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

[Cardone, Giovanni]

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
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

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