add adaptative and constante sea level elevation

src/Gargantext/Viz/AdaptativePhylo.hs

@@ -57,12 +57,22 @@ data CorpusParser =
     | Csv {_csv_limit :: Int}
     deriving (Show,Generic,Eq) 
 
+data SeaElevation = 
+      Constante  
+      { _cons_start :: Double
+      , _cons_step  :: Double }
+    | Adaptative 
+      { _adap_granularity :: Double }
+    deriving (Show,Generic,Eq)
 
 data Proximity = 
       WeightedLogJaccard 
       { _wlj_sensibility   :: Double 
-      , _wlj_thresholdInit :: Double
-      , _wlj_thresholdStep :: Double }
+      -- , _wlj_thresholdInit :: Double
+      -- , _wlj_thresholdStep :: Double
+      -- | max height for sea level in temporal matching
+      -- , _wlj_elevation     :: Double
+      }
     | Hamming 
     deriving (Show,Generic,Eq) 
 
@@ -114,6 +124,7 @@ data Config =
             , phyloName      :: Text
             , phyloLevel     :: Int
             , phyloProximity :: Proximity
+            , seaElevation   :: SeaElevation
             , phyloSynchrony :: Synchrony
             , phyloQuality   :: Quality
             , timeUnit       :: TimeUnit
@@ -132,8 +143,9 @@ defaultConfig =
             , corpusParser   = Csv 1000
             , phyloName      = pack "Default Phylo"
             , phyloLevel     = 2
-            , phyloProximity = WeightedLogJaccard 10 0 0.1
-            , phyloSynchrony = ByProximityThreshold 0.1 10 AllBranches MergeAllGroups
+            , phyloProximity = WeightedLogJaccard 10
+            , seaElevation   = Adaptative 25
+            , phyloSynchrony = ByProximityThreshold 0.6 10 SiblingBranches MergeAllGroups
             , phyloQuality   = Quality 0.1 1
             , timeUnit       = Year 3 1 5
             , clique         = Fis 1 5
@@ -148,6 +160,8 @@ instance FromJSON CorpusParser
 instance ToJSON CorpusParser
 instance FromJSON Proximity
 instance ToJSON Proximity
+instance FromJSON SeaElevation
+instance ToJSON SeaElevation
 instance FromJSON TimeUnit
 instance ToJSON TimeUnit
 instance FromJSON Clique
@@ -253,6 +267,7 @@ data Phylo =
            , _phylo_timeCooc    :: !(Map Date Cooc)
            , _phylo_timeDocs    :: !(Map Date Double)
            , _phylo_termFreq    :: !(Map Int Double)
+           , _phylo_groupsProxi :: !(Map (PhyloGroupId,PhyloGroupId) Double)
            , _phylo_param       :: PhyloParam
            , _phylo_periods     :: Map PhyloPeriodId PhyloPeriod
            }
@@ -366,9 +381,13 @@ data PhyloLabel =
 data PhyloBranch =
       PhyloBranch
       { _branch_id :: PhyloBranchId
+      , _branch_canonId  :: [Int]
+      , _branch_seaLevel :: [Double]
+      , _branch_x        :: Double
+      , _branch_y        :: Double
       , _branch_label    :: Text
       , _branch_meta     :: Map Text [Double]
-      } deriving (Generic, Show)
+      } deriving (Generic, Show, Eq)
 
 data PhyloExport =
       PhyloExport
@@ -382,6 +401,7 @@ data PhyloExport =
 
 makeLenses ''Config
 makeLenses ''Proximity
+makeLenses ''SeaElevation
 makeLenses ''Quality
 makeLenses ''Clique
 makeLenses ''PhyloLabel

src/Gargantext/Viz/Phylo/PhyloExample.hs

@@ -30,7 +30,7 @@ import Gargantext.Viz.AdaptativePhylo
 import Gargantext.Viz.Phylo.PhyloTools
 import Gargantext.Viz.Phylo.PhyloMaker
 import Gargantext.Viz.Phylo.PhyloExport
-import Gargantext.Viz.Phylo.TemporalMatching (temporalMatching)
+import Gargantext.Viz.Phylo.TemporalMatching (adaptativeTemporalMatching, constanteTemporalMatching)
 import Gargantext.Viz.Phylo.SynchronicClustering (synchronicClustering)
 
 import Control.Lens
@@ -60,7 +60,12 @@ phylo2 = synchronicClustering phylo1
 -----------------------------------------------
 
 phylo1 :: Phylo
-phylo1 = temporalMatching
+phylo1 = case (getSeaElevation phyloBase) of 
+    Constante s g   -> constanteTemporalMatching s g 
+       $ toGroupsProxi 1
+       $ appendGroups cliqueToGroup 1 phyloClique phyloBase
+    Adaptative s    -> adaptativeTemporalMatching s
+       $ toGroupsProxi 1
        $ appendGroups cliqueToGroup 1 phyloClique phyloBase
 
 

src/Gargantext/Viz/Phylo/PhyloExport.hs

@@ -17,8 +17,8 @@ Portability : POSIX
 
 module Gargantext.Viz.Phylo.PhyloExport where
 
-import Data.Map (Map, fromList, empty, fromListWith, insert, (!), elems, unionWith, findWithDefault, toList, delete)
-import Data.List ((++), sort, nub, concat, sortOn, reverse, groupBy, union, (\\), (!!), init, partition, unwords, nubBy)
+import Data.Map (Map, fromList, empty, fromListWith, insert, (!), elems, unionWith, findWithDefault, toList)
+import Data.List ((++), sort, nub, concat, sortOn, reverse, groupBy, union, (\\), (!!), init, partition, unwords, nubBy, inits)
 import Data.Vector (Vector)
 
 import Prelude (writeFile)
@@ -116,7 +116,11 @@ branchToDotNode b =
          ([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 "branchId" (pack $ unwords (map show $ snd $ b ^. branch_id)) ])
+            , 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 =
@@ -130,7 +134,7 @@ periodToDotNode prd =
 groupToDotNode :: Vector Ngrams -> PhyloGroup -> Dot DotId
 groupToDotNode fdt g = 
     node (groupIdToDotId $ getGroupId g)
-                     ([FontName "Arial", Shape BoxShape, toLabel (groupToTable fdt 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))
@@ -141,7 +145,7 @@ groupToDotNode fdt g =
 toDotEdge :: DotId -> DotId -> Text.Text -> EdgeType -> Dot DotId
 toDotEdge source target lbl edgeType = edge source target
     (case edgeType of
-        GroupToGroup   -> [ Width 10, Color [toWColor Black], Constraint True
+        GroupToGroup   -> [ Width 3, penWidth 4, Color [toWColor Black], Constraint True
                           , Label (StrLabel $ fromStrict lbl)]
         BranchToGroup  -> [ Width 3, Color [toWColor Black], ArrowHead (AType [(ArrMod FilledArrow RightSide,DotArrow)])
                           , Label (StrLabel $ fromStrict lbl)]
@@ -174,12 +178,9 @@ exportToDot phylo export =
                   <> [(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 "proxiName") $ pack $ show (getProximityName $ phyloProximity $ getConfig phylo))
-                     ,(toAttr (fromStrict "proxiInit") $ pack $ show (getProximityInit $ phyloProximity $ getConfig phylo))
-                     ,(toAttr (fromStrict "proxiStep") $ pack $ show (getProximityStep $ phyloProximity $ getConfig phylo))
-                     ,(toAttr (fromStrict "quaGranularity") $ pack $ show (_qua_granularity $ phyloQuality $ getConfig phylo))
                      ])
 
 
@@ -232,12 +233,12 @@ exportToDot phylo export =
             ) $ 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
+        -- _ <- 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]
@@ -418,8 +419,8 @@ processLabels labels foundations export =
 
 
 toDynamics :: Int -> [PhyloGroup] -> PhyloGroup -> Map Int (Date,Date) -> Double
-toDynamics n parents group m = 
-    let prd = group ^. phylo_groupPeriod
+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
@@ -467,15 +468,38 @@ toPhyloExport phylo = exportToDot phylo
                     $ processMetrics  export           
     where
         export :: PhyloExport
-        export = PhyloExport groups branches
+        export = PhyloExport groups
+               $ map (\(x,b) -> b & branch_x .~ x)
+               $ zip branchesGaps branches
+        --------------------------------------
+        branchesGaps :: [Double]
+        branchesGaps = 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) []
+                                         in (b' ^. branch_seaLevel) !! (idx - 1)
+                                        ) $ listToSeq branches))
         --------------------------------------
         branches :: [PhyloBranch]
-        branches = map (\bId -> PhyloBranch bId "" empty) $ nub $ map _phylo_groupBranchId groups
+        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 trace (show(canonId)) $ PhyloBranch (g ^. phylo_groupBranchId) 
+                                      canonId
+                                      seaLvl
+                                      0 
+                                      (last' "export" (take (round $ (last' "export" breaks) + 1) seaLvl))
+                                      "" 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
-               $ map (\g -> g & phylo_groupMeta %~ delete "dynamics")
                $ getGroupsFromLevel (phyloLevel $ getConfig phylo)
                $ tracePhyloInfo phylo
 

src/Gargantext/Viz/Phylo/PhyloMaker.hs

@@ -15,15 +15,15 @@ Portability : POSIX
 
 module Gargantext.Viz.Phylo.PhyloMaker where
 
-import Data.List (concat, nub, partition, sort, (++), group)
-import Data.Map (Map, fromListWith, keys, unionWith, fromList, empty, toList, elems, (!), restrictKeys, singleton)
+import Data.List (concat, nub, partition, sort, (++), group, intersect, null)
+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 (temporalMatching)
+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(..))
@@ -43,7 +43,8 @@ import qualified Data.Set as Set
 
 
 toPhylo :: [Document] -> TermList -> Config -> Phylo
-toPhylo docs lst conf = traceToPhylo (phyloLevel conf) $
+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 
@@ -62,8 +63,35 @@ toPhylo docs lst conf = traceToPhylo (phyloLevel conf) $
 -- | To Phylo 1 | --
 --------------------
 
-
-appendGroups :: (a -> Double -> PhyloPeriodId -> Level -> Int -> Vector Ngrams -> [Cooc] -> PhyloGroup) -> Level -> Map (Date,Date) [a] -> Phylo -> Phylo
+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
@@ -76,7 +104,7 @@ appendGroups f lvl m phylo =  trace ("\n" <> "-- | Append " <> show (length $ co
                             in  phyloLvl 
                               & phylo_levelGroups .~ (fromList $ foldl (\groups obj ->
                                     groups ++ [ (((pId,lvl),length groups)
-                                              , f obj(getPhyloThresholdInit phylo) pId lvl (length groups) (getRoots phylo) 
+                                              , f obj pId lvl (length groups) (getRoots phylo) 
                                                   (elems $ restrictKeys (phylo ^. phylo_timeCooc) $ periodsToYears [pId]))
                                               ] ) [] phyloCUnit)
                          else 
@@ -84,20 +112,25 @@ appendGroups f lvl m phylo =  trace ("\n" <> "-- | Append " <> show (length $ co
            phylo  
 
 
-cliqueToGroup :: PhyloClique -> Double -> PhyloPeriodId -> Level ->  Int -> Vector Ngrams -> [Cooc] -> PhyloGroup
-cliqueToGroup fis thr pId lvl idx fdt coocs =
+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])
-                   (singleton "thr" [thr])
+                   (fromList [("breaks",[0]),("seaLevels",[0])])
                    [] [] [] []
 
 
 toPhylo1 :: [Document] -> Phylo -> Phylo
-toPhylo1 docs phyloBase = temporalMatching
+toPhylo1 docs phyloBase = case (getSeaElevation phyloBase) of 
+    Constante start gap -> constanteTemporalMatching  start gap 
+                   $ toGroupsProxi 1
+                   $ appendGroups cliqueToGroup 1 phyloClique phyloBase    
+    Adaptative steps    -> adaptativeTemporalMatching steps
+                   $ toGroupsProxi 1
                    $ appendGroups cliqueToGroup 1 phyloClique phyloBase
     where
         --------------------------------------
@@ -247,5 +280,6 @@ toPhyloBase docs lst conf =
                (docsToTimeScaleCooc docs (foundations ^. foundations_roots))
                (docsToTimeScaleNb docs)
                (docsToTermFreq docs (foundations ^. foundations_roots))
+               empty
                params
                (fromList $ map (\prd -> (prd, PhyloPeriod prd (initPhyloLevels 1 prd))) periods)

src/Gargantext/Viz/Phylo/PhyloTools.hs

@@ -34,6 +34,7 @@ import Control.Lens hiding (Level)
 import qualified Data.Vector as Vector
 import qualified Data.List as List
 import qualified Data.Set as Set
+import qualified Data.Map as Map
 
 ------------
 -- | Io | --
@@ -66,6 +67,7 @@ roundToStr = printf "%0.*f"
 countSup :: Double -> [Double] -> Int
 countSup s l = length $ filter (>s) l
 
+
 dropByIdx :: Int -> [a] -> [a]
 dropByIdx k l = take k l ++ drop (k+1) l
 
@@ -76,6 +78,15 @@ elemIndex' e l = case (List.elemIndex e l) of
     Just i  -> i
 
 
+commonPrefix :: Eq a => [a] -> [a] -> [a] -> [a]
+commonPrefix lst lst' acc =
+    if (null lst || null lst')
+        then acc
+        else if (head' "commonPrefix" lst == head' "commonPrefix" lst')
+                then commonPrefix (tail lst) (tail lst') (acc ++ [head' "commonPrefix" lst])
+                else acc
+
+
 ---------------------
 -- | Foundations | --
 ---------------------
@@ -249,7 +260,7 @@ idToPrd :: PhyloGroupId -> PhyloPeriodId
 idToPrd id = (fst . fst) id
 
 getGroupThr :: PhyloGroup -> Double
-getGroupThr group = head' "getGroupThr" ((group ^. phylo_groupMeta) ! "thr")
+getGroupThr group = last' "getGroupThr" ((group ^. phylo_groupMeta) ! "breaks")
 
 groupByField :: Ord a => (PhyloGroup -> a) -> [PhyloGroup] ->  Map a [PhyloGroup]
 groupByField toField groups = fromListWith (++) $ map (\g -> (toField g, [g])) groups
@@ -263,28 +274,15 @@ getPeriodPointers fil group =
 filterProximity :: Proximity -> Double -> Double -> Bool
 filterProximity proximity thr local = 
     case proximity of
-        WeightedLogJaccard _ _ _ -> local >= thr
+        WeightedLogJaccard _ -> local >= thr
         Hamming -> undefined   
 
 getProximityName :: Proximity -> String
 getProximityName proximity =
     case proximity of
-        WeightedLogJaccard _ _ _ -> "WLJaccard"
+        WeightedLogJaccard _ -> "WLJaccard"
         Hamming -> "Hamming"            
 
-getProximityInit :: Proximity -> Double
-getProximityInit proximity =
-    case proximity of
-        WeightedLogJaccard _ i _ -> i
-        Hamming -> undefined  
-
-
-getProximityStep :: Proximity -> Double
-getProximityStep proximity =
-    case proximity of
-        WeightedLogJaccard _ _ s -> s
-        Hamming -> undefined               
-
 ---------------
 -- | Phylo | --
 ---------------
@@ -318,13 +316,8 @@ getLevels phylo = nub
                        .  traverse
                        . phylo_periodLevels ) phylo
 
-
-getPhyloThresholdInit :: Phylo -> Double
-getPhyloThresholdInit phylo = getThresholdInit (phyloProximity (getConfig phylo))
-
-
-getPhyloThresholdStep :: Phylo -> Double
-getPhyloThresholdStep phylo = getThresholdStep (phyloProximity (getConfig phylo))
+getSeaElevation :: Phylo -> SeaElevation
+getSeaElevation phylo = seaElevation (getConfig phylo)
 
 
 getConfig :: Phylo -> Config
@@ -350,6 +343,26 @@ getGroupsFromLevel lvl phylo =
                  . phylo_levelGroups ) phylo
 
 
+getGroupsFromLevelPeriods :: Level -> [PhyloPeriodId] -> Phylo -> [PhyloGroup]
+getGroupsFromLevelPeriods lvl periods phylo = 
+    elems $ view ( phylo_periods
+                 .  traverse
+                 .  filtered (\phyloPrd -> elem (phyloPrd ^. phylo_periodPeriod) periods)
+                 . phylo_periodLevels
+                 .  traverse
+                 .  filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == lvl)
+                 . phylo_levelGroups ) phylo    
+
+
+getGroupsFromPeriods :: Level -> Map PhyloPeriodId PhyloPeriod -> [PhyloGroup]
+getGroupsFromPeriods lvl periods = 
+    elems $ view (  traverse
+                 . phylo_periodLevels
+                 .  traverse
+                 .  filtered (\phyloLvl -> phyloLvl ^. phylo_levelLevel == lvl)
+                 . phylo_levelGroups ) periods
+
+
 updatePhyloGroups :: Level -> Map PhyloGroupId PhyloGroup -> Phylo -> Phylo
 updatePhyloGroups lvl m phylo = 
     over ( phylo_periods
@@ -407,27 +420,7 @@ traceSynchronyStart phylo =
 
 getSensibility :: Proximity -> Double
 getSensibility proxi = case proxi of 
-    WeightedLogJaccard s _ _ -> s
-    Hamming -> undefined
-
-getThresholdInit :: Proximity -> Double
-getThresholdInit proxi = case proxi of 
-    WeightedLogJaccard _ t _ -> t
-    Hamming -> undefined  
-
-getThresholdStep :: Proximity -> Double
-getThresholdStep proxi = case proxi of 
-    WeightedLogJaccard _ _ s -> s
-    Hamming -> undefined  
-
-
-traceBranchMatching :: Proximity -> Double -> [PhyloGroup] -> [PhyloGroup]
-traceBranchMatching proxi thr groups = case proxi of 
-    WeightedLogJaccard _ i s -> trace (
-            roundToStr 2 thr <> " "
-         <> foldl (\acc _ -> acc <> ".") "." [(10*i),(10*i + 10*s)..(10*thr)]
-         <> " " <>  show(length groups) <> " groups"
-        ) groups 
+    WeightedLogJaccard s -> s
     Hamming -> undefined
 
 ----------------
@@ -495,3 +488,8 @@ traceMatchEnd groups =
 traceTemporalMatching :: [PhyloGroup] -> [PhyloGroup]
 traceTemporalMatching groups = 
     trace ( "\n" <> "-- | Start temporal matching for " <> show(length groups) <> " groups" <> "\n") groups
+
+
+traceGroupsProxi :: Map (PhyloGroupId,PhyloGroupId) Double -> Map (PhyloGroupId,PhyloGroupId) Double
+traceGroupsProxi m = 
+    trace ( "\n" <> "-- | " <> show(Map.size m) <> " computed pairs of groups proximity" <> "\n") m
\ No newline at end of file

src/Gargantext/Viz/Phylo/SynchronicClustering.hs

@@ -21,8 +21,9 @@ 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 Data.List ((++), null, intersect, nub, concat, sort, sortOn, all, groupBy, group, maximum)
+import Data.Map  (Map, fromList, fromListWith, foldlWithKey, (!), insert, empty, restrictKeys, elems, mapWithKey, member)
+import Data.Text (Text)
 
 import Control.Lens hiding (Level)
 import Control.Parallel.Strategies (parList, rdeepseq, using)
@@ -37,7 +38,7 @@ import qualified Data.Set as Set
 -------------------------
 
 mergeBranchIds :: [[Int]] -> [Int]
-mergeBranchIds ids = (head' "mergeBranchIds" . sort . mostFreq) ids
+mergeBranchIds ids = (head' "mergeBranchIds" . sort . mostFreq') ids
   where
     -- | 2) find the most Up Left ids in the hierarchy of similarity
     -- mostUpLeft :: [[Int]] -> [[Int]]
@@ -46,13 +47,19 @@ mergeBranchIds ids = (head' "mergeBranchIds" . sort . mostFreq) 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' = 
+    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
 
 
+mergeMeta :: [Int] -> [PhyloGroup] -> Map Text [Double]
+mergeMeta bId groups = 
+  let ego = head' "mergeMeta" $ filter (\g -> (snd (g ^. phylo_groupBranchId)) == bId) groups  
+   in fromList [("breaks",(ego ^. phylo_groupMeta) ! "breaks"),("seaLevels",(ego ^. phylo_groupMeta) ! "seaLevels")]     
+
+
 groupsToBranches' :: Map PhyloGroupId PhyloGroup -> [[PhyloGroup]]
 groupsToBranches' groups =
     -- | run the related component algorithm
@@ -64,10 +71,8 @@ groupsToBranches' groups =
     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
+         in map (\g -> g & phylo_groupBranchId %~ (\(lvl,_) -> (lvl,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 = 
@@ -75,11 +80,15 @@ mergeGroups coocs id mapIds 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)
+                  ((snd $ fst id),bId)
+                  (mergeMeta bId childs) [] (map (\g -> (getGroupId g, 1)) childs)
                   (updatePointers $ concat $ map _phylo_groupPeriodParents childs)
                   (updatePointers $ concat $ map _phylo_groupPeriodChilds  childs)
     where
+        --------------------
+        bId :: [Int]
+        bId = mergeBranchIds $ map (\g -> snd $ g ^. phylo_groupBranchId) childs
+        --------------------
         updatePointers :: [Pointer] -> [Pointer]
         updatePointers pointers = map (\(pId,w) -> (mapIds ! pId,w)) pointers
 
@@ -163,7 +172,7 @@ groupsToEdges prox sync nbDocs diago groups =
         toEdges :: Double -> [(PhyloGroup,PhyloGroup)] -> [((PhyloGroup,PhyloGroup),Double)]
         toEdges sens edges = 
             case prox of
-                WeightedLogJaccard _ _ _ -> map (\(g,g') -> 
+                WeightedLogJaccard _ -> map (\(g,g') -> 
                                                      ((g,g'), weightedLogJaccard' sens nbDocs diago
                                                                   (g ^. phylo_groupNgrams) (g' ^. phylo_groupNgrams))) edges
                 _ -> undefined  
@@ -198,21 +207,13 @@ reduceGroups prox sync docs diagos branch =
               $ 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 
+adjustClustering :: Synchrony -> [[PhyloGroup]] -> [[PhyloGroup]]
+adjustClustering sync branches = case sync of
+  ByProximityThreshold _ _ scope _ -> case scope of 
       SingleBranch -> branches
-      SiblingBranches -> groupBy (\g g' -> (init $ getGroupRealBId step g) == (init $ getGroupRealBId step g'))
+      SiblingBranches -> groupBy (\g g' -> (last' "adjustClustering" $ (g  ^. phylo_groupMeta) ! "breaks") 
+                                        == (last' "adjustClustering" $ (g' ^. phylo_groupMeta) ! "breaks"))
                        $ sortOn _phylo_groupBranchId $ concat branches
-      -- SiblingBranches -> elems $ fromListWith (++) $ map (\b -> ((init . snd . _phylo_groupBranchId) $ head' "adjustClustering" b,b)) branches
       AllBranches -> [concat branches]
   ByProximityDistribution _ _ -> branches
 
@@ -226,7 +227,7 @@ synchronicClustering phylo =
         diagos = map coocToDiago $ phylo ^. phylo_timeCooc
         newBranches  = map (\branch -> reduceGroups prox sync docs diagos branch) 
                      $ map processDynamics
-                     $ adjustClustering sync (getPhyloThresholdStep phylo)
+                     $ adjustClustering sync
                      $ phyloToLastBranches 
                      $ traceSynchronyStart phylo
         newBranches' = newBranches `using` parList rdeepseq