{-| Module : Gargantext.Core.Viz.Phylo.PhyloExport Description : Exportation module of a Phylo Copyright : (c) CNRS, 2017-Present License : AGPL + CECILL v3 Maintainer : team@gargantext.org Stability : experimental Portability : POSIX -} {-# LANGUAGE TypeSynonymInstances #-} module Gargantext.Core.Viz.Phylo.PhyloExport where import Data.Map (Map, fromList, empty, fromListWith, insert, (!), elems, unionWith, findWithDefault, toList, member) import Data.List ((++), sort, nub, null, concat, sortOn, groupBy, union, (\\), (!!), init, partition, notElem, unwords, nubBy, inits, elemIndex) import Data.Vector (Vector) import Prelude (writeFile) import Gargantext.Prelude import Gargantext.Core.Viz.AdaptativePhylo import Gargantext.Core.Viz.Phylo.PhyloTools import Gargantext.Core.Viz.Phylo.TemporalMatching (filterDocs, filterDiago, reduceDiagos, toProximity, getNextPeriods) import Control.Lens hiding (Level) import Control.Parallel.Strategies (parList, rdeepseq, using) import Data.GraphViz hiding (DotGraph, Order) import Data.GraphViz.Types.Generalised (DotGraph) import Data.GraphViz.Attributes.Complete hiding (EdgeType, Order) import Data.GraphViz.Types.Monadic import Data.Text.Lazy (fromStrict, pack, unpack) import System.FilePath import Debug.Trace (trace) import qualified Data.Text as Text import qualified Data.Vector as Vector import qualified Data.Text.Lazy as Lazy import qualified Data.GraphViz.Attributes.HTML as H -------------------- -- | Dot export | -- -------------------- dotToFile :: FilePath -> DotGraph DotId -> IO () dotToFile filePath dotG = writeFile filePath $ dotToString dotG dotToString :: DotGraph DotId -> [Char] dotToString dotG = unpack (printDotGraph dotG) dynamicToColor :: Double -> H.Attribute dynamicToColor d | d == 0 = H.BGColor (toColor LightCoral) | d == 1 = H.BGColor (toColor Khaki) | d == 2 = H.BGColor (toColor SkyBlue) | otherwise = H.Color (toColor Black) pickLabelColor :: [Double] -> H.Attribute pickLabelColor lst | elem 0 lst = dynamicToColor 0 | elem 2 lst = dynamicToColor 2 | elem 1 lst = dynamicToColor 1 | otherwise = dynamicToColor 3 toDotLabel :: Text.Text -> Label toDotLabel lbl = StrLabel $ fromStrict lbl toAttr :: AttributeName -> Lazy.Text -> CustomAttribute toAttr k v = customAttribute k v metaToAttr :: Map Text.Text [Double] -> [CustomAttribute] metaToAttr meta = map (\(k,v) -> toAttr (fromStrict k) $ (pack . unwords) $ map show v) $ toList meta groupIdToDotId :: PhyloGroupId -> DotId groupIdToDotId (((d,d'),lvl),idx) = (fromStrict . Text.pack) $ ("group" <> (show d) <> (show d') <> (show lvl) <> (show idx)) branchIdToDotId :: PhyloBranchId -> DotId branchIdToDotId bId = (fromStrict . Text.pack) $ ("branch" <> show (snd bId)) periodIdToDotId :: PhyloPeriodId -> DotId periodIdToDotId prd = (fromStrict . Text.pack) $ ("period" <> show (fst prd) <> show (snd prd)) groupToTable :: Vector Ngrams -> PhyloGroup -> H.Label groupToTable fdt g = H.Table H.HTable { H.tableFontAttrs = Just [H.PointSize 14, H.Align H.HLeft] , H.tableAttrs = [H.Border 0, H.CellBorder 0, H.BGColor (toColor White)] , H.tableRows = [header] <> [H.Cells [H.LabelCell [H.Height 10] $ H.Text [H.Str $ fromStrict ""]]] <> ( map ngramsToRow $ splitEvery 4 $ reverse $ sortOn (snd . snd) $ zip (ngramsToText fdt (g ^. phylo_groupNgrams)) $ zip ((g ^. phylo_groupMeta) ! "dynamics") ((g ^. phylo_groupMeta) ! "inclusion"))} where -------------------------------------- ngramsToRow :: [(Ngrams,(Double,Double))] -> H.Row ngramsToRow ns = H.Cells $ map (\(n,(d,_)) -> H.LabelCell [H.Align H.HLeft,dynamicToColor d] $ H.Text [H.Str $ fromStrict n]) ns -------------------------------------- header :: H.Row header = H.Cells [ H.LabelCell [pickLabelColor ((g ^. phylo_groupMeta) ! "dynamics")] $ H.Text [H.Str $ (((fromStrict . Text.toUpper) $ g ^. phylo_groupLabel) <> (fromStrict " ( ") <> (pack $ show (fst $ g ^. phylo_groupPeriod)) <> (fromStrict " , ") <> (pack $ show (snd $ g ^. phylo_groupPeriod)) <> (fromStrict " ) ") <> (pack $ show (getGroupId g)))]] -------------------------------------- branchToDotNode :: PhyloBranch -> Int -> Dot DotId branchToDotNode b bId = node (branchIdToDotId $ b ^. branch_id) ([FillColor [toWColor CornSilk], FontName "Arial", FontSize 40, Shape Egg, Style [SItem Bold []], Label (toDotLabel $ b ^. branch_label)] <> (metaToAttr $ b ^. branch_meta) <> [ toAttr "nodeType" "branch" , toAttr "bId" (pack $ show bId) , toAttr "branchId" (pack $ unwords (map show $ snd $ b ^. branch_id)) , toAttr "branch_x" (fromStrict $ Text.pack $ (show $ b ^. branch_x)) , toAttr "branch_y" (fromStrict $ Text.pack $ (show $ b ^. branch_y)) , toAttr "label" (pack $ show $ b ^. branch_label) ]) periodToDotNode :: (Date,Date) -> Dot DotId periodToDotNode prd = node (periodIdToDotId prd) ([Shape BoxShape, FontSize 50, Label (toDotLabel $ Text.pack (show (fst prd) <> " " <> show (snd prd)))] <> [ toAttr "nodeType" "period" , toAttr "from" (fromStrict $ Text.pack $ (show $ fst prd)) , toAttr "to" (fromStrict $ Text.pack $ (show $ snd prd))]) groupToDotNode :: Vector Ngrams -> PhyloGroup -> Int -> Dot DotId groupToDotNode fdt g bId = node (groupIdToDotId $ getGroupId g) ([FontName "Arial", Shape Square, penWidth 4, toLabel (groupToTable fdt g)] <> [ toAttr "nodeType" "group" , toAttr "from" (pack $ show (fst $ g ^. phylo_groupPeriod)) , toAttr "to" (pack $ show (snd $ g ^. phylo_groupPeriod)) , toAttr "branchId" (pack $ unwords (init $ map show $ snd $ g ^. phylo_groupBranchId)) , toAttr "bId" (pack $ show bId) , toAttr "support" (pack $ show (g ^. phylo_groupSupport)) , toAttr "lbl" (pack $ show (ngramsToLabel fdt (g ^. phylo_groupNgrams))) , toAttr "foundation" (pack $ show (idxToLabel (g ^. phylo_groupNgrams))) , toAttr "role" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "dynamics"))) ]) toDotEdge :: DotId -> DotId -> [Char] -> EdgeType -> Dot DotId toDotEdge source target lbl edgeType = edge source target (case edgeType of GroupToGroup -> [ Width 3, penWidth 4, Color [toWColor Black], Constraint True] <> [toAttr "edgeType" "link", toAttr "lbl" (pack lbl)] BranchToGroup -> [ Width 3, Color [toWColor Black], ArrowHead (AType [(ArrMod FilledArrow RightSide,DotArrow)])] <> [toAttr "edgeType" "branchLink" ] BranchToBranch -> [ Width 2, Color [toWColor Black], Style [SItem Dashed []], ArrowHead (AType [(ArrMod FilledArrow BothSides,DotArrow)])] GroupToAncestor -> [ Width 3, Color [toWColor Red], Style [SItem Dashed []], ArrowHead (AType [(ArrMod FilledArrow BothSides,NoArrow)]), PenWidth 4] <> [toAttr "edgeType" "ancestorLink", toAttr "lbl" (pack lbl)] PeriodToPeriod -> [ Width 5, Color [toWColor Black]]) mergePointers :: [PhyloGroup] -> Map (PhyloGroupId,PhyloGroupId) Double mergePointers groups = let toChilds = fromList $ concat $ map (\g -> map (\(target,w) -> ((getGroupId g,target),w)) $ g ^. phylo_groupPeriodChilds) groups toParents = fromList $ concat $ map (\g -> map (\(target,w) -> ((target,getGroupId g),w)) $ g ^. phylo_groupPeriodParents) groups in unionWith (\w w' -> max w w') toChilds toParents mergeAncestors :: [PhyloGroup] -> [((PhyloGroupId,PhyloGroupId), Double)] mergeAncestors groups = concat $ map (\g -> map (\(target,w) -> ((getGroupId g,target),w)) $ g ^. phylo_groupAncestors) $ filter (\g -> (not . null) $ g ^. phylo_groupAncestors) groups toBid :: PhyloGroup -> [PhyloBranch] -> Int toBid g bs = let b' = head' "toBid" (filter (\b -> b ^. branch_id == g ^. phylo_groupBranchId) bs) in fromJust $ elemIndex b' bs exportToDot :: Phylo -> PhyloExport -> DotGraph DotId exportToDot phylo export = trace ("\n-- | Convert " <> show(length $ export ^. export_branches) <> " branches and " <> show(length $ export ^. export_groups) <> " groups " <> show(length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) $ export ^. export_groups) <> " terms to a dot file\n\n" <> "##########################") $ digraph ((Str . fromStrict) $ (phyloName $ getConfig phylo)) $ do {- 1) init the dot graph -} graphAttrs ( [ Label (toDotLabel $ (phyloName $ getConfig phylo))] <> [ FontSize 30, LabelLoc VTop, NodeSep 1, RankSep [1], Rank SameRank, Splines SplineEdges, Overlap ScaleOverlaps , Ratio FillRatio , Style [SItem Filled []],Color [toWColor White]] {-- home made attributes -} <> [(toAttr (fromStrict "phyloFoundations") $ pack $ show (length $ Vector.toList $ getRoots phylo)) ,(toAttr (fromStrict "phyloTerms") $ pack $ show (length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) $ export ^. export_groups)) ,(toAttr (fromStrict "phyloDocs") $ pack $ show (sum $ elems $ phylo ^. phylo_timeDocs)) ,(toAttr (fromStrict "phyloPeriods") $ pack $ show (length $ elems $ phylo ^. phylo_periods)) ,(toAttr (fromStrict "phyloBranches") $ pack $ show (length $ export ^. export_branches)) ,(toAttr (fromStrict "phyloGroups") $ pack $ show (length $ export ^. export_groups)) ,(toAttr (fromStrict "phyloTermsFreq") $ pack $ show (toList $ _phylo_lastTermFreq phylo)) ]) {- -- toAttr (fromStrict k) $ (pack . unwords) $ map show v -- 2) create a layer for the branches labels -} subgraph (Str "Branches peaks") $ do graphAttrs [Rank SameRank] {- -- 3) group the branches by hierarchy -- mapM (\branches -> -- subgraph (Str "Branches clade") $ do -- graphAttrs [Rank SameRank] -- -- 4) create a node for each branch -- mapM branchToDotNode branches -- ) $ elems $ fromListWith (++) $ map (\b -> ((init . snd) $ b ^. branch_id,[b])) $ export ^. export_branches -} mapM (\b -> branchToDotNode b (fromJust $ elemIndex b (export ^. export_branches))) $ export ^. export_branches {-- 5) create a layer for each period -} _ <- mapM (\period -> subgraph ((Str . fromStrict . Text.pack) $ ("Period" <> show (fst period) <> show (snd period))) $ do graphAttrs [Rank SameRank] periodToDotNode period {-- 6) create a node for each group -} mapM (\g -> groupToDotNode (getRoots phylo) g (toBid g (export ^. export_branches))) (filter (\g -> g ^. phylo_groupPeriod == period) $ export ^. export_groups) ) $ getPeriodIds phylo {-- 7) create the edges between a branch and its first groups -} _ <- mapM (\(bId,groups) -> mapM (\g -> toDotEdge (branchIdToDotId bId) (groupIdToDotId $ getGroupId g) "" BranchToGroup) groups ) $ toList $ map (\groups -> head' "toDot" $ groupBy (\g g' -> g' ^. phylo_groupPeriod == g ^. phylo_groupPeriod) $ sortOn (fst . _phylo_groupPeriod) groups) $ fromListWith (++) $ map (\g -> (g ^. phylo_groupBranchId,[g])) $ export ^. export_groups {- 8) create the edges between the groups -} _ <- mapM (\((k,k'),v) -> toDotEdge (groupIdToDotId k) (groupIdToDotId k') (show v) GroupToGroup ) $ (toList . mergePointers) $ export ^. export_groups _ <- mapM (\((k,k'),v) -> toDotEdge (groupIdToDotId k) (groupIdToDotId k') (show v) GroupToAncestor ) $ mergeAncestors $ export ^. export_groups -- 10) create the edges between the periods _ <- mapM (\(prd,prd') -> toDotEdge (periodIdToDotId prd) (periodIdToDotId prd') "" PeriodToPeriod ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ getPeriodIds phylo {- 8) create the edges between the branches -- _ <- mapM (\(bId,bId') -> -- toDotEdge (branchIdToDotId bId) (branchIdToDotId bId') -- (Text.pack $ show(branchIdsToProximity bId bId' -- (getThresholdInit $ phyloProximity $ getConfig phylo) -- (getThresholdStep $ phyloProximity $ getConfig phylo))) BranchToBranch -- ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ map _branch_id $ export ^. export_branches -} graphAttrs [Rank SameRank] ---------------- -- | Filter | -- ---------------- filterByBranchSize :: Double -> PhyloExport -> PhyloExport filterByBranchSize thr export = let splited = partition (\b -> head' "filter" ((b ^. branch_meta) ! "size") >= thr) $ export ^. export_branches in export & export_branches .~ (fst splited) & export_groups %~ (filter (\g -> not $ elem (g ^. phylo_groupBranchId) (map _branch_id $ snd splited))) processFilters :: [Filter] -> Quality -> PhyloExport -> PhyloExport processFilters filters qua export = foldl (\export' f -> case f of ByBranchSize thr -> if (thr < (fromIntegral $ qua ^. qua_minBranch)) then filterByBranchSize (fromIntegral $ qua ^. qua_minBranch) export' else filterByBranchSize thr export' ) export filters -------------- -- | Sort | -- -------------- branchToIso :: [PhyloBranch] -> [PhyloBranch] branchToIso branches = let steps = map sum $ inits $ map (\(b,x) -> b ^. branch_y + 0.05 - x) $ zip branches $ ([0] ++ (map (\(b,b') -> let idx = length $ commonPrefix (b ^. branch_canonId) (b' ^. branch_canonId) [] lmin = min (length $ b ^. branch_seaLevel) (length $ b' ^. branch_seaLevel) in if ((idx - 1) > ((length $ b' ^. branch_seaLevel) - 1)) then (b' ^. branch_seaLevel) !! (lmin - 1) else (b' ^. branch_seaLevel) !! (idx - 1) ) $ listToSeq branches)) in map (\(x,b) -> b & branch_x .~ x) $ zip steps branches branchToIso' :: Double -> Double -> [PhyloBranch] -> [PhyloBranch] branchToIso' start step branches = let bx = map (\l -> (sum l) + ((fromIntegral $ length l) * 0.5)) $ inits $ ([0] ++ (map (\(b,b') -> let root = fromIntegral $ length $ commonPrefix (snd $ b ^. branch_id) (snd $ b' ^. branch_id) [] in 1 - start - step * root) $ listToSeq branches)) in map (\(x,b) -> b & branch_x .~ x) $ zip bx branches sortByHierarchy :: Int -> [PhyloBranch] -> [PhyloBranch] sortByHierarchy depth branches = if (length branches == 1) then branches else concat $ map (\branches' -> let partitions = partition (\b -> depth + 1 == ((length . snd) $ b ^. branch_id)) branches' in (sortOn (\b -> (b ^. branch_meta) ! "birth") (fst partitions)) ++ (sortByHierarchy (depth + 1) (snd partitions))) $ groupBy (\b b' -> ((take depth . snd) $ b ^. branch_id) == ((take depth . snd) $ b' ^. branch_id) ) $ sortOn (\b -> (take depth . snd) $ b ^. branch_id) branches sortByBirthDate :: Order -> PhyloExport -> PhyloExport sortByBirthDate order export = let branches = sortOn (\b -> (b ^. branch_meta) ! "birth") $ export ^. export_branches branches' = case order of Asc -> branches Desc -> reverse branches in export & export_branches .~ branches' processSort :: Sort -> SeaElevation -> PhyloExport -> PhyloExport processSort sort' elev export = case sort' of ByBirthDate o -> sortByBirthDate o export ByHierarchy -> export & export_branches .~ (branchToIso' (_cons_start elev) (_cons_step elev) $ sortByHierarchy 0 (export ^. export_branches)) ----------------- -- | Metrics | -- ----------------- -- | Return the conditional probability of i knowing j conditional :: Ord a => Map (a,a) Double -> a -> a -> Double conditional m i j = (findWithDefault 0 (i,j) m) / (m ! (j,j)) -- | Return the genericity score of a given ngram genericity :: Map (Int, Int) Double -> [Int] -> Int -> Double genericity m l i = ( (sum $ map (\j -> conditional m i j) l) - (sum $ map (\j -> conditional m j i) l)) / (fromIntegral $ (length l) + 1) -- | Return the specificity score of a given ngram specificity :: Map (Int, Int) Double -> [Int] -> Int -> Double specificity m l i = ( (sum $ map (\j -> conditional m j i) l) - (sum $ map (\j -> conditional m i j) l)) / (fromIntegral $ (length l) + 1) -- | Return the inclusion score of a given ngram inclusion :: Map (Int, Int) Double -> [Int] -> Int -> Double inclusion m l i = ( (sum $ map (\j -> conditional m j i) l) + (sum $ map (\j -> conditional m i j) l)) / (fromIntegral $ (length l) + 1) ngramsMetrics :: PhyloExport -> PhyloExport ngramsMetrics export = over ( export_groups . traverse ) (\g -> g & phylo_groupMeta %~ insert "genericity" (map (\n -> genericity (g ^. phylo_groupCooc) ((g ^. phylo_groupNgrams) \\ [n]) n) $ g ^. phylo_groupNgrams) & phylo_groupMeta %~ insert "specificity" (map (\n -> specificity (g ^. phylo_groupCooc) ((g ^. phylo_groupNgrams) \\ [n]) n) $ g ^. phylo_groupNgrams) & phylo_groupMeta %~ insert "inclusion" (map (\n -> inclusion (g ^. phylo_groupCooc) ((g ^. phylo_groupNgrams) \\ [n]) n) $ g ^. phylo_groupNgrams) ) export branchDating :: PhyloExport -> PhyloExport branchDating export = over ( export_branches . traverse ) (\b -> let groups = sortOn fst $ foldl' (\acc g -> if (g ^. phylo_groupBranchId == b ^. branch_id) then acc ++ [g ^. phylo_groupPeriod] else acc ) [] $ export ^. export_groups periods = nub groups birth = fst $ head' "birth" groups age = (snd $ last' "age" groups) - birth in b & branch_meta %~ insert "birth" [fromIntegral birth] & branch_meta %~ insert "age" [fromIntegral age] & branch_meta %~ insert "size" [fromIntegral $ length periods] ) export processMetrics :: PhyloExport -> PhyloExport processMetrics export = ngramsMetrics $ branchDating export ----------------- -- | Taggers | -- ----------------- nk :: Int -> [[Int]] -> Int nk n groups = sum $ map (\g -> if (elem n g) then 1 else 0) groups tf :: Int -> [[Int]] -> Double tf n groups = (fromIntegral $ nk n groups) / (fromIntegral $ length $ concat groups) idf :: Int -> [[Int]] -> Double idf n groups = log ((fromIntegral $ length groups) / (fromIntegral $ nk n groups)) findTfIdf :: [[Int]] -> [(Int,Double)] findTfIdf groups = reverse $ sortOn snd $ map (\n -> (n,(tf n groups) * (idf n groups))) $ sort $ nub $ concat groups findEmergences :: [PhyloGroup] -> Map Int Double -> [(Int,Double)] findEmergences groups freq = let ngrams = map _phylo_groupNgrams groups dynamics = map (\g -> (g ^. phylo_groupMeta) ! "dynamics") groups emerging = nubBy (\n1 n2 -> fst n1 == fst n2) $ concat $ map (\g -> filter (\(_,d) -> d == 0) $ zip (fst g) (snd g)) $ zip ngrams dynamics in reverse $ sortOn snd $ map (\(n,_) -> if (member n freq) then (n,freq ! n) else (n,0)) emerging mostEmergentTfIdf :: Int -> Map Int Double -> Vector Ngrams -> PhyloExport -> PhyloExport mostEmergentTfIdf nth freq foundations export = over ( export_branches . traverse ) (\b -> let groups = filter (\g -> g ^. phylo_groupBranchId == b ^. branch_id) $ export ^. export_groups tfidf = findTfIdf (map _phylo_groupNgrams groups) emergences = findEmergences groups freq selected = if (null emergences) then map fst $ take nth tfidf else [fst $ head' "mostEmergentTfIdf" emergences] ++ (map fst $ take (nth - 1) $ filter (\(n,_) -> n /= (fst $ head' "mostEmergentTfIdf" emergences)) tfidf) in b & branch_label .~ (ngramsToLabel foundations selected)) export getNthMostMeta :: Int -> [Double] -> [Int] -> [Int] getNthMostMeta nth meta ns = map (\(idx,_) -> (ns !! idx)) $ take nth $ reverse $ sortOn snd $ zip [0..] meta mostInclusive :: Int -> Vector Ngrams -> PhyloExport -> PhyloExport mostInclusive nth foundations export = over ( export_branches . traverse ) (\b -> let groups = filter (\g -> g ^. phylo_groupBranchId == b ^. branch_id) $ export ^. export_groups cooc = foldl (\acc g -> unionWith (+) acc (g ^. phylo_groupCooc)) empty groups ngrams = sort $ foldl (\acc g -> union acc (g ^. phylo_groupNgrams)) [] groups inc = map (\n -> inclusion cooc (ngrams \\ [n]) n) ngrams lbl = ngramsToLabel foundations $ getNthMostMeta nth inc ngrams in b & branch_label .~ lbl ) export mostEmergentInclusive :: Int -> Vector Ngrams -> PhyloExport -> PhyloExport mostEmergentInclusive nth foundations export = over ( export_groups . traverse ) (\g -> let lbl = ngramsToLabel foundations $ take nth $ map (\(_,(_,idx)) -> idx) $ concat $ map (\groups -> sortOn (fst . snd) groups) $ groupBy ((==) `on` fst) $ reverse $ sortOn fst $ zip ((g ^. phylo_groupMeta) ! "inclusion") $ zip ((g ^. phylo_groupMeta) ! "dynamics") (g ^. phylo_groupNgrams) in g & phylo_groupLabel .~ lbl ) export processLabels :: [PhyloLabel] -> Vector Ngrams -> Map Int Double -> PhyloExport -> PhyloExport processLabels labels foundations freq export = foldl (\export' label -> case label of GroupLabel tagger nth -> case tagger of MostEmergentInclusive -> mostEmergentInclusive nth foundations export' _ -> panic "[ERR][Viz.Phylo.PhyloExport] unknown tagger" BranchLabel tagger nth -> case tagger of MostInclusive -> mostInclusive nth foundations export' MostEmergentTfIdf -> mostEmergentTfIdf nth freq foundations export' _ -> panic "[ERR][Viz.Phylo.PhyloExport] unknown tagger" ) export labels ------------------ -- | Dynamics | -- ------------------ toDynamics :: Int -> [PhyloGroup] -> PhyloGroup -> Map Int (Date,Date) -> Double toDynamics n parents g m = let prd = g ^. phylo_groupPeriod end = last' "dynamics" (sort $ map snd $ elems m) in if (((snd prd) == (snd $ m ! n)) && (snd prd /= end)) {- decrease -} then 2 else if ((fst prd) == (fst $ m ! n)) {- emerging -} then 0 else if isNew {- emergence -} then 1 else 3 where -------------------------------------- isNew :: Bool isNew = not $ elem n $ concat $ map _phylo_groupNgrams parents processDynamics :: [PhyloGroup] -> [PhyloGroup] processDynamics groups = map (\g -> let parents = filter (\g' -> (g ^. phylo_groupBranchId == g' ^. phylo_groupBranchId) && ((fst $ g ^. phylo_groupPeriod) > (fst $ g' ^. phylo_groupPeriod))) groups in g & phylo_groupMeta %~ insert "dynamics" (map (\n -> toDynamics n parents g mapNgrams) $ g ^. phylo_groupNgrams) ) groups where -------------------------------------- mapNgrams :: Map Int (Date,Date) mapNgrams = map (\dates -> let dates' = sort dates in (head' "dynamics" dates', last' "dynamics" dates')) $ fromListWith (++) $ foldl (\acc g -> acc ++ ( map (\n -> (n,[fst $ g ^. phylo_groupPeriod, snd $ g ^. phylo_groupPeriod])) $ (g ^. phylo_groupNgrams))) [] groups ----------------- -- | horizon | -- ----------------- getGroupThr :: Double -> PhyloGroup -> Double getGroupThr step g = let seaLvl = (g ^. phylo_groupMeta) ! "seaLevels" breaks = (g ^. phylo_groupMeta) ! "breaks" in (last' "export" (take (round $ (last' "export" breaks) + 1) seaLvl)) - step toAncestor :: Double -> Map Int Double -> Proximity -> Double -> [PhyloGroup] -> PhyloGroup -> PhyloGroup toAncestor nbDocs diago proximity step candidates ego = let curr = ego ^. phylo_groupAncestors in ego & phylo_groupAncestors .~ (curr ++ (map (\(g,w) -> (getGroupId g,w)) $ filter (\(g,w) -> (w > 0) && (w >= (min (getGroupThr step ego) (getGroupThr step g)))) $ map (\g -> (g, toProximity nbDocs diago proximity (ego ^. phylo_groupNgrams) (g ^. phylo_groupNgrams) (g ^. phylo_groupNgrams))) $ filter (\g -> g ^. phylo_groupBranchId /= ego ^. phylo_groupBranchId ) candidates)) headsToAncestors :: Double -> Map Int Double -> Proximity -> Double -> [PhyloGroup] -> [PhyloGroup] -> [PhyloGroup] headsToAncestors nbDocs diago proximity step heads acc = if (null heads) then acc else let ego = head' "headsToAncestors" heads heads' = tail' "headsToAncestors" heads in headsToAncestors nbDocs diago proximity step heads' (acc ++ [toAncestor nbDocs diago proximity step heads' ego]) toHorizon :: Phylo -> Phylo toHorizon phylo = let phyloAncestor = updatePhyloGroups level (fromList $ map (\g -> (getGroupId g, g)) $ concat $ tracePhyloAncestors newGroups) phylo reBranched = fromList $ map (\g -> (getGroupId g, g)) $ concat $ groupsToBranches $ fromList $ map (\g -> (getGroupId g, g)) $ getGroupsFromLevel level phyloAncestor in updatePhyloGroups level reBranched phylo where -- | 1) for each periods periods :: [PhyloPeriodId] periods = getPeriodIds phylo -- -- level :: Level level = getLastLevel phylo -- -- frame :: Int frame = getTimeFrame $ timeUnit $ getConfig phylo -- | 2) find ancestors between groups without parents mapGroups :: [[PhyloGroup]] mapGroups = map (\prd -> let groups = getGroupsFromLevelPeriods level [prd] phylo childs = getPreviousChildIds level frame prd periods phylo heads = filter (\g -> null (g ^. phylo_groupPeriodParents) && (notElem (getGroupId g) childs)) groups noHeads = groups \\ heads nbDocs = sum $ elems $ filterDocs (phylo ^. phylo_timeDocs) [prd] diago = reduceDiagos $ filterDiago (phylo ^. phylo_timeCooc) [prd] proximity = (phyloProximity $ getConfig phylo) step = case getSeaElevation phylo of Constante _ s -> s Adaptative _ -> undefined -- in headsToAncestors nbDocs diago proximity heads groups [] in map (\ego -> toAncestor nbDocs diago proximity step noHeads ego) $ headsToAncestors nbDocs diago proximity step heads [] ) periods -- | 3) process this task concurrently newGroups :: [[PhyloGroup]] newGroups = mapGroups `using` parList rdeepseq -------------------------------------- getPreviousChildIds :: Level -> Int -> PhyloPeriodId -> [PhyloPeriodId] -> Phylo -> [PhyloGroupId] getPreviousChildIds lvl frame curr prds phylo = concat $ map ((map fst) . _phylo_groupPeriodChilds) $ getGroupsFromLevelPeriods lvl (getNextPeriods ToParents frame curr prds) phylo --------------------- -- | phyloExport | -- --------------------- toPhyloExport :: Phylo -> DotGraph DotId toPhyloExport phylo = exportToDot phylo $ processFilters (exportFilter $ getConfig phylo) (phyloQuality $ getConfig phylo) $ processSort (exportSort $ getConfig phylo) (getSeaElevation phylo) $ processLabels (exportLabel $ getConfig phylo) (getRoots phylo) (_phylo_lastTermFreq phylo) $ processMetrics export where export :: PhyloExport export = PhyloExport groups branches -------------------------------------- branches :: [PhyloBranch] branches = map (\g -> let seaLvl = (g ^. phylo_groupMeta) ! "seaLevels" breaks = (g ^. phylo_groupMeta) ! "breaks" canonId = take (round $ (last' "export" breaks) + 2) (snd $ g ^. phylo_groupBranchId) in PhyloBranch (g ^. phylo_groupBranchId) canonId seaLvl 0 (last' "export" (take (round $ (last' "export" breaks) + 1) seaLvl)) 0 0 "" empty) $ map (\gs -> head' "export" gs) $ groupBy (\g g' -> g ^. phylo_groupBranchId == g' ^. phylo_groupBranchId) $ sortOn (\g -> g ^. phylo_groupBranchId) groups -------------------------------------- groups :: [PhyloGroup] groups = traceExportGroups $ processDynamics $ getGroupsFromLevel (phyloLevel $ getConfig phylo) $ tracePhyloInfo $ toHorizon phylo traceExportBranches :: [PhyloBranch] -> [PhyloBranch] traceExportBranches branches = trace ("\n" <> "-- | Export " <> show(length branches) <> " branches") branches tracePhyloAncestors :: [[PhyloGroup]] -> [[PhyloGroup]] tracePhyloAncestors groups = trace ("\n" <> "-- | Found " <> show(length $ concat $ map _phylo_groupAncestors $ concat groups) <> " ancestors" ) groups tracePhyloInfo :: Phylo -> Phylo tracePhyloInfo phylo = trace ("\n" <> "##########################" <> "\n\n" <> "-- | Phylo with β = " <> show(_qua_granularity $ phyloQuality $ getConfig phylo) <> " applied to " <> show(length $ Vector.toList $ getRoots phylo) <> " foundations" ) phylo traceExportGroups :: [PhyloGroup] -> [PhyloGroup] traceExportGroups groups = trace ("\n" <> "-- | Export " <> show(length $ nub $ map (\g -> g ^. phylo_groupBranchId) groups) <> " branches, " <> show(length groups) <> " groups and " <> show(length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) groups) <> " terms" ) groups