http://imagej.273.s1.nabble.com/Loci-plugin-and-macro-file-conversion-Questions-tp5003928p5003968.html
> The run('Close') suggestion was completely off my radar. Is there
Record) and then attempt to perform the operation of interest. Usually it
You can also try Googling. I searched for "imagej close non-image window"
> Thanks so much Melissa. Both suggestions worked perfectly. The quoting
> on the brackets in the open= argument makes perfect sense now that I see
> what you did, but I couldn't get there on my own when constructing a
> dynamic string from my static macro recording. Thanks for being so
> explicit!
>
> The run('Close') suggestion was completely off my radar. Is there basic
> documentation that I should have been reading prior to posting?
>
> Thanks again,
>
> Rob
>
>
> On 7/11/2013 7:02 PM, Melissa Linkert wrote:
>
>> 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.**html<
http://imagej.nih.gov/ij/list.html>
>>>
>>
>
> --
>
> 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.**html<
http://imagej.nih.gov/ij/list.html>
>