[fitsbits] BINTABLE convention for >999 columns
Rob Seaman
seaman at lpl.arizona.edu
Mon Jul 10 12:32:52 EDT 2017
I should comment that there's no reason this wouldn't compress as normal
using fpack, but the container column would not generally compress
efficiently because of the mixed data types. A future update to fpack
could become wide-table aware if deemed desirable.
Rob
--
On 7/10/17 9:25 AM, Rob Seaman wrote:
>
> Thanks for the info about usage context. Separating the tables into
> multiple files or extensions still seems a reasonable way to address
> these cases, but since Mark T's proposed convention (apparently
> originally from Bill) is legal or near-legal FITS usage, the main
> question is how best to discourage a diversity of keyword encodings, etc.
>
> Also agree with Mark C's encoding, though would suggest mono-case will
> be less of a confusing change than lower case. Mark C's option avoids
> confusing usage like TFORM0AA or whatever interrupting the sort order.
> A digit in character 6 would require digits in #7 and 8.
>
> Nobody has mentioned extremely wide table use cases (millions of
> columns), and 34695 columns is enough to cover all the wide table DB
> options listed in a previous email.
>
> Rob
> --
>
> On 7/10/17 8:34 AM, Arnold Rots wrote:
>> From all the suggestions offered so far, Mark's is by far the most
>> sensible in my opinion since it provides a significant expansion
>> while preserving full backward compatibility.
>>
>> - Arnold
>>
>> -------------------------------------------------------------------------------------------------------------
>> Arnold H. Rots Chandra X-ray
>> Science Center
>> Smithsonian Astrophysical Observatory tel: +1 617
>> 496 7701
>> 60 Garden Street, MS 67 fax: +1
>> 617 495 7356
>> Cambridge, MA 02138
>> arots at cfa.harvard.edu <mailto:arots at cfa.harvard.edu>
>> USA
>> http://hea-www.harvard.edu/~arots/ <http://hea-www.harvard.edu/%7Earots/>
>> --------------------------------------------------------------------------------------------------------------
>>
>>
>> On Fri, Jul 7, 2017 at 8:51 PM, Mark Calabretta
>> <mark at calabretta.id.au <mailto:mark at calabretta.id.au>> wrote:
>>
>> Taking into consideration what others have said on this thread, I
>> would
>> like to point out that up to 34695 bintable columns may easily be
>> accomodated, with full backward compatibility, via a simple extension
>> to the FITS standard. Namely,
>>
>> 1. When encoding bintable-related keywords such as ijPCna, allow
>> lower-case letters to represent digits in a base-36 counting
>> system.
>>
>> 2. Number bintable columns 1 to 999, followed by a00 to zzz, where an
>> offset (-11960) is applied to make a00 column 1000. The total
>> number
>> of columns is then 999 + 26*36*36 = 34695. (Alternatively,
>> the full
>> range of three-digit base-36 counting, namely 46656, could be
>> recovered with a more elaborate ordering.)
>>
>> Regards,
>> Mark Calabretta
>>
>>
>> On Fri, 7 Jul 2017 12:09:15 +0100 (BST)
>> Mark Taylor <M.B.Taylor at bristol.ac.uk
>> <mailto:M.B.Taylor at bristol.ac.uk>> wrote:
>>
>> Dear fitsbits,
>>
>> I am considering a convention for storing table data in FITS files
>> where the number of columns exceeds the 999 limit implicitly imposed
>> by the standard BINTABLE extension type. I have running code for
>> this (available on request) and plan to incorporate it in future
>> releases of STIL/STILTS/TOPCAT so that people can work with wide
>> tables in FITS while using those tools. People using software
>> that is unaware of this convention would still see a legal BINTABLE
>> but not the later columns.
>>
>> I'm posting the details here in case people want to comment,
>> or point out some major problem with the idea that I might have
>> overlooked, or tell me that there's already a convention for
>> this out there that I should be using instead. Otherwise, please
>> feel free to ignore this post. I'm not requesting that any
>> other software implements this, though if anyone wants to I
>> certainly don't object.
>>
>> Mark
>>
>> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
>>
>> Extended column convention for FITS BINTABLE
>> --------------------------------------------
>>
>> The BINTABLE extension type as described in the FITS Standard
>> (FITS Standard v3.0, sec 7.3) requires table column metadata
>> to be described using 8-character keywords of the form XXXXXnnn,
>> where XXXXX represents one of an open set of mandatory, reserved
>> or user-defined root keywords up to five characters in length,
>> for instance TFORM (mandatory), TUNIT (reserved), TUCD
>> (user-defined).
>> The nnn part is an integer between 1 and 999 indicating the
>> index of the column to which the keyword in question refers.
>> Since the header syntax confines this indexed part of the keyword
>> to three digits, there is an upper limit of 999 columns in
>> BINTABLE extensions.
>>
>> Note that the FITS/BINTABLE format does not entail any restriction on
>> the storage of column *data* beyond the 999 column limit in the data
>> part of the HDU, the problem is just that client software
>> cannot be informed about the layout of this data using the
>> header cards in the usual way.
>>
>> In some cases it is desirable to store FITS tables with a column
>> count greater than 999. Whether that's a good idea is not within
>> the scope of this discussion.
>>
>> To achieve this, I propose the following convention.
>>
>> Definitions:
>>
>> - 'BINTABLE columns' are those columns defined using the
>> FITS BINTABLE standard
>>
>> - 'Data columns' are the columns to be encoded
>>
>> - N_TOT is the total number of data columns to be stored
>>
>> - Data columns with (1-based) indexes from 999 to N_TOT inclusive
>> are known as 'extended' columns. Their data is stored
>> within the 'container' column.
>>
>> - BINTABLE column 999 is known as the 'container' column
>> It contains the byte data for all the 'extended' columns.
>>
>> Convention:
>>
>> - All column data (for columns 1 to N_TOT) is laid out in the
>> data part
>> of the HDU in exactly the same way as if there were no
>> 999-column
>> limit.
>>
>> - The TFIELDS header is declared with the value 999.
>>
>> - The container column is declared in the header with some
>> TFORM999 value corresponding to the total field length required
>> by all the extended columns ('B' is the obvious data type, but
>> any legal TFORM value that gives the right width MAY be used).
>> The byte count implied by TFORM999 MUST be equal to the
>> total byte count implied by all extended columns.
>>
>> - Other XXXXX999 headers MAY optionally be declared to describe
>> the container column in accordance with the usual rules,
>> e.g. TTYPE999 to give it a name.
>>
>> - The NAXIS1 header is declared in the usual way to give the width
>> of a table row in bytes. This is equal to the sum of
>> all the BINTABLE columns as usual. It is also equal to
>> the sum of all the data columns, which has the same value.
>>
>> - Headers for Data columns 1-998 are declared as usual,
>> corresponding to BINTABLE columns 1-998.
>>
>> - Keyword XT_ICOL indicates the index of the container column.
>> It MUST be present with the integer value 999 to indicate
>> that this convention is in use.
>>
>> - Keyword XT_NCOL indicates the total number of data columns
>> encoded.
>> It MUST be present with an integer value equal to N_TOT.
>>
>> - Metadata for each extended column is encoded with keywords
>> of the form XXXXXaaa, where XXXXX are the same keyword roots
>> as used for normal BINTABLE extensions, and aaa is a 3-digit
>> value in base 26 using the characters 'A' (0 in base 26) to
>> 'Z' (25 in base 26), and giving the 1-based data column index
>> minus 999. The sequence aaa MUST be exactly three characters
>> long (leading 'A's are required). Thus the formats for data
>> columns 999, 1000, 1001, etc are declared with the keywords
>> TFORMAAA, TFORMAAB, TFORMAAC etc.
>>
>> - This convention MUST NOT be used for N_TOT<=999.
>>
>> The resulting HDU is a completely legal FITS BINTABLE extension.
>> Readers aware of this convention may use it to extract column
>> data and metadata beyond the 999-column limit.
>> Readers unaware of this convention will see 998 columns in their
>> intended form, and an additional (possibly large) column 999
>> which contains byte data but which cannot be easily interpreted.
>>
>> This convention can therefore allow encoding of tables with data
>> column counts N_TOT up to 998+26^3 = 18574.
>>
>> An example header might look like this:
>>
>> XTENSION= 'BINTABLE' / binary table extension
>> BITPIX = 8 / 8-bit bytes
>> NAXIS = 2 / 2-dimensional table
>> NAXIS1 = 9229 / width of table in bytes
>> NAXIS2 = 26 / number of rows in table
>> PCOUNT = 0 / size of special data area
>> GCOUNT = 1 / one data group
>> TFIELDS = 999 / number of columns
>> XT_ICOL = 999 / index of container column
>> XT_NCOL = 1204 / total columns including extended
>> TTYPE1 = 'posid_1 ' / label for column 1
>> TFORM1 = 'J ' / format for column 1
>> TTYPE2 = 'instrument_1' / label for column 2
>> TFORM2 = '4A ' / format for column 2
>> TTYPE3 = 'edge_code_1' / label for column 3
>> TFORM3 = 'I ' / format for column 3
>> TUCD3 = 'meta.code.qual'
>> ...
>> TTYPE998= 'var_min_s_2' / label for column 998
>> TFORM998= 'D ' / format for column 998
>> TUNIT998= 'counts/s' / units for column 998
>> TTYPE999= 'XT_MORECOLS' / label for column 999
>> TFORM999= '813I ' / format for column 999
>> TTYPEAAA= 'var_min_u_2' / label for column 999
>> TFORMAAA= 'D ' / format for column 999
>> TUNITAAA= 'counts/s' / units for column 999
>> TTYPEAAB= 'var_prob_h_2' / label for column 1000
>> TFORMAAB= 'D ' / format for column 1000
>> ...
>> TTYPEAHW= 'var_prob_w_2' / label for column 1203
>> TFORMAHW= 'D ' / format for column 1203
>> TTYPEAHX= 'var_sigma_w_2' / label for column 1204
>> TFORMAHX= 'D ' / format for column 1204
>> TUNITAHX= 'counts/s' / units for column 1204
>> END
>>
>> This general approach was suggested by William Pence on the FITSBITS
>> list in June 2012
>> (https://listmgr.nrao.edu/pipermail/fitsbits/2012-June/002367.html
>> <https://listmgr.nrao.edu/pipermail/fitsbits/2012-June/002367.html>),
>> and by Francois-Xavier Pineau (CDS) in private conversation in 2016.
>> The details have been filled in by Mark Taylor (Bristol).
>> (F-X favours a different mechanism for encoding the extended
>> column metadata).
>>
>> --
>> Mark Taylor Astronomical Programmer Physics, Bristol
>> University, UK
>> m.b.taylor at bris.ac.uk <mailto:m.b.taylor at bris.ac.uk>
>> +44-117-9288776 <tel:%2B44-117-9288776>
>> http://www.star.bris.ac.uk/~mbt/ <http://www.star.bris.ac.uk/%7Embt/>
>>
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