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STILTS-TMATCH2(1) Stilts commands STILTS-TMATCH2(1)

NAME

stilts-tmatch2 - Crossmatches 2 tables using flexible criteria

SYNOPSIS

stilts tmatch2 [in1=<table1>] [ifmt1=<in-format>] [in2=<table2>] [ifmt2=<in-format>] [icmd1=<cmds>] [icmd2=<cmds>] [ocmd=<cmds>] [omode=out|meta|stats|count|cgi|discard|topcat|samp|tosql|gui] [out=<out-table>] [ofmt=<out-format>] [matcher=<matcher-name>] [values1=<expr-list>] [values2=<expr-list>] [params=<match-params>] [tuning=<tuning-params>] [join=1and2|1or2|all1|all2|1not2|2not1|1xor2] [find=all|best|best1|best2] [fixcols=none|dups|all] [suffix1=<label>] [suffix2=<label>] [scorecol=<col-name>] [progress=none|log|profile]

DESCRIPTION

tmatch2 is an efficient and highly configurable tool for crossmatching pairs of tables. It can match rows between tables on the basis of their relative position in the sky, or alternatively using many other criteria such as separation in some isotropic or anisotropic Cartesian space, identity of a key value, or some combination of these; the full range of match criteria is discussed in SUN/256. You can choose whether you want to identify all the matches or only the closest, and what form the output table takes, for instance matched rows only, or all rows from one or both tables, or only the unmatched rows.

If you simply want to match two tables based on sky position with a fixed maximum separation, you may find the tskymatch2 command easier to use.

Note: the duptag1 and duptag2 parameters have been replaced at version 1.4 by suffix1 and suffix2 for consistency with other table join tasks.

OPTIONS

The location of the first input table. This may take one of the following forms:

  • A filename.
  • A URL.
  • The special value "-", meaning standard input. In this case the input format must be given explicitly using the ifmt1 parameter. Note that not all formats can be streamed in this way.
  • A scheme specification of the form :<scheme-name>:<scheme-args>.
  • A system command line with either a "<" character at the start, or a "|" character at the end ("<syscmd" or "syscmd|"). This executes the given pipeline and reads from its standard output. This will probably only work on unix-like systems.

In any case, compressed data in one of the supported compression formats (gzip, Unix compress or bzip2) will be decompressed transparently.

Specifies the format of the first input table as specified by parameter in1. The known formats are listed in SUN/256. This flag can be used if you know what format your table is in. If it has the special value (auto) (the default), then an attempt will be made to detect the format of the table automatically. This cannot always be done correctly however, in which case the program will exit with an error explaining which formats were attempted. This parameter is ignored for scheme-specified tables.

The location of the second input table. This may take one of the following forms:

  • A filename.
  • A URL.
  • The special value "-", meaning standard input. In this case the input format must be given explicitly using the ifmt2 parameter. Note that not all formats can be streamed in this way.
  • A scheme specification of the form :<scheme-name>:<scheme-args>.
  • A system command line with either a "<" character at the start, or a "|" character at the end ("<syscmd" or "syscmd|"). This executes the given pipeline and reads from its standard output. This will probably only work on unix-like systems.

In any case, compressed data in one of the supported compression formats (gzip, Unix compress or bzip2) will be decompressed transparently.

Specifies the format of the second input table as specified by parameter in2. The known formats are listed in SUN/256. This flag can be used if you know what format your table is in. If it has the special value (auto) (the default), then an attempt will be made to detect the format of the table automatically. This cannot always be done correctly however, in which case the program will exit with an error explaining which formats were attempted. This parameter is ignored for scheme-specified tables.

Specifies processing to be performed on the first input table as specified by parameter in1, before any other processing has taken place. The value of this parameter is one or more of the filter commands described in SUN/256. If more than one is given, they must be separated by semicolon characters (";"). This parameter can be repeated multiple times on the same command line to build up a list of processing steps. The sequence of commands given in this way defines the processing pipeline which is performed on the table.

Commands may alteratively be supplied in an external file, by using the indirection character '@'. Thus a value of "@filename" causes the file filename to be read for a list of filter commands to execute. The commands in the file may be separated by newline characters and/or semicolons, and lines which are blank or which start with a '#' character are ignored.

Specifies processing to be performed on the second input table as specified by parameter in2, before any other processing has taken place. The value of this parameter is one or more of the filter commands described in SUN/256. If more than one is given, they must be separated by semicolon characters (";"). This parameter can be repeated multiple times on the same command line to build up a list of processing steps. The sequence of commands given in this way defines the processing pipeline which is performed on the table.

Commands may alteratively be supplied in an external file, by using the indirection character '@'. Thus a value of "@filename" causes the file filename to be read for a list of filter commands to execute. The commands in the file may be separated by newline characters and/or semicolons, and lines which are blank or which start with a '#' character are ignored.

Specifies processing to be performed on the output table, after all other processing has taken place. The value of this parameter is one or more of the filter commands described in SUN/256. If more than one is given, they must be separated by semicolon characters (";"). This parameter can be repeated multiple times on the same command line to build up a list of processing steps. The sequence of commands given in this way defines the processing pipeline which is performed on the table.

Commands may alteratively be supplied in an external file, by using the indirection character '@'. Thus a value of "@filename" causes the file filename to be read for a list of filter commands to execute. The commands in the file may be separated by newline characters and/or semicolons, and lines which are blank or which start with a '#' character are ignored.

The mode in which the result table will be output. The default mode is out, which means that the result will be written as a new table to disk or elsewhere, as determined by the out and ofmt parameters. However, there are other possibilities, which correspond to uses to which a table can be put other than outputting it, such as displaying metadata, calculating statistics, or populating a table in an SQL database. For some values of this parameter, additional parameters (<mode-args>) are required to determine the exact behaviour.

Possible values are

  • out
  • meta
  • stats
  • count
  • cgi
  • discard
  • topcat
  • samp
  • tosql
  • gui

Use the help=omode flag or see SUN/256 for more information.

The location of the output table. This is usually a filename to write to. If it is equal to the special value "-" (the default) the output table will be written to standard output.

This parameter must only be given if omode has its default value of "out".

Specifies the format in which the output table will be written (one of the ones in SUN/256 - matching is case-insensitive and you can use just the first few letters). If it has the special value "(auto)" (the default), then the output filename will be examined to try to guess what sort of file is required usually by looking at the extension. If it's not obvious from the filename what output format is intended, an error will result.

This parameter must only be given if omode has its default value of "out".

Defines the nature of the matching that will be performed. Depending on the name supplied, this may be positional matching using celestial or Cartesian coordinates, exact matching on the value of a string column, or other things. A list and explanation of the available matching algorithms is given in SUN/256. The value supplied for this parameter determines the meanings of the values required by the params, values* and tuning parameter(s).

Defines the values from table 1 which are used to determine whether a match has occurred. These will typically be coordinate values such as RA and Dec and perhaps some per-row error values as well, though exactly what values are required is determined by the kind of match as determined by matcher. Depending on the kind of match, the number and type of the values required will be different. Multiple values should be separated by whitespace; if whitespace occurs within a single value it must be 'quoted' or "quoted". Elements of the expression list are commonly just column names, but may be algebraic expressions calculated from zero or more columns as explained in SUN/256.

Defines the values from table 2 which are used to determine whether a match has occurred. These will typically be coordinate values such as RA and Dec and perhaps some per-row error values as well, though exactly what values are required is determined by the kind of match as determined by matcher. Depending on the kind of match, the number and type of the values required will be different. Multiple values should be separated by whitespace; if whitespace occurs within a single value it must be 'quoted' or "quoted". Elements of the expression list are commonly just column names, but may be algebraic expressions calculated from zero or more columns as explained in SUN/256.

Determines the parameters of this match. This is typically one or more tolerances such as error radii. It may contain zero or more values; the values that are required depend on the match type selected by the matcher parameter. If it contains multiple values, they must be separated by spaces; values which contain a space can be 'quoted' or "quoted".

Tuning values for the matching process, if appropriate. It may contain zero or more values; the values that are permitted depend on the match type selected by the matcher parameter. If it contains multiple values, they must be separated by spaces; values which contain a space can be 'quoted' or "quoted". If this optional parameter is not supplied, sensible defaults will be chosen.

Determines which rows are included in the output table. The matching algorithm determines which of the rows from the first table correspond to which rows from the second. This parameter determines what to do with that information. Perhaps the most obvious thing is to write out a table containing only rows which correspond to a row in both of the two input tables. However, you may also want to see the unmatched rows from one or both input tables, or rows present in one table but unmatched in the other, or other possibilities. The options are:

  • 1and2: An output row for each row represented in both input tables (INNER JOIN)
  • 1or2: An output row for each row represented in either or both of the input tables (FULL OUTER JOIN)
  • all1: An output row for each matched or unmatched row in table 1 (LEFT OUTER JOIN)
  • all2: An output row for each matched or unmatched row in table 2 (RIGHT OUTER JOIN)
  • 1not2: An output row only for rows which appear in the first table but are not matched in the second table
  • 2not1: An output row only for rows which appear in the second table but are not matched in the first table
  • 1xor2: An output row only for rows represented in one of the input tables but not the other one

Determines what happens when a row in one table can be matched by more than one row in the other table. The options are:

  • all: All matches. Every match between the two tables is included in the result. Rows from both of the input tables may appear multiple times in the result.
  • best: Best match, symmetric. The best pairs are selected in a way which treats the two tables symmetrically. Any input row which appears in one result pair is disqualified from appearing in any other result pair, so each row from both input tables will appear in at most one row in the result.
  • best1: Best match for each Table 1 row. For each row in table 1, only the best match from table 2 will appear in the result. Each row from table 1 will appear a maximum of once in the result, but rows from table 2 may appear multiple times.
  • best2: Best match for each Table 2 row. For each row in table 2, only the best match from table 1 will appear in the result. Each row from table 2 will appear a maximum of once in the result, but rows from table 1 may appear multiple times.

The differences between best, best1 and best2 are a bit subtle. In cases where it's obvious which object in each table is the best match for which object in the other, choosing betwen these options will not affect the result. However, in crowded fields (where the distance between objects within one or both tables is typically similar to or smaller than the specified match radius) it will make a difference. In this case one of the asymmetric options (best1 or best2) is usually more appropriate than best, but you'll have to think about which of them suits your requirements. The performance (time and memory usage) of the match may also differ between these options, especially if one table is much bigger than the other.

Determines how input columns are renamed before use in the output table. The choices are:

  • none: columns are not renamed
  • dups: columns which would otherwise have duplicate names in the output will be renamed to indicate which table they came from
  • all: all columns will be renamed to indicate which table they came from

If columns are renamed, the new ones are determined by suffix* parameters.

If the fixcols parameter is set so that input columns are renamed for insertion into the output table, this parameter determines how the renaming is done. It gives a suffix which is appended to all renamed columns from table 1.

If the fixcols parameter is set so that input columns are renamed for insertion into the output table, this parameter determines how the renaming is done. It gives a suffix which is appended to all renamed columns from table 2.

Gives the name of a column in the output table to contain the "match score" for each pairwise match. The meaning of this column is dependent on the chosen matcher, but it typically represents a distance of some kind between the two matching points. If a null value is chosen, no score column will be inserted in the output table. The default value of this parameter depends on matcher.

Determines whether information on progress of the match should be output to the standard error stream as it progresses. For lengthy matches this is a useful reassurance and can give guidance about how much longer it will take. It can also be useful as a performance diagnostic.

The options are:

  • none: no progress is shown
  • log: progress information is shown
  • profile: progress information and limited time/memory profiling information are shown

SEE ALSO

stilts(1)

If the package stilts-doc is installed, the full documentation SUN/256 is available in HTML format:
file:///usr/share/doc/stilts-doc/sun256/index.html

VERSION

STILTS version 3.4-debian

This is the Debian version of Stilts, which lack the support of some file formats and network protocols. For differences see
file:///usr/share/doc/stilts/README.Debian

AUTHOR

Mark Taylor (Bristol University)

Mar 2017