///////////////////////////////////////////////////////////////////////

// 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 L
abelling.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 website
at:
// http://rsb.info.nih.gov/ij/macros/tools/ChangeColorTool.txt
// macro SelectionColorMenuTool, from the author and available on the ImageJ web
site 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 a
pply
var 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="";
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 access
var demoimagelink1 ="http://image.bio.methods.free.fr/ij/ijmacro/zebrafish/LSM-t
imelapse-demo-movie.tif.zip",demoimagename1="LSM-timelapse-demo-movie.avi",demoi
magename11="LSM-timelapse-demo-movie.zip";
var demoimagelink2 ="http://image.bio.methods.free.fr/ij/ijmacro/zebrafish/LSM-t
imelapse-demo-movie-Arw.tif.zip",demoimagename2="LSM-timelapse-demo-movie-Arw.av
i",demoimagename22="LSM-timelapse-demo-movie-Arw.zip";
var xx = requires138p(); // check version at install time
function 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 Ar
row\(s\) Location","Draw Arrow\(s\) at the Current Location","-","Restore the La
st Cursor Location","Display Coordinates","-","New User Graphic Interface","Stan
dard User Interface","-","Change the Color of a Arrow","-","Undo the Last Arrow"
,"-", "Animation Speed Setting","Animate the Stack","-","Save a Stack as an \".a
vi\" Movie","-","Download\/Open Demo Timelapse Movie \(6 Mo\)","Download\/Open D
emo Timelapse Movie Arrowed \(6 Mo\)","-","About \"Image, Stack and Timelapse Ar
row 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;cursoro
k=0;drawok=0;dyn=1; setTool(10);}
if (cmd !="-" && cmd =="Restore the Last Cursor Location") {restoreLastC
ursor ();}
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 = "Sta
ndard 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 Labell
ing\"") {about1();}
if (cmd !="-" && cmd == "On Line Documentation") {doc ();}
}
macro " Tool-1 - " {
 if (colorok==1 && dyn ==1 && getTitle !="Arrow Palette" && getTitle !="L
ast Arrow") {changeColor ();}
if (cursorok==1 && dyn ==1 && getTitle !="Arrow Palette" && getTitle !="
Last Arrow") {Arrow (1);}
// no ansvers -> palette
if (palette==1 && getTitle =="Arrow Palette" && dyn ==1 && cancel==0 &&
reponse ==0) {
if (isOpen("Arrow Palette")) {goGraphInt ();}
}
// ansvers is cancel -> close for cancel
if (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 conditions
if (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 && re
ponse ==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 Tool
var 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 Sp
eed Setting","Animate the Stack"));
macro "Movie and Stack Menu Tool - CdccD16Dd0C999Df5CdefD3aC888D15CedeD52Db0Dc4C
abdD72CfffD3bD3cD3dD3eD3fD4cD4dD4eD4fD5dD5eD5fD68D6dD6eD6fD7dD7eD7fD8dD8eD8fD9dD
9eD9fDadDaeDafDbdDbfDceDcfDddDdeDeeDefDfeDffC17dD44CcdeD92CbbbD1bCffeD33D75C39eD
93CeeeD61D71D81D91CcccD04D0dD12D21D22Dd1Dd2Dd4De6De8Df6Df8DfcC18eD36CcddDb3CaaaD
01D03D05De7De9Df7CfeeD29DacC59dD59Dc6CeeeD1fD30D40D41D50D51D65D70D80D90Da0Da1Da2
Db1Db2Dc0Dc1Dc2DdcCccdD27D85C1aeD9bCeddD25Dd8CcccD02D09D14D1eDe2De4DebDf2Df4Cfff
D66D98DbeDcdDdfC7adDa8CeeeD42D97CccdD18D26DecC18dD47CdddD06D0bD1aD20D23DeaCaa9D1
7CeeeD0fD2aD2bD2cD2eD32D88Dc3C48dDb4CbcdD82C29dDa9CddeDdbCcbbD00Df0CfffD5cD67D79
D89C6adD77CeeeD57C09eD49CdddD08Dd5CabbDf9CfffD2dD2fDedDfdC59dD35CcceD43C3adD64Cd
eeD0aD0cD78C7bdD74CfeeDd9CcdeDa7C08eD45D48Db6CdccDd6C999D11De3Df3C59cDa3CaddD8cC
19eDaaCdddD0eD24CbbbD07D10De0C4aeD9aC19eDbaCdddD28DfaC4adD87CcddD62D6cC1aeD7bCee
dD60DdaC8bdDc5C08eDb9CaaaD1dDe1Df1C6bdD84CbceD58D76D99C29eD4aCcdeD34D4bCbcbDfbC5
aeD6aCeeeD31C0aeD6bDbbC5adDc8CcdeD56C2afD83CddeD69C8ceDa4C08eDb7Db8C999D13De5C9c
eDccC19eD38DcbCdddDd7C4aeD95C09eD46C1aeD5aD8bC7beD8aCa9aD19C49dD53CaceDc9C39dDc7
CceeD9cC5beD94C09fD54C2aeD73CddcD1cCaceDbcC4beD5bC08eD37C4adD55DabC8beD7aDcaC7ad
Da6C29eD86C6beD39C5adD96C3aeD63C8ceDa5CdcdDd3CadeD7c"{
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 \(6
Mo\)") {OpenMovieLink(1,demoimagelink2,demoimagename2,demoimagename22);}
if (cmd !="-" && cmd == "Animation Speed Setting") {setMovieSpeed ();}
if (cmd !="-" && cmd =="Animate the Stack") {AnimateStack();}
}
// macro Arrow Drawing Menu Tool
var aCmds = newMenu("Arrow Drawing Menu Tool",newArray("Set Drawing Arrow\(s\) L
ocation","Draw Arrow\(s\) at the Current Location","-","Restore the Last Cursor
Location","-","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 -C0b3D0bD1bD2bD3bD41D42D43D44D45D46D47D48D49D4aD4
bD4cD4dD4eD4fD5bD6bD7bD8bD9bDabDbbDcbDdbDebDfbCfffD00D01D02D03D04D05D06D07D08D09
D0aD0cD0dD0eD0fD10D11D12D13D14D15D16D17D18D19D1aD1cD1dD1eD1fD20D21D22D23D24D25D2
6D27D28D29D2aD2cD2dD2eD2fD30D31D32D33D34D35D36D37D38D39D3aD3cD3dD3eD3fD40D50D51D
52D53D54D55D56D57D58D5cD5dD5eD5fD60D61D62D63D64D65D6aD6cD6dD6eD6fD70D71D72D73D7a
D7cD7dD7eD7fD80D81D82D83D84D85D86D89D8aD8cD8dD8eD8fD90D91D92D93D94D95D96D99D9aD9
cD9dD9eD9fDa0Da1Da2Da3Da4Da5Da6Da9DaaDacDadDaeDafDb0Db1Db2Db3Db4Db5Db6Db8Db9DbaD
bcDbdDbeDbfDc0Dc1Dc2Dc3Dc4Dc5Dc6Dc7Dc8Dc9DcaDccDcdDceDcfDd0Dd1Dd2Dd3Dd4Dd5Dd6Dd7
Dd8Dd9DdaDdcDddDdeDdfDe0De1De2De3De4De5De6De7De8De9DeaDecDedDeeDefDf0Df1Df2Df3Df
4Df5Df6Df7Df8Df9DfaDfcDfdDfeDffC00fD59D67D68D69D74D75D76D77D78D79D87D88D97D98Da7
Db7C88fD5aD66Da8" {
cmd = getArgument();
if (cmd!="-" && cmd == "Set Drawing Arrow\(s\) Location") {colorok=0;cu
rsorok=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;cursor
ok=0;drawok=0;dyn=1; setTool(10);}
if (cmd!="-" && cmd == "Restore the Last Cursor Location") {restoreLast
Cursor ();}
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","bl
ue","magenta","cyan","orange","black","white","-","Restore Initial Selection Col
or","Get Curent Selection Color"));
macro "Cursor Color Menu Tool - C1b0D85D95Da5Db5Dc5Dd5De5Df5CfffD00D01D02D03D04D
06D07D08D09D0aD0bD0cD0dD0eD0fD10D11D12D13D14D16D17D18D19D1aD1bD1cD1dD1eD1fD20D21
D22D23D24D26D27D28D29D2aD2bD2cD2dD2eD2fD30D31D32D33D34D36D37D38D39D3aD3bD3cD3dD3
eD3fD40D41D42D43D44D46D47D48D49D4aD4bD4cD4dD4eD4fD50D51D52D53D54D56D57D58D59D5aD
5bD5cD5dD5eD5fD60D61D62D63D64D66D67D68D69D6aD6bD6cD6dD6eD6fD80D81D82D83D84D86D87
D88D89D8aD8bD8cD8dD8eD8fD90D91D92D93D94D96D97D98D99D9aD9bD9cD9dD9eD9fDa0Da1Da2Da
3Da4Da6Da7Da8Da9DaaDabDacDadDaeDafDb0Db1Db2Db3Db4Db6Db7Db8Db9DbaDbbDbcDbdDbeDbfD
c0Dc1Dc2Dc3Dc4Dc6Dc7Dc8Dc9DcaDcbDccDcdDceDcfDd0Dd1Dd2Dd3Dd4Dd6Dd7Dd8Dd9DdaDdbDdc
DddDdeDdfDe0De1De2De3De4De6De7De8De9DeaDebDecDedDeeDefDf0Df1Df2Df3Df4Df6Df7Df8Df
9DfaDfbDfcDfdDfeDffC03fD70D71D72D73D74D75Cf00D05D15D25D35D45D55D65Cf0eD76D77D78D
79D7aD7bD7cD7dD7eD7f" {
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 - C810Dc2Df7Ca55D42D51Ce20D7dD8cDd6CfffD88Da7Cd
20DadCfedD3eD55D5bDa9Dc1Ce40D63De6CfffD00D01D03D04D05D06D07D08D09D0aD0cD0dD0eD0f
D10D11D14D1cD1dD1eD1fD20D21D22D2fD31D3fD40D66D6aDaaDb0Db5DbbDc0De0DefDf0Df1Df2Df
3DfdDfeDffC811Da1Dd3Cc77D1bD6cCe20Dc7CfffD23D65D79DdfCc31D68Da4CeffDeeCd52D27D4d
C910D7fD8fDbfDf9Cd64D4bD75Db7Dc6Ce30D39D47D48D74D85Da3CfffD13D30Da6Dd0De1Cc20Dac
DbdDdaDdbCfffD98Cd42D28D52D5eDe5Ca21D71D81D91DcaCfecD5aD67D69D96Cf30D3aD3bD94Db3
Cc32D25D2bD34D9bCfffD12D50D70D80D87D89D90D99Da0Db6Dd1De2Cf63D64D72D82Db2DbeC910D
9fDafDecDf8Cb66D17D19D1aDa8Ce20D37D49Dd7Dd8CeffD6bD77D97Cd20D6dD7cDc9CffeD4fD60D
7aD9aDbaCf52D35D44D53D6eC821D5fD61De4DfbCebbD15DbcDcbDcfDdeCf30D58D73D83D93Cd41D
3cD95De7CfffD2eD78Cf53Dc3DcdDd4DebCa20D6fDccCc75D18D24D5cD7bD8aCf30D36D84Cd30D46
D59D8bDd5CfffD02D0bD2dD41D76Cf42D26D8eD9eDdcCa32D2cD3dD4eDb9CfedD56Da5Dd2DedDfcC
e31D2aD57D5dDeaCc41D43D4cD86DaeCf63D62D92Da2C810DddDf6DfaCa66D16D33Ce30Dc8Cd20D8
dD9cD9dDd9CfeeD32DabDe3Df4Cd51D29D7eC822Db1Df5Cea7Db4Dc5Ce30D4aDb8De9Cd40D38Dc4D
e8Cd53D45D54C911Dce" {
abortProcess ();
}
macro "On Line Documentation Action Tool - C000Da9DadDb6DbdDc5Dc6Dd3Dd4Dd5Dd6Ddd
C20fD11D12D13D14D15D16D17D18D19D1aD1bD1cD1dD1eD1fC0f3D42D43D44D45D46D47D48D49D4a
D4bD4cD4dD4eD4fC0feD32D33D34D35D36D37D38D39D3aD3bD3cD3dD3eC444DdeDefC73fD01Cfd0D
62D63D64D65D66D67D68D69D6aD6bD6cD6dD6eCeeeD90D95Da1Da4Db0Db2Db3De0De8Df0Df7DfaC2
22DeeC06fD22D23D24D25D26D27D28D29D2aD2bD2cD2dD2eC7f0D52D53D54D55D56D57D58D59D5aD
5bD5cD5dD5eCcccDbfDf9Cf74D70Ca99D97C888Da8CfffD9bD9cC000Dc4Dd2C64fD10C0f4D41C0ff
D31D3fCf40D71D72D73D74D75D76D77D78D79D7aD7bD7cD7dD7eD7fCa7fD00Cfd0D61D6fCfefD91C
444Db5DdaDe9C06fD21D2fC7f0D51D5fCeddD96Cf88D82D83D84D85D8bD8cCaaaDccDeaDfdC999Dc
fCfffD9fDafDb1Db8De1C666Dc7C84fD02D03D04D05D06D07D08D09D0aD0bD0cD0dD0eC333Da6Da7
DaaDb9DbcDd9DdcCdddD9aDa2Da3Dc8DdbDecCaaaDabDaeDc1De3De4De5De6Cf89D8dC222DcdDedD
feDffC4ffD30CfffDebDf1Df2Df3Df4Df5Df6DfcC48fD20C4f6D40CeeeD92D93D94Da0DcbDf8DfbC
bbbDb4Dd8C9f4D50C555Dc2C73fD0fC333DbbDc3Dc9Dd1CdddDe7Cf89D81D86D8aD8fC111DbaDd7C
deeDa5CbbbDb7Dc0De2Cf99D87D88D89C777DacDcaCcbbD9eCfaaD80C999D98Cf89D8eC999D9dC76
6D99C555DceC888DbeCfd4D60C777DdfC666Dd0"{
doc ();
}
macro "Version and Update Infos Action Tool - CcccD5fD6fD7fD8fD9fC78bD17D19D2aD3
3D37D3bD42D4cD75D95DceDd5Dd9De6Df7Df9CddeDa3C36bD27D28D3aD57D58D59D66D76D77D86D8
7Da7Db8Dd6De8De9CeeeD00D01D02D04D06D07D08D09D0bD0dD0fD10D11D12D14D1bD1dD1fD20D21
D22D2dD30D31D32D40D46D47D48D49D50D5bD60D70D71D72D74D7dD80D81D82D84D8dD90D91D92D9
4D9dDa0Da1Da2Da4Db0Db1DbbDc0Dc1Dc6Dc7Dc8Dc9Dd0Dd1Dd2De0De1De2DedDf0Df1Df2Df4DfbD
fdDffC8beD3cD3dD4dD5aD6aD79D7aD7bD85D8bD9aDaaDc3Dc4Dd3Dd4CeeeD03D05D0aD0cD0eD13D
15D1cD1eD23D2eD3eD4aD55D6cD73D7cD7eD83D8cD8eD93D9cD9eDb5DcaDdeDe3DeeDf3Df5DfcDfe
C559D18D26D34D35D36D41D51D61DafDbfDcfDdaDdbDddDeaDf8CcddD2fD5cD6dD6eDabDb2Db4Dc2
DefC99bD16D24D39D45D54D56D64D65Da5DacDb6DbcDcbDd7DecDfaCdefD67D8aC59dD29D2bD68D6
9D78D88D96D97D98D99Da6Da8Da9Db9De5De7CacdD1aD2cD38D4bD4eD5dD5eD6bD89D9bDb3DbaDc5
Dd8De4Df6C348D25D43D44Db7DccDdcDebCcccD3fD4fDdf" {
VersionInfos ();
}
macro "About \"Image, Stack and Timelapse Arrow Labelling\" Action Tool - C000D8
4Cb9fD25De7CaaaD14D2dDa0DafDecDfaCedfD49D4aD4bD4cD58D68D9bDb9DbaDbbDbcC889D2cDeb
CddfD52CcccD0bD22CeeeD00D03D0cD0fD10D1fD20D2fD30D40Dc0Dd0DdfDe0DefDf0Df1Df2Df3Df
cDfeDffC666D07D70CdcfD34D35Dc4CbacD86D91CfefD6bD6dD7cD8cD8dD8eD9cD9dDadC97aDd3De
5CedfD99CeeeD01D02D04D0dD0eD11D12D1eD21D3fDcfDd1De1De2DeeDf4DfdCfefD7dC545D94Da5
CdbeDa4Da7CbabD05D50DaeCfefD7eC98aD32Da1CecfD39D3aD3bD46D48D57D67Da8Db6Db8Dc9Dca
DcbDccCdcdD81C878D1bD60D65CdcfD29D36D38D47D77Db7Dc8Dd9DdaCcbcD7aDbfDc1De3C98bD16
D24D75DeaCedfD56D66D73D76D83D93Da3C212D7bD88D96D97CcaeD26D3cDdbCaaaD3eD5fCfdfD59
C889D15D1aD78Dc2CdcfD45Db4Db5Dc6CdddD13D31D4fDdeDedDfbC777D09D7fD85D90Df7CeceDbd
CbadD18D55Db2De9Ca9aD5eDcdDceDdcC656D08D64D80D87D8bCdbfD28D2aD37Dc7Dd8CbbbD1cD42
Dd2Df5CfdfD5aD5bD5cD5dD69D6aD6cD9aDa9DabDacC999D0aD41DddDf6CdddD1dD2eD9eDb0C888D
06D4eD6fD9fDf9CcbdD54D71D98Dc3Ca9dD17D19Dd4De6C000D74D79D95CcafDd5Dd6De8CedfD62D
72D92C889D51Db1DbeCedfD53D63Da2CdcdD6eC777D8fDf8CdcfD43D44Db3Dc5CbadD2bD33C99aD2
3De4C545D89Da6CcbfD27Dd7CbabD61CedfD82DaaC98aD3dCdceD4dD8a" {
about1 ();
}
macro "Undo Last Arrow [z]"{
run("Undo");
}
///////////////// Functions ////////////////////
// set the location
function 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 slice
if (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 parameters
function arrow (box) {
 // old interface
if (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:", arrowchoice
s3, 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<4;a++) {
builtarrow (arrowline,xfleche,yfleche,arrowwidth,arrowle
nght,tailorient,arrowconcav,tailwidth,taillenght,getRGBcolor (tailcolor));
}
}
// new interface
 if (lookInterface == newlook) {
arrowline=1;xfleche=x; yfleche=y;
setupUndo();
for (a=0;a<4;a++) {
builtarrow (arrowline,xfleche,yfleche,arrowwidth,arrowle
nght,tailorient,arrowconcav,tailwidth,taillenght,getRGBcolor (tailcolor));
}
}
}
function preview () {
prev="Arrow preview";
newImage(prev,"RGB Black",200,300,1);
image=getImageID();
xfleche=100;yfleche=75;
setFont("Serif", 12);
builtarrow (arrowline,xfleche,yfleche,arrowwidth,arrowlenght,tailorient,
arrowconcav,tailwidth,taillenght,getRGBcolor (tailcolor));
selectImage(image);
setColor(255,255,255);
drawString("Arrow lenght: "+arrowlenght + " Arrow width: "+arrowwidth
, 2,210);
drawString("Arrowhead Filling Level: "+arrowconcav,2,225);
drawString("Tail Lenght: "+taillenght+ " Tail Width: "+tailwidth,2,240);
drawString("Arrow Color: "+tailcolor,2,260);
drawString("Arrow Orientation: "+tailorient,2,275);
exit;
}
function builtarrow (arrowline,xfleche,yfleche,arrowwidth,arrowlenght,tailorient
,arrowconcav,tailwidth,taillenght,couleur) {
// convert into rgv if 8 bit grey
if (bitDepth()==8) {showMessageWithCancel ("Conversion into 24 bit (RGB)
will be performed."); run("RGB Color");}
autoUpdate(false);
setColor(rgb[0], rgb[1], rgb[2]);
if (tailorient == "North") {orientangle=0;}
if (tailorient == "N-E") {orientangle=(PI/4);arrowline=2;}
if (tailorient == "East") {orientangle=(PI/2);}
if (tailorient == "S-E") {orientangle=(PI*3/4);arrowline=2;}
if (tailorient == "South") {orientangle=(PI);}
if (tailorient == "S-W") {orientangle=(5*PI/4);arrowline=2;}
if (tailorient == "West") {orientangle=(3*PI/2);}
if (tailorient == "N-W") {orientangle=(-(PI/4));arrowline=2;}
fleche1=newArray (3);
fleche2=newArray (3);
alpha3a=(PI/2);lineWidth=1;xi=0;
setLineWidth(arrowline);
// arrowhead drawing
moveTo(xfleche, yfleche);
x1=(-1*arrowwidth);y1=(arrowlenght); alpha1a=(atan2(y1,x1)); alpha1b=(a
lpha1a+orientangle);
getxy (x1,y1,alpha1b);
fleche1[0]=(xfleche+xprime);fleche2[0]=(yfleche+ yprime);
x2=(arrowwidth);y2=(arrowlenght); alpha2a=(atan2(y2,x2));alpha2b=(alpha
2a+orientangle);
getxy (x2,y2,alpha2b);
fleche1[2]=(xfleche+xprime);fleche2[2]=(yfleche+yprime);
for (i=2; i<arrowconcav; i++) {
 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 current
slice. 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 () {
 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 location
function 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 lo
cation \nusing the \"Set Drawing Arrow\(s\) Location\" sub menu of the \n\"Arrow
Drawing Menu Tool\".");}
}
// called from the user interface tool
function changeColor () {
if (getTitle !="Arrow Palette" && getTitle !="Last Arrow") {
setupUndo();
getCursorLoc(x, y, z, flags);
doWand(x, y);
 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 arrows
function DrawTheArrows (x,y) {
nbslice= nSlices;countslc=1;
for (i=FSlice; i<= TSlice; i++) {
setSlice(i);
if (countslc ==1) {arrow (1);} else {arrow (0);}
countslc ++;
}
setSlice(curentSlice);
}
// download demo movies
function OpenMovieLink(question,demoimagelink,demoim,demoim1) {
setBatchMode(true);
// Check if already downloaded.
if (isOpen(demoim)) exit ("The \"" + demoim + "\" is already opened as a
stack.");
demoimalocation = getDirectory("startup");
ImaDemo1 = demoimalocation+"Downloaded Demo Images"+File.separator;
ImaDemo2 =ImaDemo1 + "Demo Movie Working Folder" + File.separator;
ImaDemo=ImaDemo2;
fildestination = ImaDemo + demoim;
fildestination1= ImaDemo + demoim1;
// download the demo if not already into the ImageJ folder
if (! File.exists(fildestination) || ! File.exists(fildestination1)) {
if (File.openUrlAsString(urllist) == "") exit("You need an inter
net access to run this function.");
showMessageWithCancel ("ImageJ will download a demo movie. Conti
nue?");
 run("URL...", "url=["+demoimagelink+"]");
imageid = getImageID();
nomdimage = getTitle;
// Create a <Downloaded Demo Images> 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 <Demo Movie Working Folder> repertory in ImageJ fold
er.
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 movie
if (File.exists(fildestination) && ! isOpen(demoim)) {
//if (question ==1 ) showMessageWithCancel ("The \"" + demoim +
"\" has been downloaded available at the following HD location:\n" + fildestinat
ion + "\n and:" + fildestination1+"\nOpen it now as a stack ?\n(Or \"Cancel\" an
d open it from the \"Open a Movie as Stack\" sub\-menu of the \"Movie and Stack
Menu Tool\"\) ");
if (question ==1 ) showMessageWithCancel ("- The \"" + demoim +
"\" has been downloaded and available at the following HD location:\n" + fildest
ination + "\n- A \".zip\" stack version is also available at the following HD lo
cation (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);
}
// graphic interface
function 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 ();
}
function coloBoxes(draw,detect,clickx,clicky) {
xcolorbox=20;ycolorbox=10;spcol=(Lpalette-8*xcolorbox)/9;
setLineWidth(1);detectcol=-1;democolor="";
for (a=0;a<8;a++) {
setColor(255,0,93);
if (detect==1) {
if (clicky >(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*xcol
orbox+a*spcol+spcol+1), (Hpalette-160+1), (xcolorbox-2), (ycolorbox-2));run("Sel
ect 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;
}
// location of the different interactive areas
// cancel
function 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))+(Lpal
ette-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 {test
pal=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 <
(ypreview+8) ) {testpal=1;} else {testpal=0;} return testpal;
}
function Est (clickx,clicky) {
if (clickx > ((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))+(Lpale
tte-Hprev)/6) && clicky < ((ypreview+(Hprev/2))+(Lpalette-Hprev)/6+18) ) {tes
tpal=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 < ((yprevie
w+(Hprev/2))+(Lpalette-Hprev)/6+18) ) {testpal=1;} else {testpal=0;} return test
pal;
}
function SudEst (clickx,clicky) {
if (clickx > ((Lpalette-Lprev)/3-18) && clickx < ((Lpalette-Lprev)/3)
&& clicky > ((Lpalette-Hprev)/3-18) && clicky < ((Lpalette-Hprev)/3) ) {tes
tpal=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;
}
// apply
function 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 window
newImage("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,get
RGBcolor ("Yellow"));
builtarrow (2,(Lpalette-Lprev)/3,(Lpalette-Hprev)/3,6,20,"S-E",1
5,0,0,getRGBcolor ("Yellow"));
builtarrow (2,xpreview,(Lpalette-Hprev)/3,6,20,"South",15,0,0,ge
tRGBcolor ("Yellow"));
builtarrow (2,xpreview+(Lprev/2)+(Lpalette-Lprev)/6,(Lpalette-Hp
rev)/3,6,20,"S-W",15,0,0,getRGBcolor ("Yellow"));
builtarrow (2,xpreview+(Lprev/2)+(Lpalette-Lprev)/6,ypreview,6,2
0,"West",15,0,0,getRGBcolor ("Yellow"));
builtarrow (2,xpreview+(Lprev/2)+(Lpalette-Lprev)/6,(ypreview+(H
prev/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 cancel
drawRect (distBord, (Hpalette-disthaut), largbuton, hautbuton);r
un("Select None");
setColor(0,255,0);// button apply
drawRect ((Lpalette-distBord-largbuton), (Hpalette-disthaut), la
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");}
}
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 as
a stack of images.";
about=about+"\n - \"Save a Stack as an \".avi\" Movie\" records
a stack as an avi uncompressed movie into the same\n repertory than the
original 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 trai
ning movie and an example of arrowed movie. Initial movie, obtained by\n
LSM microscopy, was provided by Tim Chico (*).";
about=about+"\n - Set the stack/movie animation speed using \"An
imation 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
 cursor points the correct target of the arrow. Unclick, and adjust settings usi
ng the\n menu and the graphic interface which then will appear.";
about=about+"\n - \"Draw Arrow(s) at the Current Location\" draw
s a arrow at the current location when the user\n graphic interface has
been canceled, or the cursor erased for any reason.";
about=about+"\n - \"Restore the Last Cursor Location\" restores
a visual (non active) cursor at the last location.";
about=about+"\n - \"New User Graphic Interface\" is the default
interface to set the arrow characteristics.";
about=about+"\n - \"Standard User Interface\" allows to use the
dialog box interface of the \"ArrowMakerTool\" instead\n of the graphica
l interface.";
about=about+"\n - \"Display Coordinates\" gives the coordinates
x, y of the current location (same as displayed in the\n status bar).";
about=about+"\n - \"Change the Color of a Arrow\" allows to chan
ge the color of a draw arrow, by clicking on it.";
about=about+"\n - \"Undo the Last Arrow\" erases the last drawn
arrow (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, de
pending 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 U
pdate Infos\" ImageJ tool bar icon to look for new beta versions.";
about=about+"\n---------------------------------------------------------
------------------------------------";
about=about+"\nThis toolset based on the \"ArrowMakerTool\" was adapted
to stacks and movies at the request of Tim Chico,\nPI in vascular biology at the
University of Sheffield, UK. Tim Chico also provided the downloadable movie\nex
ample.";
about=about + "\n-------------------------------------------------------
-------------------------------------";
about=about +"\nAuthor: Gilles Carpentier"+"\nFaculte des Sciences et Te
chnologies"+"\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 ---//

// ----------------------------------//
//
//
//
//
//
//
//
//
//
//
//
//
//
//
// -------------------*** 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 installation
Dialog.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 vers
ion).");
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
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 avai
lable on the " +giveDevInfo (macrotextdistant,5)+ " web site: ";
update=update+ "\n \nDo you want to install it?"
;
} else {
update ="\n \nThe new "+new+" beta version calle
d \"" +namedev+ "\" provided by \nthe "+giveDevInfo (macrotextdistant,5) +" web
site has already be installed";
update = update+ " in the \"" +kind+ "\" reperto
ry \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)<0) || (indexOf(text, endsign)<0) ) exit (
"Not upgradable macro code.");
for (i=0; lines[i] != endsign; i ++) {}
for (j=i; lines[j] != beginsign; j --) {}
infotext=newArray(i-j-1);
for (i=0; i < infotext.length; i ++) {infotext[i]=lines[i+j+1];}
info=infotext[n-1]; signature=":";
cut = indexOf(info, signature);
info = substring(info,(cut+lengthOf(signature)),lengthOf(info));
return info;
}
// Function giving the content of a distant macro (name) located at the distant
repertory (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(dis
tantmacrolink, " ")+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.txt
codestarter = "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 "+favoritefolderna
me+" 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 ***