/usr/share/jython/Lib/site-packages/stilts.py is in jython-stilts 3.1.2-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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10301 | # This module auto-generated by java class uk.ac.starlink.ttools.build.JyStilts.
'''Provides access to STILTS commands.
See the manual, http://www.starlink.ac.uk/stilts/sun256/
for tutorial and full usage information.
'''
__author__ = 'Mark Taylor'
import sys
import java.io
import java.nio.file
import java.util.jar
# see also http://bugs.jython.org/issue547727
def _recursivelyAddJar(jarfile):
if jarfile.canonicalPath in sys.path:
return
sys.path.append(jarfile.canonicalPath)
try:
jar = java.util.jar.JarFile(jarfile)
if jar and jar.manifest:
jarAttrs = jar.manifest.mainAttributes
jarClassPath = jarAttrs.get(java.util.jar.Attributes.Name.CLASS_PATH)
if jarClassPath:
for p in jarClassPath.split():
_recursivelyAddJar(java.io.File(jarfile.parent, p))
except java.io.FileNotFoundException:
pass # ignore jars that are not there
except java.nio.file.NoSuchFileException:
pass # ignore jars that are not there
_recursivelyAddJar(java.io.File('/usr/share/java/starlink-ttools.jar'))
del _recursivelyAddJar
del sys
import jarray.array
from org.python.core.util import StringUtil
import java.io.ByteArrayInputStream as _ByteArrayInputStream
import java.io.OutputStream as _OutputStream
import java.lang.Class as _Class
import java.lang.System as _System
import java.lang.reflect.Array as _Array
import java.util.ArrayList as _ArrayList
import uk.ac.starlink.table.ColumnInfo as _ColumnInfo
import uk.ac.starlink.table.MultiStarTableWriter as _MultiStarTableWriter
import uk.ac.starlink.table.StarTable as _StarTable
import uk.ac.starlink.table.StarTableFactory as _StarTableFactory
import uk.ac.starlink.table.StarTableOutput as _StarTableOutput
import uk.ac.starlink.table.TableSequence as _TableSequence
import uk.ac.starlink.table.Tables as _Tables
import uk.ac.starlink.table.WrapperStarTable as _WrapperStarTable
import uk.ac.starlink.table.WrapperRowSequence as _WrapperRowSequence
import uk.ac.starlink.task.InvokeUtils as _InvokeUtils
import uk.ac.starlink.ttools.Stilts as _Stilts
import uk.ac.starlink.ttools.filter.StepFactory as _StepFactory
import uk.ac.starlink.ttools.task.MapEnvironment as _MapEnvironment
import uk.ac.starlink.util.DataSource as _DataSource
import uk.ac.starlink.ttools.func.Arithmetic as Arithmetic
import uk.ac.starlink.ttools.func.Arrays as Arrays
import uk.ac.starlink.ttools.func.Conversions as Conversions
import uk.ac.starlink.ttools.func.CoordsDegrees as CoordsDegrees
import uk.ac.starlink.ttools.func.CoordsRadians as CoordsRadians
import uk.ac.starlink.ttools.func.Coverage as Coverage
import uk.ac.starlink.ttools.func.Distances as Distances
import uk.ac.starlink.ttools.func.Fluxes as Fluxes
import uk.ac.starlink.ttools.func.Formats as Formats
import uk.ac.starlink.ttools.func.KCorrections as KCorrections
import uk.ac.starlink.ttools.func.Lists as Lists
import uk.ac.starlink.ttools.func.Maths as Maths
import uk.ac.starlink.ttools.func.Strings as Strings
import uk.ac.starlink.ttools.func.Tilings as Tilings
import uk.ac.starlink.ttools.func.Times as Times
import uk.ac.starlink.ttools.func.TrigDegrees as TrigDegrees
class JyStarTable(_WrapperStarTable):
'''StarTable wrapper class for use within Jython.
Decorates a uk.ac.starlink.table.StarTable
java object with methods for use within jython.
These include special bound functions to make it an
iterable object (with items which are table rows),
arithmetic + and * overloads for concatenation,
a write method for table viewing or output,
and methods representing STILTS filter functionality,
namely cmd_* methods for filters and mode_* methods
for output modes.
As a general rule, any StarTable object which is
intented for use by JyStilts program code should be
wrapped in an instance of this class.
'''
def __init__(self, base_table):
_WrapperStarTable.__init__(self, base_table)
def __iter__(self):
rowseq = self.getRowSequence()
while rowseq.next():
yield self._create_row(rowseq.getRow())
def __str__(self):
return '%s (?x%d)' % (self.getName(), self.getColumnCount())
def __add__(self, other):
return tcat([self, other])
def __mul__(self, count):
return tcat([self] * count)
def __rmul__(self, count):
return tcat([self] * count)
def columns(self):
'''Returns a tuple of ColumnInfo objects describing the columns of this table.'''
if hasattr(self, '_columns'):
return self._columns
else:
col_list = []
for i in xrange(self.getColumnCount()):
col_list.append(_JyColumnInfo(self.getColumnInfo(i)))
self._columns = tuple(col_list)
return self.columns()
def parameters(self):
'''
Returns a mapping of table parameter names to values.
This does not provide all the information about the parameters,
for instance units and UCDs are not included.
For more detail, use the relevant StarTable methods.
Currently, this is not a live list, in the sense that changing
the returned dictionary will not affect the table parameter values.
'''
if hasattr(self, '_parameters'):
return self._parameters
else:
params = {}
for p in self.getParameters():
params[p.getInfo().getName()] = p.getValue()
self._parameters = params
return self.parameters()
def coldata(self, key):
'''Returns a sequence of all the values in a given column.'''
icol = self._column_index(key)
rowseq = self.getRowSequence()
while rowseq.next():
yield rowseq.getCell(icol)
def count_rows(self):
'''Returns the number of rows in this table.
For random access tables it calls getRowCount
which returns the value directly.
For non-random tables it may have to iterate over the rows.
That could be slow, though it should be much faster than iterating
over this table as an iterable itself, since the cell data
does not need to be made available.'''
nrow = self.getRowCount();
if nrow >= 0:
return nrow
else:
nr = 0
rseq = self.getRowSequence()
while rseq.next():
nr += 1
return nr
def _create_row(self, array):
row = _JyRow(array)
row.table = self
return row
def _column_index(self, key):
if type(key) is type(1):
if key >= 0:
return key
else:
return key + self.getColumnCount()
if hasattr(self, '_colmap'):
return self._colmap[key]
else:
colmap = {}
for ic, col in enumerate(self.columns()):
if not col in colmap:
colmap[col] = ic
colname = col.getName()
if not colname in colmap:
colmap[colname] = ic
self._colmap = colmap
return self._column_index(key)
def write(self, location=None, fmt='(auto)'):
'''Writes table to a file.
The location parameter may give a filename or a
python file object open for writing.
if it is not supplied, standard output is used.
The fmt parameter specifies output format.
Known output formats:
(auto)
jdbc
fits
fits-plus
fits-basic
fits-var
colfits-plus
colfits-basic
votable-tabledata
votable-binary-inline
votable-binary2-inline
votable-fits-href
votable-binary-href
votable-binary2-href
votable-fits-inline
text
ascii
csv
csv-noheader
ipac
tst
html
html-element
latex
latex-document
'''
sto = _StarTableOutput()
if hasattr(location, 'write') and hasattr(location, 'flush'):
ostrm = _JyOutputStream(location)
name = getattr(location, 'name', None)
handler = sto.getHandler(fmt, name)
sto.writeStarTable(self, ostrm, handler)
else:
if location is None:
location = '-'
sto.writeStarTable(self, location, fmt)
def cmd_addcol(self, *args):
'''\
Add a new column called <col-name> defined by the algebraic
expression <expr>. By default the new column appears after the last
column of the table, but you can position it either before or after
a specified column using the -before or -after flags respectively.
The -units, -ucd-utype and -desc flags can be used to define
metadata values for the new column.
Syntax for the <expr> and <col-id> arguments is described in the
manual.
The filtered table is returned.
args is a list with words as elements:
[-after <col-id> | -before <col-id>]
[-units <units>] [-ucd <ucd>] [-utype <utype>] [-desc <descrip>]
<col-name> <expr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("addcol")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_addpixsample(self, *args):
'''\
Samples pixel data from an all-sky image file in HEALPix format. The
<healpix-file> argument must be the filename of a table containing
HEALPix pixel data. The URL of such a file can be used instead, but
local files are likely to be more efficient.
The <expr-lon> and <expr-lat> arguments give expressions for the
longitude and latitude in degrees for each row of the input table;
this is usually just the column names. The long/lat must usually be
in the same coordinate system as that used for the HEALPix data, so
if the one is in galactic coordinates the other must be as well. If
this is not the case, use the -systems flag to give the input
long/lat and healpix data coordinate system names respectively. The
available coordinate system names are:
* icrs: ICRS (Hipparcos) (Right Ascension, Declination)
* fk5: FK5 J2000.0 (Right Ascension, Declination)
* fk4: FK4 B1950.0 (Right Ascension, Declination)
* galactic: IAU 1958 Galactic (Longitude, Latitude)
* supergalactic: de Vaucouleurs Supergalactic (Longitude, Latitude)
* ecliptic: Ecliptic (Longitude, Latitude)
The <expr-rad>, if present, is a constant or expression giving the
radius in degrees over which pixels will be averaged to obtain the
result values. Note that this averaging is somewhat approximate;
pixels partly covered by the specified disc are weighted the same as
those fully covered. If no radius is specified, the value of the
pixel covering the central position will be used.
The <healpix-file> file is a table with one row per HEALPix pixel
and one or more columns representing pixel data. A new column will
be added to the output table corresponding to each of these pixel
columns. This type of data is available in FITS tables for a number
of all-sky data sets, particularly from the LAMBDA archive; see for
instance the page on foreground products (including dust emission,
reddening etc) or WMAP 7 year data. If the filename given does not
appear to point to a file of the appropriate format, an error will
result. Note the LAMBDA files mostly (all?) use galactic
coordinates, so coordinate conversion using the -systems flag may be
appropriate, see above.
Syntax for the <expr-lon> , <expr-lat> and <expr-rad> arguments is
described in the manual.
This filter is somewhat experimental, and its usage may be changed
or replaced in a future version.
Note: you may prefer to use the pixsample command instead.
The filtered table is returned.
args is a list with words as elements:
[-radius <expr-rad>] [-systems <in-sys> <pix-sys>]
<expr-lon> <expr-lat> <healpix-file>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("addpixsample")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_addresolve(self, *args):
'''\
Performs name resolution on the string-valued column
<col-id-objname> and appends two new columns <col-name-ra> and
<col-name-dec> containing the resolved Right Ascension and
Declination in degrees.
Syntax for the <col-id-objname> argument is described in SUN/256.
UCDs are added to the new columns in a way which tries to be
consistent with any UCDs already existing in the table.
Since this filter works by interrogating a remote service, it will
obviously be slow. The current implementation is experimental; it
may be replaced in a future release by some way of doing the same
thing (perhaps a new STILTS task) which is able to work more
efficiently by dispatching multiple concurrent requests.
This is currently implemented using the Simbad service operated by
CDS.
The filtered table is returned.
args is a list with words as elements:
<col-id-objname> <col-name-ra> <col-name-dec>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("addresolve")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_addskycoords(self, *args):
'''\
Add new columns to the table representing position on the sky. The
values are determined by converting a sky position whose coordinates
are contained in existing columns. The <col-id> arguments give
identifiers for the two input coordinate columns in the coordinate
system named by <insys>, and the <col-name> arguments name the two
new columns, which will be in the coordinate system named by
<outsys>. The <insys> and <outsys> coordinate system specifiers are
one of
* icrs: ICRS (Hipparcos) (Right Ascension, Declination)
* fk5: FK5 J2000.0 (Right Ascension, Declination)
* fk4: FK4 B1950.0 (Right Ascension, Declination)
* galactic: IAU 1958 Galactic (Longitude, Latitude)
* supergalactic: de Vaucouleurs Supergalactic (Longitude, Latitude)
* ecliptic: Ecliptic (Longitude, Latitude)
The -inunit and -outunit flags may be used to indicate the units of
the existing coordinates and the units for the new coordinates
respectively; use one of degrees, radians or sexagesimal (may be
abbreviated), otherwise degrees will be assumed. For sexagesimal,
the two corresponding columns must be string-valued in forms like
hh:mm:ss.s and dd:mm:ss.s respectively.
For certain conversions, the value specified by the -epoch flag is
of significance. Where significant its value defaults to 2000.0.
Syntax for the <expr> , <col-id1> and <col-id2> arguments is
described in the manual.
The filtered table is returned.
args is a list with words as elements:
[-epoch <expr>] [-inunit deg|rad|sex] [-outunit deg|rad|sex]
<insys> <outsys> <col-id1> <col-id2> <col-name1> <col-name2>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("addskycoords")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_assert(self, *args):
'''\
Check that a boolean expression is true for each row. If the
expression <expr> does not evaluate true for any row of the table,
execution terminates with an error. As long as no error occurs, the
output table is identical to the input one.
The exception generated by an assertion violation is of class
uk.ac.starlink.ttools.filter.AssertException although that is not
usually obvious if you are running from the shell in the usual way.
Syntax for the <expr> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<expr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("assert")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_badval(self, *args):
'''\
For each column specified in <colid-list> any occurrence of the
value <bad-val> is replaced by a blank entry.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<bad-val> <colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("badval")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_cache(self):
'''\
Stores in memory or on disk a temporary copy of the table at this
point in the pipeline. This can provide improvements in efficiency
if there is an expensive step upstream and a step which requires
more than one read of the data downstream. If you see an error like
"Can't re-read data from stream" then adding this step near the
start of the filters might help.
The result of this filter is guaranteed to be random-access.
See also the random filter, which caches only when the input table
is not random-access.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("cache")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_check(self):
'''\
Runs checks on the table at the indicated point in the processing
pipeline. This is strictly a debugging measure, and may be
time-consuming for large tables.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("check")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_clearparams(self, *args):
'''\
Clears the value of one or more named parameters. Each of the
<pname> values supplied may be either a parameter name or a simple
wildcard expression matching parameter names. Currently the only
wildcarding is a "*" to match any sequence of characters.
clearparams * will clear all the parameters in the table.
It is not an error to supply <pname>s which do not exist in the
table - these have no effect.
The filtered table is returned.
args is a list with words as elements:
<pname> ...
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("clearparams")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_colmeta(self, *args):
'''\
Modifies the metadata of one or more columns. Some or all of the
name, units, ucd, utype and description of the column(s), identified
by <colid-list> can be set by using some or all of the listed flags.
Typically, <colid-list> will simply be the name of a single column.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-name <name>] [-units <units>] [-ucd <ucd>] [-utype <utype>]
[-desc <descrip>]
<colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("colmeta")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_delcols(self, *args):
'''\
Delete the specified columns. The same column may harmlessly be
specified more than once.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("delcols")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_every(self, *args):
'''\
Include only every <step>'th row in the result, starting with the
first row.
The filtered table is returned.
args is a list with words as elements:
<step>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("every")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_explodecols(self, *args):
'''\
Takes a list of specified columns which represent N-element arrays
and replaces each one with N scalar columns. Each of the columns
specified by <colid-list> must have a fixed-length array type,
though not all the arrays need to have the same number of elements.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("explodecols")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_explodeall(self, *args):
'''\
Replaces any columns which is an N-element arrays with N scalar
columns. Only columns with fixed array sizes are affected. The
action can be restricted to only columns of a certain shape using
the flags.
If the -ifndim flag is used, then only columns of dimensionality
<ndim> will be exploded. <ndim> may be 1, 2, ....
If the -ifshape flag is used, then only columns with a specific
shape will be exploded; <dims> is a space- or comma-separated list
of dimension extents, with the most rapidly-varying first, e.g. '2 5
' to explode all 2 x 5 element array columns.
The filtered table is returned.
args is a list with words as elements:
[-ifndim <ndim>] [-ifshape <dims>]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("explodeall")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_fixcolnames(self):
'''\
Renames all columns and parameters in the input table so that they
have names which have convenient syntax for STILTS. For the most
part this means replacing spaces and other non-alphanumeric
characters with underscores. This is a convenience which lets you
use column names in algebraic expressions and other STILTS syntax.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("fixcolnames")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_head(self, *args):
'''\
Include only the first <nrows> rows of the table. If the table has
fewer than <nrows> rows then it will be unchanged.
The filtered table is returned.
args is a list with words as elements:
<nrows>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("head")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_keepcols(self, *args):
'''\
Select the columns from the input table which will be included in
the output table. The output table will include only those columns
listed in <colid-list>, in that order. The same column may be listed
more than once, in which case it will appear in the output table
more than once.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("keepcols")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_meta(self, *args):
'''\
Provides information about the metadata for each column. This filter
turns the table sideways, so that each row of the output corresponds
to a column of the input. The columns of the output table contain
metadata items such as column name, units, UCD etc corresponding to
each column of the input table.
By default the output table contains columns for the following
items:
* Index: Position of column in table
* Name: Column name
* Class: Data type of objects in column
* Shape: Shape of array values
* ElSize: Size of each element in column (mostly useful for
strings)
* Units: Unit string
* Description: Description of data in the column
* UCD: Unified Content Descriptor
* Utype: Type in data model
as well as any table-specific column metadata items that the table
contains.
However, the output may be customised by supplying one or more
<item> headings. These may be selected from the above as well as the
following:
* UCD_desc: Textual description of UCD
as well as any table-specific metadata. It is not an error to
specify an item for which no metadata exists in any of the columns
(such entries will result in empty columns).
Any table parameters of the input table are propagated to the output
one.
The filtered table is returned.
args is a list with words as elements:
[<item> ...]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("meta")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_progress(self):
'''\
Monitors progress by displaying the number of rows processed so far
on the terminal (standard error). This number is updated every
second or thereabouts; if all the processing is done in under a
second you may not see any output. If the total number of rows in
the table is known, an ASCII-art progress bar is updated, otherwise
just the number of rows seen so far is written.
Note under some circumstances progress may appear to complete before
the actual work of the task is done since part of the processing
involves slurping up the whole table to provide random access on it.
In this case, applying the cache upstream may help.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("progress")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_random(self):
'''\
Ensures that random access is available on this table. If the table
currently has random access, it has no effect. If only sequential
access is available, the table is cached so that downstream steps
will see the cached, hence random-access, copy.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("random")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_randomview(self):
'''\
Ensures that steps downstream only use random access methods for
table access. If the table is sequential only, this will result in
an error. Only useful for debugging.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("randomview")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_repeat(self, *args):
'''\
Repeats the rows of a table multiple times to produce a longer
table. The output table will have <count> times as many rows as the
input table.
The optional flag determines the sequence of the output rows. If
<count>=2 and there are three rows, the output sequence will be
112233 for -row and 123123 for -table. The default behaviour is
currently -table.
The <count> value will usually be a constant integer value, but it
can be an expression evaluated in the context of the table.
The filtered table is returned.
args is a list with words as elements:
[-row|-table] <count>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("repeat")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_replacecol(self, *args):
'''\
Replaces the content of a column with the value of an algebraic
expression. The old values are discarded in favour of the result of
evaluating <expr>. You can specify the metadata for the new column
using the -name, -units, -ucd, -utype and -desc flags; for any of
these items which you do not specify, they will take the values from
the column being replaced.
It is legal to reference the replaced column in the expression, so
for example "replacecol pixsize pixsize*2" just multiplies the
values in column pixsize by 2.
Syntax for the <col-id> and <expr> arguments is described in the
manual.
The filtered table is returned.
args is a list with words as elements:
[-name <name>] [-units <units>] [-ucd <ucd>] [-utype <utype>]
[-desc <descrip>]
<col-id> <expr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("replacecol")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_replaceval(self, *args):
'''\
For each column specified in <colid-list> any instance of <old-val>
is replaced by <new-val>. The value string 'null' can be used for
either <old-value> or <new-value> to indicate a blank value (but see
also the badval filter).
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<old-val> <new-val> <colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("replaceval")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_rowrange(self, *args):
'''\
Includes only rows in a given range. The range can either be
supplied as "<first> <last>", where row indices are inclusive, or "
<first> +<count>". In either case, the first row is numbered 1.
Thus, to get the first hundred rows, use either "rowrange 1 100" or
"rowrange 1 +100" and to get the second hundred, either "rowrange
101 200" or "rowrange 101 +100"
The filtered table is returned.
args is a list with words as elements:
<first> <last>|+<count>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("rowrange")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_select(self, *args):
'''\
Include in the output table only rows for which the expression
<expr> evaluates to true. <expr> must be an expression which
evaluates to a boolean value (true/false).
Syntax for the <expr> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<expr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("select")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_seqview(self):
'''\
Ensures that steps downstream see the table as sequential access.
Any attempts at random access will fail. Only useful for debugging.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("seqview")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_setparam(self, *args):
'''\
Sets a named parameter in the table to a given value. The parameter
named <pname> is set to the value <pexpr>, which may be a literal
value or an expression involving mathematical operations and other
parameter names (using the param$<name> syntax). By default, the
data type of the parameter is determined by the type of the supplied
expression, but this can be overridden using the -type flag. The
parameter description, units, UCD and Utype attributes may
optionally be set using the other flags.
The filtered table is returned.
args is a list with words as elements:
[-type byte|short|int|long|float|double|boolean|string]
[-desc <descrip>] [-unit <units>] [-ucd <ucd>] [-utype <utype>]
<pname> <pexpr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("setparam")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_sort(self, *args):
'''\
Sorts the table according to the value of one or more algebraic
expressions. The sort key expressions appear, as separate
(space-separated) words, in <key-list>; sorting is done on the first
expression first, but if that results in a tie then the second one
is used, and so on.
Each expression must evaluate to a type that it makes sense to sort,
for instance numeric. If the -down flag is used, the sort order is
descending rather than ascending.
Blank entries are by default considered to come at the end of the
collation sequence, but if the -nullsfirst flag is given then they
are considered to come at the start instead.
Syntax for the <key-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-down] [-nullsfirst] <key-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("sort")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_sorthead(self, *args):
'''\
Performs a sort on the table according to the value of one or more
algebraic expressions, retaining only <nrows> rows at the head of
the resulting sorted table. The sort key expressions appear, as
separate (space-separated) words, in <key-list>; sorting is done on
the first expression first, but if that results in a tie then the
second one is used, and so on. Each expression must evaluate to a
type that it makes sense to sort, for instance numeric.
If the -tail flag is used, then the last <nrows> rows rather than
the first ones are retained.
If the -down flag is used the sort order is descending rather than
ascending.
Blank entries are by default considered to come at the end of the
collation sequence, but if the -nullsfirst flag is given then they
are considered to come at the start instead.
This filter is functionally equivalent to using sort followed by
head, but it can be done in one pass and is usually cheaper on
memory and faster, as long as <nrows> is significantly lower than
the size of the table.
Syntax for the <key-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-tail] [-down] [-nullsfirst] <nrows> <key-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("sorthead")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_stats(self, *args):
'''\
Calculates statistics on the data in the table. This filter turns
the table sideways, so that each row of the output corresponds to a
column of the input. The columns of the output table contain
statistical items such as mean, standard deviation etc corresponding
to each column of the input table.
By default the output table contains columns for the following
items:
* Name: Column name
* Mean: Average
* StDev: Population Standard deviation
* Minimum: Numeric minimum
* Maximum: Numeric maximum
* NGood: Number of non-blank cells
However, the output may be customised by supplying one or more
<item> headings. These may be selected from the above as well as the
following:
* NBad: Number of blank cells
* Variance: Population Variance
* SampStDev: Sample Standard Deviation
* SampVariance: Sample Variance
* MedAbsDev: Median Absolute Deviation
* ScMedAbsDev: Median Absolute Deviation * 1.4826
* Skew: Gamma 1 skewness measure
* Kurtosis: Gamma 2 peakedness measure
* Sum: Sum of values
* MinPos: Row index of numeric minimum
* MaxPos: Row index of numeric maximum
* Cardinality: Number of distinct values in column; values >100
ignored
* Median: Middle value in sequence
* Quartile1: First quartile
* Quartile2: Second quartile
* Quartile3: Third quartile
Additionally, the form "Q.nn" may be used to represent the quantile
corresponding to the proportion 0.nn, e.g.:
* Q.25: First quartile
* Q.625: Fifth octile
Any parameters of the input table are propagated to the output one.
Note that quantile calculations (including median and quartiles) can
be expensive on memory. If you want to calculate quantiles for large
tables, it may be wise to reduce the number of columns to only those
you need the quantiles for earlier in the pipeline. No interpolation
is performed when calculating quantiles.
The filtered table is returned.
args is a list with words as elements:
[<item> ...]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("stats")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_tablename(self, *args):
'''\
Sets the table's name attribute to the given string.
The filtered table is returned.
args is a list with words as elements:
<name>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("tablename")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_tail(self, *args):
'''\
Include only the last <nrows> rows of the table. If the table has
fewer than <nrows> rows then it will be unchanged.
The filtered table is returned.
args is a list with words as elements:
<nrows>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("tail")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_transpose(self, *args):
'''\
Transposes the input table so that columns become rows and vice
versa. The -namecol flag can be used to specify a column in the
input table which will provide the column names for the output
table. The first column of the output table will contain the column
names of the input table.
Syntax for the <col-id> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-namecol <col-id>]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("transpose")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def cmd_uniq(self, *args):
'''\
Eliminates adjacent rows which have the same values. If used with no
arguments, then any row which has identical values to its
predecessor is removed.
If the <colid-list> parameter is given then only the values in the
specified columns must be equal in order for the row to be removed.
If the -count flag is given, then an additional column with the name
DupCount will be prepended to the table giving a count of the number
of duplicated input rows represented by each output row. A unique
row has a DupCount value of 1.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-count] [<colid-list>]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("uniq")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(self))
def mode_out(self, out='-', ofmt='(auto)'):
'''\
Writes a new table.
Parameters:
out = <out-table> (uk.ac.starlink.ttools.TableConsumer)
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.
[Default: -]
ofmt = <out-format> (String)
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.
[Default: (auto)]
'''
env = _JyEnvironment()
env.setValue('out', _map_env_value(out))
env.setValue('ofmt', _map_env_value(ofmt))
mode = _stilts.getModeFactory().createObject('out')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
def mode_meta(self):
'''\
Prints the table metadata to standard output. The name and type etc
of each column is tabulated, and table parameters are also shown.
See the meta filter for more flexible output of table metadata.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('meta')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
def mode_stats(self):
'''\
Calculates and displays univariate statistics for each of the
numeric columns in the table. The following entries are shown for
each column as appropriate:
* mean
* population standard deviation
* minimum
* maximum
* number of non-null entries
See the stats filter for more flexible statistical calculations.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('stats')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
def mode_count(self):
'''\
Counts the number of rows and columns and writes the result to
standard output.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('count')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
def mode_cgi(self, ofmt='votable'):
'''\
Writes a table to standard output in a way suitable for use as
output from a CGI (Common Gateway Interface) program. This is very
much like out mode but a short CGI header giving the MIME
Content-Type is prepended to the output
Parameters:
ofmt = <out-format> (String)
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).
[Default: votable]
'''
env = _JyEnvironment()
env.setValue('ofmt', _map_env_value(ofmt))
mode = _stilts.getModeFactory().createObject('cgi')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
def mode_discard(self):
'''\
Reads all the data in the table in sequential mode and discards it.
May be useful in conjunction with the assert filter.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('discard')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
def mode_topcat(self):
'''\
Attempts to display the output table directly in TOPCAT. If a TOPCAT
instance is already running on the local host, an attempt will be
made to open the table in that. A variety of mechanisms are used to
attempt communication with an existing TOPCAT instance. In order:
* SAMP using existing hub (TOPCAT v3.4+ only, requires SAMP hub to
be running)
* SOAP (requires TOPCAT to run with somewhat deprecated -soap flag,
may be limitations on table size)
* SAMP using internal, short-lived hub (TOPCAT v3.4+ only, running
hub not required, but may be slow. It's better to start an
external hub, e.g. topcat -exthub) Failing that, an attempt
will be made to launch a new TOPCAT instance for display. This only
works if the TOPCAT classes are on the class path.
If large tables are involved, starting TOPCAT with the -disk flag is
probably a good idea.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('topcat')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
def mode_samp(self, format='votable fits', client=None):
'''\
Sends the table to registered SAMP-aware applications subscribed to
a suitable table load MType. SAMP, the Simple Application Messaging
Protocol, is a tool interoperability protocol. A SAMP Hub must be
running for this to work.
Parameters:
format = <value> (String[])
Gives one or more table format types for attempting the table
transmission over SAMP. If multiple values are supplied, they
should be separated by spaces. Each value supplied for this
parameter corresponds to a different MType which may be used
for the transmission. If a single value is used, a SAMP
broadcast will be used. If multiple values are used, each
registered client will be interrogated to see whether it
subscribes to the corresponding MTypes in order; the first one
to which it is subscribed will be used to send the table. The
standard options are
* votable: use MType table.load.votable
* fits: use MType table.load.fits
If any other string is used which corresponds to one of
STILTS's known table output formats, an attempt will be made
to use an ad-hoc MType of the form table.load.format.
[Default: votable fits]
client = <name-or-id> (String)
Identifies a registered SAMP client which is to receive the
table. Either the client ID or the (case-insensitive)
application name may be used. If a non-null value is given,
then the table will be sent to only the first client with the
given name or ID. If no value is supplied the table will be
sent to all suitably subscribed clients.
'''
env = _JyEnvironment()
env.setValue('format', _map_env_value(format))
env.setValue('client', _map_env_value(client))
mode = _stilts.getModeFactory().createObject('samp')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
def mode_tosql(self, protocol, db, dbtable, host='localhost', write='create', user='buildd', password=None):
'''\
Writes a new table to an SQL database. You need the appropriate JDBC
drivers and -Djdbc.drivers set as usual (see SUN/256).
Parameters:
protocol = <jdbc-protocol> (String)
The driver-specific sub-protocol specifier for the JDBC
connection. For MySQL's Connector/J driver, this is mysql, and
for PostgreSQL's driver it is postgresql. For other drivers,
you may have to consult the driver documentation.
host = <value> (String)
The host which is acting as a database server.
[Default: localhost]
db = <db-name> (String)
The name of the database on the server into which the new
table will be written.
The value of this parameter forms the last part of the JDBC
connection URL. That means that for some JDBC drivers, you can
append parameter specifications to it to affect the way the
connection is made to the database, e.g. "
db=some_db?useSSL=false" for MySQL's Connector/J.
dbtable = <table-name> (String)
The name of the table which will be written to the database.
write = create|dropcreate|append
(uk.ac.starlink.table.jdbc.WriteMode)
Controls how the values are written to a table in the
database. The options are:
* create: Creates a new table before writing. It is an error
if a table of the same name already exists.
* dropcreate: Creates a new database table before writing. If
a table of the same name already exists, it is dropped
first.
* append: Appends to an existing table. An error results if
the named table has the wrong structure (number or types
of columns) for the data being written.
[Default: create]
user = <username> (String)
User name for the SQL connection to the database.
[Default: buildd]
password = <passwd> (String)
Password for the SQL connection to the database.
'''
env = _JyEnvironment()
env.setValue('protocol', _map_env_value(protocol))
env.setValue('db', _map_env_value(db))
env.setValue('dbtable', _map_env_value(dbtable))
env.setValue('host', _map_env_value(host))
env.setValue('write', _map_env_value(write))
env.setValue('user', _map_env_value(user))
env.setValue('password', _map_env_value(password))
mode = _stilts.getModeFactory().createObject('tosql')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
def mode_gui(self):
'''\
Displays the table in a scrollable window.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('gui')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(self)
class RandomJyStarTable(JyStarTable):
'''Extends the JyStarTable wrapper class for random access.
Instances of this class can be subscripted.
'''
def __init__(self, base_table):
JyStarTable.__init__(self, base_table)
def __len__(self):
return int(self.getRowCount())
def __getitem__(self, key):
if type(key) is type(slice(0)):
return [self._create_row(self.getRow(irow))
for irow in _slice_range(key, len(self))]
elif key < 0:
irow = self.getRowCount() + key
return self._create_row(self.getRow(irow))
else:
return self._create_row(self.getRow(key))
def __str__(self):
return str(self.getName()) + '(' + str(self.getRowCount()) + 'x' + str(self.getColumnCount()) + ')'
def coldata(self, key):
'''Returns a sequence of all the values in a given column.'''
icol = self._column_index(key)
return _Coldata(self, icol)
class _Coldata(object):
def __init__(self, table, icol):
self.table = table
self.icol = icol
self.nrow = len(table)
def __iter__(self):
rowseq = self.table.getRowSequence()
while rowseq.next():
yield rowseq.getCell(self.icol)
def __len__(self):
return self.nrow
def __getitem__(self, key):
if type(key) is type(slice(0)):
return [self.table.getCell(irow, self.icol)
for irow in _slice_range(key, self.nrow)]
elif key < 0:
irow = self.nrow + key
return self.table.getCell(irow, self.icol)
else:
return self.table.getCell(key, self.icol)
class _JyColumnInfo(_ColumnInfo):
def __init__(self, base):
_ColumnInfo.__init__(self, base)
def __str__(self):
return self.getName()
class _JyRow(tuple):
def __init__(self, array):
tuple.__init__(self, array)
def __getitem__(self, key):
icol = self.table._column_index(key)
return tuple.__getitem__(self, icol)
class _JyEnvironment(_MapEnvironment):
def __init__(self, grab_output=False):
_MapEnvironment.__init__(self)
if grab_output:
self._out = _MapEnvironment.getOutputStream(self)
else:
self._out = _System.out
self._err = _System.err
self._used = {}
def getOutputStream(self):
return self._out
def getErrorStream(self):
return self._err
def acquireValue(self, param):
_MapEnvironment.acquireValue(self, param)
self._used[param.getName()] = True
def getUnusedArgs(self):
return filter(lambda n: n not in self._used, self.getNames())
def _check_unused_args(env):
names = env.getUnusedArgs()
if (names):
raise SyntaxError('Unused STILTS parameters %s' % str(tuple([str(n) for n in names])))
def _check_multi_handler(handler):
if not _MultiStarTableWriter.isInstance(handler):
raise TypeError('Handler %s cannot write multiple tables' % handler.getFormatName())
def _slice_range(slice, leng):
start = slice.start
stop = slice.stop
step = slice.step
if start is None:
start = 0
elif start < 0:
start += leng
if stop is None:
stop = leng
elif stop < 0:
stop += leng
if step is None:
return xrange(start, stop)
else:
return xrange(start, stop, step)
class _JyOutputStream(_OutputStream):
def __init__(self, file):
self._file = file
def write(self, *args):
narg = len(args)
if narg is 1:
arg0 = args[0]
if type(arg0) is type(1):
pyarg = chr(arg0)
else:
pyarg = arg0
elif narg is 3:
buf, off, leng = args
pyarg = buf[off:off + leng].tostring()
else:
raise SyntaxError('%d args?' % narg)
self._file.write(pyarg)
def close(self):
self._file.close()
def flush(self):
self._file.flush()
class _JyTableSequence(_TableSequence):
def __init__(self, seq):
self._iter = iter(seq)
def nextTable(self):
try:
return self._iter.next()
except StopIteration:
return None
class _JyDataSource(_DataSource):
def __init__(self, file):
buf = file.read(-1)
self._buffer = StringUtil.toBytes(buf)
if hasattr(file, 'name'):
self.setName(file.name)
def getRawInputStream(self):
return _ByteArrayInputStream(self._buffer)
def import_star_table(table):
'''Imports a StarTable instance for use with JyStilts.
This factory function takes an instance of the Java class
uk.ac.starlink.table.StarTable
and returns an instance of a wrapper subclass which has some
decorations useful in a python environment.
This includes stilts cmd_* and mode_* methods, as well as
python-friendly standard methods to make it behave as an
iterable, and where possible a container, of data rows,
and overloaded addition and multiplication operators
with the semantics of concatenation.
'''
if table.isRandom():
return RandomJyStarTable(table)
else:
return JyStarTable(table)
def _map_env_value(pval):
if pval is None:
return None
elif pval is True:
return 'true'
elif pval is False:
return 'false'
elif isinstance(pval, _StarTable):
return pval
elif _is_container(pval, _StarTable):
return jarray.array(pval, _StarTable)
else:
return str(pval)
def _is_container(value, type):
try:
if len(value) > 0:
for item in value:
if not isinstance(item, type):
return False
return True
else:
return False
except TypeError:
return False
_stilts = _Stilts()
_InvokeUtils.configureLogging(0, False)
_param_alias_dict = {}
_param_alias_dict['in']='in_'
_stilts_lib_version = _stilts.getVersion()
_stilts_script_version = '3.1-2-debian'
if _stilts_lib_version != _stilts_script_version:
print('WARNING: STILTS script/class library version mismatch (' + _stilts_script_version + '/' + _stilts_lib_version + ').')
print(' This may or may not cause trouble.')
def tread(location, fmt='(auto)', random=False):
'''Reads a table from a filename, URL or python file object.
The random argument determines whether random access is required
for the table.
Setting it true may improve efficiency, but perhaps at the cost
of memory usage and load time for large tables.
The fmt argument must be supplied if the table format cannot
be auto-detected.
In general supplying a filename is preferred; the current implementation
may be much more expensive on memory if a python file object is used.
Auto-detected in-formats:
fits-plus
colfits-plus
colfits-basic
fits
votable
Known in-formats:
fits-plus
colfits-plus
colfits-basic
fits
votable
ascii
csv
tst
ipac
wdc
The result of the function is a JyStilts table object.
'''
fact = _StarTableFactory(random)
if hasattr(location, 'read'):
datsrc = _JyDataSource(location)
table = fact.makeStarTable(datsrc, fmt)
else:
table = fact.makeStarTable(location, fmt)
return import_star_table(table)
def treads(location, fmt='(auto)', random=False):
'''Reads multiple tables from a filename, URL or python file object.
It only makes sense to use this function rather than tread() if the
format is, or may be, one which can contain multiple tables.
Generally this means VOTable or FITS or one of their variants.
The random argument determines whether random access is required
for the table.
Setting it true may improve efficiency, but perhaps at the cost
of memory usage and load time for large tables.
The fmt argument must be supplied if the table format cannot
be auto-detected.
In general supplying a filename is preferred; the current implementation
may be much more expensive on memory if a python file object is used.
The result of the function is a list of JyStilts table objects.
'''
fact = _StarTableFactory(random)
if hasattr(location, 'read'):
datsrc = _JyDataSource(location)
else:
datsrc = _DataSource.makeDataSource(location)
tseq = fact.makeStarTables(datsrc, fmt)
tables = _Tables.tableArray(tseq)
return map(import_star_table, tables)
def twrite(table, location=None, fmt='(auto)'):
'''Writes table to a file.
The location parameter may give a filename or a
python file object open for writing.
if it is not supplied, standard output is used.
The fmt parameter specifies output format.
Known output formats:
(auto)
jdbc
fits
fits-plus
fits-basic
fits-var
colfits-plus
colfits-basic
votable-tabledata
votable-binary-inline
votable-binary2-inline
votable-fits-href
votable-binary-href
votable-binary2-href
votable-fits-inline
text
ascii
csv
csv-noheader
ipac
tst
html
html-element
latex
latex-document
'''
sto = _StarTableOutput()
if hasattr(location, 'write') and hasattr(location, 'flush'):
ostrm = _JyOutputStream(location)
name = getattr(location, 'name', None)
handler = sto.getHandler(fmt, name)
sto.writeStarTable(table, ostrm, handler)
else:
if location is None:
location = '-'
sto.writeStarTable(table, location, fmt)
def twrites(tables, location=None, fmt='(auto)'):
'''Writes a sequence of tables to a single container file.
The tables parameter gives an iterable over JyStilts table objects
The location parameter may give a filename or a python file object
open for writing. If it is not supplied, standard output is used.
The fmt parameter specifies output format.
Note that not all formats can write multiple tables;
an error will result if an attempt is made to write
multiple tables to a single-table only format.
Known multi-table output formats:
(auto)
fits
fits-plus
fits-basic
fits-var
colfits-plus
colfits-basic
votable-tabledata
votable-binary-inline
votable-binary2-inline
votable-fits-href
votable-binary-href
votable-binary2-href
votable-fits-inline
text
html
html-element
'''
sto = _StarTableOutput()
tseq = _JyTableSequence(tables)
if hasattr(location, 'write') and hasattr(location, 'flush'):
ostrm = _JyOutputStream(location)
name = getattr(location, 'name', None)
handler = sto.getHandler(fmt, name)
_check_multi_handler(handler)
handler.writeStarTables(tseq, ostrm)
else:
if location is None:
location = '-'
handler = sto.getHandler(fmt, location)
_check_multi_handler(handler)
handler.writeStarTables(tseq, location, sto)
def tfilter(table, cmd):
'''Applies a filter operation to a table and returns the result.
In most cases, it's better to use one of the cmd_* functions.
'''
step = _StepFactory.getInstance().createStep(cmd)
return import_star_table(step.wrap(table))
def calc(expression, **kwargs):
'''\
Evaluates expressions.
The return value is the output string.
Parameters:
expression = <expr> (String)
An expression to evaluate. The functions in SUN/256 can be
used.
table = <table> (uk.ac.starlink.table.StarTable)
Input table.
'''
task = _stilts.getTaskFactory().createObject('calc')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment(grab_output=True)
env.setValue('expression', _map_env_value(expression))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
txt = env.getOutputText()
return str(txt.strip())
def cdsskymatch(in_, **kwargs):
'''\
Crossmatches table on sky position against VizieR/SIMBAD table.
The return value is the resulting table.
Parameters:
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
ra = <expr> (String)
Right ascension in degrees in the ICRS coordinate system for
the position of each row of the input table. This may simply
be a column name, or it may be an algebraic expression
calculated from columns as explained in SUN/256. If left
blank, an attempt is made to guess from UCDs, column names and
unit annotations what expression to use.
dec = <expr> (String)
Declination in degrees in the ICRS coordinate system for the
position of each row of the input table. This may simply be a
column name, or it may be an algebraic expression calculated
from columns as explained in SUN/256. If left blank, an
attempt is made to guess from UCDs, column names and unit
annotations what expression to use.
radius = <value/arcsec> (Double)
Maximum distance from the local table (ra,dec) position at
which counterparts from the remote table will be identified.
This is a fixed value given in arcseconds, and must be in the
range [0,180] (this limit is currently enforced by the CDS
Xmatch service).
cdstable = <value> (String)
Identifier of the table from the CDS crossmatch service that
is to be matched against the local table. This identifier may
be the standard VizieR identifier (e.g. "II/246/out" for the
2MASS Point Source Catalogue) or "simbad" to indicate SIMBAD
data.
See for instance the TAPVizieR table searching facility at
http://tapvizier.u-strasbg.fr/adql/ to find VizieR catalogue
identifiers.
find = all|best|best-remote|each|each-dist
(uk.ac.starlink.ttools.task.UserFindMode)
Determines which pair matches are included in the result.
* all: All matches
* best: Matched rows, best remote row for each input row
* best-remote: Matched rows, best input row for each remote
row
* each: One row per input row, contains best remote match or
blank
* each-dist: One row per input row, column giving distance
only for best match
Note only the all mode is symmetric between the two tables.
Note also that there is a bug in best-remote matching. If the
match is done in multiple blocks, it's possible for a remote
table row to appear matched against one local table row per
uploaded block, rather than just once for the whole result. If
you're worried about that, set blocksize >=rowCount. This may
be fixed in a future release.
[Default: all]
blocksize = <int-value> (Integer)
The CDS Xmatch service operates limits on the maximum number
of rows that can be uploaded and the maximum number of rows
that is returned as a result from a single query. In the case
of large input tables, they are broken down into smaller
blocks, and one request is sent to the external service for
each block. This parameter controls the number of rows in each
block. For an input table with fewer rows than this value, the
whole thing is done as a single request.
At time of writing, the maximum upload size is 100Mb (about
3Mrow; this does not depend on the width of your table), and
the maximum return size is 2Mrow.
Large blocksizes tend to be good (up to a point) for reducing
the total amount of time a large xmatch operation takes, but
they can make it harder to see the job progressing. There is
also the danger (for ALL-type find modes) of exceeding the
return size limit, which will result in truncation of the
returned result.
[Default: 50000]
maxrec = <int-value> (Integer)
Limit to the number of rows resulting from this operation. If
the value is negative (the default) no limit is imposed. Note
however that there can be truncation of the result if the
number of records returned from a single chunk exceeds the
service hard limit (2,000,000 at time of writing).
[Default: -1]
compress = true|false (Boolean)
If true, the service is requested to provide HTTP-level
compression for the response stream (Accept-Encoding header is
set to "gzip", see RFC 2616). This does not guarantee that
compression will happen but if the service honours this
request it may result in a smaller amount of network traffic
at the expense of more processing on the server and client.
[Default: true]
serviceurl = <url-value> (java.net.URL)
The URL at which the CDS Xmatch service can be found. Normally
this should not be altered from the default, but if other
implementations of the same service are known, this parameter
can be used to access them.
[Default: http://cdsxmatch.u-strasbg.fr/xmatch/api/v1/sync]
usemoc = true|false (Boolean)
If true, first acquire a MOC coverage map from CDS, and use
that to pre-filter rows before uploading them for matching.
This should improve efficiency, but have no effect on the
result.
[Default: true]
presort = true|false (Boolean)
If true, the rows are sorted by HEALPix index before they are
uploaded to the CDS X-Match service. If the match is done in
multiple blocks, this may improve efficiency, since when
matching against a large remote catalogue the X-Match service
likes to process requests in which sources are grouped into a
small region rather than scattered all over the sky.
Note this will have a couple of other side effects that may be
undesirable: it will read all the input rows into the task at
once, which may make it harder to assess progress, and it will
affect the order of the rows in the output table.
It is probably only worth setting true for rather large
(multi-million-row?) multi-block matches, where both local and
remote catalogues are spread over a significant fraction of
the sky. But feel free to experiment.
[Default: false]
fixcols = none|dups|all
(uk.ac.starlink.ttools.task.JoinFixActionParameter$Fixer)
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.
[Default: dups]
suffixin = <label> (String)
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 the input table.
[Default: _in]
suffixremote = <label> (String)
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 the CDS result table.
[Default: _cds]
'''
task = _stilts.getTaskFactory().createObject('cdsskymatch')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def coneskymatch(in_, **kwargs):
'''\
Crossmatches table on sky position against remote cone service.
The return value is the resulting table.
Parameters:
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
ra = <expr> (String)
Right ascension in degrees in the ICRS coordinate system for
the position of each row of the input table. This may simply
be a column name, or it may be an algebraic expression
calculated from columns as explained in SUN/256. If left
blank, an attempt is made to guess from UCDs, column names and
unit annotations what expression to use.
dec = <expr> (String)
Declination in degrees in the ICRS coordinate system for the
position of each row of the input table. This may simply be a
column name, or it may be an algebraic expression calculated
from columns as explained in SUN/256. If left blank, an
attempt is made to guess from UCDs, column names and unit
annotations what expression to use.
sr = <expr/deg> (String)
Expression which evaluates to the search radius in degrees for
the request at each row of the input table. This will often be
a constant numerical value, but may be the name or ID of a
column in the input table, or a function involving one.
find = best|all|each (String)
Determines which matches are retained.
* best: Only the matching query table row closest to the
input table row will be output. Input table rows with no
matches will be omitted. (Note this corresponds to the
best1 option in the pair matching commands, and best1 is
a permitted alias).
* all: All query table rows which match the input table row
will be output. Input table rows with no matches will be
omitted.
* each: There will be one output table row for each input
table row. If matches are found, the closest one from
the query table will be output, and in the case of no
matches, the query table columns will be blank.
[Default: all]
usefoot = true|false (Boolean)
Determines whether an attempt will be made to restrict
searches in accordance with available footprint information.
If this is set true, then before any of the per-row queries
are performed, an attempt may be made to acquire footprint
information about the servce. If such information can be
obtained, then queries which fall outside the footprint, and
hence which are known to yield no results, are skipped. This
can speed up the search considerably.
Currently, the only footprints available are those provided by
the CDS MOC (Multi-Order Coverage map) service, which covers
VizieR and a few other cone search services.
[Default: true]
footnside = <int-value> (Integer)
Determines the HEALPix Nside parameter for use with the MOC
footprint service. This tuning parameter determines the
resolution of the footprint if available. Larger values give
better resolution, hence a better chance of avoiding
unnecessary queries, but processing them takes longer and
retrieving and storing them is more expensive.
The value must be a power of 2, and at the time of writing,
the MOC service will not supply footprints at resolutions
greater than nside=512, so it should be <=512.
Only used if usefoot=true.
copycols = <colid-list> (String)
List of columns from the input table which are to be copied to
the output table. Each column identified here will be
prepended to the columns of the combined output table, and its
value for each row taken from the input table row which
provided the parameters of the query which produced it. See
SUN/256 for list syntax. The default setting is "*", which
means that all columns from the input table are included in
the output.
[Default: *]
scorecol = <col-name> (String)
Gives the name of a column in the output table to contain the
distance between the requested central position and the actual
position of the returned row. The distance returned is an
angular distance in degrees. If a null value is chosen, no
distance column will appear in the output table.
[Default: Separation]
parallel = <n> (Integer)
Allows multiple cone searches to be performed concurrently. If
set to the default value, 1, the cone query corresponding to
the first row of the input table will be dispatched, when that
is completed the query corresponding to the second row will be
dispatched, and so on. If set to <n>, then queries will be
overlapped in such a way that up to approximately <n> may be
running at any one time.
Whether increasing <n> is a good idea, and what might be a
sensible maximum value, depends on the characteristics of the
service being queried. In particular, setting it to too large
a number may overload the service resulting in some
combination of failed queries, ultimately slower runtimes, and
unpopularity with server admins.
The maximum value permitted for this parameter by default is
10. This limit may be raised by use of the service.maxparallel
system property but use that option with great care since you
may overload services and make yourself unpopular with data
centre admins. As a rule, you should only increase this value
if you have obtained permission from the data centres whose
services on which you will be using the increased parallelism.
[Default: 1]
erract = abort|ignore|retry|retry<n>
(uk.ac.starlink.ttools.cone.ConeErrorPolicy)
Determines what will happen if any of the individual cone
search requests fails. By default the task aborts. That may be
the best thing to do, but for unreliable or poorly implemented
services you may find that some searches fail and others
succeed so it can be best to continue operation in the face of
a few failures. The options are:
* abort: failure of any query terminates the task
* ignore: failure of a query is treated the same as a query
which returns no rows
* retry: failed queries are retried until they succeed; use
with care - if the failure is for some good, or at least
reproducible reason this could prevent the task from
ever completing
* retry<n>: failed queries are retried at most a fixed number
<n> of times If they still fail the task terminates.
[Default: abort]
ostream = true|false (Boolean)
If set true, this will cause the operation to stream on
output, so that the output table is built up as the results
are obtained from the cone search service. The disadvantage of
this is that some output modes and formats need multiple
passes through the data to work, so depending on the output
destination, the operation may fail if this is set. Use with
care (or be prepared for the operation to fail).
[Default: false]
fixcols = none|dups|all
(uk.ac.starlink.ttools.task.JoinFixActionParameter$Fixer)
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.
[Default: dups]
suffix0 = <label> (String)
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 the input table.
[Default: _0]
suffix1 = <label> (String)
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 the cone result table.
[Default: _1]
servicetype = cone|sia|ssa (ServiceType)
Selects the type of data access service to contact. Most
commonly this will be the Cone Search service itself, but
there are one or two other possibilities:
* cone: Cone Search protocol - returns a table of objects
found near each location. See Cone Search standard.
* sia: Simple Image Access protocol - returns a table of
images near each location. See SIA standard.
* ssa: Simple Spectral Access protocol - returns a table of
spectra near each location. See SSA standard.
[Default: cone]
serviceurl = <url-value> (java.net.URL)
The base part of a URL which defines the queries to be made.
Additional parameters will be appended to this using CGI
syntax ("name=value", separated by '&' characters). If this
value does not end in either a '?' or a '&', one will be added
as appropriate.
See SUN/256 for discussion of how to locate service URLs
corresponding to given datasets.
verb = 1|2|3 (String)
Verbosity level of the tables returned by the query service. A
value of 1 indicates the bare minimum and 3 indicates all
available information.
dataformat = <value> (String)
Indicates the format of data objects described in the returned
table. The meaning of this is dependent on the value of the
servicetype parameter:
* servicetype=cone: not used
* servicetype=sia: gives the MIME type of images referenced
in the output table, also special values "GRAPHIC" and "
ALL".(value of the SIA FORMAT parameter)
* servicetype=ssa: gives the MIME type of spectra referenced
in the output table, also special values "votable", "
fits", "compliant", "graphic", "all", and others (value
of the SSA FORMAT parameter).
emptyok = true|false (Boolean)
Whether the table metadata which is returned from a search
result with zero rows is to be believed. According to the
spirit, though not the letter, of the cone search standard, a
cone search service which returns no data ought nevertheless
to return the correct column headings. Unfortunately this is
not always the case. If this parameter is set true, it is
assumed that the service behaves properly in this respect; if
it does not an error may result. In that case, set this
parameter false. A consequence of setting it false is that in
the event of no results being returned, the task will return
no table at all, rather than an empty one.
[Default: true]
compress = true|false (Boolean)
If true, the service is requested to provide HTTP-level
compression for the response stream (Accept-Encoding header is
set to "gzip", see RFC 2616). This does not guarantee that
compression will happen but if the service honours this
request it may result in a smaller amount of network traffic
at the expense of more processing on the server and client.
[Default: true]
'''
task = _stilts.getTaskFactory().createObject('coneskymatch')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def funcs(**kwargs):
'''\
Browses functions used by algebraic expression language.
'''
task = _stilts.getTaskFactory().createObject('funcs')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def pixfoot(in_, **kwargs):
'''\
Generates Multi-Order Coverage maps.
Parameters:
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
order = <int-value> (Integer)
Maximum HEALPix order for the MOC. This defines the maximum
resolution of the output coverage map. The angular resolution
corresponding to order k is approximately 180/sqrt(3.Pi)/2^k
(3520*2^-k arcmin).
[Default: 13]
ra = <expr> (String)
Right ascension in degrees for the position of each row of the
input table. This may simply be a column name, or it may be an
algebraic expression calculated from columns as explained in
SUN/256. If left blank, an attempt is made to guess from UCDs,
column names and unit annotations what expression to use.
dec = <expr> (String)
Declination in degrees for the position of each row of the
input table. This may simply be a column name, or it may be an
algebraic expression calculated from columns as explained in
SUN/256. If left blank, an attempt is made to guess from UCDs,
column names and unit annotations what expression to use.
radius = <expr> (String)
Expression which evaluates to the radius in degrees of the
cone at each row of the input table. The default is "0", which
treats each position as a point rather than a cone, but a
constant or an expression as described in SUN/256 may be used
instead.
[Default: 0]
mocfmt = fits|json (uk.ac.starlink.ttools.cone.MocFormat)
Determines the output format for the MOC file.
[Default: fits]
out = <out-file> (uk.ac.starlink.util.Destination)
The location of the output file. This is usually a filename to
write to. If it is equal to the special value "-" the output
will be written to standard output.
[Default: -]
'''
task = _stilts.getTaskFactory().createObject('pixfoot')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def pixsample(in_, **kwargs):
'''\
Samples from a HEALPix pixel data file.
The return value is the resulting table.
Parameters:
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
pixdata = <pix-table> (uk.ac.starlink.table.StarTable)
Input table.
pixorder = nested|ring|(auto) (HealpixScheme)
Selects the pixel ordering scheme used by the pixel data file.
There are two different ways of ordering pixels in a HEALPix
file, "ring" and "nested", and the sampler needs to know which
one is in use. If you know which is in use, choose the
appropriate value for this parameter; if (auto) is used it
will attempt to work it out from headers in the file (the
ORDERING header). If no reliable ordering scheme can be
determined, the command will fail with an error.
[Default: (auto)]
stat = point|mean
(uk.ac.starlink.ttools.task.PixSampler$StatMode)
Determines how the pixel values will be sampled to generate an
output value. The options are:
* point: Uses the value at the pixel covering the supplied
position. In this case the radius parameter is not used.
* mean: Averages the values over all the pixels within a
radius given by the radius parameter. This averaging is
somewhat approximate; all pixels which are mostly within
the radius are averaged with equal weights.
[Default: point]
lon = <expr> (String)
Expression which evaluates to the longitude coordinate in
degrees in the input table at which positions are to be
sampled from the pixel data table. This will usually be the
name or ID of a column in the input table, or an expression
involving one. If this coordinate does not match the
coordinate system used by the pixel data table, both
coordinate systems must be set using the insys and pixsys
parameters.
lat = <expr> (String)
Expression which evaluates to the latitude coordinate in
degrees in the input table at which positions are to be
sampled from the pixel data table. This will usually be the
name or ID of a column in the input table, or an expression
involving one. If this coordinate does not match the
coordinate system used by the pixel data table, both
coordinate systems must be set using the insys and pixsys
parameters.
insys = icrs|fk5|fk4|galactic|supergalactic|ecliptic
(uk.ac.starlink.ttools.convert.SkySystem)
Specifies the sky coordinate system in which sample positions
are provided by the lon/lat parameters. If the sample
positions are given in the same coordinate system as that
given by the pixel data table, both the insys and pixsys
parameters may be set null.
The available coordinate systems are:
* icrs: ICRS (Hipparcos) (Right Ascension, Declination)
* fk5: FK5 J2000.0 (Right Ascension, Declination)
* fk4: FK4 B1950.0 (Right Ascension, Declination)
* galactic: IAU 1958 Galactic (Longitude, Latitude)
* supergalactic: de Vaucouleurs Supergalactic (Longitude,
Latitude)
* ecliptic: Ecliptic (Longitude, Latitude)
pixsys = icrs|fk5|fk4|galactic|supergalactic|ecliptic
(uk.ac.starlink.ttools.convert.SkySystem)
Specifies the sky coordinate system used for the HEALPix data
in the pixdata file. If the sample positions are given in the
same coordinate system as that given by the pixel data table,
both the insys and pixsys parameters may be set null.
The available coordinate systems are:
* icrs: ICRS (Hipparcos) (Right Ascension, Declination)
* fk5: FK5 J2000.0 (Right Ascension, Declination)
* fk4: FK4 B1950.0 (Right Ascension, Declination)
* galactic: IAU 1958 Galactic (Longitude, Latitude)
* supergalactic: de Vaucouleurs Supergalactic (Longitude,
Latitude)
* ecliptic: Ecliptic (Longitude, Latitude)
radius = <expr> (String)
Determines the radius in degrees over which pixels will be
sampled to generate the output statistic in accordance with
the value of the stat parameter. This will typically be a
constant value, but it may be an algebraic expression based on
columns from the input table.
Not used if stat=point.
'''
task = _stilts.getTaskFactory().createObject('pixsample')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def plot2d(**kwargs):
'''\
Old-style 2D Scatter Plot.
Parameters:
xpix = <int-value> (Integer)
The width of the output graphic in pixels.
[Default: 400]
ypix = <int-value> (Integer)
The height of the output graphic in pixels.
[Default: 300]
font = dialog|serif|... (String)
Determines the font that will be used for textual annotation
of the plot, including axes etc. At least the following fonts
will be available:
* serif
* sansserif
* monospaced
* dialog
* dialoginput
as well as a range of system-dependent fonts, possibly
including
* dejavu_sans
* dejavu_sans_mono
* dejavu_serif
[Default: dialog]
fontsize = <int-value> (Integer)
Sets the font size used for plot annotations.
[Default: 12]
fontstyle = plain|bold|italic|bold-italic (Integer)
Gives a style in which the font is to be applied for plot
annotations. Options are plain, bold, italic and bold-italic.
[Default: plain]
legend = true|false (Boolean)
Determines whether a legend showing which plotting style is
used for each data set. Defaults to true if there is more than
one set, false otherwise.
title = <value> (String)
A one-line title to display at the top of the plot.
omode = swing|out|cgi|discard|auto
(uk.ac.starlink.ttools.plottask.PaintMode)
Determines how the drawn plot will be output, see SUN/256.
* swing: Plot will be displayed in a window on the screen.
This plot is "live"; it can be resized and (except for
old-style plots) navigated around with mouse actions in
the same way as plots in TOPCAT.
* out: Plot will be written to a file given by out using the
graphics format given by ofmt.
* cgi: Plot will be written in a way suitable for CGI use
direct from a web server. The output is in the graphics
format given by ofmt, preceded by a suitable
"Content-type" declaration.
* discard: Plot is drawn, but discarded. There is no output.
* auto: Behaves as swing or out mode depending on presence of
out parameter
[Default: auto]
out = <out-file> (uk.ac.starlink.util.Destination)
The location of the output file. This is usually a filename to
write to. If it is equal to the special value "-" the output
will be written to standard output.
ofmt = png|png-transp|gif|jpeg|pdf|eps|eps-gzip
(uk.ac.starlink.ttools.plot.GraphicExporter)
Graphics format in which the plot is written to the output
file, see SUN/256. One of:
* png: PNG
* png-transp: PNG with transparent background
* gif: GIF
* jpeg: JPEG
* pdf: Portable Document Format
* eps: Encapsulated PostScript
* eps-gzip: Gzipped Encapsulated PostScript
May default to a sensible value depending on the filename
given by out.
inN = <table> (uk.ac.starlink.table.StarTable)
Input table.
xdataN = <expr> (String)
Gives a column name or expression for the x axis data for
table N. The expression is a numeric algebraic expression
based on column names as described in SUN/256
ydataN = <expr> (String)
Gives a column name or expression for the y axis data for
table N. The expression is a numeric algebraic expression
based on column names as described in SUN/256
auxdataN = <expr> (String)
Gives a column name or expression for the aux axis data for
table N. The expression is a numeric algebraic expression
based on column names as described in SUN/256
xlo = <float-value> (Double)
The lower limit for the plotted x axis. If not set, a value
will be chosen which is low enough to accommodate all the
data.
ylo = <float-value> (Double)
The lower limit for the plotted y axis. If not set, a value
will be chosen which is low enough to accommodate all the
data.
auxlo = <float-value> (Double)
The lower limit for the plotted aux axis. If not set, a value
will be chosen which is low enough to accommodate all the
data.
xhi = <float-value> (Double)
The upper limit for the plotted x axis. If not set, a value
will be chosen which is high enough to accommodate all the
data.
yhi = <float-value> (Double)
The upper limit for the plotted y axis. If not set, a value
will be chosen which is high enough to accommodate all the
data.
auxhi = <float-value> (Double)
The upper limit for the plotted aux axis. If not set, a value
will be chosen which is high enough to accommodate all the
data.
xlog = true|false (Boolean)
If false (the default), the scale on the x axis is linear; if
true it is logarithmic.
[Default: false]
ylog = true|false (Boolean)
If false (the default), the scale on the y axis is linear; if
true it is logarithmic.
[Default: false]
auxlog = true|false (Boolean)
If false (the default), the scale on the aux axis is linear;
if true it is logarithmic.
[Default: false]
xflip = true|false (Boolean)
If set true, the scale on the x axis will increase in the
opposite sense from usual (e.g. right to left rather than left
to right).
[Default: false]
yflip = true|false (Boolean)
If set true, the scale on the y axis will increase in the
opposite sense from usual (e.g. right to left rather than left
to right).
[Default: false]
auxflip = true|false (Boolean)
If set true, the scale on the aux axis will increase in the
opposite sense from usual (e.g. right to left rather than left
to right).
[Default: false]
xlabel = <value> (String)
Specifies a label to be used for annotating axis x. A default
values based on the plotted data will be used if no value is
supplied for this parameter.
ylabel = <value> (String)
Specifies a label to be used for annotating axis y. A default
values based on the plotted data will be used if no value is
supplied for this parameter.
auxlabel = <value> (String)
Specifies a label to be used for annotating axis aux. A
default values based on the plotted data will be used if no
value is supplied for this parameter.
xerrorN = <expr>|[<lo-expr>],[<hi-expr>] (String)
Gives expressions for the errors on X coordinates for table N.
The following forms are permitted:
* <expr>: symmetric error value
* <lo-expr>,<hi-expr>:distinct lower and upper error values
* <lo-expr>,: lower error value only
* ,<hi-expr>: upper error value only
* null: no errors
The expression in each case is a numeric algebraic expression
based on column names as described in SUN/256.
yerrorN = <expr>|[<lo-expr>],[<hi-expr>] (String)
Gives expressions for the errors on Y coordinates for table N.
The following forms are permitted:
* <expr>: symmetric error value
* <lo-expr>,<hi-expr>:distinct lower and upper error values
* <lo-expr>,: lower error value only
* ,<hi-expr>: upper error value only
* null: no errors
The expression in each case is a numeric algebraic expression
based on column names as described in SUN/256.
auxshader = rainbow|pastel|...
(uk.ac.starlink.ttools.plot.Shader)
Determines how data from auxiliary axes will be displayed.
Generally this is some kind of colour ramp. These are the
available colour fixing options:
* rainbow
* pastel
* standard
* heat
* colour
* hue
* greyscale
* red-blue
and these are the available colour modifying options:
* hsv_h
* hsv_s
* hsv_v
* intensity
* rgb_red
* rgb_green
* rgb_blue
* yuv_y
* yuv_u
* yuv_v
* transparency
[Default: rainbow]
txtlabelN = <value> (String)
Gives an expression which will label each plotted point. If
given, the text (or number) resulting from evaluating the
expression will be written near each point which is plotted.
subsetNS = <expr> (String)
Gives the selection criterion for the subset labelled "NS".
This is a boolean expression which may be the name of a
boolean-valued column or any other boolean-valued expression.
Rows for which the expression evaluates true will be included
in the subset, and those for which it evaluates false will
not.
nameNS = <value> (String)
Provides a name to use for a subset with the symbolic label
NS. This name will be used for display in the legend, if one
is displayed.
colourNS = <rrggbb>|red|blue|... (java.awt.Color)
Defines the colour of markers plotted. The value may be a
6-digit hexadecimal number giving red, green and blue
intensities, e.g. "ff00ff" for magenta. Alternatively it may
be the name of one of the pre-defined colours. These are
currently red, blue, green, grey, magenta, cyan, orange, pink,
yellow, black and white.
For most purposes, either the American or the British spelling
is accepted for this parameter name.
shapeNS = filled_circle|open_circle|...
(uk.ac.starlink.ttools.plot.MarkShape)
Defines the shapes for the markers that are plotted in data
set NS. The following shapes are available:
* filled_circle
* open_circle
* cross
* x
* open_square
* open_diamond
* open_triangle_up
* open_triangle_down
* filled_square
* filled_diamond
* filled_triangle_up
* filled_triangle_down
sizeNS = <int-value> (Integer)
Defines the marker size in pixels for markers plotted in data
set NS. If the value is negative, an attempt will be made to
use a suitable size according to how many points there are to
be plotted.
[Default: -1]
transparencyNS = <int-value> (Integer)
Determines the transparency of plotted markers for data set
NS. A value of <n> means that opacity is only achieved (the
background is only blotted out) when <n> pixels of this colour
have been plotted on top of each other.
The minimum value is 1, which means opaque markers.
lineNS = DotToDot|LinearRegression
(uk.ac.starlink.ttools.plot.MarkStyle$Line)
Determines what line if any will be plotted along with the
data points. The options are:
* null: No line is plotted.
* DotToDot: Each point is joined to the next one in sequence
by a straight line.
* LinearRegression: A linear regression line is plotted based
on all the points which are visible in the plot. Note
that the regression coefficients take no account of
points out of the visible range.
linewidthNS = <int-value> (Integer)
Sets the line width in pixels for any lines drawn in data set
NS.
Only has an effect if the lineNS parameter is set to draw
lines.
[Default: 1]
dashNS = dot|dash|...|<a,b,...> (float[])
Defines the dash style for any lines drawn in data set NS To
generate a dashed line the value may be one of the named dash
types:
* dot
* dash
* longdash
* dotdash
or may be a comma-separated string of on/off length values
such as "4,2,8,2". A null value indicates a solid line.
Only has an effect if the lineNS parameter is set to draw
lines.
hideNS = true|false (Boolean)
Indicates whether the actual markers plotted for each point
should be hidden. Normally this is false, but you may want to
set it to true if the point positions are being revealed in
some other way, for instance by error markers or lines drawn
between them.
[Default: false]
errstyleNS = lines|capped_lines|...
(uk.ac.starlink.ttools.plot.ErrorRenderer)
Defines the way in which error bars (or ellipses, or...) will
be represented for data set NS if errors are being displayed.
The following options are available:
* none
* lines
* capped_lines
* caps
* arrows
* ellipse
* crosshair_ellipse
* rectangle
* crosshair_rectangle
* filled_ellipse
* filled_rectangle
[Default: lines]
grid = true|false (Boolean)
If true, grid lines are drawn on the plot. If false, they are
absent.
[Default: true]
antialias = true|false (Boolean)
Controls whether lines are drawn using antialiasing, where
applicable. If lines are drawn to a bitmapped-type graphics
output format setting this parameter to true smooths the lines
out by using gradations of colour for diagonal lines, and
setting it false simply sets each pixel in the line to on or
off. For vector-type graphics output formats, or for cases in
which no diagonal lines are drawn, the setting of this
parameter has no effect. Setting it true may slow the plot
down slightly.
[Default: true]
sequence = <suffix>,<suffix>,... (String[])
Can be used to control the sequence in which different
datasets and subsets are plotted. This will affect which
symbols are plotted on top of, and so potentially obscure,
which other ones. The value of this parameter is a
comma-separated list of the "NS" suffixes which appear on the
parameters which apply to subsets. The sets which are named
will be plotted in order, so the first-named one will be at
the bottom (most likely to be obscured). Note that if this
parameter is supplied, then only those sets which are named
will be plotted, so this parameter may also be used to
restrict which plots appear (though it may not be the most
efficient way of doing this). If no explicit value is supplied
for this parameter, sets will be plotted in some sequence
decided by STILTS (probably alphabetic by suffix).
'''
task = _stilts.getTaskFactory().createObject('plot2d')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def plot3d(**kwargs):
'''\
Old-style 3D Scatter Plot.
Parameters:
xpix = <int-value> (Integer)
The width of the output graphic in pixels.
[Default: 300]
ypix = <int-value> (Integer)
The height of the output graphic in pixels.
[Default: 300]
font = dialog|serif|... (String)
Determines the font that will be used for textual annotation
of the plot, including axes etc. At least the following fonts
will be available:
* serif
* sansserif
* monospaced
* dialog
* dialoginput
as well as a range of system-dependent fonts, possibly
including
* dejavu_sans
* dejavu_sans_mono
* dejavu_serif
[Default: dialog]
fontsize = <int-value> (Integer)
Sets the font size used for plot annotations.
[Default: 12]
fontstyle = plain|bold|italic|bold-italic (Integer)
Gives a style in which the font is to be applied for plot
annotations. Options are plain, bold, italic and bold-italic.
[Default: plain]
legend = true|false (Boolean)
Determines whether a legend showing which plotting style is
used for each data set. Defaults to true if there is more than
one set, false otherwise.
title = <value> (String)
A one-line title to display at the top of the plot.
omode = swing|out|cgi|discard|auto
(uk.ac.starlink.ttools.plottask.PaintMode)
Determines how the drawn plot will be output, see SUN/256.
* swing: Plot will be displayed in a window on the screen.
This plot is "live"; it can be resized and (except for
old-style plots) navigated around with mouse actions in
the same way as plots in TOPCAT.
* out: Plot will be written to a file given by out using the
graphics format given by ofmt.
* cgi: Plot will be written in a way suitable for CGI use
direct from a web server. The output is in the graphics
format given by ofmt, preceded by a suitable
"Content-type" declaration.
* discard: Plot is drawn, but discarded. There is no output.
* auto: Behaves as swing or out mode depending on presence of
out parameter
[Default: auto]
out = <out-file> (uk.ac.starlink.util.Destination)
The location of the output file. This is usually a filename to
write to. If it is equal to the special value "-" the output
will be written to standard output.
ofmt = png|png-transp|gif|jpeg|pdf|eps|eps-gzip
(uk.ac.starlink.ttools.plot.GraphicExporter)
Graphics format in which the plot is written to the output
file, see SUN/256. One of:
* png: PNG
* png-transp: PNG with transparent background
* gif: GIF
* jpeg: JPEG
* pdf: Portable Document Format
* eps: Encapsulated PostScript
* eps-gzip: Gzipped Encapsulated PostScript
May default to a sensible value depending on the filename
given by out.
inN = <table> (uk.ac.starlink.table.StarTable)
Input table.
xdataN = <expr> (String)
Gives a column name or expression for the x axis data for
table N. The expression is a numeric algebraic expression
based on column names as described in SUN/256
ydataN = <expr> (String)
Gives a column name or expression for the y axis data for
table N. The expression is a numeric algebraic expression
based on column names as described in SUN/256
zdataN = <expr> (String)
Gives a column name or expression for the z axis data for
table N. The expression is a numeric algebraic expression
based on column names as described in SUN/256
auxdataN = <expr> (String)
Gives a column name or expression for the aux axis data for
table N. The expression is a numeric algebraic expression
based on column names as described in SUN/256
xlo = <float-value> (Double)
The lower limit for the plotted x axis. If not set, a value
will be chosen which is low enough to accommodate all the
data.
ylo = <float-value> (Double)
The lower limit for the plotted y axis. If not set, a value
will be chosen which is low enough to accommodate all the
data.
zlo = <float-value> (Double)
The lower limit for the plotted z axis. If not set, a value
will be chosen which is low enough to accommodate all the
data.
auxlo = <float-value> (Double)
The lower limit for the plotted aux axis. If not set, a value
will be chosen which is low enough to accommodate all the
data.
xhi = <float-value> (Double)
The upper limit for the plotted x axis. If not set, a value
will be chosen which is high enough to accommodate all the
data.
yhi = <float-value> (Double)
The upper limit for the plotted y axis. If not set, a value
will be chosen which is high enough to accommodate all the
data.
zhi = <float-value> (Double)
The upper limit for the plotted z axis. If not set, a value
will be chosen which is high enough to accommodate all the
data.
auxhi = <float-value> (Double)
The upper limit for the plotted aux axis. If not set, a value
will be chosen which is high enough to accommodate all the
data.
xlog = true|false (Boolean)
If false (the default), the scale on the x axis is linear; if
true it is logarithmic.
[Default: false]
ylog = true|false (Boolean)
If false (the default), the scale on the y axis is linear; if
true it is logarithmic.
[Default: false]
zlog = true|false (Boolean)
If false (the default), the scale on the z axis is linear; if
true it is logarithmic.
[Default: false]
auxlog = true|false (Boolean)
If false (the default), the scale on the aux axis is linear;
if true it is logarithmic.
[Default: false]
xflip = true|false (Boolean)
If set true, the scale on the x axis will increase in the
opposite sense from usual (e.g. right to left rather than left
to right).
[Default: false]
yflip = true|false (Boolean)
If set true, the scale on the y axis will increase in the
opposite sense from usual (e.g. right to left rather than left
to right).
[Default: false]
zflip = true|false (Boolean)
If set true, the scale on the z axis will increase in the
opposite sense from usual (e.g. right to left rather than left
to right).
[Default: false]
auxflip = true|false (Boolean)
If set true, the scale on the aux axis will increase in the
opposite sense from usual (e.g. right to left rather than left
to right).
[Default: false]
xlabel = <value> (String)
Specifies a label to be used for annotating axis x. A default
values based on the plotted data will be used if no value is
supplied for this parameter.
ylabel = <value> (String)
Specifies a label to be used for annotating axis y. A default
values based on the plotted data will be used if no value is
supplied for this parameter.
zlabel = <value> (String)
Specifies a label to be used for annotating axis z. A default
values based on the plotted data will be used if no value is
supplied for this parameter.
auxlabel = <value> (String)
Specifies a label to be used for annotating axis aux. A
default values based on the plotted data will be used if no
value is supplied for this parameter.
xerrorN = <expr>|[<lo-expr>],[<hi-expr>] (String)
Gives expressions for the errors on X coordinates for table N.
The following forms are permitted:
* <expr>: symmetric error value
* <lo-expr>,<hi-expr>:distinct lower and upper error values
* <lo-expr>,: lower error value only
* ,<hi-expr>: upper error value only
* null: no errors
The expression in each case is a numeric algebraic expression
based on column names as described in SUN/256.
yerrorN = <expr>|[<lo-expr>],[<hi-expr>] (String)
Gives expressions for the errors on Y coordinates for table N.
The following forms are permitted:
* <expr>: symmetric error value
* <lo-expr>,<hi-expr>:distinct lower and upper error values
* <lo-expr>,: lower error value only
* ,<hi-expr>: upper error value only
* null: no errors
The expression in each case is a numeric algebraic expression
based on column names as described in SUN/256.
zerrorN = <expr>|[<lo-expr>],[<hi-expr>] (String)
Gives expressions for the errors on Z coordinates for table N.
The following forms are permitted:
* <expr>: symmetric error value
* <lo-expr>,<hi-expr>:distinct lower and upper error values
* <lo-expr>,: lower error value only
* ,<hi-expr>: upper error value only
* null: no errors
The expression in each case is a numeric algebraic expression
based on column names as described in SUN/256.
auxshader = rainbow|pastel|...
(uk.ac.starlink.ttools.plot.Shader)
Determines how data from auxiliary axes will be displayed.
Generally this is some kind of colour ramp. These are the
available colour fixing options:
* rainbow
* pastel
* standard
* heat
* colour
* hue
* greyscale
* red-blue
and these are the available colour modifying options:
* hsv_h
* hsv_s
* hsv_v
* intensity
* rgb_red
* rgb_green
* rgb_blue
* yuv_y
* yuv_u
* yuv_v
* transparency
[Default: rainbow]
txtlabelN = <value> (String)
Gives an expression which will label each plotted point. If
given, the text (or number) resulting from evaluating the
expression will be written near each point which is plotted.
subsetNS = <expr> (String)
Gives the selection criterion for the subset labelled "NS".
This is a boolean expression which may be the name of a
boolean-valued column or any other boolean-valued expression.
Rows for which the expression evaluates true will be included
in the subset, and those for which it evaluates false will
not.
nameNS = <value> (String)
Provides a name to use for a subset with the symbolic label
NS. This name will be used for display in the legend, if one
is displayed.
colourNS = <rrggbb>|red|blue|... (java.awt.Color)
Defines the colour of markers plotted. The value may be a
6-digit hexadecimal number giving red, green and blue
intensities, e.g. "ff00ff" for magenta. Alternatively it may
be the name of one of the pre-defined colours. These are
currently red, blue, green, grey, magenta, cyan, orange, pink,
yellow, black and white.
For most purposes, either the American or the British spelling
is accepted for this parameter name.
shapeNS = filled_circle|open_circle|...
(uk.ac.starlink.ttools.plot.MarkShape)
Defines the shapes for the markers that are plotted in data
set NS. The following shapes are available:
* filled_circle
* open_circle
* cross
* x
* open_square
* open_diamond
* open_triangle_up
* open_triangle_down
* filled_square
* filled_diamond
* filled_triangle_up
* filled_triangle_down
sizeNS = <int-value> (Integer)
Defines the marker size in pixels for markers plotted in data
set NS. If the value is negative, an attempt will be made to
use a suitable size according to how many points there are to
be plotted.
[Default: -1]
transparencyNS = <int-value> (Integer)
Determines the transparency of plotted markers for data set
NS. A value of <n> means that opacity is only achieved (the
background is only blotted out) when <n> pixels of this colour
have been plotted on top of each other.
The minimum value is 1, which means opaque markers.
lineNS = DotToDot|LinearRegression
(uk.ac.starlink.ttools.plot.MarkStyle$Line)
Determines what line if any will be plotted along with the
data points. The options are:
* null: No line is plotted.
* DotToDot: Each point is joined to the next one in sequence
by a straight line.
* LinearRegression: A linear regression line is plotted based
on all the points which are visible in the plot. Note
that the regression coefficients take no account of
points out of the visible range.
linewidthNS = <int-value> (Integer)
Sets the line width in pixels for any lines drawn in data set
NS.
Only has an effect if the lineNS parameter is set to draw
lines.
[Default: 1]
dashNS = dot|dash|...|<a,b,...> (float[])
Defines the dash style for any lines drawn in data set NS To
generate a dashed line the value may be one of the named dash
types:
* dot
* dash
* longdash
* dotdash
or may be a comma-separated string of on/off length values
such as "4,2,8,2". A null value indicates a solid line.
Only has an effect if the lineNS parameter is set to draw
lines.
hideNS = true|false (Boolean)
Indicates whether the actual markers plotted for each point
should be hidden. Normally this is false, but you may want to
set it to true if the point positions are being revealed in
some other way, for instance by error markers or lines drawn
between them.
[Default: false]
errstyleNS = lines|capped_lines|...
(uk.ac.starlink.ttools.plot.ErrorRenderer)
Defines the way in which error bars (or ellipses, or...) will
be represented for data set NS if errors are being displayed.
The following options are available:
* none
* lines
* capped_lines
* caps
* arrows
* cuboid
* ellipse
* crosshair_ellipse
* rectangle
* crosshair_rectangle
* filled_ellipse
* filled_rectangle
[Default: lines]
grid = true|false (Boolean)
If true, grid lines are drawn on the plot. If false, they are
absent.
[Default: true]
antialias = true|false (Boolean)
Controls whether lines are drawn using antialiasing, where
applicable. If lines are drawn to a bitmapped-type graphics
output format setting this parameter to true smooths the lines
out by using gradations of colour for diagonal lines, and
setting it false simply sets each pixel in the line to on or
off. For vector-type graphics output formats, or for cases in
which no diagonal lines are drawn, the setting of this
parameter has no effect. Setting it true may slow the plot
down slightly.
[Default: true]
sequence = <suffix>,<suffix>,... (String[])
Can be used to control the sequence in which different
datasets and subsets are plotted. This will affect which
symbols are plotted on top of, and so potentially obscure,
which other ones. The value of this parameter is a
comma-separated list of the "NS" suffixes which appear on the
parameters which apply to subsets. The sets which are named
will be plotted in order, so the first-named one will be at
the bottom (most likely to be obscured). Note that if this
parameter is supplied, then only those sets which are named
will be plotted, so this parameter may also be used to
restrict which plots appear (though it may not be the most
efficient way of doing this). If no explicit value is supplied
for this parameter, sets will be plotted in some sequence
decided by STILTS (probably alphabetic by suffix).
fog = <float-value> (Double)
Sets the level of fogging used to provide a visual indication
of depth. Object plotted further away from the viewer appear
more washed-out by a white fog. The default value gives a bit
of fogging; increase it to make the fog thicker, or set to
zero if no fogging is required.
[Default: 1.0]
phi = <float-value> (Double)
Angle in degrees through which the 3D plot is rotated abound
the Z axis prior to drawing.
[Default: 30.0]
theta = <float-value> (Double)
Angle in degrees through which the 3D plot is rotated towards
the viewer (i.e. about the horizontal axis of the viewing
plane) prior to drawing.
[Default: 15.0]
'''
task = _stilts.getTaskFactory().createObject('plot3d')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def plothist(**kwargs):
'''\
Old-style Histogram.
Parameters:
xpix = <int-value> (Integer)
The width of the output graphic in pixels.
[Default: 400]
ypix = <int-value> (Integer)
The height of the output graphic in pixels.
[Default: 300]
font = dialog|serif|... (String)
Determines the font that will be used for textual annotation
of the plot, including axes etc. At least the following fonts
will be available:
* serif
* sansserif
* monospaced
* dialog
* dialoginput
as well as a range of system-dependent fonts, possibly
including
* dejavu_sans
* dejavu_sans_mono
* dejavu_serif
[Default: dialog]
fontsize = <int-value> (Integer)
Sets the font size used for plot annotations.
[Default: 12]
fontstyle = plain|bold|italic|bold-italic (Integer)
Gives a style in which the font is to be applied for plot
annotations. Options are plain, bold, italic and bold-italic.
[Default: plain]
legend = true|false (Boolean)
Determines whether a legend showing which plotting style is
used for each data set. Defaults to true if there is more than
one set, false otherwise.
title = <value> (String)
A one-line title to display at the top of the plot.
omode = swing|out|cgi|discard|auto
(uk.ac.starlink.ttools.plottask.PaintMode)
Determines how the drawn plot will be output, see SUN/256.
* swing: Plot will be displayed in a window on the screen.
This plot is "live"; it can be resized and (except for
old-style plots) navigated around with mouse actions in
the same way as plots in TOPCAT.
* out: Plot will be written to a file given by out using the
graphics format given by ofmt.
* cgi: Plot will be written in a way suitable for CGI use
direct from a web server. The output is in the graphics
format given by ofmt, preceded by a suitable
"Content-type" declaration.
* discard: Plot is drawn, but discarded. There is no output.
* auto: Behaves as swing or out mode depending on presence of
out parameter
[Default: auto]
out = <out-file> (uk.ac.starlink.util.Destination)
The location of the output file. This is usually a filename to
write to. If it is equal to the special value "-" the output
will be written to standard output.
ofmt = png|png-transp|gif|jpeg|pdf|eps|eps-gzip
(uk.ac.starlink.ttools.plot.GraphicExporter)
Graphics format in which the plot is written to the output
file, see SUN/256. One of:
* png: PNG
* png-transp: PNG with transparent background
* gif: GIF
* jpeg: JPEG
* pdf: Portable Document Format
* eps: Encapsulated PostScript
* eps-gzip: Gzipped Encapsulated PostScript
May default to a sensible value depending on the filename
given by out.
inN = <table> (uk.ac.starlink.table.StarTable)
Input table.
xdataN = <expr> (String)
Gives a column name or expression for the x axis data for
table N. The expression is a numeric algebraic expression
based on column names as described in SUN/256
xlo = <float-value> (Double)
The lower limit for the plotted x axis. If not set, a value
will be chosen which is low enough to accommodate all the
data.
xhi = <float-value> (Double)
The upper limit for the plotted x axis. If not set, a value
will be chosen which is high enough to accommodate all the
data.
xlog = true|false (Boolean)
If false (the default), the scale on the x axis is linear; if
true it is logarithmic.
[Default: false]
xflip = true|false (Boolean)
If set true, the scale on the x axis will increase in the
opposite sense from usual (e.g. right to left rather than left
to right).
[Default: false]
xlabel = <value> (String)
Specifies a label to be used for annotating axis x. A default
values based on the plotted data will be used if no value is
supplied for this parameter.
subsetNS = <expr> (String)
Gives the selection criterion for the subset labelled "NS".
This is a boolean expression which may be the name of a
boolean-valued column or any other boolean-valued expression.
Rows for which the expression evaluates true will be included
in the subset, and those for which it evaluates false will
not.
nameNS = <value> (String)
Provides a name to use for a subset with the symbolic label
NS. This name will be used for display in the legend, if one
is displayed.
colourNS = <rrggbb>|red|blue|... (java.awt.Color)
Defines the colour of bars plotted for data set NS. The value
may be a 6-digit hexadecimal number giving red, green and blue
intensities, e.g. "ff00ff" for magenta. Alternatively it may
be the name of one of the pre-defined colours. These are
currently red, blue, green, grey, magenta, cyan, orange, pink,
yellow, black and white.
For most purposes, either the American or the British spelling
is accepted for this parameter name.
barstyleNS = fill|open|... (BarShape)
Defines how histogram bars will be drawn for dataset NS. The
options are:
* fill
* open
* tops
* semi
* semitops
* spikes
* fillover
* openover
[Default: fill]
linewidthNS = <int-value> (Integer)
Defines the line width for lines drawn as part of the bars for
dataset NS. Only certain bar styles are affected by the line
width.
[Default: 2]
dashNS = dot|dash|...|<a,b,...> (float[])
Defines the dashing pattern for lines drawn for dataset NS. To
generate a dashed line the value may be one of the named dash
types:
* dot
* dash
* longdash
* dotdash
or may be a comma-separated string of on/off length values
such as "4,2,8,2". A null value indicates a solid line. Only
certain bar styles are affected by the dash pattern.
grid = true|false (Boolean)
If true, grid lines are drawn on the plot. If false, they are
absent.
[Default: true]
antialias = true|false (Boolean)
Controls whether lines are drawn using antialiasing, where
applicable. If lines are drawn to a bitmapped-type graphics
output format setting this parameter to true smooths the lines
out by using gradations of colour for diagonal lines, and
setting it false simply sets each pixel in the line to on or
off. For vector-type graphics output formats, or for cases in
which no diagonal lines are drawn, the setting of this
parameter has no effect. Setting it true may slow the plot
down slightly.
[Default: true]
sequence = <suffix>,<suffix>,... (String[])
Can be used to control the sequence in which different
datasets and subsets are plotted. This will affect which
symbols are plotted on top of, and so potentially obscure,
which other ones. The value of this parameter is a
comma-separated list of the "NS" suffixes which appear on the
parameters which apply to subsets. The sets which are named
will be plotted in order, so the first-named one will be at
the bottom (most likely to be obscured). Note that if this
parameter is supplied, then only those sets which are named
will be plotted, so this parameter may also be used to
restrict which plots appear (though it may not be the most
efficient way of doing this). If no explicit value is supplied
for this parameter, sets will be plotted in some sequence
decided by STILTS (probably alphabetic by suffix).
ylo = <float-value> (Double)
Lower bound for Y axis.
[Default: 0.0]
yhi = <float-value> (Double)
Upper bound for Y axis. Autogenerated from the data if not
supplied.
ylog = true|false (Boolean)
Whether to use a logarithmic scale for the Y axis.
[Default: false]
ylabel = <value> (String)
Specifies a label for annotating the vertical axis. A default
value based on the type of histogram will be used if no value
is supplied for this parameter.
[Default: Count]
weightN = <value> (String)
Defines a weighting for each point accumulated to determine
the height of plotted bars. If this parameter has a value
other than 1 (the default) then instead of simply accumulating
the number of points per bin to determine bar height, the bar
height will be the sum over the weighting expression for the
points in each bin. Note that with weighting, the figure drawn
is no longer strictly speaking a histogram.
When weighted, bars can be of negative height. An anomaly of
the plot as currently implemented is that the Y axis never
descends below zero, so any such bars are currently invisible.
This may be amended in a future release (contact the author to
lobby for such an amendment).
[Default: 1]
binwidth = <float-value> (Double)
Defines the width on the X axis of histogram bins. If the X
axis is logarithmic, then this is a multiplicative value.
norm = true|false (Boolean)
Determines whether bin counts are normalised. If true,
histogram bars are scaled such that summed height of all bars
over the whole dataset is equal to one. Otherwise (the
default), no scaling is done.
[Default: false]
cumulative = true|false (Boolean)
Determines whether historams are cumulative. When false (the
default), the height of each bar is determined by counting the
number of points which fall into the range on the X axis that
it covers. When true, the height is determined by counting all
the points between negative infinity and the upper bound of
the range on the X axis that it covers.
[Default: false]
binbase = <float-value> (Double)
Adjusts the offset of the bins. By default zero (or one for
logarithmic X axis) is a boundary between bins; other
boundaries are defined by this and the bin width. If this
value is adjusted, the lower bound of one of the bins will be
set to this value, so all the bins move along by the
corresponding distance.
[Default: 0.0]
'''
task = _stilts.getTaskFactory().createObject('plothist')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def regquery(**kwargs):
'''\
Queries the VO registry.
The return value is the resulting table.
Parameters:
query = <value> (String)
Text of an ADQL WHERE clause targeted at the VOResource 1.0
schema defining which resource records you wish to retrieve
from the registry. Some examples are:
* @xsi:type like '%Organisation%'
* capability/@standardID = 'ivo://ivoa.net/std/ConeSearch'
and title like '%SDSS%'
* curation/publisher like 'CDS%' and title like '%galax%'
A full description of ADQL syntax and of the VOResource schema
is well beyond the scope of this documentation, but in general
you want to use <field-name> like '<value>' where '%' is a
wildcard character. Logical operators and and or and
parentheses can be used to group and combine expressions. To
work out the various <field-name>s you need to look at the
VOResource 1.0 schema; you can find some more discussion in
the documentation of the NVO IVOARegistry package.
regurl = <url-value> (java.net.URL)
The URL of a SOAP endpoint which provides a VOResource1.0 IVOA
registry service. Some known suitable registry endpoints at
time of writing are
*
http://registry.astrogrid.org/astrogrid-registry/services/RegistryQueryv1_0
* http://registry.euro-vo.org/services/RegistrySearch
* http://vao.stsci.edu/directory/ristandardservice.asmx
[Default:
http://registry.astrogrid.org/astrogrid-registry/services/RegistryQueryv1_0
]
soapout = <out-file> (uk.ac.starlink.util.Destination)
If set to a non-null value, this gives the destination for the
text of the request and response SOAP messages. The special
value "-" indicates standard output.
'''
task = _stilts.getTaskFactory().createObject('regquery')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def sqlclient(**kwargs):
'''\
Executes SQL statements.
Parameters:
db = <jdbc-url> (java.sql.Connection)
URL which defines a connection to a database. This has the
form jdbc:<subprotocol>:<subname> - the details are database-
and driver-dependent. Consult Sun's JDBC documentation and
that for the particular JDBC driver you are using for details.
Note that the relevant driver class will need to be on your
classpath and referenced in the jdbc.drivers system property
as well for the connection to be made.
user = <value> (String)
User name for logging in to SQL database. Defaults to the
current username.
[Default: buildd]
password = <value> (String)
Password for logging in to SQL database.
sql = <sql> (String)
Text of an SQL statement for execution. This parameter may be
repeated, or statements may be separated by semicolon (";")
characters.
'''
task = _stilts.getTaskFactory().createObject('sqlclient')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def sqlskymatch(in_, **kwargs):
'''\
Crossmatches table on sky position against SQL table.
The return value is the resulting table.
Parameters:
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
ra = <expr> (String)
Right ascension in degrees in the coordinate system for the
position of each row of the input table. This may simply be a
column name, or it may be an algebraic expression calculated
from columns as explained in SUN/256. If left blank, an
attempt is made to guess from UCDs, column names and unit
annotations what expression to use.
dec = <expr> (String)
Declination in degrees in the coordinate system for the
position of each row of the input table. This may simply be a
column name, or it may be an algebraic expression calculated
from columns as explained in SUN/256. If left blank, an
attempt is made to guess from UCDs, column names and unit
annotations what expression to use.
sr = <expr/deg> (String)
Expression which evaluates to the search radius in degrees for
the request at each row of the input table. This will often be
a constant numerical value, but may be the name or ID of a
column in the input table, or a function involving one.
find = best|all|each (String)
Determines which matches are retained.
* best: Only the matching query table row closest to the
input table row will be output. Input table rows with no
matches will be omitted. (Note this corresponds to the
best1 option in the pair matching commands, and best1 is
a permitted alias).
* all: All query table rows which match the input table row
will be output. Input table rows with no matches will be
omitted.
* each: There will be one output table row for each input
table row. If matches are found, the closest one from
the query table will be output, and in the case of no
matches, the query table columns will be blank.
[Default: all]
usefoot = true|false (Boolean)
Determines whether an attempt will be made to restrict
searches in accordance with available footprint information.
If this is set true, then before any of the per-row queries
are performed, an attempt may be made to acquire footprint
information about the servce. If such information can be
obtained, then queries which fall outside the footprint, and
hence which are known to yield no results, are skipped. This
can speed up the search considerably.
Currently, the only footprints available are those provided by
the CDS MOC (Multi-Order Coverage map) service, which covers
VizieR and a few other cone search services.
[Default: true]
footnside = <int-value> (Integer)
Determines the HEALPix Nside parameter for use with the MOC
footprint service. This tuning parameter determines the
resolution of the footprint if available. Larger values give
better resolution, hence a better chance of avoiding
unnecessary queries, but processing them takes longer and
retrieving and storing them is more expensive.
The value must be a power of 2, and at the time of writing,
the MOC service will not supply footprints at resolutions
greater than nside=512, so it should be <=512.
Only used if usefoot=true.
copycols = <colid-list> (String)
List of columns from the input table which are to be copied to
the output table. Each column identified here will be
prepended to the columns of the combined output table, and its
value for each row taken from the input table row which
provided the parameters of the query which produced it. See
SUN/256 for list syntax. The default setting is "*", which
means that all columns from the input table are included in
the output.
[Default: *]
scorecol = <col-name> (String)
Gives the name of a column in the output table to contain the
distance between the requested central position and the actual
position of the returned row. The distance returned is an
angular distance in degrees. If a null value is chosen, no
distance column will appear in the output table.
[Default: Separation]
erract = abort|ignore|retry|retry<n>
(uk.ac.starlink.ttools.cone.ConeErrorPolicy)
Determines what will happen if any of the individual cone
search requests fails. By default the task aborts. That may be
the best thing to do, but for unreliable or poorly implemented
services you may find that some searches fail and others
succeed so it can be best to continue operation in the face of
a few failures. The options are:
* abort: failure of any query terminates the task
* ignore: failure of a query is treated the same as a query
which returns no rows
* retry: failed queries are retried until they succeed; use
with care - if the failure is for some good, or at least
reproducible reason this could prevent the task from
ever completing
* retry<n>: failed queries are retried at most a fixed number
<n> of times If they still fail the task terminates.
[Default: abort]
ostream = true|false (Boolean)
If set true, this will cause the operation to stream on
output, so that the output table is built up as the results
are obtained from the cone search service. The disadvantage of
this is that some output modes and formats need multiple
passes through the data to work, so depending on the output
destination, the operation may fail if this is set. Use with
care (or be prepared for the operation to fail).
[Default: false]
fixcols = none|dups|all
(uk.ac.starlink.ttools.task.JoinFixActionParameter$Fixer)
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.
[Default: dups]
suffix0 = <label> (String)
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 the input table.
[Default: _0]
suffix1 = <label> (String)
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 the cone result table.
[Default: _1]
db = <jdbc-url> (java.sql.Connection)
URL which defines a connection to a database. This has the
form jdbc:<subprotocol>:<subname> - the details are database-
and driver-dependent. Consult Sun's JDBC documentation and
that for the particular JDBC driver you are using for details.
Note that the relevant driver class will need to be on your
classpath and referenced in the jdbc.drivers system property
as well for the connection to be made.
user = <value> (String)
User name for logging in to SQL database. Defaults to the
current username.
[Default: buildd]
password = <value> (String)
Password for logging in to SQL database.
dbtable = <table-name> (String)
The name of the table in the SQL database which provides the
remote data.
dbra = <sql-col> (String)
The name of a column in the SQL database table dbtable which
gives the right ascension. Units are given by dbunit.
dbdec = <sql-col> (String)
The name of a column in the SQL database table dbtable which
gives the declination. Units are given by dbunit.
dbunit = deg|rad (uk.ac.starlink.ttools.cone.AngleUnits)
Units of the right ascension and declination columns
identified in the database table. May be either deg[rees] (the
default) or rad[ians].
[Default: deg]
tiling = hpx<K>|healpixnest<K>|healpixring<K>|htm<K>
(uk.ac.starlink.ttools.cone.SkyTiling)
Describes the sky tiling scheme that is in use. One of the
following values may be used:
* hpxK: alias for healpixnestK
* healpixnestK: HEALPix using the Nest scheme at order K
* healpixringK: HEALPix using the Ring scheme at order K
* htmK: Hierarchical Triangular Mesh at level K
So for instance hpx5 or healpixnest5 would both indicate the
HEALPix NEST tiling scheme at order 5.
At level K, there are 12*4^K HEALPix pixels, or 8*4^K HTM
pixels on the sky. More information about these tiling schemes
can be found at the HEALPix and HTM web sites.
dbtile = <sql-col> (String)
The name of a column in the SQL database table dbtable which
contains a sky tiling pixel index. The tiling scheme is given
by the tiling parameter. Use of a tiling column is optional,
but if present (and if the column is indexed in the database
table) it may serve to speed up searches. Set to null if the
database table contains no tiling column or if you do not wish
to use one.
selectcols = <sql-cols> (String)
An SQL expression for the list of columns to be selected from
the table in the database. A value of "*" retrieves all
columns.
[Default: *]
where = <sql-condition> (String)
An SQL expression further limiting the rows to be selected
from the database. This will be combined with the constraints
on position implied by the cone search centres and radii. The
value of this parameter should just be a condition, it should
not contain the WHERE keyword. A null value indicates no
additional criteria.
preparesql = true|false (Boolean)
If true, the JDBC connection will use PreparedStatements for
the SQL SELECTs otherwise it will use simple Statements. This
is a tuning parameter and affects only performance. On some
database/driver combinations it's a lot faster set false (the
default); on others it may be faster, who knows?
[Default: false]
'''
task = _stilts.getTaskFactory().createObject('sqlskymatch')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def sqlupdate(**kwargs):
'''\
Updates values in an SQL table.
Parameters:
db = <jdbc-url> (java.sql.Connection)
URL which defines a connection to a database. This has the
form jdbc:<subprotocol>:<subname> - the details are database-
and driver-dependent. Consult Sun's JDBC documentation and
that for the particular JDBC driver you are using for details.
Note that the relevant driver class will need to be on your
classpath and referenced in the jdbc.drivers system property
as well for the connection to be made.
user = <value> (String)
User name for logging in to SQL database. Defaults to the
current username.
[Default: buildd]
password = <value> (String)
Password for logging in to SQL database.
select = <select-stmt> (String)
Gives the full text (including "SELECT") of the SELECT
statement to identify which rows undergo updates.
assign = <col>=<expr> (Assignment[])
Assigns new values for a given column. The assignment is made
in the form <colname>=<expr> where <colname> is the name of a
column in the SQL table and <expr> is the text of an
expression using STILTS's expression language, as described in
SUN/256. SQL table column names or $ID identifiers may be used
as variables in the usual way.
This parameter may be supplied more than once to effect
multiple assignments, or multiple assignments may be made by
separating them with semicolons in the value of this
parameter.
progress = true|false (Boolean)
If true, a spinner will be drawn on standard error which shows
how many rows have been updated so far.
[Default: true]
'''
task = _stilts.getTaskFactory().createObject('sqlupdate')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def taplint(tapurl, **kwargs):
'''\
Tests TAP services.
Parameters:
tapurl = <url-value> (java.net.URL)
The base URL of a Table Access Protocol service. This is the
bare URL without a trailing "/[a]sync".
The default values of the various endpoints (sync and async
query submission, tables metadata, service-provided examples
etc) use this URL as a parent and append standard sub-paths.
However, other parameters (syncurl, asyncurl, ...) are
provided so that the different endpoints can be set
individually if required.
stages =
TMV|TME|TMS|TMC|CPV|CAP|AVV|QGE|QPO|QAS|UWS|MDQ|OBS|UPL|EXA[ ...]
(String[])
Lists the validation stages which the validator will perform.
Each stage is represented by a short code, as follows:
* TMV: Validate table metadata against XML schema (on)
* TME: Check content of tables metadata from /tables (on)
* TMS: Check content of tables metadata from TAP_SCHEMA (on)
* TMC: Compare table metadata from /tables and TAP_SCHEMA
(on)
* CPV: Validate capabilities against XML schema (on)
* CAP: Check content of TAPRegExt capabilities record (on)
* AVV: Validate availability against XML schema (on)
* QGE: Make ADQL queries in sync GET mode (on)
* QPO: Make ADQL queries in sync POST mode (on)
* QAS: Make ADQL queries in async mode (on)
* UWS: Test asynchronous UWS/TAP behaviour (on)
* MDQ: Check table query result columns against declared
metadata (on)
* OBS: Test implementation of ObsCore Data Model (on)
* UPL: Make queries with table uploads (on)
* EXA: Check content of examples document (on)
You can specify a list of stage codes, separated by spaces.
Order is not significant.
Note that removing some stages may affect the operation of
others; for instance table metadata is acquired from the
metadata stages, and avoiding those will mean that later
stages that use the table metadata to pose queries will not be
able to do so with knowledge of the database schema.
[Default: TMV TME TMS TMC CPV CAP AVV QGE QPO QAS UWS MDQ OBS
UPL EXA]
maxtable = <int-value> (Integer)
Limits the number of tables from the service that will be
tested. Currently, this only affects stage MDQ. If the value
is left blank (the default), or if it is larger than the
number of tables actually present in the service, it will have
no effect.
format = text|json
(uk.ac.starlink.ttools.taplint.OutputReporter)
Determines the format of the output. Possible values are text
, json.
Note not all of the other parameters may be applicable to all
output formats.
[Default: text]
report = [EWISF]+ (String)
Letters indicating which message types should be listed. Each
character of the string is one of the letters , , , , with the
following meanings:
* E: Error in operation or standard compliance of the
service.
* W: Warning that service behaviour is questionable, or
contravenes a standard recommendation, but is not in
actual violation of the standard.
* I: Information about progress, for instance details of
queries made.
* S: Summary of previous successful/unsuccessful reports.
* F: Failure of the validator to perform some testing. The
cause is either some error internal to the validator, or
some error or missing functionality in the service which
has already been reported.
[Default: EWISF]
maxrepeat = <int-value> (Integer)
Puts a limit on the number of times that a single message will
be repeated. By setting this to some reasonably small number,
you can ensure that the output does not get cluttered up by
millions of repetitions of essentially the same error.
[Default: 9]
truncate = <int-value> (Integer)
Limits the line length written to the output.
[Default: 640]
debug = true|false (Boolean)
If true, debugging output including stack traces will be
output along with the normal validation messages.
[Default: false]
syncurl = <url-value> (java.net.URL)
Sets the URL to use for the sync endpoint of the TAP service.
By default, this would be <tapurl>/sync but you can set this
parameter to some other location if required. If left blank,
the default value is used.
asyncurl = <url-value> (java.net.URL)
Sets the URL to use for the async endpoint of the TAP service.
By default, this would be <tapurl>/async but you can set this
parameter to some other location if required. If left blank,
the default value is used.
tablesurl = <url-value> (java.net.URL)
Sets the URL to use for the tables endpoint of the TAP
service. By default, this would be <tapurl>/tables but you can
set this parameter to some other location if required. If left
blank, the default value is used.
capabilitiesurl = <url-value> (java.net.URL)
Sets the URL to use for the capabilities endpoint of the TAP
service. By default, this would be <tapurl>/capabilities but
you can set this parameter to some other location if required.
If left blank, the default value is used.
availabilityurl = <url-value> (java.net.URL)
Sets the URL to use for the availability endpoint of the TAP
service. By default, this would be <tapurl>/availability but
you can set this parameter to some other location if required.
If left blank, the default value is used.
examplesurl = <url-value> (java.net.URL)
Sets the URL to use for the examples endpoint of the TAP
service. By default, this would be <tapurl>/examples but you
can set this parameter to some other location if required. If
left blank, the default value is used.
'''
task = _stilts.getTaskFactory().createObject('taplint')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('tapurl', _map_env_value(tapurl))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def tapquery(**kwargs):
'''\
Queries a Table Access Protocol server.
The return value is the resulting table.
Parameters:
nupload = <count> (Integer)
The number of upload tables for this task. For each of the
upload tables N there will be associated parameters ufmtN,
uploadN and ucmdN.
[Default: 0]
uploadN = <tableN> (uk.ac.starlink.table.StarTable)
Input table.
upnameN = <adql-identifier> (String)
Identifier to use in server-side expressions for uploaded
table #N. In ADQL expressions, the table should be referred to
as "TAP_UPLOAD.<label>".
The value must syntactically be an ADQL identifier (
[A-Za-z][A-Za-z0-9_]*).
[Default: upN]
tapurl = <url-value> (java.net.URL)
The base URL of a Table Access Protocol service. This is the
bare URL without a trailing "/[a]sync".
The default values of the various endpoints (sync and async
query submission, tables metadata, service-provided examples
etc) use this URL as a parent and append standard sub-paths.
However, other parameters (syncurl, asyncurl, ...) are
provided so that the different endpoints can be set
individually if required.
adql = <query-text> (String)
Astronomical Data Query Language string specifying the TAP
query to execute. ADQL/S resembles SQL, so this string will
likely start with "SELECT".
parse = true|false (Boolean)
Determines whether an attempt will be made to check the syntax
of the ADQL prior to submitting the query. If this is set
true, and if a syntax error is found, the task will fail with
an error before any attempt is made to submit the query.
[Default: false]
sync = true|false (Boolean)
Determines whether the TAP query is submitted in synchronous
or asynchronous mode. Synchronous (true) means that the result
is retrieved over the same HTTP connection that the query is
submitted from. This is uncomplicated, but means if the query
takes a long time it may time out and the results will be
lost. Asynchronous (false) means that the job is queued and
results may be retrieved later. Normally this command does the
necessary waiting around and recovery of the result, though
with appropriate settings you can get tapresume to pick it up
for you later instead. In most cases false (the default) is
preferred.
[Default: false]
maxrec = <nrow> (Long)
Sets the requested maximum row count for the result of the
query. The service is not obliged to respect this, but in the
case that it has a default maximum record count, setting this
value may raise the limit. If no value is set, the service's
default policy will be used.
destruction = <iso8601> (String)
Posts an updated value of the UWS DESTRUCTION parameter to the
query job before it starts. This only makes sense for
asynchronous jobs (sync=false).
The supplied value should be an ISO-8601-like string, giving
the new requested job destruction time. The service is not
obliged to honour this request. See UWS v1.0, sec 2.2.3.3.
executionduration = <seconds> (Long)
Posts an updated value of the UWS EXECUTIONDURATION parameter
to the query job before it starts. This only makes sense for
asynchronous jobs (sync=false).
The supplied value is an integer giving the maximum number of
wall-clock seconds for which the job is permitted to execute
before being forcibly terminated. A value of zero indicates
unlimited duration. The service is not obliged to honour this
request. See UWS v1.0, sec 2.2.3.4.
compress = true|false (Boolean)
If true, the service is requested to provide HTTP-level
compression for the response stream (Accept-Encoding header is
set to "gzip", see RFC 2616). This does not guarantee that
compression will happen but if the service honours this
request it may result in a smaller amount of network traffic
at the expense of more processing on the server and client.
[Default: true]
upvotformat = TABLEDATA|BINARY|BINARY2
(uk.ac.starlink.votable.VOTableWriter)
Determines how any uploaded tables will be serialized for
transmission to the TAP server. The supplied string is the
name of one of the defined VOTable serialization formats. The
choice shouldn't affect any results, though it may affect
required bandwidth, and some services may (though should not)
have non-standard requirements for serialization format.
[Default: TABLEDATA]
language = <lang-name> (String)
Language to use for the ADQL-like query. This will usually be
"ADQL" (the default), but may be set to some other value
supported by the service, for instance a variant indicating a
different ADQL version. Note that at present, setting it to
"PQL" is not sufficient to submit a PQL query.
[Default: ADQL]
poll = <millisec> (Integer)
Interval to wait between polling attempts, in milliseconds.
Asynchronous TAP queries can only find out when they are
complete by repeatedly polling the server to find out the
job's status. This parameter allows you to set how often that
happens. Attempts to set it too low (<50) will be rejected on
the assumption that you're thinking in seconds.
[Default: 5000]
progress = true|false (Boolean)
If this parameter is set true, progress of the job is reported
to standard output as it happens.
[Default: true]
delete = finished|never|always (DeleteMode)
Determines under what circumstances the UWS job is to be
deleted from the server when its data is no longer required.
If it is not deleted, then the job is left on the TAP server
and it can be accessed via the normal UWS REST endpoints until
it is destroyed by the server.
Possible values:
* finished: delete only if the job finished, successfully or
not
* never: do not delete
* always: delete in any case
[Default: finished]
'''
task = _stilts.getTaskFactory().createObject('tapquery')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tapresume(**kwargs):
'''\
Resumes a previous query to a Table Access Protocol server.
The return value is the resulting table.
Parameters:
joburl = <url-value> (java.net.URL)
The URL of a job created by submission of a TAP query which
was created earlier and has not yet been deleted (by the
client) or destroyed (by the server). This will usually be of
the form <tap-url>/async/<job-id>. You can also find out, and
possibly retrieve results from the job by pointing a web
browser at this URL.
compress = true|false (Boolean)
If true, the service is requested to provide HTTP-level
compression for the response stream (Accept-Encoding header is
set to "gzip", see RFC 2616). This does not guarantee that
compression will happen but if the service honours this
request it may result in a smaller amount of network traffic
at the expense of more processing on the server and client.
[Default: true]
poll = <millisec> (Integer)
Interval to wait between polling attempts, in milliseconds.
Asynchronous TAP queries can only find out when they are
complete by repeatedly polling the server to find out the
job's status. This parameter allows you to set how often that
happens. Attempts to set it too low (<50) will be rejected on
the assumption that you're thinking in seconds.
[Default: 5000]
progress = true|false (Boolean)
If this parameter is set true, progress of the job is reported
to standard output as it happens.
[Default: true]
delete = finished|never|always (DeleteMode)
Determines under what circumstances the UWS job is to be
deleted from the server when its data is no longer required.
If it is not deleted, then the job is left on the TAP server
and it can be accessed via the normal UWS REST endpoints until
it is destroyed by the server.
Possible values:
* finished: delete only if the job finished, successfully or
not
* never: do not delete
* always: delete in any case
[Default: finished]
'''
task = _stilts.getTaskFactory().createObject('tapresume')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tapskymatch(in_, **kwargs):
'''\
Crossmatches table on sky position against TAP table.
The return value is the resulting table.
Parameters:
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
inlon = <expr/deg> (String)
Longitude in degrees for the position of each row in the input
table. This may simply be a column name, or it may be an
algebraic expression as explained in SUN/256. The coordinate
system must match that used for the coordinates in the remote
table.
inlat = <expr/deg> (String)
Longitude in degrees for the position of each row in the input
table. This may simply be a column name, or it may be an
algebraic expression as explained in SUN/256. The coordinate
system must match that used for the coordinates in the remote
table.
tapurl = <url-value> (java.net.URL)
The base URL of a Table Access Protocol service. This is the
bare URL without a trailing "/[a]sync".
The default values of the various endpoints (sync and async
query submission, tables metadata, service-provided examples
etc) use this URL as a parent and append standard sub-paths.
However, other parameters (syncurl, asyncurl, ...) are
provided so that the different endpoints can be set
individually if required.
taptable = <name> (String)
Name of the table in the given TAP service against which the
matching will be performed.
taplon = <column> (String)
Longitude in degrees for the position of each row in the
remote table. This is an ADQL expression interpreted within
the TAP service, typically just a column name. The coordinate
system must match that used for the input table.
taplat = <column> (String)
Latitude in degrees for the position of each row in the remote
table. This is an ADQL expression interpreted within the TAP
service, typically just a column name. The coordinate system
must match that used for the input table.
tapcols = <colname,...> (String[])
Comma-separated list of column names to retrieve from the
remote table. If no value is supplied (the default), all
columns from the remote table will be returned.
sr = <expr/deg> (String)
Maximum distance in degrees from the local table (lat,lon)
position at which counterparts from the remote table will be
identified. This is an ADQL expression interpreted within the
TAP service, so it may be a constant value or may involve
columns in the remote table.
find = all|best|each|each-dist
(uk.ac.starlink.ttools.task.UserFindMode)
Determines which pair matches are included in the result.
* all: All matches
* best: Matched rows, best remote row for each input row
* each: One row per input row, contains best remote match or
blank
* each-dist: One row per input row, column giving distance
only for best match
Note only the all mode is symmetric between the two tables.
[Default: all]
blocksize = <int-value> (Integer)
The number of rows uploaded in each TAP query. TAP services
may have limits on the number of rows in a table uploaded for
matching. This command can therefore break up input tables
into blocks and make a number of individual TAP queries to
generate the result. This parameter controls the maximum
number of rows uploaded in each individual request. For an
input table with fewer rows than this value, the whole thing
is done as a single query.
[Default: 5000]
maxrec = <int-value> (Integer)
Limit to the number of rows resulting from this operation. If
the value is negative (the default) no limit is imposed. Note
however that there can be truncation of the result if the
number of records returned from a single chunk exceeds limits
imposed by the service.
[Default: -1]
sync = true|false (Boolean)
Determines whether the TAP queries are submitted in
synchronous or asynchronous mode. Since this command uses
chunking to keep requests to a reasonable size, hopefully
requests will not take too long to execute, therefore the
default is synchronous (true).
[Default: true]
blockmaxrec = <nrow> (Long)
Sets the MAXREC parameter passed to the TAP service for each
uploaded block. This allows you to request that the service
overrides its default limit for the number of rows output from
a single query. The service may still impose some "hard" limit
beyond which the output row count cannot be increased.
Note this differs from the maxrec parameter, which gives the
maximum total number of rows to be returned from this command.
compress = true|false (Boolean)
If true, the service is requested to provide HTTP-level
compression for the response stream (Accept-Encoding header is
set to "gzip", see RFC 2616). This does not guarantee that
compression will happen but if the service honours this
request it may result in a smaller amount of network traffic
at the expense of more processing on the server and client.
[Default: true]
fixcols = none|dups|all
(uk.ac.starlink.ttools.task.JoinFixActionParameter$Fixer)
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.
[Default: dups]
suffixin = <label> (String)
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 the input table.
[Default: _in]
suffixremote = <label> (String)
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 the TAP result table.
[Default: _tap]
'''
task = _stilts.getTaskFactory().createObject('tapskymatch')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tcat(in_, **kwargs):
'''\
Concatenates multiple similar tables.
The return value is the resulting table.
Parameters:
in_ = <table> [<table> ...]
(uk.ac.starlink.ttools.task.TableProducer[])
Array of input tables.
multi = true|false (Boolean)
Determines whether all tables, or just the first one, from
input table files will be used. If set false, then just the
first table from each file named by in will be used. If true,
then all tables present in those input files will be used.
This only has an effect for file formats which are capable of
containing more than one table, which effectively means FITS
and VOTable and their variants.
[Default: false]
seqcol = <colname> (String)
Name of a column to be added to the output table which will
contain the sequence number of the input table from which each
row originated. This column will contain 1 for the rows from
the first concatenated table, 2 for the second, and so on.
loccol = <colname> (String)
Name of a column to be added to the output table which will
contain the location (as specified in the input parameter(s))
of the input table from which each row originated.
uloccol = <colname> (String)
Name of a column to be added to the output table which will
contain the unique part of the location (as specified in the
input parameter(s)) of the input table from which each row
originated. If not null, parameters will also be added to the
output table giving the pre- and post-fix string common to all
the locations. For example, if the input tables are
"/data/cat_a1.fits" and "/data/cat_b2.fits" then the output
table will contain a new column <colname> which takes the
value "a1" for rows from the first table and "b2" for rows
from the second, and new parameters "<colname>_prefix" and
"<colname>_postfix" with the values "/data/cat_" and ".fits"
respectively.
lazy = true|false (Boolean)
Whether to perform table resolution lazily. If true, each
table is only accessed when the time comes to add its rows to
the output; if false, then all the tables are accessed up
front. This is mostly a tuning parameter, and on the whole it
doesn't matter much how it is set, but for joining an enormous
number of tables setting it true may avoid running out of
resources.
[Default: false]
countrows = true|false (Boolean)
Whether to count the rows in the table before starting the
output. This is essentially a tuning parameter - if writing to
an output format which requires the number of rows up front
(such as normal FITS) it may result in skipping the number of
passes through the input files required for processing. Unless
you have a good understanding of the internals of the
software, your best bet for working out whether to set this
true or false is to try it both ways
[Default: false]
'''
task = _stilts.getTaskFactory().createObject('tcat')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tcatn(**kwargs):
'''\
Concatenates multiple tables.
The return value is the resulting table.
Parameters:
nin = <count> (Integer)
The number of input tables for this task. For each of the
input tables N there will be associated parameters ifmtN, inN
and icmdN.
inN = <tableN> (uk.ac.starlink.table.StarTable)
Input table.
seqcol = <colname> (String)
Name of a column to be added to the output table which will
contain the sequence number of the input table from which each
row originated. This column will contain 1 for the rows from
the first concatenated table, 2 for the second, and so on.
loccol = <colname> (String)
Name of a column to be added to the output table which will
contain the location (as specified in the input parameter(s))
of the input table from which each row originated.
uloccol = <colname> (String)
Name of a column to be added to the output table which will
contain the unique part of the location (as specified in the
input parameter(s)) of the input table from which each row
originated. If not null, parameters will also be added to the
output table giving the pre- and post-fix string common to all
the locations. For example, if the input tables are
"/data/cat_a1.fits" and "/data/cat_b2.fits" then the output
table will contain a new column <colname> which takes the
value "a1" for rows from the first table and "b2" for rows
from the second, and new parameters "<colname>_prefix" and
"<colname>_postfix" with the values "/data/cat_" and ".fits"
respectively.
countrows = true|false (Boolean)
Whether to count the rows in the table before starting the
output. This is essentially a tuning parameter - if writing to
an output format which requires the number of rows up front
(such as normal FITS) it may result in skipping the number of
passes through the input files required for processing. Unless
you have a good understanding of the internals of the
software, your best bet for working out whether to set this
true or false is to try it both ways
[Default: false]
'''
task = _stilts.getTaskFactory().createObject('tcatn')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tcopy(in_, **kwargs):
'''\
Converts between table formats.
Parameters:
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
'''
task = _stilts.getTaskFactory().createObject('tcopy')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def tcube(in_, **kwargs):
'''\
Calculates N-dimensional histograms.
Parameters:
cols = <col-id> ... (String[])
Columns to use for this task. One or more <col-id> elements,
separated by spaces, should be given. Each one represents a
column in the table, using either its name or index.
The number of columns listed in the value of this parameter
defines the dimensionality of the output data cube.
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
bounds = [<lo>]:[<hi>] ... (String[])
Gives the bounds for each dimension of the cube in data
coordinates. The form of the value is a space-separated list
of words, each giving an optional lower bound, then a colon,
then an optional upper bound, for instance "1:100 0:20" to
represent a range for two-dimensional output between 1 and 100
of the first coordinate (table column) and between 0 and 20
for the second. Either or both numbers may be omitted to
indicate that the bounds should be determined automatically by
assessing the range of the data in the table. A null value for
the parameter indicates that all bounds should be determined
automatically for all the dimensions.
If any of the bounds need to be determined automatically in
this way, two passes through the data will be required, the
first to determine bounds and the second to populate the cube.
binsizes = <size> ... (String[])
Gives the extent of of the data bins (cube pixels) in each
dimension in data coordinates. The form of the value is a
space-separated list of values, giving a list of extents for
the first, second, ... dimension. Either this parameter or the
nbins parameter must be supplied.
nbins = <num> ... (String[])
Gives the number of bins (cube pixels) in each dimension. The
form of the value is a space-separated list of integers,
giving the number of pixels for the output cube in the first,
second, ... dimension. Either this parameter or the binsizes
parameter must be supplied.
out = <out-file> (uk.ac.starlink.util.Destination)
The location of the output file. This is usually a filename to
write to. If it is equal to the special value "-" the output
will be written to standard output.
The output cube is currently written as a single-HDU FITS
file.
[Default: -]
otype = byte|short|int|long|float|double (Class)
The type of numeric value which will fill the output array. If
no selection is made, the output type will be determined
automatically as the shortest type required to hold all the
values in the array. Currently, integers are always signed (no
BSCALE/BZERO), so for instance the largest value that can be
recorded in 8 bits is 127.
scale = <col-id> (String)
Optionally gives a value by which the count in each bin is
scaled. If this value is null (the default) then for each row
that falls within the bounds of a pixel, the pixel value will
be incremented by 1. If a column ID is given, then instead of
1 being added, the value of that column for the row in
question is added. The effect of this is that the output image
contains the mean of the given column for the rows
corresponding to each pixel rather than just a count of them.
'''
task = _stilts.getTaskFactory().createObject('tcube')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def tjoin(**kwargs):
'''\
Joins multiple tables side-to-side.
The return value is the resulting table.
Parameters:
nin = <count> (Integer)
The number of input tables for this task. For each of the
input tables N there will be associated parameters ifmtN, inN
and icmdN.
inN = <tableN> (uk.ac.starlink.table.StarTable)
Input table.
fixcols = none|dups|all
(uk.ac.starlink.ttools.task.JoinFixActionParameter$Fixer)
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.
[Default: dups]
suffixN = <label> (String)
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 N.
[Default: _N]
'''
task = _stilts.getTaskFactory().createObject('tjoin')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tloop(end, colname='i', start=0.0, step=1.0, **kwargs):
'''\
Generates a single-column table from a loop variable.
The return value is the resulting table.
Parameters:
colname = <value> (String)
Gives the name of the single column produced by this command.
[Default: i]
start = <float-value> (Double)
Gives the starting value of the loop variable. This will the
the value in the first row of the table.
[Default: 0.0]
end = <float-value> (Double)
Gives the value which the loop variable will not exceed.
Exceeding is in the positive or negative sense according to
the sense of the step parameter, as usual for a for-type loop.
step = <float-value> (Double)
Amount by which the loop variable will be incremented at each
iteration, i.e. each table row.
[Default: 1.0]
forcefloat = true|false (Boolean)
Affects the data type of the loop variable column. If true,
the column is always floating point. If false, and if the
other parameters are all of integer type, the column will be
an integer column.
[Default: false]
'''
task = _stilts.getTaskFactory().createObject('tloop')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('end', _map_env_value(end))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tmatch1(in_, **kwargs):
'''\
Performs a crossmatch internal to a single table.
The return value is the resulting table.
Parameters:
matcher = <matcher-name>
(uk.ac.starlink.table.join.MatchEngine)
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).
[Default: sky]
params = <match-params> (String[])
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 = <tuning-params> (String[])
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.
values = <expr-list> (String[])
Defines the values from the input table 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.
action = identify|keep0|keep1|wide2|wideN
(uk.ac.starlink.table.join.Match1Type)
Determines the form of the table which will be output as a
result of the internal match.
* identify: The output table is the same as the input table
except that it contains two additional columns, GroupID
and GroupSize, following the input columns. Each group
of rows which matched is assigned a unique integer,
recorded in the GroupID column, and the size of each
group is recorded in the GroupSize column. Rows which
don't match any others (singles) have null values in
both these columns.
* keep0: The result is a new table containing only "single"
rows, that is ones which don't match any other rows in
the table. Any other rows are thrown out.
* keep1: The result is a new table in which only one row (the
first in the input table order) from each group of
matching ones is retained. A subsequent intra-table
match with the same criteria would therefore show no
matches.
* wideN: The result is a new "wide" table consisting of
matched rows in the input table stacked next to each
other. Only groups of exactly N rows in the input table
are used to form the output table; each row of the
output table consists of the columns of the first group
member, followed by the columns of the second group
member and so on. The output table therefore has N times
as many columns as the input table. The column names in
the new table have _1, _2, ... appended to them to avoid
duplication.
[Default: identify]
progress = none|log|profile (String)
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
[Default: log]
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
'''
task = _stilts.getTaskFactory().createObject('tmatch1')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tmatch2(in1, in2, **kwargs):
'''\
Crossmatches 2 tables using flexible criteria.
The return value is the resulting table.
Parameters:
in1 = <table1> (uk.ac.starlink.table.StarTable)
Input table.
in2 = <table2> (uk.ac.starlink.table.StarTable)
Input table.
matcher = <matcher-name>
(uk.ac.starlink.table.join.MatchEngine)
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).
[Default: sky]
values1 = <expr-list> (String[])
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.
values2 = <expr-list> (String[])
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.
params = <match-params> (String[])
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 = <tuning-params> (String[])
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.
join = 1and2|1or2|all1|all2|1not2|2not1|1xor2
(uk.ac.starlink.table.join.JoinType)
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
[Default: 1and2]
find = all|best|best1|best2
(uk.ac.starlink.table.join.PairMode)
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.
[Default: best]
fixcols = none|dups|all
(uk.ac.starlink.ttools.task.JoinFixActionParameter$Fixer)
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.
[Default: dups]
suffix1 = <label> (String)
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.
[Default: _1]
suffix2 = <label> (String)
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.
[Default: _2]
scorecol = <col-name> (String)
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.
[Default: Score]
progress = none|log|profile (String)
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
[Default: log]
'''
task = _stilts.getTaskFactory().createObject('tmatch2')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in1', _map_env_value(in1))
env.setValue('in2', _map_env_value(in2))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tmatchn(**kwargs):
'''\
Crossmatches multiple tables using flexible criteria.
The return value is the resulting table.
Parameters:
nin = <count> (Integer)
The number of input tables for this task. For each of the
input tables N there will be associated parameters ifmtN, inN
and icmdN.
inN = <tableN> (uk.ac.starlink.table.StarTable)
Input table.
multimode = pairs|group (String)
Defines what is meant by a multi-table match. There are two
possibilities:
* pairs: Each output row corresponds to a single row of the
reference table (see parameter iref) and contains
entries from other tables which are pair matches to
that. If a reference table row matches multiple rows
from one of the other tables, only the best one is
included.
* group: Each output row corresponds to a group of entries
from the input tables which are mutually linked by pair
matches between them. This means that although you can
get from any entry to any other entry via one or more
pair matches, there is no guarantee that any entry is a
pair match with any other entry. No table has privileged
status in this case. If there are multiple entries from
a given table in the match group, an arbitrary one is
chosen for inclusion (there is no unique way to select
the best). See SUN/256 for more discussion.
In the case of well-separated objects these modes will give
the same results. For crowded fields however it will make a
difference which is chosen.
Note that which rows actually appear in the output is also
influenced by the joinN parameter.
[Default: pairs]
iref = <table-index> (Integer)
If multimode=pairs this parameter gives the index of the table
in the input table list which is to serve as the reference
table (the one which must be matched by other tables). Ignored
in other modes.
Row ordering in the output table is usually tidiest if the
default setting of 1 is used (i.e. if the first input table is
used as the reference table).
[Default: 1]
matcher = <matcher-name>
(uk.ac.starlink.table.join.MatchEngine)
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).
[Default: sky]
params = <match-params> (String[])
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 = <tuning-params> (String[])
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.
valuesN = <expr-list> (String[])
Defines the values from table N 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.
joinN = default|match|nomatch|always
(uk.ac.starlink.table.join.MultiJoinType)
Determines which rows from input table N are included in the
output table. The matching algorithm determines which of the
rows in each of the input tables correspond to which rows in
the other input tables, and this parameter determines what to
do with that information.
The default behaviour is that a row will appear in the output
table if it represents a match of rows from two or more of the
input tables. This can be altered on a per-input-table basis
however by choosing one of the non-default options below:
* match: Rows are included only if they contain an entry from
input table N.
* nomatch: Rows are included only if they do not contain an
entry from input table N.
* always: Rows are included if they contain an entry from
input table N (overrides any match and nomatch settings
of other tables).
* default: Input table N has no special effect on whether
rows are included.
[Default: default]
fixcols = none|dups|all
(uk.ac.starlink.ttools.task.JoinFixActionParameter$Fixer)
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.
[Default: dups]
suffixN = <label> (String)
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 N.
[Default: _N]
progress = none|log|profile (String)
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
[Default: log]
'''
task = _stilts.getTaskFactory().createObject('tmatchn')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tmulti(in_, **kwargs):
'''\
Writes multiple tables to a single container file.
Parameters:
in_ = <table> [<table> ...]
(uk.ac.starlink.ttools.task.TableProducer[])
Array of input tables.
multi = true|false (Boolean)
Determines whether all tables, or just the first one, from
input table files will be used. If set false, then just the
first table from each file named by in will be used. If true,
then all tables present in those input files will be used.
This only has an effect for file formats which are capable of
containing more than one table, which effectively means FITS
and VOTable and their variants.
[Default: false]
out = <out-file> (uk.ac.starlink.util.Destination)
The location of the output file. This is usually a filename to
write to. If it is equal to the special value "-" the output
will be written to standard output.
[Default: -]
'''
task = _stilts.getTaskFactory().createObject('tmulti')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def tmultin(**kwargs):
'''\
Writes multiple processed tables to single container file.
Parameters:
nin = <count> (Integer)
The number of input tables for this task. For each of the
input tables N there will be associated parameters ifmtN, inN
and icmdN.
inN = <tableN> (uk.ac.starlink.table.StarTable)
Input table.
out = <out-file> (uk.ac.starlink.util.Destination)
The location of the output file. This is usually a filename to
write to. If it is equal to the special value "-" the output
will be written to standard output.
[Default: -]
'''
task = _stilts.getTaskFactory().createObject('tmultin')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def tpipe(in_, **kwargs):
'''\
Performs pipeline processing on a table.
The return value is the resulting table.
Parameters:
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
'''
task = _stilts.getTaskFactory().createObject('tpipe')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tskymap(in_, **kwargs):
'''\
Calculates sky density maps.
The return value is the resulting table.
Parameters:
in_ = <table> (uk.ac.starlink.table.StarTable)
Input table.
lon = <expr/deg> (String)
Longitude in degrees for the position of each row in the input
table. This may simply be a column name, or it may be an
algebraic expression as explained in SUN/256. The sky system
used here will determine the grid on which the output map is
built.
lat = <expr/deg> (String)
Latitude in degrees for the position of each row in the input
table. This may simply be a column name, or it may be an
algebraic expression as explained in SUN/256. The sky system
used here will determine the grid on which the output map is
built.
tiling = hpx<K>|healpixnest<K>|healpixring<K>|htm<K>
(uk.ac.starlink.ttools.cone.SkyTiling)
Describes the sky tiling scheme that is in use. One of the
following values may be used:
* hpxK: alias for healpixnestK
* healpixnestK: HEALPix using the Nest scheme at order K
* healpixringK: HEALPix using the Ring scheme at order K
* htmK: Hierarchical Triangular Mesh at level K
So for instance hpx5 or healpixnest5 would both indicate the
HEALPix NEST tiling scheme at order 5.
At level K, there are 12*4^K HEALPix pixels, or 8*4^K HTM
pixels on the sky. More information about these tiling schemes
can be found at the HEALPix and HTM web sites.
[Default: hpx5]
count = true|false (Boolean)
Controls whether a COUNT column is added to the output table
along with any other columns that may have been requested. If
included, this reports the number of rows from the input table
that fell within the corresponding bin.
[Default: true]
cols = <expr> ... (String[])
Selects the columns to be aggregated into bins. The value is a
space-separated list of items, where each item may be either a
column name or an expression using the expression language.
The output table will have one column for each of the items in
this list.
combine = sum|mean|median|min|max|stdev|count|hit
(uk.ac.starlink.ttools.plot2.layer.Combiner)
Combination mode for aggregating binned quantities. Possible
values are:
* sum: the sum of all the combined values
* mean: the mean of the combined values
* median: the median of the combined values (may be slow)
* min: the minimum of all the combined values
* max: the maximum of all the combined values
* stdev: the sample standard deviation of the combined values
* count: the number of non-blank values (weight is ignored)
* hit: 1 if any values present, NaN otherwise (weight is
ignored)
[Default: mean]
complete = true|false (Boolean)
Determines whether the output table contains a row for every
pixel in the tiling, or only the rows for pixels in which some
of the input data fell.
The value of this parameter may affect performance as well as
output. If you know that most pixels on the sky will be
covered, it's probably a good idea to set this true, and if
you know that only a small patch of sky will be covered, it's
better to set it false.
[Default: false]
'''
task = _stilts.getTaskFactory().createObject('tskymap')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in_', _map_env_value(in_))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def tskymatch2(in1, in2, **kwargs):
'''\
Crossmatches 2 tables on sky position.
The return value is the resulting table.
Parameters:
in1 = <table1> (uk.ac.starlink.table.StarTable)
Input table.
in2 = <table2> (uk.ac.starlink.table.StarTable)
Input table.
ra1 = <expr> (String)
Right ascension in degrees for the position of each row of
table 1. This may simply be a column name, or it may be an
algebraic expression calculated from columns as explained in
SUN/256. If left blank, an attempt is made to guess from UCDs,
column names and unit annotations what expression to use.
dec1 = <expr> (String)
Declination in degrees for the position of each row of table
1. This may simply be a column name, or it may be an algebraic
expression calculated from columns as explained in SUN/256. If
left blank, an attempt is made to guess from UCDs, column
names and unit annotations what expression to use.
ra2 = <expr> (String)
Right ascension in degrees for the position of each row of
table 2. This may simply be a column name, or it may be an
algebraic expression calculated from columns as explained in
SUN/256. If left blank, an attempt is made to guess from UCDs,
column names and unit annotations what expression to use.
dec2 = <expr> (String)
Declination in degrees for the position of each row of table
2. This may simply be a column name, or it may be an algebraic
expression calculated from columns as explained in SUN/256. If
left blank, an attempt is made to guess from UCDs, column
names and unit annotations what expression to use.
error = <value/arcsec> (Double)
The maximum separation permitted between two objects for them
to count as a match. Units are arc seconds.
tuning = <healpix-k> (Integer)
Tuning parameter that controls the pixel size used when
binning the rows. The legal range is from 0 (corresponding to
pixel size of about 60 degrees) to 20 (about 0.2 arcsec). The
value of this parameter will not affect the result but may
affect the performance in terms of CPU and memory resources
required. A default value will be chosen based on the size of
the error parameter, but it may be possible to improve
performance by adjusting the default value. The value used can
be seen by examining the progress output. If your match is
taking a long time or is failing from lack of memory it may be
worth trying different values for this parameter.
join = 1and2|1or2|all1|all2|1not2|2not1|1xor2
(uk.ac.starlink.table.join.JoinType)
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
[Default: 1and2]
find = all|best|best1|best2
(uk.ac.starlink.table.join.PairMode)
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.
[Default: best]
'''
task = _stilts.getTaskFactory().createObject('tskymatch2')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
env.setValue('in1', _map_env_value(in1))
env.setValue('in2', _map_env_value(in2))
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
table = task.createProducer(env).getTable()
_check_unused_args(env)
return import_star_table(table)
def votcopy(in_='-', out='-', format='TABLEDATA', **kwargs):
'''\
Transforms between VOTable encodings.
Parameters:
in_ = <location> (String)
Location of the input VOTable. May be a URL, filename, or "-"
to indicate standard input. The input table may be compressed
using one of the known compression formats (Unix compress,
gzip or bzip2).
[Default: -]
out = <location> (String)
Location of the output VOTable. May be a filename or "-" to
indicate standard output.
[Default: -]
format = TABLEDATA|BINARY|BINARY2|FITS
(uk.ac.starlink.votable.DataFormat)
Determines the encoding format of the table data in the output
document. If null is selected, then the tables will be
data-less (will contain no DATA element), leaving only the
document structure. Data-less tables are legal VOTable
elements.
The BINARY2 format is only available for version=1.3
[Default: TABLEDATA]
version = 1.0|1.1|1.2|1.3
(uk.ac.starlink.votable.VOTableVersion)
Determines the version of the VOTable standard to which the
output will conform. If null (the default), the output table
will have the same version as the input table.
charset = <xml-encoding> (java.nio.charset.Charset)
Selects the Unicode encoding used for the output XML. The
available options are dependent on your JVM, use help=charset
for a full listing. Setting the value null will use the JVM's
system default.
[Default: UTF-8]
cache = true|false (Boolean)
Determines whether the input tables are read into a cache
prior to being written out. The default is selected
automatically depending on the input table; so you should
normally leave this flag alone.
href = true|false (Boolean)
In the case of BINARY or FITS encoding, this determines
whether the STREAM elements output will contain their data
inline or externally. If set false, the output document will
be self-contained, with STREAM data inline as base64-encoded
characters. If true, then for each TABLE in the document the
binary data will be written to a separate file and referenced
by an href attribute on the corresponding STREAM element. The
name of these files is usually determined by the name of the
main output file; but see also the base flag.
nomagic = true|false (Boolean)
Eliminate the null attributes of VALUES elements where they
are no longer required. In VOTable versions <=1.2, the only
way to specify null values for integer-type scalar columns was
to use the null attribute of the VALUES element to indicate an
in-band magic value representing null. From VOTable v1.3, null
values can be represented using empty <TD> elements or flagged
specially in BINARY2 streams. In these cases, it is
recommended (though not required) not to use the VALUES/null
mechanism.
If this parameter is set true, then any VALUES/null attributes
will be removed in VOTable 1.3 BINARY2 or TABLEDATA output. If
this results in an empty VALUES element, it too will be
removed.
This parameter is ignored if the output VOTable version is
lower than 1.3 or if format=BINARY/FITS.
[Default: true]
base = <location> (String)
Determines the name of external output files written when the
href flag is true. Normally these are given names based on the
name of the output file. But if this flag is given, the names
will be based on the <location> string. This flag is
compulsory if href is true and out=- (output is to standard
out), since in this case there is no default base name to use.
'''
task = _stilts.getTaskFactory().createObject('votcopy')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def votlint(votable='-', **kwargs):
'''\
Validates VOTable documents.
Parameters:
votable = <location> (java.io.InputStream)
Location of the VOTable to be checked. This may be a filename,
URL or "-" (the default), to indicate standard input. The
input may be compressed using one of the known compression
formats (Unix compress, gzip or bzip2).
[Default: -]
validate = true|false (Boolean)
Whether to validate the input document aganist the VOTable
DTD. If true (the default), then as well as votlint's own
checks, it is validated against an appropriate version of the
VOTable DTD which picks up such things as the presence of
unknown elements and attributes, elements in the wrong place,
and so on. Sometimes however, particularly when XML namespaces
are involved, the validator can get confused and may produce a
lot of spurious errors. Setting this flag false prevents this
validation step so that only votlint's own checks are
performed. In this case many violations of the VOTable
standard concerning document structure will go unnoticed.
[Default: true]
version = 1.0|1.1|1.2|1.3
(uk.ac.starlink.votable.VOTableVersion)
Selects the version of the VOTable standard which the input
table is supposed to exemplify. The version may also be
specified within the document using the "version" attribute of
the document's VOTABLE element; if it is and it conflicts with
the value specified by this flag, a warning is issued.
If no value is provided for this parameter (the default), the
version will be determined from the VOTable itself.
out = <location> (uk.ac.starlink.util.Destination)
Destination file for output messages. May be a filename or "-"
to indicate standard output.
[Default: -]
'''
task = _stilts.getTaskFactory().createObject('votlint')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def plot2plane(**kwargs):
'''\
Draws a plane plot.
Parameters:
xpix = <int-value> (Integer)
Size of the output image in the X direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 500]
ypix = <int-value> (Integer)
Size of the output image in the Y direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 400]
insets = <top>,<left>,<bottom>,<right>
(uk.ac.starlink.ttools.plot2.Padding)
Defines the amount of space in pixels around the actual
plotting area. This space is used for axis labels, and other
decorations and any left over forms an empty border.
The size and position of the actual plotting area is
determined by this parameter along with xpix and ypix.
The value of this parameter is 4 comma separated integers:
<top>,<left>,<bottom>,<right>. Any or all of these values may
be left blank, in which case the corresponding margin will be
calculated automatically according to how much space is
required.
omode = swing|out|cgi|discard|auto
(uk.ac.starlink.ttools.plottask.PaintMode)
Determines how the drawn plot will be output, see SUN/256.
* swing: Plot will be displayed in a window on the screen.
This plot is "live"; it can be resized and (except for
old-style plots) navigated around with mouse actions in
the same way as plots in TOPCAT.
* out: Plot will be written to a file given by out using the
graphics format given by ofmt.
* cgi: Plot will be written in a way suitable for CGI use
direct from a web server. The output is in the graphics
format given by ofmt, preceded by a suitable
"Content-type" declaration.
* discard: Plot is drawn, but discarded. There is no output.
* auto: Behaves as swing or out mode depending on presence of
out parameter
[Default: auto]
storage = simple|cache|basic-cache
(uk.ac.starlink.ttools.plot2.data.DataStoreFactory)
Determines the way that data is accessed when constructing the
plot. There are two basic options, cached or not.
If no caching is used (simple) then rows are read sequentially
from the specified input table(s) every time they are
required. This generally requires a small memory footprint
(though that can depend on how the table is specified) and
makes sense if the data only needs to be scanned once or
perhaps if the table is very large.
If caching is used (cache) then the required data is read once
from the specified input table(s) and cached before any
plotting is performed, and plots are done using this cached
data. This may use a significant amount of memory for large
tables but it's usually more sensible (faster) if the data
will need to be scanned multiple times.
The default value is cache if a live plot is being generated (
omode=swing), since in that case the plot needs to be redrawn
every time the user performs plot navigation actions or
resizes the window, or if animations are being produced.
Otherwise (e.g. output to a graphics file) the default is
simple.
[Default: simple]
seq = <suffix>[,...] (String[])
Contains a comma-separated list of layer suffixes to determine
the order in which layers are drawn on the plot. This can
affect which symbol are plotted on top of, and so potentially
obscure, which other ones.
When specifying a plot, multiple layers may be specified, each
introduced by a parameter layer<N>, where <N> is a different
(arbitrary) suffix labelling the layer, and is appended to all
the parameters specific to defining that layer.
By default the layers are drawn on the plot in the order in
which the layer* parameters appear on the command line.
However if this parameter is specified, each comma-separated
element is interpreted as a layer suffix, giving the ordered
list of layers to plot. Every element of the list must be a
suffix with a corresponding layer parameter, but missing or
repeated elements are allowed.
legend = true|false (Boolean)
Whether to draw a legend or not. If no value is supplied, the
decision is made automatically: a legend is drawn only if it
would have more than one entry.
legborder = true|false (Boolean)
If true, a line border is drawn around the legend.
[Default: true]
legopaque = true|false (Boolean)
If true, the background of the legend is opaque, and the
legend obscures any plot components behind it. Otherwise, it's
transparent.
[Default: true]
legseq = <suffix>[,...] (String[])
Determines which layers are represented in the legend (if
present) and in which order they appear. The legend has a line
for each layer label (as determined by the leglabelN
parameter). If multiple layers have the same label, they will
contribute to the same entry in the legend, with style icons
plotted over each other. The value of this parameter is a
comma-separated sequence of layer suffixes, which determines
the order in which the legend entries appear. Layers with
suffixes missing from this list do not show up in the legend
at all.
If no value is supplied (the default), the sequence is the
same as the layer plotting sequence (see seq).
legpos = <xfrac,yfrac> (double[])
Determines the internal position of the legend on the plot.
The value is a comma-separated pair of values giving the X and
Y positions of the legend within the plotting bounds, so for
instance "0.5,0.5" will put the legend right in the middle of
the plot. If no value is supplied, the legend will appear
outside the plot boundary.
title = <value> (String)
Text of a title to be displayed at the top of the plot. If
null, the default, no title is shown and there's more space
for the graphics.
auxmap = <map-name>|<color>-<color>[-<color>...]
(uk.ac.starlink.ttools.plot.Shader)
Color map used for Aux axis shading.
A mixed bag of colour ramps are available: inferno, magma,
plasma, viridis, cubehelix, sron, rainbow, rainbow2, rainbow3
, pastel, accent, gnuplot, gnuplot2, specxby, set1, paired,
hotcold, rdbu, piyg, brbg, cyan-magenta, red-blue, brg, heat,
cold, light, greyscale, colour, standard, bugn, bupu, orrd,
pubu, purd, huecl, hue, intensity, rgb_red, rgb_green,
rgb_blue, hsv_h, hsv_s, hsv_v, yuv_y, yuv_u, yuv_v,
scale_hsv_s, scale_hsv_v, scale_yuv_y, mask, blacker, whiter,
transparency. Note: many of these, including rainbow-like
ones, are frowned upon by the visualisation community.
You can also construct your own custom colour map by giving a
sequence of colour names separated by minus sign ("-")
characters. In this case the ramp is a linear interpolation
between each pair of colours named, using the same syntax as
when specifying a colour value. So for instance "
yellow-hotpink-#0000ff" would shade from yellow via hot pink
to blue.
[Default: inferno]
auxclip = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a subrange of the colour ramp to be used for Aux
shading. The value is specified as a (low,high)
comma-separated pair of two numbers between 0 and 1.
If the full range 0,1 is used, the whole range of colours
specified by the selected shader will be used. But if for
instance a value of 0,0.5 is given, only those colours at the
left hand end of the ramp will be seen.
If the null (default) value is chosen, a default clip will be
used. This generally covers most or all of the range 0-1 but
for colour maps which fade to white, a small proportion of the
lower end may be excluded, to ensure that all the colours are
visually distinguishable from a white background. This default
is usually a good idea if the colour map is being used with
something like a scatter plot, where markers are plotted
against a white background. However, for something like a
density map when the whole plotting area is tiled with colours
from the map, it may be better to supply the whole range 0,1
explicitly.
auxflip = true|false (Boolean)
If true, the colour map on the Aux axis will be reversed.
[Default: false]
auxquant = <number> (Double)
Allows the colour map used for the Aux axis to be quantised.
If an integer value N is chosen then the colour map will be
viewed as N discrete evenly-spaced levels, so that only N
different colours will appear in the plot. This can be used to
generate a contour-like effect, and may make it easier to
trace the boundaries of regions of interest by eye.
If left blank, the colour map is nominally continuous (though
in practice it may be quantised to a medium-sized number like
256).
auxfunc = log|linear|sqrt|square
(uk.ac.starlink.ttools.plot2.Scaling)
Defines the way that values in the Aux range are mapped to the
selected colour ramp.
The available options are:
* log: Logarithmic scaling
* linear: Linear scaling
* sqrt: Square root scaling
* square: Square scaling
[Default: linear]
auxmin = <number> (Double)
Minimum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
auxmax = <number> (Double)
Maximum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
auxlabel = <text> (String)
Sets the label used to annotate the aux axis, if it is
visible.
auxcrowd = <factor> (Double)
Determines how closely the tick marks are spaced on the Aux
axis, if visible. The default value is 1, meaning normal
crowding. Larger values result in more ticks, and smaller
values fewer ticks. Tick marks will not however be spaced so
closely that the labels overlap each other, so to get very
closely spaced marks you may need to reduce the font size as
well.
[Default: 1.0]
auxwidth = <pixels> (Integer)
Determines the lateral size of the aux colour ramp, if
visible, in pixels.
[Default: 15]
auxvisible = true|false (Boolean)
Determines whether the aux axis colour ramp is displayed
alongside the plot.
If not supplied (the default), the aux axis will be visible
when aux shading is used in any of the plotted layers.
forcebitmap = true|false (Boolean)
Affects whether rendering of the data contents of a plot
(though not axis labels etc) is always done to an intermediate
bitmap rather than, where possible, being painted using
graphics primitives. This is a rather arcane setting that may
nevertheless have noticeable effects on the appearance and
size of an output graphics file, as well as plotting time. For
some types of plot (e.g. shadingN=auto or shadingN=density) it
will have no effect, since this kind of rendering happens in
any case.
When writing to vector graphics formats (PDF and PostScript),
setting it true will force the data contents to be bitmapped.
This may make the output less beautiful (round markers will no
longer be perfectly round), but it may result in a much
smaller file if there are very many data points.
When writing to bitmapped output formats (PNG, GIF, JPEG,
...), it fixes shapes to be the same as seen on the screen
rather than be rendered at the mercy of the graphics system,
which sometimes introduces small distortions.
[Default: false]
compositor = 0..1
(uk.ac.starlink.ttools.plot2.paper.Compositor)
Defines how multiple overplotted partially transparent pixels
are combined to form a resulting colour. The way this is used
depends on the details of the specified plot.
Currently, this parameter takes a "boost" value in the range
0..1. If the value is zero, saturation semantics are used: RGB
colours are added in proporition to their associated alpha
value until the total alpha is saturated (reaches 1), after
which additional pixels have no further effect. For larger
boost values, the effect is similar, but any non-zero alpha in
the output is boosted to the given minimum value. The effect
of this is that even very slightly populated pixels can be
visually distinguished from unpopulated ones which may not be
the case for saturation composition.
[Default: 0.05]
animate = <table> (uk.ac.starlink.table.StarTable)
Input table.
parallel = <int-value> (Integer)
Determines how many threads will run in parallel if animation
output is being produced. Only used if the animate parameter
is supplied. The default value is the number of processors
apparently available to the JVM.
[Default: 4]
xlog = true|false (Boolean)
If false (the default), the scale on the X axis is linear, if
true it is logarithmic.
[Default: false]
ylog = true|false (Boolean)
If false (the default), the scale on the Y axis is linear, if
true it is logarithmic.
[Default: false]
xflip = true|false (Boolean)
If true, the scale on the X axis will increase in the opposite
sense from usual (e.g. right to left rather than left to
right).
[Default: false]
yflip = true|false (Boolean)
If true, the scale on the Y axis will increase in the opposite
sense from usual (e.g. right to left rather than left to
right).
[Default: false]
xlabel = <text> (String)
Gives a label to be used for annotating axis X A default value
based on the plotted data will be used if no value is
supplied.
[Default: X]
ylabel = <text> (String)
Gives a label to be used for annotating axis Y A default value
based on the plotted data will be used if no value is
supplied.
[Default: Y]
aspect = <number> (Double)
Ratio of the unit length on the X axis to the unit length on
the Y axis. If set to 1, the space will be isotropic. If not
set (the default) the ratio will be determined by the given or
calculated data bounds on both axes and the shape of the
plotting region.
grid = true|false (Boolean)
If true, grid lines are drawn on the plot at positions
determined by the major tick marks. If false, they are absent.
[Default: false]
xcrowd = <number> (Double)
Determines how closely the tick marks are spaced on the X
axis. The default value is 1, meaning normal crowding. Larger
values result in more ticks, and smaller values fewer ticks.
Tick marks will not however be spaced so closely that the
labels overlap each other, so to get very closely spaced marks
you may need to reduce the font size as well.
[Default: 1]
ycrowd = <number> (Double)
Determines how closely the tick marks are spaced on the Y
axis. The default value is 1, meaning normal crowding. Larger
values result in more ticks, and smaller values fewer ticks.
Tick marks will not however be spaced so closely that the
labels overlap each other, so to get very closely spaced marks
you may need to reduce the font size as well.
[Default: 1]
minor = true|false (Boolean)
If true, minor tick marks are painted along the axes as well
as the major tick marks. Minor tick marks do not have
associated grid lines.
[Default: true]
gridcolor = <rrggbb>|red|blue|... (java.awt.Color)
The color of the plot grid, given by name or as a hexadecimal
RGB value.
The standard plotting colour names are red, blue, green, grey
, magenta, cyan, orange, pink, yellow, black, light_grey,
white. However, many other common colour names (too many to
list here) are also understood. The list currently contains
those colour names understood by most web browsers, from
AliceBlue to YellowGreen, listed e.g. in the Extended color
keywords section of the CSS3 standard.
Alternatively, a six-digit hexadecimal number RRGGBB may be
supplied, optionally prefixed by "#" or "0x", giving red,
green and blue intensities, e.g. "ff00ff", "#ff00ff" or "
0xff00ff" for magenta.
[Default: light_grey]
labelcolor = <rrggbb>|red|blue|... (java.awt.Color)
The color of axis labels and other plot annotations, given by
name or as a hexadecimal RGB value.
The standard plotting colour names are red, blue, green, grey
, magenta, cyan, orange, pink, yellow, black, light_grey,
white. However, many other common colour names (too many to
list here) are also understood. The list currently contains
those colour names understood by most web browsers, from
AliceBlue to YellowGreen, listed e.g. in the Extended color
keywords section of the CSS3 standard.
Alternatively, a six-digit hexadecimal number RRGGBB may be
supplied, optionally prefixed by "#" or "0x", giving red,
green and blue intensities, e.g. "ff00ff", "#ff00ff" or "
0xff00ff" for magenta.
[Default: black]
texttype = plain|antialias|latex (TextSyntax)
Determines how to turn label text into characters on the plot.
Plain and Antialias both take the text at face value, but
Antialias smooths the characters. LaTeX interprets the text as
LaTeX source code and typesets it accordingly.
When not using LaTeX, antialiased text usually looks nicer,
but can be perceptibly slower to plot. At time of writing, on
MacOS antialiased text seems to be required to stop the
writing coming out upside-down for non-horizontal text (MacOS
java bug).
[Default: plain]
fontsize = <int-value> (Integer)
Size of the text font in points.
[Default: 12]
fontstyle = standard|serif|mono (FontType)
Font style for text.
The available options are:
* standard
* serif
* mono
[Default: standard]
fontweight = plain|bold|italic|bold_italic (FontWeight)
Font weight for text.
The available options are:
* plain
* bold
* italic
* bold_italic
[Default: plain]
xmin = <number> (Double)
Minimum value of the data coordinate on the X axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
xmax = <number> (Double)
Maximum value of the data coordinate on the X axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
xsub = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a normalised adjustment to the data range of the X
axis. The value may be specified as a comma-separated pair of
two numbers, giving the lower and upper bounds of the range of
of interest respectively. This sub-range is applied to the
data range that would otherwise be used, either automatically
calculated or explicitly supplied; zero corresponds to the
lower bound and one to the upper.
The default value "0,1" therefore has no effect. The range
could be restricted to its lower half with the value 0,0.5.
[Default: 0,1]
ymin = <number> (Double)
Minimum value of the data coordinate on the Y axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
ymax = <number> (Double)
Maximum value of the data coordinate on the Y axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
ysub = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a normalised adjustment to the data range of the Y
axis. The value may be specified as a comma-separated pair of
two numbers, giving the lower and upper bounds of the range of
of interest respectively. This sub-range is applied to the
data range that would otherwise be used, either automatically
calculated or explicitly supplied; zero corresponds to the
lower bound and one to the upper.
The default value "0,1" therefore has no effect. The range
could be restricted to its lower half with the value 0,0.5.
[Default: 0,1]
navaxes = xy|x|y (boolean[])
Determines the axes which are affected by the interactive
navigation actions (pan and zoom). The default is xy, which
means that the various mouse gestures will provide panning and
zooming in both X and Y directions. However, if it is set to
(for instance) x then the mouse will only allow panning and
zooming in the horizontal direction, with the vertical extent
fixed.
[Default: xy]
xanchor = true|false (Boolean)
If true, then zoom actions will work in such a way that the
zero point on the X axis stays in the same position on the
plot.
[Default: false]
yanchor = true|false (Boolean)
If true, then zoom actions will work in such a way that the
zero point on the Y axis stays in the same position on the
plot.
[Default: false]
zoomfactor = <number> (Double)
Sets the amount by which the plot view zooms in or out for
each unit of mouse wheel movement. A value of 1 means that
mouse wheel zooming has no effect. A higher value means that
the mouse wheel zooms faster and a value nearer 1 means it
zooms slower. Values below 1 are not permitted.
[Default: 1.2]
leglabelN = <text> (String)
Sets the presentation label for the layer with a given suffix.
This is the text which is displayed in the legend, if present.
Multiple layers may use the same label, in which case they
will be combined to form a single legend entry.
If no value is supplied (the default), the suffix itself is
used as the label.
layerN = <layer-type> <layerN-specific-params>
(uk.ac.starlink.ttools.plot2.task.LayerType)
Selects one of the available plot types for layerN. A plot
consists of a plotting surface, set up using the various
unsuffixed parameters of the plotting command, and zero or
more plot layers. Each layer is introduced by a parameter with
the name layer<N> where the suffix "<N>" is a label
identifying the layer and is appended to all the parameter
names which configure that layer. Suffixes may be any string,
including the empty string.
This parameter may take one of the following values, described
in more detail in SUN/256:
* mark
* size
* sizexy
* xyvector
* xyerror
* xyellipse
* xycorr
* link2
* mark2
* line
* linearfit
* label
* contour
* grid
* fill
* quantile
* histogram
* kde
* knn
* densogram
* gaussian
* function
Each of these layer types comes with a list of type-specific
parameters to define the details of that layer, including some
or all of the following groups:
* input table parameters (e.g. inN, icmdN)
* coordinate params referring to input table columns (e.g.
xN, yN)
* layer style parameters (e.g. shadingN, colorN)
Every parameter notionally carries the same suffix N. However,
if the suffix is not present, the application will try looking
for a parameter with the same name with no suffix instead. In
this way, if several layers have the same value for a given
parameter (for instance input table), you can supply it using
one unsuffixed parameter to save having to supply several
parameters with the same value but different suffixes.
'''
task = _stilts.getTaskFactory().createObject('plot2plane')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def plot2sky(**kwargs):
'''\
Draws a sky plot.
Parameters:
xpix = <int-value> (Integer)
Size of the output image in the X direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 500]
ypix = <int-value> (Integer)
Size of the output image in the Y direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 400]
insets = <top>,<left>,<bottom>,<right>
(uk.ac.starlink.ttools.plot2.Padding)
Defines the amount of space in pixels around the actual
plotting area. This space is used for axis labels, and other
decorations and any left over forms an empty border.
The size and position of the actual plotting area is
determined by this parameter along with xpix and ypix.
The value of this parameter is 4 comma separated integers:
<top>,<left>,<bottom>,<right>. Any or all of these values may
be left blank, in which case the corresponding margin will be
calculated automatically according to how much space is
required.
omode = swing|out|cgi|discard|auto
(uk.ac.starlink.ttools.plottask.PaintMode)
Determines how the drawn plot will be output, see SUN/256.
* swing: Plot will be displayed in a window on the screen.
This plot is "live"; it can be resized and (except for
old-style plots) navigated around with mouse actions in
the same way as plots in TOPCAT.
* out: Plot will be written to a file given by out using the
graphics format given by ofmt.
* cgi: Plot will be written in a way suitable for CGI use
direct from a web server. The output is in the graphics
format given by ofmt, preceded by a suitable
"Content-type" declaration.
* discard: Plot is drawn, but discarded. There is no output.
* auto: Behaves as swing or out mode depending on presence of
out parameter
[Default: auto]
storage = simple|cache|basic-cache
(uk.ac.starlink.ttools.plot2.data.DataStoreFactory)
Determines the way that data is accessed when constructing the
plot. There are two basic options, cached or not.
If no caching is used (simple) then rows are read sequentially
from the specified input table(s) every time they are
required. This generally requires a small memory footprint
(though that can depend on how the table is specified) and
makes sense if the data only needs to be scanned once or
perhaps if the table is very large.
If caching is used (cache) then the required data is read once
from the specified input table(s) and cached before any
plotting is performed, and plots are done using this cached
data. This may use a significant amount of memory for large
tables but it's usually more sensible (faster) if the data
will need to be scanned multiple times.
The default value is cache if a live plot is being generated (
omode=swing), since in that case the plot needs to be redrawn
every time the user performs plot navigation actions or
resizes the window, or if animations are being produced.
Otherwise (e.g. output to a graphics file) the default is
simple.
[Default: simple]
seq = <suffix>[,...] (String[])
Contains a comma-separated list of layer suffixes to determine
the order in which layers are drawn on the plot. This can
affect which symbol are plotted on top of, and so potentially
obscure, which other ones.
When specifying a plot, multiple layers may be specified, each
introduced by a parameter layer<N>, where <N> is a different
(arbitrary) suffix labelling the layer, and is appended to all
the parameters specific to defining that layer.
By default the layers are drawn on the plot in the order in
which the layer* parameters appear on the command line.
However if this parameter is specified, each comma-separated
element is interpreted as a layer suffix, giving the ordered
list of layers to plot. Every element of the list must be a
suffix with a corresponding layer parameter, but missing or
repeated elements are allowed.
legend = true|false (Boolean)
Whether to draw a legend or not. If no value is supplied, the
decision is made automatically: a legend is drawn only if it
would have more than one entry.
legborder = true|false (Boolean)
If true, a line border is drawn around the legend.
[Default: true]
legopaque = true|false (Boolean)
If true, the background of the legend is opaque, and the
legend obscures any plot components behind it. Otherwise, it's
transparent.
[Default: true]
legseq = <suffix>[,...] (String[])
Determines which layers are represented in the legend (if
present) and in which order they appear. The legend has a line
for each layer label (as determined by the leglabelN
parameter). If multiple layers have the same label, they will
contribute to the same entry in the legend, with style icons
plotted over each other. The value of this parameter is a
comma-separated sequence of layer suffixes, which determines
the order in which the legend entries appear. Layers with
suffixes missing from this list do not show up in the legend
at all.
If no value is supplied (the default), the sequence is the
same as the layer plotting sequence (see seq).
legpos = <xfrac,yfrac> (double[])
Determines the internal position of the legend on the plot.
The value is a comma-separated pair of values giving the X and
Y positions of the legend within the plotting bounds, so for
instance "0.5,0.5" will put the legend right in the middle of
the plot. If no value is supplied, the legend will appear
outside the plot boundary.
title = <value> (String)
Text of a title to be displayed at the top of the plot. If
null, the default, no title is shown and there's more space
for the graphics.
auxmap = <map-name>|<color>-<color>[-<color>...]
(uk.ac.starlink.ttools.plot.Shader)
Color map used for Aux axis shading.
A mixed bag of colour ramps are available: inferno, magma,
plasma, viridis, cubehelix, sron, rainbow, rainbow2, rainbow3
, pastel, accent, gnuplot, gnuplot2, specxby, set1, paired,
hotcold, rdbu, piyg, brbg, cyan-magenta, red-blue, brg, heat,
cold, light, greyscale, colour, standard, bugn, bupu, orrd,
pubu, purd, huecl, hue, intensity, rgb_red, rgb_green,
rgb_blue, hsv_h, hsv_s, hsv_v, yuv_y, yuv_u, yuv_v,
scale_hsv_s, scale_hsv_v, scale_yuv_y, mask, blacker, whiter,
transparency. Note: many of these, including rainbow-like
ones, are frowned upon by the visualisation community.
You can also construct your own custom colour map by giving a
sequence of colour names separated by minus sign ("-")
characters. In this case the ramp is a linear interpolation
between each pair of colours named, using the same syntax as
when specifying a colour value. So for instance "
yellow-hotpink-#0000ff" would shade from yellow via hot pink
to blue.
[Default: inferno]
auxclip = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a subrange of the colour ramp to be used for Aux
shading. The value is specified as a (low,high)
comma-separated pair of two numbers between 0 and 1.
If the full range 0,1 is used, the whole range of colours
specified by the selected shader will be used. But if for
instance a value of 0,0.5 is given, only those colours at the
left hand end of the ramp will be seen.
If the null (default) value is chosen, a default clip will be
used. This generally covers most or all of the range 0-1 but
for colour maps which fade to white, a small proportion of the
lower end may be excluded, to ensure that all the colours are
visually distinguishable from a white background. This default
is usually a good idea if the colour map is being used with
something like a scatter plot, where markers are plotted
against a white background. However, for something like a
density map when the whole plotting area is tiled with colours
from the map, it may be better to supply the whole range 0,1
explicitly.
auxflip = true|false (Boolean)
If true, the colour map on the Aux axis will be reversed.
[Default: false]
auxquant = <number> (Double)
Allows the colour map used for the Aux axis to be quantised.
If an integer value N is chosen then the colour map will be
viewed as N discrete evenly-spaced levels, so that only N
different colours will appear in the plot. This can be used to
generate a contour-like effect, and may make it easier to
trace the boundaries of regions of interest by eye.
If left blank, the colour map is nominally continuous (though
in practice it may be quantised to a medium-sized number like
256).
auxfunc = log|linear|sqrt|square
(uk.ac.starlink.ttools.plot2.Scaling)
Defines the way that values in the Aux range are mapped to the
selected colour ramp.
The available options are:
* log: Logarithmic scaling
* linear: Linear scaling
* sqrt: Square root scaling
* square: Square scaling
[Default: linear]
auxmin = <number> (Double)
Minimum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
auxmax = <number> (Double)
Maximum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
auxlabel = <text> (String)
Sets the label used to annotate the aux axis, if it is
visible.
auxcrowd = <factor> (Double)
Determines how closely the tick marks are spaced on the Aux
axis, if visible. The default value is 1, meaning normal
crowding. Larger values result in more ticks, and smaller
values fewer ticks. Tick marks will not however be spaced so
closely that the labels overlap each other, so to get very
closely spaced marks you may need to reduce the font size as
well.
[Default: 1.0]
auxwidth = <pixels> (Integer)
Determines the lateral size of the aux colour ramp, if
visible, in pixels.
[Default: 15]
auxvisible = true|false (Boolean)
Determines whether the aux axis colour ramp is displayed
alongside the plot.
If not supplied (the default), the aux axis will be visible
when aux shading is used in any of the plotted layers.
forcebitmap = true|false (Boolean)
Affects whether rendering of the data contents of a plot
(though not axis labels etc) is always done to an intermediate
bitmap rather than, where possible, being painted using
graphics primitives. This is a rather arcane setting that may
nevertheless have noticeable effects on the appearance and
size of an output graphics file, as well as plotting time. For
some types of plot (e.g. shadingN=auto or shadingN=density) it
will have no effect, since this kind of rendering happens in
any case.
When writing to vector graphics formats (PDF and PostScript),
setting it true will force the data contents to be bitmapped.
This may make the output less beautiful (round markers will no
longer be perfectly round), but it may result in a much
smaller file if there are very many data points.
When writing to bitmapped output formats (PNG, GIF, JPEG,
...), it fixes shapes to be the same as seen on the screen
rather than be rendered at the mercy of the graphics system,
which sometimes introduces small distortions.
[Default: false]
compositor = 0..1
(uk.ac.starlink.ttools.plot2.paper.Compositor)
Defines how multiple overplotted partially transparent pixels
are combined to form a resulting colour. The way this is used
depends on the details of the specified plot.
Currently, this parameter takes a "boost" value in the range
0..1. If the value is zero, saturation semantics are used: RGB
colours are added in proporition to their associated alpha
value until the total alpha is saturated (reaches 1), after
which additional pixels have no further effect. For larger
boost values, the effect is similar, but any non-zero alpha in
the output is boosted to the given minimum value. The effect
of this is that even very slightly populated pixels can be
visually distinguished from unpopulated ones which may not be
the case for saturation composition.
[Default: 0.05]
animate = <table> (uk.ac.starlink.table.StarTable)
Input table.
parallel = <int-value> (Integer)
Determines how many threads will run in parallel if animation
output is being produced. Only used if the animate parameter
is supplied. The default value is the number of processors
apparently available to the JVM.
[Default: 4]
projection = sin|aitoff|car
(uk.ac.starlink.ttools.plot2.geom.Projection)
Sky projection used to display the plot.
The available options are:
* sin: rotatable sphere
* aitoff: Hammer-Aitoff projection
* car: Plate Carree projection (lon/lat on Cartesian axes)
[Default: sin]
viewsys = equatorial|galactic|supergalactic|ecliptic
(uk.ac.starlink.ttools.plot2.geom.SkySys)
The sky coordinate system used for the generated plot.
Choice of this value goes along with the data coordinate
system that may be specified for plot layers. If unspecified,
a generic longitude/latitude system is used, and all lon/lat
coordinates in the plotted data layers are assumed to be in
the same system. If a value is supplied for this parameter,
then a sky system must (implicitly or explicitly) be supplied
for each data layer, and the coordinates are converted from
data to view system before being plotted.
The available options are:
* equatorial: J2000 equatorial system
* galactic: IAU 1958 galactic system
* supergalactic: De Vaucouleurs supergalactic system
* ecliptic: ecliptic system based on conversion at 2000.0
reflectlon = true|false (Boolean)
Whether to invert the celestial sphere by displaying the
longitude axis increasing right-to-left rather than
left-to-right. It is conventional to display the celestial
sphere in this way because that's what it looks like from the
earth, so the default is true. Set it false to see the sphere
from the outside.
[Default: true]
grid = true|false (Boolean)
If true, sky coordinate grid lines are drawn on the plot. If
false, they are absent.
[Default: true]
labelpos = Auto|External|Internal|Basic|Hybrid|None
(uk.ac.starlink.ttools.plot2.geom.SkyAxisLabeller)
Controls whether and where the numeric annotations of the
lon/lat axes are displayed. The default option Auto usually
does the sensible thing, but other options exist to force
labelling internally or externally to the plot region, or to
remove numeric labels altogether.
The available options are:
* Auto: Uses External or Internal policy according to whether
the sky fills the plot bounds or not
* External: Labels are drawn outside the plot bounds
* Internal: Labels are drawn inside the plot bounds
* Basic: Labels are drawn somewhere near the grid line
* Hybrid: Grid lines are labelled outside the plot bounds
where possible, but inside if they would otherwise be
invisible
* None: Axes are not labelled
[Default: Auto]
sex = true|false (Boolean)
If true, grid line labels are written in sexagesimal notation,
if false in decimal degrees.
[Default: true]
crowd = <number> (Double)
Determines how closely sky grid lines are spaced. The default
value is 1, meaning normal crowding. Larger values result in
more grid lines, and smaller values in fewer grid lines.
[Default: 1]
gridcolor = <rrggbb>|red|blue|... (java.awt.Color)
The color of the plot grid, given by name or as a hexadecimal
RGB value.
The standard plotting colour names are red, blue, green, grey
, magenta, cyan, orange, pink, yellow, black, light_grey,
white. However, many other common colour names (too many to
list here) are also understood. The list currently contains
those colour names understood by most web browsers, from
AliceBlue to YellowGreen, listed e.g. in the Extended color
keywords section of the CSS3 standard.
Alternatively, a six-digit hexadecimal number RRGGBB may be
supplied, optionally prefixed by "#" or "0x", giving red,
green and blue intensities, e.g. "ff00ff", "#ff00ff" or "
0xff00ff" for magenta.
[Default: light_grey]
labelcolor = <rrggbb>|red|blue|... (java.awt.Color)
The color of axis labels and other plot annotations, given by
name or as a hexadecimal RGB value.
The standard plotting colour names are red, blue, green, grey
, magenta, cyan, orange, pink, yellow, black, light_grey,
white. However, many other common colour names (too many to
list here) are also understood. The list currently contains
those colour names understood by most web browsers, from
AliceBlue to YellowGreen, listed e.g. in the Extended color
keywords section of the CSS3 standard.
Alternatively, a six-digit hexadecimal number RRGGBB may be
supplied, optionally prefixed by "#" or "0x", giving red,
green and blue intensities, e.g. "ff00ff", "#ff00ff" or "
0xff00ff" for magenta.
[Default: black]
gridaa = true|false (Boolean)
If true, grid lines are drawn with antialiasing. Antialiased
lines look smoother, but may take perceptibly longer to draw.
Only has any effect for bitmapped output formats.
[Default: false]
texttype = plain|antialias|latex (TextSyntax)
Determines how to turn label text into characters on the plot.
Plain and Antialias both take the text at face value, but
Antialias smooths the characters. LaTeX interprets the text as
LaTeX source code and typesets it accordingly.
When not using LaTeX, antialiased text usually looks nicer,
but can be perceptibly slower to plot. At time of writing, on
MacOS antialiased text seems to be required to stop the
writing coming out upside-down for non-horizontal text (MacOS
java bug).
[Default: plain]
fontsize = <int-value> (Integer)
Size of the text font in points.
[Default: 12]
fontstyle = standard|serif|mono (FontType)
Font style for text.
The available options are:
* standard
* serif
* mono
[Default: standard]
fontweight = plain|bold|italic|bold_italic (FontWeight)
Font weight for text.
The available options are:
* plain
* bold
* italic
* bold_italic
[Default: plain]
clon = <degrees> (Double)
Longitude of the central position of the plot in decimal
degrees. Use with clat and radius. If the center is not
specified, the field of view is determined from the data.
clat = <degrees> (Double)
Latitude of the central position of the plot in decimal
degrees. Use with clon and radius. If the center is not
specified, the field of view is determined from the data.
radius = <degrees> (Double)
Approximate radius of the plot field of view in degrees. Only
used if clon and clat are also specified.
[Default: 1]
zoomfactor = <number> (Double)
Sets the amount by which the plot view zooms in or out for
each unit of mouse wheel movement. A value of 1 means that
mouse wheel zooming has no effect. A higher value means that
the mouse wheel zooms faster and a value nearer 1 means it
zooms slower. Values below 1 are not permitted.
[Default: 1.2]
leglabelN = <text> (String)
Sets the presentation label for the layer with a given suffix.
This is the text which is displayed in the legend, if present.
Multiple layers may use the same label, in which case they
will be combined to form a single legend entry.
If no value is supplied (the default), the suffix itself is
used as the label.
layerN = <layer-type> <layerN-specific-params>
(uk.ac.starlink.ttools.plot2.task.LayerType)
Selects one of the available plot types for layerN. A plot
consists of a plotting surface, set up using the various
unsuffixed parameters of the plotting command, and zero or
more plot layers. Each layer is introduced by a parameter with
the name layer<N> where the suffix "<N>" is a label
identifying the layer and is appended to all the parameter
names which configure that layer. Suffixes may be any string,
including the empty string.
This parameter may take one of the following values, described
in more detail in SUN/256:
* mark
* size
* sizexy
* skyvector
* skyellipse
* skycorr
* link2
* mark2
* label
* contour
* skydensity
* healpix
* skygrid
Each of these layer types comes with a list of type-specific
parameters to define the details of that layer, including some
or all of the following groups:
* input table parameters (e.g. inN, icmdN)
* coordinate params referring to input table columns (e.g.
xN, yN)
* layer style parameters (e.g. shadingN, colorN)
Every parameter notionally carries the same suffix N. However,
if the suffix is not present, the application will try looking
for a parameter with the same name with no suffix instead. In
this way, if several layers have the same value for a given
parameter (for instance input table), you can supply it using
one unsuffixed parameter to save having to supply several
parameters with the same value but different suffixes.
'''
task = _stilts.getTaskFactory().createObject('plot2sky')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def plot2cube(**kwargs):
'''\
Draws a cube plot.
Parameters:
xpix = <int-value> (Integer)
Size of the output image in the X direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 500]
ypix = <int-value> (Integer)
Size of the output image in the Y direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 400]
insets = <top>,<left>,<bottom>,<right>
(uk.ac.starlink.ttools.plot2.Padding)
Defines the amount of space in pixels around the actual
plotting area. This space is used for axis labels, and other
decorations and any left over forms an empty border.
The size and position of the actual plotting area is
determined by this parameter along with xpix and ypix.
The value of this parameter is 4 comma separated integers:
<top>,<left>,<bottom>,<right>. Any or all of these values may
be left blank, in which case the corresponding margin will be
calculated automatically according to how much space is
required.
omode = swing|out|cgi|discard|auto
(uk.ac.starlink.ttools.plottask.PaintMode)
Determines how the drawn plot will be output, see SUN/256.
* swing: Plot will be displayed in a window on the screen.
This plot is "live"; it can be resized and (except for
old-style plots) navigated around with mouse actions in
the same way as plots in TOPCAT.
* out: Plot will be written to a file given by out using the
graphics format given by ofmt.
* cgi: Plot will be written in a way suitable for CGI use
direct from a web server. The output is in the graphics
format given by ofmt, preceded by a suitable
"Content-type" declaration.
* discard: Plot is drawn, but discarded. There is no output.
* auto: Behaves as swing or out mode depending on presence of
out parameter
[Default: auto]
storage = simple|cache|basic-cache
(uk.ac.starlink.ttools.plot2.data.DataStoreFactory)
Determines the way that data is accessed when constructing the
plot. There are two basic options, cached or not.
If no caching is used (simple) then rows are read sequentially
from the specified input table(s) every time they are
required. This generally requires a small memory footprint
(though that can depend on how the table is specified) and
makes sense if the data only needs to be scanned once or
perhaps if the table is very large.
If caching is used (cache) then the required data is read once
from the specified input table(s) and cached before any
plotting is performed, and plots are done using this cached
data. This may use a significant amount of memory for large
tables but it's usually more sensible (faster) if the data
will need to be scanned multiple times.
The default value is cache if a live plot is being generated (
omode=swing), since in that case the plot needs to be redrawn
every time the user performs plot navigation actions or
resizes the window, or if animations are being produced.
Otherwise (e.g. output to a graphics file) the default is
simple.
[Default: simple]
seq = <suffix>[,...] (String[])
Contains a comma-separated list of layer suffixes to determine
the order in which layers are drawn on the plot. This can
affect which symbol are plotted on top of, and so potentially
obscure, which other ones.
When specifying a plot, multiple layers may be specified, each
introduced by a parameter layer<N>, where <N> is a different
(arbitrary) suffix labelling the layer, and is appended to all
the parameters specific to defining that layer.
By default the layers are drawn on the plot in the order in
which the layer* parameters appear on the command line.
However if this parameter is specified, each comma-separated
element is interpreted as a layer suffix, giving the ordered
list of layers to plot. Every element of the list must be a
suffix with a corresponding layer parameter, but missing or
repeated elements are allowed.
legend = true|false (Boolean)
Whether to draw a legend or not. If no value is supplied, the
decision is made automatically: a legend is drawn only if it
would have more than one entry.
legborder = true|false (Boolean)
If true, a line border is drawn around the legend.
[Default: true]
legopaque = true|false (Boolean)
If true, the background of the legend is opaque, and the
legend obscures any plot components behind it. Otherwise, it's
transparent.
[Default: true]
legseq = <suffix>[,...] (String[])
Determines which layers are represented in the legend (if
present) and in which order they appear. The legend has a line
for each layer label (as determined by the leglabelN
parameter). If multiple layers have the same label, they will
contribute to the same entry in the legend, with style icons
plotted over each other. The value of this parameter is a
comma-separated sequence of layer suffixes, which determines
the order in which the legend entries appear. Layers with
suffixes missing from this list do not show up in the legend
at all.
If no value is supplied (the default), the sequence is the
same as the layer plotting sequence (see seq).
legpos = <xfrac,yfrac> (double[])
Determines the internal position of the legend on the plot.
The value is a comma-separated pair of values giving the X and
Y positions of the legend within the plotting bounds, so for
instance "0.5,0.5" will put the legend right in the middle of
the plot. If no value is supplied, the legend will appear
outside the plot boundary.
title = <value> (String)
Text of a title to be displayed at the top of the plot. If
null, the default, no title is shown and there's more space
for the graphics.
auxmap = <map-name>|<color>-<color>[-<color>...]
(uk.ac.starlink.ttools.plot.Shader)
Color map used for Aux axis shading.
A mixed bag of colour ramps are available: inferno, magma,
plasma, viridis, cubehelix, sron, rainbow, rainbow2, rainbow3
, pastel, accent, gnuplot, gnuplot2, specxby, set1, paired,
hotcold, rdbu, piyg, brbg, cyan-magenta, red-blue, brg, heat,
cold, light, greyscale, colour, standard, bugn, bupu, orrd,
pubu, purd, huecl, hue, intensity, rgb_red, rgb_green,
rgb_blue, hsv_h, hsv_s, hsv_v, yuv_y, yuv_u, yuv_v,
scale_hsv_s, scale_hsv_v, scale_yuv_y, mask, blacker, whiter,
transparency. Note: many of these, including rainbow-like
ones, are frowned upon by the visualisation community.
You can also construct your own custom colour map by giving a
sequence of colour names separated by minus sign ("-")
characters. In this case the ramp is a linear interpolation
between each pair of colours named, using the same syntax as
when specifying a colour value. So for instance "
yellow-hotpink-#0000ff" would shade from yellow via hot pink
to blue.
[Default: inferno]
auxclip = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a subrange of the colour ramp to be used for Aux
shading. The value is specified as a (low,high)
comma-separated pair of two numbers between 0 and 1.
If the full range 0,1 is used, the whole range of colours
specified by the selected shader will be used. But if for
instance a value of 0,0.5 is given, only those colours at the
left hand end of the ramp will be seen.
If the null (default) value is chosen, a default clip will be
used. This generally covers most or all of the range 0-1 but
for colour maps which fade to white, a small proportion of the
lower end may be excluded, to ensure that all the colours are
visually distinguishable from a white background. This default
is usually a good idea if the colour map is being used with
something like a scatter plot, where markers are plotted
against a white background. However, for something like a
density map when the whole plotting area is tiled with colours
from the map, it may be better to supply the whole range 0,1
explicitly.
auxflip = true|false (Boolean)
If true, the colour map on the Aux axis will be reversed.
[Default: false]
auxquant = <number> (Double)
Allows the colour map used for the Aux axis to be quantised.
If an integer value N is chosen then the colour map will be
viewed as N discrete evenly-spaced levels, so that only N
different colours will appear in the plot. This can be used to
generate a contour-like effect, and may make it easier to
trace the boundaries of regions of interest by eye.
If left blank, the colour map is nominally continuous (though
in practice it may be quantised to a medium-sized number like
256).
auxfunc = log|linear|sqrt|square
(uk.ac.starlink.ttools.plot2.Scaling)
Defines the way that values in the Aux range are mapped to the
selected colour ramp.
The available options are:
* log: Logarithmic scaling
* linear: Linear scaling
* sqrt: Square root scaling
* square: Square scaling
[Default: linear]
auxmin = <number> (Double)
Minimum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
auxmax = <number> (Double)
Maximum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
auxlabel = <text> (String)
Sets the label used to annotate the aux axis, if it is
visible.
auxcrowd = <factor> (Double)
Determines how closely the tick marks are spaced on the Aux
axis, if visible. The default value is 1, meaning normal
crowding. Larger values result in more ticks, and smaller
values fewer ticks. Tick marks will not however be spaced so
closely that the labels overlap each other, so to get very
closely spaced marks you may need to reduce the font size as
well.
[Default: 1.0]
auxwidth = <pixels> (Integer)
Determines the lateral size of the aux colour ramp, if
visible, in pixels.
[Default: 15]
auxvisible = true|false (Boolean)
Determines whether the aux axis colour ramp is displayed
alongside the plot.
If not supplied (the default), the aux axis will be visible
when aux shading is used in any of the plotted layers.
forcebitmap = true|false (Boolean)
Affects whether rendering of the data contents of a plot
(though not axis labels etc) is always done to an intermediate
bitmap rather than, where possible, being painted using
graphics primitives. This is a rather arcane setting that may
nevertheless have noticeable effects on the appearance and
size of an output graphics file, as well as plotting time. For
some types of plot (e.g. shadingN=auto or shadingN=density) it
will have no effect, since this kind of rendering happens in
any case.
When writing to vector graphics formats (PDF and PostScript),
setting it true will force the data contents to be bitmapped.
This may make the output less beautiful (round markers will no
longer be perfectly round), but it may result in a much
smaller file if there are very many data points.
When writing to bitmapped output formats (PNG, GIF, JPEG,
...), it fixes shapes to be the same as seen on the screen
rather than be rendered at the mercy of the graphics system,
which sometimes introduces small distortions.
[Default: false]
compositor = 0..1
(uk.ac.starlink.ttools.plot2.paper.Compositor)
Defines how multiple overplotted partially transparent pixels
are combined to form a resulting colour. The way this is used
depends on the details of the specified plot.
Currently, this parameter takes a "boost" value in the range
0..1. If the value is zero, saturation semantics are used: RGB
colours are added in proporition to their associated alpha
value until the total alpha is saturated (reaches 1), after
which additional pixels have no further effect. For larger
boost values, the effect is similar, but any non-zero alpha in
the output is boosted to the given minimum value. The effect
of this is that even very slightly populated pixels can be
visually distinguished from unpopulated ones which may not be
the case for saturation composition.
[Default: 0.05]
animate = <table> (uk.ac.starlink.table.StarTable)
Input table.
parallel = <int-value> (Integer)
Determines how many threads will run in parallel if animation
output is being produced. Only used if the animate parameter
is supplied. The default value is the number of processors
apparently available to the JVM.
[Default: 4]
xlog = true|false (Boolean)
If false (the default), the scale on the X axis is linear, if
true it is logarithmic.
[Default: false]
ylog = true|false (Boolean)
If false (the default), the scale on the Y axis is linear, if
true it is logarithmic.
[Default: false]
zlog = true|false (Boolean)
If false (the default), the scale on the Z axis is linear, if
true it is logarithmic.
[Default: false]
xflip = true|false (Boolean)
If true, the scale on the X axis will increase in the opposite
sense from usual (e.g. right to left rather than left to
right).
[Default: false]
yflip = true|false (Boolean)
If true, the scale on the Y axis will increase in the opposite
sense from usual (e.g. right to left rather than left to
right).
[Default: false]
zflip = true|false (Boolean)
If true, the scale on the Z axis will increase in the opposite
sense from usual (e.g. right to left rather than left to
right).
[Default: false]
xlabel = <text> (String)
Gives a label to be used for annotating axis X A default value
based on the plotted data will be used if no value is
supplied.
[Default: X]
ylabel = <text> (String)
Gives a label to be used for annotating axis Y A default value
based on the plotted data will be used if no value is
supplied.
[Default: Y]
zlabel = <text> (String)
Gives a label to be used for annotating axis Z A default value
based on the plotted data will be used if no value is
supplied.
[Default: Z]
xcrowd = <number> (Double)
Determines how closely the tick marks are spaced on the X
axis. The default value is 1, meaning normal crowding. Larger
values result in more ticks, and smaller values fewer ticks.
Tick marks will not however be spaced so closely that the
labels overlap each other, so to get very closely spaced marks
you may need to reduce the font size as well.
[Default: 1]
ycrowd = <number> (Double)
Determines how closely the tick marks are spaced on the Y
axis. The default value is 1, meaning normal crowding. Larger
values result in more ticks, and smaller values fewer ticks.
Tick marks will not however be spaced so closely that the
labels overlap each other, so to get very closely spaced marks
you may need to reduce the font size as well.
[Default: 1]
zcrowd = <number> (Double)
Determines how closely the tick marks are spaced on the Z
axis. The default value is 1, meaning normal crowding. Larger
values result in more ticks, and smaller values fewer ticks.
Tick marks will not however be spaced so closely that the
labels overlap each other, so to get very closely spaced marks
you may need to reduce the font size as well.
[Default: 1]
frame = true|false (Boolean)
If true, a cube wire frame with labelled axes is drawn to
indicate the limits of the plotted 3D region. If false, no
wire frame and no axes are drawn.
[Default: true]
minor = true|false (Boolean)
If true, minor tick marks are painted along the axes as well
as the major tick marks. Minor tick marks do not have
associated grid lines.
[Default: true]
gridaa = true|false (Boolean)
If true, grid lines are drawn with antialiasing. Antialiased
lines look smoother, but may take perceptibly longer to draw.
Only has any effect for bitmapped output formats.
[Default: false]
texttype = plain|antialias|latex (TextSyntax)
Determines how to turn label text into characters on the plot.
Plain and Antialias both take the text at face value, but
Antialias smooths the characters. LaTeX interprets the text as
LaTeX source code and typesets it accordingly.
When not using LaTeX, antialiased text usually looks nicer,
but can be perceptibly slower to plot. At time of writing, on
MacOS antialiased text seems to be required to stop the
writing coming out upside-down for non-horizontal text (MacOS
java bug).
[Default: plain]
fontsize = <int-value> (Integer)
Size of the text font in points.
[Default: 12]
fontstyle = standard|serif|mono (FontType)
Font style for text.
The available options are:
* standard
* serif
* mono
[Default: standard]
fontweight = plain|bold|italic|bold_italic (FontWeight)
Font weight for text.
The available options are:
* plain
* bold
* italic
* bold_italic
[Default: plain]
xmin = <number> (Double)
Minimum value of the data coordinate on the X axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
xmax = <number> (Double)
Maximum value of the data coordinate on the X axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
xsub = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a normalised adjustment to the data range of the X
axis. The value may be specified as a comma-separated pair of
two numbers, giving the lower and upper bounds of the range of
of interest respectively. This sub-range is applied to the
data range that would otherwise be used, either automatically
calculated or explicitly supplied; zero corresponds to the
lower bound and one to the upper.
The default value "0,1" therefore has no effect. The range
could be restricted to its lower half with the value 0,0.5.
[Default: 0,1]
ymin = <number> (Double)
Minimum value of the data coordinate on the Y axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
ymax = <number> (Double)
Maximum value of the data coordinate on the Y axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
ysub = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a normalised adjustment to the data range of the Y
axis. The value may be specified as a comma-separated pair of
two numbers, giving the lower and upper bounds of the range of
of interest respectively. This sub-range is applied to the
data range that would otherwise be used, either automatically
calculated or explicitly supplied; zero corresponds to the
lower bound and one to the upper.
The default value "0,1" therefore has no effect. The range
could be restricted to its lower half with the value 0,0.5.
[Default: 0,1]
zmin = <number> (Double)
Minimum value of the data coordinate on the Z axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
zmax = <number> (Double)
Maximum value of the data coordinate on the Z axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
zsub = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a normalised adjustment to the data range of the Z
axis. The value may be specified as a comma-separated pair of
two numbers, giving the lower and upper bounds of the range of
of interest respectively. This sub-range is applied to the
data range that would otherwise be used, either automatically
calculated or explicitly supplied; zero corresponds to the
lower bound and one to the upper.
The default value "0,1" therefore has no effect. The range
could be restricted to its lower half with the value 0,0.5.
[Default: 0,1]
phi = <degrees> (Double)
First of the Euler angles, in the ZXZ sequence, defining the
rotation of the plotted 3d space. Units are degrees. This is
the rotation around the initial Z axis applied before the plot
is viewed.
[Default: 30]
theta = <degrees> (Double)
Second of the Euler angles, in the ZXZ sequence, defining the
rotation of the plotted 3d space. Units are degrees. This is
the rotation towards the viewer.
[Default: -15]
psi = <degrees> (Double)
Second of the Euler angles, in the ZXZ sequence, defining the
rotation of the plotted 3d space. Units are degrees.
[Default: 0]
zoom = <factor> (Double)
Sets the magnification factor at which the the plotted 3D
region itself is viewed, without affecting its contents. The
default value is 1, which means the cube fits into the
plotting space however it is rotated. Much higher zoom factors
will result in parts of the plotting region and axes being
drawn outside of the plotting region (so invisible).
[Default: 1]
xoff = <pixels> (Double)
Shifts the whole plot within the plotting region by the given
number of pixels in the horizontal direction.
[Default: 0]
yoff = <pixels> (Double)
Shifts the whole plot within the plotting region by the given
number of pixels in the vertical direction.
[Default: 0]
zoomaxes = [[x][y][z]] (boolean[])
Determines which axes are affected by zoom navigation actions.
If no value is supplied (the default), the mouse wheel zooms
around the center of the cube, and right-button (or CTRL-)
drag zooms in the two dimensions most closely aligned with the
plane of the screen, with the reference position set by the
initial position of the mouse.
If this value is set (legal values are x, y, z, xy, yz, xz and
xyz) then all zoom operations are around the cube center and
affect the axes named.
zoomfactor = <number> (Double)
Sets the amount by which the plot view zooms in or out for
each unit of mouse wheel movement. A value of 1 means that
mouse wheel zooming has no effect. A higher value means that
the mouse wheel zooms faster and a value nearer 1 means it
zooms slower. Values below 1 are not permitted.
[Default: 1.2]
leglabelN = <text> (String)
Sets the presentation label for the layer with a given suffix.
This is the text which is displayed in the legend, if present.
Multiple layers may use the same label, in which case they
will be combined to form a single legend entry.
If no value is supplied (the default), the suffix itself is
used as the label.
layerN = <layer-type> <layerN-specific-params>
(uk.ac.starlink.ttools.plot2.task.LayerType)
Selects one of the available plot types for layerN. A plot
consists of a plotting surface, set up using the various
unsuffixed parameters of the plotting command, and zero or
more plot layers. Each layer is introduced by a parameter with
the name layer<N> where the suffix "<N>" is a label
identifying the layer and is appended to all the parameter
names which configure that layer. Suffixes may be any string,
including the empty string.
This parameter may take one of the following values, described
in more detail in SUN/256:
* mark
* size
* sizexy
* xyzvector
* xyzerror
* link2
* mark2
* label
* contour
Each of these layer types comes with a list of type-specific
parameters to define the details of that layer, including some
or all of the following groups:
* input table parameters (e.g. inN, icmdN)
* coordinate params referring to input table columns (e.g.
xN, yN)
* layer style parameters (e.g. shadingN, colorN)
Every parameter notionally carries the same suffix N. However,
if the suffix is not present, the application will try looking
for a parameter with the same name with no suffix instead. In
this way, if several layers have the same value for a given
parameter (for instance input table), you can supply it using
one unsuffixed parameter to save having to supply several
parameters with the same value but different suffixes.
'''
task = _stilts.getTaskFactory().createObject('plot2cube')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def plot2sphere(**kwargs):
'''\
Draws a sphere plot.
Parameters:
xpix = <int-value> (Integer)
Size of the output image in the X direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 500]
ypix = <int-value> (Integer)
Size of the output image in the Y direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 400]
insets = <top>,<left>,<bottom>,<right>
(uk.ac.starlink.ttools.plot2.Padding)
Defines the amount of space in pixels around the actual
plotting area. This space is used for axis labels, and other
decorations and any left over forms an empty border.
The size and position of the actual plotting area is
determined by this parameter along with xpix and ypix.
The value of this parameter is 4 comma separated integers:
<top>,<left>,<bottom>,<right>. Any or all of these values may
be left blank, in which case the corresponding margin will be
calculated automatically according to how much space is
required.
omode = swing|out|cgi|discard|auto
(uk.ac.starlink.ttools.plottask.PaintMode)
Determines how the drawn plot will be output, see SUN/256.
* swing: Plot will be displayed in a window on the screen.
This plot is "live"; it can be resized and (except for
old-style plots) navigated around with mouse actions in
the same way as plots in TOPCAT.
* out: Plot will be written to a file given by out using the
graphics format given by ofmt.
* cgi: Plot will be written in a way suitable for CGI use
direct from a web server. The output is in the graphics
format given by ofmt, preceded by a suitable
"Content-type" declaration.
* discard: Plot is drawn, but discarded. There is no output.
* auto: Behaves as swing or out mode depending on presence of
out parameter
[Default: auto]
storage = simple|cache|basic-cache
(uk.ac.starlink.ttools.plot2.data.DataStoreFactory)
Determines the way that data is accessed when constructing the
plot. There are two basic options, cached or not.
If no caching is used (simple) then rows are read sequentially
from the specified input table(s) every time they are
required. This generally requires a small memory footprint
(though that can depend on how the table is specified) and
makes sense if the data only needs to be scanned once or
perhaps if the table is very large.
If caching is used (cache) then the required data is read once
from the specified input table(s) and cached before any
plotting is performed, and plots are done using this cached
data. This may use a significant amount of memory for large
tables but it's usually more sensible (faster) if the data
will need to be scanned multiple times.
The default value is cache if a live plot is being generated (
omode=swing), since in that case the plot needs to be redrawn
every time the user performs plot navigation actions or
resizes the window, or if animations are being produced.
Otherwise (e.g. output to a graphics file) the default is
simple.
[Default: simple]
seq = <suffix>[,...] (String[])
Contains a comma-separated list of layer suffixes to determine
the order in which layers are drawn on the plot. This can
affect which symbol are plotted on top of, and so potentially
obscure, which other ones.
When specifying a plot, multiple layers may be specified, each
introduced by a parameter layer<N>, where <N> is a different
(arbitrary) suffix labelling the layer, and is appended to all
the parameters specific to defining that layer.
By default the layers are drawn on the plot in the order in
which the layer* parameters appear on the command line.
However if this parameter is specified, each comma-separated
element is interpreted as a layer suffix, giving the ordered
list of layers to plot. Every element of the list must be a
suffix with a corresponding layer parameter, but missing or
repeated elements are allowed.
legend = true|false (Boolean)
Whether to draw a legend or not. If no value is supplied, the
decision is made automatically: a legend is drawn only if it
would have more than one entry.
legborder = true|false (Boolean)
If true, a line border is drawn around the legend.
[Default: true]
legopaque = true|false (Boolean)
If true, the background of the legend is opaque, and the
legend obscures any plot components behind it. Otherwise, it's
transparent.
[Default: true]
legseq = <suffix>[,...] (String[])
Determines which layers are represented in the legend (if
present) and in which order they appear. The legend has a line
for each layer label (as determined by the leglabelN
parameter). If multiple layers have the same label, they will
contribute to the same entry in the legend, with style icons
plotted over each other. The value of this parameter is a
comma-separated sequence of layer suffixes, which determines
the order in which the legend entries appear. Layers with
suffixes missing from this list do not show up in the legend
at all.
If no value is supplied (the default), the sequence is the
same as the layer plotting sequence (see seq).
legpos = <xfrac,yfrac> (double[])
Determines the internal position of the legend on the plot.
The value is a comma-separated pair of values giving the X and
Y positions of the legend within the plotting bounds, so for
instance "0.5,0.5" will put the legend right in the middle of
the plot. If no value is supplied, the legend will appear
outside the plot boundary.
title = <value> (String)
Text of a title to be displayed at the top of the plot. If
null, the default, no title is shown and there's more space
for the graphics.
auxmap = <map-name>|<color>-<color>[-<color>...]
(uk.ac.starlink.ttools.plot.Shader)
Color map used for Aux axis shading.
A mixed bag of colour ramps are available: inferno, magma,
plasma, viridis, cubehelix, sron, rainbow, rainbow2, rainbow3
, pastel, accent, gnuplot, gnuplot2, specxby, set1, paired,
hotcold, rdbu, piyg, brbg, cyan-magenta, red-blue, brg, heat,
cold, light, greyscale, colour, standard, bugn, bupu, orrd,
pubu, purd, huecl, hue, intensity, rgb_red, rgb_green,
rgb_blue, hsv_h, hsv_s, hsv_v, yuv_y, yuv_u, yuv_v,
scale_hsv_s, scale_hsv_v, scale_yuv_y, mask, blacker, whiter,
transparency. Note: many of these, including rainbow-like
ones, are frowned upon by the visualisation community.
You can also construct your own custom colour map by giving a
sequence of colour names separated by minus sign ("-")
characters. In this case the ramp is a linear interpolation
between each pair of colours named, using the same syntax as
when specifying a colour value. So for instance "
yellow-hotpink-#0000ff" would shade from yellow via hot pink
to blue.
[Default: inferno]
auxclip = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a subrange of the colour ramp to be used for Aux
shading. The value is specified as a (low,high)
comma-separated pair of two numbers between 0 and 1.
If the full range 0,1 is used, the whole range of colours
specified by the selected shader will be used. But if for
instance a value of 0,0.5 is given, only those colours at the
left hand end of the ramp will be seen.
If the null (default) value is chosen, a default clip will be
used. This generally covers most or all of the range 0-1 but
for colour maps which fade to white, a small proportion of the
lower end may be excluded, to ensure that all the colours are
visually distinguishable from a white background. This default
is usually a good idea if the colour map is being used with
something like a scatter plot, where markers are plotted
against a white background. However, for something like a
density map when the whole plotting area is tiled with colours
from the map, it may be better to supply the whole range 0,1
explicitly.
auxflip = true|false (Boolean)
If true, the colour map on the Aux axis will be reversed.
[Default: false]
auxquant = <number> (Double)
Allows the colour map used for the Aux axis to be quantised.
If an integer value N is chosen then the colour map will be
viewed as N discrete evenly-spaced levels, so that only N
different colours will appear in the plot. This can be used to
generate a contour-like effect, and may make it easier to
trace the boundaries of regions of interest by eye.
If left blank, the colour map is nominally continuous (though
in practice it may be quantised to a medium-sized number like
256).
auxfunc = log|linear|sqrt|square
(uk.ac.starlink.ttools.plot2.Scaling)
Defines the way that values in the Aux range are mapped to the
selected colour ramp.
The available options are:
* log: Logarithmic scaling
* linear: Linear scaling
* sqrt: Square root scaling
* square: Square scaling
[Default: linear]
auxmin = <number> (Double)
Minimum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
auxmax = <number> (Double)
Maximum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
auxlabel = <text> (String)
Sets the label used to annotate the aux axis, if it is
visible.
auxcrowd = <factor> (Double)
Determines how closely the tick marks are spaced on the Aux
axis, if visible. The default value is 1, meaning normal
crowding. Larger values result in more ticks, and smaller
values fewer ticks. Tick marks will not however be spaced so
closely that the labels overlap each other, so to get very
closely spaced marks you may need to reduce the font size as
well.
[Default: 1.0]
auxwidth = <pixels> (Integer)
Determines the lateral size of the aux colour ramp, if
visible, in pixels.
[Default: 15]
auxvisible = true|false (Boolean)
Determines whether the aux axis colour ramp is displayed
alongside the plot.
If not supplied (the default), the aux axis will be visible
when aux shading is used in any of the plotted layers.
forcebitmap = true|false (Boolean)
Affects whether rendering of the data contents of a plot
(though not axis labels etc) is always done to an intermediate
bitmap rather than, where possible, being painted using
graphics primitives. This is a rather arcane setting that may
nevertheless have noticeable effects on the appearance and
size of an output graphics file, as well as plotting time. For
some types of plot (e.g. shadingN=auto or shadingN=density) it
will have no effect, since this kind of rendering happens in
any case.
When writing to vector graphics formats (PDF and PostScript),
setting it true will force the data contents to be bitmapped.
This may make the output less beautiful (round markers will no
longer be perfectly round), but it may result in a much
smaller file if there are very many data points.
When writing to bitmapped output formats (PNG, GIF, JPEG,
...), it fixes shapes to be the same as seen on the screen
rather than be rendered at the mercy of the graphics system,
which sometimes introduces small distortions.
[Default: false]
compositor = 0..1
(uk.ac.starlink.ttools.plot2.paper.Compositor)
Defines how multiple overplotted partially transparent pixels
are combined to form a resulting colour. The way this is used
depends on the details of the specified plot.
Currently, this parameter takes a "boost" value in the range
0..1. If the value is zero, saturation semantics are used: RGB
colours are added in proporition to their associated alpha
value until the total alpha is saturated (reaches 1), after
which additional pixels have no further effect. For larger
boost values, the effect is similar, but any non-zero alpha in
the output is boosted to the given minimum value. The effect
of this is that even very slightly populated pixels can be
visually distinguished from unpopulated ones which may not be
the case for saturation composition.
[Default: 0.05]
animate = <table> (uk.ac.starlink.table.StarTable)
Input table.
parallel = <int-value> (Integer)
Determines how many threads will run in parallel if animation
output is being produced. Only used if the animate parameter
is supplied. The default value is the number of processors
apparently available to the JVM.
[Default: 4]
crowd = <number> (Double)
Determines how closely tick marks are spaced on the wire frame
axes. The default value is 1, meaning normal crowding. Larger
values result in more grid lines, and smaller values in fewer
grid lines.
[Default: 1]
frame = true|false (Boolean)
If true, a cube wire frame with labelled axes is drawn to
indicate the limits of the plotted 3D region. If false, no
wire frame and no axes are drawn.
[Default: true]
minor = true|false (Boolean)
If true, minor tick marks are painted along the axes as well
as the major tick marks. Minor tick marks do not have
associated grid lines.
[Default: true]
gridaa = true|false (Boolean)
If true, grid lines are drawn with antialiasing. Antialiased
lines look smoother, but may take perceptibly longer to draw.
Only has any effect for bitmapped output formats.
[Default: false]
texttype = plain|antialias|latex (TextSyntax)
Determines how to turn label text into characters on the plot.
Plain and Antialias both take the text at face value, but
Antialias smooths the characters. LaTeX interprets the text as
LaTeX source code and typesets it accordingly.
When not using LaTeX, antialiased text usually looks nicer,
but can be perceptibly slower to plot. At time of writing, on
MacOS antialiased text seems to be required to stop the
writing coming out upside-down for non-horizontal text (MacOS
java bug).
[Default: plain]
fontsize = <int-value> (Integer)
Size of the text font in points.
[Default: 12]
fontstyle = standard|serif|mono (FontType)
Font style for text.
The available options are:
* standard
* serif
* mono
[Default: standard]
fontweight = plain|bold|italic|bold_italic (FontWeight)
Font weight for text.
The available options are:
* plain
* bold
* italic
* bold_italic
[Default: plain]
cx = <number> (Double)
Gives the central coordinate in the X dimension. This will be
determined from the data range if not supplied.
cy = <number> (Double)
Gives the central coordinate in the Y dimension. This will be
determined from the data range if not supplied.
cz = <number> (Double)
Gives the central coordinate in the Z dimension. This will be
determined from the data range if not supplied.
scale = <number> (Double)
The length of the cube sides in data coordinates. This will be
determined from the data range if not supplied.
phi = <degrees> (Double)
First of the Euler angles, in the ZXZ sequence, defining the
rotation of the plotted 3d space. Units are degrees. This is
the rotation around the initial Z axis applied before the plot
is viewed.
[Default: 30]
theta = <degrees> (Double)
Second of the Euler angles, in the ZXZ sequence, defining the
rotation of the plotted 3d space. Units are degrees. This is
the rotation towards the viewer.
[Default: -15]
psi = <degrees> (Double)
Second of the Euler angles, in the ZXZ sequence, defining the
rotation of the plotted 3d space. Units are degrees.
[Default: 0]
zoom = <factor> (Double)
Sets the magnification factor at which the the plotted 3D
region itself is viewed, without affecting its contents. The
default value is 1, which means the cube fits into the
plotting space however it is rotated. Much higher zoom factors
will result in parts of the plotting region and axes being
drawn outside of the plotting region (so invisible).
[Default: 1]
xoff = <pixels> (Double)
Shifts the whole plot within the plotting region by the given
number of pixels in the horizontal direction.
[Default: 0]
yoff = <pixels> (Double)
Shifts the whole plot within the plotting region by the given
number of pixels in the vertical direction.
[Default: 0]
zoomfactor = <number> (Double)
Sets the amount by which the plot view zooms in or out for
each unit of mouse wheel movement. A value of 1 means that
mouse wheel zooming has no effect. A higher value means that
the mouse wheel zooms faster and a value nearer 1 means it
zooms slower. Values below 1 are not permitted.
[Default: 1.2]
leglabelN = <text> (String)
Sets the presentation label for the layer with a given suffix.
This is the text which is displayed in the legend, if present.
Multiple layers may use the same label, in which case they
will be combined to form a single legend entry.
If no value is supplied (the default), the suffix itself is
used as the label.
layerN = <layer-type> <layerN-specific-params>
(uk.ac.starlink.ttools.plot2.task.LayerType)
Selects one of the available plot types for layerN. A plot
consists of a plotting surface, set up using the various
unsuffixed parameters of the plotting command, and zero or
more plot layers. Each layer is introduced by a parameter with
the name layer<N> where the suffix "<N>" is a label
identifying the layer and is appended to all the parameter
names which configure that layer. Suffixes may be any string,
including the empty string.
This parameter may take one of the following values, described
in more detail in SUN/256:
* mark
* size
* sizexy
* link2
* mark2
* label
* contour
Each of these layer types comes with a list of type-specific
parameters to define the details of that layer, including some
or all of the following groups:
* input table parameters (e.g. inN, icmdN)
* coordinate params referring to input table columns (e.g.
xN, yN)
* layer style parameters (e.g. shadingN, colorN)
Every parameter notionally carries the same suffix N. However,
if the suffix is not present, the application will try looking
for a parameter with the same name with no suffix instead. In
this way, if several layers have the same value for a given
parameter (for instance input table), you can supply it using
one unsuffixed parameter to save having to supply several
parameters with the same value but different suffixes.
'''
task = _stilts.getTaskFactory().createObject('plot2sphere')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def plot2time(**kwargs):
'''\
Draws a time plot.
Parameters:
xpix = <int-value> (Integer)
Size of the output image in the X direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 500]
ypix = <int-value> (Integer)
Size of the output image in the Y direction in pixels. This
includes space for any axis labels, padding and other
decoration outside the plot area itself. See also insets.
[Default: 400]
insets = <top>,<left>,<bottom>,<right>
(uk.ac.starlink.ttools.plot2.Padding)
Defines the amount of space in pixels around the actual
plotting area. This space is used for axis labels, and other
decorations and any left over forms an empty border.
The size and position of the actual plotting area is
determined by this parameter along with xpix and ypix.
The value of this parameter is 4 comma separated integers:
<top>,<left>,<bottom>,<right>. Any or all of these values may
be left blank, in which case the corresponding margin will be
calculated automatically according to how much space is
required.
omode = swing|out|cgi|discard|auto
(uk.ac.starlink.ttools.plottask.PaintMode)
Determines how the drawn plot will be output, see SUN/256.
* swing: Plot will be displayed in a window on the screen.
This plot is "live"; it can be resized and (except for
old-style plots) navigated around with mouse actions in
the same way as plots in TOPCAT.
* out: Plot will be written to a file given by out using the
graphics format given by ofmt.
* cgi: Plot will be written in a way suitable for CGI use
direct from a web server. The output is in the graphics
format given by ofmt, preceded by a suitable
"Content-type" declaration.
* discard: Plot is drawn, but discarded. There is no output.
* auto: Behaves as swing or out mode depending on presence of
out parameter
[Default: auto]
storage = simple|cache|basic-cache
(uk.ac.starlink.ttools.plot2.data.DataStoreFactory)
Determines the way that data is accessed when constructing the
plot. There are two basic options, cached or not.
If no caching is used (simple) then rows are read sequentially
from the specified input table(s) every time they are
required. This generally requires a small memory footprint
(though that can depend on how the table is specified) and
makes sense if the data only needs to be scanned once or
perhaps if the table is very large.
If caching is used (cache) then the required data is read once
from the specified input table(s) and cached before any
plotting is performed, and plots are done using this cached
data. This may use a significant amount of memory for large
tables but it's usually more sensible (faster) if the data
will need to be scanned multiple times.
The default value is cache if a live plot is being generated (
omode=swing), since in that case the plot needs to be redrawn
every time the user performs plot navigation actions or
resizes the window, or if animations are being produced.
Otherwise (e.g. output to a graphics file) the default is
simple.
[Default: simple]
seq = <suffix>[,...] (String[])
Contains a comma-separated list of layer suffixes to determine
the order in which layers are drawn on the plot. This can
affect which symbol are plotted on top of, and so potentially
obscure, which other ones.
When specifying a plot, multiple layers may be specified, each
introduced by a parameter layer<N>, where <N> is a different
(arbitrary) suffix labelling the layer, and is appended to all
the parameters specific to defining that layer.
By default the layers are drawn on the plot in the order in
which the layer* parameters appear on the command line.
However if this parameter is specified, each comma-separated
element is interpreted as a layer suffix, giving the ordered
list of layers to plot. Every element of the list must be a
suffix with a corresponding layer parameter, but missing or
repeated elements are allowed.
legend = true|false (Boolean)
Whether to draw a legend or not. If no value is supplied, the
decision is made automatically: a legend is drawn only if it
would have more than one entry.
legborder = true|false (Boolean)
If true, a line border is drawn around the legend.
[Default: true]
legopaque = true|false (Boolean)
If true, the background of the legend is opaque, and the
legend obscures any plot components behind it. Otherwise, it's
transparent.
[Default: true]
legseq = <suffix>[,...] (String[])
Determines which layers are represented in the legend (if
present) and in which order they appear. The legend has a line
for each layer label (as determined by the leglabelN
parameter). If multiple layers have the same label, they will
contribute to the same entry in the legend, with style icons
plotted over each other. The value of this parameter is a
comma-separated sequence of layer suffixes, which determines
the order in which the legend entries appear. Layers with
suffixes missing from this list do not show up in the legend
at all.
If no value is supplied (the default), the sequence is the
same as the layer plotting sequence (see seq).
legpos = <xfrac,yfrac> (double[])
Determines the internal position of the legend on the plot.
The value is a comma-separated pair of values giving the X and
Y positions of the legend within the plotting bounds, so for
instance "0.5,0.5" will put the legend right in the middle of
the plot. If no value is supplied, the legend will appear
outside the plot boundary.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. legposZ affects only zone Z.
title = <value> (String)
Text of a title to be displayed at the top of the plot. If
null, the default, no title is shown and there's more space
for the graphics.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. titleZ affects only zone Z.
auxmap = <map-name>|<color>-<color>[-<color>...]
(uk.ac.starlink.ttools.plot.Shader)
Color map used for Aux axis shading.
A mixed bag of colour ramps are available: inferno, magma,
plasma, viridis, cubehelix, sron, rainbow, rainbow2, rainbow3
, pastel, accent, gnuplot, gnuplot2, specxby, set1, paired,
hotcold, rdbu, piyg, brbg, cyan-magenta, red-blue, brg, heat,
cold, light, greyscale, colour, standard, bugn, bupu, orrd,
pubu, purd, huecl, hue, intensity, rgb_red, rgb_green,
rgb_blue, hsv_h, hsv_s, hsv_v, yuv_y, yuv_u, yuv_v,
scale_hsv_s, scale_hsv_v, scale_yuv_y, mask, blacker, whiter,
transparency. Note: many of these, including rainbow-like
ones, are frowned upon by the visualisation community.
You can also construct your own custom colour map by giving a
sequence of colour names separated by minus sign ("-")
characters. In this case the ramp is a linear interpolation
between each pair of colours named, using the same syntax as
when specifying a colour value. So for instance "
yellow-hotpink-#0000ff" would shade from yellow via hot pink
to blue.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxmapZ affects only zone Z.
[Default: inferno]
auxclip = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a subrange of the colour ramp to be used for Aux
shading. The value is specified as a (low,high)
comma-separated pair of two numbers between 0 and 1.
If the full range 0,1 is used, the whole range of colours
specified by the selected shader will be used. But if for
instance a value of 0,0.5 is given, only those colours at the
left hand end of the ramp will be seen.
If the null (default) value is chosen, a default clip will be
used. This generally covers most or all of the range 0-1 but
for colour maps which fade to white, a small proportion of the
lower end may be excluded, to ensure that all the colours are
visually distinguishable from a white background. This default
is usually a good idea if the colour map is being used with
something like a scatter plot, where markers are plotted
against a white background. However, for something like a
density map when the whole plotting area is tiled with colours
from the map, it may be better to supply the whole range 0,1
explicitly.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxclipZ affects only zone Z.
auxflip = true|false (Boolean)
If true, the colour map on the Aux axis will be reversed.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxflipZ affects only zone Z.
[Default: false]
auxquant = <number> (Double)
Allows the colour map used for the Aux axis to be quantised.
If an integer value N is chosen then the colour map will be
viewed as N discrete evenly-spaced levels, so that only N
different colours will appear in the plot. This can be used to
generate a contour-like effect, and may make it easier to
trace the boundaries of regions of interest by eye.
If left blank, the colour map is nominally continuous (though
in practice it may be quantised to a medium-sized number like
256).
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxquantZ affects only zone Z.
auxfunc = log|linear|sqrt|square
(uk.ac.starlink.ttools.plot2.Scaling)
Defines the way that values in the Aux range are mapped to the
selected colour ramp.
The available options are:
* log: Logarithmic scaling
* linear: Linear scaling
* sqrt: Square root scaling
* square: Square scaling
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxfuncZ affects only zone Z.
[Default: linear]
auxmin = <number> (Double)
Minimum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxminZ affects only zone Z.
auxmax = <number> (Double)
Maximum value of the data coordinate on the Aux axis. This
sets the value before any subranging is applied. If not
supplied, the value is determined from the plotted data.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxmaxZ affects only zone Z.
auxlabel = <text> (String)
Sets the label used to annotate the aux axis, if it is
visible.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxlabelZ affects only zone Z.
auxcrowd = <factor> (Double)
Determines how closely the tick marks are spaced on the Aux
axis, if visible. The default value is 1, meaning normal
crowding. Larger values result in more ticks, and smaller
values fewer ticks. Tick marks will not however be spaced so
closely that the labels overlap each other, so to get very
closely spaced marks you may need to reduce the font size as
well.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxcrowdZ affects only zone Z.
[Default: 1.0]
auxwidth = <pixels> (Integer)
Determines the lateral size of the aux colour ramp, if
visible, in pixels.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxwidthZ affects only zone Z.
[Default: 15]
auxvisible = true|false (Boolean)
Determines whether the aux axis colour ramp is displayed
alongside the plot.
If not supplied (the default), the aux axis will be visible
when aux shading is used in any of the plotted layers.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. auxvisibleZ affects only zone Z.
forcebitmap = true|false (Boolean)
Affects whether rendering of the data contents of a plot
(though not axis labels etc) is always done to an intermediate
bitmap rather than, where possible, being painted using
graphics primitives. This is a rather arcane setting that may
nevertheless have noticeable effects on the appearance and
size of an output graphics file, as well as plotting time. For
some types of plot (e.g. shadingN=auto or shadingN=density) it
will have no effect, since this kind of rendering happens in
any case.
When writing to vector graphics formats (PDF and PostScript),
setting it true will force the data contents to be bitmapped.
This may make the output less beautiful (round markers will no
longer be perfectly round), but it may result in a much
smaller file if there are very many data points.
When writing to bitmapped output formats (PNG, GIF, JPEG,
...), it fixes shapes to be the same as seen on the screen
rather than be rendered at the mercy of the graphics system,
which sometimes introduces small distortions.
[Default: false]
compositor = 0..1
(uk.ac.starlink.ttools.plot2.paper.Compositor)
Defines how multiple overplotted partially transparent pixels
are combined to form a resulting colour. The way this is used
depends on the details of the specified plot.
Currently, this parameter takes a "boost" value in the range
0..1. If the value is zero, saturation semantics are used: RGB
colours are added in proporition to their associated alpha
value until the total alpha is saturated (reaches 1), after
which additional pixels have no further effect. For larger
boost values, the effect is similar, but any non-zero alpha in
the output is boosted to the given minimum value. The effect
of this is that even very slightly populated pixels can be
visually distinguished from unpopulated ones which may not be
the case for saturation composition.
[Default: 0.05]
animate = <table> (uk.ac.starlink.table.StarTable)
Input table.
parallel = <int-value> (Integer)
Determines how many threads will run in parallel if animation
output is being produced. Only used if the animate parameter
is supplied. The default value is the number of processors
apparently available to the JVM.
[Default: 4]
ylog = true|false (Boolean)
If false (the default), the scale on the Y axis is linear, if
true it is logarithmic.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. ylogZ affects only zone Z.
[Default: false]
yflip = true|false (Boolean)
If true, the scale on the Y axis will increase in the opposite
sense from usual (e.g. right to left rather than left to
right).
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. yflipZ affects only zone Z.
[Default: false]
tlabel = <text> (String)
Gives a label to be used for annotating the Time axis. If not
supplied no label will be drawn.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. tlabelZ affects only zone Z.
ylabel = <text> (String)
Gives a label to be used for annotating axis Y A default value
based on the plotted data will be used if no value is
supplied.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. ylabelZ affects only zone Z.
[Default: Y]
grid = true|false (Boolean)
If true, grid lines are drawn on the plot at positions
determined by the major tick marks. If false, they are absent.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. gridZ affects only zone Z.
[Default: false]
tcrowd = <number> (Double)
Determines how closely the tick marks are spaced on the Time
axis. The default value is 1, meaning normal crowding. Larger
values result in more ticks, and smaller values fewer ticks.
Tick marks will not however be spaced so closely that the
labels overlap each other, so to get very closely spaced marks
you may need to reduce the font size as well.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. tcrowdZ affects only zone Z.
[Default: 1]
ycrowd = <number> (Double)
Determines how closely the tick marks are spaced on the Y
axis. The default value is 1, meaning normal crowding. Larger
values result in more ticks, and smaller values fewer ticks.
Tick marks will not however be spaced so closely that the
labels overlap each other, so to get very closely spaced marks
you may need to reduce the font size as well.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. ycrowdZ affects only zone Z.
[Default: 1]
tformat = iso-8601|year|mjd|unix
(uk.ac.starlink.ttools.plot2.geom.TimeFormat)
Selects the way in which time values are represented when
using them to label the time axis.
The available options are:
* iso-8601: ISO 8601 date, of the form yyyy-mm-ddThh:mm:ss.s
(e.g. "2012-03-13T04")
* year: Decimal year (e.g. "2012.197")
* mjd: Modified Julian Date (e.g. "55999.2")
* unix: Seconds since midnight of 1 Jan 1970 (e.g.
"1331613420")
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. tformatZ affects only zone Z.
[Default: iso-8601]
minor = true|false (Boolean)
If true, minor tick marks are painted along the axes as well
as the major tick marks. Minor tick marks do not have
associated grid lines.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. minorZ affects only zone Z.
[Default: true]
texttype = plain|antialias|latex (TextSyntax)
Determines how to turn label text into characters on the plot.
Plain and Antialias both take the text at face value, but
Antialias smooths the characters. LaTeX interprets the text as
LaTeX source code and typesets it accordingly.
When not using LaTeX, antialiased text usually looks nicer,
but can be perceptibly slower to plot. At time of writing, on
MacOS antialiased text seems to be required to stop the
writing coming out upside-down for non-horizontal text (MacOS
java bug).
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. texttypeZ affects only zone Z.
[Default: plain]
fontsize = <int-value> (Integer)
Size of the text font in points.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. fontsizeZ affects only zone Z.
[Default: 12]
fontstyle = standard|serif|mono (FontType)
Font style for text.
The available options are:
* standard
* serif
* mono
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. fontstyleZ affects only zone Z.
[Default: standard]
fontweight = plain|bold|italic|bold_italic (FontWeight)
Font weight for text.
The available options are:
* plain
* bold
* italic
* bold_italic
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. fontweightZ affects only zone Z.
[Default: plain]
tmin = <year-or-iso8601> (Double)
Minimum value of the time coordinate plotted. This sets the
value before any subranging is applied. If not supplied, the
value is determined from the plotted data.
The value may be set with a string that can be interpreted as
a decimal year (e.g. "2007.521") or an ISO-8601 string (e.g. "
2007-07-10T03:57:36", "2007-07-10T03" or "2007-07-10"). Note
however that the numeric value of this configuration item if
accessed programmatically is seconds since 1 Jan 1970.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. tminZ affects only zone Z.
tmax = <year-or-iso8601> (Double)
Maximum value of the time coordinate plotted. This sets the
value before any subranging is applied. If not supplied, the
value is determined from the plotted data.
The value may be set with a string that can be interpreted as
a decimal year (e.g. "2007.521") or an ISO-8601 string (e.g. "
2007-07-10T03:57:36", "2007-07-10T03" or "2007-07-10"). Note
however that the numeric value of this configuration item if
accessed programmatically is seconds since 1 Jan 1970.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. tmaxZ affects only zone Z.
tsub = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a normalised adjustment to the data range of the Time
axis. The value may be specified as a comma-separated pair of
two numbers, giving the lower and upper bounds of the range of
of interest respectively. This sub-range is applied to the
data range that would otherwise be used, either automatically
calculated or explicitly supplied; zero corresponds to the
lower bound and one to the upper.
The default value "0,1" therefore has no effect. The range
could be restricted to its lower half with the value 0,0.5.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. tsubZ affects only zone Z.
[Default: 0,1]
ymin = <number> (Double)
Minimum value of the data coordinate on the Y axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. yminZ affects only zone Z.
ymax = <number> (Double)
Maximum value of the data coordinate on the Y axis. This sets
the value before any subranging is applied. If not supplied,
the value is determined from the plotted data.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. ymaxZ affects only zone Z.
ysub = <lo>,<hi> (uk.ac.starlink.ttools.plot2.Subrange)
Defines a normalised adjustment to the data range of the Y
axis. The value may be specified as a comma-separated pair of
two numbers, giving the lower and upper bounds of the range of
of interest respectively. This sub-range is applied to the
data range that would otherwise be used, either automatically
calculated or explicitly supplied; zero corresponds to the
lower bound and one to the upper.
The default value "0,1" therefore has no effect. The range
could be restricted to its lower half with the value 0,0.5.
If a zone suffix is appended to the parameter name, only that
zone is affected, e.g. ysubZ affects only zone Z.
[Default: 0,1]
navaxes = t|y|ty (boolean[])
Determines the axes which are affected by the interactive
navigation actions (pan and zoom). The default is t which
means that the various mouse gestures will provide panning and
zooming in the Time direction only. However, if it is set to
ty mouse actions will affect both the horizontal and vertical
axes.
[Default: t]
zoomfactor = <number> (Double)
Sets the amount by which the plot view zooms in or out for
each unit of mouse wheel movement. A value of 1 means that
mouse wheel zooming has no effect. A higher value means that
the mouse wheel zooms faster and a value nearer 1 means it
zooms slower. Values below 1 are not permitted.
[Default: 1.2]
leglabelN = <text> (String)
Sets the presentation label for the layer with a given suffix.
This is the text which is displayed in the legend, if present.
Multiple layers may use the same label, in which case they
will be combined to form a single legend entry.
If no value is supplied (the default), the suffix itself is
used as the label.
layerN = <layer-type> <layerN-specific-params>
(uk.ac.starlink.ttools.plot2.task.LayerType)
Selects one of the available plot types for layerN. A plot
consists of a plotting surface, set up using the various
unsuffixed parameters of the plotting command, and zero or
more plot layers. Each layer is introduced by a parameter with
the name layer<N> where the suffix "<N>" is a label
identifying the layer and is appended to all the parameter
names which configure that layer. Suffixes may be any string,
including the empty string.
This parameter may take one of the following values, described
in more detail in SUN/256:
* mark
* line
* fill
* quantile
* grid
* histogram
* kde
* knn
* densogram
* gaussian
* yerror
* spectrogram
* label
* function
Each of these layer types comes with a list of type-specific
parameters to define the details of that layer, including some
or all of the following groups:
* input table parameters (e.g. inN, icmdN)
* coordinate params referring to input table columns (e.g.
xN, yN)
* layer style parameters (e.g. shadingN, colorN)
Every parameter notionally carries the same suffix N. However,
if the suffix is not present, the application will try looking
for a parameter with the same name with no suffix instead. In
this way, if several layers have the same value for a given
parameter (for instance input table), you can supply it using
one unsuffixed parameter to save having to supply several
parameters with the same value but different suffixes.
zoneN = <text> (String)
Defines which plot zone the layer with suffix N will appear
in. This only makes sense for multi-zone plots. The actual
value of the parameter is not significant, it just serves as a
label, but different layers will end up in the same plot zone
if they give the same values for this parameter.
'''
task = _stilts.getTaskFactory().createObject('plot2time')
for param in task.getParameters():
pname = param.getName()
if pname in _param_alias_dict:
param.setName(_param_alias_dict[pname])
env = _JyEnvironment()
for kw in kwargs.iteritems():
key = kw[0]
value = kw[1]
env.setValue(key, _map_env_value(value))
exe = task.createExecutable(env)
_check_unused_args(env)
exe.execute()
def cmd_addcol(table, *args):
'''\
Add a new column called <col-name> defined by the algebraic
expression <expr>. By default the new column appears after the last
column of the table, but you can position it either before or after
a specified column using the -before or -after flags respectively.
The -units, -ucd-utype and -desc flags can be used to define
metadata values for the new column.
Syntax for the <expr> and <col-id> arguments is described in the
manual.
The filtered table is returned.
args is a list with words as elements:
[-after <col-id> | -before <col-id>]
[-units <units>] [-ucd <ucd>] [-utype <utype>] [-desc <descrip>]
<col-name> <expr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("addcol")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_addpixsample(table, *args):
'''\
Samples pixel data from an all-sky image file in HEALPix format. The
<healpix-file> argument must be the filename of a table containing
HEALPix pixel data. The URL of such a file can be used instead, but
local files are likely to be more efficient.
The <expr-lon> and <expr-lat> arguments give expressions for the
longitude and latitude in degrees for each row of the input table;
this is usually just the column names. The long/lat must usually be
in the same coordinate system as that used for the HEALPix data, so
if the one is in galactic coordinates the other must be as well. If
this is not the case, use the -systems flag to give the input
long/lat and healpix data coordinate system names respectively. The
available coordinate system names are:
* icrs: ICRS (Hipparcos) (Right Ascension, Declination)
* fk5: FK5 J2000.0 (Right Ascension, Declination)
* fk4: FK4 B1950.0 (Right Ascension, Declination)
* galactic: IAU 1958 Galactic (Longitude, Latitude)
* supergalactic: de Vaucouleurs Supergalactic (Longitude, Latitude)
* ecliptic: Ecliptic (Longitude, Latitude)
The <expr-rad>, if present, is a constant or expression giving the
radius in degrees over which pixels will be averaged to obtain the
result values. Note that this averaging is somewhat approximate;
pixels partly covered by the specified disc are weighted the same as
those fully covered. If no radius is specified, the value of the
pixel covering the central position will be used.
The <healpix-file> file is a table with one row per HEALPix pixel
and one or more columns representing pixel data. A new column will
be added to the output table corresponding to each of these pixel
columns. This type of data is available in FITS tables for a number
of all-sky data sets, particularly from the LAMBDA archive; see for
instance the page on foreground products (including dust emission,
reddening etc) or WMAP 7 year data. If the filename given does not
appear to point to a file of the appropriate format, an error will
result. Note the LAMBDA files mostly (all?) use galactic
coordinates, so coordinate conversion using the -systems flag may be
appropriate, see above.
Syntax for the <expr-lon> , <expr-lat> and <expr-rad> arguments is
described in the manual.
This filter is somewhat experimental, and its usage may be changed
or replaced in a future version.
Note: you may prefer to use the pixsample command instead.
The filtered table is returned.
args is a list with words as elements:
[-radius <expr-rad>] [-systems <in-sys> <pix-sys>]
<expr-lon> <expr-lat> <healpix-file>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("addpixsample")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_addresolve(table, *args):
'''\
Performs name resolution on the string-valued column
<col-id-objname> and appends two new columns <col-name-ra> and
<col-name-dec> containing the resolved Right Ascension and
Declination in degrees.
Syntax for the <col-id-objname> argument is described in SUN/256.
UCDs are added to the new columns in a way which tries to be
consistent with any UCDs already existing in the table.
Since this filter works by interrogating a remote service, it will
obviously be slow. The current implementation is experimental; it
may be replaced in a future release by some way of doing the same
thing (perhaps a new STILTS task) which is able to work more
efficiently by dispatching multiple concurrent requests.
This is currently implemented using the Simbad service operated by
CDS.
The filtered table is returned.
args is a list with words as elements:
<col-id-objname> <col-name-ra> <col-name-dec>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("addresolve")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_addskycoords(table, *args):
'''\
Add new columns to the table representing position on the sky. The
values are determined by converting a sky position whose coordinates
are contained in existing columns. The <col-id> arguments give
identifiers for the two input coordinate columns in the coordinate
system named by <insys>, and the <col-name> arguments name the two
new columns, which will be in the coordinate system named by
<outsys>. The <insys> and <outsys> coordinate system specifiers are
one of
* icrs: ICRS (Hipparcos) (Right Ascension, Declination)
* fk5: FK5 J2000.0 (Right Ascension, Declination)
* fk4: FK4 B1950.0 (Right Ascension, Declination)
* galactic: IAU 1958 Galactic (Longitude, Latitude)
* supergalactic: de Vaucouleurs Supergalactic (Longitude, Latitude)
* ecliptic: Ecliptic (Longitude, Latitude)
The -inunit and -outunit flags may be used to indicate the units of
the existing coordinates and the units for the new coordinates
respectively; use one of degrees, radians or sexagesimal (may be
abbreviated), otherwise degrees will be assumed. For sexagesimal,
the two corresponding columns must be string-valued in forms like
hh:mm:ss.s and dd:mm:ss.s respectively.
For certain conversions, the value specified by the -epoch flag is
of significance. Where significant its value defaults to 2000.0.
Syntax for the <expr> , <col-id1> and <col-id2> arguments is
described in the manual.
The filtered table is returned.
args is a list with words as elements:
[-epoch <expr>] [-inunit deg|rad|sex] [-outunit deg|rad|sex]
<insys> <outsys> <col-id1> <col-id2> <col-name1> <col-name2>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("addskycoords")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_assert(table, *args):
'''\
Check that a boolean expression is true for each row. If the
expression <expr> does not evaluate true for any row of the table,
execution terminates with an error. As long as no error occurs, the
output table is identical to the input one.
The exception generated by an assertion violation is of class
uk.ac.starlink.ttools.filter.AssertException although that is not
usually obvious if you are running from the shell in the usual way.
Syntax for the <expr> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<expr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("assert")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_badval(table, *args):
'''\
For each column specified in <colid-list> any occurrence of the
value <bad-val> is replaced by a blank entry.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<bad-val> <colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("badval")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_cache(table):
'''\
Stores in memory or on disk a temporary copy of the table at this
point in the pipeline. This can provide improvements in efficiency
if there is an expensive step upstream and a step which requires
more than one read of the data downstream. If you see an error like
"Can't re-read data from stream" then adding this step near the
start of the filters might help.
The result of this filter is guaranteed to be random-access.
See also the random filter, which caches only when the input table
is not random-access.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("cache")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_check(table):
'''\
Runs checks on the table at the indicated point in the processing
pipeline. This is strictly a debugging measure, and may be
time-consuming for large tables.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("check")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_clearparams(table, *args):
'''\
Clears the value of one or more named parameters. Each of the
<pname> values supplied may be either a parameter name or a simple
wildcard expression matching parameter names. Currently the only
wildcarding is a "*" to match any sequence of characters.
clearparams * will clear all the parameters in the table.
It is not an error to supply <pname>s which do not exist in the
table - these have no effect.
The filtered table is returned.
args is a list with words as elements:
<pname> ...
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("clearparams")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_colmeta(table, *args):
'''\
Modifies the metadata of one or more columns. Some or all of the
name, units, ucd, utype and description of the column(s), identified
by <colid-list> can be set by using some or all of the listed flags.
Typically, <colid-list> will simply be the name of a single column.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-name <name>] [-units <units>] [-ucd <ucd>] [-utype <utype>]
[-desc <descrip>]
<colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("colmeta")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_delcols(table, *args):
'''\
Delete the specified columns. The same column may harmlessly be
specified more than once.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("delcols")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_every(table, *args):
'''\
Include only every <step>'th row in the result, starting with the
first row.
The filtered table is returned.
args is a list with words as elements:
<step>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("every")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_explodecols(table, *args):
'''\
Takes a list of specified columns which represent N-element arrays
and replaces each one with N scalar columns. Each of the columns
specified by <colid-list> must have a fixed-length array type,
though not all the arrays need to have the same number of elements.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("explodecols")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_explodeall(table, *args):
'''\
Replaces any columns which is an N-element arrays with N scalar
columns. Only columns with fixed array sizes are affected. The
action can be restricted to only columns of a certain shape using
the flags.
If the -ifndim flag is used, then only columns of dimensionality
<ndim> will be exploded. <ndim> may be 1, 2, ....
If the -ifshape flag is used, then only columns with a specific
shape will be exploded; <dims> is a space- or comma-separated list
of dimension extents, with the most rapidly-varying first, e.g. '2 5
' to explode all 2 x 5 element array columns.
The filtered table is returned.
args is a list with words as elements:
[-ifndim <ndim>] [-ifshape <dims>]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("explodeall")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_fixcolnames(table):
'''\
Renames all columns and parameters in the input table so that they
have names which have convenient syntax for STILTS. For the most
part this means replacing spaces and other non-alphanumeric
characters with underscores. This is a convenience which lets you
use column names in algebraic expressions and other STILTS syntax.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("fixcolnames")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_head(table, *args):
'''\
Include only the first <nrows> rows of the table. If the table has
fewer than <nrows> rows then it will be unchanged.
The filtered table is returned.
args is a list with words as elements:
<nrows>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("head")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_keepcols(table, *args):
'''\
Select the columns from the input table which will be included in
the output table. The output table will include only those columns
listed in <colid-list>, in that order. The same column may be listed
more than once, in which case it will appear in the output table
more than once.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("keepcols")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_meta(table, *args):
'''\
Provides information about the metadata for each column. This filter
turns the table sideways, so that each row of the output corresponds
to a column of the input. The columns of the output table contain
metadata items such as column name, units, UCD etc corresponding to
each column of the input table.
By default the output table contains columns for the following
items:
* Index: Position of column in table
* Name: Column name
* Class: Data type of objects in column
* Shape: Shape of array values
* ElSize: Size of each element in column (mostly useful for
strings)
* Units: Unit string
* Description: Description of data in the column
* UCD: Unified Content Descriptor
* Utype: Type in data model
as well as any table-specific column metadata items that the table
contains.
However, the output may be customised by supplying one or more
<item> headings. These may be selected from the above as well as the
following:
* UCD_desc: Textual description of UCD
as well as any table-specific metadata. It is not an error to
specify an item for which no metadata exists in any of the columns
(such entries will result in empty columns).
Any table parameters of the input table are propagated to the output
one.
The filtered table is returned.
args is a list with words as elements:
[<item> ...]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("meta")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_progress(table):
'''\
Monitors progress by displaying the number of rows processed so far
on the terminal (standard error). This number is updated every
second or thereabouts; if all the processing is done in under a
second you may not see any output. If the total number of rows in
the table is known, an ASCII-art progress bar is updated, otherwise
just the number of rows seen so far is written.
Note under some circumstances progress may appear to complete before
the actual work of the task is done since part of the processing
involves slurping up the whole table to provide random access on it.
In this case, applying the cache upstream may help.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("progress")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_random(table):
'''\
Ensures that random access is available on this table. If the table
currently has random access, it has no effect. If only sequential
access is available, the table is cached so that downstream steps
will see the cached, hence random-access, copy.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("random")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_randomview(table):
'''\
Ensures that steps downstream only use random access methods for
table access. If the table is sequential only, this will result in
an error. Only useful for debugging.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("randomview")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_repeat(table, *args):
'''\
Repeats the rows of a table multiple times to produce a longer
table. The output table will have <count> times as many rows as the
input table.
The optional flag determines the sequence of the output rows. If
<count>=2 and there are three rows, the output sequence will be
112233 for -row and 123123 for -table. The default behaviour is
currently -table.
The <count> value will usually be a constant integer value, but it
can be an expression evaluated in the context of the table.
The filtered table is returned.
args is a list with words as elements:
[-row|-table] <count>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("repeat")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_replacecol(table, *args):
'''\
Replaces the content of a column with the value of an algebraic
expression. The old values are discarded in favour of the result of
evaluating <expr>. You can specify the metadata for the new column
using the -name, -units, -ucd, -utype and -desc flags; for any of
these items which you do not specify, they will take the values from
the column being replaced.
It is legal to reference the replaced column in the expression, so
for example "replacecol pixsize pixsize*2" just multiplies the
values in column pixsize by 2.
Syntax for the <col-id> and <expr> arguments is described in the
manual.
The filtered table is returned.
args is a list with words as elements:
[-name <name>] [-units <units>] [-ucd <ucd>] [-utype <utype>]
[-desc <descrip>]
<col-id> <expr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("replacecol")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_replaceval(table, *args):
'''\
For each column specified in <colid-list> any instance of <old-val>
is replaced by <new-val>. The value string 'null' can be used for
either <old-value> or <new-value> to indicate a blank value (but see
also the badval filter).
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<old-val> <new-val> <colid-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("replaceval")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_rowrange(table, *args):
'''\
Includes only rows in a given range. The range can either be
supplied as "<first> <last>", where row indices are inclusive, or "
<first> +<count>". In either case, the first row is numbered 1.
Thus, to get the first hundred rows, use either "rowrange 1 100" or
"rowrange 1 +100" and to get the second hundred, either "rowrange
101 200" or "rowrange 101 +100"
The filtered table is returned.
args is a list with words as elements:
<first> <last>|+<count>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("rowrange")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_select(table, *args):
'''\
Include in the output table only rows for which the expression
<expr> evaluates to true. <expr> must be an expression which
evaluates to a boolean value (true/false).
Syntax for the <expr> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
<expr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("select")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_seqview(table):
'''\
Ensures that steps downstream see the table as sequential access.
Any attempts at random access will fail. Only useful for debugging.
The filtered table is returned.
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("seqview")
sargs = []
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_setparam(table, *args):
'''\
Sets a named parameter in the table to a given value. The parameter
named <pname> is set to the value <pexpr>, which may be a literal
value or an expression involving mathematical operations and other
parameter names (using the param$<name> syntax). By default, the
data type of the parameter is determined by the type of the supplied
expression, but this can be overridden using the -type flag. The
parameter description, units, UCD and Utype attributes may
optionally be set using the other flags.
The filtered table is returned.
args is a list with words as elements:
[-type byte|short|int|long|float|double|boolean|string]
[-desc <descrip>] [-unit <units>] [-ucd <ucd>] [-utype <utype>]
<pname> <pexpr>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("setparam")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_sort(table, *args):
'''\
Sorts the table according to the value of one or more algebraic
expressions. The sort key expressions appear, as separate
(space-separated) words, in <key-list>; sorting is done on the first
expression first, but if that results in a tie then the second one
is used, and so on.
Each expression must evaluate to a type that it makes sense to sort,
for instance numeric. If the -down flag is used, the sort order is
descending rather than ascending.
Blank entries are by default considered to come at the end of the
collation sequence, but if the -nullsfirst flag is given then they
are considered to come at the start instead.
Syntax for the <key-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-down] [-nullsfirst] <key-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("sort")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_sorthead(table, *args):
'''\
Performs a sort on the table according to the value of one or more
algebraic expressions, retaining only <nrows> rows at the head of
the resulting sorted table. The sort key expressions appear, as
separate (space-separated) words, in <key-list>; sorting is done on
the first expression first, but if that results in a tie then the
second one is used, and so on. Each expression must evaluate to a
type that it makes sense to sort, for instance numeric.
If the -tail flag is used, then the last <nrows> rows rather than
the first ones are retained.
If the -down flag is used the sort order is descending rather than
ascending.
Blank entries are by default considered to come at the end of the
collation sequence, but if the -nullsfirst flag is given then they
are considered to come at the start instead.
This filter is functionally equivalent to using sort followed by
head, but it can be done in one pass and is usually cheaper on
memory and faster, as long as <nrows> is significantly lower than
the size of the table.
Syntax for the <key-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-tail] [-down] [-nullsfirst] <nrows> <key-list>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("sorthead")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_stats(table, *args):
'''\
Calculates statistics on the data in the table. This filter turns
the table sideways, so that each row of the output corresponds to a
column of the input. The columns of the output table contain
statistical items such as mean, standard deviation etc corresponding
to each column of the input table.
By default the output table contains columns for the following
items:
* Name: Column name
* Mean: Average
* StDev: Population Standard deviation
* Minimum: Numeric minimum
* Maximum: Numeric maximum
* NGood: Number of non-blank cells
However, the output may be customised by supplying one or more
<item> headings. These may be selected from the above as well as the
following:
* NBad: Number of blank cells
* Variance: Population Variance
* SampStDev: Sample Standard Deviation
* SampVariance: Sample Variance
* MedAbsDev: Median Absolute Deviation
* ScMedAbsDev: Median Absolute Deviation * 1.4826
* Skew: Gamma 1 skewness measure
* Kurtosis: Gamma 2 peakedness measure
* Sum: Sum of values
* MinPos: Row index of numeric minimum
* MaxPos: Row index of numeric maximum
* Cardinality: Number of distinct values in column; values >100
ignored
* Median: Middle value in sequence
* Quartile1: First quartile
* Quartile2: Second quartile
* Quartile3: Third quartile
Additionally, the form "Q.nn" may be used to represent the quantile
corresponding to the proportion 0.nn, e.g.:
* Q.25: First quartile
* Q.625: Fifth octile
Any parameters of the input table are propagated to the output one.
Note that quantile calculations (including median and quartiles) can
be expensive on memory. If you want to calculate quantiles for large
tables, it may be wise to reduce the number of columns to only those
you need the quantiles for earlier in the pipeline. No interpolation
is performed when calculating quantiles.
The filtered table is returned.
args is a list with words as elements:
[<item> ...]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("stats")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_tablename(table, *args):
'''\
Sets the table's name attribute to the given string.
The filtered table is returned.
args is a list with words as elements:
<name>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("tablename")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_tail(table, *args):
'''\
Include only the last <nrows> rows of the table. If the table has
fewer than <nrows> rows then it will be unchanged.
The filtered table is returned.
args is a list with words as elements:
<nrows>
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("tail")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_transpose(table, *args):
'''\
Transposes the input table so that columns become rows and vice
versa. The -namecol flag can be used to specify a column in the
input table which will provide the column names for the output
table. The first column of the output table will contain the column
names of the input table.
Syntax for the <col-id> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-namecol <col-id>]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("transpose")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def cmd_uniq(table, *args):
'''\
Eliminates adjacent rows which have the same values. If used with no
arguments, then any row which has identical values to its
predecessor is removed.
If the <colid-list> parameter is given then only the values in the
specified columns must be equal in order for the row to be removed.
If the -count flag is given, then an additional column with the name
DupCount will be prepended to the table giving a count of the number
of duplicated input rows represented by each output row. A unique
row has a DupCount value of 1.
Syntax for the <colid-list> argument is described in SUN/256.
The filtered table is returned.
args is a list with words as elements:
[-count] [<colid-list>]
'''
pfilt = _StepFactory.getInstance().getFilterFactory().createObject("uniq")
sargs = [str(a) for a in args]
argList = _ArrayList(sargs)
step = pfilt.createStep(argList.iterator())
return import_star_table(step.wrap(table))
def mode_out(table, out='-', ofmt='(auto)'):
'''\
Writes a new table.
Parameters:
out = <out-table> (uk.ac.starlink.ttools.TableConsumer)
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.
[Default: -]
ofmt = <out-format> (String)
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.
[Default: (auto)]
'''
env = _JyEnvironment()
env.setValue('out', _map_env_value(out))
env.setValue('ofmt', _map_env_value(ofmt))
mode = _stilts.getModeFactory().createObject('out')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
def mode_meta(table):
'''\
Prints the table metadata to standard output. The name and type etc
of each column is tabulated, and table parameters are also shown.
See the meta filter for more flexible output of table metadata.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('meta')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
def mode_stats(table):
'''\
Calculates and displays univariate statistics for each of the
numeric columns in the table. The following entries are shown for
each column as appropriate:
* mean
* population standard deviation
* minimum
* maximum
* number of non-null entries
See the stats filter for more flexible statistical calculations.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('stats')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
def mode_count(table):
'''\
Counts the number of rows and columns and writes the result to
standard output.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('count')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
def mode_cgi(table, ofmt='votable'):
'''\
Writes a table to standard output in a way suitable for use as
output from a CGI (Common Gateway Interface) program. This is very
much like out mode but a short CGI header giving the MIME
Content-Type is prepended to the output
Parameters:
ofmt = <out-format> (String)
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).
[Default: votable]
'''
env = _JyEnvironment()
env.setValue('ofmt', _map_env_value(ofmt))
mode = _stilts.getModeFactory().createObject('cgi')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
def mode_discard(table):
'''\
Reads all the data in the table in sequential mode and discards it.
May be useful in conjunction with the assert filter.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('discard')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
def mode_topcat(table):
'''\
Attempts to display the output table directly in TOPCAT. If a TOPCAT
instance is already running on the local host, an attempt will be
made to open the table in that. A variety of mechanisms are used to
attempt communication with an existing TOPCAT instance. In order:
* SAMP using existing hub (TOPCAT v3.4+ only, requires SAMP hub to
be running)
* SOAP (requires TOPCAT to run with somewhat deprecated -soap flag,
may be limitations on table size)
* SAMP using internal, short-lived hub (TOPCAT v3.4+ only, running
hub not required, but may be slow. It's better to start an
external hub, e.g. topcat -exthub) Failing that, an attempt
will be made to launch a new TOPCAT instance for display. This only
works if the TOPCAT classes are on the class path.
If large tables are involved, starting TOPCAT with the -disk flag is
probably a good idea.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('topcat')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
def mode_samp(table, format='votable fits', client=None):
'''\
Sends the table to registered SAMP-aware applications subscribed to
a suitable table load MType. SAMP, the Simple Application Messaging
Protocol, is a tool interoperability protocol. A SAMP Hub must be
running for this to work.
Parameters:
format = <value> (String[])
Gives one or more table format types for attempting the table
transmission over SAMP. If multiple values are supplied, they
should be separated by spaces. Each value supplied for this
parameter corresponds to a different MType which may be used
for the transmission. If a single value is used, a SAMP
broadcast will be used. If multiple values are used, each
registered client will be interrogated to see whether it
subscribes to the corresponding MTypes in order; the first one
to which it is subscribed will be used to send the table. The
standard options are
* votable: use MType table.load.votable
* fits: use MType table.load.fits
If any other string is used which corresponds to one of
STILTS's known table output formats, an attempt will be made
to use an ad-hoc MType of the form table.load.format.
[Default: votable fits]
client = <name-or-id> (String)
Identifies a registered SAMP client which is to receive the
table. Either the client ID or the (case-insensitive)
application name may be used. If a non-null value is given,
then the table will be sent to only the first client with the
given name or ID. If no value is supplied the table will be
sent to all suitably subscribed clients.
'''
env = _JyEnvironment()
env.setValue('format', _map_env_value(format))
env.setValue('client', _map_env_value(client))
mode = _stilts.getModeFactory().createObject('samp')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
def mode_tosql(table, protocol, db, dbtable, host='localhost', write='create', user='buildd', password=None):
'''\
Writes a new table to an SQL database. You need the appropriate JDBC
drivers and -Djdbc.drivers set as usual (see SUN/256).
Parameters:
protocol = <jdbc-protocol> (String)
The driver-specific sub-protocol specifier for the JDBC
connection. For MySQL's Connector/J driver, this is mysql, and
for PostgreSQL's driver it is postgresql. For other drivers,
you may have to consult the driver documentation.
host = <value> (String)
The host which is acting as a database server.
[Default: localhost]
db = <db-name> (String)
The name of the database on the server into which the new
table will be written.
The value of this parameter forms the last part of the JDBC
connection URL. That means that for some JDBC drivers, you can
append parameter specifications to it to affect the way the
connection is made to the database, e.g. "
db=some_db?useSSL=false" for MySQL's Connector/J.
dbtable = <table-name> (String)
The name of the table which will be written to the database.
write = create|dropcreate|append
(uk.ac.starlink.table.jdbc.WriteMode)
Controls how the values are written to a table in the
database. The options are:
* create: Creates a new table before writing. It is an error
if a table of the same name already exists.
* dropcreate: Creates a new database table before writing. If
a table of the same name already exists, it is dropped
first.
* append: Appends to an existing table. An error results if
the named table has the wrong structure (number or types
of columns) for the data being written.
[Default: create]
user = <username> (String)
User name for the SQL connection to the database.
[Default: buildd]
password = <passwd> (String)
Password for the SQL connection to the database.
'''
env = _JyEnvironment()
env.setValue('protocol', _map_env_value(protocol))
env.setValue('db', _map_env_value(db))
env.setValue('dbtable', _map_env_value(dbtable))
env.setValue('host', _map_env_value(host))
env.setValue('write', _map_env_value(write))
env.setValue('user', _map_env_value(user))
env.setValue('password', _map_env_value(password))
mode = _stilts.getModeFactory().createObject('tosql')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
def mode_gui(table):
'''\
Displays the table in a scrollable window.
'''
env = _JyEnvironment()
mode = _stilts.getModeFactory().createObject('gui')
consumer = mode.createConsumer(env)
_check_unused_args(env)
consumer.consume(table)
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