) expected in line 20 but all parentheses are there in the code. Pls help!

[nhasan]

Hi All

I am not very  experienced in writing macros, so I used the macro recorder
to create a simple macro (code below). However, when I run it, I get this
error that says ")" expected in line 20. i double-checked the code, but
seems like all the brackets/parentheses are accounted for in the code. Any
suggestions? Really appreciate the help!


run("Open...");
title=getTitle()
selectWindow(title);
run("Split Channels");
selectWindow(title+" (blue)");
close();
selectWindow(title+" (green)");
close();
selectWindow(title+" (red)");
run("16-bit");
run("Duplicate..."," ");
selectWindow(title+" (red)-1");
setAutoThreshold("Default dark");
//run("Threshold...");
setThreshold(51, 254);
//setThreshold(51, 254);
setOption("BlackBackground", true);
run("Convert to Mask");
run("Watershed");
//line below giving ")" expected error
run("Set Measurements...", "area mean standard min limit redirect=[title+ "
(red)"] decimal=3");
run("Analyze Particles...", "pixel show=Outlines display clear summarize");
selectWindow(title+ " (red)");
close();
selectWindow(title+ " (red)-1");
close();





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[Herbie]

Good day,

the following works for me:

title+=" (red)";
run("Set Measurements...", "area mean standard min limit
redirect=[title] decimal=3");
run("Analyze Particles...", "pixel show=Outlines display clear summarize");
selectWindow(title);
close();
selectWindow(title+ "-1");
close();

(Please watch for line breaks introduced by the mailer.)

This is not a good idea:

setAutoThreshold("Default dark");
setThreshold(51, 254);

First you use an automatic threshold scheme (Default), then you set the
threshold to fixed values.
Fixed thresholds should be avoided because they don't generalize to
similar images. If you are not happy with the automatic
"Default"-scheme, try one of the other automatic schemes.

Regards

Herbie

:::::::::::::::::::::::::::::::::::
Am 13.11.19 um 18:30 schrieb nhasan:

> run("Open...");
> title=getTitle()
> selectWindow(title);
> run("Split Channels");
> selectWindow(title+" (blue)");
> close();
> selectWindow(title+" (green)");
> close();
> selectWindow(title+" (red)");
> run("16-bit");
> run("Duplicate..."," ");
> selectWindow(title+" (red)-1");
> setAutoThreshold("Default dark");
> //run("Threshold...");
> setThreshold(51, 254);
> //setThreshold(51, 254);
> setOption("BlackBackground", true);
> run("Convert to Mask");
> run("Watershed");
> //line below giving ")" expected error
> run("Set Measurements...", "area mean standard min limit redirect=[title+ "
> (red)"] decimal=3");
> run("Analyze Particles...", "pixel show=Outlines display clear summarize");
> selectWindow(title+ " (red)");
> close();
> selectWindow(title+ " (red)-1");
> close();

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[nhasan]

Thank you Herbie!

Just to clarify, where would i put the title+=" (red)"; ? should that be
right above line 20?

Also, thanks for the tip on the thresholding - the reason why I set the
threshold was to be able to get a quantitative estimate of particles across
images that fall within the thresholded area. Is there a better way of doing
that using automatic thresholding?





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[Herbie]

Here is the code that works for me:

/////////////////////////
run("Open...");
title=getTitle()
run("Split Channels");
close(title+" (blue)");
close(title+" (green)");
title+=" (red)";
run("16-bit"); // not sure if this is reasonable
run("Duplicate..."," ");
selectImage(title+"-1");
setThreshold(51, 254);
setOption("BlackBackground", true);
run("Convert to Mask");
run("Watershed");
run("Set Measurements...", "area mean standard min limit
redirect=[title] decimal=3");
run("Analyze Particles...", "pixel show=Outlines display clear summarize");
close(title);
close(title+"-1");
exit();
/////////////////////////

"Is there a better way of doing that using automatic thresholding?"

Yes!

Run the first part of the macro, i.e.:

/////////////////////////
run("Open...");
title=getTitle()
run("Split Channels");
close(title+" (blue)");
close(title+" (green)");
title+=" (red)";
run("16-bit"); // not sure if this is reasonable
run("Duplicate..."," ");
selectImage(title+"-1");
/////////////////////////

Then go to "Image >> Adjust >> Threshold...", check "Dark background"
and choose a scheme from the left drop-down menu and look if the
threshold suits your needs. If you've found an automatic threshold that
is adequate, then exchange the macro code-line

setThreshold(51, 254);

by this line

setAutoThreshold("XXXXX dark");

where XXXXX is the name of the automatic threshold-scheme.

I'm not sure if you really need the code line:

run("16-bit");

Finally, please try to understand what your macro is doing!

Regards

Herbie

::::::::::::::::::::::::::::::::::::
Am 13.11.19 um 19:24 schrieb nhasan:

> Thank you Herbie!
>
> Just to clarify, where would i put the title+=" (red)"; ? should that be
> right above line 20?
>
> Also, thanks for the tip on the thresholding - the reason why I set the
> threshold was to be able to get a quantitative estimate of particles across
> images that fall within the thresholded area. Is there a better way of doing
> that using automatic thresholding?
>
>
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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