Re: cannot open FITS image with extended header

Posted by Sergei Goshko on Jun 02, 2009; 3:12am
URL: http://imagej.273.s1.nabble.com/cannot-open-FITS-image-with-extended-header-tp3692336p3692338.html

Hi,

I used nom.tam.fits package that worked for me just file.

The simplified code that I used is following:

import nom.tam.fits.BasicHDU;
import nom.tam.fits.Fits;
import nom.tam.fits.FitsException;
import nom.tam.fits.Header;

    public ImagePlus readFITS(String fitsFile) throws FitsException {
        Fits f = new Fits(fitsFile);
        try {
            BasicHDU[] hh = f.read();
            for (BasicHDU bh: hh) {
                Header h = bh.getHeader();
                int naxis = h.getIntValue("NAXIS");
                if (naxis >= 2 && bh.getData().getData()!=null) {
                    return new ImagePlus(path, new
FloatProcessor((float[][])bh.getData().getData()));
                }
            }
        } finally {
            try { f.getStream().close(); } catch(Exception e) {}
        }
        return null;
    }

It can open only FITS with data type float that is enough for me, but with
little extra code it is possible to handle any data types.


Sergei

----- Original Message -----
From: "Adrian Martin" <[hidden email]>
To: <[hidden email]>
Sent: Monday, June 01, 2009 12:45
Subject: Re: cannot open FITS image with extended header

> ImageJ does not handle extensions, as far as I can know.  Your file  has
> an "image" extension where the data is held,  so that's why it  gets
> confused (it also has -32bits which might be confusing too).  I  use table
> extensions regularly, and am working on a plugin to deal  with those, but
> the FITS standards cover many cases and writing  something to suit
> everyone's FITs files would take a lot of work.
>
> I'd be interested to hear from anyone who has written an even half-
> working version of code to do this!
>
> Dr Adrian Martin
> Sensor Sciences,  3333 Vincent Road, Suite 103, Pleasant Hill, CA 94523
> [phone] phone, [phone] fax
>
>
> On Jun 1, 2009, at 12:02 AM, Sergei Goshko wrote:
>
>> Hi,
>>
>> I cannot open FITS file downloaded from HLA (i.e.
>> http://archive.stsci.edu/cgi-bin/hla/getdata.cgi?download=1&dataset=hlsp_coma_hst_acs-wfc_v19_f814w&filename=hlsp_coma_hst_acs-wfc_v19_f814w_v1_ivm-drz-cl.fits )
>>
>> The file has extended FITS header and I believe it confuses ImageJ.
>> The message I get is "This does not appear to be a FITS file."
>> The image can be opened with no problem by SAO DS9 viewer. SAO shows
>> both headers.
>> I just downloaded latest release of ImageJ 1.41 and the problem is  still
>> there.
>> Is there any work around?
>>
>> Thank you.
>> Sergei
>>
>>
>> The header of the image above looks like:
>>
>> SIMPLE  =                    T / Fits standard
>> BITPIX  =                   16 / Bits per pixel
>> NAXIS   =                    0 / Number of axes
>> EXTEND  =                    T / File may contain extensions
>> ORIGIN  = 'NOAO-IRAF FITS Image Kernel July 2003' / FITS file  originator
>> IRAF-TLM= '10:58:58 (24/07/2007)' / Time of last modification
>> NEXTEND =                    3 / Number of standard extensions
>> DATE    = '2007-02-19T22:26:34' / date this file was written (yyyy-
>> mm-dd)
>> .............
>> END
>> XTENSION= 'IMAGE   '           / Image extension
>> BITPIX  =                  -32 / Bits per pixel
>> NAXIS   =                    2 / Number of axes
>> NAXIS1  =                 4225 / Axis length
>> NAXIS2  =                 4300 / Axis length
>> PCOUNT  =                    0 / No 'random' parameters
>> GCOUNT  =                    1 / Only one group
>> ORIGIN  = 'NOAO-IRAF FITS Image Kernel July 2003' / FITS file  originator
>> EXTNAME = 'SCI     '           / Extension name
>> EXTVER  =                    1 / Extension version
>> DATE    = '2007-02-19T22:26:35' / Date FITS file was generated
>> IRAF-TLM= '11:00:08 (24/07/2007)' / Time of last modification
>> INHERIT =                    T / inherit the primary header
>> EXPNAME = 'j9ty19xyq                ' / exposure identifier
>> BUNIT   = 'ELECTRONS'          / brightness units
>> ....................
>> END
>> <binary data>
>