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

[Kai Schleicher]

Hi Jean-Marie,

thanks for your reply and the updated scripts! I switched to the newer 
version you mentioned and it works like a charm, it was easy to adept to 
fetch only the time points that I like to have!

I would like to further extend it and get the ROIs associated to that 
image from OMERO into the ROI manger of ImageJ.

I found how this could be done in the example scripts, i.e 
https://github.com/ome/training-scripts/blob/master/practical/jython/omero_rois_to_imagej_roi.jy

Just as a question, is this script already available as a class in 
OMER.insight?
Like a "ROIwriter class", as opposed to the ROIreader class from 
org.openmicroscopy.shoola.util.roi.io

Since this is a feature that is already in OMERO.insight, I figure there 
must be such a class, I just don't know its name :)

I apologize in advance, as these type of questions must be tedious to 
answer one by one (you are not a class/command/package lookup service), 
but I just started trying to find my way through the documentation.

Thanks and cheers,
Kai

On 05/17/2018 10:11 PM, Jean-Marie Burel (Staff) wrote:
> 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  |www.biozentrum.unibas.ch  |www.microscopynetwork.unibas.ch
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
>
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