[Matplotlib-users] Images, FITS files, and so on

[Stephen W. <ste...@cs...>]

This was originally a much longer message with a great deal of context, 
but I'm going to make it a lot shorter as a series of questions in the 
hopes of getting a Socratic dialog going?

1.  Is anyone else bothered by the fact that imshow(array) displays 
array[i,j] at Cartesian coordinates [j,shape(array)[0]-i] if origin is 
'upper' and at [j,i] if origin is 'lower'?

2.  In light of the above, how do you handle overlaying contours on an 
image?  I see by experiment that contour(array) also treats array[i,j] 
the same way as imshow.

3.  Are the astronomers as confused by all of this in relation to the 
FITS WCS standard as I seem to be?  How do I do the computation 
correctly so that x[i,j] is the first WCS coordinate of FITS pixel (i,j) 
(which is at array[j-1,i-1] after a PyFITS read)?