<div dir="ltr"><div><div><div><div>Hi All,<br><br></div>thank you for your replies.<br></div>Once available I will test the function and let you know.<br></div>Thank you once more for your help.<br><br></div>Antonio<br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-05-06 19:59 GMT+01:00 Mark Carroll <span dir="ltr"><<a href="mailto:m.t.b.carroll@dundee.ac.uk" target="_blank">m.t.b.carroll@dundee.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I can confirm that the fix will be in the forthcoming 5.1.2 release.<br>
Do let us know if it gives you any further problems.<br>
<br>
-- Mark<span class=""><br>
<br>
<br>
On 05/06/2015 05:52 PM, Antonio Trabalza wrote:<br>
</span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">
Dear Jean-Marie,<br>
<br>
thank you for your reply.<br>
I am using version 5.0.8 and it is working.<br>
Yes please keep me in the loop.<br>
<br>
Antonio<br>
<br>
2015-05-02 21:03 GMT+01:00 Jean-Marie Burel (Staff)<br></span>
<<a href="mailto:j.burel@dundee.ac.uk" target="_blank">j.burel@dundee.ac.uk</a> <mailto:<a href="mailto:j.burel@dundee.ac.uk" target="_blank">j.burel@dundee.ac.uk</a>>>:<span class=""><br>
<br>
Dear Antonio<br>
<br>
I have created a ticket<br>
<a href="https://trac.openmicroscopy.org.uk/ome/ticket/12865" target="_blank">https://trac.openmicroscopy.org.uk/ome/ticket/12865</a><br>
If you wish to be cc'd, let us know<br>
<br>
We should have it fixed in the next release (in few weeks)<br>
If you use the 5.0.x version, it should work<br>
<br>
Regards<br>
<br>
Jmarie<br>
<br>
<br>
From: Antonio Trabalza <<a href="mailto:antoniotrabalza@gmail.com" target="_blank">antoniotrabalza@gmail.com</a><br></span>
<mailto:<a href="mailto:antoniotrabalza@gmail.com" target="_blank">antoniotrabalza@gmail.com</a>>><span class=""><br>
Reply-To: OME User Support List<br>
<<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br></span>
<mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>>><span class=""><br>
Date: Friday, 1 May 2015 09:37<br>
To: OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br></span>
<mailto:<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>>><span class=""><br>
Subject: Re: [ome-users] Fwd: Ext.getPlanePositionX(positionX, no)<br>
problems<br>
<br>
Hi Curtis,<br>
<br>
Thank you !<br>
You spared me a lot of mental health!<br>
<br>
How long this fix would take?<br>
Can I use an earlier version for the time being?<br>
Antonio<br>
<br>
On 30 Apr 2015 23:36, "Curtis Rueden" <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a><br></span><span class="">
<mailto:<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>>> wrote:<br>
<br>
Hi Antonio,<br>
<br>
> I am getting this error:<br>
><br>
> ')' expected in line ...<br>
> Ext.getPlanePositionX( <positionX> [no], no);<br>
<br>
Unfortunately, it appears that the Ext.getPlanePosition* methods<br>
are broken since v5.1.0 [1]. (The error ImageJ gives here is<br>
misleading.) This will need to be fixed on the Bio-Formats side.<br>
<br>
Regards,<br>
Curtis<br>
<br>
[1] Commit introducing the breakage:<br>
<a href="https://github.com/openmicroscopy/bioformats/commit/70c134c04030f093d19ffeb8df0d99eda9ba4441" target="_blank">https://github.com/openmicroscopy/bioformats/commit/70c134c04030f093d19ffeb8df0d99eda9ba4441</a><br>
<br>
<br>
On Thu, Apr 30, 2015 at 8:15 AM, Antonio Trabalza<br></span><div><div class="h5">
<<a href="mailto:a.trabalza@csc.mrc.ac.uk" target="_blank">a.trabalza@csc.mrc.ac.uk</a> <mailto:<a href="mailto:a.trabalza@csc.mrc.ac.uk" target="_blank">a.trabalza@csc.mrc.ac.uk</a>>> wrote:<br>
<br>
<br>
Dear OME users,<br>
<br>
I am a postdoc in neurodisease lab at CSC MRC London.<br>
I am trying to write a IJ macro to organize several stacks<br>
taken by prairie 2 photon microscope in a format nice for<br>
the stitching plugin to process<br>
<br>
I am having serious problems with the IJ macro external<br>
commands Ext.getPlanePositionX, Y and Z. I can't get them to<br>
work.<br>
<br>
I wrote (just to set up the concept, it will be a part of a<br>
longer macro):<br>
<br>
id = File.openDialog("Choose a file");<br>
run("Bio-Formats Macro Extensions")<br>
run("Bio-Formats Importer", "open=[" + id + "]<br>
color_mode=Default open_all_series view=[Standard ImageJ]<br>
stack_order=Default");<br>
Ext.setId(id);<br>
Ext.getImageCount(imageCount);<br>
positionX = newArray(imageCount);<br>
positionY = newArray(imageCount);<br>
positionZ = newArray(imageCount);<br>
for (no=0; no<imageCount; no++) {<br>
Ext.getPlanePositionX(positionX[no], no);<br>
Ext.getPlanePositionY(positionY[no], no);<br>
Ext.getPlanePositionZ(positionZ[no], no);<br>
}<br>
<br>
ideally I would like to print the data to a tile<br>
configuration file (CSV).<br>
<br>
I am getting this error:<br>
<br>
')' expected in line ...<br>
Ext.getPlanePositionX( <positionX> [no], no);<br>
<br>
this should work similarly to<br>
<a href="https://github.com/openmicroscopy/bioformats/blob/v5.1.1/components/bio-formats-plugins/utils/macros/planeTimings.txt" target="_blank">https://github.com/openmicroscopy/bioformats/blob/v5.1.1/components/bio-formats-plugins/utils/macros/planeTimings.txt</a>,<br>
but it complains about positionX....<br>
<br>
Maybe I am doing something very stupid, but please can<br>
anybody help me? I am getting mad....<br>
<br>
Thank you in advance for your time and kind regards.<br>
<br>
<br>
--<br>
Antonio Trabalza, Ph.D.<br>
Room 3009<br>
Neuroplasticity & Disease Group<br>
Clinical Sciences Centre - MRC<br>
Imperial College<br>
Hammersmith Hospital Campus<br>
Du Cane Road<br>
London W12 0NN<br></div></div>
Tel <a href="tel:%2B44%280%292083838294" value="+442083838294" target="_blank">+44(0)2083838294</a> <tel:%2B44%280%292083838294><br>
Mobile <a href="tel:%2B44%280%297577833827" value="+447577833827" target="_blank">+44(0)7577833827</a> <tel:%2B44%280%297577833827><br>
Mobile (IT) <a href="tel:%2B393204516210" value="+393204516210" target="_blank">+393204516210</a> <tel:%2B393204516210><br>
</blockquote>
(snip)<div class="HOEnZb"><div class="h5"><br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr">Antonio Trabalza, Ph.D.<br>Room 3009<br>Neuroplasticity & Disease Group<br>Clinical Sciences Centre - MRC<br>Imperial College<br>Hammersmith Hospital Campus<br>Du Cane Road<br>London W12 0NN<br>Tel +44(0)2083838294<br>Mobile +44(0)7577833827<br>Mobile (IT) +393204516210<br></div></div>
</div>