{-|
Module : Gargantext.Viz.Phylo.Tools
Description : Phylomemy Tools to build/manage it
Copyright : (c) CNRS, 2017-Present
License : AGPL + CECILL v3
Maintainer : team@gargantext.org
Stability : experimental
Portability : POSIX
-}
{-# LANGUAGE NoImplicitPrelude #-}
{-# LANGUAGE FlexibleContexts #-}
{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE TypeSynonymInstances #-}
{-# LANGUAGE FlexibleInstances #-}
module Gargantext.Viz.Phylo.LevelMaker
where
import Control.Parallel.Strategies
import Control.Lens hiding (both, Level)
import Data.List ((++), sort, concat, nub, zip, last, null)
import Data.Map (Map, (!), empty, singleton, size)
import Data.Text (Text)
import Data.Tuple.Extra
import Data.Vector (Vector)
import Gargantext.Prelude
import Gargantext.Viz.Phylo
import Gargantext.Viz.Phylo.Metrics
import Gargantext.Viz.Phylo.Aggregates
import Gargantext.Viz.Phylo.Cluster
import Gargantext.Viz.Phylo.BranchMaker
import Gargantext.Viz.Phylo.LinkMaker
import Gargantext.Viz.Phylo.Tools
import Gargantext.Text.Context (TermList)
import qualified Data.Vector.Storable as VS
import qualified Data.Set as Set
import qualified Data.Vector as Vector
import Debug.Trace (trace)
import Numeric.Statistics (percentile)
-------------------------
-- | PhyloLevelMaker | --
-------------------------
-- | A typeClass for polymorphic PhyloLevel functions
class PhyloLevelMaker aggregate
where
-- | To add a new Level of PhyloGroups to a Phylo based on a list of Aggregates
addPhyloLevel :: Level -> Map (Date,Date) [aggregate] -> Phylo -> Phylo
-- | To create a list of PhyloGroups based on a list of aggregates a
toPhyloGroups :: Level -> (Date,Date) -> [aggregate] -> Map (Date,Date) [aggregate] -> Phylo -> [PhyloGroup]
instance PhyloLevelMaker PhyloCluster
where
--------------------------------------
-- | Level -> Map (Date,Date) [Cluster] -> Phylo -> Phylo
addPhyloLevel lvl m p
| lvl > 1 = addPhyloLevel' lvl m p
| otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Clusters at level < 2")
--------------------------------------
-- | Level -> (Date,Date) -> [Cluster] -> Map (Date,Date) [Cluster] -> Phylo -> [PhyloGroup]
toPhyloGroups lvl (d,d') l m p =
let clusters = map (\(idx,cluster) -> clusterToGroup (d,d') lvl idx "" cluster m p) $ zip [1..] l
clusters' = clusters `using` parList rdeepseq
in clusters'
--------------------------------------
instance PhyloLevelMaker PhyloFis
where
--------------------------------------
-- | Level -> Map (Date,Date) [Fis] -> Phylo -> Phylo
addPhyloLevel lvl m p
| lvl == 1 = addPhyloLevel' lvl m p
| otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Fis at level <> 1")
--------------------------------------
-- | Level -> (Date,Date) -> [Fis] -> Map (Date,Date) [Fis] -> Phylo -> [PhyloGroup]
toPhyloGroups lvl (d,d') l _ p =
let groups = map (\(idx,fis) -> cliqueToGroup (d,d') lvl idx "" fis (getPhyloCooc p) (getFoundationsRoots p)) $ zip [1..] l
groups' = groups `using` parList rdeepseq
in groups'
--------------------------------------
instance PhyloLevelMaker Document
where
--------------------------------------
-- | Level -> Map (Date,Date) [Document] -> Phylo -> Phylo
addPhyloLevel lvl m p
| lvl == 0 = addPhyloLevel' lvl m p
| otherwise = panic ("[ERR][Viz.Phylo.Example.addPhyloLevel] No process declared for adding Documents at level <> 0")
--------------------------------------
-- | Level -> (Date,Date) -> [Document] -> Map (Date,Date) [Fis] -> Phylo -> [PhyloGroup]
toPhyloGroups lvl (d,d') l _m p = map (\ngram -> ngramsToGroup (d,d') lvl (getIdxInRoots ngram p) ngram [ngram] p)
$ (nub . concat)
$ map text l
--------------------------------------
-- | To traverse a Phylo and add a new PhyloLevel linked to a new list of PhyloGroups
addPhyloLevel' :: PhyloLevelMaker a => Level -> Map (Date, Date) [a] -> Phylo -> Phylo
addPhyloLevel' lvl m p = alterPhyloPeriods
(\period -> let pId = _phylo_periodId period
in over (phylo_periodLevels)
(\phyloLevels ->
let groups = toPhyloGroups lvl pId (m ! pId) m p
in trace (show (length groups) <> " groups for " <> show (pId) ) $ phyloLevels ++ [PhyloLevel (pId, lvl) groups]
) period) p
----------------------
-- | toPhyloGroup | --
----------------------
-- | To transform a Clique into a PhyloGroup
cliqueToGroup :: PhyloPeriodId -> Level -> Int -> Text -> PhyloFis -> Map Date (Map (Int,Int) Double) -> Vector Ngrams -> PhyloGroup
cliqueToGroup prd lvl idx lbl fis cooc' root = PhyloGroup ((prd, lvl), idx) lbl ngrams
(getNgramsMeta cooc ngrams)
-- empty
(singleton "support" (fromIntegral $ getSupport fis))
Nothing
cooc
[] [] [] childs
where
--------------------------------------
cooc :: Map (Int, Int) Double
cooc = getMiniCooc (listToFullCombi ngrams) (periodsToYears [prd]) cooc'
--------------------------------------
ngrams :: [Int]
ngrams = sort $ map (\x -> getIdxInRoots' x root)
$ Set.toList
$ getClique fis
--------------------------------------
childs :: [Pointer]
childs = map (\n -> (((prd, lvl - 1), n),1)) ngrams
--------------------------------------
-- | To transform a Cluster into a Phylogroup
clusterToGroup :: PhyloPeriodId -> Level -> Int -> Text -> PhyloCluster -> Map (Date,Date) [PhyloCluster]-> Phylo-> PhyloGroup
clusterToGroup prd lvl idx lbl groups _m p =
PhyloGroup ((prd, lvl), idx) lbl ngrams
(getNgramsMeta cooc ngrams)
-- empty
empty
Nothing
cooc
ascLink desLink [] childs
where
--------------------------------------
cooc :: Map (Int, Int) Double
cooc = getMiniCooc (listToFullCombi ngrams) (periodsToYears [prd]) (getPhyloCooc p)
--------------------------------------
childs :: [Pointer]
childs = map (\g -> (getGroupId g, 1)) groups
ascLink = concat $ map getGroupPeriodParents groups
desLink = concat $ map getGroupPeriodChilds groups
--------------------------------------
ngrams :: [Int]
ngrams = (sort . nub . concat) $ map getGroupNgrams groups
--------------------------------------
-- | To transform a list of Ngrams into a PhyloGroup
ngramsToGroup :: PhyloPeriodId -> Level -> Int -> Text -> [Ngrams] -> Phylo -> PhyloGroup
ngramsToGroup prd lvl idx lbl ngrams p = PhyloGroup ((prd, lvl), idx) lbl (sort $ map (\x -> getIdxInRoots x p) ngrams) empty empty Nothing
(getMiniCooc (listToFullCombi $ sort $ map (\x -> getIdxInRoots x p) ngrams) (periodsToYears [prd]) (getPhyloCooc p))
[] [] [] []
----------------------
-- | toPhyloLevel | --
----------------------
-- | To reconstruct the Phylo from a set of Document to a given Level
toPhylo :: PhyloQueryBuild -> [Document] -> TermList -> Map (Date,Date) [PhyloFis] -> Phylo
toPhylo q c termList fis = toNthLevel (getNthLevel q) (getInterTemporalMatching q) (getNthCluster q) phylo1
where
--------------------------------------
phylo1 :: Phylo
phylo1 = toPhylo1 (getContextualUnit q) (getInterTemporalMatching q) phyloDocs phyloBase
-- phylo1 = toPhylo1 (getContextualUnit q) (getInterTemporalMatching q) phyloDocs phylo
--------------------------------------
-- phylo0 :: Phylo
-- phylo0 = tracePhyloN 0
-- $ addPhyloLevel 0 phyloDocs phyloBase
--------------------------------------
phyloDocs :: Map (Date, Date) [Document]
phyloDocs = groupDocsByPeriod date (getPhyloPeriods phyloBase) c
--------------------------------------
phyloBase :: Phylo
phyloBase = tracePhyloBase
$ toPhyloBase q (initPhyloParam (Just defaultPhyloVersion) (Just defaultSoftware) (Just q)) c termList fis
--------------------------------------
-- | To incrementally add new Levels to a Phylo by making all the linking and aggregation tasks
toNthLevel :: Level -> Proximity -> Cluster -> Phylo -> Phylo
toNthLevel lvlMax prox clus p
| lvl >= lvlMax = p
| otherwise = toNthLevel lvlMax prox clus
$ traceBranches (lvl + 1)
$ setPhyloBranches (lvl + 1)
-- $ transposePeriodLinks (lvl + 1)
$ traceTranspose (lvl + 1) Descendant
$ transposeLinks (lvl + 1) Descendant
$ traceTranspose (lvl + 1) Ascendant
$ transposeLinks (lvl + 1) Ascendant
$ tracePhyloN (lvl + 1)
$ setLevelLinks (lvl, lvl + 1)
$ addPhyloLevel (lvl + 1)
(clusters) p
where
--------------------------------------
clusters :: Map (Date,Date) [PhyloCluster]
clusters = phyloToClusters lvl clus p
--------------------------------------
lvl :: Level
lvl = getLastLevel 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 k s t) -> traceBranches 1
-- $ reLinkPhyloBranches 1
-- $ traceBranches 1
$ setPhyloBranches 1
$ traceTempoMatching Descendant 1
$ interTempoMatching Descendant 1 prox
$ traceTempoMatching Ascendant 1
$ interTempoMatching Ascendant 1 prox
$ tracePhyloN 1
-- $ setLevelLinks (0,1)
$ addPhyloLevel 1 (getPhyloFis phyloFis)
$ trace (show (size $ getPhyloFis phyloFis) <> " Fis created") $ phyloFis
where
--------------------------------------
phyloFis :: Phylo
phyloFis = if (null $ getPhyloFis p)
then p & phylo_fis .~ refineFis (docsToFis d p) k s t
else p & phylo_fis .~ docsToFis d p
--------------------------------------
_ -> panic "[ERR][Viz.Phylo.LevelMaker.toPhylo1] fst clustering not recognized"
-- | To create the base of the Phylo (foundations, periods, cooc, etc)
toPhyloBase :: PhyloQueryBuild -> PhyloParam -> [Document] -> TermList -> Map (Date,Date) [PhyloFis] -> Phylo
toPhyloBase q p c termList fis = initPhyloBase periods foundations nbDocs cooc fis p
where
--------------------------------------
cooc :: Map Date (Map (Int,Int) Double)
cooc = docsToCooc c (foundations ^. phylo_foundationsRoots)
--------------------------------------
nbDocs :: Map Date Double
nbDocs = countDocs $ map (\doc -> (date doc, text doc)) c
--------------------------------------
foundations :: PhyloFoundations
foundations = PhyloFoundations (initFoundationsRoots (termListToNgrams termList)) termList
--------------------------------------
periods :: [(Date,Date)]
periods = initPeriods (getPeriodGrain q) (getPeriodSteps q)
$ both date (head' "toPhyloBase" c, last' "toPhyloBase" c)
--------------------------------------
-----------------
-- | Tracers | --
-----------------
tracePhyloN :: Level -> Phylo -> Phylo
tracePhyloN lvl p = trace ("\n---------------\n--| Phylo " <> show (lvl) <> " |--\n---------------\n\n"
<> show (length $ getGroupsWithLevel lvl p) <> " groups created \n") p
traceTranspose :: Level -> Filiation -> Phylo -> Phylo
traceTranspose lvl fil p = trace ("----\n Transpose " <> show (fil) <> " links for " <> show (length $ getGroupsWithLevel lvl p) <> " groups\n") p
tracePhyloBase :: Phylo -> Phylo
tracePhyloBase p = trace ( "\n-------------\n--| Phylo |--\n-------------\n\n"
<> show (length $ _phylo_periods p) <> " periods from "
<> show (getPhyloPeriodId $ (head' "PhyloMaker") $ _phylo_periods p)
<> " to "
<> show (getPhyloPeriodId $ last $ _phylo_periods p)
<> "\n"
<> show ( Vector.length $ getFoundationsRoots p) <> " foundations roots \n") p
traceTempoMatching :: Filiation -> Level -> Phylo -> Phylo
traceTempoMatching fil lvl p = trace ( "----\n" <> show (fil) <> " filtered temporal Matching in Phylo" <> show (lvl) <> " :\n"
<> "count : " <> show (length pts) <> " pointers\n") p
where
--------------------------------------
pts :: [Pointer]
pts = concat $ map (\g -> getGroupPointers PeriodEdge fil g) $ getGroupsWithLevel lvl p
--------------------------------------
traceBranches :: Level -> Phylo -> Phylo
traceBranches lvl p = trace ( "----\n" <> "Branches in Phylo" <> show lvl <> " :\n"
<> "count : " <> show (length $ filter (\(lvl',_) -> lvl' == lvl ) $ getBranchIds p) <> " branches\n"
<> "count : " <> show (length $ getGroupsWithLevel lvl p) <> " groups\n"
<> "groups by branch : " <> show (percentile 25 (VS.fromList brs)) <> " (25%) "
<> show (percentile 50 (VS.fromList brs)) <> " (50%) "
<> show (percentile 75 (VS.fromList brs)) <> " (75%) "
<> show (percentile 90 (VS.fromList brs)) <> " (90%)\n") p
where
--------------------------------------
brs :: [Double]
brs = sort $ map (\(_,gs) -> fromIntegral $ length gs)
$ filter (\(id,_) -> (fst id) == lvl)
$ getGroupsByBranches p
--------------------------------------