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<p>Hi Jean-Marie,</p>
<p>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!</p>
<p>I would like to further extend it and get the ROIs associated to
that image from OMERO into the ROI manger of ImageJ.</p>
<p>I found how this could be done in the example scripts, i.e
<a class="moz-txt-link-freetext" href="https://github.com/ome/training-scripts/blob/master/practical/jython/omero_rois_to_imagej_roi.jy">https://github.com/ome/training-scripts/blob/master/practical/jython/omero_rois_to_imagej_roi.jy</a><br>
</p>
Just as a question, is this script already available as a class in
OMER.insight?<br>
Like a "ROIwriter class", as opposed to the ROIreader class from
org.openmicroscopy.shoola.util.roi.io<br>
<br>
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 :)<br>
<br>
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.<br>
<br>
Thanks and cheers,<br>
Kai<br>
<br>
<div class="moz-cite-prefix">On 05/17/2018 10:11 PM, Jean-Marie
Burel (Staff) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:D7239E31.7660E%25j.burel@dundee.ac.uk">
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<div>Hi Kai</div>
<div><br>
</div>
<div><br>
</div>
<div>All the scripts are now available at <a
href="https://github.com/ome/training-scripts"
moz-do-not-send="true">https://github.com/ome/training-scripts</a></div>
<div><br>
</div>
<div>I did a bit of digging and it seems that the option
specifyRanges=true is taken into account only when
windowless=false</div>
<div>In that case the values in the range dialog are read.</div>
<div><br>
</div>
<div>We have written a new version of the script you mentioned</div>
<div>The new version does not use the BF-importer plugin</div>
<div><a
href="https://github.com/ome/training-scripts/blob/master/practical/jython/analyse_particles_from_dataset.jy"
moz-do-not-send="true">https://github.com/ome/training-scripts/blob/master/practical/jython/analyse_particles_from_dataset.jy</a></div>
<div>This should hopefully allow you to only retrieve the planes
you want</div>
<div><br>
</div>
<div>Cheers</div>
<div>Jmarie</div>
<div><br>
</div>
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<span style="font-weight:bold">From: </span>ome-users <<a
href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"
moz-do-not-send="true">ome-users-bounces@lists.openmicroscopy.org.uk</a>>
on behalf of Kai Schleicher <<a
href="mailto:kai.schleicher@unibas.ch"
moz-do-not-send="true">kai.schleicher@unibas.ch</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME User
Support List <<a
href="mailto:ome-users@lists.openmicroscopy.org.uk"
moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 17 May
2018 at 18:11<br>
<span style="font-weight:bold">To: </span>"<a
href="mailto:ome-users@lists.openmicroscopy.org.uk"
moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a>"
<<a href="mailto:ome-users@lists.openmicroscopy.org.uk"
moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>[ome-users]
syntax for scripting the windowless importer in Jython<br>
</div>
<div><br>
</div>
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<p>Dear OME-team,</p>
<p>To script the windowless BF-importer in Jython I am
building on the cool <a moz-do-not-send="true"
href="https://github.com/bramalingam/Omero-Imagej-Scripts/blob/master/omero_batch_analysis.py">script
by Balaji</a>.</p>
<p>I specifically wish to limit the import to the first
time-point of my datasets, but I am struggling at getting
the syntax right.</p>
<p>In IJ1-macro language it works like this:<br>
</p>
<blockquote type="cite">run("Bio-Formats Importer",
"open=V:/small5Dstack.tif specify_range t_begin=1 t_end=1
t_step=1");</blockquote>
In the jython script I tried to add a line 53:<br>
<blockquote type="cite">options += " specifyranges=true
tbegin=1 tend=1 tstep=1 "</blockquote>
But it still loads the entire dataset.<br>
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.
<p>Thanks and see you soon at the meeting,<br>
Kai</p>
<pre class="moz-signature" cols="72">--
>>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) | <a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch" moz-do-not-send="true">kai.schleicher@unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch" moz-do-not-send="true">www.biozentrum.unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch" moz-do-not-send="true">www.microscopynetwork.unibas.ch</a></pre>
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