Re: Creating individual tiles from large montage file

Posted by Jacqueline Ross on Jul 29, 2016; 8:03am
URL: http://imagej.273.s1.nabble.com/Creating-individual-tiles-from-large-montage-file-tp5016947p5016949.html

Thanks Jerome,

I can now get the correct naming! The extension is still there as part of the name but that doesn't matter.

I'd like to have the files going into a specified Destination folder, dir2 so that it's a bit more generic.

How would I add in that step?

I've used the code below before for saving individual files into folders but not for a sequence;

saveAs("TIFF", dir2 + title);
close();

}

So, I’m assuming I can somehow adapt this...?

Cheers,

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 Jerome Mutterer
Sent: Friday, 29 July 2016 7:19 p.m.
To: [hidden email]
Subject: Re: Creating individual tiles from large montage file

Dear Jacqui,
the getTilte() function works as expected, but because you have spaces in
the tilte, you should add square brackets in the "Image Sequence..."
command arguments. You can also specify the output folder using the save
parameter, like this:

run("Image Sequence... ", "format=TIFF name=["+ imgName +"] start=0 digits=4
save=/Users/jmutterer/Desktop/aaa");

Sincerely,

Jerome


On 29 July 2016 at 09:05, Jacqui Ross <[hidden email]> wrote:

> Dear All,
>
> We have a system that creates very large stitched images from individual
> raw data files. I'm helping one of our graduate students to do some image
> analysis and unfortunately her files are far too large to be able to
> process the stitched image and she has somehow forgotten to copy and store
> safely the raw data, which we often use for the analysis.
>
> So, I would like to create a macro that will cut these large images into
> tiles of a size that can be managed, i.e. reverse the process.
>
> I've made some progress but have two issues. One is that her file names
> have spaces in them. When I use the ImgName=getTitle() command, it seems to
> cut off the title at the space. Is there another command that can be used
> that will get the full name including spaces? If not, is there an easy way
> to rename these images with underscore or hyphens in place of spaces as a
> first step?
>
> The second problem is that instead of saving the image stack automatically
> as a sequence, it's asking me to confirm the file name. It might just be
> that it's late on a Friday afternoon (for me) but I can't work out what
> I've done wrong.
>
> I've copied the macro below and I would very much appreciate some help !
> I've also attached it as a text file in case something goes wrong with the
> lines..
>
>
> //This macro splits a stitched image into 5 x 5 individual tiles and saves
> as a sequence into a Destination folder
> 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]);
> imgName=getTitle();
> run("Montage to Stack...", "images_per_row=5 images_per_column=5
> border=0");
> run("Image Sequence... ", "format=TIFF name="+imgName+"start=0 digits=3");
> close();
>
> }
>
> 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/
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Jerome Mutterer
CNRS - Institut de biologie moléculaire des plantes
12, rue du Général Zimmer
67084 Strasbourg Cedex
www.ibmp.cnrs.fr

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