Greetings,
> run("Set...", "value=25 slice");
As to setting an RGB in this fashion, how?
It would be nice in macros/plugins, the color in question can be passed in
as a parameter, e.g., run("Fill", "value=black"). Setting a default colors
for the GUI is convenient, albeit, having to save, set, reset defaults in
code is a pain, especially when things don't go perfectly...
When 32bit I use:
run("Macro...", "code=[if (v<0.5) v=1; else v=NaN;]");
It would be nice to have a macro variable, say 'r', which is true within
an ROI and false otherwise.
Also, RGB???
Thanks for listening,
Fred
On Mon, February 19, 2024 5:25 pm, Cammer, Michael wrote:
> 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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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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