[fitsbits] BINTABLE convention for >999 columns
Francois-Xavier PINEAU
francois-xavier.pineau at astro.unistra.fr
Fri Jul 7 09:49:21 EDT 2017
Because:
- I do not see any good conceptual reason why not accept more than 999
columns in a FITS table.
The reason appears to be purely technical: only 3 characters
provided to encode the column index.
- It would be a forced denormalization of the relational model (a fits
reader will see 2 or more tables)
- It would convoluted the data access algorithm (need to perform joins)
- It would imply to read multiple blocks on the HDD, which is less
effective than a simple sequential read (depending buffer sizes, ...; on
a HDD reading at 150 MB/s with an access time of 10 ms, each
displacement of the heads <=> the time to read 1.5 MB of data)
I agree with this solution if one knows that a sub-part of the columns
are not very interesting and will almost never be read (on purpose
denormalization).
fx
Le 07/07/2017 à 14:51, Rob Seaman a écrit :
> Why not simply split such tables into two+ extensions and join as needed?
>
> Rob
>
> --
>
>
> On 7/7/17 4:09 AM, 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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