src/Gargantext/Viz/Phylo/PhyloExport.hs

   1 {-|
   2 Module      : Gargantext.Viz.Phylo.PhyloExport
   3 Description : Exportation module 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 {-# LANGUAGE TypeSynonymInstances #-}
  12
  13 module Gargantext.Viz.Phylo.PhyloExport where
  14
  15 import Data.Map (Map, fromList, empty, fromListWith, insert, (!), elems, unionWith, findWithDefault, toList)
  16 import Data.List ((++), sort, nub, null, concat, sortOn, reverse, groupBy, union, (\\), (!!), init, partition, notElem, unwords, nubBy, inits, elemIndex)
  17 import Data.Vector (Vector)
  18
  19 import Prelude (writeFile)
  20 import Gargantext.Prelude
  21 import Gargantext.Viz.AdaptativePhylo
  22 import Gargantext.Viz.Phylo.PhyloTools
  23 import Gargantext.Viz.Phylo.TemporalMatching (filterDocs, filterDiago, reduceDiagos, toProximity, getNextPeriods)
  24
  25 import Control.Lens hiding (Level)
  26 import Control.Parallel.Strategies (parList, rdeepseq, using)
  27 import Data.GraphViz hiding (DotGraph, Order)
  28 import Data.GraphViz.Types.Generalised (DotGraph)
  29 import Data.GraphViz.Attributes.Complete hiding (EdgeType, Order)
  30 import Data.GraphViz.Types.Monadic
  31 import Data.Text.Lazy (fromStrict, pack, unpack)
  32 import System.FilePath
  33 import Debug.Trace (trace)
  34
  35 import qualified Data.Text as Text
  36 import qualified Data.Vector as Vector
  37 import qualified Data.Text.Lazy as Lazy
  38 import qualified Data.GraphViz.Attributes.HTML as H
  39
  40 --------------------
  41 -- | Dot export | --
  42 --------------------
  43
  44 dotToFile :: FilePath -> DotGraph DotId -> IO ()
  45 dotToFile filePath dotG = writeFile filePath $ dotToString dotG
  46
  47 dotToString :: DotGraph DotId  -> [Char]
  48 dotToString dotG = unpack (printDotGraph dotG)
  49
  50 dynamicToColor :: Double -> H.Attribute
  51 dynamicToColor d
  52   | d == 0    = H.BGColor (toColor LightCoral)
  53   | d == 1    = H.BGColor (toColor Khaki)
  54   | d == 2    = H.BGColor (toColor SkyBlue)
  55   | otherwise = H.Color   (toColor Black)
  56
  57 pickLabelColor :: [Double] -> H.Attribute
  58 pickLabelColor lst
  59   | elem 0 lst = dynamicToColor 0
  60   | elem 2 lst = dynamicToColor 2
  61   | elem 1 lst = dynamicToColor 1
  62   | otherwise  = dynamicToColor 3
  63
  64 toDotLabel :: Text.Text -> Label
  65 toDotLabel lbl = StrLabel $ fromStrict lbl
  66
  67 toAttr :: AttributeName -> Lazy.Text -> CustomAttribute
  68 toAttr k v = customAttribute k v
  69
  70 metaToAttr :: Map Text.Text [Double] -> [CustomAttribute]
  71 metaToAttr meta = map (\(k,v) -> toAttr (fromStrict k) $ (pack . unwords) $ map show v) $ toList meta
  72
  73 groupIdToDotId :: PhyloGroupId -> DotId
  74 groupIdToDotId (((d,d'),lvl),idx) = (fromStrict . Text.pack) $ ("group" <> (show d) <> (show d') <> (show lvl) <> (show idx))
  75
  76 branchIdToDotId :: PhyloBranchId -> DotId
  77 branchIdToDotId bId = (fromStrict . Text.pack) $ ("branch" <> show (snd bId))
  78
  79 periodIdToDotId :: PhyloPeriodId -> DotId
  80 periodIdToDotId prd = (fromStrict . Text.pack) $ ("period" <> show (fst prd) <> show (snd prd))
  81
  82 groupToTable :: Vector Ngrams -> PhyloGroup -> H.Label
  83 groupToTable fdt g = H.Table H.HTable
  84                     { H.tableFontAttrs = Just [H.PointSize 14, H.Align H.HLeft]
  85                     , H.tableAttrs = [H.Border 0, H.CellBorder 0, H.BGColor (toColor White)]
  86                     , H.tableRows = [header]
  87                                  <> [H.Cells [H.LabelCell [H.Height 10] $ H.Text [H.Str $ fromStrict ""]]]
  88                                  <> ( map ngramsToRow $ splitEvery 4
  89                                     $ reverse $ sortOn (snd . snd)
  90                                     $ zip (ngramsToText fdt (g ^. phylo_groupNgrams))
  91                                     $ zip ((g ^. phylo_groupMeta) ! "dynamics") ((g ^. phylo_groupMeta) ! "inclusion"))}
  92     where
  93         --------------------------------------
  94         ngramsToRow :: [(Ngrams,(Double,Double))] -> H.Row
  95         ngramsToRow ns = H.Cells $ map (\(n,(d,_)) ->
  96                             H.LabelCell [H.Align H.HLeft,dynamicToColor d] $ H.Text [H.Str $ fromStrict n]) ns
  97         --------------------------------------
  98         header :: H.Row
  99         header =
 100             H.Cells [ H.LabelCell [pickLabelColor ((g ^. phylo_groupMeta) ! "dynamics")]
 101                     $ H.Text [H.Str $ (((fromStrict . Text.toUpper) $ g ^. phylo_groupLabel)
 102                                    <> (fromStrict " ( ")
 103                                    <> (pack $ show (fst $ g ^. phylo_groupPeriod))
 104                                    <> (fromStrict " , ")
 105                                    <> (pack $ show (snd $ g ^. phylo_groupPeriod))
 106                                    <> (fromStrict " ) ")
 107                                    <> (pack $ show (getGroupId g)))]]
 108         --------------------------------------
 109
 110 branchToDotNode :: PhyloBranch -> Int -> Dot DotId
 111 branchToDotNode b bId =
 112     node (branchIdToDotId $ b ^. branch_id)
 113          ([FillColor [toWColor CornSilk], FontName "Arial", FontSize 40, Shape Egg, Style [SItem Bold []], Label (toDotLabel $ b ^. branch_label)]
 114          <> (metaToAttr $ b ^. branch_meta)
 115          <> [ toAttr "nodeType" "branch"
 116             , toAttr "bId"      (pack $ show bId)
 117             , toAttr "branchId" (pack $ unwords (map show $ snd $ b ^. branch_id))
 118             , toAttr "branch_x" (fromStrict $ Text.pack $ (show $ b ^. branch_x))
 119             , toAttr "branch_y" (fromStrict $ Text.pack $ (show $ b ^. branch_y))
 120             , toAttr "label"    (pack $ show $ b ^. branch_label)
 121             ])
 122
 123 periodToDotNode :: (Date,Date) -> Dot DotId
 124 periodToDotNode prd =
 125     node (periodIdToDotId prd)
 126          ([Shape BoxShape, FontSize 50, Label (toDotLabel $ Text.pack (show (fst prd) <> " " <> show (snd prd)))]
 127          <> [ toAttr "nodeType" "period"
 128             , toAttr "from" (fromStrict $ Text.pack $ (show $ fst prd))
 129             , toAttr "to"   (fromStrict $ Text.pack $ (show $ snd prd))])
 130
 131
 132 groupToDotNode :: Vector Ngrams -> PhyloGroup -> Int -> Dot DotId
 133 groupToDotNode fdt g bId =
 134     node (groupIdToDotId $ getGroupId g)
 135                      ([FontName "Arial", Shape Square, penWidth 4,  toLabel (groupToTable fdt g)]
 136                       <> [ toAttr "nodeType" "group"
 137                          , toAttr "from" (pack $ show (fst $ g ^. phylo_groupPeriod))
 138                          , toAttr "to"   (pack $ show (snd $ g ^. phylo_groupPeriod))
 139                          , toAttr "branchId" (pack $ unwords (init $ map show $ snd $ g ^. phylo_groupBranchId))
 140                          , toAttr "bId" (pack $ show bId)
 141                          , toAttr "support" (pack $ show (g ^. phylo_groupSupport))
 142                          , toAttr "label" (pack $ show (ngramsToLabel fdt (g ^. phylo_groupNgrams)))
 143                          , toAttr "foundation" (pack $ show (idxToLabel (g ^. phylo_groupNgrams)))
 144                          , toAttr "role" (pack $ show (idxToLabel' ((g ^. phylo_groupMeta) ! "dynamics")))
 145                          ])
 146
 147
 148 toDotEdge :: DotId -> DotId -> Text.Text -> EdgeType -> Dot DotId
 149 toDotEdge source target lbl edgeType = edge source target
 150     (case edgeType of
 151         GroupToGroup    -> [ Width 3, penWidth 4, Color [toWColor Black], Constraint True
 152                           , Label (StrLabel $ fromStrict lbl)] <> [toAttr "edgeType" "link" ]
 153         BranchToGroup   -> [ Width 3, Color [toWColor Black], ArrowHead (AType [(ArrMod FilledArrow RightSide,DotArrow)])
 154                           , Label (StrLabel $ fromStrict lbl)] <> [toAttr "edgeType" "branchLink" ]
 155         BranchToBranch  -> [ Width 2, Color [toWColor Black], Style [SItem Dashed []], ArrowHead (AType [(ArrMod FilledArrow BothSides,DotArrow)])
 156                           , Label (StrLabel $ fromStrict lbl)]
 157         GroupToAncestor -> [ Width 3, Color [toWColor Red], Style [SItem Dashed []], ArrowHead (AType [(ArrMod FilledArrow BothSides,NoArrow)])
 158                           , Label (StrLabel $ fromStrict lbl), PenWidth 4] <> [toAttr "edgeType" "ancestorLink" ]
 159         PeriodToPeriod  -> [ Width 5, Color [toWColor Black]])
 160
 161
 162 mergePointers :: [PhyloGroup] -> Map (PhyloGroupId,PhyloGroupId) Double
 163 mergePointers groups =
 164     let toChilds  = fromList $ concat $ map (\g -> map (\(target,w) -> ((getGroupId g,target),w)) $ g ^. phylo_groupPeriodChilds) groups
 165         toParents = fromList $ concat $ map (\g -> map (\(target,w) -> ((target,getGroupId g),w)) $ g ^. phylo_groupPeriodParents) groups
 166     in  unionWith (\w w' -> max w w') toChilds toParents
 167
 168 mergeAncestors :: [PhyloGroup] -> [((PhyloGroupId,PhyloGroupId), Double)]
 169 mergeAncestors groups = concat
 170                       $ map (\g -> map (\(target,w) -> ((getGroupId g,target),w)) $ g ^. phylo_groupAncestors)
 171                       $ filter (\g -> (not . null) $ g ^. phylo_groupAncestors) groups
 172
 173
 174 toBid :: PhyloGroup -> [PhyloBranch] -> Int
 175 toBid g bs =
 176   let b' = head' "toBid" (filter (\b -> b ^. branch_id == g ^. phylo_groupBranchId) bs)
 177    in fromJust $ elemIndex b' bs
 178
 179 exportToDot :: Phylo -> PhyloExport -> DotGraph DotId
 180 exportToDot phylo export =
 181     trace ("\n-- | Convert " <> show(length $ export ^. export_branches) <> " branches and "
 182          <> show(length $ export ^. export_groups) <> " groups "
 183          <> show(length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) $ export ^. export_groups) <> " terms to a dot file\n\n"
 184          <> "##########################") $
 185     digraph ((Str . fromStrict) $ (phyloName $ getConfig phylo)) $ do
 186
 187         {- 1) init the dot graph -}
 188         graphAttrs ( [ Label (toDotLabel $ (phyloName $ getConfig phylo))]
 189                   <> [ FontSize 30, LabelLoc VTop, NodeSep 1, RankSep [1], Rank SameRank, Splines SplineEdges, Overlap ScaleOverlaps
 190                      , Ratio FillRatio
 191                      , Style [SItem Filled []],Color [toWColor White]]
 192                   {-- home made attributes -}
 193                   <> [(toAttr (fromStrict "phyloFoundations") $ pack $ show (length $ Vector.toList $ getRoots phylo))
 194                      ,(toAttr (fromStrict "phyloTerms") $ pack $ show (length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) $ export ^. export_groups))
 195                      ,(toAttr (fromStrict "phyloDocs") $ pack $ show (sum $ elems $ phylo ^. phylo_timeDocs))
 196                      ,(toAttr (fromStrict "phyloPeriods") $ pack $ show (length $ elems $ phylo ^. phylo_periods))
 197                      ,(toAttr (fromStrict "phyloBranches") $ pack $ show (length $ export ^. export_branches))
 198                      ,(toAttr (fromStrict "phyloGroups") $ pack $ show (length $ export ^. export_groups))
 199                      ,(toAttr (fromStrict "phyloTermsFreq") $ pack $ show (toList $ _phylo_lastTermFreq phylo))
 200                      ])
 201
 202 {-
 203  -- toAttr (fromStrict k) $ (pack . unwords) $ map show v
 204
 205         --  2) create a layer for the branches labels -}
 206         subgraph (Str "Branches peaks") $ do
 207
 208             graphAttrs [Rank SameRank]
 209 {-
 210             --  3) group the branches by hierarchy
 211             -- mapM (\branches ->
 212             --         subgraph (Str "Branches clade") $ do
 213             --             graphAttrs [Rank SameRank]
 214
 215             --             --  4) create a node for each branch
 216             --             mapM branchToDotNode branches
 217             --     ) $ elems $ fromListWith (++) $ map (\b -> ((init . snd) $ b ^. branch_id,[b])) $ export ^. export_branches
 218 -}
 219             mapM (\b -> branchToDotNode b (fromJust $ elemIndex b (export ^. export_branches))) $ export ^. export_branches
 220
 221         {--  5) create a layer for each period -}
 222         _ <- mapM (\period ->
 223                 subgraph ((Str . fromStrict . Text.pack) $ ("Period" <> show (fst period) <> show (snd period))) $ do
 224                     graphAttrs [Rank SameRank]
 225                     periodToDotNode period
 226
 227                     {--  6) create a node for each group -}
 228                     mapM (\g -> groupToDotNode (getRoots phylo) g (toBid g (export ^. export_branches))) (filter (\g -> g ^. phylo_groupPeriod == period) $ export ^. export_groups)
 229             ) $ getPeriodIds phylo
 230
 231         {--  7) create the edges between a branch and its first groups -}
 232         _ <- mapM (\(bId,groups) ->
 233                 mapM (\g -> toDotEdge (branchIdToDotId bId) (groupIdToDotId $ getGroupId g) "" BranchToGroup) groups
 234              )
 235            $ toList
 236            $ map (\groups -> head' "toDot"
 237                            $ groupBy (\g g' -> g' ^. phylo_groupPeriod == g ^. phylo_groupPeriod)
 238                            $ sortOn (fst . _phylo_groupPeriod) groups)
 239            $ fromListWith (++) $ map (\g -> (g ^. phylo_groupBranchId,[g])) $ export ^. export_groups
 240
 241         {-  8) create the edges between the groups -}
 242         _ <- mapM (\((k,k'),_) ->
 243                 toDotEdge (groupIdToDotId k) (groupIdToDotId k') "" GroupToGroup
 244             ) $ (toList . mergePointers) $ export ^. export_groups
 245
 246         _ <- mapM (\((k,k'),_) ->
 247                 toDotEdge (groupIdToDotId k) (groupIdToDotId k') "" GroupToAncestor
 248           ) $ mergeAncestors $ export ^. export_groups
 249
 250         -- | 10) create the edges between the periods
 251         _ <- mapM (\(prd,prd') ->
 252                 toDotEdge (periodIdToDotId prd) (periodIdToDotId prd') "" PeriodToPeriod
 253             ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ getPeriodIds phylo
 254
 255         {-  8) create the edges between the branches
 256         -- _ <- mapM (\(bId,bId') ->
 257         --         toDotEdge (branchIdToDotId bId) (branchIdToDotId bId')
 258         --         (Text.pack $ show(branchIdsToProximity bId bId'
 259         --                             (getThresholdInit $ phyloProximity $ getConfig phylo)
 260         --                             (getThresholdStep $ phyloProximity $ getConfig phylo))) BranchToBranch
 261         --     ) $ nubBy (\combi combi' -> fst combi == fst combi') $ listToCombi' $ map _branch_id $ export ^. export_branches
 262         -}
 263
 264
 265         graphAttrs [Rank SameRank]
 266
 267
 268 ----------------
 269 -- | Filter | --
 270 ----------------
 271
 272 filterByBranchSize :: Double -> PhyloExport -> PhyloExport
 273 filterByBranchSize thr export =
 274     let splited  = partition (\b -> head' "filter" ((b ^. branch_meta) ! "size") >= thr) $ export ^. export_branches
 275      in export & export_branches .~ (fst splited)
 276                & export_groups %~ (filter (\g -> not $ elem  (g ^. phylo_groupBranchId) (map _branch_id $ snd splited)))
 277
 278
 279 processFilters :: [Filter] -> Quality -> PhyloExport -> PhyloExport
 280 processFilters filters qua export =
 281     foldl (\export' f -> case f of
 282                 ByBranchSize thr -> if (thr < (fromIntegral $ qua ^. qua_minBranch))
 283                                       then filterByBranchSize (fromIntegral $ qua ^. qua_minBranch) export'
 284                                       else filterByBranchSize thr export'
 285         ) export filters
 286
 287 --------------
 288 -- | Sort | --
 289 --------------
 290
 291 branchToIso :: [PhyloBranch] -> [PhyloBranch]
 292 branchToIso branches =
 293     let steps = map sum
 294               $ inits
 295               $ map (\(b,x) -> b ^. branch_y + 0.05 - x)
 296               $ zip branches
 297               $ ([0] ++ (map (\(b,b') ->
 298                                  let idx = length $ commonPrefix (b ^. branch_canonId) (b' ^. branch_canonId) []
 299                                   in (b' ^. branch_seaLevel) !! (idx - 1)
 300                                  ) $ listToSeq branches))
 301      in map (\(x,b) -> b & branch_x .~ x)
 302       $ zip steps branches
 303
 304
 305 sortByHierarchy :: Int -> [PhyloBranch] -> [PhyloBranch]
 306 sortByHierarchy depth branches =
 307     if (length branches == 1)
 308         then branchToIso branches
 309         else branchToIso $ concat
 310            $ map (\branches' ->
 311                     let partitions = partition (\b -> depth + 1 == ((length . snd) $ b ^. branch_id)) branches'
 312                     in  (sortOn (\b -> (b ^. branch_meta) ! "birth") (fst partitions))
 313                     ++  (sortByHierarchy (depth + 1) (snd partitions)))
 314             $ groupBy (\b b' -> ((take depth . snd) $ b ^. branch_id) == ((take depth . snd) $ b' ^. branch_id) )
 315             $ sortOn (\b -> (take depth . snd) $ b ^. branch_id) branches
 316
 317
 318 sortByBirthDate :: Order -> PhyloExport -> PhyloExport
 319 sortByBirthDate order export =
 320     let branches  = sortOn (\b -> (b ^. branch_meta) ! "birth") $ export ^. export_branches
 321         branches' = case order of
 322                     Asc  -> branches
 323                     Desc -> reverse branches
 324     in  export & export_branches .~ branches'
 325
 326 processSort :: Sort -> PhyloExport -> PhyloExport
 327 processSort sort' export = case sort' of
 328     ByBirthDate o -> sortByBirthDate o export
 329     ByHierarchy   -> export & export_branches .~ sortByHierarchy 0 (export ^. export_branches)
 330
 331
 332 -----------------
 333 -- | Metrics | --
 334 -----------------
 335
 336 -- | Return the conditional probability of i knowing j
 337 conditional :: Ord a => Map (a,a) Double -> a -> a -> Double
 338 conditional m i j = (findWithDefault 0 (i,j) m)
 339                   / (m ! (j,j))
 340
 341
 342 -- | Return the genericity score of a given ngram
 343 genericity :: Map (Int, Int) Double -> [Int] -> Int -> Double
 344 genericity m l i = ( (sum $ map (\j -> conditional m i j) l)
 345                    - (sum $ map (\j -> conditional m j i) l)) / (fromIntegral $ (length l) + 1)
 346
 347
 348 -- | Return the specificity score of a given ngram
 349 specificity :: Map (Int, Int) Double -> [Int] -> Int -> Double
 350 specificity m l i = ( (sum $ map (\j -> conditional m j i) l)
 351                     - (sum $ map (\j -> conditional m i j) l)) / (fromIntegral $ (length l) + 1)
 352
 353
 354 -- | Return the inclusion score of a given ngram
 355 inclusion :: Map (Int, Int) Double -> [Int] -> Int -> Double
 356 inclusion m l i = ( (sum $ map (\j -> conditional m j i) l)
 357                   + (sum $ map (\j -> conditional m i j) l)) / (fromIntegral $ (length l) + 1)
 358
 359
 360 ngramsMetrics :: PhyloExport -> PhyloExport
 361 ngramsMetrics export =
 362     over ( export_groups
 363          .  traverse )
 364     (\g -> g & phylo_groupMeta %~ insert "genericity"
 365                                   (map (\n -> genericity  (g ^. phylo_groupCooc) ((g ^. phylo_groupNgrams) \\ [n]) n) $ g ^. phylo_groupNgrams)
 366              & phylo_groupMeta %~ insert "specificity"
 367                                   (map (\n -> specificity (g ^. phylo_groupCooc) ((g ^. phylo_groupNgrams) \\ [n]) n) $ g ^. phylo_groupNgrams)
 368              & phylo_groupMeta %~ insert "inclusion"
 369                                   (map (\n -> inclusion   (g ^. phylo_groupCooc) ((g ^. phylo_groupNgrams) \\ [n]) n) $ g ^. phylo_groupNgrams)
 370         ) export
 371
 372
 373 branchDating :: PhyloExport -> PhyloExport
 374 branchDating export =
 375     over ( export_branches
 376          .  traverse )
 377     (\b ->
 378         let groups = sortOn fst
 379                    $ foldl' (\acc g -> if (g ^. phylo_groupBranchId == b ^. branch_id)
 380                                       then acc ++ [g ^. phylo_groupPeriod]
 381                                       else acc ) [] $ export ^. export_groups
 382             periods = nub groups
 383             birth = fst $ head' "birth" groups
 384             age   = (snd $ last' "age"  groups) - birth
 385         in b & branch_meta %~ insert "birth" [fromIntegral birth]
 386              & branch_meta %~ insert "age"   [fromIntegral age]
 387              & branch_meta %~ insert "size"  [fromIntegral $ length periods] ) export
 388
 389 processMetrics :: PhyloExport -> PhyloExport
 390 processMetrics export = ngramsMetrics
 391                       $ branchDating export
 392
 393
 394 -----------------
 395 -- | Taggers | --
 396 -----------------
 397
 398 getNthMostMeta :: Int -> [Double] -> [Int] -> [Int]
 399 getNthMostMeta nth meta ns = map (\(idx,_) -> (ns !! idx))
 400                            $ take nth
 401                            $ reverse
 402                            $ sortOn snd $ zip [0..] meta
 403
 404
 405 mostInclusive :: Int -> Vector Ngrams -> PhyloExport -> PhyloExport
 406 mostInclusive nth foundations export =
 407     over ( export_branches
 408          .  traverse )
 409          (\b ->
 410             let groups = filter (\g -> g ^. phylo_groupBranchId == b ^. branch_id) $ export ^. export_groups
 411                 cooc   = foldl (\acc g -> unionWith (+) acc (g ^. phylo_groupCooc)) empty groups
 412                 ngrams = sort $ foldl (\acc g -> union acc (g ^. phylo_groupNgrams)) [] groups
 413                 inc    = map (\n -> inclusion cooc (ngrams \\ [n]) n) ngrams
 414                 lbl    = ngramsToLabel foundations $ getNthMostMeta nth inc ngrams
 415             in b & branch_label .~ lbl ) export
 416
 417
 418 mostEmergentInclusive :: Int -> Vector Ngrams -> PhyloExport -> PhyloExport
 419 mostEmergentInclusive nth foundations export =
 420     over ( export_groups
 421          .  traverse )
 422          (\g ->
 423             let lbl = ngramsToLabel foundations
 424                     $ take nth
 425                     $ map (\(_,(_,idx)) -> idx)
 426                     $ concat
 427                     $ map (\groups -> sortOn (fst . snd) groups)
 428                     $ groupBy ((==) `on` fst) $ reverse $ sortOn fst
 429                     $ zip ((g ^. phylo_groupMeta) ! "inclusion")
 430                     $ zip ((g ^. phylo_groupMeta) ! "dynamics") (g ^. phylo_groupNgrams)
 431             in g & phylo_groupLabel .~ lbl ) export
 432
 433
 434 processLabels :: [PhyloLabel] -> Vector Ngrams -> PhyloExport -> PhyloExport
 435 processLabels labels foundations export =
 436     foldl (\export' label ->
 437                 case label of
 438                     GroupLabel  tagger nth ->
 439                         case tagger of
 440                             MostEmergentInclusive -> mostEmergentInclusive nth foundations export'
 441                             _ -> panic "[ERR][Viz.Phylo.PhyloExport] unknown tagger"
 442                     BranchLabel tagger nth ->
 443                         case tagger of
 444                             MostInclusive -> mostInclusive nth foundations export'
 445                             _ -> panic "[ERR][Viz.Phylo.PhyloExport] unknown tagger" ) export labels
 446
 447
 448 ------------------
 449 -- | Dynamics | --
 450 ------------------
 451
 452
 453 toDynamics :: Int -> [PhyloGroup] -> PhyloGroup -> Map Int (Date,Date) -> Double
 454 toDynamics n parents g m =
 455     let prd = g ^. phylo_groupPeriod
 456         end = last' "dynamics" (sort $ map snd $ elems m)
 457     in  if (((snd prd) == (snd $ m ! n)) && (snd prd /= end))
 458             {- decrease -}
 459             then 2
 460         else if ((fst prd) == (fst $ m ! n))
 461             {- recombination -}
 462             then 0
 463         else if isNew
 464             {- emergence -}
 465             then 1
 466         else 3
 467     where
 468         --------------------------------------
 469         isNew :: Bool
 470         isNew = not $ elem n $ concat $ map _phylo_groupNgrams parents
 471
 472
 473 processDynamics :: [PhyloGroup] -> [PhyloGroup]
 474 processDynamics groups =
 475     map (\g ->
 476         let parents = filter (\g' -> (g ^. phylo_groupBranchId == g' ^. phylo_groupBranchId)
 477                                   && ((fst $ g ^. phylo_groupPeriod) > (fst $ g' ^. phylo_groupPeriod))) groups
 478         in  g & phylo_groupMeta %~ insert "dynamics" (map (\n -> toDynamics n parents g mapNgrams) $ g ^. phylo_groupNgrams) ) groups
 479     where
 480         --------------------------------------
 481         mapNgrams :: Map Int (Date,Date)
 482         mapNgrams = map (\dates ->
 483                         let dates' = sort dates
 484                         in (head' "dynamics" dates', last' "dynamics" dates'))
 485                   $ fromListWith (++)
 486                   $ foldl (\acc g -> acc ++ ( map (\n -> (n,[fst $ g ^. phylo_groupPeriod, snd $ g ^. phylo_groupPeriod]))
 487                                             $ (g ^. phylo_groupNgrams))) [] groups
 488
 489
 490 -----------------
 491 -- | horizon | --
 492 -----------------
 493
 494 getGroupThr :: Double -> PhyloGroup -> Double
 495 getGroupThr step g =
 496     let seaLvl = (g ^. phylo_groupMeta) ! "seaLevels"
 497         breaks = (g ^. phylo_groupMeta) ! "breaks"
 498      in (last' "export" (take (round $ (last' "export" breaks) + 1) seaLvl)) - step
 499
 500 toAncestor :: Double -> Map Int Double -> Proximity -> Double -> [PhyloGroup] -> PhyloGroup -> PhyloGroup
 501 toAncestor nbDocs diago proximity step candidates ego =
 502   let curr = ego ^. phylo_groupAncestors
 503    in ego & phylo_groupAncestors .~ (curr ++ (map (\(g,w) -> (getGroupId g,w))
 504          $ filter (\(g,w) -> (w > 0) && (w >= (min (getGroupThr step ego) (getGroupThr step g))))
 505          $ map (\g -> (g, toProximity nbDocs diago proximity (ego ^. phylo_groupNgrams) (g ^. phylo_groupNgrams) (g ^. phylo_groupNgrams)))
 506          $ filter (\g -> g ^. phylo_groupBranchId /= ego ^. phylo_groupBranchId ) candidates))
 507
 508
 509 headsToAncestors :: Double -> Map Int Double -> Proximity -> Double -> [PhyloGroup] -> [PhyloGroup] -> [PhyloGroup]
 510 headsToAncestors nbDocs diago proximity step heads acc =
 511   if (null heads)
 512     then acc
 513     else
 514       let ego    = head' "headsToAncestors" heads
 515           heads' = tail' "headsToAncestors" heads
 516        in headsToAncestors nbDocs diago proximity step heads' (acc ++ [toAncestor nbDocs diago proximity step heads' ego])
 517
 518
 519 toHorizon :: Phylo -> Phylo
 520 toHorizon phylo =
 521   let phyloAncestor = updatePhyloGroups
 522                     level
 523                     (fromList $ map (\g -> (getGroupId g, g))
 524                               $ concat
 525                               $ tracePhyloAncestors newGroups) phylo
 526       reBranched = fromList $ map (\g -> (getGroupId g, g)) $ concat
 527                  $ groupsToBranches $ fromList $ map (\g -> (getGroupId g, g)) $ getGroupsFromLevel level phyloAncestor
 528    in updatePhyloGroups level reBranched phylo
 529   where
 530     -- | 1) for each periods
 531     periods :: [PhyloPeriodId]
 532     periods = getPeriodIds phylo
 533     -- --
 534     level :: Level
 535     level = getLastLevel phylo
 536     -- --
 537     frame :: Int
 538     frame = getTimeFrame $ timeUnit $ getConfig phylo
 539     -- | 2) find ancestors between groups without parents
 540     mapGroups :: [[PhyloGroup]]
 541     mapGroups = map (\prd ->
 542       let groups  = getGroupsFromLevelPeriods level [prd] phylo
 543           childs  = getPreviousChildIds level frame prd periods phylo
 544           heads   = filter (\g -> null (g ^. phylo_groupPeriodParents) && (notElem (getGroupId g) childs)) groups
 545           noHeads = groups \\ heads
 546           nbDocs  = sum $ elems  $ filterDocs  (phylo ^. phylo_timeDocs) [prd]
 547           diago   = reduceDiagos $ filterDiago (phylo ^. phylo_timeCooc) [prd]
 548           proximity = (phyloProximity $ getConfig phylo)
 549           step = case getSeaElevation phylo of
 550             Constante  _ s -> s
 551             Adaptative _ -> undefined
 552        -- in headsToAncestors nbDocs diago proximity heads groups []
 553        in map (\ego -> toAncestor nbDocs diago proximity step noHeads ego)
 554         $ headsToAncestors nbDocs diago proximity step heads []
 555       ) periods
 556     -- | 3) process this task concurrently
 557     newGroups :: [[PhyloGroup]]
 558     newGroups = mapGroups `using` parList rdeepseq
 559     --------------------------------------
 560
 561 getPreviousChildIds :: Level -> Int -> PhyloPeriodId -> [PhyloPeriodId] -> Phylo -> [PhyloGroupId]
 562 getPreviousChildIds lvl frame curr prds phylo =
 563     concat $ map ((map fst) . _phylo_groupPeriodChilds)
 564            $ getGroupsFromLevelPeriods lvl (getNextPeriods ToParents frame curr prds) phylo
 565
 566 ---------------------
 567 -- | phyloExport | --
 568 ---------------------
 569
 570 toPhyloExport :: Phylo -> DotGraph DotId
 571 toPhyloExport phylo = exportToDot phylo
 572                     $ processFilters (exportFilter $ getConfig phylo) (phyloQuality $ getConfig phylo)
 573                     $ processSort    (exportSort   $ getConfig phylo)
 574                     $ processLabels  (exportLabel  $ getConfig phylo) (getRoots phylo)
 575                     $ processMetrics  export
 576     where
 577         export :: PhyloExport
 578         export = PhyloExport groups branches
 579         --------------------------------------
 580         branches :: [PhyloBranch]
 581         branches = map (\g ->
 582                       let seaLvl = (g ^. phylo_groupMeta) ! "seaLevels"
 583                           breaks = (g ^. phylo_groupMeta) ! "breaks"
 584                           canonId = take (round $ (last' "export" breaks) + 2) (snd $ g ^. phylo_groupBranchId)
 585                        in PhyloBranch (g ^. phylo_groupBranchId)
 586                                       canonId
 587                                       seaLvl
 588                                       0
 589                                       (last' "export" (take (round $ (last' "export" breaks) + 1) seaLvl))
 590                                       0
 591                                       0
 592                                       "" empty)
 593                   $ map (\gs -> head' "export" gs)
 594                   $ groupBy (\g g' -> g ^. phylo_groupBranchId == g' ^. phylo_groupBranchId)
 595                   $ sortOn (\g -> g ^. phylo_groupBranchId) groups
 596         --------------------------------------
 597         groups :: [PhyloGroup]
 598         groups = traceExportGroups
 599                $ processDynamics
 600                $ getGroupsFromLevel (phyloLevel $ getConfig phylo)
 601                $ tracePhyloInfo
 602                $ toHorizon phylo
 603
 604
 605 traceExportBranches :: [PhyloBranch] -> [PhyloBranch]
 606 traceExportBranches branches = trace ("\n"
 607   <> "-- | Export " <> show(length branches) <> " branches") branches
 608
 609 tracePhyloAncestors :: [[PhyloGroup]] -> [[PhyloGroup]]
 610 tracePhyloAncestors groups = trace ("\n"
 611   <> "-- | Found " <> show(length $ concat $ map _phylo_groupAncestors $ concat groups) <> " ancestors"
 612   ) groups
 613
 614 tracePhyloInfo :: Phylo -> Phylo
 615 tracePhyloInfo phylo = trace ("\n"  <> "##########################" <> "\n\n" <> "-- | Phylo with β = "
 616     <> show(_qua_granularity $ phyloQuality $ getConfig phylo) <> " applied to "
 617     <> show(length $ Vector.toList $ getRoots phylo) <> " foundations"
 618   ) phylo
 619
 620
 621 traceExportGroups :: [PhyloGroup] -> [PhyloGroup]
 622 traceExportGroups groups = trace ("\n" <> "-- | Export "
 623     <> show(length $ nub $ map (\g -> g ^. phylo_groupBranchId) groups) <> " branches, "
 624     <> show(length groups) <> " groups and "
 625     <> show(length $ nub $ concat $ map (\g -> g ^. phylo_groupNgrams) groups) <> " terms"
 626   ) groups
 627