[ome-users] FIJI bio-formats importer cannot open paths with spaces (from macro)

[Clark Andrew]

Hi Giovanni,

thanks for your quick response. Yes, that did the trick. Sorry, I should have caught that myself using the recorder. Thanks a lot for your help!

best,
Andy

On 12 Feb 2019, at 13:11, Cardone, Giovanni <cardone at biochem.mpg.de<mailto:cardone at biochem.mpg.de>> wrote:

Hi Andy,

I think that you should try to include the full name of the file between square brackets. I didn’t try for this specific command, but this is the common practice when file names contain spaces (otherwise the script interpreter reads only the substring before the space).

run(“Bio-Formats”, “open=[/path/to my/file]”);

I hope it helps,
Giovanni

From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Clark Andrew
Sent: Dienstag, 12. Februar 2019 13:02
To: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: [ome-users] FIJI bio-formats importer cannot open paths with spaces (from macro)

There’s a small issue with calling the bio-formats importer from a FIJI macro. It will not open a file if there is a space anywhere in the file path. For example:

run(“Bio-Formats”, “open=/path/to my/file”);

will raise the following error:

The specified file (/path/to) does not exist.

I tried replacing the spaces with “\ “ or putting the filepath in double quotes, but I get the same error.

This is on a freshly updated FIJI and bio-formats on OSX. There is no problem opening the file using the Bio-Formats importer from the dropdown plugins menu, only running it from a macro script.

Thanks!
andy
____________________
Andrew G. CLARK, PhD
Postdoctoral Fellow
VIGNJEVIC Group

+33 (0) 156 24 67 70
andrew.clark at curie.fr<mailto:andrew.clark at curie.fr>
www.andrewgclark.info<http://www.andrewgclark.info/>

Institut Curie / UMR 144
12, Rue Lhomond
75005 Paris
FRANCE

_______________________________________________
ome-users mailing list
ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

____________________
Andrew G. CLARK, PhD
Postdoctoral Fellow
VIGNJEVIC Group

+33 (0) 156 24 67 70
andrew.clark at curie.fr<mailto:andrew.clark at curie.fr>
www.andrewgclark.info<http://www.andrewgclark.info>

Institut Curie / UMR 144
12, Rue Lhomond
75005 Paris
FRANCE

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20190212/464a01a8/attachment.html>