3D numpy array and axes

[dorai iyer]

Hi,

I am having a problem that appears to have been discussed at least twice with the link to 

http://docs.glueviz.org/en/stable/customizing_guide/coordinates.html 

My data is in the form of 3D numpy array [260,128,256] where the 260 are the 260 points where I change the electrical bias from negative to  positive values through 0 in mV and the other two  are simply typical image coordinates in microns. 

I  have been able to visualize the data as array points now I would like to put the coordinates in and this is where things got really difficult for me.

I am not able to translate the coordinates to WCS in 3D. it is most probably because i am not familiar with WCS. Is there an example other than the abstract concept in the docs?

One way out would be to convert each slice into a FITS image but then I would still be struggling to label the bias axis.

Thanks in advance

Dorai

[Thomas Robitaille]

Hi Dorai,

(Apologies for the very delayed reply to your question - even though this may no longer be useful for you, I am replying in case anyone has the same question)

Since you sent this, the coordinate handling in glue has improved, and you can use for example the AffineCoordinates class:

http://docs.glueviz.org/en/stable/customizing_guide/coordinates.html#affine-coordinates

to set up a transformation between pixel and world coordinates, if the transformation is indeed an affine transform. If it is a more complex transformation, you can use CustomCoordinates:

http://docs.glueviz.org/en/stable/customizing_guide/coordinates.html#custom-coordinates

Neither of these requires any knowledge of WCS transformations.

Cheers,

Tom

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