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gargantext
haskell-gargantext
Commits
41908d30
Commit
41908d30
authored
3 years ago
by
Alexandre Delanoë
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Plain Diff
[FIX] Order 1 and Order 2, node size ok.
parent
083c1f50
Changes
4
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4 changed files
with
98 additions
and
103 deletions
+98
-103
MaxClique.hs
src/Gargantext/Core/Methods/Graph/MaxClique.hs
+1
-0
API.hs
src/Gargantext/Core/Viz/Graph/API.hs
+3
-15
Index.hs
src/Gargantext/Core/Viz/Graph/Index.hs
+7
-4
Tools.hs
src/Gargantext/Core/Viz/Graph/Tools.hs
+87
-84
No files found.
src/Gargantext/Core/Methods/Graph/MaxClique.hs
View file @
41908d30
...
...
@@ -71,6 +71,7 @@ type Neighbor = Node
-- | getMaxCliques
-- TODO chose distance order
getMaxCliques
::
Ord
a
=>
CliqueFilter
->
Distance
->
Threshold
->
Map
(
a
,
a
)
Int
->
[[
a
]]
getMaxCliques
f
d
t
m
=
map
fromIndices
$
getMaxCliques'
t
m'
where
...
...
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Click to expand it.
src/Gargantext/Core/Viz/Graph/API.hs
View file @
41908d30
...
...
@@ -9,7 +9,6 @@ Portability : POSIX
-}
{-# LANGUAGE OverloadedLists #-}
-- allows to write Map and HashMap as lists
{-# LANGUAGE TypeOperators #-}
...
...
@@ -159,13 +158,6 @@ recomputeGraph _uId nId maybeDistance = do
pure
$
trace
"[G.V.G.API] Graph exists, recomputing"
graph'''
-- TODO use Database Monad only here ?
--computeGraph :: HasNodeError err
-- => CorpusId
-- -> Distance
-- -> NgramsType
-- -> NodeListStory
-- -> Cmd err Graph
computeGraph
::
FlowCmdM
env
err
m
=>
CorpusId
->
Distance
...
...
@@ -180,7 +172,9 @@ computeGraph cId d nt repo = do
$
mapTermListRoot
[
lId
]
nt
repo
myCooc
<-
HashMap
.
filter
(
>
1
)
-- Removing the hapax (ngrams with 1 cooc)
<$>
getCoocByNgrams
(
if
d
==
Conditional
then
Diagonal
True
else
Diagonal
False
)
-- <$> HashMap.filterWithKey (\(x,y) _ -> x /= y)
-- <$> getCoocByNgrams (if d == Conditional then Diagonal True else Diagonal False)
<$>
getCoocByNgrams
(
Diagonal
True
)
<$>
groupNodesByNgrams
ngs
<$>
getNodesByNgramsOnlyUser
cId
(
lIds
<>
[
lId
])
nt
(
HashMap
.
keys
ngs
)
...
...
@@ -220,7 +214,6 @@ defaultGraphMetadata cId t repo gm = do
}
-- (map (\n -> LegendField n "#FFFFFF" (pack $ show n)) [1..10])
------------------------------------------------------------
type
GraphAsyncAPI
=
Summary
"Recompute graph"
:>
"recompute"
...
...
@@ -339,8 +332,3 @@ getGraphGexf uId nId = do
HyperdataGraphAPI
{
_hyperdataAPIGraph
=
graph
}
<-
getGraph
uId
nId
pure
$
addHeader
"attachment; filename=graph.gexf"
graph
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src/Gargantext/Core/Viz/Graph/Index.hs
View file @
41908d30
...
...
@@ -28,7 +28,7 @@ import qualified Data.Array.Accelerate as A
import
qualified
Data.Array.Accelerate.Interpreter
as
A
import
Data.Array.Accelerate
(
Matrix
,
Elt
,
Shape
,
(
:.
)(
..
),
Z
(
..
))
import
Data.Maybe
(
fromMaybe
)
import
Data.Maybe
(
fromMaybe
,
catMaybes
)
import
Data.Set
(
Set
)
import
qualified
Data.Set
as
S
...
...
@@ -69,7 +69,7 @@ map2mat sym def n m = A.fromFunction shape getData
case
sym
of
Triangle
->
fromMaybe
def
(
M
.
lookup
(
x
,
y
)
m
)
Square
->
fromMaybe
(
fromMaybe
def
$
M
.
lookup
(
y
,
x
)
m
)
$
M
.
lookup
(
x
,
y
)
m
$
M
.
lookup
(
x
,
y
)
m
)
shape
=
(
Z
:.
n
:.
n
)
...
...
@@ -93,8 +93,11 @@ fromIndex ni ns = indexConversion ni ns
indexConversion
::
(
Ord
b
,
Ord
k
)
=>
Map
k
b
->
Map
(
k
,
k
)
a
->
Map
(
b
,
b
)
a
indexConversion
index
ms
=
M
.
fromList
$
map
(
\
((
k1
,
k2
),
c
)
->
(
((
M
.!
)
index
k1
,
(
M
.!
)
index
k2
),
c
))
(
M
.
toList
ms
)
$
catMaybes
$
map
(
\
((
k1
,
k2
),
c
)
->
((,)
<$>
((,)
<$>
M
.
lookup
k1
index
<*>
M
.
lookup
k2
index
)
<*>
Just
c
)
)
$
M
.
toList
ms
---------------------------------------------------------------------------------
-------------------------------------------------------------------------------
...
...
This diff is collapsed.
Click to expand it.
src/Gargantext/Core/Viz/Graph/Tools.hs
View file @
41908d30
...
...
@@ -80,75 +80,6 @@ cooc2graphWith Louvain = undefined
cooc2graphWith
Spinglass
=
cooc2graphWith'
(
spinglass
1
)
-- cooc2graphWith Bac = cooc2graphWith' (\x -> pure $ BAC.defaultClustering x)
cooc2graph''
::
Ord
t
=>
Distance
->
Double
->
Map
(
t
,
t
)
Int
->
Map
(
Index
,
Index
)
Double
cooc2graph''
distance
threshold
myCooc
=
neighbourMap
where
(
ti
,
_
)
=
createIndices
myCooc
myCooc'
=
toIndex
ti
myCooc
matCooc
=
map2mat
Triangle
0
(
Map
.
size
ti
)
$
Map
.
filter
(
>
1
)
myCooc'
distanceMat
=
measure
distance
matCooc
neighbourMap
=
filterByNeighbours
threshold
$
mat2map
distanceMat
-- Quentin
filterByNeighbours
::
Double
->
Map
(
Index
,
Index
)
Double
->
Map
(
Index
,
Index
)
Double
filterByNeighbours
threshold
distanceMap
=
filteredMap
where
indexes
::
[
Index
]
indexes
=
List
.
nub
$
List
.
concat
$
map
(
\
(
idx
,
idx'
)
->
[
idx
,
idx'
]
)
$
Map
.
keys
distanceMap
filteredMap
::
Map
(
Index
,
Index
)
Double
filteredMap
=
Map
.
fromList
$
List
.
concat
$
map
(
\
idx
->
let
selected
=
List
.
reverse
$
List
.
sortOn
snd
$
Map
.
toList
$
Map
.
filter
(
>
0
)
$
Map
.
filterWithKey
(
\
(
from
,
_
)
_
->
idx
==
from
)
distanceMap
in
List
.
take
(
round
threshold
)
selected
)
indexes
doDistanceMap
::
Distance
->
Threshold
->
HashMap
(
NgramsTerm
,
NgramsTerm
)
Int
->
(
Map
(
Int
,
Int
)
Double
,
Map
(
Index
,
Index
)
Int
,
Map
NgramsTerm
Index
)
doDistanceMap
distance
threshold
myCooc
=
(
distanceMap
,
myCooc'
,
ti
)
where
-- TODO remove below
theMatrix
=
Map
.
fromList
$
HashMap
.
toList
myCooc
(
ti
,
_
)
=
createIndices
theMatrix
tiSize
=
Map
.
size
ti
myCooc'
=
toIndex
ti
theMatrix
matCooc
=
case
distance
of
-- Shape of the Matrix
Conditional
->
map2mat
Triangle
0
tiSize
Distributional
->
map2mat
Square
0
tiSize
$
case
distance
of
-- Removing the Diagonal ?
Conditional
->
Map
.
filterWithKey
(
\
(
a
,
b
)
_
->
a
/=
b
)
Distributional
->
identity
$
Map
.
filter
(
>
1
)
myCooc'
similarities
=
measure
distance
matCooc
links
=
round
(
let
n
::
Double
=
fromIntegral
tiSize
in
n
*
log
n
)
distanceMap
=
Map
.
fromList
$
List
.
take
links
$
List
.
sortOn
snd
$
Map
.
toList
$
case
distance
of
Conditional
->
Map
.
filter
(
>
threshold
)
Distributional
->
Map
.
filter
(
>
0
)
$
mat2map
similarities
cooc2graphWith'
::
ToComId
a
=>
Partitions
a
...
...
@@ -158,7 +89,7 @@ cooc2graphWith' :: ToComId a
->
IO
Graph
cooc2graphWith'
doPartitions
distance
threshold
myCooc
=
do
let
(
distanceMap
,
myCooc'
,
ti
)
=
doDistanceMap
distance
threshold
myCooc
(
distanceMap
,
diag
,
ti
)
=
doDistanceMap
distance
threshold
myCooc
nodesApprox
::
Int
nodesApprox
=
n'
...
...
@@ -184,7 +115,48 @@ cooc2graphWith' doPartitions distance threshold myCooc = do
confluence'
=
confluence
(
Map
.
keys
bridgeness'
)
3
True
False
pure
$
data2graph
(
Map
.
toList
$
Map
.
mapKeys
unNgramsTerm
ti
)
myCooc'
bridgeness'
confluence'
partitions
diag
bridgeness'
confluence'
partitions
doDistanceMap
::
Distance
->
Threshold
->
HashMap
(
NgramsTerm
,
NgramsTerm
)
Int
->
(
Map
(
Int
,
Int
)
Double
,
Map
(
Index
,
Index
)
Int
,
Map
NgramsTerm
Index
)
doDistanceMap
distance
threshold
myCooc
=
(
distanceMap
,
toIndex
ti
diag
,
ti
)
where
-- TODO remove below
(
diag
,
theMatrix
)
=
Map
.
partitionWithKey
(
\
(
x
,
y
)
_
->
x
==
y
)
$
Map
.
fromList
$
HashMap
.
toList
myCooc
(
ti
,
_it
)
=
createIndices
theMatrix
tiSize
=
Map
.
size
ti
matCooc
=
case
distance
of
-- Shape of the Matrix
Conditional
->
map2mat
Triangle
0
tiSize
Distributional
->
map2mat
Square
0
tiSize
{-$ case distance of -- Removing the Diagonal ?
Conditional -> Map.filterWithKey (\(a,b) _ -> a /= b)
Distributional -> Map.filterWithKey (\(a,b) _ -> a /= b)
-}
$
toIndex
ti
theMatrix
similarities
=
measure
distance
matCooc
links
=
round
(
let
n
::
Double
=
fromIntegral
tiSize
in
n
*
log
n
)
distanceMap
=
Map
.
fromList
$
List
.
take
links
$
List
.
sortOn
snd
$
Map
.
toList
$
Map
.
filter
(
>
threshold
)
$
mat2map
similarities
------------------------------------------------------------------------
------------------------------------------------------------------------
...
...
@@ -204,22 +176,26 @@ clustersParams x = ClustersParams (fromIntegral x) "0.00000001" -- y
----------------------------------------------------------
-- | From data to Graph
type
Occurrences
=
Map
(
Int
,
Int
)
Int
data2graph
::
ToComId
a
=>
[(
Text
,
Int
)]
->
Map
(
Int
,
Int
)
Int
->
Occurrences
->
Map
(
Int
,
Int
)
Double
->
Map
(
Int
,
Int
)
Double
->
[
a
]
->
Graph
data2graph
labels
cooc
s
bridge
conf
partitions
=
Graph
{
_graph_nodes
=
nodes
data2graph
labels
occurence
s
bridge
conf
partitions
=
Graph
{
_graph_nodes
=
nodes
,
_graph_edges
=
edges
,
_graph_metadata
=
Nothing
}
where
community_id_by_node_id
=
Map
.
fromList
$
map
nodeId2comId
partitions
community_id_by_node_id
=
Map
.
fromList
$
map
nodeId2comId
partitions
nodes
=
map
(
setCoord
ForceAtlas
labels
bridge
)
[
(
n
,
Node
{
node_size
=
maybe
0
identity
(
Map
.
lookup
(
n
,
n
)
cooc
s
)
[
(
n
,
Node
{
node_size
=
maybe
0
identity
(
Map
.
lookup
(
n
,
n
)
occurence
s
)
,
node_type
=
Terms
-- or Unknown
,
node_id
=
cs
(
show
n
)
,
node_label
=
l
...
...
@@ -313,14 +289,41 @@ layout m n gen = maybe (panic "") identity $ Map.lookup n $ coord
--p = Layout.defaultLGL
p
=
Layout
.
kamadaKawai
g
=
mkGraphUfromEdges
$
map
fst
$
List
.
filter
(
\
e
->
snd
e
>
0
)
$
Map
.
toList
m
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
-----------------------------------------------------------------------------
-- Debug
{-
-- measure logDistributional
dataDebug = map2mat Square (0::Int) 19 dataBug'
-- MISC Tools
cooc2graph''
::
Ord
t
=>
Distance
->
Double
->
Map
(
t
,
t
)
Int
->
Map
(
Index
,
Index
)
Double
cooc2graph''
distance
threshold
myCooc
=
neighbourMap
where
(
ti
,
_
)
=
createIndices
myCooc
myCooc'
=
toIndex
ti
myCooc
matCooc
=
map2mat
Triangle
0
(
Map
.
size
ti
)
$
Map
.
filter
(
>
1
)
myCooc'
distanceMat
=
measure
distance
matCooc
neighbourMap
=
filterByNeighbours
threshold
$
mat2map
distanceMat
-- Quentin
filterByNeighbours
::
Double
->
Map
(
Index
,
Index
)
Double
->
Map
(
Index
,
Index
)
Double
filterByNeighbours
threshold
distanceMap
=
filteredMap
where
indexes
::
[
Index
]
indexes
=
List
.
nub
$
List
.
concat
$
map
(
\
(
idx
,
idx'
)
->
[
idx
,
idx'
]
)
$
Map
.
keys
distanceMap
filteredMap
::
Map
(
Index
,
Index
)
Double
filteredMap
=
Map
.
fromList
$
List
.
concat
$
map
(
\
idx
->
let
selected
=
List
.
reverse
$
List
.
sortOn
snd
$
Map
.
toList
$
Map
.
filter
(
>
0
)
$
Map
.
filterWithKey
(
\
(
from
,
_
)
_
->
idx
==
from
)
distanceMap
in
List
.
take
(
round
threshold
)
selected
)
indexes
dataBug' :: Map (Int, Int) Int
dataBug' = Map.fromList [((0,0),28),((0,1),8),((0,2),6),((0,3),2),((0,5),4),((0,6),4),((0,7),2),((0,9),7),((0,10),4),((0,13),4),((0,14),2),((0,15),5),((0,16),8),((0,17),3),((1,1),28),((1,2),6),((1,3),7),((1,4),5),((1,5),7),((1,6),5),((1,7),2),((1,9),6),((1,10),7),((1,11),5),((1,13),6),((1,15),6),((1,16),14),((1,18),4),((2,2),39),((2,3),5),((2,4),4),((2,5),3),((2,6),4),((2,7),4),((2,8),3),((2,9),17),((2,10),4),((2,11),8),((2,12),2),((2,13),15),((2,14),4),((2,15),5),((2,16),21),((2,18),4),((3,3),48),((3,4),10),((3,5),7),((3,6),3),((3,7),7),((3,8),6),((3,9),12),((3,10),9),((3,11),8),((3,12),5),((3,13),15),((3,14),5),((3,15),9),((3,16),17),((3,18),4),((4,4),33),((4,5),2),((4,6),5),((4,7),7),((4,8),4),((4,9),6),((4,10),12),((4,11),8),((4,12),3),((4,13),16),((4,14),4),((4,15),4),((4,16),5),((4,17),2),((4,18),12),((5,5),27),((5,6),2),((5,8),3),((5,9),12),((5,10),6),((5,11),9),((5,13),4),((5,14),2),((5,15),7),((5,16),11),((5,18),4),((6,6),34),((6,7),4),((6,8),3),((6,9),12),((6,10),8),((6,11),2),((6,12),5),((6,13),6),((6,14),6),((6,15),5),((6,16),22),((6,17),8),((6,18),4),((7,7),27),((7,8),2),((7,9),6),((7,10),2),((7,11),4),((7,13),13),((7,15),2),((7,16),8),((7,17),6),((7,18),4),((8,8),30),((8,9),9),((8,10),6),((8,11),9),((8,12),6),((8,13),3),((8,14),3),((8,15),4),((8,16),15),((8,17),3),((8,18),5),((9,9),69),((9,10),9),((9,11),22),((9,12),15),((9,13),18),((9,14),10),((9,15),14),((9,16),48),((9,17),6),((9,18),9),((10,10),39),((10,11),15),((10,12),5),((10,13),11),((10,14),2),((10,15),4),((10,16),19),((10,17),3),((10,18),11),((11,11),48),((11,12),9),((11,13),20),((11,14),2),((11,15),13),((11,16),29),((11,18),13),((12,12),30),((12,13),4),((12,15),5),((12,16),16),((12,17),6),((12,18),2),((13,13),65),((13,14),10),((13,15),14),((13,16),23),((13,17),6),((13,18),10),((14,14),25),((14,16),9),((14,17),3),((14,18),3),((15,15),38),((15,16),17),((15,18),4),((16,16),99),((16,17),11),((16,18),14),((17,17),29),((18,18),23)]
-}
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