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

[Jean-Marie Burel (Staff)]

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>

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