http://imagej.273.s1.nabble.com/Loci-plugin-and-macro-file-conversion-Questions-tp5003928p5003965.html
Thanks so much Melissa. Both suggestions worked perfectly. The quoting
dynamic string from my static macro recording. Thanks for being so
The run('Close') suggestion was completely off my radar. Is there basic
> Hi Rob,
>
>> I wrote a short macro to convert a set of images from Zeiss .zvi to
>> .tiff format (code below). The macro works, but I have two minor
>> issues I can not overcome. If prior to running my macro, I load an
>> image with Loci Bioformats plutgin and uncheck show metadata and
>> then load a second image with the windowless format turned on, I can
>> process my whole directory of images without manual intervention.
>> However, I can not figure out how to set these defaults within the
>> context of the macro. Can anyone point me to the proper way to set
>> defaults for the Loci plugins?
> Probably the easiest thing to do is to use the macro recorder to open a
> file with the desired options set, and then paste the output into your
> macro in place of the 'open(...)' command. Something like this:
>
> run("Bio-Formats Importer", "open=["+dir1+list[i]+"]");
>
> may be sufficient.
>
>> The second issue is that if I choose to let the metadata show in
>> windows as the conversion goes on, I can't figure out how to close
>> the files. Is there way to close these files other than one by one?
>> close and closeAll seem to only work with image windows.
> Have you tried:
>
> run("Close");
>
> instead? That should allow you to close any non-image windows.
>
> Regards,
> -Melissa
>
> On Thu, Jul 11, 2013 at 02:27:03PM -0500, Robert Baer wrote:
>> I wrote a short macro to convert a set of images from Zeiss .zvi to
>> .tiff format (code below). The macro works, but I have two minor
>> issues I can not overcome. If prior to running my macro, I load an
>> image with Loci Bioformats plutgin and uncheck show metadata and
>> then load a second image with the windowless format turned on, I can
>> process my whole directory of images without manual intervention.
>> However, I can not figure out how to set these defaults within the
>> context of the macro. Can anyone point me to the proper way to set
>> defaults for the Loci plugins?
>>
>> The second issue is that if I choose to let the metadata show in
>> windows as the conversion goes on, I can't figure out how to close
>> the files. Is there way to close these files other than one by one?
>> close and closeAll seem to only work with image windows.
>>
>> Thanks for any pointers,
>>
>> Rob
>>
>> // The macro code
>> //
>>
>> macro "Batch Convert .zvi to .tif"{
>> requires("1.33s");
>> dir1 = getDirectory("Choose Source Directory ");
>> dir2 = getDirectory("Choose Destination Directory ");
>> print(dir1 + " -> " + dir2);
>> list = getFileList(dir1);
>> setBatchMode(true);
>>
>> for (i=0; i < list.length; i++) {
>> showProgress(i + 1, list.length);
>> print(dir1 + list[i]);
>> if (endsWith(toLowerCase(list[i]), ".zvi")){
>> open(dir1 + list[i]);
>> dotIndex = lastIndexOf(list[i], ".");
>> if (dotIndex!=-1){
>> list[i] = substring(list[i], 0, dotIndex); // remove .zvi
>> saveAs ("Tiff", dir2 + list[i]+'.tif');
>> }
>> }
>> close();
>> }
>> }
>>
>>
>> --
>>
>> Robert W. Baer, Ph.D.
>> Professor of Physiology
>> Kirksille College of Osteopathic Medicine
>> A. T. Still University of Health Sciences
>> Kirksville, MO 63501 USA
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.htmlRobert W. Baer, Ph.D.
A. T. Still University of Health Sciences