ targets = map (\g -> (getGroupId g, g ^. phylo_groupNgrams)) $ getGroupsFromLevelPeriods lvl next phylo
+ docs = filterDocs (phylo ^. phylo_timeDocs) ([pId] ++ next)
+ diagos = filterDiago (phylo ^. phylo_timeCooc) ([pId] ++ next)
+ -- 2) compute the pairs in parallel
+ pairs = map (\(id,ngrams) ->
+ map (\(id',ngrams') ->
+ let nbDocs = (sum . elems) $ filterDocs docs ([idToPrd id, idToPrd id'])
+ diago = reduceDiagos $ filterDiago diagos ([idToPrd id, idToPrd id'])
+ in ((id,id'),toProximity nbDocs diago proximity ngrams ngrams' ngrams')
+ ) $ filter (\(_,ngrams') -> (not . null) $ intersect ngrams ngrams') targets
+ ) egos
+ pairs' = pairs `using` parList rdeepseq
+ in acc ++ (concat pairs')
+ ) [] $ phylo ^. phylo_periods
+ in phylo & phylo_groupsProxi .~ ((traceGroupsProxi . fromList) groupsProxi)
+
+
+appendGroups :: (a -> PhyloPeriodId -> Level -> Int -> Vector Ngrams -> [Cooc] -> PhyloGroup) -> Level -> Map (Date,Date) [a] -> Phylo -> Phylo
+appendGroups f lvl m phylo = trace ("\n" <> "-- | Append " <> show (length $ concat $ elems m) <> " groups to Level " <> show (lvl) <> "\n")
+ $ over ( phylo_periods
+ . traverse
+ . phylo_periodLevels
+ . traverse)
+ (\phyloLvl -> if lvl == (phyloLvl ^. phylo_levelLevel)
+ then
+ let pId = phyloLvl ^. phylo_levelPeriod
+ phyloCUnit = m ! pId
+ in phyloLvl
+ & phylo_levelGroups .~ (fromList $ foldl (\groups obj ->
+ groups ++ [ (((pId,lvl),length groups)
+ , f obj pId lvl (length groups) (getRoots phylo)
+ (elems $ restrictKeys (phylo ^. phylo_timeCooc) $ periodsToYears [pId]))
+ ] ) [] phyloCUnit)
+ else
+ phyloLvl )
+ phylo
+
+
+cliqueToGroup :: PhyloClique -> PhyloPeriodId -> Level -> Int -> Vector Ngrams -> [Cooc] -> PhyloGroup
+cliqueToGroup fis pId lvl idx fdt coocs =
+ let ngrams = ngramsToIdx (Set.toList $ fis ^. phyloClique_nodes) fdt
+ in PhyloGroup pId lvl idx ""
+ (fis ^. phyloClique_support)
+ ngrams
+ (ngramsToCooc ngrams coocs)
+ (1,[0]) -- | branchid (lvl,[path in the branching tree])
+ (fromList [("breaks",[0]),("seaLevels",[0])])
+ [] [] [] []
+
+
+toPhylo1 :: [Document] -> Phylo -> Phylo
+toPhylo1 docs phyloBase = case (getSeaElevation phyloBase) of
+ Constante start gap -> constanteTemporalMatching start gap
+ $ appendGroups cliqueToGroup 1 phyloClique phyloBase
+ Adaptative steps -> adaptativeTemporalMatching steps
+ $ toGroupsProxi 1
+ $ appendGroups cliqueToGroup 1 phyloClique phyloBase
+ where
+ --------------------------------------
+ phyloClique :: Map (Date,Date) [PhyloClique]
+ phyloClique = toPhyloClique phyloBase docs'
+ --------------------------------------
+ docs' :: Map (Date,Date) [Document]
+ docs' = groupDocsByPeriod' date (getPeriodIds phyloBase) docs
+ --------------------------------------
+
+
+---------------------------
+-- | Frequent Item Set | --
+---------------------------
+
+
+-- | 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
+filterCliqueBySupport :: Int -> [PhyloClique] -> [PhyloClique]
+filterCliqueBySupport thr l = filter (\clq -> (clq ^. phyloClique_support) >= thr) l
+
+
+-- | 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
+filterCliqueByNested :: Map (Date, Date) [PhyloClique] -> Map (Date, Date) [PhyloClique]
+filterCliqueByNested m =
+ let clq = map (\l ->
+ foldl (\mem f -> if (any (\f' -> isNested (Set.toList $ f' ^. phyloClique_nodes) (Set.toList $ f ^. phyloClique_nodes)) mem)
+ then mem
+ else
+ let fMax = filter (\f' -> not $ isNested (Set.toList $ f ^. phyloClique_nodes) (Set.toList $ f' ^. phyloClique_nodes)) mem
+ in fMax ++ [f] ) [] l)
+ $ elems m
+ clq' = clq `using` parList rdeepseq
+ in fromList $ zip (keys m) clq'
+
+
+-- | 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"
+ $ filterClique True s' (filterCliqueBySize)
+ -- $ traceFis "Filtered by support"
+ $ filterClique True s (filterCliqueBySupport)
+ -- $ traceFis "Unfiltered Fis"
+ phyloClique
+ MaxClique _ -> undefined
+ where
+ --------------------------------------
+ phyloClique :: Map (Date,Date) [PhyloClique]
+ phyloClique = case (clique $ getConfig phylo) of
+ Fis _ _ -> let fis = map (\(prd,docs) ->
+ let lst = toList $ fisWithSizePolyMap (Segment 1 20) 1 (map text docs)
+ in (prd, map (\f -> PhyloClique (fst f) (snd f) prd) lst))
+ $ toList phyloDocs
+ fis' = fis `using` parList rdeepseq
+ in fromList fis'
+ MaxClique _ -> undefined
+ --------------------------------------
+
+
+--------------------
+-- | Coocurency | --
+--------------------
+
+
+-- | 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
+ $ map (\(_d,l) -> (_d, listToMatrix l))
+ $ map (\doc -> (date doc, sort $ ngramsToIdx (text doc) fdt)) docs
+ mCooc' = fromList
+ $ map (\t -> (t,empty))
+ $ toTimeScale (map date docs) 1
+ in trace ("\n" <> "-- | Build the coocurency matrix for " <> show (length $ keys mCooc') <> " unit of time" <> "\n")
+ $ unionWith sumCooc mCooc mCooc'
+
+
+-----------------------
+-- | to Phylo Base | --
+-----------------------
+
+-- | 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
+ periods = map (inPeriode f docs') pds
+ periods' = periods `using` parList rdeepseq
+ in trace ("\n" <> "-- | Group " <> show(length docs) <> " docs by " <> show(length pds) <> " periods" <> "\n")
+ $ fromList $ zip pds periods'
+ where
+ --------------------------------------
+ inPeriode :: Ord b => (t -> b) -> [[t]] -> (b, b) -> [t]
+ inPeriode f' h (start,end) =
+ concat $ fst $ partition (\d -> f' (head' "inPeriode" d) >= start && f' (head' "inPeriode" d) <= end) h
+
+
+
+-- | 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 =
+ let periods = map (inPeriode f es) pds
+ periods' = periods `using` parList rdeepseq
+
+ in trace ("\n" <> "-- | Group " <> show(length es) <> " docs by " <> show(length pds) <> " periods" <> "\n")
+ $ fromList $ zip pds periods'
+ where
+ --------------------------------------
+ inPeriode :: Ord b => (t -> b) -> [t] -> (b, b) -> [t]
+ inPeriode f' h (start,end) =
+ fst $ partition (\d -> f' d >= start && f' d <= end) h
+ --------------------------------------
+
+
+docsToTermFreq :: [Document] -> Vector Ngrams -> Map Int Double
+docsToTermFreq docs fdt =
+ let nbDocs = fromIntegral $ length docs
+ freqs = map (/(nbDocs))
+ $ fromList
+ $ map (\lst -> (head' "docsToTermFreq" lst, fromIntegral $ length lst))
+ $ group $ sort $ concat $ map (\d -> nub $ ngramsToIdx (text d) fdt) docs
+ sumFreqs = sum $ elems freqs
+ in map (/sumFreqs) freqs
+
+
+-- | 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
- time = fromList $ map (\t -> (t,0)) $ toTimeScale (keys docs') step
- in unionWith (+) time docs'
+ time = fromList $ map (\t -> (t,0)) $ toTimeScale (keys docs') 1
+ in trace ("\n" <> "-- | Group " <> show(length docs) <> " docs by " <> show(length time) <> " unit of time" <> "\n")
+ $ unionWith (+) time docs'
+
+
+initPhyloLevels :: Int -> PhyloPeriodId -> Map PhyloLevelId PhyloLevel
+initPhyloLevels lvlMax pId =
+ fromList $ map (\lvl -> ((pId,lvl),PhyloLevel pId lvl empty)) [1..lvlMax]
+-- | 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
+ params = defaultPhyloParam { _phyloParam_config = conf }
+ periods = toPeriods (sort $ nub $ map date docs) (getTimePeriod $ timeUnit conf) (getTimeStep $ timeUnit conf)
+ in trace ("\n" <> "-- | Create PhyloBase out of " <> show(length docs) <> " docs \n")
+ $ Phylo foundations
+ (docsToTimeScaleCooc docs (foundations ^. foundations_roots))
+ (docsToTimeScaleNb docs)
+ (docsToTermFreq docs (foundations ^. foundations_roots))
+ empty
+ params
+ (fromList $ map (\prd -> (prd, PhyloPeriod prd (initPhyloLevels 1 prd))) periods)