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// This macro runs "Measure" on a all the slices in a stack. With a
// hyperstack, it runs "Measure" in a user-selected (c,t,z) order.
// Unchecking "Channels", "Slices" or "Frames" will select the
// current channel, slice or frame while running "Measure".
//
// Ved P. Sharma, March 21, 2012
// Albert Einstein College of Medicine, New York
saveSettings;
setOption("Stack position", true);
if (!Stack.isHyperstack) {
getVoxelSize(width, height, depth, unit);
for (n=1; n<=nSlices; n++) {
setSlice(n);
run("Measure");
}
if (unit!="pixels") {
depths = newArray(Table.size);
for (i=0; i<Table.size; i++)
depths[i] = i*depth;
Table.setColumn(unit, depths);
Table.update;
}
restoreSettings;
exit;
}
Stack.getDimensions(w, h, channels, slices, frames);
Stack.getPosition(ch, sl, fr);
Dialog.create("Measure Hyperstack");
Dialog.addCheckbox("Channels ("+channels+")", true);
Dialog.addCheckbox("Slices ("+slices+")", true);
Dialog.addCheckbox("Frames ("+frames+")", true);
choices = newArray("czt(default)", "ctz", "zct", "ztc", "tcz", "tzc");
Dialog.addChoice("Order:", choices, choices[0]);
Dialog.show();
state1 = Dialog.getCheckbox();
state2 = Dialog.getCheckbox();
state3 = Dialog.getCheckbox();
order = Dialog.getChoice();
if(state1) {startCh = 1; endCh = channels;}
else {startCh = ch; endCh = ch;}
if(state2) {startSl = 1; endSl = slices;}
else {startSl = sl; endSl = sl;}
if(state3) {startFr = 1; endFr = frames;}
else {startFr = fr; endFr = fr;}
if(order == "czt(default)") {
for (u=startFr; u<=endFr; u++) {
Stack.setFrame(u);
for (v=startSl; v<=endSl; v++) {
Stack.setSlice(v);
for (w=startCh; w<=endCh; w++) {
Stack.setChannel(w);
run("Measure");
}
}
}
}
if(order == "ctz") {
for (u=startSl; u<=endSl; u++) {
Stack.setSlice(u);
for (v=startFr; v<=endFr; v++) {
Stack.setFrame(v);
for (w=startCh; w<=endCh; w++) {
Stack.setChannel(w);
run("Measure");
}
}
}
}
if(order == "zct") {
for (u=startFr; u<=endFr; u++) {
Stack.setFrame(u);
for (v=startCh; v<=endCh; v++) {
Stack.setChannel(v);
for (w=startSl; w<=endSl; w++) {
Stack.setSlice(w);
run("Measure");
}
}
}
}
if(order == "ztc") {
for (u=startCh; u<=endCh; u++) {
Stack.setChannel(u);
for (v=startFr; v<=endFr; v++) {
Stack.setFrame(v);
for (w=startSl; w<=endSl; w++) {
Stack.setSlice(w);
run("Measure");
}
}
}
}
if(order == "tcz") {
for (u=startSl; u<=endSl; u++) {
Stack.setSlice(u);
for (v=startCh; v<=endCh; v++) {
Stack.setChannel(v);
for (w=startFr; w<=endFr; w++) {
Stack.setFrame(w);
run("Measure");
}
}
}
}
if(order == "tzc") {
for (u=startCh; u<=endCh; u++) {
Stack.setChannel(u);
for (v=startSl; v<=endSl; v++) {
Stack.setSlice(v);
for (w=startFr; w<=endFr; w++) {
Stack.setFrame(w);
run("Measure");
}
}
}
}
Stack.setPosition(ch, sl, fr);
restoreSettings;
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