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

[Curtis Rueden]

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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