I often use
run("Set...", "value=25 slice");
instead of clear or clear outside to avoid issues with LUTs or users changing
colors.
Cheers-
Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, New York, NY 10016
[email protected]<mailto:[email protected]>
http://nyulmc.org/micros http://microscopynotes.com/
Cell voice (no text) 1-914-309-3270
Office 1-646-501-0567
________________________________
From: Stein Rørvik <[email protected]>
Sent: Monday, February 19, 2024 4:17:37 PM
To: [email protected]
Subject: Problem with Fill and Clear Outside in macros
[EXTERNAL]
I have encountered a problem with "Fill" and "Clear Outside" in a macro.
What I want to do is to create a ROI on each slice in a stack based on fitting
around the outline of a thresholded object,
and fill inside and clear outside to create a mask, leaving an overlay of the
selection.
The problem is that "Fill" fills with the background color instead of the
foreground color. It fills correctly on the first selected slice.
The problem does not occur if either the "Fill" or "Clear Outside" command is
removed. It also does not occur if done manually via the GUI.
The following macro reproduces the problem:
close("*t1*");
run("T1 Head (16-bits)");
run("8-bit");
setSlice(nSlices/2);
setAutoThreshold("IJ_IsoData dark no-reset");
Color.setForeground("white");
Color.setBackground("black");
for (s = 50; s <= 100; s++) {
setSlice(s);
run("Create Selection");
if (selectionType >= 0) {
run("Fit Ellipse");
run("Clear Outside", "slice");
run("Fill", "slice"); //bug? this
fills with black, except for on slice 50
}
Overlay.addSelection("red");
Overlay.setPosition(s);
}
setSlice(nSlices/2);
resetThreshold;
Roi.remove;
I am on Windows 10/64 using the latest daily build under Java 8 jre.
Stein
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