Arrow Labelling Tools

8/9/2019 Arrow Labelling Tools

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///////////////////////////////////////////////////////////////////////// Image, Stack and Timelapse Arrow Labelling//// avaible in the IJ macros toolsets repertory at// http://rsb.info.nih.gov/ij/macros/toolsets/Image, Stack and Timelapse Arrow Labelling.txt///////////////////////////////////////////////////////////////////////

// Author: Gilles Carpentier, Faculte des Sciences et// Technologies, Universite Paris 12 Val de Marne, France

// More information is available at// http://image.bio.methods.free.fr/arrows.html

// First version 24 04 2007// Requires the ImageJ 1.38p// Based on the following macros:// macro ArrowMakerTool, from the author and available on the ImageJ website at:// http://rsb.info.nih.gov/ij/macros/tools/ArrowMakerTool.txt// Macro BigCursorTool writen by Wayne Rasband, and avaible on the ImageJ websit

e at:// http://rsb.info.nih.gov/ij/macros/tools/BigCursorTool.txt// macro change Color tool, from the author and available on the ImageJ websiteat:// http://rsb.info.nih.gov/ij/macros/tools/ChangeColorTool.txt// macro SelectionColorMenuTool, from the author and available on the ImageJ website at:// http://rsbweb.nih.gov/ij/macros/tools/SelectionColorMenuTool.txt

var x, y, quadrantx,xlocation,ylocation,xinit,yinit,xprime,yprime,arrowline ;//spacer,var arrowlenght=20, arrowwidth=6, arrowconcav=21, taillenght=20,previewarrow=0,speed=15,defaultspeed=15;

var tailwidth=4, tailcolor="Cyan", tailorient="East", orientangle=0,newcolor = "Magenta", stackchoice="All the stack";var colorchoices=newArray("Magenta","Cyan","Yellow","Black","White","Red","Green","Blue"),rgb=newArray(3);var fromSlice ="", toSlice="",FSlice=0,TSlice=0,curentSlice=0;var lastx=-1,lasty=-1,h=-1,w=-1;var dyn=0,colorok=0,cursorok=0,drawok=0;var px = newArray(6), py = newArray(6);var ImaDemo="";

var newlook="New User Graphic Interface";var oldlook="Standard User Interface";

var interface=newArray("New User Graphic Interface","Standard User Interface");var lookInterface = "New User Graphic Interface";

var palette=0,reponse=0,cancel=0,apply=0;var targetWindow=0,tempPalette=0,paletteID=0;var Lpalette=250,Hpalette=420,Lprev=156,Hprev=156,xpreview=0,ypreview=0;

var distBord=15,disthaut=30,largbuton=53,hautbuton=25;// button cancel and applyvar box1x=99,box1y=(Hpalette-135);var box2x=222,box2y=(Hpalette-135);var box3x=160,box3y=(Hpalette-115);var box4x=89,box4y=(Hpalette-95);

var box5x=205,box5y=(Hpalette-95);

var Red="", Green="", Blue="", color ="", previousColor="";


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var onlinedoclink = "http://image.bio.methods.free.fr/arrows.html";var urllist = "http://image.bio.methods.free.fr/ij/ijupdatetest/ListOfMacros.txt";// to check the internet accessvar demoimagelink1 ="http://image.bio.methods.free.fr/ij/ijmacro/zebrafish/LSM-timelapse-demo-movie.tif.zip",demoimagename1="LSM-timelapse-demo-movie.avi",demoimagename11="LSM-timelapse-demo-movie.zip";

var demoimagelink2 ="http://image.bio.methods.free.fr/ij/ijmacro/zebrafish/LSM-timelapse-demo-movie-Arw.tif.zip",demoimagename2="LSM-timelapse-demo-movie-Arw.avi",demoimagename22="LSM-timelapse-demo-movie-Arw.zip";

var xx = requires138p(); // check version at install timefunction requires138p() {requires("1.38p"); return 0;}

// menu popup summering every commands of the the toolset menu bar (click right)var pmCmds = newMenu("Popup Menu", newArray("Abort Download","-","Set Drawing Arrow\(s\) Location","Draw Arrow\(s\) at the Current Location","-","Restore the Last Cursor Location","Display Coordinates","-","New User Graphic Interface","Standard User Interface","-","Change the Color of a Arrow","-","Undo the Last Arrow"

,"-", "Animation Speed Setting","Animate the Stack","-","Save a Stack as an \".avi\" Movie","-","Download\/Open Demo Timelapse Movie \(6 Mo\)","Download\/Open Demo Timelapse Movie Arrowed \(6 Mo\)","-","About \"Image, Stack and Timelapse Arrow Labelling\"","-","On Line Documentation"));

// click right menu, (ctrl click)macro "Popup Menu" {

cmd = getArgument();if (cmd !="-" && cmd =="Abort Download") {abortProcess ();}if (cmd !="-" && cmd =="Set Drawing Arrow\(s\) Location") {colorok=0;cur

sorok=1;drawok=0;dyn=1;setTool(10);}if (cmd !="-" && cmd =="Draw Arrow\(s\) at the Current Location") {draw

Arrow();}

if (cmd !="-" && cmd =="Change the Color of a Arrow") {colorok=1;cursorok=0;drawok=0;dyn=1; setTool(10);}

if (cmd !="-" && cmd =="Restore the Last Cursor Location") {restoreLastCursor ();}

if (cmd !="-" && cmd =="Display Coordinates") {DisplayCo ();}if (cmd !="-" && cmd == "Undo the Last Arrow") {UndoLast ();}if (cmd !="-" && cmd =="Save a Stack as an \".avi\" Movie") {saveAsAvi

();}

if (cmd !="-" && cmd == "New User Graphic Interface") {lookInterface = "New User Graphic Interface";}

if (cmd !="-" && cmd == "Standard User Interface") {lookInterface = "Standard User Interface";}

if (cmd !="-" && cmd =="Animation Speed Setting") {setMovieSpeed ();}if (cmd !="-" && cmd =="Animate the Stack") {AnimateStack();}if (cmd !="-" && cmd == "Download\/Open Demo Timelapse Movie \(6 Mo\)")

{OpenMovieLink(1,demoimagelink1,demoimagename1,demoimagename11);}if (cmd !="-" && cmd == "Download\/Open Demo Timelapse Movie Arrowed \(6

Mo\)") {OpenMovieLink(1,demoimagelink2,demoimagename2,demoimagename22);}

if (cmd !="-" && cmd == "About \"Image, Stack and Timelapse Arrow Labelling\"") {about1();}

if (cmd !="-" && cmd == "On Line Documentation") {doc ();}}

macro " Tool-1 - " {


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if (colorok==1 && dyn ==1 && getTitle !="Arrow Palette" && getTitle !="Last Arrow") {changeColor ();}

if (cursorok==1 && dyn ==1 && getTitle !="Arrow Palette" && getTitle !="Last Arrow") {Arrow (1);}

// no ansvers -> paletteif (palette==1 && getTitle =="Arrow Palette" && dyn ==1 && cancel==0 &&

reponse ==0) {if (isOpen("Arrow Palette")) {goGraphInt ();}

}

// ansvers is cancel -> close for cancelif (palette==0 && getTitle =="Arrow Palette" && dyn ==1 && cancel==1 &&

reponse ==1) {palette=0;cursorok=1;if (isOpen("Arrow Palette")) {

selectImage ("Arrow Palette");close ();

}

}// close for bad conditionsif (palette==1 && (getTitle !="Arrow Palette" ! isOpen("Arrow Palett

e")) && dyn ==1 && cancel==0 && reponse ==0) {palette=0;cursorok=0;if (isOpen("Arrow Palette")) {

selectImage ("Arrow Palette");close ();showMessage("No user ansvers from the \"Arrow Palette\".

\nThe tool has been unselected.");}

}// apply a user choose

if (palette==0 && getTitle =="Last Arrow" && dyn ==1 && cancel==0 && reponse ==1 && apply==1) {

if (isOpen(targetWindow)) {selectImage(targetWindow);DrawTheArrows (x,y);apply=0;reponse=0;cursorok=1;

}}

} // leave slot between ImageJ tools, and allow user interaction

// macro Open/Save a Movie Menu Toolvar mCmds = newMenu("Movie and Stack Menu Tool",newArray("Open a Movie as Stack","Save a Stack as an \".avi\" Movie","-","Download\/Open Demo Timelapse Movie \(6 Mo\)","Download\/Open Demo Timelapse Movie Arrowed \(6 Mo\)","-","Animation Speed Setting","Animate the Stack"));macro "Movie and Stack Menu Tool - CdccD16Dd0C999Df5CdefD3aC888D15CedeD52Db0Dc4CabdD72CfffD3bD3cD3dD3eD3fD4cD4dD4eD4fD5dD5eD5fD68D6dD6eD6fD7dD7eD7fD8dD8eD8fD9dD9eD9fDadDaeDafDbdDbfDceDcfDddDdeDeeDefDfeDffC17dD44CcdeD92CbbbD1bCffeD33D75C39eD93CeeeD61D71D81D91CcccD04D0dD12D21D22Dd1Dd2Dd4De6De8Df6Df8DfcC18eD36CcddDb3CaaaD01D03D05De7De9Df7CfeeD29DacC59dD59Dc6CeeeD1fD30D40D41D50D51D65D70D80D90Da0Da1Da2Db1Db2Dc0Dc1Dc2DdcCccdD27D85C1aeD9bCeddD25Dd8CcccD02D09D14D1eDe2De4DebDf2Df4CfffD66D98DbeDcdDdfC7adDa8CeeeD42D97CccdD18D26DecC18dD47CdddD06D0bD1aD20D23DeaCaa9D17CeeeD0fD2aD2bD2cD2eD32D88Dc3C48dDb4CbcdD82C29dDa9CddeDdbCcbbD00Df0CfffD5cD67D79D89C6adD77CeeeD57C09eD49CdddD08Dd5CabbDf9CfffD2dD2fDedDfdC59dD35CcceD43C3adD64CdeeD0aD0cD78C7bdD74CfeeDd9CcdeDa7C08eD45D48Db6CdccDd6C999D11De3Df3C59cDa3CaddD8cC

19eDaaCdddD0eD24CbbbD07D10De0C4aeD9aC19eDbaCdddD28DfaC4adD87CcddD62D6cC1aeD7bCeedD60DdaC8bdDc5C08eDb9CaaaD1dDe1Df1C6bdD84CbceD58D76D99C29eD4aCcdeD34D4bCbcbDfbC5aeD6aCeeeD31C0aeD6bDbbC5adDc8CcdeD56C2afD83CddeD69C8ceDa4C08eDb7Db8C999D13De5C9c


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eDccC19eD38DcbCdddDd7C4aeD95C09eD46C1aeD5aD8bC7beD8aCa9aD19C49dD53CaceDc9C39dDc7CceeD9cC5beD94C09fD54C2aeD73CddcD1cCaceDbcC4beD5bC08eD37C4adD55DabC8beD7aDcaC7adDa6C29eD86C6beD39C5adD96C3aeD63C8ceDa5CdcdDd3CadeD7c"{

cmd = getArgument();if (cmd!="-" && cmd == "Open a Movie as Stack") {openMovie ();}if (cmd!="-" && cmd == "Save a Stack as an \".avi\" Movie") {saveAsAvi

();}

if (cmd !="-" && cmd == "Download\/Open Demo Timelapse Movie \(6 Mo\)"){OpenMovieLink(1,demoimagelink1,demoimagename1,demoimagename11);}

if (cmd !="-" && cmd == "Download\/Open Demo Timelapse Movie Arrowed \(6Mo\)") {OpenMovieLink(1,demoimagelink2,demoimagename2,demoimagename22);}

if (cmd !="-" && cmd == "Animation Speed Setting") {setMovieSpeed ();}if (cmd !="-" && cmd =="Animate the Stack") {AnimateStack();}

}

// macro Arrow Drawing Menu Toolvar aCmds = newMenu("Arrow Drawing Menu Tool",newArray("Set Drawing Arrow\(s\) Location","Draw Arrow\(s\) at the Current Location","-","Restore the Last CursorLocation","-","New User Graphic Interface","Standard User Interface","-","Displa

y Coordinates","-","Change the Color of a Arrow","-","Undo the Last Arrow"));macro "Arrow Drawing Menu Tool -C0b3D0bD1bD2bD3bD41D42D43D44D45D46D47D48D49D4aD4bD4cD4dD4eD4fD5bD6bD7bD8bD9bDabDbbDcbDdbDebDfbCfffD00D01D02D03D04D05D06D07D08D09D0aD0cD0dD0eD0fD10D11D12D13D14D15D16D17D18D19D1aD1cD1dD1eD1fD20D21D22D23D24D25D26D27D28D29D2aD2cD2dD2eD2fD30D31D32D33D34D35D36D37D38D39D3aD3cD3dD3eD3fD40D50D51D52D53D54D55D56D57D58D5cD5dD5eD5fD60D61D62D63D64D65D6aD6cD6dD6eD6fD70D71D72D73D7aD7cD7dD7eD7fD80D81D82D83D84D85D86D89D8aD8cD8dD8eD8fD90D91D92D93D94D95D96D99D9aD9cD9dD9eD9fDa0Da1Da2Da3Da4Da5Da6Da9DaaDacDadDaeDafDb0Db1Db2Db3Db4Db5Db6Db8Db9DbaDbcDbdDbeDbfDc0Dc1Dc2Dc3Dc4Dc5Dc6Dc7Dc8Dc9DcaDccDcdDceDcfDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7Dd8Dd9DdaDdcDddDdeDdfDe0De1De2De3De4De5De6De7De8De9DeaDecDedDeeDefDf0Df1Df2Df3Df4Df5Df6Df7Df8Df9DfaDfcDfdDfeDffC00fD59D67D68D69D74D75D76D77D78D79D87D88D97D98Da7Db7C88fD5aD66Da8" {

cmd = getArgument();

if (cmd!="-" && cmd == "Set Drawing Arrow\(s\) Location") {colorok=0;cursorok=1;drawok=0;dyn=1; setTool(10);}

if (cmd!="-" && cmd == "Draw Arrow\(s\) at the Current Location") {drawArrow();}

if (cmd!="-" && cmd == "Change the Color of a Arrow") {colorok=1;cursorok=0;drawok=0;dyn=1; setTool(10);}

if (cmd!="-" && cmd == "Restore the Last Cursor Location") {restoreLastCursor ();}

if (cmd!="-" && cmd == "Display Coordinates") {DisplayCo ();}if (cmd!="-" && cmd == "Undo the Last Arrow") {UndoLast ();}if (cmd !="-" && cmd == "New User Graphic Interface") {lookInterface = "

New User Graphic Interface";}if (cmd !="-" && cmd == "Standard User Interface") {lookInterface = "Sta

ndard User Interface";}}

var cCmds = newMenu("Cursor Color Menu Tool",newArray("yellow","red","green","blue","magenta","cyan","orange","black","white","-","Restore Initial Selection Color","Get Curent Selection Color"));macro "Cursor Color Menu Tool - C1b0D85D95Da5Db5Dc5Dd5De5Df5CfffD00D01D02D03D04D06D07D08D09D0aD0bD0cD0dD0eD0fD10D11D12D13D14D16D17D18D19D1aD1bD1cD1dD1eD1fD20D21D22D23D24D26D27D28D29D2aD2bD2cD2dD2eD2fD30D31D32D33D34D36D37D38D39D3aD3bD3cD3dD3eD3fD40D41D42D43D44D46D47D48D49D4aD4bD4cD4dD4eD4fD50D51D52D53D54D56D57D58D59D5aD5bD5cD5dD5eD5fD60D61D62D63D64D66D67D68D69D6aD6bD6cD6dD6eD6fD80D81D82D83D84D86D87D88D89D8aD8bD8cD8dD8eD8fD90D91D92D93D94D96D97D98D99D9aD9bD9cD9dD9eD9fDa0Da1Da2Da

3Da4Da6Da7Da8Da9DaaDabDacDadDaeDafDb0Db1Db2Db3Db4Db6Db7Db8Db9DbaDbbDbcDbdDbeDbfDc0Dc1Dc2Dc3Dc4Dc6Dc7Dc8Dc9DcaDcbDccDcdDceDcfDd0Dd1Dd2Dd3Dd4Dd6Dd7Dd8Dd9DdaDdbDdcDddDdeDdfDe0De1De2De3De4De6De7De8De9DeaDebDecDedDeeDefDf0Df1Df2Df3Df4Df6Df7Df8Df


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9DfaDfbDfcDfdDfeDffC03fD70D71D72D73D74D75Cf00D05D15D25D35D45D55D65Cf0eD76D77D78D79D7aD7bD7cD7dD7eD7f" {

cmd=getArgument();if (previousColor == "") {previousColor= call("ij.gui.Roi.getColor");}if (cmd != "Restore Initial Selection Color" && cmd != "Get Curent Selec

tion Color" && cmd != "-") run("Colors...", "selection=["+cmd+"]");if (cmd == "Restore Initial Selection Color" && cmd != "-") RestoreInitC

olor ();if (cmd == "Get Curent Selection Color" && cmd != "-") GetCurentSelectio

nColor ();getSelectionColors(call("ij.gui.Roi.getColor"));showStatus("Selection color is now " + getColorName(Red,Green,Blue));

}

macro "Abort Process Action Tool - C810Dc2Df7Ca55D42D51Ce20D7dD8cDd6CfffD88Da7Cd20DadCfedD3eD55D5bDa9Dc1Ce40D63De6CfffD00D01D03D04D05D06D07D08D09D0aD0cD0dD0eD0fD10D11D14D1cD1dD1eD1fD20D21D22D2fD31D3fD40D66D6aDaaDb0Db5DbbDc0De0DefDf0Df1Df2Df3DfdDfeDffC811Da1Dd3Cc77D1bD6cCe20Dc7CfffD23D65D79DdfCc31D68Da4CeffDeeCd52D27D4dC910D7fD8fDbfDf9Cd64D4bD75Db7Dc6Ce30D39D47D48D74D85Da3CfffD13D30Da6Dd0De1Cc20Dac

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" {

abortProcess ();}

macro "On Line Documentation Action Tool - C000Da9DadDb6DbdDc5Dc6Dd3Dd4Dd5Dd6Ddd

C20fD11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD1fC0f3D42D43D44D45D46D47D48D49D4aD4bD4cD4dD4eD4fC0feD32D33D34D35D36D37D38D39D3aD3bD3cD3dD3eC444DdeDefC73fD01Cfd0D62D63D64D65D66D67D68D69D6aD6bD6cD6dD6eCeeeD90D95Da1Da4Db0Db2Db3De0De8Df0Df7DfaC222DeeC06fD22D23D24D25D26D27D28D29D2aD2bD2cD2dD2eC7f0D52D53D54D55D56D57D58D59D5aD5bD5cD5dD5eCcccDbfDf9Cf74D70Ca99D97C888Da8CfffD9bD9cC000Dc4Dd2C64fD10C0f4D41C0ffD31D3fCf40D71D72D73D74D75D76D77D78D79D7aD7bD7cD7dD7eD7fCa7fD00Cfd0D61D6fCfefD91C444Db5DdaDe9C06fD21D2fC7f0D51D5fCeddD96Cf88D82D83D84D85D8bD8cCaaaDccDeaDfdC999DcfCfffD9fDafDb1Db8De1C666Dc7C84fD02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eC333Da6Da7DaaDb9DbcDd9DdcCdddD9aDa2Da3Dc8DdbDecCaaaDabDaeDc1De3De4De5De6Cf89D8dC222DcdDedDfeDffC4ffD30CfffDebDf1Df2Df3Df4Df5Df6DfcC48fD20C4f6D40CeeeD92D93D94Da0DcbDf8DfbCbbbDb4Dd8C9f4D50C555Dc2C73fD0fC333DbbDc3Dc9Dd1CdddDe7Cf89D81D86D8aD8fC111DbaDd7CdeeDa5CbbbDb7Dc0De2Cf99D87D88D89C777DacDcaCcbbD9eCfaaD80C999D98Cf89D8eC999D9dC766D99C555DceC888DbeCfd4D60C777DdfC666Dd0"{

doc ();}

macro "Version and Update Infos Action Tool - CcccD5fD6fD7fD8fD9fC78bD17D19D2aD33D37D3bD42D4cD75D95DceDd5Dd9De6Df7Df9CddeDa3C36bD27D28D3aD57D58D59D66D76D77D86D87Da7Db8Dd6De8De9CeeeD00D01D02D04D06D07D08D09D0bD0dD0fD10D11D12D14D1bD1dD1fD20D21D22D2dD30D31D32D40D46D47D48D49D50D5bD60D70D71D72D74D7dD80D81D82D84D8dD90D91D92D94D9dDa0Da1Da2Da4Db0Db1DbbDc0Dc1Dc6Dc7Dc8Dc9Dd0Dd1Dd2De0De1De2DedDf0Df1Df2Df4DfbDfdDffC8beD3cD3dD4dD5aD6aD79D7aD7bD85D8bD9aDaaDc3Dc4Dd3Dd4CeeeD03D05D0aD0cD0eD13D15D1cD1eD23D2eD3eD4aD55D6cD73D7cD7eD83D8cD8eD93D9cD9eDb5DcaDdeDe3DeeDf3Df5DfcDfeC559D18D26D34D35D36D41D51D61DafDbfDcfDdaDdbDddDeaDf8CcddD2fD5cD6dD6eDabDb2Db4Dc2DefC99bD16D24D39D45D54D56D64D65Da5DacDb6DbcDcbDd7DecDfaCdefD67D8aC59dD29D2bD68D6

9D78D88D96D97D98D99Da6Da8Da9Db9De5De7CacdD1aD2cD38D4bD4eD5dD5eD6bD89D9bDb3DbaDc5Dd8De4Df6C348D25D43D44Db7DccDdcDebCcccD3fD4fDdf" {

VersionInfos ();


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}

macro "About \"Image, Stack and Timelapse Arrow Labelling\" Action Tool - C000D84Cb9fD25De7CaaaD14D2dDa0DafDecDfaCedfD49D4aD4bD4cD58D68D9bDb9DbaDbbDbcC889D2cDebCddfD52CcccD0bD22CeeeD00D03D0cD0fD10D1fD20D2fD30D40Dc0Dd0DdfDe0DefDf0Df1Df2Df3DfcDfeDffC666D07D70CdcfD34D35Dc4CbacD86D91CfefD6bD6dD7cD8cD8dD8eD9cD9dDadC97aDd3De5CedfD99CeeeD01D02D04D0dD0eD11D12D1eD21D3fDcfDd1De1De2DeeDf4DfdCfefD7dC545D94Da5

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" {

about1 ();}

macro "Undo Last Arrow [z]"{run("Undo");}

///////////////// Functions ////////////////////

// set the locationfunction Arrow (curs) {

targetWindow=getImageID();if (curs == 1) {

getCursorLoc(x, y, z, flags);xstart=x; ystart=y;w = getWidth(); h = getHeight();

x2=x; y2=y;while (flags&16!=0) {

getCursorLoc(x, y, z, flags);if (x!=x2 y!=y2) {

makeCursor(x,y,w,h);}x2=x; y2=y;wait(10);

};} else {xstart =-1; ystart=-1;}

// choose sliceif (x!=xstart && y!=ystart) {

lastx=x;lasty=y;nbslice= nSlices;curentSlice= getSliceNumber();if (nbslice >1) {chooseStack(curentSlice,nbslice);} else {FSlice

=nbslice;TSlice=nbslice;}if (lookInterface == oldlook) {DrawTheArrows (x,y);}if (lookInterface == newlook) {

palette=1;dyn=1;reponse=0;cancel=0;cursorok=0;if (! isOpen("Arrow Palette")) {updatePalette (1);}setTool(10);

}}

}

// set the parametersfunction arrow (box) {


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// old interfaceif (lookInterface == oldlook) {

if (box == 1) {previewarrow=0;arrowchoices1=newArray("3","6","10","15","20","25","30")

;arrowchoices2=newArray("10","15","20","25","30");

arrowchoices3=newArray("6","11","16","21","26","31");arrowchoices4=newArray("0","5","10","15","20","25","30")

;arrowchoices5=newArray("0","2","4","6","12");arrowchoices7=newArray("North","N-E","East","S-E","South

","S-W","West","N-W");

Dialog.create("Arrow Size and Form");Dialog.addChoice("Arrow length:", arrowchoices2, toStri

ng(arrowlenght));Dialog.addChoice("Arrow width:", arrowchoices1, toStrin

g(arrowwidth));

Dialog.addChoice("Arrowhead Filling Level:", arrowchoices3, toString(arrowconcav));Dialog.addChoice("Tail Size (Length):", arrowchoices4,

toString(taillenght));Dialog.addChoice("Tail Size (Width):", arrowchoices5, t

oString(tailwidth));Dialog.addChoice("Arrow Color:",colorchoices, tailcolor)

;Dialog.addChoice("Arrow Orientation:",arrowchoices7, tai

lorient);Dialog.addCheckbox("Preview", false);Dialog.addMessage(" Press 'z' to Undo (only the

last arrow)");

Dialog.show();

arrowlenght = parseFloat (Dialog.getChoice());arrowwidth = parseFloat (Dialog.getChoice());arrowconcav = parseFloat( Dialog.getChoice());taillenght = parseFloat(Dialog.getChoice());tailwidth = parseFloat(Dialog.getChoice());tailcolor = Dialog.getChoice();tailorient = Dialog.getChoice();previewarrow = parseFloat (Dialog.getCheckbox());

}if (arrowconcav > (arrowlenght+1)) arrowconcav=(arrowlenght+1);if (tailwidth > arrowwidth) tailwidth = (arrowwidth-3);arrowline=1;xfleche=x; yfleche=y;if (previewarrow == true) {preview();}selectImage(targetWindow);setupUndo();

if (arrowconcav > (arrowlenght+1)) arrowconcav=(arrowlenght+1);if (tailwidth > arrowwidth) tailwidth = (arrowwidth-3);

for (a=0;a


8/22

if (lookInterface == newlook) {arrowline=1;xfleche=x; yfleche=y;setupUndo();for (a=0;a


9/22

getxy (xi,i,alpha3a);getxy (xprime,yprime,(alpha3a+orientangle));fleche1[1]=(xfleche + xprime);fleche2[1]=(yfleche + yprime);drawLine(fleche1[0], fleche2[0], fleche1[1], fleche2[1]);drawLine(fleche1[2],fleche2[2], fleche1[1], fleche2[1]);

}// tail drawing

if (tailwidth != 0) {getxy (0,arrowconcav,alpha3a);getxy (xprime,yprime,(alpha3a+orientangle));x3a=xprime;y3a=yprime;getxy (0,(arrowconcav+taillenght),alpha3a);getxy (xprime,yprime,(alpha3a+orientangle));x3b=xprime;y3b=yprime;lineWidth=tailwidth;setLineWidth(tailwidth);drawLine ((xfleche+x3a), (yfleche + y3a), (xfleche+x3b),(yfleche

+y3b));}

updateDisplay;}

function getxy (xxx,yyy,beta) {if (xxx==0) xxx=1;if (yyy==0) yyy=1;xprime=round( (cos(beta) *(xxx/(cos(atan2(yyy,xxx))))));yprime=round( (sin(beta) *(xxx/(cos(atan2(yyy,xxx))))));

}

function getRGBcolor (couleur) {if (couleur=="Magenta") {rgb[0] = 255; rgb[1]= 0; rgb[2] = 225;}if (couleur=="Cyan") {rgb[0]=0; rgb[1]=255; rgb[2]=255;}

if (couleur=="Yellow") {rgb[0]=255; rgb[1]=255; rgb[2]=0;}if (couleur=="White") {rgb[0] =255; rgb[1] =255; rgb[2]=255;}if (couleur=="Black") {rgb[0]=0; rgb[1]=0; rgb[2]=0;}if (couleur=="Red") {rgb[0]=255; rgb[1]=0; rgb[2]=0;}if (couleur=="Green") {rgb[0]=0; rgb[1]=255; rgb[2]=0;}if (couleur=="Blue") {rgb[0]=0; rgb[1]=0; rgb[2]=255;}return rgb;

}

function chooseStack(curentSlc,nbslices) {SliceMenu=newArray(nbslices);fromSlice=curentSlc;toSlice=curentSlc;for (i=0; i < nbslices ; i++) {SliceMenu[i]=toString(i+1);}Dialog.create("User Choices");if (nbslices >1) {

Dialog.addMessage("You are working with a stack of " + nbslices+" slices . Choose \nto draw an arrowonto the current slice or other slices:");

Dialog.addMessage("the default values correspond to the currentslice. Set the\nsame slicenumber to draw an arrow onto a single slice.");

Dialog.addMessage("Arrow drawing");Dialog.addChoice("from the slice", SliceMenu,toString(fromSlice)

); Dialog.addChoice("to the slice",SliceMenu,toString(toSlice));}Dialog.show();fromSlice= Dialog.getChoice(); FSlice=parseFloat (fromSlice);toSlice= Dialog.getChoice(); TSlice=parseFloat (toSlice);

}

function openMovie () {


10/22

if (ImaDemo != "") {run("Using QuickTime...", "open...");//run("Using QuickTime...", "open=["+ImaDemo+"]");

} else {run("Using QuickTime...", "open..."); }ImaDemo="";

}

function saveAsAvi () {theStack= getTitle;if (nSlices == 1) exit ("You can\'t make a movie with a single image. Fi

st make a stack.");folderTreatedpath =getDirectory("current");if (ImaDemo != "") folderTreatedpath =ImaDemo;if (endsWith(theStack, ".tif") == 1) {theStack = substring (theStack,0,(

indexOf(theStack, ".tif")));}if (endsWith(theStack, ".avi") == 1) {theStack = substring (theStack,0,(

indexOf(theStack, ".avi")));}kind=lastIndexOf(theStack, "-Arw-");if (kind>0) {theStack = substring (theStack,0,kind);}

n=1;checkpath= folderTreatedpath + theStack + "-Arw-"+n+".avi";while (File.exists(checkpath)) {

n++;checkpath= folderTreatedpath + theStack + "-Arw-"+n+".avi";

}// set the rate speed of the movie (image/sec)userspeed=15;speed=0;while (speed < 1 speed > 60) {

Dialog.create("Save Movie Settings");Dialog.addMessage("File destination\:\n"+checkpath);Dialog.addNumber("Speed of the movie 1 ... 60 ?", defaultspeed,

0, 2, "(image\/sec)");

Dialog.show();speed=Dialog.getNumber();

}defaultspeed=speed;run("Animation Options...", "speed=["+speed+"]");saveAs ("avi", checkpath);

}

// to draw a arrow at the curent locationfunction drawArrow() {

if (getTitle =="Arrow Palette" getTitle =="Last Arrow") exit;targetWindow=getImageID();makeCursor(lastx,lasty,w,h);if (lastx != -1 && lasty!= -1) {

x=lastx;y=lasty;Arrow (0);

} else {showMessage ("No current location coordinates found. Choose a location \nusing the \"Set Drawing Arrow\(s\) Location\" sub menu of the \n\"ArrowDrawing Menu Tool\".");}}

// called from the user interface toolfunction changeColor () {

if (getTitle !="Arrow Palette" && getTitle !="Last Arrow") {

setupUndo();getCursorLoc(x, y, z, flags);doWand(x, y);


11/22

Dialog.create("New Color Choice");Dialog.addChoice("Color?",colorchoices, toString(newcolor));Dialog.addMessage(" Press 'z' to Undo");Dialog.show();newcolor = Dialog.getChoice();rgb=getRGBcolor (newcolor);setColor(rgb[0], rgb[1], rgb[2]);

fill();run("Select None");

}}

function makeCursor(x,y,w,h) {px[0]=0; py[0]=y;px[1]=w; py[1]=y;px[2]=x; py[2]=y;px[3]=x; py[3]=0;px[4]=x; py[4]=h;px[5]=x; py[5]=y;

makeSelection("polgon", px, py);showStatus("Target coodinates: x="+x+", y="+y);}

function restoreLastCursor () {if (getTitle =="Arrow Palette" getTitle =="Last Arrow") exit;if (lastx != -1 && lasty!= -1) {

makeCursor(lastx,lasty,w,h);} else {exit ("No previous cursor available.");}

}

// draw the arrowsfunction DrawTheArrows (x,y) {

nbslice= nSlices;countslc=1;for (i=FSlice; i


12/22

run("URL...", "url=["+demoimagelink+"]");imageid = getImageID();nomdimage = getTitle;// Create a repertory in ImageJ folder.File.makeDirectory(ImaDemo1);if (!File.exists(ImaDemo1)) exit ("Unable to create the director

y \""+ImaDemo1+"\" , something wrong in the ImageJ folder");

// Create a repertory in ImageJ folder.

File.makeDirectory(ImaDemo2);if (!File.exists(ImaDemo2)) exit ("Unable to create the director

y \""+ImaDemo2+"\" , something wrong in the ImageJ folder");selectWindow(nomdimage);speed=15;run("Animation Options...", "speed=["+speed+"]");saveAs ("avi", fildestination);saveAs ("zip", fildestination1);close();

}

// create a working folder with the dowloaded movieif (File.exists(fildestination) && ! isOpen(demoim)) {//if (question ==1 ) showMessageWithCancel ("The \"" + demoim +

"\" has been downloaded available at the following HD location:\n" + fildestination + "\n and:" + fildestination1+"\nOpen it now as a stack ?\n(Or \"Cancel\" and open it from the \"Open a Movie as Stack\" sub\-menu of the \"Movie and StackMenu Tool\"\) ");

if (question ==1 ) showMessageWithCancel ("- The \"" + demoim +"\" has been downloaded and available at the following HD location:\n" + fildestination + "\n- A \".zip\" stack version is also available at the following HD location (for computer without required QuickTime resources):\n"+ fildestination1+"\n \nOpen the stack now? ");

//run("Using QuickTime...", "open=["+fildestination+"]");

open(fildestination1);}setBatchMode("exit and display");

}

function setMovieSpeed () {userspeed=15;speed=0;while (speed < 1 speed > 60) {

Dialog.create("Movie\/Stack Animation Speed Settings");Dialog.addNumber("Speed of the movie\/stack animation 1 ... 60

?", defaultspeed, 0, 2, "(image\/sec)");Dialog.show();speed=Dialog.getNumber();

}defaultspeed=speed;run("Animation Options...", "speed=["+speed+"]");

}

function AnimateStack() {run("Start Animation");

}

function UndoLast () {run("Undo");

}

function DisplayCo () {showMessage("X Coordinate: "+x + "\nY Coordinate: "+y);


13/22

}

// graphic interfacefunction goGraphInt () {

clickx=0;clicky=0;reponse=0;cancel=0;dyn =0;if (! isOpen("Arrow Palette")) {reponse=1;cancel=1;}

getCursorLoc(clickx, clicky, z, flags);

if (Nord(clickx,clicky) ==1) {tailorient="North";updatePalette (0);}if (Sud (clickx,clicky) ==1) {tailorient="South";updatePalette (0);}if (Est (clickx,clicky) ==1) {tailorient="East";updatePalette (0);}if (Ouest (clickx,clicky) ==1) {tailorient="West";updatePalette (0);}if (NordOuest (clickx,clicky) ==1) {tailorient="N-W";updatePalette (0);}if (NordEst (clickx,clicky) ==1) {tailorient="N-E";updatePalette (0);}if (SudEst (clickx,clicky) ==1) {tailorient="S-E";updatePalette (0);}if (SudOuest (clickx,clicky) ==1) {tailorient="S-W";updatePalette (0);}

testcolor= coloBoxes(0,1,clickx,clicky);

if (testcolor != "") {tailcolor=testcolor;updatePalette (0);}

boxstatut=adjustBoxes(box1x,box1y,0,1,clickx,clicky);if (boxstatut == 2) {arrowlenght=arrowlenght-1;updatePalette (0);}if (boxstatut == 3) {arrowlenght=arrowlenght+1;updatePalette (0);}

boxstatut=adjustBoxes(box2x,box2y,0,1,clickx,clicky);if (boxstatut == 2) {arrowwidth=arrowwidth-1;updatePalette (0);}if (boxstatut == 3) {arrowwidth=arrowwidth+1;updatePalette (0);}

boxstatut=adjustBoxes(box3x,box3y,0,1,clickx,clicky);if (boxstatut == 2) {arrowconcav=arrowconcav-1;updatePalette (0);}if (boxstatut == 3) {arrowconcav=arrowconcav+1;updatePalette (0);}

boxstatut=adjustBoxes(box4x,box4y,0,1,clickx,clicky);if (boxstatut == 2) {taillenght=taillenght-1;updatePalette (0);}if (boxstatut == 3) {taillenght=taillenght+1;updatePalette (0);}

boxstatut=adjustBoxes(box5x,box5y,0,1,clickx,clicky);if (boxstatut == 2) {tailwidth=tailwidth-1;updatePalette (0);}if (boxstatut == 3) {tailwidth=tailwidth+1;updatePalette (0);}

if (Cancel (clickx,clicky) == 1) {cancel=1;reponse=1;palette=0;}if (Apply (clickx,clicky) ==1) {cancel=0;reponse=1;palette=0;apply=1;cur

sorok=1;}dyn =1;

}

function getSample () {selectImage (targetWindow);xtemp=getWidth(); ytemp=getHeight();run("Select None");setBatchMode(true);run("Duplicate...", "title=temp");run("Select All");run("Copy");close ();newImage("tempSample","RGB Black",xtemp+2*Lprev,ytemp+2*Hprev,1);setForegroundColor(62,10,113);run("Select All");run("Fill");run("Select None");

run("Paste");run("Select None");makeRectangle ((x+(Lprev/2)+1), (y+(Lprev/2)+1), Lprev-2, Hprev-2);run("Copy");close ();


14/22

}

function coloBoxes(draw,detect,clickx,clicky) {xcolorbox=20;ycolorbox=10;spcol=(Lpalette-8*xcolorbox)/9;setLineWidth(1);detectcol=-1;democolor="";for (a=0;a(Hpalette-160) && clicky < (Hpalette-160+yco

lorbox)) {if (clickx > (a*xcolorbox+a*spcol+spcol) && clic

kx < ((a*xcolorbox+a*spcol+spcol)+xcolorbox)) detectcol=a;}

}if (draw==1) {drawRect ((a*xcolorbox+a*spcol+spcol), (Hpalette-1

60), xcolorbox, ycolorbox);run("Select None");}if (a==0) {getRGBcolor ("Red");if (detect==1 && detectcol==0) {d

emocolor ="Red";}}if (a==1) {getRGBcolor ("Green");if (detect==1 && detectcol==1)

{democolor ="Green";}}if (a==2) {getRGBcolor ("Blue");if (detect==1 && detectcol==2) {democolor ="Blue";}}

if (a==3) {getRGBcolor ("Cyan");if (detect==1 && detectcol==3) {democolor ="Cyan";}}

if (a==4) {getRGBcolor ("Yellow");if (detect==1 && detectcol==4){democolor ="Yellow";}}

if (a==5) {getRGBcolor ("Magenta");if (detect==1 && detectcol==5) {democolor ="Magenta";}}

if (a==6) {getRGBcolor ("Black");if (detect==1 && detectcol==6){democolor ="Black";}}

if (a==7) {getRGBcolor ("White");if (detect==1 && detectcol==7){democolor ="White";}}

if (draw==1) {setColor(rgb[0], rgb[1], rgb[2]);fillRect ((a*xcolorbox+a*spcol+spcol+1), (Hpalette-160+1), (xcolorbox-2), (ycolorbox-2));run("Select None");}

}return democolor;

}

function adjustBoxes(xbx,ybx,draw,detect,clickx,clicky) {xadjustbox=25;yadjustbox=14;setLineWidth(1);status=0;if (detect==1) {

if (clicky >(ybx) && clicky < (ybx+yadjustbox) && clickx > (xbx+xadjustbox/2) && clickx < (xbx+xadjustbox)) {status=3;}

if (clicky >(ybx) && clicky < (ybx+yadjustbox) && clickx > xbx && clickx < (xbx+xadjustbox/2)) {status=2;}

}if (draw==1) {

setColor(100,50,50);fillRect ((xbx+1), (ybx+1), (xadjustbox-1),(yadjustbox-1));run("Select None");

setColor(255,0,93);drawRect (xbx, ybx, xadjustbox, yadjustbox);run("Select None");

drawLine ((xbx+xadjustbox/2-1), ybx, (xbx+xadjustbox/2-1), (ybx+yadjustbox-1));

setFont("SansSerif", 15,"antialiased");setColor(0,255,0);drawString("-",(xbx+2),(ybx+15));

drawString("+",(xbx+xadjustbox/2-1),(ybx+15));}return status;


15/22

}

// location of the different interactive areas// cancelfunction Cancel (clickx,clicky) {

testcancel=0;if (clickx > distBord && clickx < (distBord+largbuton) && clicky > (Hpa

lette-disthaut) && clicky < (Hpalette-disthaut+hautbuton)) {testcancel=1;}return testcancel;

}

function Nord (clickx,clicky) {if (clickx > (xpreview-8) && clickx < (xpreview +8) && clicky > ((yp

review+(Hprev/2))+(Lpalette-Hprev)/6) && clicky < ((ypreview+(Hprev/2))+(Lpalette-Hprev)/6+20)) {testpal=1;} else {testpal=0;} return testpal;}

function Sud (clickx,clicky) {if (clickx > (xpreview-8) && clickx < (xpreview +8) && clicky > ((Lp

alette-Hprev)/3-20) && clicky < ((Lpalette-Hprev)/3)) {testpal=1;} else {testpal=0;} return testpal;}

function Ouest (clickx,clicky) {if (clickx > (xpreview+(Lprev/2)+(Lpalette-Lprev)/6) && clickx < (xpre

view+(Lprev/2)+(Lpalette-Lprev)/6+20) && clicky > (ypreview-8) && clicky ((Lpalette-Lprev)/3-20) && clickx < ((Lpalette-Lprev)/3)

&& clicky > (ypreview-8) && clicky < (ypreview+8) ) {testpal=1;} else {test

pal=0;} return testpal;}

function NordOuest (clickx,clicky) {if (clickx > (xpreview+(Lprev/2)+(Lpalette-Lprev)/6) && clickx < (xpre

view+(Lprev/2)+(Lpalette-Lprev)/6+18) && clicky > ((ypreview+(Hprev/2))+(Lpalette-Hprev)/6) && clicky < ((ypreview+(Hprev/2))+(Lpalette-Hprev)/6+18) ) {testpal=1;} else {testpal=0;} return testpal;}

function NordEst (clickx,clicky) {if (clickx > ((Lpalette-Lprev)/3-18) && clickx < ((Lpalette-Lprev)/3)

&& clicky > ((ypreview+(Hprev/2))+(Lpalette-Hprev)/6) && clicky < ((ypreview+(Hprev/2))+(Lpalette-Hprev)/6+18) ) {testpal=1;} else {testpal=0;} return testpal;}

function SudEst (clickx,clicky) {if (clickx > ((Lpalette-Lprev)/3-18) && clickx < ((Lpalette-Lprev)/3)

&& clicky > ((Lpalette-Hprev)/3-18) && clicky < ((Lpalette-Hprev)/3) ) {testpal=1;} else {testpal=0;} return testpal;}

function SudOuest (clickx,clicky) {if (clickx > (xpreview+(Lprev/2)+(Lpalette-Lprev)/6) && clickx < (xpre

view+(Lprev/2)+(Lpalette-Lprev)/6+18) && clicky > ((Lpalette-Lprev)/3-18) &&clicky < ((Lpalette-Lprev)/3) ) {testpal=1;} else {testpal=0;} return testpal;}


16/22

// applyfunction Apply (clickx,clicky) {

testapply=0;if (clickx > (Lpalette-distBord-largbuton) && clickx < (Lpalette-distBor

d) && clicky > (Hpalette-disthaut) && clicky < (Hpalette-disthaut+hautbuton)) {makeRectangle (0,0,Lpalette,(Hpalette-36));

run("Crop");if (isOpen("Last Arrow")) {selectWindow("Last Arrow");close ();}selectImage (paletteID);rename ("Last Arrow");testapply=1;

}return testapply;

}

function updatePalette (draw) {setBatchMode(true);if (draw ==1) {

setBatchMode(true);

getSample ();restoreLastCursor ();setLineWidth(arrowline);// make the palette windownewImage("Arrow Palette","RGB Black",Lpalette,Hpalette,1);paletteID=getImageID();setForegroundColor(32,0,93);run("Select All");run("Fill");run("Select None");setColor(255,0,93);drawRect ( (Lpalette-Lprev)/2, (Lpalette-Lprev)/2, Lprev, Hprev)

;run("Select None");xpreview=((Lpalette-Lprev)/2 + Lprev/2);ypreview=((Lpalette-Lprev)/2 + Hprev/2);

// draw orientation arrows

builtarrow (2,(Lpalette-Lprev)/3,ypreview,6,20,"East",15,0,0,getRGBcolor ("Yellow"));

builtarrow (2,(Lpalette-Lprev)/3,(Lpalette-Hprev)/3,6,20,"S-E",15,0,0,getRGBcolor ("Yellow"));

builtarrow (2,xpreview,(Lpalette-Hprev)/3,6,20,"South",15,0,0,getRGBcolor ("Yellow"));

builtarrow (2,xpreview+(Lprev/2)+(Lpalette-Lprev)/6,(Lpalette-Hprev)/3,6,20,"S-W",15,0,0,getRGBcolor ("Yellow"));

builtarrow (2,xpreview+(Lprev/2)+(Lpalette-Lprev)/6,ypreview,6,20,"West",15,0,0,getRGBcolor ("Yellow"));

builtarrow (2,xpreview+(Lprev/2)+(Lpalette-Lprev)/6,(ypreview+(Hprev/2))+(Lpalette-Hprev)/6,6,20,"N-W",15,0,0,getRGBcolor ("Yellow"));

builtarrow (2,xpreview,(ypreview+(Hprev/2))+(Lpalette-Hprev)/6,6,20,"North",15,0,0,getRGBcolor ("Yellow"));

builtarrow (2,(Lpalette-Lprev)/3,(ypreview+(Hprev/2))+(Lpalette-Hprev)/6,6,20,"N-E",15,0,0,getRGBcolor ("Yellow"));

coloBoxes(1,0,0,0);

setLineWidth(arrowline);setColor(255,0,0);// button canceldrawRect (distBord, (Hpalette-disthaut), largbuton, hautbuton);r

un("Select None");setColor(0,255,0);// button applydrawRect ((Lpalette-distBord-largbuton), (Hpalette-disthaut), la


17/22

rgbuton, hautbuton);run("Select None");setColor(100,0,133);fillRect (distBord+1, Hpalette-disthaut+1, largbuton-2, hautbuto

n-2);fillRect (Lpalette-distBord-largbuton+1, Hpalette-disthaut+1, la

rgbuton-2, hautbuton-2);setFont("SansSerif", 12,"bold");

setColor(255,60,60);drawString("Cancel",(distBord+5),(Hpalette-10));run("Select None

");setColor(0,255,0);drawString("Apply",(Lpalette-distBord-largbuton+7),(Hpalette-10)

);run("Select None");}

makeRectangle ( ((Lpalette-Lprev)/2+1), ((Lpalette-Lprev)/2+1), Lprev-2,Hprev-2);

run("Paste");run("Select None");if (arrowconcav > (arrowlenght+1)) arrowconcav=(arrowlenght+1);

if (tailwidth > arrowwidth) tailwidth = (arrowwidth-3);if (arrowwidth < 0) arrowwidth=0;if (arrowlenght < 0) arrowwidth=0;if (arrowconcav < 0) arrowconcav=0;if (tailwidth < 0) tailwidth=0;if (taillenght < 0) taillenght=0;builtarrow (arrowline,xpreview,ypreview,arrowwidth,arrowlenght,tailorien

t,arrowconcav,tailwidth,taillenght,getRGBcolor (tailcolor));

setColor(32,0,93); //setColor(150,0,93);fillRect(0, (Hpalette-140), Lpalette,103);

adjustBoxes(box1x,box1y,1,0,0,0);

adjustBoxes(box2x,box2y,1,0,0,0);adjustBoxes(box3x,box3y,1,0,0,0);adjustBoxes(box4x,box4y,1,0,0,0);adjustBoxes(box5x,box5y,1,0,0,0);

setColor(255,255,255);setFont("SansSerif", 12);drawString("Arrow Lenght:"+arrowlenght, 2,(Hpalette-120));drawString("Arrow Width:"+arrowwidth, 130,(Hpalette-120));

drawString("Arrowhead Filling Level:"+arrowconcav,2,(Hpalette-120+20));drawString("Tail Lenght:"+taillenght,2,(Hpalette-120+40));drawString("Tail Width:"+tailwidth,125,(Hpalette-120+40));drawString("Arrow Color:"+tailcolor,2,(Hpalette-120+60));

drawString("Arrow Orientation:"+tailorient,2,(Hpalette-120+80));setBatchMode("exit and display");

}

function RestoreInitColor () {if (previousColor !="") {

getSelectionColors (previousColor);run("Colors...", "selection=["+getColorName(Red,Green,Blue)+"]")

;showMessage ("Previous selection color \"" + getColorName(Red,Gr

een,Blue) + "\" has been restored");} else {showMessage ("Selection Color has not been changed");}

}


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function GetCurentSelectionColor () {color= call("ij.gui.Roi.getColor");getSelectionColors (color);showMessage ("Curent selection color: "+ getColorName(Red,Green,Blue) +

" \(Red="+Red+" Green="+Green+" Blue="+Blue+"\)");}

// decodes a color in the form "java.awt.Color[r=255,g=255,b=0]"function getSelectionColors (color) {

Red = substring(color, (indexOf(color, "r=")+2), (indexOf(color, "g=")-1));

Green= substring(color, (indexOf(color, "g=")+2), (indexOf(color, "b=")-1));

Blue= substring(color, (indexOf(color, "b=")+2), indexOf(color, "]"));}

function getColorName(r,g,b) {if (r=="255" && g=="255" && b=="0") ColorName ="yellow";

if (r=="255" && g=="0" && b=="0") ColorName ="red";if (r=="0" && g=="255" && b=="0") ColorName ="green";if (r=="0" && g=="0" && b=="255") ColorName ="blue";if (r=="255" && g=="0" && b=="255") ColorName ="magenta";if (r=="0" && g=="255" && b=="255") ColorName ="cyan";if (r=="255" && g=="200" && b=="0") ColorName ="orange";if (r=="0" && g=="0" && b=="0") ColorName ="black";if (r=="255" && g=="255" && b=="255") ColorName ="white";return ColorName;

}

function abortProcess () {setKeyDown("Esc");}

function about1() {about="";about=about+"

-- Image, Stack and Timelapse Arrow Labelling --";about=about+"\n* Description:";about=about+"\nThis toolset allows to draw, with an interactive graphic

interface, \"histological\" arrows on images,\nstacks and movies.";about=about+"\n* Notice:";about=about+"\n - The \"Movie and Stack Menu\" regroups the functions

specific to movies and stack:";about=about+"\n - \"Open a Movie as Stack\" displays a dialog bo

x to open a movie, using QuickTime resources,\n which will be opened asa stack of images.";

about=about+"\n - \"Save a Stack as an \".avi\" Movie\" recordsa stack as an avi uncompressed movie into the same\n repertory than theoriginal one, with an incremented suffix number.";

about=about+"\n - \"Download\/Open Demo Timelapse Movie\" and \"Download\/Open Demo Timelapse Movie Arrowed\"\n give respectively a training movie and an example of arrowed movie. Initial movie, obtained by\nLSM microscopy, was provided by Tim Chico (*).";

about=about+"\n - Set the stack/movie animation speed using \"Animation Speed Setting\".";

about=about+"\n - Check for the arrow effect on a stack using \"Animate the Stack\". ";

about=about+"\n - The \"Arrow Drawing Menu\" regroups the arrow drawin

g utilities:";about=about+"\n - \"Set Drawing Arrow(s) Location\" is the first

step to draw arrows: move, staying clicked, onto the\n image, until the


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cursor points the correct target of the arrow. Unclick, and adjust settings using the\n menu and the graphic interface which then will appear.";

about=about+"\n - \"Draw Arrow(s) at the Current Location\" draws a arrow at the current location when the user\n graphic interface hasbeen canceled, or the cursor erased for any reason.";

about=about+"\n - \"Restore the Last Cursor Location\" restoresa visual (non active) cursor at the last location.";

about=about+"\n - \"New User Graphic Interface\" is the defaultinterface to set the arrow characteristics.";

about=about+"\n - \"Standard User Interface\" allows to use thedialog box interface of the \"ArrowMakerTool\" instead\n of the graphical interface.";

about=about+"\n - \"Display Coordinates\" gives the coordinatesx, y of the current location (same as displayed in the\n status bar).";

about=about+"\n - \"Change the Color of a Arrow\" allows to change the color of a draw arrow, by clicking on it.";

about=about+"\n - \"Undo the Last Arrow\" erases the last drawnarrow (only for single image or slice).";

about=about+"\n - The \"Cursor Color Menu Menu\" allows to manage the

cursor color to make easier the visual location\n of the target area, depending of the background color of the image.";about=about+"\n - Click on the \"Abort Process\" ImageJ tool bar icon

to cancel too long processes.";about=about+"\n - Click on the \"On Line Documentation\" ImageJ tool b

ar icon for more details."; about=about+"\n - Click on the \"Version and Update Infos\" ImageJ tool bar icon to look for new beta versions.";

about=about+"\n---------------------------------------------------------------------------------------------";

about=about+"\nThis toolset based on the \"ArrowMakerTool\" was adaptedto stacks and movies at the request of Tim Chico,\nPI in vascular biology at theUniversity of Sheffield, UK. Tim Chico also provided the downloadable movie\nexample.";

about=about + "\n--------------------------------------------------------------------------------------------";

about=about +"\nAuthor: Gilles Carpentier"+"\nFaculte des Sciences et Technologies"+"\nUniversite Paris 12 Val de Marne, France.";

showMessage(about);//print (about);

}

function doc () {if (File.openUrlAsString(urllist) == "") exit("You need an internet acce

ss to run this function.");showMessageWithCancel ("A notice is avaible on line. Open it with your

default web browser?");run("URL...", "url=["+onlinedoclink +"]");

}

// --- End of code of the macro project ---//// ----------------------------------////////////

//////


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////////////// -------------------*** Additionnal code for on line update resources ***-----

------------------------

//Developer info//Kind:Toolset//Title:"Image, Stack and Timelapse Arrow Labelling"//Version:1.0//Date: 28 April 2007//Origin:NIH//End info

function VersionInfos () {// variables for on line update resources

beginsign="//Developer info";endsign="//End info";kind="toolsets/";urlrep="http://image.bio.methods.free.fr/ij/ijmacro/zebrafish/";name="Image, Stack and Timelapse Arrow Labelling.txt";namedev="Image, Stack and Timelapse Arrow Labelling-dev.txt";favoritefoldername= "Image.Bio.Methods";

version=versionMessage();if (indexOf(version, "install it?" ) > 0 ) {

macrotext=getdistantmacro (namedev,urlrep);macrolocal="";macropath=getDirectory("macros")+kind+namedev;if (File.exists(macropath)) {macrolocal=File.openAsString(macrop

ath);}

if (macrotext != macrolocal) {//perfom the installationDialog.create("New version installation option");Dialog.addMessage(version);Dialog.addCheckbox("Install a Plugin Shortcut?", 0);Dialog.addMessage("(This option provides a shortcut in t

he plugins menu of ImageJ, making easier\nthe next use of the new installed version).");

Dialog.show();plugin= Dialog.getCheckbox();f= File.open(macropath);print (f,macrotext);File.close(f);if (plugin ==1) {InstallPluginsStarter(namedev);}message="The installation of the "+giveDevInfo (macrotex

t,1)+ " "+ giveDevInfo (macrotext,2)+ "is completed.";message=message+ " Do you want to run it?";showMessageWithCancel(message);run("Install...", "install=["+macropath+"]");

}} else {showMessage (version); // comment without installation available

}}

function versionMessage() {

version="";if (getDirectory("startup") == 0) exit ("Unable to find the startup dire


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ctory, something wrong in the ImageJ folder");if (getDirectory("macros") == 0) exit ("Unable to find the macros direct

ory, something wrong in the ImageJ folder");MacroPath=getDirectory("macros");thismacropath=MacroPath+kind+name;if (! File.exists(thismacropath)) exit ("This macro has to be recorded u

nder the name of \"" +name+"\"\ninto the \"macros/"+kind+"\" folder of ImageJ.");

macrotext=File.openAsString(thismacropath);macrotextdistant=getdistantmacro (namedev,urlrep);

version="";macrolocal="";version=version + "\n \nThis version of the " + giveDevInfo (macrotext,1

) + " " + giveDevInfo (macrotext,2);version=version + "is provided by the " + giveDevInfo (macrotext,5)+ " w

eb site.";version=version + "\nVersion number: " + giveDevInfo (macrotext,3)+ " -

" + giveDevInfo (macrotext,4) +".";

if (macrotextdistant !="" ) {new=giveDevInfo (macrotextdistant,3);old=giveDevInfo (macrotext,3);

if (new > old) {macropath=getDirectory("macros")+kind+namedev;if (File.exists(macropath)) {macrolocal=File.openAsStrin

g(macropath);}if (macrotextdistant != macrolocal) {

update="\n \nA new beta version "+new+ " is available on the " +giveDevInfo (macrotextdistant,5)+ " web site: ";

update=update+ "\n \nDo you want to install it?";

} else {

update ="\n \nThe new "+new+" beta version called \"" +namedev+ "\" provided by \nthe "+giveDevInfo (macrotextdistant,5) +" website has already be installed";

update = update+ " in the \"" +kind+ "\" repertory \nof ImageJ.";

}} else {

update="No new Beta version available.";}version=version +"\n" + update ;

}return version;

}

function giveDevInfo (text,n) {lines=split(text,"\n");if ( (indexOf(text, beginsign)


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// Function giving the content of a distant macro (name) located at the distantrepertory (urlrep).function getdistantmacro (name,urlrep) {

macrotextnih="";if (File.openUrlAsString("http://rsb.info.nih.gov/ij/macros/Arrays.txt")

!= "") {distantmacrolink = urlrep + name;

if (indexOf(distantmacrolink, " ") > -1) {while (indexOf(distantmacrolink, " ") > -1) {

distantmacrolink=substring(distantmacrolink, 0,(indexOf(distantmacrolink, " ")))+"%20"+substring(distantmacrolink, (indexOf(distantmacrolink, " ")+1),lengthOf(distantmacrolink) );

}}showStatus("Internet link...");macrotextnih =File.openUrlAsString(distantmacrolink);showStatus("");

} else { showMessage ("No internet connection to looks for beta version.");}

return macrotextnih;}

function InstallPluginsStarter(macroname) {// from MacroPluginShortcutsTool.txtcodestarter = "run\(\"Install...\", \"install=[\"+getDirectory(\"macros\

")+\""+kind+ macroname + "\]\"\);";if (getDirectory("plugins") == "") exit ("Unable to find the Plugins dir

ectory; something wrong in the ImageJ folder.");if (endsWith(macroname, ".txt") endsWith(macroname, ".ijm")) pluginna

me = substring(macroname, 0, (lengthOf(macroname)-4));StarterDir = getDirectory("plugins")+favoritefoldername+File.separator;File.makeDirectory(StarterDir);

if (!File.exists(StarterDir)) exit ("Unable to create "+favoritefoldername+" Macros directory, something wrong in the ImageJ folder.");

starterplugin = StarterDir + pluginname +"_ .ijm";f= File.open(StarterDir + pluginname +"_ .ijm");print (f,codestarter);File.close(f);showMessage ("The plugin shortcut \"" +pluginname+ "\" will be available

after\nImageJ restarting, in the \"Plugins->" + favoritefoldername + "\" menu.");}

// *** End of additionnal code for on line update ressources ***

Arrow Labelling Tools

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Transcript of Arrow Labelling Tools