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

[Antonio Trabalza]

Hi All,

thank you for your replies.
Once available I will test the function and let you know.
Thank you once more for your help.

Antonio

2015-05-06 19:59 GMT+01:00 Mark Carroll <m.t.b.carroll at dundee.ac.uk>:

> 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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-- 
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
Mobile +44(0)7577833827
Mobile (IT) +393204516210
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