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documents:110822jsip_cooking:javascript_imagej_cookbook [2016/05/24 12:46] – external edit 127.0.0.1documents:110822jsip_cooking:javascript_imagej_cookbook [2020/11/26 08:24] (current) – kota
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 ====== Javascript (+ ImageJ) Cookbook ====== ====== Javascript (+ ImageJ) Cookbook ======
  
Line 23: Line 13:
 ==== Getting Directory Path Interactively ==== ==== Getting Directory Path Interactively ====
  
-<sxh javascript>+<code javascript>
 dc = DirectoryChooser("Select an output folder..."); dc = DirectoryChooser("Select an output folder...");
 dir = dc.getDirectory(); dir = dc.getDirectory();
 IJ.log(dir); IJ.log(dir);
-</sxh>+</code>
  
 ==== Getting File Path Interactively ==== ==== Getting File Path Interactively ====
  
-<sxh js>+<code js>
 importClass(Packages.ij.io.OpenDialog); importClass(Packages.ij.io.OpenDialog);
  
Line 39: Line 29:
 path = directory + name; path = directory + name;
 IJ.log(path); IJ.log(path);
-</sxh>+</code>
  
 ==== Path String Management ==== ==== Path String Management ====
-<sxh javascript>+<code javascript>
 // Example code for managing path strings.  // Example code for managing path strings. 
 // Kota Miura (miura@embl.de) // Kota Miura (miura@embl.de)
Line 68: Line 58:
 IJ.log(traindata); IJ.log(traindata);
  
-</sxh>+</code>
  
-[[https://github.com/cmci/ijmacros/blob/master/PathStringManagement.js]]+[[https://github.com/miura/ijmacros/blob/master/PathStringManagement.js]]
  
 ==== Loading CSV file (data table) ==== ==== Loading CSV file (data table) ====
Line 76: Line 66:
 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.   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>+<code javascript>
 // Example javascript for loading data from a series of CSV files in a folder. // Example javascript for loading data from a series of CSV files in a folder.
 //  // 
Line 127: Line 117:
     }         }    
 }     }    
-</sxh>+</code>
  
-[[https://github.com/cmci/ijmacros/blob/master/CSVloader.js]]+[[https://github.com/miura/ijmacros/blob/master/CSVloader.js]]
  
 ==== Saving CSV file (data table) ==== ==== Saving CSV file (data table) ====
  
 This example is in Jython (Python style Java scripting). This example is in Jython (Python style Java scripting).
-<sxh python>+<code python>
 from util.opencsv import CSVWriter from util.opencsv import CSVWriter
 from java.io import FileWriter from java.io import FileWriter
Line 148: Line 138:
 writer.writeNext(data) writer.writeNext(data)
 writer.close() writer.close()
-</sxh>+</code>
  
  
Line 158: Line 148:
 Bitwise AND is often used as switching ON/OFF multiple options. For Example: Bitwise AND is often used as switching ON/OFF multiple options. For Example:
  
-<sxh javascript>+<code javascript>
 DISPLAY_SUMMARY = 256; DISPLAY_SUMMARY = 256;
 SHOW_ROI_MASKS = 4096; SHOW_ROI_MASKS = 4096;
Line 164: Line 154:
 if ((options&SHOW_ROI_MASKS)!=0) if ((options&SHOW_ROI_MASKS)!=0)
  IJ.log("SHOW_ROI_MASKS selected");  IJ.log("SHOW_ROI_MASKS selected");
-</sxh>+</code>
  
 Switching ON/OFF is controlled using 16bit binary a.k.a 16 digit binary number. 256 is  Switching ON/OFF is controlled using 16bit binary a.k.a 16 digit binary number. 256 is 
Line 194: Line 184:
 </code> </code>
 meaning that meaning that
-<sxh javascript>+<code javascript>
 ((options&SHOW_ROI_MASKS)!=0) ((options&SHOW_ROI_MASKS)!=0)
-</sxh>+</code>
 is true. is true.
  
Line 205: Line 195:
 Javascript Function is a class that takes variable length of arguments. Even if there is no arguments declared in the function, one could add ones in runtime and could be retrieved from inside the function using Functions object 'Arguments'. Javascript Function is a class that takes variable length of arguments. Even if there is no arguments declared in the function, one could add ones in runtime and could be retrieved from inside the function using Functions object 'Arguments'.
  
-<sxh javascript>+<code javascript>
 // normal way of writing function  // normal way of writing function 
 function add01(a, b) { function add01(a, b) {
Line 233: Line 223:
 IJ.log(sum(1, 2, 3)); // prints 6 IJ.log(sum(1, 2, 3)); // prints 6
 IJ.log(sum(1, 2, 3, 4, 5, 6)); // prints 21 IJ.log(sum(1, 2, 3, 4, 5, 6)); // prints 21
-</sxh>+</code>
 ===== Writing Values in the Results Table ===== ===== Writing Values in the Results Table =====
  
-<sxh javascript>+<code javascript>
 rt = ResultsTable(); rt = ResultsTable();
 for (var i = 0; i < 10; i++){ for (var i = 0; i < 10; i++){
Line 244: Line 234:
 } }
 rt.show("Results"); rt.show("Results");
-</sxh>+</code>
  
 ===== Aborting the script ===== ===== Aborting the script =====
Line 250: Line 240:
 To abort the running script, use the following function.  To abort the running script, use the following function. 
 I got this from [[http://vikku.info/codesnippets/javascript/forcing-javascript-to-abort-stop-javascript-execution-at-any-time/|here]].  I got this from [[http://vikku.info/codesnippets/javascript/forcing-javascript-to-abort-stop-javascript-execution-at-any-time/|here]]. 
-<sxh javascript>+<code javascript>
 function javascript_abort(){ function javascript_abort(){
    throw new Error('This is not an error. This is just to abort javascript');    throw new Error('This is not an error. This is just to abort javascript');
-}</sxh>+}</code>
 ===== Arrays ===== ===== Arrays =====
  
Line 262: Line 252:
 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, [[http://pacific.mpi-cbg.de/wiki/index.php/Javascript_Scripting#Native_Java_arrays|see here]].  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, [[http://pacific.mpi-cbg.de/wiki/index.php/Javascript_Scripting#Native_Java_arrays|see here]]. 
    
-<sxh javascript>+<code javascript>
 //as an example, you first get an array from  //as an example, you first get an array from 
 //Results table in ImageJ.  //Results table in ImageJ. 
Line 279: Line 269:
 IJ.log("sliceA class: " + Object.prototype.toString.call(sliceA)); IJ.log("sliceA class: " + Object.prototype.toString.call(sliceA));
 IJ.log("sliceJSA class: " + Object.prototype.toString.call(sliceJSA)); IJ.log("sliceJSA class: " + Object.prototype.toString.call(sliceJSA));
-</sxh>+</code>
 ==== Sorting Numerical Array ==== ==== Sorting Numerical Array ====
-<sxh javascript>+<code javascript>
 //prepare some data //prepare some data
 data = [10.0, 100.0, -1.0, 9.0, 200.0, 1.0]; data = [10.0, 100.0, -1.0, 9.0, 200.0, 1.0];
Line 303: Line 293:
 IJ.log(data.valueOf()); //prints -1,1,9,10,100,200 IJ.log(data.valueOf()); //prints -1,1,9,10,100,200
  
-</sxh>+</code>
  
 ==== Sorting a List of Numbered Files ==== ==== Sorting a List of Numbered Files ====
Line 323: Line 313:
 Such sorting could be done by combining regular expression matching. Such sorting could be done by combining regular expression matching.
  
-<sxh javascript>+<code javascript>
 importPackage(java.io); importPackage(java.io);
 path = "c:\\files"; path = "c:\\files";
Line 347: Line 337:
  return (regexa[1] - regexb[1])   return (regexa[1] - regexb[1]) 
 } }
-</sxh>+</code>
  
 Above code will then prints out: Above code will then prints out:
Line 369: Line 359:
  
 I thought of Math.max(array.valueOf()) seemingly should work, but it doesn't. It should be like this: I thought of Math.max(array.valueOf()) seemingly should work, but it doesn't. It should be like this:
-<sxh javascript>+<code javascript>
 var testa = Array(); var testa = Array();
  
Line 381: Line 371:
 IJ.log("Minimum value: " + minval); IJ.log("Minimum value: " + minval);
 IJ.log("Maximum value: " + maxval); IJ.log("Maximum value: " + maxval);
-</sxh>+</code>
  
 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.  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> +<code javascript> 
 var sum = function(){ var sum = function(){
   var result = 0;   var result = 0;
Line 402: Line 392:
 ans = sum.apply(sum, data02); ans = sum.apply(sum, data02);
 IJ.log(ans); IJ.log(ans);
-</sxh>+</code>
  
 ... 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.  ... 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. 
Line 410: Line 400:
 Use Array.forEach(function) method.  Use Array.forEach(function) method. 
  
-<sxh javascript>+<code javascript>
 data = [10.0, 100.0, -1.0, 9.0, 200.0, 1.0]; data = [10.0, 100.0, -1.0, 9.0, 200.0, 1.0];
  
Line 424: Line 414:
    IJ.log('['+idx+'] = '+ Math.pow(x,2));    IJ.log('['+idx+'] = '+ Math.pow(x,2));
 } }
-</sxh>+</code>
  
 Output: Output:
Line 450: Line 440:
 map() function is convenient if you want to have an output array after processing each element.  map() function is convenient if you want to have an output array after processing each element. 
  
-<sxh javascript>+<code javascript>
 // this will be an example array // this will be an example array
 xA = [5, 25, 75, 100]; xA = [5, 25, 75, 100];
Line 474: Line 464:
 IJ.log(array.join()); //prints 20,100,300,400 IJ.log(array.join()); //prints 20,100,300,400
  
-</sxh>+</code>
  
 ==== Slicing Multidimensional Array ==== ==== Slicing Multidimensional Array ====
Line 482: Line 472:
 If you know one, please tell me. What supposed to be something like v1 = allA[:, 1] in Python would be much easier.  If you know one, please tell me. What supposed to be something like v1 = allA[:, 1] in Python would be much easier. 
  
-<sxh javascript>+<code javascript>
 //multidimensional array slicing //multidimensional array slicing
  
Line 518: Line 508:
  return a[id][this.sliceindex];  return a[id][this.sliceindex];
 } }
-</sxh>+</code>
  
 ==== Matrix Transpose ==== ==== Matrix Transpose ====
  
 An application of vertical slicing, matrix transposition.  An application of vertical slicing, matrix transposition. 
-<sxh javascript>+<code javascript>
 //transposing data matrix //transposing data matrix
  
Line 553: Line 543:
 2,5,8 2,5,8
 */ */
-</sxh>+</code>
  
 ===== Windows ===== ===== Windows =====
Line 559: Line 549:
 ==== Duplicating current Results table with different title ==== ==== Duplicating current Results table with different title ====
  
-<sxh js>+<code js>
 ResultsTable.getResultsTable().clone().show("duplicated"); ResultsTable.getResultsTable().clone().show("duplicated");
-</sxh>+</code>
  
 ==== Activating / Deactivating BatchMode ==== ==== Activating / Deactivating BatchMode ====
Line 567: Line 557:
 To suppress creation of image windows, you could activate BatchMode. Corresponding function in ImageJ is setBatchMode(true) and setBatchMode(false). To suppress creation of image windows, you could activate BatchMode. Corresponding function in ImageJ is setBatchMode(true) and setBatchMode(false).
  
-<sxh javascript>+<code javascript>
 importClass(Packages.ij.macro.Interpreter); importClass(Packages.ij.macro.Interpreter);
 macro = new Interpreter();  macro = new Interpreter(); 
Line 588: Line 578:
 //deactivate batchmode //deactivate batchmode
 macro.batchMode = false; macro.batchMode = false;
-</sxh>+</code>
  
  
 ==== Closing All Image Windows ==== ==== Closing All Image Windows ====
  
-<sxh javascript>+<code javascript>
 function imagewinKiller(){ function imagewinKiller(){
  var wins = WindowManager.getIDList();  var wins = WindowManager.getIDList();
Line 599: Line 589:
  WindowManager.getImage(wins[i]).close();  WindowManager.getImage(wins[i]).close();
 } }
-</sxh>+</code>
  
 ==== Adding Mouse Listener to an Image ==== ==== Adding Mouse Listener to an Image ====
  
-<sxh javascript>+<code javascript>
 // example of implementing and extending java interface // example of implementing and extending java interface
  
Line 626: Line 616:
 win.getCanvas().addMouseMotionListener(mouseListener); win.getCanvas().addMouseMotionListener(mouseListener);
  
-</sxh>+</code>
  
 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! 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>+<code javascript>
 var mouseListener = new JavaAdapter(MouseListener, /*MouseMotionListener,*/ { var mouseListener = new JavaAdapter(MouseListener, /*MouseMotionListener,*/ {
     mouseClicked: function(event) {     mouseClicked: function(event) {
Line 641: Line 631:
     }     }
 }); });
-</sxh>+</code>
  
 ==== Adding Overlays to an Image ==== ==== Adding Overlays to an Image ====
Line 648: Line 638:
 For drawing Arrows, use commented out lines. For drawing Arrows, use commented out lines.
  
-<sxh javascript>+<code javascript>
 overlayLine(10, 10, 40, 40); overlayLine(10, 10, 40, 40);
 overlayLine(40, 40, 10, 70); overlayLine(40, 40, 10, 70);
Line 674: Line 664:
 //IJ.log("head " + roi1.getDefaultWidth()); //IJ.log("head " + roi1.getDefaultWidth());
 } }
-</sxh>+</code>
  
 ===== Image Processing ===== ===== Image Processing =====
Line 680: Line 670:
 ==== Creating a Partial Stack of an Original Stack with shared ImageProcessor objects ==== ==== Creating a Partial Stack of an Original Stack with shared ImageProcessor objects ====
  
-<sxh javascript>+<code javascript>
 function alias2frames(imp, i){ function alias2frames(imp, i){
  var stack = imp.getStack();  var stack = imp.getStack();
Line 689: Line 679:
  return imp2   return imp2
 } }
-</sxh> +</code> 
  
 ==== Background Subtraction by ImageMath ==== ==== Background Subtraction by ImageMath ====
  
-<sxh javascript>+<code javascript>
 //Example Javascript for Background substraction using ImageMath  //Example Javascript for Background substraction using ImageMath 
 // Kota Miura (miura@embl.de) // Kota Miura (miura@embl.de)
Line 711: Line 701:
  ic.run("Subtract", imp, blurrimp);  ic.run("Subtract", imp, blurrimp);
 } }
-</sxh>+</code>
  
-[[https://github.com/cmci/ijmacros/blob/master/ImageMath.js]]+[[https://github.com/miura/ijmacros/blob/master/ImageMath.js]]
  
 ==== Batch Trainable Segmentation using Trained Data ==== ==== Batch Trainable Segmentation using Trained Data ====
  
-<sxh javascript>+<code javascript>
 // Example script for using trainable segmentation // Example script for using trainable segmentation
 // -- assumes that an extra plugin by Kota is installed // -- assumes that an extra plugin by Kota is installed
Line 734: Line 724:
 binimp = dbt.runsilent(); binimp = dbt.runsilent();
 binimp.show(); binimp.show();
-</sxh>+</code>
  
-[[https://github.com/cmci/ijmacros/blob/master/TrainableSegmentationByTrained.js]]+[[https://github.com/miura/ijmacros/blob/master/TrainableSegmentationByTrained.js]]
  
 Another version without using the plugin above.  Another version without using the plugin above. 
-<sxh javascript>+<code javascript>
 importClass(Packages.trainableSegmentation.WekaSegmentation); importClass(Packages.trainableSegmentation.WekaSegmentation);
 imp = IJ.getImage(); imp = IJ.getImage();
Line 752: Line 742:
  }  }
 }  }
-</sxh>+</code>
  
 ==== Using 3D processor plugin ==== ==== Using 3D processor plugin ====
Line 759: Line 749:
  
 %gist(1663061)% %gist(1663061)%
 +
 +https://gist.github.com/miura/1663061
 +<code:js>
 +importClass(Packages.ij3d.image3d.IntImage3D);
 +imp=IJ.getImage();
 +ima=new IntImage3D(imp.getStack());
 +r=3;
 +ima2=ima.createLocalMaximaImage(r,r,r, true);
 +plus=new ImagePlus("localmaxima",ima2.getStack());
 +plus.show();
 +</code>
  
 ==== Transformation of 3D stack according to given landmark pairs ==== ==== Transformation of 3D stack according to given landmark pairs ====
Line 764: Line 765:
 Works in Fiji. Note the use of JavaImporter() from line 12 to 15 for avoiding conflicts in name space.  Works in Fiji. Note the use of JavaImporter() from line 12 to 15 for avoiding conflicts in name space. 
  
-<sxh javascript>+<code javascript>
 //  affinetransform3D.js //  affinetransform3D.js
 //  Created: 201107120 by Kota Miura (CMCI, EMBL miura@embl.de) //  Created: 201107120 by Kota Miura (CMCI, EMBL miura@embl.de)
Line 882: Line 883:
   transM.preConcatenate(shift);   transM.preConcatenate(shift);
 } }
-</sxh>+</code>
  
-[[https://github.com/cmci/ijmacros/blob/master/affinetransform3Dv2.js]]+[[https://github.com/miura/ijmacros/blob/master/affinetransform3Dv2.js]]
  
 ==== 3D tracking of spots, and plotting of the resulted spots in a new Stack ==== ==== 3D tracking of spots, and plotting of the resulted spots in a new Stack ====
  
-<sxh javascript>+<code javascript>
 /* /*
 * script for creating a stack with same size of the current stack, and plot xyz dots listed in results window.\ * script for creating a stack with same size of the current stack, and plot xyz dots listed in results window.\
Line 929: Line 930:
 } }
 imp2.show(); imp2.show();
-</sxh>+</code>
  
-[[https://github.com/cmci/ijmacros/blob/master/3Ddots.js]]+[[https://github.com/miura/ijmacros/blob/master/3Ddots.js]]
  
 ===== Math ===== ===== Math =====
Line 938: Line 939:
  
 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.   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>+<code javascript>
 //first example, using static methods "StatUtils".  //first example, using static methods "StatUtils". 
 importClass(Packages.org.apache.commons.math.stat.StatUtils); importClass(Packages.org.apache.commons.math.stat.StatUtils);
Line 965: Line 966:
 IJ.log(mean); IJ.log(mean);
 IJ.log(std); IJ.log(std);
-</sxh>+</code>
  
 ==== 3D vector ==== ==== 3D vector ====
  
 Using 3D vector class in apache commons math.  Using 3D vector class in apache commons math. 
-<sxh javascript>+<code javascript>
 importClass(Packages.org.apache.commons.math.geometry.euclidean.threed.Vector3D); importClass(Packages.org.apache.commons.math.geometry.euclidean.threed.Vector3D);
  
Line 994: Line 995:
 vd = va.crossProduct(vb); vd = va.crossProduct(vb);
 IJ.log("" + vd.getX()+ "," + vd.getY()+ "," + vd.getZ()); IJ.log("" + vd.getX()+ "," + vd.getY()+ "," + vd.getZ());
-</sxh>+</code>
  
 ==== Solving Quadratic Formula ==== ==== Solving Quadratic Formula ====
Line 1001: Line 1002:
 [[http://code.garyjones.co.uk/category/javascript/]] [[http://code.garyjones.co.uk/category/javascript/]]
  
-<sxh javascript>+<code javascript>
 //Solving quadratic formula //Solving quadratic formula
 /** /**
Line 1059: Line 1060:
  return lambda; // Returns either root based on parameter "root" passed to function.  return lambda; // Returns either root based on parameter "root" passed to function.
 } }
-</sxh>+</code>
  
-[[https://github.com/cmci/ijmacros/blob/master/roiProfileGaussFitterV3.js]]+[[https://github.com/miura/ijmacros/blob/master/roiProfileGaussFitterV3.js]]
  
 ==== Gaussian fitting of Intensity Profile ==== ==== Gaussian fitting of Intensity Profile ====
Line 1069: Line 1070:
 Note Line 18 and 19, where type conversion between Java array and javascript array is done.  Note Line 18 and 19, where type conversion between Java array and javascript array is done. 
  
-<sxh javascript>+<code javascript>
 // cf: class CurveFitter // cf: class CurveFitter
 // cfp: fitted parameter array // cfp: fitted parameter array
Line 1110: Line 1111:
   return resA;     return resA;  
 } }
-</sxh>+</code>
  
-[[https://github.com/cmci/ijmacros/blob/master/roiProfileGaussFitterV3.js]]+[[https://github.com/miura/ijmacros/blob/master/roiProfileGaussFitterV3.js]]
  
  
Line 1125: Line 1126:
  
 %gist(1663134)% %gist(1663134)%
 +[gist cmci/1663134]
  
 ==== Plotting Mesh shapes: an example with tubes ==== ==== Plotting Mesh shapes: an example with tubes ====
Line 1131: Line 1133:
 It seems that there will be newer class called [[http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=blob;f=src-plugins/3D_Viewer/customnode/Tube.java;h=674156cee4131181336c36a6a65cdb2c807f510d;hb=HEAD|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.  It seems that there will be newer class called [[http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=blob;f=src-plugins/3D_Viewer/customnode/Tube.java;h=674156cee4131181336c36a6a65cdb2c807f510d;hb=HEAD|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>+<code javascript>
 // test for Mesh_Maker,createTube // test for Mesh_Maker,createTube
  
Line 1169: Line 1171:
 } }
  
-</sxh>+</code>
 [{{ :documents:figure20111219:figure20111219:track2frames.gif?250| Plotting of tracks}}] [{{ :documents:figure20111219:figure20111219:track2frames.gif?250| Plotting of tracks}}]
documents/110822jsip_cooking/javascript_imagej_cookbook.1464094015.txt.gz · Last modified: 2016/05/25 10:07 (external edit)
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