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cluster analysis - Finding connected components in an array


I have an $w\times h$ array with non-negative integers.


I wish to partition the set of coordinates $(c,r)$ with $1\leq c \leq w$ and $1\leq r \leq h$, in subsets, so that each subset corresponds to a cluster of the same value in the array.


Two coordinates are neighbouring if they either are on top of another, or one is down-left of the other. This corresponds to finding clusters in a parallelogram.


belisarius was nice to provide a picture:


enter image description here


I have some code to find one connected cluster in an array (I call it gt):


FloodFillExtractTile[gt_, {sr_, sc_}] := 
Module[{r, c, toExplore, visited = {}},
toExplore = {{sr, sc}};

While[Length@toExplore > 0,
(* Pop *)
{r, c} = Last@toExplore;
toExplore = Most[toExplore];
AppendTo[visited, {r, c}];
(* Down-left *)

If[c > 1 && r < h &&
gt[[r + 1, c - 1]] == gt[[r, c]] && !
MemberQ[visited, {r + 1, c - 1}],

AppendTo[toExplore, {r + 1, c - 1}];
];
(* Down-right *)

If[ r < h &&
gt[[r + 1, c]] == gt[[r, c]] && ! MemberQ[visited, {r + 1, c}],
AppendTo[toExplore, {r + 1, c}];
];
(* Up-right *)


If[r > 1 && c < w &&
gt[[r - 1, c + 1]] == gt[[r, c]] && !
MemberQ[visited, {r - 1, c + 1}],
AppendTo[toExplore, {r - 1, c + 1}];
];
(* Up-left *)

If[ r > 1 &&
gt[[r - 1, c]] == gt[[r, c]] && ! MemberQ[visited, {r - 1, c}],
AppendTo[toExplore, {r - 1, c}];

];
];
Return@visited;
];

Then FloodFillExtractTile[gtp, {1, 1}] gives the component connected to the upper left hand corner. However, this method feels ugly, and extending it to all components feels even uglier.


I was looking at Gather, but the problem is that it wants all points in a cluster to be equal, see for example Gather dependency on list order?


Edit: So this is the type of arrays I am looking at. The $6$, the $3$'s, the $2$'s and the $0$'s are in one component respectively, but there are two components with $1$'s.


Being neighbours means being adjacent down-left, down-right, up-left and up-right.


Now, the rows is stored just like regular rows in a rectangular matrix, so that is why this translates to a bit strange criteria for being neighbours. GT-pattern



This is the best code I have so far, first extract points with the same value, then do connected-component analysis on those parts.


GetGTTiles[gtp_] := 
Module[{testSame, testEdge, h, w, pts, sameClusters, getEdges,
tiles},
{h, w} = Dimensions[gtp];
pts = Join @@ Table[{r, c}, {r, h}, {c, w}];
testSame[{r1_, c1_}, {r2_, c2_}] := (gtp[[r1, c1]] ==
gtp[[r2, c2]]);
testEdge[{r1_, c1_}, {r2_,
c2_}] := (gtp[[r1, c1]] ==

gtp[[r2, c2]]) &&
((c1 == c2 &&
Abs[r1 - r2] <= 1) || (c1 == c2 - 1 &&
r1 == r2 + 1) || (c1 == c2 + 1 && r1 == r2 - 1));
sameClusters = Gather[pts, testSame];
getEdges[clust_] :=
Join @@ Outer[If[testEdge[#1, #2], #1 -> #2, Sequence @@ {}] &,
clust, clust, 1];
tiles =
Join @@ (ConnectedComponents[Graph@getEdges[#]] & /@ sameClusters);

Return@tiles;
];

This is the output I expect for the example given (5 clusters found):


{{{1, 1}}, {{1, 2}, {2, 1}}, 
{{1, 3}, {2, 3}, {3, 2}, {4, 1}, {3, 1}, {2, 2}},
{{1, 4}},
{{2, 4}, {3, 4}, {4, 4}, {5, 4}, {5, 3}, {4,3}},
{{3, 3}, {4, 2}, {5, 2}, {5, 1}}}


EDIT: So this is the final code, based on belisarius solution:


GTTiles[gtp_List] := Module[{fromEuclidean, toEuclidean,
getOneTile, elements, elmPos, pts, tile, tiles},

(* This is used to changefrom different coordinate systems. *)

fromEuclidean[{r_, c_}] := {r, (c - r)/2 + 1};
toEuclidean[{r_, c_}] := {r, 2 c + r - 2};

getOneTile[pts_List, maxDist_?NumericQ] := Module[{f},

f = Nearest[pts];
FixedPoint[
Union@Flatten[f[#, {Infinity, maxDist}] & /@ #, 1] &, {First@
pts}]];

elements = Union @@ gtp;
elmPos = (toEuclidean /@ Position[gtp, #]) & /@ elements;
(* This is really strange code. *)
tiles = Flatten[Flatten[
Reap[NestWhile[Complement[#,

Sow@getOneTile[#, N@Sqrt@2]] &, #, # != {} &]][[2]],
1] & /@ elmPos, 1];
tiles = Map[fromEuclidean, tiles, {2}];
Return@tiles;
];

Answer



l1 = {{6, 3, 2, 1}, {3, 2, 2, 0}, {2, 2, 1, 0}, {2, 1, 0, 0}, {1, 1, 0, 0}};
l = Riffle[#, ""] & /@ l1;
els = Union @@ l;
par = MapIndexed[PadRight[PadLeft[#1, #2[[1]] + Length@#1 - 1, ""],

Length@l + Length@#1 - 1, ""] &, l];
eachElm = Position[par, #] & /@ els;
getOneCluster[pts_List, maxDist_?NumericQ] :=
Module[{f},
f = Nearest[pts];
FixedPoint[Union@Flatten[f[#, {Infinity, maxDist}] & /@ #, 1] &, {First@pts}]];
clusters =
Flatten[Flatten[
Reap[NestWhile[
Complement[#,

Sow@getOneCluster[#, N@Sqrt@2]] &, #, # != {} &]][[2]], 1] & /@ eachElm, 1];
Grid[par,
ItemStyle -> {Automatic, Automatic, Flatten@MapIndexed[#1 -> Hue[#2[[1]]/3] &,
clusters, {2}]}]

Mathematica graphics


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