For scripting with ImageJ and Fiji using Javascript, an concise introduction is available at the ImageJ website. An excellent tutorial could be found at the Fiji website. Assuming that you have done this tutorial already, I list some practical usage examples in below.

If you need more examples, Jython examples are recommended. Their usage of ImageJ Java classes provides many hints.

• A Fiji Scripting Tutorial
• Jython Scripting tutorial @Fiji site

<sxh javascript> dc = DirectoryChooser(“Select an output folder…”); dir = dc.getDirectory(); IJ.log(dir); </sxh>

<sxh js> importClass(Packages.ij.io.OpenDialog);

od = new OpenDialog(“Open As String”, “”); directory = od.getDirectory(); name = od.getFileName(); path = directory + name; IJ.log(path); </sxh>

<sxh javascript> Example code for managing path strings. Kota Miura (miura@embl.de) … assumes Unix style path … assumes that the script is executed from command line. … argment should be in the form <a path>:<another path> args = getArgument(); importClass(Packages.ij.util.Tools); argA = Tools.split(args, “:”); IJ.log(argA[0]); IJ.log(argA[1]); fpA = Tools.split(argA[0], “/”); path = “/”; for (i in fpA){ if (i != (fpA.length - 1)) path = path + fpA[i] + “/”; else file = fpA[i]; } traindata =argA[1]; IJ.log(path); IJ.log(file); IJ.log(traindata); </sxh> https://github.com/cmci/ijmacros/blob/master/PathStringManagement.js ==== Loading CSV file (data table) ==== Note that line 21 uses java.lang.String class explicitly, for using endsWith() method in the line 22. Otherwise the string variable “filepath” is a type of JS string which does not have endsWith() method. <sxh javascript> Example javascript for loading data from a series of CSV files in a folder. Assumes that these files are data output from other processing, and all data has same format. This script uses openCSV, which is included in Fiji. for more details on openCSV, visit the URLbelow. http://opencsv.sourceforge.net/ 20110822 Kota Miura (miura@embl.de) importPackage(Packages.util.opencsv); importPackage(java.io); path = “/Users/miura/Dropbox/data”; unix path = “C:/dropbox/My\ Dropbox/data”; win

dir = new File(path); filesA = dir.list(); sp = File.separator;

for (var i=0; i<filesA.length; i++) {

filepath = java.lang.String(dir + sp + filesA[i]);
if (filepath.endsWith(".txt") || filepath.endsWith(".csv")) {
      	IJ.log(filepath);
      	readCSV(filepath);
} else {
      	IJ.log("Igonored: " + filepath);
}

}

reads out 5th column in the CSV file using readALL method function readCSV(filepath) {

var reader = new CSVReader(new FileReader(filepath), " ");
var ls = reader.readAll();
var it = ls.iterator(); 
while (it.hasNext()){
	var carray = it.next();
	IJ.log(carray[4]); 
}

}

reads out 5th column in the CSV file using readNext method, output is similar to readAll function readCSVbyLine(filepath) {

var reader = new CSVReader(new FileReader(filepath), " ");
while ((nextLine = reader.readNext()) != null) {
      	// nextLine[] is an array of values from the line
      	IJ.log(nextLine[4]);
  	}    

} </sxh>

https://github.com/cmci/ijmacros/blob/master/CSVloader.js

This example is in Jython (Python style Java scripting). <sxh python> from util.opencsv import CSVWriter from java.io import FileWriter from java.lang.reflect import Array from java.lang import String, Class

writer = CSVWriter(FileWriter(“c:/temp/testcsv.csv”), ',') data = Array.newInstance(Class.forName(“java.lang.String”), 3) #String[] entries = “first#second#third”.split(“#”); data[0] = str(11) data[1] = str(23) data[2] = str(5555) writer.writeNext(data) writer.close() </sxh>

Bitwise AND is often used as switching ON/OFF multiple options. For Example:

<sxh javascript> DISPLAY_SUMMARY = 256; SHOW_ROI_MASKS = 4096; options = SHOW_ROI_MASKS + DISPLAY_SUMMARY; if ¹⁾; prints 3 IJ.log(add02(1, 2)); prints 3 as well

IJ.log(“——”);

a bit more with arguments to show that 'arguments' could be with any length function sum() {

var result = 0;
for (var i = 0, n = arguments.length; i < n; i++) {
  result += arguments[i];
}
return result;

}

IJ.log(sum(1, 2, 3)); prints 6 IJ.log(sum(1, 2, 3, 4, 5, 6)); prints 21 </sxh>

<sxh javascript> rt = ResultsTable(); for (var i = 0; i < 10; i++){

rt.incrementCounter();
rownum = rt.getCounter()-1;
rt.setValue("testcol", rownum, Double.valueOf(i*i));	

} rt.show(“Results”); </sxh>

To abort the running script, use the following function. I got this from here. <sxh javascript> function javascript_abort(){

 throw new Error('This is not an error. This is just to abort javascript');

}</sxh>

Keep in mind that java array and Javascript array are different types.

For some array treatments, this matters a lot and keeping your arrays either Java array or Javascript array is pretty important. Below is an example of Java > javascript array conversion and also how to check the object type. For constructing Java array in javascript, see here.

<sxh javascript> as an example, you first get an array from Results table in ImageJ. this array is Java array. rt = ResultsTable.getResultsTable(); sliceA = rt.getColumn(rt.getColumnIndex(“Slice”)); converting java array to javascript array

sliceJSA = []; for (var i =0; i < sliceA.length; i++)

sliceJSA.push(sliceA[i]);

check object types IJ.log(“sliceA class: ” + Object.prototype.toString.call(sliceA)); IJ.log(“sliceJSA class: ” + Object.prototype.toString.call(sliceJSA)); </sxh> ==== Sorting Numerical Array ==== <sxh javascript> prepare some data data = [10.0, 100.0, -1.0, 9.0, 200.0, 1.0];

data.sort();

IJ.log(data.valueOf()); prints -1,1,10,100,200,9 Comparator should be created. here we go again data = [10.0, 100.0, -1.0, 9.0, 200.0, 1.0]; create a comparator function comp(a, b){

return (a - b); 

}

data.sort(comp);

IJ.log(data.valueOf()); prints -1,1,9,10,100,200 </sxh> ==== Sorting a List of Numbered Files ==== Consider a situation of having a list of file names in an array filesA in the follwoing order, and we want to sort the name so the numbering is in ascending order. <code> 110608wt2.tif.proc.tif.noseg.tif8_9.txt 110608wt2.tif.proc.tif.noseg.tif9_10.txt 110608wt2.tif.proc.tif.noseg.tif10_11.txt 110608wt2.tif.proc.tif.noseg.tif0_1.txt 110608wt2.tif.proc.tif.noseg.tif1_2.txt 110608wt2.tif.proc.tif.noseg.tif2_3.txt 110608wt2.tif.proc.tif.noseg.tif3_4.txt 110608wt2.tif.proc.tif.noseg.tif4_5.txt 110608wt2.tif.proc.tif.noseg.tif5_6.txt 110608wt2.tif.proc.tif.noseg.tif6_7.txt 110608wt2.tif.proc.tif.noseg.tif7_8.txt </code> Such sorting could be done by combining regular expression matching. <sxh javascript> importPackage(java.io); path = “c:\\files”; dir = new File(path); filesA = dir.list(); sp = File.separator; filesA.sort(comparator); for (var i=0; i<filesA.length; i++) { filepath = java.lang.String(dir + sp + filesA[i]); if (filepath.endsWith(“.txt”)) IJ.log(filesA[i]); else IJ.log(“Igonored: ” + filepath); } function comparator(stra, strb){ regular expression to extract numberings

var patt1 = /\.tif([0-9]{1,10})_/i;
regexa = stra.match(patt1);
regexb = strb.match(patt1);	
return (regexa[1] - regexb[1]) 

} </sxh>

Above code will then prints out:

110608wt2.tif.proc.tif.noseg.tif0_1.txt
110608wt2.tif.proc.tif.noseg.tif1_2.txt
110608wt2.tif.proc.tif.noseg.tif2_3.txt
110608wt2.tif.proc.tif.noseg.tif3_4.txt
110608wt2.tif.proc.tif.noseg.tif4_5.txt
110608wt2.tif.proc.tif.noseg.tif5_6.txt
110608wt2.tif.proc.tif.noseg.tif6_7.txt
110608wt2.tif.proc.tif.noseg.tif7_8.txt
110608wt2.tif.proc.tif.noseg.tif8_9.txt
110608wt2.tif.proc.tif.noseg.tif9_10.txt
110608wt2.tif.proc.tif.noseg.tif10_11.txt

To study more about Javascript regular expression, maybe visit here.

I thought of Math.max(array.valueOf()) seemingly should work, but it doesn't. It should be like this: <sxh javascript> var testa = Array();

testa[0] = 10.3; testa[1] = 20.1; testa[2] = 100.9; testa[3] = 5.1;

minval = Math.min.apply(Math, testa); maxval = Math.max.apply(Math, testa); IJ.log(“Minimum value: ” + minval); IJ.log(“Maximum value: ” + maxval); </sxh>

This is because Math.min and Math.max methods only takes individual numbers, not an array. To unpack an array, apply() method of class Function is used. An example below depicts its usage.

<sxh javascript> var sum = function(){

var result = 0;
for (var i = 0, n = arguments.length; i < n; i++) {
  result += arguments[i];
}
return result;

};

data01 = [1, 2, 3]; data02 = [1, 2, 3, 4, 5, 6];

ans = sum.apply(sum, data01); IJ.log(ans);

ans = sum.apply(sum, data02); IJ.log(ans); </sxh>

… I mean if you want to sum up, you don't really have to be bulky but method apply() has so many flexibility in applying methods to any objects.

Use Array.forEach(function) method.

<sxh javascript> data = [10.0, 100.0, -1.0, 9.0, 200.0, 1.0];

data.forEach(printArray); IJ.log(“—”) data.forEach(squaredArray);

function printArray(x, idx) {

 IJ.log('['+idx+'] = '+x);

}

function squaredArray(x, idx) {

 IJ.log('['+idx+'] = '+ Math.pow(x,2));

} </sxh>

Output:

[0] = 10
[1] = 100
[2] = -1
[3] = 9
[4] = 200
[5] = 1
---
[0] = 100
[1] = 10000
[2] = 1
[3] = 81
[4] = 40000
[5] = 1

Source array is not affected in this case. If you want to modify the array itself, use Array.map(function) examples in the following. See more examples at this site.

map() function is convenient if you want to have an output array after processing each element.

<sxh javascript> this will be an example array xA = [5, 25, 75, 100]; create an object with a field 'factor' and a method 'multiply' var obj = {

factor: 2,
multiply: function (x){
	return x * this.factor;
}

} … factor 2 will then be the default value. use Array.map(function, obj) to calculate all elements at once.

array = xA.map(obj.multiply, obj); IJ.log(array.join()); prints 10,50,150,200 replace the factor. obj.factor = 4;

array = xA.map(obj.multiply, obj); IJ.log(array.join()); prints 20,100,300,400 </sxh> ==== Slicing Multidimensional Array ==== Here are examples of horizontal and vertical slicing of a 2D array. Vertical slicing is a bit complex, but I could not figure out other ways. If you know one, please tell me. What supposed to be something like v1 = allA[:, 1] in Python would be much easier. <sxh javascript> multidimensional array slicing

print = IJ.log;

xA = [1, 2, 3]; yA = [40, 50, 60]; zA = [-1, -2, -3]; allA = [xA, yA, zA]; this is a multidimensional array print(allA[1][2]); prints 60 print(allA[1]); prints 40,50,60, (sliced horizontally) v1 = allA.map(function (v){return v[1];});(sliced vertically) print(v1); prints 2,50,-2 print(v1[2]); prints -2

— here is another way of vartical slicing, longer but more clear with what's happening.

var obj = {sliceindex:1}; prepare an aboject with variable v1 = allA.map(returnVert, obj); use map function returnVert(see below)

			//with context of object 'obj'
                              //prints three lines of 'slice index:1' during map exexution

print(v1); prints 2,50,-2 v: one dimensional array passed from map function id: index of the one dimensional array passed, within the multidimensional array a: parent array (= itself, in our case allA) function returnVert(v, id, a){ print(“slice index:” + this.sliceindex); this.sliceindex will be passed from obj

return a[id][this.sliceindex];

} </sxh>

An application of vertical slicing, matrix transposition. <sxh javascript> transposing data matrix function transp(incoords){ var transposed = [] for(var i = 0; i < incoords[0].length; i++){

for(var i in incoords[0]){
	transposed.push(incoords.map(function(v){return v[i];}));
}
return transposed;

}

data = [ [0, 1, 2],

	[3, 4, 5],
	[6, 7, 8]];

var tdata = transp(data);

for (i in data) IJ.log(data[i]); for (i in tdata) IJ.log(tdata[i]); </sxh>

<sxh js> ResultsTable.getResultsTable().clone().show(“duplicated”); </sxh>

To suppress creation of image windows, you could activate BatchMode. Corresponding function in ImageJ is setBatchMode(true) and setBatchMode(false).

<sxh javascript> importClass(Packages.ij.macro.Interpreter); macro = new Interpreter();

activate batchmode (= setBatchMode(true) in IJ macro) macro.batchMode = true; when error occurrs and execution is terminated during batchmode=true, you might not see any images anymore (even if you try to open a new one manually). To avoid, do something like below to catch error and deactivate the batchmode. try {

IJ.run(imp, "do process...", op);

catch(err){

	macro.batchMode = false;
	IJ.log("!Error with do process...");
	IJ.log(err.rhinoException.toString());
	IJ.log(err.javaException.toString());		

}

deactivate batchmode macro.batchMode = false; </sxh> ==== Closing All Image Windows ==== <sxh javascript> function imagewinKiller(){ var wins = WindowManager.getIDList(); for (var i = 0; i < wins.length; i++) WindowManager.getImage(wins[i]).close(); } </sxh> ==== Adding Mouse Listener to an Image ==== <sxh javascript> example of implementing and extending java interface

importPackage(java.awt.event);

extends MouseAdapter, implements MouseMotionListener var mouseListener = new JavaAdapter(MouseAdapter, MouseMotionListener, { mouseClicked: function(event) { IJ.log(“clicked” + “ (” + event.getX() + “,” + event.getY() + “)”); }, mouseDragged: function(event) { IJ.log(“dragged”); }, mouseMoved: function(event) { } }); imp = IJ.getImage(); var win = imp.getWindow(); win.getCanvas().addMouseListener(mouseListener); win.getCanvas().addMouseMotionListener(mouseListener); </sxh> As of 20131120, above code works with “Run” in Fiji script editor, but it DOES NOT work if you save the script as a file and run it using [Macro > Plugins > Run]. This probably is caused by the difference in javascript engine version: Fiji script editor uses jar/js.jar, but the latter method uses JS evaluator packaged with JRE. Following code works with [Macro > Plugins > Run…]. Difference is that the constructor for JavaAdaptor in this case uses two arguments, rather than three arguments. This problem was pointed out by Torsten Stöter (Uni. Magdeburg) and following fix was contributed by him. Thanks to Torsten! <sxh javascript> var mouseListener = new JavaAdapter(MouseListener, /*MouseMotionListener,*/ { mouseClicked: function(event) { IJ.log(“clicked” + “ (” + event.getX() + “,” + event.getY() + “)”); }, mouseDragged: function(event) { IJ.log(“dragged”); }, mouseMoved: function(event) { } }); </sxh> ==== Adding Overlays to an Image ==== An example of overlay function in ImageJ / Fiji.
For drawing Arrows, use commented out lines. <sxh javascript> overlayLine(10, 10, 40, 40); overlayLine(40, 40, 10, 70); function overlayLine(x1, y1, x2, y2){ importClass(Packages.ij.gui.Overlay); importClass(Packages.java.awt.Color); imp = IJ.getImage(); roi1 = Arrow( 110, 245, 111, 246);

roi1 = Line(x1, y1, x2, y2);

roi1.setWidth(1.5); roi1.setHeadSize(3);

imp.setRoi(roi1);
overlay = imp.getOverlay();
if (overlay != null)
	overlay.add(roi1);
else
	overlay = Overlay(roi1);
red = Color(1, 0, 0);
overlay.setStrokeColor(red); 
imp.setOverlay(overlay);
imp.updateAndDraw() ;

IJ.log(“head ” + roi1.getDefaultHeadSize()); IJ.log(“head ” + roi1.getDefaultWidth()); } </sxh>

<sxh javascript> function alias2frames(imp, i){

var stack = imp.getStack();
var tempstk = new ImageStack(imp.getWidth(), imp.getHeight());
tempstk.addSlice(String(i), stack.getProcessor(i).clone());
tempstk.addSlice(String(i+1), stack.getProcessor(i+1).clone());
var imp2 = new ImagePlus("temp", tempstk);	
return imp2	

} </sxh>

<sxh javascript> Example Javascript for Background substraction using ImageMath Kota Miura (miura@embl.de)

get ImagePlus of the active window imp = IJ.getImage(); duplicate and blurr images blurrimp = imp.duplicate(); IJ.run(blurrimp, “Gaussian Blur…”, “sigma=15 stack”);

subtract the blurred from the original ic = new ImageCalculator(); for (var i=1; i⇐imp.getStackSize(); i++){ imp.setSlice(i); blurrimp.setSlice(i); ic.run(“Subtract”, imp, blurrimp); } </sxh> https://github.com/cmci/ijmacros/blob/master/ImageMath.js ==== Batch Trainable Segmentation using Trained Data ==== <sxh javascript> Example script for using trainable segmentation – assumes that an extra plugin by Kota is installed – assumes that you already have “trained data” arff 20110819 Kota Miura (miura@embl.de)

get currently active image / image stack imp = IJ.getImage(); path to the arff data traindata = “D:\\People\\Tina\\20110813\\data02.arff”;

importClass(Packages.emblcmci.DotSegmentByTrained); dbt = new DotSegmentByTrained(traindata, imp); binimp = dbt.runsilent(); binimp.show(); </sxh>

https://github.com/cmci/ijmacros/blob/master/TrainableSegmentationByTrained.js

Another version without using the plugin above. <sxh javascript> importClass(Packages.trainableSegmentation.WekaSegmentation); imp = IJ.getImage(); ws = WekaSegmentation(imp); ws.loadTrainingData('C:\\t\\data.arff'); if (ws.trainClassifier()){

impout = ws.getClassifiedImage();
if (impout == null) 
	IJ.log("failed retrieving output");
else {
	impout.show();
}

} </sxh>

3D processing generally consumes long long time for calculation, so better been done silently and headlessly. Here is one recipe using 3D processor plugin, which could be a good hint for doing it in headless (batch) mode. Does not use IJ.rin method, so ImagePlus instance is handed over explicitly.

%gist(1663061)%

Works in Fiji. Note the use of JavaImporter() from line 12 to 15 for avoiding conflicts in name space.

<sxh javascript> affinetransform3D.js Created: 201107120 by Kota Miura (CMCI, EMBL miura@embl.de) Collaborater: Oleg written according to the advice from Stephan Saalfeld@mpicbg http://groups.google.com/group/fiji-users/browse_thread/thread/4e70cd4caf96d180 TODO try using moving least square. http://pacific.mpi-cbg.de/javadoc/mpicbg/models/MovingLeastSquaresTransform.html http://www.ini.uzh.ch/~acardona/api/mpicbg/trakem2/transform/MovingLeastSquaresTransform.html importPackage(Packages.java.util); var mpimodel = new JavaImporter(); var trakmodel = new JavaImporter(); var mpistack = new JavaImporter(); var jarray = new JavaImporter(); mpimodel.importPackage(Packages.mpicbg.models); trakmodel.importPackage(Packages.mpicbg.trakem2.transform); mpistack.importPackage(Packages.mpicbg.ij.stack); jarray.importPackage(Packages.java.lang.reflect);

pointPairs = new ArrayList(); testFillPoints(pointPairs);

LS fitting modelM = new trakmodel.AffineModel3D(); use Albert's class, for printing out matrix modelM.fit( pointPairs ); IJ.log(modelM.toDataString());

— preparing target stack size, offsets — imp = IJ.getImage(); move this later to the beginning to check if there is indeed an image stack opened ww = imp.getWidth(); hh = imp.getHeight(); dd = imp.getImageStackSize();

need to use java native array for estimateBounds() method. minA = jarray.Array.newInstance(java.lang.Float.TYPE, 3); maxA = jarray.Array.newInstance(java.lang.Float.TYPE, 3); minA[0] = 0.0; minA[1] = 0.0; minA[2] = 0.0; maxA[0] = ww; maxA[1] = hh; maxA[2] = dd; IJ.log(“original:”+ ww.toString() +“,” + hh.toString()+ “,” + dd.toString()); destsizeA = ReCalcStackSize(modelM, minA, maxA); ww = destsizeA[0]; hh = destsizeA[1]; dd = destsizeA[2]; for (var i in minA) IJ.log(minA[i]); for (var i in maxA) IJ.log(maxA[i]); outstr = “after: ”; for (var i in minA) outstr = outstr + destsizeA[i] + “,”; IJ.log(outstr); ReCalcOffset(modelM, minA); IJ.log(modelM.toDataString()); — stack transformation —

mapping = mpistack.InverseTransformMapping( modelM );

ip = imp.getStack().getProcessor( 1 ).createProcessor( 1, 1 ); target = new ImageStack(ww, hh); for ( var s = 0; s < dd; ++s ) {

ip = ip.createProcessor( ww, hh ); 
mapping.setSlice( s ); 
try { 
  mapping.mapInterpolated( imp.getStack(), ip ); 
} catch ( err ) { 
  alert('An error has occurred: '+err.message); 
} 
target.addSlice( "", ip ); 

} impout = ImagePlus(“out”, target); impout.show();

function testFillPoints(pointPairs) {

var p11 = [1, 0, 0];
var p12 = [0, 1, 0];

var p21 = [0, 1, 0];
var p22 = [0, 0, 1];

var p31 = [0, 0, 1];
var p32 = [1, 0, 0];

var p41 = [0.5, 0, 0];
var p42 = [0, 0.5, 0];

pointPairs.add(mpimodel.PointMatch(mpimodel.Point(p11), mpimodel.Point(p12)));
pointPairs.add(mpimodel.PointMatch(mpimodel.Point(p21), mpimodel.Point(p22)));
pointPairs.add(mpimodel.PointMatch(mpimodel.Point(p31), mpimodel.Point(p32)));
pointPairs.add(mpimodel.PointMatch(mpimodel.Point(p41), mpimodel.Point(p42)));
IJ.log(pointPairs.toString());

}

function ReCalcStackSize(transM, minA, maxA){

transM.estimateBounds(minA, maxA);
var newsizeA = [0.0, 0.0, 0.0];  
for (var i in newsizeA) 
  newsizeA[i] = Math.ceil(maxA[i] - minA[i]);
return newsizeA;

}

function ReCalcOffset(transM, minA){

var shift = new mpimodel.TranslationModel3D();
var shift.set( -1*minA[0], -1*minA[1], -1*minA[2] );
transM.preConcatenate(shift);

} </sxh>

https://github.com/cmci/ijmacros/blob/master/affinetransform3Dv2.js

<sxh javascript>

imp = IJ.getImage(); impdimA = imp.getDimensions();

pt = IJ.runPlugIn(imp, “mosaic.plugins.ParticleTracker3DModular_”, “radius=3 cutoff=3 percentile=0.01 link=2 displacement=10”); pt.transferParticlesToResultsTable();

imp2 = imp.createImagePlus(); ims = imp.createEmptyStack(); for (var i = 0; i < impdimA[3]; i++) ims.addSlice(i, new ByteProcessor(impdimA[0], impdimA[1])); imp2 = new ImagePlus(“test”, ims); nSlices = imp2.getNSlices(); rt = ResultsTable.getResultsTable(); xindex = rt.getColumnIndex(“x”); yindex = rt.getColumnIndex(“y”); zindex = rt.getColumnIndex(“z”); xA = rt.getColumn(xindex); yA = rt.getColumn(yindex); zA = rt.getColumn(zindex); for (var i = 0; i < xA.length; i++){ IJ.log(xA[i]); cslice=Math.round(zA[i])+1; z seems to statrt from 0 in tracker result, so add 1.

if ((cslice > 0) && (cslice <= nSlices)) {
	ip = imp2.getStack().getProcessor(cslice);
	//ip.setColor(255);
	//ip.drawOval(Math.round(yA[i]), Math.round(xA[i]), 1, 1); //x and y is inverted.
	ip.set(Math.round(yA[i]), Math.round(xA[i]), 255); //x and y is inverted.

}

} imp2.show(); </sxh>

https://github.com/cmci/ijmacros/blob/master/3Ddots.js

Below is an example of calculating statistical values using Apache Commons Math library (already included in Fiji). There are many more you could do with it so explore the API. <sxh javascript> first example, using static methods “StatUtils”. importClass(Packages.org.apache.commons.math.stat.StatUtils); test = [1 , 3, 4, 8, 100]; IJ.log(test[2]); mn = StatUtils.mean(test); IJ.log(mn); above static method is limited with number of things that could be done. use DescriptiveStatistics then (but consumes more memory) importClass(Packages.org.apache.commons.math.stat.descriptive.DescriptiveStatistics); stats = new DescriptiveStatistics(); Add the data from the array for(i = 0; i < test.length; i++) {

      stats.addValue(test[i]);

}

Compute some statistics mean = stats.getMean(); std = stats.getStandardDeviation(); median = stats.getPercentile(50); IJ.log(mean); IJ.log(std); </sxh> ==== 3D vector ==== Using 3D vector class in apache commons math. <sxh javascript> importClass(Packages.org.apache.commons.math.geometry.euclidean.threed.Vector3D); construct 2 vectors va = new Vector3D(0.0, 0.0, 2.0); vb = new Vector3D(2.0, 0.0, 0.0);

angle between va and vb ang = Vector3D.angle(va, vb); IJ.log(ang); add va and vb, and out puts a new vector as a result vc = new Vector3D(1.0, va, 1.0, vb);

prints out elements of the vector vc IJ.log(“” + vc.getX()+ “,” + vc.getY()+ “,” + vc.getZ()); dot (inner) product of va abd vb dp = va.dotProduct(vb); IJ.log(dp);

cross product of va abd vb vd = va.crossProduct(vb); IJ.log(“” + vd.getX()+ “,” + vd.getY()+ “,” + vd.getZ()); </sxh> ==== Solving Quadratic Formula ==== For this, I borrowed a code by Gary Jones published in http://code.garyjones.co.uk/category/javascript/ <sxh javascript> Solving quadratic formula function chop(number, decimal_places) {

var multiplier = Math.pow(10, decimal_places) // makes multiplier = 10^decimal_places.
number = ( Math.round( number * multiplier ) ) / multiplier;

return number; }

function quadratic(aq, bq, cq, root) {

var complex,
	lambda,
	lambdaone,
	lambdatwo,
	plusminusone,
	plusminustwo,
	bsmfac = bq * bq - 4 * aq * cq,
	precision = 3;
if ( bsmfac < 0 ) { // Accounts for complex roots.
	plusminusone = " + ";
	plusminustwo = " - ";
	bsmfac *= -1;
	complex = Math.sqrt( bsmfac ) / ( 2 * aq );
	if ( aq < 0 ){ // if negative imaginary term, tidies appearance.
		plusminusone = " - ";
		plusminustwo = " + ";
		complex *= -1;
	}
	lambdaone = chop( -bq / ( 2 * aq ), precision ) + plusminusone + chop( complex, precision ) + 'i';
	lambdatwo = chop( -bq / ( 2 * aq ), precision ) + plusminustwo + chop( complex, precision ) + 'i';
} else if ( 0 == bsmfac ){ // Simplifies if b^2 = 4ac (real roots).
	lambdaone = chop( -bq / ( 2 * aq ), precision );
	lambdatwo = chop( -bq / ( 2 * aq ), precision );
} else { // Finds real roots when b^2 != 4ac.
	lambdaone = (-bq + (Math.sqrt( bsmfac ))) / ( 2 * aq );
	lambdaone = chop( lambdaone, precision );
	lambdatwo = (-bq - (Math.sqrt( bsmfac ))) / ( 2 * aq );
	lambdatwo = chop( lambdatwo, precision );
}
( '+' == root ) ? lambda = lambdaone : lambda = lambdatwo;
return lambda; // Returns either root based on parameter "root" passed to function.

} </sxh>

https://github.com/cmci/ijmacros/blob/master/roiProfileGaussFitterV3.js

In the second function, profileA is an array with intensity profile, and doPlot is an boolean flag for plotting the curve fitting result.

Note Line 18 and 19, where type conversion between Java array and javascript array is done.

<sxh javascript> cf: class CurveFitter cfp: fitted parameter array estD: estimated diameter function PlotFitted(xA, yA, cf, cfp, estD){ var fitA = []; for (i in yA) fitA[i] = cf.f(cfp, i); fitplot = Plot(“fitted”, “pixels”, “intensity”, xA, fitA) fitplot.addPoints(xA, yA, fitplot.CIRCLE) fitplot.addLabel(0.1, 0.1, estD) fitplot.show() } returns diameter and goodness of fit in addition to the fit results parameters. function GaussFitReturnPara(profileA, doPlot){

//var pixx = [];
var resultsA = [];
var pixx = java.lang.reflect.Array.newInstance(java.lang.Double.TYPE, profileA.length);
for (var i=0; i<profileA.length ; i++) pixx[i] = Number(i); 
cf = new CurveFitter(pixx, profileA);
cf.doFit(cf.GAUSSIAN);
IJ.log(cf.getResultString()); //debugging
cfp = cf.getParams();
//diameter = 2.355*cfp[3]; half max
diameter = 4*cfp[3];	// 2*sigma 
EstimatedDiameter = "Diameter =" + diameter;
IJ.log("Goodness of Fit (1.0 is the best): " + cf.getFitGoodness());
IJ.log("Estiamted Diameter = " + diameter);
if (doPlot) PlotFitted(pixx, profileA, cf, cfp, EstimatedDiameter);

var resA = HashMap();
resA.put(headerA[0], cf.getIterations());
resA.put(headerA[1], cf.getRestarts());
resA.put(headerA[2], sqsum(cf.getResiduals()));
resA.put(headerA[3], cf.getSD());
resA.put(headerA[4], cf.getRSquared());
resA.put(headerA[5], cf.getFitGoodness());
resA.put(headerA[6], diameter);
return resA;  

} </sxh>

https://github.com/cmci/ijmacros/blob/master/roiProfileGaussFitterV3.js

3DViewer has many capability in plotting 3D scenes, including time series. Api is available at here. Examples could be found in the website.

Version of Java3D is a critical issue for programming 3DViewer. Since upgrading Java does not in many cases means automatic upgrading of Java3D in your Java extension folder, this could be a problem during development. Here is a way to check your Java3D version.

%gist(1663134)%

3D viewer Tube example

I use tubes for plotting trajectories. Here is an example. It seems that there will be newer class called customnode.Tube becoming available soon (as of 20111219). Since Point3d class is directly used in this new class, I will replace the code below, but this old one might still is informative as an example of using Java array.

<sxh javascript> test for Mesh_Maker,createTube importClass(Packages.java.util.Vector); importPackage(Packages.ij3d); importClass(Packages.customnode.CustomTriangleMesh); importClass(Packages.javax.vecmath.Color3f); col = Color3f(0, 1.0, 0.5); col2 = Color3f(1.0, 0, 0); colw = Color3f(1.0, 1.0, 1.0); var xA = javaArray(1, 10); var yA = javaArray(1, 10); var zA = javaArray(1, 10); var rA = javaArray(1, 1); var tube = Mesh_Maker.createTube(xA, yA, zA, rA, 20, false); var xA = javaArray(10, 20); var yA = javaArray(10, 20); var zA = javaArray(10, 10); var rA = javaArray(1, 1); var tube2 = Mesh_Maker.createTube(xA, yA, zA, rA, 20, false); var tubes = Vector(); tubes.addAll(tube); tubes.addAll(tube2); var csp = CustomTriangleMesh(tubes, colw, 0.0); var ccs = ContentCreator.createContent(csp, “tubetime test”, 0); univ = new Image3DUniverse(); univ.show(); univ.addContent(ccs); function javaArray(sp, ep){ ja = new java.lang.reflect.Array.newInstance(java.lang.Double.TYPE, 2); ja[0] = sp; ja[1] = ep; return ja; } </sxh> []