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Fix the ImgLib2 benchmarks charts
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@ctrueden
ctrueden committed Jan 23, 2023
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182 changes: 152 additions & 30 deletions _pages/libs/imglib2/benchmarks.md
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---
mediawiki: ImgLib2_Benchmarks
title: ImgLib2 Benchmarks
section: Explore:Libraries:ImgLib2
---



{% include notice icon="info" content='This page was last updated 2016 May 3.' %}

This page compares the time performance of image processing operations using raw byte arrays, [ImageJ](/software/imagej) and [ImgLib2](/libs/imglib2). The benchmark tests these various methods for a "cheap" per-pixel operation (inverting an 8-bit image) as well as an "expensive" operation (some calls to `java.util.Math`) at several image resolutions.
Expand Down Expand Up @@ -59,40 +56,165 @@ The shell script also uses a Python script to transform the CSV output into the

## Cheap operation results

<div style="float: left">

<pLines ymin=0 title="Iteration x Time (ms) at 1 Mpx" size=300x250 plots> ImageJ, ImgLib2 Array, ImgLib2 Cell, ImgLib2 ImagePlus, ImgLib2 Planar, Raw 9, 15, 15, 12, 12, 4 5, 5, 9, 8, 5, 0 0, 0, 2, 1, 0, 0 0, 0, 3, 0, 0, 0 0, 0, 3, 0, 0, 0 0, 0, 3, 0, 0, 0 0, 0, 3, 0, 0, 0 0, 0, 2, 0, 1, 0 0, 0, 3, 0, 0, 0 0, 0, 2, 0, 0, 1 </pLines>

<style type="text/css">
.dygraph {
display: inline-block;
max-width: 100%;
width: 435px;
height: 250px;
}
.dygraph-legend {
background-color: rgba(200, 200, 255, 0.75) !important;
padding: 4px;
border: 1px solid #000;
border-radius: 10px;
box-shadow: 4px 4px 4px #888;
pointer-events: none;
width: 12em;
}
.dygraph-legend > span.highlight { background-color: rgba(255, 255, 200, 0.75) !important; }
.dygraph-legend > span.highlight { display: inline; }
</style>

<div>
<div class="dygraph" id="cheapIterationVsTime1"></div>
<div class="dygraph" id="cheapIterationVsTime25"></div>
</div>

<pLines ymin=0 title="Iteration x Time (ms) at 25 Mpx" size=435x250 plots legend> ImageJ, ImgLib2 Array, ImgLib2 Cell, ImgLib2 ImagePlus, ImgLib2 Planar, Raw 10, 42, 92, 39, 40, 7 5, 35, 78, 33, 30, 5 2, 2, 79, 2, 3, 3 2, 2, 78, 2, 3, 3 2, 2, 78, 2, 2, 3 1, 2, 79, 3, 3, 3 2, 1, 75, 2, 2, 4 1, 2, 79, 2, 3, 3 2, 2, 78, 4, 2, 3 1, 3, 83, 3, 3, 4 </pLines> {% include clear%}


<div style="float: left">

<pLines ymin=0 title="Resolution x Time (ms) at iteration #1" size=300x250 angle=90 cubic plots> , ImageJ, ImgLib2 Array, ImgLib2 Cell, ImgLib2 ImagePlus, ImgLib2 Planar, Raw 1 Mpx, 9, 15, 15, 12, 12, 4 4 Mpx, 8, 16, 25, 14, 15, 5 7 Mpx, 9, 18, 36, 17, 17, 5 10 Mpx, 9, 25, 38, 23, 21, 5 13 Mpx, 9, 28, 49, 24, 23, 6 16 Mpx, 9, 31, 60, 28, 27, 6 19 Mpx, 9, 36, 66, 31, 31, 6 22 Mpx, 10, 37, 74, 35, 33, 7 25 Mpx, 10, 42, 92, 39, 40, 7 </pLines>

<div>
<div class="dygraph" id="cheapResolutionVsTime1"></div>
<div class="dygraph" id="cheapResolutionVsTime10"></div>
</div>

<pLines ymin=0 title="Resolution x Time (ms) at iteration #10" size=435x250 angle=90 cubic plots legend> , ImageJ, ImgLib2 Array, ImgLib2 Cell, ImgLib2 ImagePlus, ImgLib2 Planar, Raw 1 Mpx, 0, 0, 2, 0, 0, 1 4 Mpx, 0, 0, 15, 1, 0, 1 7 Mpx, 1, 0, 21, 2, 0, 0 10 Mpx, 1, 0, 30, 1, 1, 1 13 Mpx, 1, 1, 39, 1, 2, 1 16 Mpx, 1, 1, 52, 1, 2, 2 19 Mpx, 1, 1, 65, 1, 2, 2 22 Mpx, 2, 1, 70, 2, 2, 2 25 Mpx, 1, 3, 83, 3, 3, 4 </pLines> {% include clear%}


## Expensive operation results

<div style="float: left">

<pLines ymin=0 title="Iteration x Time (ms) at 1 Mpx" size=300x250 plots> ImageJ, ImgLib2 Array, ImgLib2 Cell, ImgLib2 ImagePlus, ImgLib2 Planar, Raw 61, 61, 68, 58, 56, 58 43, 44, 55, 52, 49, 50 39, 41, 50, 43, 43, 41 42, 44, 47, 42, 39, 40 40, 43, 41, 39, 41, 43 38, 43, 44, 43, 44, 40 40, 44, 41, 42, 41, 41 39, 38, 40, 42, 40, 41 45, 39, 43, 43, 47, 43 38, 43, 47, 43, 46, 40 </pLines>

<div>
<div class="dygraph" id="expensiveIterationVsTime1"></div>
<div class="dygraph" id="expensiveIterationVsTime25"></div>
</div>

<pLines ymin=0 title="Iteration x Time (ms) at 25 Mpx" size=435x250 plots legend> ImageJ, ImgLib2 Array, ImgLib2 Cell, ImgLib2 ImagePlus, ImgLib2 Planar, Raw 1161, 1171, 1332, 1126, 1162, 1277 1052, 1062, 1210, 1066, 1069, 1024 1037, 1044, 1174, 1030, 1033, 1000 1008, 1038, 1137, 1033, 1026, 978 1027, 1041, 1137, 1037, 1037, 997 1017, 1034, 1096, 1031, 1058, 984 978, 1049, 1079, 1060, 1042, 983 999, 1040, 1072, 1046, 1030, 989 993, 1071, 1100, 1047, 1042, 983 989, 1037, 1061, 1030, 1041, 973 </pLines> {% include clear%}


<div style="float: left">

<pLines ymin=0 title="Resolution x Time (ms) at iteration #1" size=300x250 angle=90 cubic plots> , ImageJ, ImgLib2 Array, ImgLib2 Cell, ImgLib2 ImagePlus, ImgLib2 Planar, Raw 1 Mpx, 61, 61, 68, 58, 56, 58 4 Mpx, 185, 196, 232, 202, 190, 222 7 Mpx, 323, 338, 379, 336, 324, 365 10 Mpx, 477, 485, 595, 457, 458, 508 13 Mpx, 608, 615, 692, 601, 614, 667 16 Mpx, 747, 766, 944, 723, 750, 831 19 Mpx, 871, 884, 1019, 849, 878, 1075 22 Mpx, 1013, 1045, 1170, 973, 1013, 1090 25 Mpx, 1161, 1171, 1332, 1126, 1162, 1277 </pLines>

<div>
<div class="dygraph" id="expensiveResolutionVsTime1"></div>
<div class="dygraph" id="expensiveResolutionVsTime10"></div>
</div>

<pLines ymin=0 title="Resolution x Time (ms) at iteration #10" size=435x250 angle=90 cubic plots legend> , ImageJ, ImgLib2 Array, ImgLib2 Cell, ImgLib2 ImagePlus, ImgLib2 Planar, Raw 1 Mpx, 38, 43, 47, 43, 46, 40 4 Mpx, 165, 169, 173, 157, 180, 167 7 Mpx, 286, 292, 298, 284, 299, 279 10 Mpx, 390, 435, 423, 412, 420, 397 13 Mpx, 518, 589, 529, 535, 547, 512 16 Mpx, 646, 655, 668, 652, 661, 636 19 Mpx, 764, 779, 799, 775, 774, 745 22 Mpx, 866, 913, 922, 911, 909, 859 25 Mpx, 989, 1037, 1061, 1030, 1041, 973 </pLines> {% include clear%}

<script type="text/javascript">
function plot(id, title, xlabel, data) {
new Dygraph(document.getElementById(id), data, {
title: title,
titleHeight: 24,
xlabel: xlabel,
ylabel: "Time",
labelsSeparateLines: true,
drawPoints: true,
pointSize: 3,
highlightCircleSize: 2,
strokeWidth: 1,
strokeBorderWidth: 1,
highlightSeriesOpts: {
strokeWidth: 3,
strokeBorderWidth: 1,
highlightCircleSize: 5
}
});
}
plot("cheapIterationVsTime1", "Iteration x Time (ms) at 1 Mpx", "Iteration",
"Iteration,ImageJ,ImgLib2 Array,ImgLib2 Cell,ImgLib2 ImagePlus,ImgLib2 Planar,Raw\n" +
"1,9,15,15,12,12,4\n" +
"2,5,5,9,8,5,0\n" +
"3,0,0,2,1,0,0\n" +
"4,0,0,3,0,0,0\n" +
"5,0,0,3,0,0,0\n" +
"6,0,0,3,0,0,0\n" +
"7,0,0,3,0,0,0\n" +
"8,0,0,2,0,1,0\n" +
"9,0,0,3,0,0,0\n" +
"10,0,0,2,0,0,1");

plot("cheapIterationVsTime25", "Iteration x Time (ms) at 25 Mpx", "Iteration",
"Iteration,ImageJ,ImgLib2 Array,ImgLib2 Cell,ImgLib2 ImagePlus,ImgLib2 Planar,Raw\n" +
"1,10,42,92,39,40,7\n" +
"2,5,35,78,33,30,5\n" +
"3,2,2,79,2,3,3\n" +
"4,2,2,78,2,3,3\n" +
"5,2,2,78,2,2,3\n" +
"6,1,2,79,3,3,3\n" +
"7,2,1,75,2,2,4\n" +
"8,1,2,79,2,3,3\n" +
"9,2,2,78,4,2,3\n" +
"10,1,3,83,3,3,4");

plot("cheapResolutionVsTime1", "Resolution x Time (ms) at iteration #1", "Mpx",
"Mpx,ImageJ,ImgLib2 Array,ImgLib2 Cell,ImgLib2 ImagePlus,ImgLib2 Planar,Raw\n" +
"1 Mpx,9,15,15,12,12,4\n" +
"4 Mpx,8,16,25,14,15,5\n" +
"7 Mpx,9,18,36,17,17,5\n" +
"10 Mpx,9,25,38,23,21,5\n" +
"13 Mpx,9,28,49,24,23,6\n" +
"16 Mpx,9,31,60,28,27,6\n" +
"19 Mpx,9,36,66,31,31,6\n" +
"22 Mpx,10,37,74,35,33,7\n" +
"25 Mpx,10,42,92,39,40,7");

plot("cheapResolutionVsTime10", "Resolution x Time (ms) at iteration #10", "Mpx",
"Mpx,ImageJ,ImgLib2 Array,ImgLib2 Cell,ImgLib2 ImagePlus,ImgLib2 Planar,Raw\n" +
"1 Mpx,0,0,2,0,0,1\n" +
"4 Mpx,0,0,15,1,0,1\n" +
"7 Mpx,1,0,21,2,0,0\n" +
"10 Mpx,1,0,30,1,1,1\n" +
"13 Mpx,1,1,39,1,2,1\n" +
"16 Mpx,1,1,52,1,2,2\n" +
"19 Mpx,1,1,65,1,2,2\n" +
"22 Mpx,2,1,70,2,2,2\n" +
"25 Mpx,1,3,83,3,3,4");

plot("expensiveIterationVsTime1", "Iteration x Time (ms) at 1 Mpx", "Iteration",
"Iteration,ImageJ,ImgLib2 Array,ImgLib2 Cell,ImgLib2 ImagePlus,ImgLib2 Planar,Raw\n" +
"1,61,61,68,58,56,58\n" +
"2,43,44,55,52,49,50\n" +
"3,39,41,50,43,43,41\n" +
"4,42,44,47,42,39,40\n" +
"5,40,43,41,39,41,43\n" +
"6,38,43,44,43,44,40\n" +
"7,40,44,41,42,41,41\n" +
"8,39,38,40,42,40,41\n" +
"9,45,39,43,43,47,43\n" +
"10,38,43,47,43,46,40");

plot("expensiveIterationVsTime25", "Iteration x Time (ms) at 25 Mpx", "Iteration",
"Iteration,ImageJ,ImgLib2 Array,ImgLib2 Cell,ImgLib2 ImagePlus,ImgLib2 Planar,Raw\n" +
"1,1161,1171,1332,1126,1162,1277\n" +
"2,1052,1062,1210,1066,1069,1024\n" +
"3,1037,1044,1174,1030,1033,1000\n" +
"4,1008,1038,1137,1033,1026,978\n" +
"5,1027,1041,1137,1037,1037,997\n" +
"6,1017,1034,1096,1031,1058,984\n" +
"7,978,1049,1079,1060,1042,983\n" +
"8,999,1040,1072,1046,1030,989\n" +
"9,993,1071,1100,1047,1042,983\n" +
"10,989,1037,1061,1030,1041,973");

plot("expensiveResolutionVsTime1", "Resolution x Time (ms) at iteration #1", "Mpx",
"Mpx,ImageJ,ImgLib2 Array,ImgLib2 Cell,ImgLib2 ImagePlus,ImgLib2 Planar,Raw\n" +
"1 Mpx,61,61,68,58,56,58\n" +
"4 Mpx,185,196,232,202,190,222\n" +
"7 Mpx,323,338,379,336,324,365\n" +
"10 Mpx,477,485,595,457,458,508\n" +
"13 Mpx,608,615,692,601,614,667\n" +
"16 Mpx,747,766,944,723,750,831\n" +
"19 Mpx,871,884,1019,849,878,1075\n" +
"22 Mpx,1013,1045,1170,973,1013,1090\n" +
"25 Mpx,1161,1171,1332,1126,1162,1277");

plot("expensiveResolutionVsTime10", "Resolution x Time (ms) at iteration #10", "Mpx",
"Mpx,ImageJ,ImgLib2 Array,ImgLib2 Cell,ImgLib2 ImagePlus,ImgLib2 Planar,Raw\n" +
"1 Mpx,38,43,47,43,46,40\n" +
"4 Mpx,165,169,173,157,180,167\n" +
"7 Mpx,286,292,298,284,299,279\n" +
"10 Mpx,390,435,423,412,420,397\n" +
"13 Mpx,518,589,529,535,547,512\n" +
"16 Mpx,646,655,668,652,661,636\n" +
"19 Mpx,764,779,799,775,774,745\n" +
"22 Mpx,866,913,922,911,909,859\n" +
"25 Mpx,989,1037,1061,1030,1041,973");
</script>

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