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

[Antonio Trabalza]

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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>>
>>
>
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