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list manipulation - Optimising 2D binning code


I have a set of (x,y,z) data, 45,000 to be precise and I want to bin the z values in 256 equidistant bins based on their (x,y) values. The final array should be a set of 256x256 array with each slot containing an average of binned z values.


Being new to mathematica, I came up with the following code:


 data = RandomReal[{12000, 35000}, {45000, 3}];

data1 = data[[All, {1, 2}]];(*strip the zvalues from the set*)
xValues = data[[All, 1]];
yValues = data[[All, 2]];
zValues = data[[All, 3]];
(*Compute maximum/minimum of x values*)
maxXvalue = Max[xValues];
minXvalue = Min[xValues];

(*Compute maximum/minimum of y values*)
maxYvalue = Max[yValues];

minYvalue = Min [yValues];

(*Compute maximum/minimum of z values*)
maxZvalue = Max[zValues];
minZValue = Min[zValues];

bbx = {Floor[minXvalue], Floor[maxXvalue],
Floor[((maxXvalue - minXvalue)/256)]}; (* equidistant x bins*)
bby = {Floor[minYvalue], Floor[maxYvalue],
Floor[((maxYvalue - minYvalue)/256)]};(* equidistant y bins*)

bList = BinLists[data1, {bbx}, {bby}];
bCount = BinCounts[data1, {bbx}, {bby}];(*Gives a count of the number of items in \
each bins*)

(*Defining array to contain final z average values*)
meanZValues = Table[0, {Length[bList]}, {Length[bList]}];

i = 0; (*initialising loop variables*)
j = 0;
k = 0;


f[x_] := zValues[[x]];(*Defining function to get z values back*)

For[i = 1, i <= Length[bList], i++,
For [j = 1, j <= Length[bList], j++, m1 = {}; (*Re-empty m1 list*)
For [k = 1, k <= Length[bList[[i, j]]], k++,
AppendTo[m1, Position[data1, bList[[i, j]][[k]]] (*accessing only the x-
coordinate index of the position on original matrix*)
];
(*Getting the indices of the binned values*)

indices = Flatten[DeleteDuplicates[Take[m1, All]]]; (*Position command above gives multiple indices if these values occur more than once, hence deleting the duplicate ones*)

meanZValues[[i, j]] = Mean[Map[f,indices]]; (*Compute average values of Z by accessing the original array, getting the z values *)
]
]
]
meanZValues

It gives an output in a reasonable amount of time for up to couple of thousand values, however, it lags and maybe crashes without any output for 45,000 set of data.


How do I make this code more efficient? Thank you




Answer



Modifying @ruebenko's answer in the StackOverflow Q/A linked in Faysal's comment (Mathematica fast 2D binning algorithm) to get the means of z-values for each bin (using yet another undocumented setting for the option "TreatRepeatedEntries" that works in version 9 only):


 zvalues = data[[All, 3]];
epsilon = 1*^-10;
indexes = 1 + Floor[(1 - epsilon) 256 Rescale[data[[All, {1, 2}]]]];
System`SetSystemOptions["SparseArrayOptions" -> {"TreatRepeatedEntries" -> (Mean[{##}] &)}];
binmeansZ = SparseArray[indexes -> zvalues];
System`SetSystemOptions["SparseArrayOptions" -> {"TreatRepeatedEntries" -> First}];

A picture:



 MatrixPlot[binmeansZ]

enter image description here


Update: Timings


Mr.Wizards's version 7 settings (also works in versions 8.0.4.0 and 9):


  SetSystemOptions["SparseArrayOptions" -> {"TreatRepeatedEntries" -> 2}];
AbsoluteTiming[binmeans = Normal[SparseArray[indexes -> zvalues]] /.
"List"[x__] :> Mean@{x};]
SetSystemOptions["SparseArrayOptions" -> {"TreatRepeatedEntries" -> 0}];
(* {0.086009, Null} *)


Version 9 settings:


  System`SetSystemOptions["SparseArrayOptions" -> {"TreatRepeatedEntries" -> (Mean[{##}] &)}]; 
AbsoluteTiming[binmeansZ = SparseArray[indexes -> zvalues];]
System`SetSystemOptions["SparseArrayOptions" -> {"TreatRepeatedEntries" -> First}];
(* {0.035003, Null}*)
binmeansZ == SparseArray[binmeans]
(* True *)

Update 2: Default settings in versions 8.0.4.0 and 9:



  "TreatRepeatedEntries" /. SystemOptions["SparseArrayOptions"][[1, 2]]
(* 0 (Version 8.0.4.0) *)
(* First (Version 9) *)

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