Re: Batch split channels and save

Posted by Dr D.J. Metcalf on Aug 06, 2010; 12:35pm
URL: http://imagej.273.s1.nabble.com/Batch-split-channels-and-save-tp3687341p3687343.html

Dear Kees,

Thanks for your reply. I've just tried the macro but I get an error message:
 
'(' expected in line 19.

title= File . nameWithoutExtension <;>

Regards,

Dan

On Aug 6 2010, Straatman, Kees R. (Dr.) wrote:

>Dear Dan,
>
> See if the macro below does what you want. At the moment it saves the
> results to a new directory called "analysed". If you want to save the
> result files in the same directory as your original files delete the line
> "dir2 = ....." and change in the first lane "dir1" into "dir2"
>
>
>dir1 = getDirectory("Choose Source Directory ");
>list = getFileList(dir1);
>dir2 = dir1+"analysed"+File.separator;
>File.makeDirectory(dir2);
>for (i=0; i<list.length; i++)
> {
>
> if (File.isDirectory(dir1+list[i])){}
> else{
>
> path = dir1+list[i];
> if (endsWith(path, ".db")){}
> else{
>
> open(path);
> if (bitDepth!=24){}  
> else {
> setBatchMode(true);
> title = File.nameWithoutExtension ;
> run("Split Channels");
> close();
>
> saveAs("Tiff", dir2+title+"d0.tif");
> saveAs("Tiff", dir2+title+"d1.tif");
> close();
> saveAs("Tiff", dir2+title+"d2.tif");
> close();
> setBatchMode(false);
>
> }
> }
> }
> }
>
>Best wishes
>
>Kees
>
>
>Dr K.R. Straatman
>Senior Experimental Officer
>Centre for Core Biotechnology Services
>College of Medicine, Biological Sciences and Psychology
>http://www.le.ac.uk/biochem/microscopy/home.html
>
>
> -----Original Message----- From: ImageJ Interest Group
> [mailto:[hidden email]] On Behalf Of Dr D.J. Metcalf Sent: 04 August
> 2010 17:14 To: [hidden email] Subject: Batch split channels and save
>
>Hi,
>
>I'd be grateful for some help on making my macro capable of batch
>processing a folder of images. I'm not sure if it's possible to modify the
>one I've written or if another approach is required.
>
>The aim is to open RGB tif files and then save the individual channels but
>with the added complication of discarding the blue image and saving the
>green and red images. Ideally I'd like to save the green image twice with
>different file names (see below).
>
>My starting file names are A_A##f##.tif My result file names are
>A_A##f##d0.tif, A_A##f##d1.tif, A_A##f##d2.tif (where d0 is the green
>chanel, d1 is the green channel and d2 is the red channel)
>
>Thanks,
>
>Dan
>
>
> open("V:\\Dan\\tif_files\\A_A06f12.tif"); run("Split Channels");
> run("Save", "save=V:\\Dan\\tif_files\\discards\\C3-A_A06f12.tif");
> close(); close(); run("Save",
> "save=[V:\\Dan\\tif_files\\discards\\C1-A_A06f12.tif]"); close();
> open("V:\\Dan\\tif_files\\discards\\C1-A_A06f12.tif");
> open("V:\\Dan\\tif_files\\discards\\C3-A_A06f12.tif"); run("Merge
> Channels...", "red=C3-A_A06f12.tif green=C1-A_A06f12.tif
> blue=C1-A_A06f12.tif gray=*None* create"); run("Split Channels");
> run("Save", "save=[V:\\Dan\\new files\\A_A06f12d0.tif]"); close();
> run("Save", "save=[V:\\Dan\\new files\\A_A06f12d1.tif]"); close();
> run("Save", "save=[V:\\Dan\\new files\\A_A06f12d2.tif]"); close();