I just found a new case when this does not work:
If the image is binary, it works if the order is "Fill" and then "Clear
Outside" but not the other way around.
close("*t1*");
run("T1 Head (16-bits)");
run("8-bit");
setSlice(nSlices/2);
setAutoThreshold("IJ_IsoData dark no-reset");
run("Convert to Mask", "method=IJ_IsoData background=Dark black create");
//2024-02-20
Color.setForeground("white");
Color.setBackground("black");
for (s = 50; s <= 100; s++) {
setSlice(s);
run("Create Selection");
if (selectionType >= 0) {
run("Fit Ellipse");
Overlay.addSelection("red");
Overlay.setPosition(s);
if (true) {
run("Clear Outside", "slice");
run("Fill", "slice"); //fills with black
} else {
run("Fill", "slice"); //fills with white
run("Clear Outside", "slice");
}
}
}
setSlice(nSlices/2);
resetThreshold;
Roi.remove;
Stein
-----Original Message-----
From: Stein Rørvik <[email protected]>
Sent: 20. februar 2024 19:07
Subject: Re: Problem with Fill and Clear Outside in macros
Thanks for the quick response,
it works fine after this update!
Stein
-----Original Message-----
From: Wayne Rasband <[email protected]>
Sent: 20. februar 2024 16:53
Subject: Re: Problem with Fill and Clear Outside in macros
> On Feb 19, 2024, at 5:20 PM, Stein Rørvik
> <[email protected]> wrote:
>
> I have encountered a problem with "Fill" and "Clear Outside" in a macro.
The latest daily build (1.54i17) fixes a bug where calling run("Clear
Outside","slice") set the foreground color to the background color.
-wayne
> 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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