add the mecanisms for filtering the FIS if needed

src/Gargantext/Viz/Phylo.hs

@@ -201,8 +201,11 @@ 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) 
-type PhyloFis = (Clique,Support)
-
+data PhyloFis = PhyloFis 
+  { _phyloFis_clique  :: Clique
+  , _phyloFis_support :: Support
+  , _phyloFis_metrics :: Map (Int,Int) (Map Text [Double]) 
+  } deriving (Show)
 
 -- | A list of clustered PhyloGroup 
 type PhyloCluster = [PhyloGroup]
@@ -239,8 +242,7 @@ data Cluster = Fis FisParams
 
 -- | Parameters for Fis clustering
 data FisParams = FisParams
-  { _fis_filtered     :: Bool
-  , _fis_keepMinorFis :: Bool
+  { _fis_keepMinorFis :: Bool
   , _fis_minSupport   :: Support 
   } deriving (Show)
 
@@ -334,6 +336,8 @@ data PhyloQuery = PhyloQuery
     
     -- Clustering method for building the contextual unit of Phylo (ie: level 1) 
     , _q_contextualUnit :: Cluster
+    , _q_contextualUnitMetrics :: [Metric]
+    , _q_contextualUnitFilters :: [Filter]    
     
     -- Inter-temporal matching method of the Phylo
     , _q_interTemporalMatching :: Proximity
@@ -438,6 +442,7 @@ makeLenses ''PhyloPeaks
 makeLenses ''PhyloGroup
 makeLenses ''PhyloLevel
 makeLenses ''PhyloPeriod
+makeLenses ''PhyloFis
 -- 
 makeLenses ''Proximity
 makeLenses ''Cluster
@@ -463,10 +468,13 @@ $(deriveJSON defaultOptions ''Tree  )
 $(deriveJSON (unPrefix "_phylo_period" ) ''PhyloPeriod )
 $(deriveJSON (unPrefix "_phylo_level"  ) ''PhyloLevel  )
 $(deriveJSON (unPrefix "_phylo_group"  ) ''PhyloGroup  )
+$(deriveJSON (unPrefix "_phyloFis_"    ) ''PhyloFis    )
 -- 
 $(deriveJSON (unPrefix "_software_"    ) ''Software    )
 $(deriveJSON (unPrefix "_phyloParam_"  ) ''PhyloParam  )
 --
+$(deriveJSON defaultOptions ''Filter    )
+$(deriveJSON defaultOptions ''Metric    )
 $(deriveJSON defaultOptions ''Cluster   )
 $(deriveJSON defaultOptions ''Proximity )
 --
@@ -475,6 +483,7 @@ $(deriveJSON (unPrefix "_hamming_" ) ''HammingParams )
 $(deriveJSON (unPrefix "_louvain_" ) ''LouvainParams )
 $(deriveJSON (unPrefix "_rc_" )      ''RCParams      )
 $(deriveJSON (unPrefix "_wlj_" )     ''WLJParams     )
+$(deriveJSON (unPrefix "_sb_" )      ''SBParams      )
 --
 $(deriveJSON (unPrefix "_q_" ) ''PhyloQuery )
 

src/Gargantext/Viz/Phylo/Aggregates/Cooc.hs

@@ -37,15 +37,15 @@ fisToCooc :: Map (Date, Date) [PhyloFis] -> Phylo -> Map (Int, Int) Double
 fisToCooc m p = map   (/docs)
               $ foldl (\mem x -> adjust (+1) (getKeyPair x mem) mem) cooc
               $ concat
-              $ map (\x -> listToUnDirectedCombiWith (\x -> getIdxInPeaks x p) $ (Set.toList . fst) x) 
+              $ map (\x -> listToUnDirectedCombiWith (\x -> getIdxInPeaks x p) $ (Set.toList . getClique) x) 
               $ (concat . elems) m
   where
     --------------------------------------
     fisNgrams :: [Ngrams]
-    fisNgrams = foldl (\mem x -> union mem $ (Set.toList . fst) x) [] $ (concat . elems) m
+    fisNgrams = foldl (\mem x -> union mem $ (Set.toList . getClique) x) [] $ (concat . elems) m
     --------------------------------------
     docs :: Double
-    docs = fromIntegral $ foldl (\mem x -> mem + (snd x)) 0 $ (concat . elems) m
+    docs = fromIntegral $ foldl (\mem x -> mem + (getSupport x)) 0 $ (concat . elems) m
     --------------------------------------
     cooc :: Map (Int, Int) (Double)
     cooc = Map.fromList $ map (\x -> (x,0)) (listToUnDirectedCombiWith (\x -> getIdxInPeaks x p) fisNgrams)

src/Gargantext/Viz/Phylo/Aggregates/Fis.hs

@@ -17,8 +17,8 @@ Portability : POSIX
 module Gargantext.Viz.Phylo.Aggregates.Fis
   where
 
-import Data.List        (last,head)
-import Data.Map         (Map)
+import Data.List        (last,head,null)
+import Data.Map         (Map, empty)
 import Data.Text        (Text, unwords, toLower, words)
 import Data.Tuple       (fst, snd)
 import Data.Tuple.Extra
@@ -44,16 +44,39 @@ filterFisBySupport keep min m = case keep of
 
 -- | To filter Fis with small Support, to preserve nonempty periods please use : filterFisBySupport true
 filterMinorFis :: Int -> [PhyloFis] -> [PhyloFis]
-filterMinorFis min l = filter (\fis -> snd fis > min) l
+filterMinorFis min l = filter (\fis -> getSupport fis > min) l
 
 
 -- | To filter nested Fis 
 filterFisByNested :: Map (Date, Date) [PhyloFis] -> Map (Date, Date) [PhyloFis]
-filterFisByNested = map (\l -> let cliqueMax = filterNestedSets (head $ map fst l) (map fst l) []
-                               in  filter (\fis -> elem (fst fis) cliqueMax) l)
+filterFisByNested = map (\l -> let cliqueMax = filterNestedSets (head $ map getClique l) (map getClique l) []
+                               in  filter (\fis -> elem (getClique fis) cliqueMax) l)
 
 
 -- | To transform a list of Documents into a Frequent Items Set 
 docsToFis :: Map (Date, Date) [Document] -> Map (Date, Date) [PhyloFis]
-docsToFis docs = map (\d -> Map.toList 
-                          $ fisWithSizePolyMap (Segment 1 20) 1 (map text d)) docs
+docsToFis docs = map (\d -> let fs = Map.toList $ fisWithSizePolyMap (Segment 1 20) 1 (map text d)
+                            in map (\f -> PhyloFis (fst f) (snd f) empty) fs) docs
\ No newline at end of file
+
+
+-- | To process a list of Filters on top of the PhyloFis
+processFilters :: [Filter] -> Map (Date, Date) [PhyloFis] -> Map (Date, Date) [PhyloFis]
+processFilters filters phyloFis
+  | null filters = phyloFis
+  | otherwise    = panic "[ERR][Viz.Phylo.LevelMaker.processFilters] please add some filters for the Fis"
+
+
+-- | To process a list of Metrics on top of the PhyloFis
+processMetrics :: [Metric] -> Map (Date, Date) [PhyloFis] -> Map (Date, Date) [PhyloFis]
+processMetrics metrics phyloFis
+  | null metrics = phyloFis
+  | otherwise    = panic "[ERR][Viz.Phylo.LevelMaker.processMetrics] please add some metrics for the Fis"
+
+
+-- | To transform some Documents into PhyloFis and apply a List of Metrics and Filters
+toPhyloFis :: Map (Date, Date) [Document] -> Bool -> Support -> [Metric] -> [Filter] -> Map (Date, Date) [PhyloFis]
+toPhyloFis ds k s ms fs = processFilters fs  
+                        $ processMetrics ms
+                        $ filterFisByNested 
+                        $ filterFisBySupport k s
+                        $ docsToFis ds  
\ No newline at end of file

src/Gargantext/Viz/Phylo/Example.hs

@@ -123,7 +123,7 @@ queryEx = "title=Cesar et Cleôpatre"
 
 phyloQuery :: PhyloQuery
 phyloQuery = PhyloQuery "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)"
-             5 3 defaultFis defaultWeightedLogJaccard 3 defaultRelatedComponents
+             5 3 defaultFis [] [] defaultWeightedLogJaccard 3 defaultRelatedComponents
 
 
 
@@ -221,7 +221,7 @@ phylo1 =  addPhyloLevel (1) phyloFis phylo
 
 
 phyloFis :: Map (Date, Date) [PhyloFis]
-phyloFis = filterFisBySupport False 1 (filterFisByNested (docsToFis phyloDocs))
+phyloFis = filterFisByNested $ filterFisBySupport False 1 (docsToFis phyloDocs)
 
 
 ----------------------------------------

src/Gargantext/Viz/Phylo/LevelMaker.hs

@@ -111,15 +111,15 @@ clusterToGroup prd lvl idx lbl groups m p =
 
 
 -- | To transform a Clique into a PhyloGroup
-cliqueToGroup :: PhyloPeriodId -> Level -> Int -> Text -> (Clique,Support) -> Map (Date, Date) [PhyloFis] -> Phylo -> PhyloGroup
+cliqueToGroup :: PhyloPeriodId -> Level -> Int -> Text -> PhyloFis -> Map (Date, Date) [PhyloFis] -> Phylo -> PhyloGroup
 cliqueToGroup prd lvl idx lbl fis m p = 
-    PhyloGroup ((prd, lvl), idx) lbl ngrams (singleton "support" (fromIntegral $ snd fis)) cooc Nothing [] [] [] []
+    PhyloGroup ((prd, lvl), idx) lbl ngrams (singleton "support" (fromIntegral $ getSupport fis)) cooc Nothing [] [] [] []
       where
         --------------------------------------
         ngrams :: [Int]
         ngrams = sort $ map (\x -> getIdxInPeaks x p)
                       $ Set.toList
-                      $ fst fis
+                      $ getClique fis
         --------------------------------------
         cooc :: Map (Int, Int) Double 
         cooc =  filterWithKey (\k _ -> elem (fst k) ngrams && elem (snd k) ngrams) 
@@ -163,23 +163,21 @@ toNthLevel lvlMax prox clus p
 
 
 -- | To reconstruct the Level 1 of a Phylo based on a Clustering Method
-toPhylo1 :: Cluster -> Proximity -> Map (Date, Date) [Document] -> Phylo -> Phylo
-toPhylo1 clus prox d p = case clus of 
-  Fis (FisParams f k s) -> setPhyloBranches 1
-                            $ interTempoMatching Descendant 1 prox
-                            $ interTempoMatching Ascendant 1 prox
-                            $ setLevelLinks (0,1)
-                            $ setLevelLinks (1,0)
-                            $ addPhyloLevel 1 phyloFis p
-    where 
+toPhylo1 :: Cluster -> Proximity -> [Metric] -> [Filter] -> Map (Date, Date) [Document] -> Phylo -> Phylo
+toPhylo1 clus prox metrics filters d p = case clus of 
+  Fis (FisParams k s) -> setPhyloBranches 1
+                       $ interTempoMatching Descendant 1 prox
+                       $ interTempoMatching Ascendant 1 prox
+                       $ setLevelLinks (0,1)
+                       $ setLevelLinks (1,0)
+                       $ addPhyloLevel 1 phyloFis p
+    where
       --------------------------------------
       phyloFis :: Map (Date, Date) [PhyloFis]
-      phyloFis = if f
-                 then filterFisBySupport k s (filterFisByNested (docsToFis d))
-                 else docsToFis d
+      phyloFis = toPhyloFis d k s metrics filters 
       --------------------------------------
 
-  _   -> panic "[ERR][Viz.Phylo.PhyloMaker.toPhylo1] fst clustering not recognized"
+  _   -> panic "[ERR][Viz.Phylo.LevelMaker.toPhylo1] fst clustering not recognized"
 
 
 -- | To reconstruct the Level 0 of a Phylo
@@ -210,7 +208,7 @@ toPhylo q c a ts = toNthLevel (getNthLevel q) (getInterTemporalMatching q) (getN
   where
     --------------------------------------
     phylo1 :: Phylo
-    phylo1 = toPhylo1 (getFstCluster q) (getInterTemporalMatching q) phyloDocs phylo0    
+    phylo1 = toPhylo1 (getContextualUnit q) (getInterTemporalMatching q) (getContextualUnitMetrics q) (getContextualUnitFilters q) phyloDocs phylo0    
     --------------------------------------
     phylo0 :: Phylo
     phylo0 = toPhylo0 phyloDocs phyloBase

src/Gargantext/Viz/Phylo/Tools.hs

@@ -451,6 +451,24 @@ setPhyloLevelId lvl' (PhyloLevel (id, lvl) groups)
             groups' = over (traverse . phylo_groupId) (\((period, lvl), idx) -> ((period, lvl'), idx)) groups 
 
 
+------------------
+-- | PhyloFis | --
+------------------
+
+
+-- | To get the clique of a PhyloFis
+getClique :: PhyloFis -> Clique
+getClique = _phyloFis_clique
+
+-- | To get the metrics of a PhyloFis
+getFisMetrics :: PhyloFis -> Map (Int,Int) (Map Text [Double])
+getFisMetrics = _phyloFis_metrics
+
+-- | To get the support of a PhyloFis
+getSupport :: PhyloFis -> Support
+getSupport = _phyloFis_support
+
+
 ----------------------------
 -- | PhyloNodes & Edges | --
 ----------------------------
@@ -558,9 +576,19 @@ getViewBranchIds v = map getBranchId $ v ^. phylo_viewBranches
 -- | PhyloQuery & QueryView | --
 --------------------------------
 
--- | To get the first clustering method to apply to get the level 1 of a Phylo
-getFstCluster :: PhyloQuery -> Cluster
-getFstCluster q = q ^. q_contextualUnit
+-- | To get the first clustering method to apply to get the contextual units of a Phylo
+getContextualUnit :: PhyloQuery -> Cluster
+getContextualUnit q = q ^. q_contextualUnit
+
+
+-- | To get the metrics to apply to contextual units
+getContextualUnitMetrics :: PhyloQuery -> [Metric]
+getContextualUnitMetrics q = q ^. q_contextualUnitMetrics
+
+
+-- | To get the filters to apply to contextual units
+getContextualUnitFilters :: PhyloQuery -> [Filter]
+getContextualUnitFilters q = q ^. q_contextualUnitFilters
 
 
 -- | To get the cluster methods to apply to the Nths levels of a Phylo
@@ -602,8 +630,8 @@ getProximity cluster = case cluster of
 
 
 -- | To initialize all the Cluster / Proximity with their default parameters
-initFis :: Maybe Bool -> Maybe Bool -> Maybe Support -> FisParams
-initFis (def True -> flt) (def True -> kmf) (def 1 -> min) = FisParams flt kmf min
+initFis :: Maybe Bool -> Maybe Support -> FisParams
+initFis (def True -> kmf) (def 1 -> min) = FisParams kmf min
 
 initHamming :: Maybe Double -> HammingParams
 initHamming (def 0.01 -> sens) = HammingParams sens
@@ -622,10 +650,10 @@ initWeightedLogJaccard (def 0 -> thr) (def 0.01 -> sens) = WLJParams thr sens
 
 
 -- | To initialize a PhyloQuery from given and default parameters
-initPhyloQuery :: Text -> Text -> Maybe Int -> Maybe Int -> Maybe Cluster -> Maybe Proximity -> Maybe Level -> Maybe Cluster -> PhyloQuery
-initPhyloQuery name desc (def 5 -> grain) (def 3 -> steps) (def defaultFis -> cluster)
+initPhyloQuery :: Text -> Text -> Maybe Int -> Maybe Int -> Maybe Cluster -> Maybe [Metric] -> Maybe [Filter] -> Maybe Proximity -> Maybe Level -> Maybe Cluster -> PhyloQuery
+initPhyloQuery name desc (def 5 -> grain) (def 3 -> steps) (def defaultFis -> cluster) (def [] -> metrics) (def [] -> filters)
   (def defaultWeightedLogJaccard -> matching) (def 2 -> nthLevel) (def defaultRelatedComponents -> nthCluster) =
-    PhyloQuery name desc grain steps cluster matching nthLevel nthCluster
+    PhyloQuery name desc grain steps cluster metrics filters matching nthLevel nthCluster
 
 
 -- | To initialize a PhyloQueryView default parameters
@@ -635,9 +663,6 @@ initPhyloQueryView (def 2 -> lvl) (def Descendant -> f) (def False -> c) (def 1
 
 
 -- | To define some obvious boolean getters
-shouldFilterFis :: FisParams -> Bool
-shouldFilterFis = _fis_filtered
-
 shouldKeepMinorFis :: FisParams -> Bool
 shouldKeepMinorFis = _fis_keepMinorFis
 
@@ -648,7 +673,7 @@ shouldKeepMinorFis = _fis_keepMinorFis
 -- Clusters
 
 defaultFis :: Cluster
-defaultFis = Fis (initFis Nothing Nothing Nothing)
+defaultFis = Fis (initFis Nothing Nothing)
 
 defaultLouvain :: Cluster
 defaultLouvain = Louvain (initLouvain Nothing)
@@ -678,7 +703,7 @@ defaultWeightedLogJaccard = WeightedLogJaccard (initWeightedLogJaccard Nothing N
 
 defaultQuery :: PhyloQuery
 defaultQuery = initPhyloQuery "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)" 
-                              Nothing Nothing Nothing Nothing Nothing Nothing
+                              Nothing Nothing Nothing Nothing Nothing Nothing Nothing Nothing
 
 defaultQueryView :: PhyloQueryView
 defaultQueryView = initPhyloQueryView Nothing Nothing Nothing Nothing Nothing Nothing Nothing Nothing Nothing Nothing