[ome-users] Fwd: Ext.getPlanePositionX(positionX, no) problems

[Mark Carroll]

I can confirm that the fix will be in the forthcoming 5.1.2 release.
Do let us know if it gives you any further problems.

-- Mark


On 05/06/2015 05:52 PM, Antonio Trabalza wrote:
> Dear Jean-Marie,
>
> thank you for your reply.
> I am using version 5.0.8 and it is working.
> Yes please keep me in the loop.
>
> Antonio
>
> 2015-05-02 21:03 GMT+01:00 Jean-Marie Burel (Staff)
> <j.burel at dundee.ac.uk <mailto:j.burel at dundee.ac.uk>>:
>
>     Dear Antonio
>
>     I have created a ticket
>     https://trac.openmicroscopy.org.uk/ome/ticket/12865
>     If you wish to be cc'd, let us know
>
>     We should have it fixed in the next release (in few weeks)
>     If you use the 5.0.x version, it should work
>
>     Regards
>
>     Jmarie
>
>
>     From: Antonio Trabalza <antoniotrabalza at gmail.com
>     <mailto:antoniotrabalza at gmail.com>>
>     Reply-To: OME User Support List
>     <ome-users at lists.openmicroscopy.org.uk
>     <mailto:ome-users at lists.openmicroscopy.org.uk>>
>     Date: Friday, 1 May 2015 09:37
>     To: OME User Support List <ome-users at lists.openmicroscopy.org.uk
>     <mailto:ome-users at lists.openmicroscopy.org.uk>>
>     Subject: Re: [ome-users] Fwd: Ext.getPlanePositionX(positionX, no)
>     problems
>
>     Hi Curtis,
>
>     Thank you !
>     You spared me a lot of mental health!
>
>     How long this fix would take?
>     Can I use an earlier version for the time being?
>     Antonio
>
>     On 30 Apr 2015 23:36, "Curtis Rueden" <ctrueden at wisc.edu
>     <mailto:ctrueden at wisc.edu>> wrote:
>
>         Hi Antonio,
>
>         > I am getting this error:
>         >
>         > ')' expected in line ...
>         > Ext.getPlanePositionX( <positionX> [no], no);
>
>         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.
>
>         Regards,
>         Curtis
>
>         [1] Commit introducing the breakage:
>         https://github.com/openmicroscopy/bioformats/commit/70c134c04030f093d19ffeb8df0d99eda9ba4441
>
>
>         On Thu, Apr 30, 2015 at 8:15 AM, Antonio Trabalza
>         <a.trabalza at csc.mrc.ac.uk <mailto:a.trabalza at csc.mrc.ac.uk>> wrote:
>
>
>             Dear OME users,
>
>             I am a postdoc in neurodisease lab at CSC MRC London.
>             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
>
>             I am having serious problems with the IJ macro external
>             commands Ext.getPlanePositionX, Y and Z. I can't get them to
>             work.
>
>             I wrote (just to set up the concept, it will be a part of a
>             longer macro):
>
>             id = File.openDialog("Choose a file");
>             run("Bio-Formats Macro Extensions")
>             run("Bio-Formats Importer", "open=[" + id + "]
>             color_mode=Default open_all_series view=[Standard ImageJ]
>             stack_order=Default");
>             Ext.setId(id);
>             Ext.getImageCount(imageCount);
>             positionX = newArray(imageCount);
>             positionY = newArray(imageCount);
>             positionZ = newArray(imageCount);
>             for (no=0; no<imageCount; no++) {
>                Ext.getPlanePositionX(positionX[no], no);
>                Ext.getPlanePositionY(positionY[no], no);
>                Ext.getPlanePositionZ(positionZ[no], no);
>             }
>
>             ideally I would like to print the data to a tile
>             configuration file (CSV).
>
>             I am getting this error:
>
>             ')' expected in line ...
>             Ext.getPlanePositionX( <positionX> [no], no);
>
>             this should work similarly to
>             https://github.com/openmicroscopy/bioformats/blob/v5.1.1/components/bio-formats-plugins/utils/macros/planeTimings.txt,
>             but it complains about positionX....
>
>             Maybe I am doing something very stupid, but please can
>             anybody help me? I am getting mad....
>
>             Thank you in advance for your time and kind regards.
>
>
>             --
>             Antonio Trabalza, Ph.D.
>             Room 3009
>             Neuroplasticity & Disease Group
>             Clinical Sciences Centre - MRC
>             Imperial College
>             Hammersmith Hospital Campus
>             Du Cane Road
>             London W12 0NN
>             Tel +44(0)2083838294 <tel:%2B44%280%292083838294>
>             Mobile +44(0)7577833827 <tel:%2B44%280%297577833827>
>             Mobile (IT) +393204516210 <tel:%2B393204516210>
(snip)

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