ImageJ base code to get access to all the classes and their methods to test new Plugins. https://imagejdocu.tudor.lu/howto/plugins/the_imagej_eclipse_howto
You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
448 lines
12 KiB
448 lines
12 KiB
//--version--1.6
|
|
// 1.6 adds the '?' button that points to the wiki page
|
|
// panel labels are now drawn on an overlay
|
|
// added overlay commands and copy to system clipboard to the rightclick menu
|
|
// Montage tools for easy montage manipulation
|
|
// jerome.mutterer at ibmp.fr
|
|
|
|
var str="ABCDEFGHIJKLMNOPQRSTUVWXYZ";
|
|
var lcas=false;
|
|
var antialiasedLabels = true;
|
|
var n=0;
|
|
var xoffset=0.05;
|
|
var yoffset=0.05;
|
|
var pos="Clicked quadrant";
|
|
|
|
var commands = newArray("Copy", "Paste","-", "Scale Bar...",
|
|
"Brightness/Contrast...", "-", "Extract Selected Panels","Crop Montage [F3]","-",
|
|
"Add Panel to Manager [F1]","Selected panels to stack [F2]", "Montage to Stack", "-",
|
|
"Fit Clipboard content into panel [F4]","Fill Panel with Clipboard content [F5]","-",
|
|
"Set Montage Layout","Change Montage Layout","-",
|
|
"Hide Overlay","Show Overlay", "Remove Overlay", "Flatten", "-",
|
|
"Copy to System"));
|
|
|
|
var toolCmds = newMenu("Magic Montage Menu Tool",commands);
|
|
var pmCmds = newMenu("Popup Menu",commands);
|
|
|
|
macro "Popup Menu" {
|
|
runCommand();
|
|
}
|
|
|
|
macro "Auto Montage Action Tool - C66fF0077C6f6F9977Cf66F9077C888F0977" {
|
|
setBatchMode(true);
|
|
b=bitDepth;
|
|
if ((b!=24)&&(nSlices==1)) { exit("Stack, Composite, or RGB image required.");}
|
|
if ((b==24)&&(nSlices==1)) { run("Make Composite"); b=8;}
|
|
Stack.getDimensions(width, height, channels, slices, frames);
|
|
getVoxelSize(xp,yp,zp,unit);
|
|
if (channels==1) { channels = channels* frames*slices; Stack.setDimensions(channels,1,1); }
|
|
id=getImageID;
|
|
t=getTitle;
|
|
if (b!=24) {
|
|
newImage("tempmont", "RGB", width, height,channels);
|
|
id2=getImageID;
|
|
for (i=1;i<=channels;i++) {
|
|
setPasteMode("copy");
|
|
selectImage(id);
|
|
Stack.setChannel(i);
|
|
getLut(r,g,b);
|
|
run("Duplicate...", "title=temp"+i);
|
|
setLut(r,g,b);
|
|
run("RGB Color");
|
|
run("Copy");
|
|
selectImage(id2);
|
|
setSlice(i);
|
|
run("Paste");
|
|
}
|
|
}
|
|
run("Make Montage...", "scale=1 border=0");
|
|
rename(getTitle+" of "+t);
|
|
setVoxelSize(xp,yp,zp,unit);
|
|
setBatchMode(false);
|
|
}
|
|
|
|
macro "Select Panels Tool - Cf44R0077R9077C888R9977R0977"{
|
|
run("Select None");
|
|
setPasteMode("copy");
|
|
w = getWidth;
|
|
h = getHeight;
|
|
getCursorLoc(x, y, z, flags);
|
|
id=getImageID;
|
|
t=getTitle;
|
|
selectImage(id);
|
|
xn = info("xMontage");
|
|
yn = info("yMontage");
|
|
if ((xn==0)||(yn==0))
|
|
exit;
|
|
xc = floor(x/(w/xn));
|
|
yc = floor(y/(h/yn));
|
|
makeRectangle(xc*(w/xn),yc*(h/yn),(w/xn),(h/yn));
|
|
xstart = x; ystart = y;
|
|
x2=x; y2=y;
|
|
x2c=xc;y2c=yc;
|
|
while (flags&16 !=0) {
|
|
getCursorLoc(x, y, z, flags);
|
|
if (x!=x2 || y!=y2) {
|
|
x2c = floor(x/(w/xn));
|
|
y2c = floor(y/(h/yn));
|
|
makeRectangle(xc*(w/xn),yc*(h/yn),(w/xn)*(x2c-xc+1),(h/yn)*(y2c-yc+1));
|
|
x2=x; y2=y;
|
|
wait(10);
|
|
}
|
|
}
|
|
setPasteMode("add");
|
|
}
|
|
|
|
macro "Extract Selected Panels"{
|
|
t=getTitle;
|
|
xn = info("xMontage");
|
|
yn = info("yMontage");
|
|
pw = getWidth/xn;
|
|
ph = getHeight/yn;
|
|
run("Duplicate...", "title=[Extract of "+t+"]");
|
|
setMetadata("Info","xMontage="+getWidth/pw+"\nyMontage="+getHeight/ph+"\n");
|
|
}
|
|
|
|
macro "Montage Shuffler Tool - C888R0077R9977C44fR0977R9077"{
|
|
id=getImageID;
|
|
run("Select None");
|
|
setPasteMode("copy");
|
|
w = getWidth;
|
|
h = getHeight;
|
|
getCursorLoc(x, y, z, flags);
|
|
xn = info("xMontage");
|
|
yn = info("yMontage");
|
|
if ((xn==0)||(yn==0))
|
|
exit;
|
|
xstart = x; ystart = y;
|
|
x2=x; y2=y;
|
|
while (flags&16 !=0) {
|
|
getCursorLoc(x, y, z, flags);
|
|
if (x!=x2 || y!=y2) spring(xstart, ystart, x, y);
|
|
x2=x; y2=y;
|
|
wait(10);
|
|
}
|
|
if (x!=xstart || y!=ystart) {
|
|
xext=0;
|
|
yext=0;
|
|
if (x>w) xext=1;
|
|
if (y>h) yext=1;
|
|
if ((xext>0)||(yext>0)) {
|
|
run("Canvas Size...", "width="+w+xext*(w/xn)+" height="+h+yext*(h/yn)+" position=Top-Left zero");
|
|
setMetadata("Info","xMontage="+(parseInt(xn)+parseInt(xext))+"\nyMontage="+(parseInt(yn)+parseInt(yext))+"\n");
|
|
exit;
|
|
}
|
|
sc = floor(xstart/(w/xn));
|
|
tc = floor(x/(w/xn));
|
|
sr = floor(ystart/(h/yn));
|
|
tr = floor(y/(h/yn));
|
|
swap(sc,sr,tc,tr);
|
|
|
|
}
|
|
}
|
|
|
|
macro "Annotation Tool - C700 T2709A T8709B T1f09C T8f09D" {
|
|
xn = info("xMontage");
|
|
yn = info("yMontage");
|
|
|
|
getCursorLoc(x, y, z, flags);
|
|
iw = getWidth/xn;
|
|
ih = getHeight/yn;
|
|
|
|
co = floor(x/iw);
|
|
li = floor(y/ih);
|
|
|
|
fontsize = ih/10;
|
|
if (fontsize<12) fontsize=12;
|
|
marque = substring(str,n,n+1);
|
|
if (lcas==1) marque= toLowerCase(marque);
|
|
opt="";
|
|
|
|
if (pos == "Clicked quadrant") {
|
|
xoffset=0.05; yoffset=0.05;
|
|
if (x>((co+0.5)*iw)) xoffset=0.90;
|
|
if (y<((li+0.5)*ih)) yoffset=0.85;
|
|
}
|
|
|
|
if (antialiasedLabels==true) opt=opt+"antialiased";
|
|
setFont("SanSerif",fontsize, opt);
|
|
fg = getValue("rgb.foreground");
|
|
makeText(marque ,co*iw+xoffset*iw,(li+1)*ih-yoffset*ih-getValue("font.height"));
|
|
Roi.setStrokeColor(fg&0xff0000>>16,fg&0x00ff00>>8,fg&0x0000ff);
|
|
Overlay.addSelection("",0);
|
|
run("Select None");
|
|
n++; if (n>lengthOf(str)) n=0;
|
|
}
|
|
|
|
macro "Annotation Tool Options" {
|
|
if (nImages>0) setupUndo;
|
|
Dialog.create("Annotation - Options");
|
|
Dialog.addString("Labels",str);
|
|
Dialog.addCheckbox("Lowercase labels",lcas);
|
|
Dialog.addCheckbox("Reset label counter",true);
|
|
Dialog.addCheckbox("Antialiased",true);
|
|
Dialog.addChoice("Position",newArray("Clicked quadrant","Lower left","Lower right","Upper right","Upper left"),pos);
|
|
Dialog.show;
|
|
str = Dialog.getString;
|
|
lcas = Dialog.getCheckbox;
|
|
resetCounter = Dialog.getCheckbox;
|
|
if (resetCounter==true) n=0;
|
|
antialiasedLabels = Dialog.getCheckbox;
|
|
pos=Dialog.getChoice();
|
|
if (pos=="Lower left") {xoffset=0.05; yoffset=0.05;}
|
|
else if (pos=="Lower right") {xoffset=0.90; yoffset=0.05;}
|
|
else if (pos=="Upper left") {xoffset=0.05; yoffset=0.85;}
|
|
else if (pos=="Upper right") {xoffset=0.90; yoffset=0.85;}
|
|
|
|
}
|
|
|
|
macro "Montage Sync Tool - C800L07f7L707fG" {
|
|
w=getWidth;
|
|
h= getHeight;
|
|
getCursorLoc(x,y,z,flags);
|
|
xn = info("xMontage");
|
|
yn = info("yMontage");
|
|
if ((xn==0)||(yn==0)) {
|
|
run("Set Montage Layout");
|
|
exit;
|
|
}
|
|
xc = floor(x/(w/xn));
|
|
yc = floor(y/(h/yn));
|
|
x0 = x-xc*w/xn;
|
|
y0 = y-yc*h/yn;
|
|
np = 1*xn*yn;
|
|
xp =newArray(np);
|
|
yp =newArray(np);
|
|
for (i=0;i<xn;i++) {
|
|
for (j=0;j<yn;j++) {
|
|
xp[j*xn+i] = x0+i*(w/xn);
|
|
yp[j*xn+i] = y0+j*(h/yn);
|
|
}
|
|
}
|
|
makeSelection("point yellow large hybred",xp,yp);
|
|
}
|
|
|
|
macro "Magic Montage Menu Tool - C800G027ff200" {
|
|
runCommand();
|
|
}
|
|
|
|
function runCommand() {
|
|
cmd = getArgument();
|
|
if (cmd=="Scale Bar...")
|
|
doCommand(cmd);
|
|
else
|
|
run(getArgument());
|
|
}
|
|
|
|
macro "Magic Montage Help Action Tool - C911T4e18?"{
|
|
run("URL...", "url=http://wsr.imagej.net/macros/toolsets/MagicMontage.pdf");
|
|
//run("URL...", "url=http://imagejdocu.tudor.lu/doku.php?id=howto:working:work_with_magic_montage");
|
|
}
|
|
|
|
// Returns numeric value associated with 'key' or 0 if not found.
|
|
function info(key) {
|
|
value = getInfo(key);
|
|
if (value=="")
|
|
return 0;
|
|
else
|
|
return parseInt(value);
|
|
}
|
|
|
|
function swap(a,b,c,d) {
|
|
setupUndo;
|
|
setBatchMode(true);
|
|
makeRectangle(a*(w/xn),b*(h/yn),(w/xn),(h/yn));
|
|
run("Duplicate...", "title=tmp");
|
|
selectImage(id);
|
|
makeRectangle(c*(w/xn),d*(h/yn),(w/xn),(h/yn));
|
|
run("Copy");
|
|
makeRectangle(a*(w/xn),b*(h/yn),(w/xn),(h/yn));
|
|
run("Paste");
|
|
selectWindow("tmp");
|
|
run("Select All");
|
|
run("Copy");
|
|
selectImage(id);
|
|
makeRectangle(c*(w/xn),d*(h/yn),(w/xn),(h/yn));
|
|
run("Paste");
|
|
run("Select None");
|
|
setBatchMode(false);
|
|
}
|
|
|
|
function spring(x0,y0,x1,y1) {
|
|
d = sqrt((y1-y0)*(y1-y0)+(x1-x0)*(x1-x0));
|
|
step=3;
|
|
r=15;
|
|
xa = newArray(floor(d/step));
|
|
ya = newArray(xa.length);
|
|
for (i=0;i<xa.length;i++) {
|
|
j=i*step;
|
|
xa[i]=x0+j*(x1-x0)/d+sin(j/7)*r;
|
|
ya[i]=y0+j*(y1-y0)/d+cos(j/7)*r;
|
|
}
|
|
if (xa.length>1) {
|
|
xa[0]=x0;
|
|
ya[0]=y0;
|
|
xa[xa.length-1]=x1;
|
|
ya[ya.length-1]=y1;
|
|
}
|
|
makeSelection("freeline",xa,ya);
|
|
}
|
|
|
|
macro "Add Panel to Manager [F1]" {
|
|
roiManager("Add");
|
|
setOption("Show All",true);
|
|
}
|
|
|
|
macro "Montage to Stack" {
|
|
columns = info("xMontage");
|
|
rows = info("yMontage");
|
|
if (rows==0 || columns==0) {
|
|
run("Set Montage Layout");
|
|
columns = info("xMontage");
|
|
rows = info("yMontage");
|
|
}
|
|
run("Montage to Stack...", "columns=&columns rows=&rows");
|
|
}
|
|
|
|
macro "Selected panels to stack [F2]" {
|
|
id=getImageID;
|
|
t=getTitle;
|
|
selectImage(id);
|
|
roiManager("select",0);
|
|
getSelectionBounds(x,y,sw,sh);
|
|
setBatchMode(true);
|
|
newImage("Extracted Panels of "+t, "RGB", sw,sh,roiManager("count"));
|
|
id2=getImageID;
|
|
setPasteMode("copy");
|
|
for (i=0;i<roiManager("count");i++) {
|
|
selectImage(id);
|
|
roiManager("select",i);
|
|
run("Copy");
|
|
selectImage(id2);
|
|
setSlice(i+1);
|
|
run("Paste");
|
|
}
|
|
setBatchMode(false);
|
|
}
|
|
|
|
macro "Crop Montage [F3]" {
|
|
setBatchMode(true);
|
|
setPasteMode("copy");
|
|
w=getWidth;
|
|
h= getHeight;
|
|
b=bitDepth;
|
|
getSelectionBounds(x,y,sw,sh);
|
|
t=getTitle;
|
|
id=getImageID;
|
|
getVoxelSize(xp,yp,zp,unit);
|
|
xn = info("xMontage");
|
|
yn = info("yMontage");
|
|
xc = floor(x/(w/xn));
|
|
yc = floor(y/(h/yn));
|
|
xpa = x-xc*(w/xn);
|
|
ypa= y-yc*(h/yn);
|
|
newImage("Crop of "+t,b+"RGB",sw,sh,(xn)*(yn));
|
|
id2=getImageID;
|
|
for (j=0;j<yn;j++) {
|
|
for (i=0;i<xn;i++) {
|
|
selectImage(id);
|
|
makeRectangle(i*(w/xn)+xpa,j*(h/yn)+ypa,sw,sh);
|
|
run("Copy");
|
|
selectImage(id2);
|
|
setSlice(j*(xn)+i+1);
|
|
run("Paste");
|
|
}
|
|
}
|
|
setVoxelSize(xp,yp,zp,unit);
|
|
setBatchMode(false);
|
|
setSlice(nSlices);
|
|
setSlice(1);
|
|
}
|
|
|
|
macro "Fit Clipboard content into panel [F4]" {
|
|
getSelectionBounds(x,y,sw,sh);
|
|
id=getImageID;
|
|
setBatchMode(true);
|
|
ffp=sw/sh;
|
|
run("Internal Clipboard");
|
|
run("RGB Color");
|
|
ffc=getWidth/getHeight;
|
|
if (ffc>ffp) {
|
|
run("Size...", "width="+sw+" height="+sw/ffc+" constrain interpolate");
|
|
run("Canvas Size...", "width="+sw+" height="+sh+" position=Center zero");
|
|
} else {
|
|
run("Size...", "width="+sh*ffc+" height="+sh+" constrain interpolate");
|
|
run("Canvas Size...", "width="+sw+" height="+sh+" position=Center zero");
|
|
}
|
|
run("Copy");
|
|
close;
|
|
selectImage(id);
|
|
setBatchMode(false);
|
|
setPasteMode("Copy");
|
|
run("Paste");
|
|
}
|
|
|
|
macro "Fill Panel with Clipboard content [F5]" {
|
|
getSelectionBounds(x,y,sw,sh);
|
|
id=getImageID;
|
|
setBatchMode(true);
|
|
ffp=sw/sh;
|
|
run("Internal Clipboard");
|
|
run("RGB Color");
|
|
ffc=getWidth/getHeight;
|
|
if (ffc>ffp) {
|
|
run("Size...", "width="+sw*ffc+" height="+sh+" constrain interpolate");
|
|
run("Canvas Size...", "width="+sw+" height="+sh+" position=Center zero");
|
|
} else {
|
|
run("Size...", "width="+sw+" height="+sh/ffc+" constrain interpolate");
|
|
run("Canvas Size...", "width="+sw+" height="+sh+" position=Center zero");
|
|
}
|
|
run("Copy");
|
|
close;
|
|
selectImage(id);
|
|
setBatchMode(false);
|
|
setPasteMode("Copy");
|
|
run("Paste");
|
|
|
|
}
|
|
|
|
macro "Set Montage Layout" {
|
|
columns = info("xMontage");
|
|
rows = info("yMontage");
|
|
if (columns>0 && rows>0)
|
|
exit("Layout ("+columns+"x"+rows+") is already set");
|
|
Dialog.create("Set Montage Layout");
|
|
Dialog.addNumber("Width:", 2);
|
|
Dialog.addNumber("Height:", 2);
|
|
Dialog.show;
|
|
mw = Dialog.getNumber;
|
|
mh = Dialog.getNumber;
|
|
setMetadata("Info","xMontage="+mw+"\nyMontage="+mh+"\n");
|
|
}
|
|
|
|
macro "Change Montage Layout" {
|
|
columns = info("xMontage");
|
|
rows = info("yMontage");
|
|
if (rows==0 || columns==0) {
|
|
run("Set Montage Layout");
|
|
columns = info("xMontage");
|
|
rows = info("yMontage");
|
|
}
|
|
id1 = getImageID;
|
|
title = getTitle;
|
|
getVoxelSize(xp,yp,zp,unit);
|
|
Dialog.create("Change Montage Layout");
|
|
Dialog.addNumber("Columns:", columns);
|
|
Dialog.addNumber("Rows:", rows);
|
|
Dialog.show;
|
|
columns2 = Dialog.getNumber;
|
|
rows2 = Dialog.getNumber;
|
|
run("Montage to Stack...", "columns=&columns rows=&rows");
|
|
id2 = getImageID;
|
|
run("Make Montage...", "columns=&columns2 rows=&rows2 scale=1.0");
|
|
rename(title);
|
|
setVoxelSize(xp,yp,zp,unit);
|
|
selectImage(id1); close;
|
|
selectImage(id2); close;
|
|
}
|
|
|