howto: write out a cutout subset of an image with a new header

[richardgmcmahon]

Hi Erin,

I want to use use fitsio to create a 'FITs object' in memory of a cutout.

With pyfits I do this:

fh = pyfits.open(filename)
head = fh[ext].header.copy()
...
various header manipulations to work out the pixel ranges
and update the new header
...
cutout = fh[ext].data[ymin:ymax,xmin:xmax]
newfh = pyfits.PrimaryHDU(data=cutout,header=head)

with fitsio I do

fh=fitsio.FITS(filename)
head = fh[ext].read_header()
....
work out the pixel range I want and update the header
....
cutout=fh[ext][ymin:ymax,xmin:xmax]

how do I make a FITs object from cutout, newhead that I can then pass out of my
function?

Also how do I write this to a new fits file?

This would be a useful example of how to create and write out a image cutout.

Thanks, r.

[esheldon]

On Sat, Jun 29, 2013 at 5:36 PM, richardgmcmahon
notifications@github.comwrote:

Hi Erin,

I want to use use fitsio to create a 'FITs object' in memory of a cutout.

With pyfits I do this:

fh = pyfits.open(filename)
head = fh[ext].header.copy()
...
various header manipulations to work out the pixel ranges
and update the new header
...
cutout = fh[ext].data[ymin:ymax,xmin:xmax]
newfh = pyfits.PrimaryHDU(data=cutout,header=head)

with fitsio I do

fh=fitsio.FITS(filename)
head = fh[ext].read_header()
....
work out the pixel range I want and update the header
....
cutout=fh[ext][ymin:ymax,xmin:xmax]

how do I make a FITs object from cutout, newhead that I can then pass out
of my
function?

You get a numpy array from fh[ext][ymin:ymax,xmin:xmax]. The easiest
thing to do is just write that along with the header

fitsio.write(filename, cutout, header=head)

If the file already exists, that will add a new extension. You can add
clobber=True to over-write the file.

If you want to create a new FITS object directly, you can just do the
following

fits=FITS(filename, 'rw', clobber=clobber, **other_keywords)
fits.write(cutout, **other_keywords)

Note the FITS object represents file structure, not data in memory. I
intentionally separated that; you create your data structures separately
and then write them into the file. The documentation for this
functionality is available on the front page, but more readily using ? in
ipython or help().

Also how do I write this to a new fits file?

This would be a useful example of how to create and write out a image
cutout.

good idea!

-e

Thanks, r.

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Reply to this email directly or view it on GitHubhttps://github.com//issues/10
.

Erin Scott Sheldon
Brookhaven National Laboratory erin dot sheldon at gmail dot com

[esheldon]

I'm going to close this since I haven't heard any complaints.