[ome-users] syntax for scripting the windowless importer in Jython

[Jean-Marie Burel (Staff)]

Hi Kai


All the scripts are now available at https://github.com/ome/training-scripts

I did a bit of digging and it seems that the option specifyRanges=true is taken into account only when windowless=false
In that case the values in the range dialog are read.

We have written a new version of the script you mentioned
The new version  does not use the BF-importer plugin
https://github.com/ome/training-scripts/blob/master/practical/jython/analyse_particles_from_dataset.jy
This should hopefully allow you to only retrieve the planes you want

Cheers
Jmarie

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>>
Reply-To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Date: Thursday, 17 May 2018 at 18:11
To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>" <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: [ome-users] syntax for scripting the windowless importer in Jython


Dear OME-team,

To script the windowless BF-importer in Jython I am building on the cool script by Balaji<https://github.com/bramalingam/Omero-Imagej-Scripts/blob/master/omero_batch_analysis.py>.

I specifically wish to limit the import to the first time-point of my datasets, but I am struggling at getting the syntax right.

In IJ1-macro language it works like this:

run("Bio-Formats Importer", "open=V:/small5Dstack.tif specify_range t_begin=1 t_end=1 t_step=1");
In the jython script I tried to add a line 53:

options += " specifyranges=true tbegin=1 tend=1 tstep=1 "
But it still loads the entire dataset.
I tried a few other strings without luck and was wondering if you could maybe just point me to the proper way of doing it.

Thanks and see you soon at the meeting,
Kai

--
>>Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch>

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