add the maxClique (in progress)

src/Gargantext/Viz/AdaptativePhylo.hs

@@ -88,12 +88,14 @@ data ContextualUnit =
       Fis 
       { _fis_support :: Int
       , _fis_size    :: Int }
+    | MaxClique
+      { _clique_size :: Int } 
       deriving (Show,Generic,Eq)      
 
 
 data Quality = 
-     Quality { _qua_relevance :: Double
-             , _qua_minBranch :: Int }
+     Quality { _qua_granularity :: Double
+             , _qua_minBranch   :: Int }
       deriving (Show,Generic,Eq)   
 
 
@@ -125,7 +127,7 @@ defaultConfig =
             , phyloLevel     = 2
             , phyloProximity = WeightedLogJaccard 10 0 0.1
             , phyloSynchrony = ByProximityDistribution 0
-            , phyloQuality   = Quality 10 3
+            , phyloQuality   = Quality 0 3
             , timeUnit       = Year 3 1 5
             , contextualUnit = Fis 1 5
             , exportLabel    = [BranchLabel MostInclusive 2, GroupLabel MostEmergentInclusive 2]
@@ -315,17 +317,13 @@ data PointerType = TemporalPointer | LevelPointer deriving (Generic, Show)
 -- | Frequent Item Set | --
 ---------------------------
 
--- | Clique : Set of ngrams cooccurring in the same Document
-type Clique   = Set Ngrams
-
 -- | Support : Number of Documents where a Clique occurs
 type Support  = Int
 
--- | Fis : Frequent Items Set (ie: the association between a Clique and a Support)
-data PhyloFis = PhyloFis
-  { _phyloFis_clique  :: Clique
-  , _phyloFis_support :: Support
-  , _phyloFis_period  :: (Date,Date)
+data PhyloCUnit = PhyloCUnit
+  { _phyloCUnit_nodes   :: Set Ngrams
+  , _phyloCUnit_support :: Support
+  , _phyloCUnit_period  :: (Date,Date)
   } deriving (Generic,NFData,Show,Eq)
 
 
@@ -378,7 +376,7 @@ makeLenses ''ContextualUnit
 makeLenses ''PhyloLabel
 makeLenses ''TimeUnit
 makeLenses ''PhyloFoundations
-makeLenses ''PhyloFis
+makeLenses ''PhyloCUnit
 makeLenses ''Phylo
 makeLenses ''PhyloPeriod
 makeLenses ''PhyloLevel

src/Gargantext/Viz/Phylo/PhyloExample.hs

@@ -62,8 +62,8 @@ phylo1 = temporalMatching
 ---------------------------------------------
 
 
-phyloFis :: Map (Date,Date) [PhyloFis]
-phyloFis = toPhyloFis docsByPeriods (getFisSupport $ contextualUnit config) (getFisSize $ contextualUnit config) 
+phyloFis :: Map (Date,Date) [PhyloCUnit]
+phyloFis = toPhyloFis docsByPeriods (getContextualUnitSupport $ contextualUnit config) (getContextualUnitSize $ contextualUnit config) 
 
 
 docsByPeriods :: Map (Date,Date) [Document]

src/Gargantext/Viz/Phylo/PhyloExport.hs

@@ -171,7 +171,7 @@ exportToDot phylo export =
                      ,(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 "quaFactor") $ pack $ show (_qua_relevance $ phyloQuality $ getConfig phylo))
+                     ,(toAttr (fromStrict "quaFactor") $ pack $ show (_qua_granularity $ phyloQuality $ getConfig phylo))
                      ])
 
 

src/Gargantext/Viz/Phylo/PhyloMaker.hs

@@ -72,23 +72,23 @@ appendGroups f lvl m phylo =  trace ("\n" <> "-- | Append " <> show (length $ co
            (\phyloLvl -> if lvl == (phyloLvl ^. phylo_levelLevel)
                          then
                             let pId = phyloLvl ^. phylo_levelPeriod
-                                phyloFis = m ! pId
+                                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]))
-                                              ] ) [] phyloFis)
+                                              ] ) [] phyloCUnit)
                          else 
                             phyloLvl )
            phylo  
 
 
-fisToGroup :: PhyloFis -> PhyloPeriodId -> Level ->  Int -> Vector Ngrams -> [Cooc] -> PhyloGroup
+fisToGroup :: PhyloCUnit -> PhyloPeriodId -> Level ->  Int -> Vector Ngrams -> [Cooc] -> PhyloGroup
 fisToGroup fis pId lvl idx fdt coocs =
-    let ngrams = ngramsToIdx (Set.toList $ fis ^. phyloFis_clique) fdt
+    let ngrams = ngramsToIdx (Set.toList $ fis ^. phyloCUnit_nodes) fdt
     in  PhyloGroup pId lvl idx ""
-                   (fis ^. phyloFis_support)
+                   (fis ^. phyloCUnit_support)
                    ngrams
                    (ngramsToCooc ngrams coocs)
                    (1,[0])
@@ -98,11 +98,13 @@ fisToGroup fis pId lvl idx fdt coocs =
 
 toPhylo1 :: [Document] -> Phylo -> Phylo
 toPhylo1 docs phyloBase = temporalMatching
-                        $ appendGroups fisToGroup 1 phyloFis phyloBase
+                        $ appendGroups fisToGroup 1 phyloCUnit phyloBase
     where
         --------------------------------------
-        phyloFis :: Map (Date,Date) [PhyloFis]
-        phyloFis =  toPhyloFis docs' (getFisSupport $ contextualUnit $ getConfig phyloBase) (getFisSize $ contextualUnit $ getConfig phyloBase)
+        phyloCUnit :: Map (Date,Date) [PhyloCUnit]
+        phyloCUnit =  case (contextualUnit $ getConfig phyloBase) of
+          Fis s s' ->  toPhyloFis docs' s s'
+          MaxClique _ -> undefined
         --------------------------------------
         docs' :: Map (Date,Date) [Document]
         docs' =  groupDocsByPeriod date (getPeriodIds phyloBase) docs
@@ -115,30 +117,30 @@ toPhylo1 docs phyloBase = temporalMatching
 
 
 -- | To apply a filter with the possibility of keeping some periods non empty (keep : True|False)
-filterFis :: Bool -> Int -> (Int -> [PhyloFis] -> [PhyloFis]) -> Map (Date, Date) [PhyloFis] -> Map (Date, Date) [PhyloFis]
+filterFis :: Bool -> Int -> (Int -> [PhyloCUnit] -> [PhyloCUnit]) -> Map (Date, Date) [PhyloCUnit] -> Map (Date, Date) [PhyloCUnit]
 filterFis 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
-filterFisBySupport :: Int -> [PhyloFis] -> [PhyloFis]
-filterFisBySupport thr l = filter (\fis -> (fis ^. phyloFis_support) >= thr) l
+filterFisBySupport :: Int -> [PhyloCUnit] -> [PhyloCUnit]
+filterFisBySupport thr l = filter (\fis -> (fis ^. phyloCUnit_support) >= thr) l
 
 
 -- | To filter Fis with small Clique size
-filterFisByClique :: Int -> [PhyloFis] -> [PhyloFis]
-filterFisByClique thr l = filter (\fis -> (size $ fis ^. phyloFis_clique) >= thr) l
+filterFisByClique :: Int -> [PhyloCUnit] -> [PhyloCUnit]
+filterFisByClique thr l = filter (\fis -> (size $ fis ^. phyloCUnit_nodes) >= thr) l
 
 
 -- | To filter nested Fis
-filterFisByNested :: Map (Date, Date) [PhyloFis] -> Map (Date, Date) [PhyloFis]
+filterFisByNested :: Map (Date, Date) [PhyloCUnit] -> Map (Date, Date) [PhyloCUnit]
 filterFisByNested m = 
   let fis  = map (\l -> 
-                foldl (\mem f -> if (any (\f' -> isNested (Set.toList $ f' ^. phyloFis_clique) (Set.toList $ f ^. phyloFis_clique)) mem)
+                foldl (\mem f -> if (any (\f' -> isNested (Set.toList $ f' ^. phyloCUnit_nodes) (Set.toList $ f ^. phyloCUnit_nodes)) mem)
                                  then mem
                                  else 
-                                    let fMax = filter (\f' -> not $ isNested (Set.toList $ f ^. phyloFis_clique) (Set.toList $ f' ^. phyloFis_clique)) mem
+                                    let fMax = filter (\f' -> not $ isNested (Set.toList $ f ^. phyloCUnit_nodes) (Set.toList $ f' ^. phyloCUnit_nodes)) mem
                                     in  fMax ++ [f] ) [] l)
            $ elems m 
       fis' = fis `using` parList rdeepseq
@@ -146,7 +148,7 @@ filterFisByNested m =
 
 
 -- | To transform a time map of docs innto a time map of Fis with some filters
-toPhyloFis :: Map (Date, Date) [Document] -> Int -> Int -> Map (Date,Date) [PhyloFis]
+toPhyloFis :: Map (Date, Date) [Document] -> Int -> Int -> Map (Date,Date) [PhyloCUnit]
 toPhyloFis phyloDocs support clique = traceFis "Filtered Fis"
                 $ filterFisByNested 
                 $ traceFis "Filtered by clique size"
@@ -156,10 +158,10 @@ toPhyloFis phyloDocs support clique = traceFis "Filtered Fis"
                 $ traceFis "Unfiltered Fis" phyloFis
     where
         -------------------------------------- 
-        phyloFis :: Map (Date,Date) [PhyloFis]
+        phyloFis :: Map (Date,Date) [PhyloCUnit]
         phyloFis = 
             let fis  = map (\(prd,docs) -> let lst = toList $ fisWithSizePolyMap (Segment 1 20) 1 (map text docs)
-                                           in (prd, map (\f -> PhyloFis (fst f) (snd f) prd) lst))
+                                           in (prd, map (\f -> PhyloCUnit (fst f) (snd f) prd) lst))
                      $ toList phyloDocs
                 fis' = fis `using` parList rdeepseq
             in fromList fis'
@@ -209,9 +211,9 @@ groupDocsByPeriod f pds es =
 docsToTermFreq :: [Document] -> Vector Ngrams -> Map Int Double
 docsToTermFreq docs fdt =
   let nbDocs = fromIntegral $ length docs
-      freqs = map (/nbDocs)
+      freqs = map (/(log nbDocs))
              $ fromList
-             $ map (\lst -> (head' "docsToTermFreq" lst, fromIntegral $ length lst)) 
+             $ map (\lst -> (head' "docsToTermFreq" lst, log $ fromIntegral $ length lst)) 
              $ group $ sort $ concat $ map (\d -> nub $ ngramsToIdx (text d) fdt) docs
       sumFreqs = sum $ elems freqs
    in map (/sumFreqs) freqs

src/Gargantext/Viz/Phylo/PhyloTools.hs

@@ -162,28 +162,28 @@ keepFilled f thr l = if (null $ f thr l) && (not $ null l)
                      else f thr l
 
 
-traceClique :: Map (Date, Date) [PhyloFis] -> String
+traceClique :: Map (Date, Date) [PhyloCUnit] -> String
 traceClique mFis = foldl (\msg cpt -> msg <> show (countSup cpt cliques) <> " (>" <> show (cpt) <> ") "  ) "" [1..6]
     where
         --------------------------------------
         cliques :: [Double]
-        cliques = sort $ map (fromIntegral . size . _phyloFis_clique) $ concat $ elems mFis
+        cliques = sort $ map (fromIntegral . size . _phyloCUnit_nodes) $ concat $ elems mFis
         -------------------------------------- 
 
 
-traceSupport :: Map (Date, Date) [PhyloFis] -> String
+traceSupport :: Map (Date, Date) [PhyloCUnit] -> String
 traceSupport mFis = foldl (\msg cpt -> msg <> show (countSup cpt supports) <> " (>" <> show (cpt) <> ") "  ) "" [1..6]
     where
         --------------------------------------
         supports :: [Double]
-        supports = sort $ map (fromIntegral . _phyloFis_support) $ concat $ elems mFis
+        supports = sort $ map (fromIntegral . _phyloCUnit_support) $ concat $ elems mFis
         -------------------------------------- 
 
 
-traceFis :: [Char] -> Map (Date, Date) [PhyloFis] -> Map (Date, Date) [PhyloFis]
+traceFis :: [Char] -> Map (Date, Date) [PhyloCUnit] -> Map (Date, Date) [PhyloCUnit]
 traceFis msg mFis = trace ( "\n" <> "-- | " <> msg <> " : " <> show (sum $ map length $ elems mFis) <> "\n"
                          <> "Support : " <> (traceSupport mFis) <> "\n"
-                         <> "Clique : "  <> (traceClique mFis)  <> "\n" ) mFis
+                         <> "Nb Ngrams : "  <> (traceClique mFis)  <> "\n" ) mFis
 
 
 -------------------------
@@ -191,15 +191,15 @@ traceFis msg mFis = trace ( "\n" <> "-- | " <> msg <> " : " <> show (sum $ map l
 -------------------------
 
 
-getFisSupport :: ContextualUnit -> Int
-getFisSupport unit = case unit of 
+getContextualUnitSupport :: ContextualUnit -> Int
+getContextualUnitSupport unit = case unit of 
     Fis s _ -> s
-    -- _       -> panic ("[ERR][Viz.Phylo.PhyloTools.getFisSupport] Only Fis has a support")
+    MaxClique _ -> 0
 
-getFisSize :: ContextualUnit -> Int
-getFisSize unit = case unit of 
+getContextualUnitSize :: ContextualUnit -> Int
+getContextualUnitSize unit = case unit of 
     Fis _ s -> s
-    -- _       -> panic ("[ERR][Viz.Phylo.PhyloTools.getFisSupport] Only Fis has a clique size")  
+    MaxClique s -> s
 
 
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