ROI Manager does not work headless

ctrueden commented 7 years ago

The ROI Manager cannot work headless, since it extends PlugInFrame, and unlike GenericDialog, this library does not runtime patch it. We could do so.

For example, any of the following macro calls:

roiManager("reset");
roiManager(("count");
roiManager("select", index);

will throw an exception like:

java.awt.HeadlessException
        at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
        at java.awt.Window.<init>(Window.java:536)
        at java.awt.Frame.<init>(Frame.java:420)
        at ij.plugin.frame.PlugInFrame.<init>(PlugInFrame.java:13)
        at ij.plugin.frame.RoiManager.<init>(RoiManager.java:90)
        at ij.macro.Functions.roiManager(Functions.java:2748)
        at ij.macro.Functions.getFunctionValue(Functions.java:230)
        at ij.macro.Interpreter.getFactor(Interpreter.java:1385)
        at ij.macro.Interpreter.getTerm(Interpreter.java:1356)
        at ij.macro.Interpreter.getStringExpression(Interpreter.java:1496)
        at ij.macro.Interpreter.getStringTerm(Interpreter.java:1315)
        at ij.macro.Interpreter.getString(Interpreter.java:1272)
        at ij.macro.Interpreter.doStatement(Interpreter.java:281)
        at ij.macro.Interpreter.doBlock(Interpreter.java:608)
        at ij.macro.Interpreter.doStatement(Interpreter.java:272)
        at ij.macro.Interpreter.doFor(Interpreter.java:530)
        at ij.macro.Interpreter.doStatement(Interpreter.java:254)
        at ij.macro.Interpreter.doBlock(Interpreter.java:608)
        at ij.macro.Interpreter.doStatement(Interpreter.java:272)
        at ij.macro.Interpreter.doFor(Interpreter.java:530)
        at ij.macro.Interpreter.doStatement(Interpreter.java:254)
        at ij.macro.Interpreter.doBlock(Interpreter.java:608)
        at ij.macro.Interpreter.doStatement(Interpreter.java:272)
        at ij.macro.Interpreter.doFor(Interpreter.java:530)
        at ij.macro.Interpreter.doStatement(Interpreter.java:254)
        at ij.macro.Interpreter.doStatements(Interpreter.java:218)
        at ij.macro.Interpreter.run(Interpreter.java:115)
        at ij.macro.Interpreter.run(Interpreter.java:85)
        at ij.macro.Interpreter.run(Interpreter.java:96)
        at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
        at ij.plugin.Macro_Runner.runMacroFile(Macro_Runner.java:139)
        at ij.IJ.runMacroFile(IJ.java:148)
        at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:1056)
        at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:1052)
        at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:986)
        at net.imagej.legacy.IJ1Helper.runMacroFile(IJ1Helper.java:1052)
        at net.imagej.legacy.LegacyCommandline$Macro.handle(LegacyCommandline.java:188)
        at org.scijava.console.DefaultConsoleService.processArgs(DefaultConsoleS ervice.java:93)
        at net.imagej.legacy.LegacyConsoleService.processArgs(LegacyConsoleService.java:81)
        at org.scijava.AbstractGateway.launch(AbstractGateway.java:95)
        at net.imagej.Main.launch(Main.java:62)
        at net.imagej.Main.main(Main.java:68)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl. java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:497)
        at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)

ctrueden commented 7 years ago

One reason we have not implemented this patching yet is because you can use overlays as a workaround. For example, the following code adds ROIs to an overlay, transfers the overlay to another image, and then measures the mean of each ROI in the overlay.

run("Blobs (25K)");
setAutoThreshold("Default");
run("Analyze Particles...", "  show=Overlay");
Overlay.copy
newImage("Untitled", "8-bit ramp", 256, 254, 1);
Overlay.paste
for (i=0; i<Overlay.size; i++) {
  Overlay.activateSelection(i);
  List.setMeasurements;
  mean = List.getValue("Mean");
  print(i+"  "+mean);
}

See this forum thread for details and discussion.

imagesc-bot commented 3 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/redirect-imagej-fiji-print-macro-to-console/47012/1

imagesc-bot commented 3 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/headless-roimanager-open-file-path/46561/2

imagej / imagej-legacy

ROI Manager does not work headless #153