Ubuntu Manpage: stilts-tgroup - Calculates aggregate functions on groups of rows

NAME

       stilts-tgroup - Calculates aggregate functions on groups of rows

SYNOPSIS

       stilts tgroup [ifmt=<in-format>] [istream=true|false] [in=<table>] [icmd=<cmds>]
                     [ocmd=<cmds>]
                     [omode=out|meta|stats|count|checksum|cgi|discard|topcat|samp|tosql|gui]
                     [out=<out-table>] [ofmt=<out-format>] [keys=<expr> ...]
                     [aggcols=<expr>;<aggregator>[;<name>] ...]
                     [runner=sequential|parallel|parallel<n>|partest] [sort=true|false]
                     [cache=true|false]

DESCRIPTION

       tgroup  identifies  groups  of  rows  in  a table based on the values in a given column or
       columns, and calculates statistical quantities or otherwise collapses  down  the  multiple
       values from other columns into single values representing each group. It does the same job
       as a SELECT ... GROUP BY statement with aggregate functions in ADQL/SQL.

       The keys parameter defines how input rows are grouped, and the aggcols  parameter  defines
       what  quantities  to  aggregate  from  the  rows in each group. keys specifies one or more
       values (column names or expresssions) that must be the same  for  rows  grouped  together,
       while  aggcols  specifies zero or more columns to be added based on the content of rows in
       each group. The output table therefore contains one column for each entry in keys and  one
       column for each entry in aggcols, and has one row for each group identified.

       This  command  can therefore be used to count rows or calculate statistical quantities per
       group. A number of statistical aggregation methods are  provided  such  as  mean,  median,
       minimum,  maximum etc. For more specialised requirements, for instance quantiles or custom
       statistics, you can also use the array aggregators which generate an array containing  all
       of the values in the group, and operate on the resulting column using one of the functions
       in the Arrays class.

       By way of comparison, the tgroup  invocation:  stilts  tgroup  in=t  keys="year  detector"
       aggcols="0;count;num  gmag;min;min_gmag  gmag;mean" corresponds roughly to the ADQL query:
       SELECT COUNT(*) AS num, MIN(gmag) AS min_gmag, MEAN(gmag), FROM t GROUP BY year, detector

       See also the tgridmap and tskymap commands, which provide similar functionality where  the
       grouping is over evenly spaced numeric/coordinate values.

OPTIONS

ifmt=<in-format>
Specifies the format of the input table as specified by parameter in. 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.

istream=true|false
If set true, the input table specified by the in parameter will be read as a
stream. It is necessary to give the ifmt parameter in this case. Depending on the
required operations and processing mode, this may cause the read to fail (sometimes
it is necessary to read the table more than once). It is not normally necessary to
set this flag; in most cases the data will be streamed automatically if that is the
best thing to do. However it can sometimes result in less resource usage when
processing large files in certain formats (such as VOTable). This parameter is
ignored for scheme-specified tables.

in=<table>
The location of the 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 ifmt 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.

icmd=<cmds>
Specifies processing to be performed on the input table as specified by parameter
in, 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 alternatively 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. A backslash character '\fR' at the
end of a line joins it with the following line.

ocmd=<cmds>
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.

omode=out|meta|stats|count|checksum|cgi|discard|topcat|samp|tosql|gui
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

* checksum

* cgi

* discard

* topcat

* samp

* tosql

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

out=<out-table>
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".

ofmt=<out-format>
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".

keys=<expr> ...
List of one or more space-separated words defining the groups within which
aggregation should be done. Each word can be a column name or an expression using
the expression language. Each expression will appear as one of the columns in the
output table. This list corresponds to the contents of an ADQL/SQL GROUP BY clause.

aggcols=<expr>;<aggregator>[;<name>] ...
Defines the aggregate quantities to be calculated for each group of input rows.
Each quantity is defined by one entry in this list; entries are space-separated, or
can be given by multiple instances of this parameter on the command line.

Each entry is composed of two or three tokens, separated by semicolon (";")
characters:

* <expr>: (required) column name, or expression using the expression language,
for the quantity to be aggregated

* <aggregator>: (required) aggregation method

* <name>: (optional) name of output column; if omitted, a name based on the
<expr> value will be used

The available <aggregator> values are as follows:

* count: counts the number of rows

* ngood: counts the number of non-blank items

* sum: the sum of all the combined values per bin

* mean: the mean of the combined values

* median: the median

* stdev: the sample standard deviation of the combined values

* stdev-pop: the population standard deviation of the combined values

* max: records the maximum value

* min: records the minimum value

* array: collects all non-blank values into an array

* array-withblanks: collects all values into an array; blank values are
represented as zero for integers

* count-long: counts the number of rows, works for >2 billion

* ngood-long: counts the number of non-blank items, works for >2 billion

* Q.nnn: quantile nnn (e.g. Q.05 is the fifth percentile)

runner=sequential|parallel|parallel<n>|partest
Selects the threading implementation, i.e. to what extent processing is done in
parallel. The options are currently:

* sequential: runs using only a single thread

* parallel: runs using multiple threads for large tables, with parallelism given
by the number of available processors

* parallel<n>: runs using multiple threads for large tables, with parallelism
given by the supplied value <n>

* partest: runs using multiple threads even when tables are small (only intended
for testing purposes)

Using parallel processing can speed up execution considerably; however, depending
on the I/O operations required, it can also slow it down by disrupting patterns of
disk access. If the content of a file is on a solid state disk, or is already in
cache for instance because a similar command has been run recently, then parallel
will probably be faster. However, if the data is being read directly from a
spinning disk, for instance because the file is too large to fit in RAM, then
sequential or parallel<n> with a small <n> may be faster.

The value of this parameter should make only very tiny differences to the output
table. If you notice significant discrepancies please report them.

sort=true|false
Determines whether an attempt is made to sort the output table by the values of the
keys expressions. This may not be possible if no sort order is defined on the keys.

In most cases such sorting will be a small overhead on the rest of the work done by
this task, so the default is true but if ordering by key is not useful you may save
some resources by setting it false. If no sorting is done, the output row order is
undefined.

cache=true|false
Determines whether the results of the aggregation operation will be cached in
random-access storage before output. This is set true by default, since accessing
rows of the calculated table may be somewhat expensive, and most uses of the
results will need all of the cells. But if you anticipate making only a small
number of accesses to the output table cells, it could be more efficient to set
this false.

VERSION

       STILTS version 3.5.1-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