to the level 1

src/Gargantext/Viz/AdaptativePhylo.hs

@@ -172,7 +172,7 @@ data Phylo =
            , _phylo_timeCooc    :: !(Map Date Cooc)
            , _phylo_timeDocs    :: !(Map Date Double)
            , _phylo_param       :: PhyloParam
-           , _phylo_periods     :: [PhyloPeriod]
+           , _phylo_periods     :: Map PhyloPeriodId PhyloPeriod
            }
            deriving (Generic, Show, Eq)
 
@@ -184,10 +184,9 @@ type PhyloPeriodId = (Date,Date)
 --  id: tuple (start date, end date) of the temporal step of the phylomemy
 --  levels: levels of granularity
 data PhyloPeriod =
-     PhyloPeriod { _phylo_periodId     :: PhyloPeriodId
-                 , _phylo_periodLevels :: [PhyloLevel]
-                 }
-                 deriving (Generic, Show, Eq)   
+     PhyloPeriod { _phylo_periodPeriod :: (Date,Date)
+                 , _phylo_periodLevels :: Map PhyloLevelId PhyloLevel
+                 } deriving (Generic, Show, Eq)   
 
 
 -- | Level : a level of clustering
@@ -202,26 +201,41 @@ type PhyloLevelId  = (PhyloPeriodId,Level)
 -- Level 1: First level of clustering (the Fis)
 -- Level [2..N]: Nth level of synchronic clustering (cluster of Fis)
 data PhyloLevel =
-     PhyloLevel { _phylo_levelId     :: PhyloLevelId
-                , _phylo_levelGroups :: [PhyloGroup]
-                }
+     PhyloLevel { _phylo_levelPeriod :: (Date,Date)
+                , _phylo_levelLevel  :: Level 
+                , _phylo_levelGroups :: Map PhyloGroupId PhyloGroup
+                } 
                 deriving (Generic, Show, Eq)   
 
 
---------------------
--- | PhyloGroup | --
--------------------- 
-
+type PhyloGroupId  = (PhyloLevelId, Int)
 
-type Index = Int
-type PhyloGroupId  = (PhyloLevelId, Index)
+-- | BranchId : (a level, a sequence of branch index)
+-- the sequence is a path of heritage from the most to the less specific branch
+type PhyloBranchId = (Level, [Int])
 
 -- | PhyloGroup : group of ngrams at each level and period
 data PhyloGroup = 
-      PhyloGroup { _phylo_groupId :: PhyloGroupId
+      PhyloGroup { _phylo_groupPeriod   :: (Date,Date)
+                 , _phylo_groupLevel    :: Level
+                 , _phylo_groupIndex    :: Int
+                 , _phylo_groupSupport  :: Support
+                 , _phylo_groupNgrams   :: [Int]
+                 , _phylo_groupBranchId :: PhyloBranchId
+                 , _phylo_groupLevelParents  :: [Pointer]
+                 , _phylo_groupLevelChilds   :: [Pointer]
+                 , _phylo_groupPeriodParents :: [Pointer]
+                 , _phylo_groupPeriodChilds  :: [Pointer]
+                 , _phylo_groupBreakPointer  :: Maybe Pointer
                  }
                  deriving (Generic, Show, Eq)
 
+-- | Weight : A generic mesure that can be associated with an Id
+type Weight = Double
+
+-- | Pointer : A weighted pointer to a given PhyloGroup
+type Pointer = (PhyloGroupId, Weight)                 
+
 
 ---------------------------
 -- | Frequent Item Set | --

src/Gargantext/Viz/Phylo/PhyloExample.hs

@@ -35,6 +35,14 @@ import Control.Lens
 import qualified Data.Vector as Vector
 
 
+-----------------------------------------------
+-- | STEP 3 | -- Build the Level 1 of the Phylo
+-----------------------------------------------
+
+phylo1 :: Phylo
+phylo1 = appendGroups fisToGroup 1 phyloFis phyloBase
+
+
 ---------------------------------------------
 -- | STEP 2 | -- Build the frequent items set
 ---------------------------------------------

src/Gargantext/Viz/Phylo/PhyloMaker.hs

@@ -16,7 +16,7 @@ Portability : POSIX
 module Gargantext.Viz.Phylo.PhyloMaker where
 
 import Data.List (concat, nub, partition, sort, (++))
-import Data.Map (Map, fromListWith, keys, unionWith, fromList, empty, mapWithKey, toList, elems)
+import Data.Map (Map, fromListWith, keys, unionWith, fromList, empty, toList, elems, (!))
 import Data.Set (size)
 import Data.Vector (Vector)
 
@@ -29,7 +29,7 @@ import Gargantext.Text.Metrics.FrequentItemSet (fisWithSizePolyMap, Size(..))
 import Control.DeepSeq (NFData)
 import Control.Parallel.Strategies (parList, rdeepseq, using)
 import Debug.Trace (trace)
-import Control.Lens
+import Control.Lens hiding (Level)
 
 import qualified Data.Vector as Vector
 import qualified Data.Set as Set
@@ -41,11 +41,11 @@ import qualified Data.Set as Set
 
 
 toPhylo :: [Document] -> TermList -> Config -> Phylo
-toPhylo docs lst conf = phyloBase
+toPhylo docs lst conf = phylo1
     where
         --------------------------------------
-        _phylo1 :: Phylo
-        _phylo1 = toPhylo1 docs phyloBase
+        phylo1 :: Phylo
+        phylo1 = toPhylo1 docs phyloBase
         --------------------------------------
         phyloBase :: Phylo 
         phyloBase = toPhyloBase docs lst conf
@@ -58,15 +58,43 @@ toPhylo docs lst conf = phyloBase
 --------------------
 
 
+appendGroups :: (a -> PhyloPeriodId -> Level -> Int -> Vector Ngrams -> 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
+           . phylo_periodLevels
+           .  traverse)
+           (\phyloLvl -> if lvl == (phyloLvl ^. phylo_levelLevel)
+                         then
+                            let pId = phyloLvl ^. phylo_levelPeriod
+                                phyloFis = m ! pId
+                            in  phyloLvl 
+                              & phylo_levelGroups .~ (fromList $ foldl (\groups obj ->
+                                    groups ++ [(((pId,lvl),length groups),f obj pId lvl (length groups) (getRoots phylo))] ) [] phyloFis)
+                         else 
+                            phyloLvl )
+           phylo  
+
+
+fisToGroup :: PhyloFis -> PhyloPeriodId -> Level ->  Int -> Vector Ngrams -> PhyloGroup
+fisToGroup fis pId lvl idx fdt = 
+    PhyloGroup pId lvl idx
+               (fis ^. phyloFis_support)
+               (ngramsToIdx (Set.toList $ fis ^. phyloFis_clique) fdt)
+               (1,[])
+               [] [] [] []
+               Nothing
+
+
 toPhylo1 :: [Document] -> Phylo -> Phylo
-toPhylo1 docs phyloBase = undefined
+toPhylo1 docs phyloBase = appendGroups fisToGroup 1 phyloFis phyloBase
     where
         --------------------------------------
-        _mFis :: Map (Date,Date) [PhyloFis]
-        _mFis =  toPhyloFis _docs' (fisSupport $ getConfig phyloBase) (fisSize $ getConfig phyloBase)
+        phyloFis :: Map (Date,Date) [PhyloFis]
+        phyloFis =  toPhyloFis docs' (fisSupport $ getConfig phyloBase) (fisSize $ getConfig phyloBase)
         --------------------------------------
-        _docs' :: Map (Date,Date) [Document]
-        _docs' =  groupDocsByPeriod date (getPeriodIds phyloBase) docs
+        docs' :: Map (Date,Date) [Document]
+        docs' =  groupDocsByPeriod date (getPeriodIds phyloBase) docs
         --------------------------------------
 
 
@@ -108,19 +136,22 @@ 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 mDocs support clique = traceFis "Filtered Fis"
-                                $ filterFisByNested 
-                                $ traceFis "Filtered by clique size"
-                                $ filterFis True clique (filterFisByClique)
-                                $ traceFis "Filtered by support"
-                                $ filterFis True support (filterFisBySupport)
-                                $ traceFis "Unfiltered Fis" mFis
+toPhyloFis phyloDocs support clique = traceFis "Filtered Fis"
+                $ filterFisByNested 
+                $ traceFis "Filtered by clique size"
+                $ filterFis True clique (filterFisByClique)
+                $ traceFis "Filtered by support"
+                $ filterFis True support (filterFisBySupport)
+                $ traceFis "Unfiltered Fis" phyloFis
     where
-        --------------------------------------
-        -- | create the fis from the docs for each period
-        mFis :: Map (Date,Date) [PhyloFis]
-        mFis = mapWithKey (\prd docs -> let fis = toList $ fisWithSizePolyMap (Segment 1 20) 1 (map text docs)
-                                        in  map (\f -> PhyloFis (fst f) (snd f) prd) fis ) mDocs
+        -------------------------------------- 
+        phyloFis :: Map (Date,Date) [PhyloFis]
+        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))
+                     $ toList phyloDocs
+                fis' = fis `using` parList rdeepseq
+            in fromList fis'
         -------------------------------------- 
 
 
@@ -173,6 +204,11 @@ nbDocsByTime docs step =
       $ unionWith (+) time docs'
 
 
+initPhyloLevels :: Int -> PhyloPeriodId -> Map PhyloLevelId PhyloLevel
+initPhyloLevels lvlMax pId = 
+    fromList $ map (\lvl -> ((pId,lvl),PhyloLevel pId lvl empty)) [1..lvlMax]
+
+
 -- | To init the basic elements of a Phylo
 toPhyloBase :: [Document] -> TermList -> Config -> Phylo
 toPhyloBase docs lst conf = 
@@ -184,4 +220,4 @@ toPhyloBase docs lst conf =
                (docsToCoocByYear docs (foundations ^. foundations_roots) conf)
                (nbDocsByTime docs $ timeUnit conf)
                params
-               (map (\prd -> PhyloPeriod prd []) periods)
+               (fromList $ map (\prd -> (prd, PhyloPeriod prd (initPhyloLevels (phyloLevel conf) prd))) periods)

src/Gargantext/Viz/Phylo/PhyloTools.hs

@@ -19,7 +19,7 @@ module Gargantext.Viz.Phylo.PhyloTools where
 import Data.Vector (Vector, elemIndex)
 import Data.List (sort, concat, null, union, (++), tails, sortOn)
 import Data.Set (size)
-import Data.Map (Map, elems, fromList, unionWith)
+import Data.Map (Map, elems, fromList, unionWith, keys)
 import Data.String (String)
 
 import Gargantext.Prelude
@@ -150,8 +150,13 @@ sumCooc cooc cooc' = unionWith (+) cooc cooc'
 
 getPeriodIds :: Phylo -> [(Date,Date)]
 getPeriodIds phylo = sortOn fst
-                   $ map (\prd -> prd ^. phylo_periodId)
+                   $ keys
                    $ phylo ^. phylo_periods
 
+
 getConfig :: Phylo -> Config
-getConfig phylo = (phylo ^. phylo_param) ^. phyloParam_config
\ No newline at end of file
+getConfig phylo = (phylo ^. phylo_param) ^. phyloParam_config
+
+
+getRoots :: Phylo -> Vector Ngrams
+getRoots phylo = (phylo ^. phylo_foundations) ^. foundations_roots
\ No newline at end of file