Colour Deconvolution Macro - help with saving files

[Jacqueline Ross]

Hi All,

I'm helping one of our researchers with a macro to split Haematoxylin/DAB images into the 3 separate images and save Colour1 and Colour2 as separate files into a destination folder.

What I can't seem to be able to do is just give the destination directory using Dir2

saveAs("TIFF", "dir2+list[i]" +title);

so I am having to use a specified path. This is working but I'd like to be able to do it properly. I think it's something to do with the titles...

Can anyone point me in the direction of my error? I'm having a mental block with this one!

This is the macro;

dir1 = getDirectory("Choose Source Directory ");
dir2 = getDirectory("Choose Destination Directory ");
list = getFileList(dir1);
setBatchMode(true);
for (i=0; i<list.length; i++) {
showProgress(i+1, list.length);
open(dir1+list[i]);
makeRectangle(1386, 702, 2952, 2958);
run("Crop");
run("Subtract Background...", "rolling=50 light");
imgName=getTitle();
run("Colour Deconvolution", "vectors=[H DAB]");
//close windows we don't need
selectWindow(imgName + " (Colour[3])");
close();
selectWindow(imgName +" (Colour[1])");
title = getTitle();
print("title: " + title);
saveAs("Tiff", "C:\\Users\\jros013\\Desktop\\Rachel_output\\"+title);
close();
selectWindow(imgName + " (Colour[2])");
title = getTitle();
print("title: " + title);
saveAs("Tiff", "C:\\Users\\jros013\\Desktop\\Rachel_output\\"+title);
close();
saveAs("TIFF", "dir2+list[i]" +title);
close();
}


Thanks!

Kind regards,

Jacqui
Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


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[Tiago Ferreira-2]

On 2012.10.08, at 18:49 , Jacqui Ross wrote:
>
> What I can't seem to be able to do is just give the destination directory
> saveAs("TIFF", "dir2+list[i]" +title);

Hi Jacqui,

I haven't read your macro, but if you quote "dir2+list[i]" then <<dir2>> and the
item <<i>> in the array <<list>> are no longer variables, they simply become one
string, containing no file name separators. You may just need to unquote them.

Also, if <<title>> already includes the <<list[i]>> filename, you may want to
just use:

saveAs("TIFF", dir2 + title);

This kind of frustrations are easily avoidable by using a text editor w/ syntax
highlighting, such as the Fiji script editor.

HTH,
-tiago

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[Jacqueline Ross]

Thanks Tiago and Wayne!

Your suggestions have solved the problem.

I just needed to put;

title = getTitle();

saveAs("TIFF", dir2 + title);

Now, it's working fine. Just a bit puzzled by the loss of one of the square brackets in the file name...

I have to admit that I haven't used the Fiji script editor as yet but will give it a try next time.

I do use the "evaluate line" and debugging in the standard ImageJ.

Kind regards,

Jacqui

Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Tiago Ferreira
Sent: Tuesday, 9 October 2012 4:34 p.m.
To: [hidden email]
Subject: Re: Colour Deconvolution Macro - help with saving files

On 2012.10.08, at 18:49 , Jacqui Ross wrote:
>
> What I can't seem to be able to do is just give the destination
> directory saveAs("TIFF", "dir2+list[i]" +title);

Hi Jacqui,

I haven't read your macro, but if you quote "dir2+list[i]" then <<dir2>> and the item <<i>> in the array <<list>> are no longer variables, they simply become one string, containing no file name separators. You may just need to unquote them.

Also, if <<title>> already includes the <<list[i]>> filename, you may want to just use:

saveAs("TIFF", dir2 + title);

This kind of frustrations are easily avoidable by using a text editor w/ syntax highlighting, such as the Fiji script editor.

HTH,
-tiago

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