<div dir="ltr"><div><div><div><div>Dear Jean-Marie,<br><br></div>thank you for your reply.<br></div>I am using version 5.0.8 and it is working.<br></div>Yes please keep me in the loop.<br><br></div>Antonio<br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-05-02 21:03 GMT+01:00 Jean-Marie Burel (Staff) <span dir="ltr"><<a href="mailto:j.burel@dundee.ac.uk" target="_blank">j.burel@dundee.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>Dear Antonio</div>
<div><br>
</div>
<div>I have created a ticket <a href="https://trac.openmicroscopy.org.uk/ome/ticket/12865" target="_blank">https://trac.openmicroscopy.org.uk/ome/ticket/12865</a></div>
<div>If you wish to be cc'd, let us know</div>
<div><br>
</div>
<div>We should have it fixed in the next release (in few weeks)</div>
<div>If you use the 5.0.x version, it should work</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Jmarie</div>
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</div>
<div><br>
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<span style="font-weight:bold">From: </span>Antonio Trabalza <<a href="mailto:antoniotrabalza@gmail.com" target="_blank">antoniotrabalza@gmail.com</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Friday, 1 May 2015 09:37<br>
<span style="font-weight:bold">To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-users] Fwd: Ext.getPlanePositionX(positionX, no) problems<br>
</div><div><div class="h5">
<div><br>
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<p dir="ltr">Hi Curtis,</p>
<p dir="ltr">Thank you !<br>
You spared me a lot of mental health!</p>
<p dir="ltr">How long this fix would take?<br>
Can I use an earlier version for the time being?<br>
Antonio</p>
<div class="gmail_quote">On 30 Apr 2015 23:36, "Curtis Rueden" <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>> wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Antonio,
<div><br>
</div>
<div>
<div>> I am getting this error:</div>
<div>></div>
<div>> ')' expected in line ...</div>
<div>> Ext.getPlanePositionX( <positionX> [no], no);</div>
</div>
<div><br>
</div>
<div>Unfortunately, it appears that the Ext.getPlanePosition* methods are broken since v5.1.0 [1]. (The error ImageJ gives here is misleading.) This will need to be fixed on the Bio-Formats side.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Curtis</div>
<div><br>
</div>
<div>[1] Commit introducing the breakage:</div>
<div><a href="https://github.com/openmicroscopy/bioformats/commit/70c134c04030f093d19ffeb8df0d99eda9ba4441" target="_blank">https://github.com/openmicroscopy/bioformats/commit/70c134c04030f093d19ffeb8df0d99eda9ba4441</a><br>
</div>
<div><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Apr 30, 2015 at 8:15 AM, Antonio Trabalza <span dir="ltr">
<<a href="mailto:a.trabalza@csc.mrc.ac.uk" target="_blank">a.trabalza@csc.mrc.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><br>
<div class="gmail_quote">
<div dir="ltr">
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<div>
<div>Dear OME users,<br>
<br>
</div>
I am a postdoc in neurodisease lab at CSC MRC London.<br>
</div>
I am trying to write a IJ macro to organize several stacks taken by prairie 2 photon microscope in a format nice for the stitching plugin to process<br>
<br>
</div>
I am having serious problems with the IJ macro external commands Ext.getPlanePositionX, Y and Z. I can't get them to work.<br>
<br>
</div>
I wrote (just to set up the concept, it will be a part of a longer macro):<br>
<br>
id = File.openDialog("Choose a file");<br>
run("Bio-Formats Macro Extensions") <br>
run("Bio-Formats Importer", "open=[" + id + "] color_mode=Default open_all_series view=[Standard ImageJ] 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 clear="all">
<div>
<div>
<div>
<div>
<div><br>
ideally I would like to print the data to a tile configuration file (CSV).<br>
<br>
</div>
<div>I am getting this error:<br>
</div>
<div><br>
')' expected in line ...<br>
</div>
<div>Ext.getPlanePositionX( <positionX> [no], no);<br>
</div>
<div><br>
</div>
<div>this should work similarly to <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>, but it complains about positionX....<br>
</div>
<div><br>
Maybe I am doing something very stupid, but please can anybody help me? I am getting mad....<br>
</div>
<div><br>
</div>
<div>Thank you in advance for your time and kind regards.<span><font color="#888888"><span><font color="#888888"><br>
<br>
</font></span></font></span></div>
<span><font color="#888888"><br>
</font></span></div>
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</div>
</div>
</div>
<span><font color="#888888">-- <br>
<div>
<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 <a href="tel:%2B44%280%292083838294" value="+442083838294" target="_blank">+44(0)2083838294</a><br>
Mobile <a href="tel:%2B44%280%297577833827" value="+447577833827" target="_blank">
+44(0)7577833827</a><br>
Mobile (IT) <a href="tel:%2B393204516210" value="+393204516210" target="_blank">+393204516210</a><br>
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<br></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>
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