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

[Antonio Trabalza]

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>:

>  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>
> Reply-To: OME User Support List <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>
> 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> 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> 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
>>> Mobile +44(0)7577833827
>>> Mobile (IT) +393204516210
>>>
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>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>
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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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