[fitsbits] BINTABLE convention for >999 columns
Tom McGlynn (NASA/GSFC Code 660.1)
tom.mcglynn at nasa.gov
Fri Jul 7 13:20:26 EDT 2017
Hi Mark,
I think this is an interesting and valuable way to address a key limit on FITS tables.
To my mind, the alternative that some suggested of using multiple HDUs is not really viable. It has
two major
problems for me:
First it scales poorly. It might be okay when you just exceed the current limit, but soon you be
carrying around dozens of HDU's.
It seems very cumbersome.
Second, the whole idea of a table is that a row is localized -- we can efficiently process row by
row. Once we split the table into multiple
pieces which are put sequentially in a file, we may need to read almost the entire file just to read
the first row. Losing the ability to do stream processing
on tables is fatal for me.
The alternative of using Compressed Tables is interesting, but I think it has some of the same
problems. It's not very
efficient for row-by-row processing and something still needs to be done to get around the limit 999
limit for many of the keywords.
Your approach is clean with regard to table processing. It's fully compatible with existing FITS
and enables easy access to the first 998 tables
for existing readers. However I agree with the commenters who noted that while this significantly
increases
the limit, it leaves it at less than 2^16. That's not a very big number any more. Also, the
numbering for the columns is rather kludgy to my eye.
Both of these issues are addressed by Francois-Xavier Pineau's suggestion of using HIEARACH
keywords. There's no longer any limit on
the number of columns, and the column names are completely natural. As you note at the bottom this
is identical structurally -- only
the metadata description is different. It seems like the only problem is that you have to commit to
using HIERARCH, but that's pretty
broadly supported.
Overall I think what you are doing is clever and reasonable, but I think the HIERARCH metadata might
be a better way to go.
One final question... Is there any thought that the same approach might be used for ASCII tables?
In principle it's a little easier
since the length of ASCII tables rows is not required to be defined by the concatenation of the
columns. There are some cases where
ASCII tables can is useful: e.g., very large integers or 128 bit floats, but I imagine it would be
fairly rare to have both this kind of column
and need more than 999 columns total. However since ASCII tables are not deprecated, it seems more
elegant to define this model for FITS
tables, rather than for just one of the two formats that FITS supports.
Tom
Mark Taylor 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),
> 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 +44-117-9288776 http://www.star.bris.ac.uk/~mbt/
>
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