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haskell-gargantext
Commit 38d3a9cd authored by qlobbe's avatar qlobbe
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remove bad tracers

parent 5e332ef8
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    bin/gargantext-phylo/Main.hs
    View file @ 38d3a9cd
    ......@@ -115,7 +115,9 @@ filterTerms patterns (y,d) = (y,termsInText patterns d)
    -- | To transform a Csv nfile into a readable corpus
    csvToCorpus :: Limit -> CorpusPath -> IO ([(Int,Text)])
    csvToCorpus limit csv = DV.toList
    -- . DV.reverse
    . DV.take limit
    -- . DV.reverse
    . DV.map (\n -> (csv_publication_year n, (csv_title n) <> " " <> (csv_abstract n)))
    . snd <$> CSV.readFile csv
    ......
    src/Gargantext/Viz/Phylo/Aggregates/Cluster.hs
    View file @ 38d3a9cd
    ......@@ -49,10 +49,12 @@ graphToClusters clust (nodes,edges) = case clust of
    -- | To transform a list of PhyloGroups into a Graph of Proximity
    groupsToGraph :: Proximity -> [PhyloGroup] -> Map (Int, Int) Double -> Phylo -> ([GroupNode],[GroupEdge])
    groupsToGraph prox gs cooc p = case prox of
    WeightedLogJaccard (WLJParams _ sens) -> (gs, map (\(x,y) -> ((x,y), traceSim x y (getSubCooc (getGroupNgrams x) cooc) (getSubCooc (getGroupNgrams y) cooc) p
    $ weightedLogJaccard sens (getSubCooc (getGroupNgrams x) cooc) (getSubCooc (getGroupNgrams y) cooc)))
    groupsToGraph :: Proximity -> [PhyloGroup] -> Map (Int, Int) Double -> ([GroupNode],[GroupEdge])
    groupsToGraph prox gs cooc = case prox of
    -- WeightedLogJaccard (WLJParams _ sens) -> (gs, map (\(x,y) -> ((x,y), traceSim x y (getSubCooc (getGroupNgrams x) cooc) (getSubCooc (getGroupNgrams y) cooc) p
    -- $ weightedLogJaccard sens (getSubCooc (getGroupNgrams x) cooc) (getSubCooc (getGroupNgrams y) cooc)))
    -- $ getCandidates gs)
    WeightedLogJaccard (WLJParams _ sens) -> (gs, map (\(x,y) -> ((x,y), weightedLogJaccard' sens (getGroupNgrams x) (getGroupNgrams y) cooc))
    $ getCandidates gs)
    Hamming (HammingParams _) -> (gs, map (\(x,y) -> ((x,y), hamming (getSubCooc (getGroupNgrams x) cooc) (getSubCooc (getGroupNgrams y) cooc)))
    $ getCandidates gs)
    ......@@ -82,7 +84,7 @@ phyloToClusters lvl clus p = Map.fromList
    --------------------------------------
    graphs :: [([GroupNode],[GroupEdge])]
    graphs = traceGraph lvl (getThreshold prox)
    $ map (\prd -> groupsToGraph prox (getGroupsWithFilters lvl prd p) (getCooc [prd] p) p) periods
    $ map (\prd -> groupsToGraph prox (getGroupsWithFilters lvl prd p) (getCooc [prd] p)) periods
    --------------------------------------
    prox :: Proximity
    prox = getProximity clus
    ......@@ -100,7 +102,6 @@ phyloToClusters lvl clus p = Map.fromList
    traceGraph :: Level -> Double -> [([GroupNode],[GroupEdge])] -> [([GroupNode],[GroupEdge])]
    traceGraph lvl thr g = trace ( "----\nUnfiltered clustering in Phylo" <> show (lvl) <> " :\n"
    <> "count : " <> show (length lst) <> " potential edges (" <> show (length $ filter (>= thr) lst) <> " >= " <> show (thr) <> ")\n"
    <> show (lst) <> "\n"
    <> "similarity : " <> show (percentile 25 (VS.fromList lst)) <> " (25%) "
    <> show (percentile 50 (VS.fromList lst)) <> " (50%) "
    <> show (percentile 75 (VS.fromList lst)) <> " (75%) "
    ......@@ -120,7 +121,5 @@ traceGraphFiltered lvl g = trace ( "----\nClustering in Phylo" <> show (lvl) <>
    lst = sort $ map snd $ concat $ map snd g
    traceSim :: PhyloGroup -> PhyloGroup -> Map (Int, Int) Double -> Map (Int, Int) Double -> Phylo -> Double -> Double
    traceSim g g' _ _ p sim = trace (show (getGroupText g p) <> " [vs] " <> show (getGroupText g' p) <> " = " <> show (sim) <> "\n"
    -- <> show (c) <> " [vs] " <> show (c') <> " = " <> show (sim)
    ) sim
    -- traceSim :: PhyloGroup -> PhyloGroup -> Phylo -> Double -> Double
    -- traceSim g g' p sim = trace (show (getGroupText g p) <> " [vs] " <> show (getGroupText g' p) <> " = " <> show (sim) <> "\n") sim
    src/Gargantext/Viz/Phylo/Example.hs
    View file @ 38d3a9cd
    ......@@ -55,7 +55,7 @@ import qualified Data.List as List
    ------------------------------------------------------
    export :: IO ()
    export = dotToFile "/home/qlobbe/data/epique/output/cesar_cleopatre.dot" phyloDot
    export = dotToFile "/home/qlobbe/data/phylo/output/cesar_cleopatre.dot" phyloDot
    phyloDot :: DotGraph DotId
    phyloDot = viewToDot phyloView
    ......@@ -77,7 +77,7 @@ queryViewEx = "level=3"
    phyloQueryView :: PhyloQueryView
    phyloQueryView = PhyloQueryView 1 Merge False 1 [BranchAge] [] [BranchPeakFreq,GroupLabelCooc] (Just (ByBranchAge,Asc)) Json Flat True
    phyloQueryView = PhyloQueryView 2 Merge False 1 [BranchAge] [] [BranchPeakFreq,GroupLabelCooc] (Just (ByBranchAge,Asc)) Json Flat True
    --------------------------------------------------
    ......@@ -104,7 +104,7 @@ queryEx = "title=Cesar et Cleôpatre"
    phyloQueryBuild :: PhyloQueryBuild
    phyloQueryBuild = PhyloQueryBuild "Cesar et Cleôpatre" "An example of Phylomemy (french without accent)"
    5 3 defaultFis [] [] (WeightedLogJaccard $ WLJParams 0.1 10) 2 (RelatedComponents $ RCParams $ WeightedLogJaccard $ WLJParams 0.13 0)
    5 3 defaultFis [] [] (WeightedLogJaccard $ WLJParams 0.3 10) 2 (RelatedComponents $ RCParams $ WeightedLogJaccard $ WLJParams 0.5 0)
    ......
    src/Gargantext/Viz/Phylo/LinkMaker.hs
    View file @ 38d3a9cd
    ......@@ -89,7 +89,8 @@ setLevelLinks (lvl,lvl') p = alterPhyloGroups (\gs -> map (\g -> if getGroupLeve
    -- | To apply the corresponding proximity function based on a given Proximity
    applyProximity :: Proximity -> PhyloGroup -> PhyloGroup -> Map (Int, Int) Double -> (PhyloGroupId, Double)
    applyProximity prox g1 g2 cooc = case prox of
    WeightedLogJaccard (WLJParams _ s) -> ((getGroupId g2), weightedLogJaccard s (getSubCooc (getGroupNgrams g1) cooc) (getSubCooc (getGroupNgrams g2) cooc))
    -- WeightedLogJaccard (WLJParams _ s) -> ((getGroupId g2), weightedLogJaccard s (getSubCooc (getGroupNgrams g1) cooc) (getSubCooc (getGroupNgrams g2) cooc))
    WeightedLogJaccard (WLJParams _ s) -> ((getGroupId g2), weightedLogJaccard' s (getGroupNgrams g1) (getGroupNgrams g2) cooc)
    Hamming (HammingParams _) -> ((getGroupId g2), hamming (getSubCooc (getGroupNgrams g1) cooc) (getSubCooc (getGroupNgrams g2) cooc))
    _ -> panic ("[ERR][Viz.Phylo.Example.applyProximity] Proximity function not defined")
    ......@@ -166,6 +167,51 @@ filterCandidates g gs = filter (\g' -> (not . null) $ intersect (getGroupNgrams
    $ delete g gs
    -- | a init avec la [[head groups]] et la tail groups
    toBranches :: [[PhyloGroup]] -> [PhyloGroup] -> [[PhyloGroup]]
    toBranches mem gs
    | null gs = mem
    | otherwise = toBranches mem' $ tail gs
    where
    --------------------------------------
    mem' :: [[PhyloGroup]]
    mem' = if (null withHead)
    then mem ++ [[head' "toBranches" gs]]
    else (filter (\gs' -> not $ elem gs' withHead) mem)
    ++
    [(concat withHead) ++ [head' "toBranches" gs]]
    --------------------------------------
    withHead :: [[PhyloGroup]]
    withHead = filter (\gs' -> (not . null)
    $ intersect (concat $ map getGroupNgrams gs')
    (getGroupNgrams $ (head' "toBranches" gs))
    ) mem
    --------------------------------------
    -- | a init avec la [[head groups]] et la tail groups
    toBranches' :: [[[Int]]] -> [[Int]] -> [[[Int]]]
    toBranches' mem gs
    | null gs = mem
    | otherwise = toBranches' mem' $ tail gs
    where
    --------------------------------------
    mem' :: [[[Int]]]
    mem' = if (null withHead)
    then mem ++ [[head' "toBranches" gs]]
    else (filter (\gs' -> not $ elem gs' withHead) mem)
    ++
    [(concat withHead) ++ [head' "toBranches" gs]]
    --------------------------------------
    withHead :: [[[Int]]]
    withHead = filter (\gs' -> (not . null)
    $ intersect (concat gs')
    (head' "toBranches" gs)
    ) mem
    --------------------------------------
    -- | To apply the intertemporal matching to Phylo at a given level
    interTempoMatching :: Filiation -> Level -> Proximity -> Phylo -> Phylo
    ......@@ -179,12 +225,18 @@ interTempoMatching fil lvl prox p = traceMatching fil lvl (getThreshold prox) sc
    scores :: [Double]
    scores = sort $ concat $ map (snd . snd) candidates
    --------------------------------------
    -- candidates' :: [(PhyloGroupId,([Pointer],[Double]))]
    -- candidates' = map (\g -> ( getGroupId g, findBestCandidates' fil 1 5 prox (getNextPeriods fil (getGroupPeriod g) prds) (filterCandidates g gs) g p)) gs
    --------------------------------------
    candidates :: [(PhyloGroupId,([Pointer],[Double]))]
    candidates = map (\g -> ( getGroupId g, findBestCandidates' fil 1 5 prox (getNextPeriods fil (getGroupPeriod g) prds) (filterCandidates g gs) g p)) gs
    candidates = concat $ map (\b -> map (\g -> ( getGroupId g, findBestCandidates' fil 1 5 prox (getNextPeriods fil (getGroupPeriod g) prds) (filterCandidates g gs) g p)) b) bs
    --------------------------------------
    gs :: [PhyloGroup]
    gs = getGroupsWithLevel lvl p
    --------------------------------------
    bs :: [[PhyloGroup]]
    bs = tracePreBranches $ toBranches [[head' "interTempoMatching" gs]] $ tail gs
    --------------------------------------
    prds :: [PhyloPeriodId]
    prds = getPhyloPeriods p
    --------------------------------------
    ......@@ -230,3 +282,7 @@ traceMatching fil lvl thr lst p = trace ( "----\n" <> show (fil) <> " unfiltered
    <> show (percentile 75 (VS.fromList lst)) <> " (75%) "
    <> show (percentile 90 (VS.fromList lst)) <> " (90%)\n") p
    tracePreBranches :: [[PhyloGroup]] -> [[PhyloGroup]]
    tracePreBranches bs = trace (show (length bs) <> " pre-branches" <> "\n"
    <> "with sizes : " <> show (map length bs) <> "\n") bs
    src/Gargantext/Viz/Phylo/Metrics/Proximity.hs
    View file @ 38d3a9cd
    ......@@ -17,18 +17,19 @@ Portability : POSIX
    module Gargantext.Viz.Phylo.Metrics.Proximity
    where
    import Data.List (null)
    import Data.List (null,intersect,union)
    import Data.Map (Map,elems,unionWith,intersectionWith,intersection,size)
    import Gargantext.Prelude
    import Debug.Trace (trace)
    import Gargantext.Viz.Phylo.Aggregates.Cooc
    -- import Debug.Trace (trace)
    -- | To process the weightedLogJaccard between two PhyloGroup fields
    weightedLogJaccard :: Double -> Map (Int, Int) Double -> Map (Int, Int) Double -> Double
    weightedLogJaccard s f1 f2
    | null wUnion = 0
    | wUnion == wInter = 1
    | s == 0 = trace ("==0") $ (fromIntegral $ length wInter)/(fromIntegral $ length wUnion)
    | s > 0 = trace (">0") $ (sumInvLog wInter)/(sumInvLog wUnion)
    | s == 0 = (fromIntegral $ length wInter)/(fromIntegral $ length wUnion)
    | s > 0 = (sumInvLog wInter)/(sumInvLog wUnion)
    | otherwise = (sumLog wInter)/(sumLog wUnion)
    where
    --------------------------------------
    ......@@ -46,6 +47,37 @@ weightedLogJaccard s f1 f2
    --------------------------------------
    -- | To process the weightedLogJaccard between two PhyloGroup fields
    weightedLogJaccard' :: Double -> [Int] -> [Int] -> Map (Int, Int) Double -> Double
    weightedLogJaccard' s idx idx' cooc
    | null idxUnion = 0
    | idxUnion == idxInter = 1
    | s == 0 = (fromIntegral $ length idxInter)/(fromIntegral $ length idxUnion)
    | s > 0 = (sumInvLog wInter)/(sumInvLog wUnion)
    | otherwise = (sumLog wInter)/(sumLog wUnion)
    where
    --------------------------------------
    wInter :: [Double]
    wInter = elems $ getSubCooc idxInter cooc
    --------------------------------------
    wUnion :: [Double]
    wUnion = elems $ getSubCooc idxUnion cooc
    --------------------------------------
    idxInter :: [Int]
    idxInter = intersect idx idx'
    --------------------------------------
    idxUnion :: [Int]
    idxUnion = union idx idx'
    --------------------------------------
    sumInvLog :: [Double] -> Double
    sumInvLog l = foldl (\mem x -> mem + (1 / log (s + x))) 0 l
    --------------------------------------
    sumLog :: [Double] -> Double
    sumLog l = foldl (\mem x -> mem + log (s + x)) 0 l
    --------------------------------------
    -- | To process the Hamming distance between two PhyloGroup fields
    hamming :: Map (Int, Int) Double -> Map (Int, Int) Double -> Double
    hamming f1 f2 = fromIntegral $ max ((size inter) - (size f1)) ((size inter) - (size f2))
    ......
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