Re: Open gzipped FITS image files

Posted by Gregory Jefferis on
URL: http://imagej.273.s1.nabble.com/Open-gzipped-FITS-image-files-tp3699348p3699350.html

Hi Leonard,

I forgot the first version I sent needs an extra library for the zlib
encoding that you don't want anyway.  Here is the very basic version I used
to use which should do just what you want.  In the past I have added it as a
private class within the body of an existing class like the Biorad_Reader ­
it should work fine in the same way with the FITS_Reader.  Best,

Greg.

PS watch line breaks!

--

class FlexibleFileOpener extends FileOpener {
    // private class which determines if the file is gzipped or not
    // and adds a GZIPInputStream if required
    public FlexibleFileOpener(FileInfo fi) {
        super(fi);
    }
   
    public InputStream createInputStream(FileInfo fi) throws IOException,
MalformedURLException {
        // use the method in the FileOpener class to generate an input
stream
        InputStream is=super.createInputStream(fi);
        if (is!=null & fi.fileName.toLowerCase().endsWith(".gz")) {
            // then stick a GZIPInputStream on top of it!
            return new GZIPInputStream(is);
        } else {
            // Just return plain input stream
            return is;
        }
    }
}

--

On 23/5/07 22:44, "Gregory Jefferis" <[hidden email]> wrote:

> Dear Leonard,
>
> I have done this for various readers using the attached code.  It has more
> functionality than you want but it might be useful.
>
> Just replace any FileOpener object in the FITS opener plugin with
> FlexibleFileOpener and you are there (it will automatically add a GZFileOpener
> if the file name ends in .gz).  Something like this
>
>     fo = new FlexibleFileOpener(fi);
>     imp = fo.open(false);
>
> Feel free to contact me if you would like more assistance.  I may see if Wayne
> would be interested in adding this functionality to ImageJ.
>
> Best wishes,
>
> Greg.
>
> The additional functionality allows you to use it to open ZLIB compressed data
> (gzip without the full header) and to specify an offset for the start of the
> compressed block in the file and a separate offset for the start of the image
> data within the compressed block.
>
>
>
>> Date:    Tue, 22 May 2007 10:58:49 -0600
>> From:    Leonard Sitongia <[hidden email]>
>> Subject: Open gzipped FITS image files
>>
>> Hi,
>>
>> I'd like to be able to read gzipped FITS image files, decompressing the files
>> on the fly.  Is this already possible (I don't see it)?  If not, then it
>> seems like this would be pretty easy to add to the code, by wrapping
>> something like "new GZIPInputStream()" around the existing input stream (with
>> the necessary logic to check for a compressed file, and such).
>>
>> Has this been done/can this be done?
>>
>> Thanks!
>> --
>> ==Leonard E. Sitongia
>>   High Altitude Observatory
>>   National Center for Atmospheric Research
>>   P.O. Box 3000 Boulder CO 80307  USA
>>   [hidden email]    voice: [phone]   fax: [phone]
>>
>> -------------
>
>  

--
Gregory Jefferis, PhD                                   and:
Research Fellow    
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University of Cambridge                                 Cambridge
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United Kingdom

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