Now I understand.
I also tried adding
resetThreshold;
and
close("Threshold");
before each method and the pull down menu in the GUI does not update.
And all that shows up in the Recorder is
run("script:Macro.ijm.ijm");
Cheers-
Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
-----Original Message-----
From: CARL Philippe (LBP) <[email protected]>
Sent: Thursday, January 11, 2024 9:36 AM
To: [email protected]
Subject: Re: setAutoThreshold through macro code
[EXTERNAL]
Hi Michael,
Sorry if my text wasn't clear enough and I confirm that "command does update
the histogram display" (as I wrote "As the min and max levels seem to be
updated").
The issue is that the method name doesn't get updated within the "Threshold..."
window.
Thus a user can't know "which" or "if" a given method had been set by the macro
code.
Kindest regards,
Philippe
----- Mail original -----
De: "Michael Schmid" <[email protected]>
À: "imagej" <[email protected]>
Envoyé: Jeudi 11 Janvier 2024 15:25:01
Objet: Re: setAutoThreshold through macro code
Hi Philippe,
as far as I can see, the run("Threshold...") command does update the histogram
display. You won't see much difference with the Blobs sample and these
thresholding methods because they all yield essentially the same threshold. If
you use a different image like the M51 galaxy sample, you can better see it.
Michael
________________________________________________________________
On 11.01.24 14:23, CARL Philippe (LBP) wrote:
> Dear all,
> Isn't it possible to perform a setAutoThreshold within a macro and visualyze
> this selection within the Threshold... window ?
> As the min and max levels seem to be updated, it is not the case of the
> threshold method as illustrated by the following small macro code:
> run("Blobs (25K)");
> setAutoThreshold("Otsu dark");
> run("Threshold...");
> waitForUser;
> setAutoThreshold("Minimum dark");
> run("Threshold...");
> waitForUser;
> setAutoThreshold("Default dark");
> run("Threshold...");
> waitForUser;
> setAutoThreshold("Huang dark");
> run("Threshold...");
> waitForUser;
> setAutoThreshold("Intermodes dark");
> run("Threshold...");
> waitForUser;
> setAutoThreshold("IsoData dark");
> run("Threshold...");
> Looking briefly within the code, I found the setMethod method within the
> ij.process.AutoThresholder which could be doing the job (through the
> "instance.methodChoice.select(method);" line).
> But the setAutoThreshold of the ij.macro.Functions class is calling the
> setAutoThreshold method of the ij.process.ImageProcessor class which will
> finally be calling the getThreshold method of the AutoThresholder class.
> And there is no call to a "instance.methodChoice.select(method);" instruction
> or equivalent.
> Looking forward for your lightings on this, please receive my best wishes for
> this new year!
> My best regards,
> Philippe
>
> Philippe CARL
> Laboratoire de Bioimagerie et Pathologies UMR 7021 CNRS - Université
> de Strasbourg Faculté de Pharmacie
> 74 route du Rhin
> 67401 ILLKIRCH
> Tel : +33(0)3 68 85 41 41
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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