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