Re: Batch split channels and save

Posted by BenTupper on Aug 06, 2010; 1:51pm
URL: http://imagej.273.s1.nabble.com/Batch-split-channels-and-save-tp3687341p3687344.html

Hi,

On Aug 6, 2010, at 8:35 AM, Dr D.J. Metcalf wrote:

> 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 <;>
>

It might be that you have a different version of ImageJ than that  
required.  The File.nameWithoutExtension requires at least 1.42d  
according to ...

http://rsb.info.nih.gov/ij/developer/macro/functions.html#F

Cheers,
Ben

> 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();