Changeset 1265 for branches


Ignore:
Timestamp:
09/11/06 23:16:06 (18 years ago)
Author:
phi196
Message:

Release 2.1 updates

File:
1 edited

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  • branches/Release2.1/doc/userguide.tex

    r1264 r1265  
    6767updated to Debian Sarge and are using the ``DEBIANsarge''
    6868/usr/local. If your favourite machine has not been upgraded, send a
    69 request your your friendly IT support.}
     69request your your friendly IT support. At the time of writing asap 2.1
     70does not run on hydra, bourbon or kaputar.}
    7071
    7172\index{Running}To start asap log onto one of these Linux hosts and enter
     
    12651266}
    12661267
    1267 
    1268 
    12691268These functions all take a set of \cmd{kwargs} commands. These can be
    12701269used to set colour, linewidth fontsize etc. These are standard
     
    12901289\index{Linecatalog}ASAP can load and manipulate line catlogs to
    12911290retrieve rest frequencies for \cmd{set\_restfreqs} and for line
    1292 identification in the plotter. No line catalogs are built into ASAP,
    1293 the user must load a ASCII based table (which can optionally be saved
    1294 in an internal format) either of the users own creation or a standard
    1295 line catalog such as the JPL line catalog or Lovas. The ATNF asap ftp
    1296 area as copies of the JPL and Lovas catalog in the appropriate
    1297 format. All line catalogs are loaded into a ``linecatalog'' object.
     1291identification in the plotter. All line catalogs are loaded into a ``linecatalog'' object.
     1292
     1293No line catalogs are built into ASAP, the user must load a ASCII based
     1294table (which can optionally be saved in an internal format) either of
     1295the users own creation or a standard line catalog such as the JPL line
     1296catalog or Lovas. The ATNF asap ftp area as copies of the JPL and
     1297Lovas catalog in the appropriate format
     1298(\cmd{ftp://ftp.atnf.csiro.au/pub/software/asap/data})
    12981299
    12991300\subsection{Loading a Line Catalog}
    13001301
    1301 \index{Linecatalog|loading}The ASCII text line catalog must have at
     1302\index{Linecatalog!loading}The ASCII text line catalog must have at
    13021303least 4 columns. The first four columns must contain (in order):
    13031304Molecule name, frequency in MHz, frequency error and ``intensity''
     
    13301331\end{verbatim}
    13311332
     1333{\em NOTE:} Due to a bug in ipython, if you do not \cmd{del} the
     1334linecatalog table before quiting asap, you will be left with temporary
     1335files. It is safe to delete these once asap has finished.
     1336
    13321337\subsection{Line selection}
    13331338
    1334 \index{Linecatalog|line selection}The linecatalog has a number of
     1339\index{Linecatalog!line selection}The linecatalog has a number of
    13351340selection functions to select a range of lines from a larger catalog
    13361341(the JPL catalog has $>$180000 lines for
     
    13591364\subsubsection{Plotting linecatalog}
    13601365
    1361 \index{Linecatalog|plotting}
     1366\index{Linecatalog!plotting}
    13621367
    13631368The plotter \cmd{plot\_lines} function takes a line catalog as an
     
    13851390\subsubsection{Setting Rest Frequencies}
    13861391
    1387 \index{Linecatalog|set_restfreq}
     1392\index{Linecatalog!set\_restfreq}A linecatalog can be used as an
     1393argument for \cmd{set\_restfreqs}. If a personal line catalog has been
     1394used (which has the same size as the number of number of IFs) or
     1395linecatalog selection has been used to reduce the number of entries,
     1396the line catalog can be used directly as an argument to
     1397\cmd{set\_restfreqs}, e.g.:
     1398\begin{verbatim}
     1399  ASAP>jpl = linecatalog('jpl.tbl')
     1400  ASAP>jpl.set_frequency_limits(23.66,23.75,'GHz')
     1401  ASAP>data = scantable('data.rpf')
     1402  ASAP>data.set_restfreqs(jpl)
     1403\end{verbatim}
     1404
     1405If a larger linecatalog is used, individual elements can be used. Use
     1406the \cmd{summary} to get the index number of the rest frequency you
     1407wish to use. E.g.:
     1408
     1409\begin{verbatim}
     1410  ASAP>jpl.summary()
     1411  ASAP>data.set_restfreqs([jpl[11],[jpl[21]])
     1412\end{verbatim}
     1413
     1414
     1415
    13881416
    13891417\section{Fitting}
     
    16451673
    16461674\subsection{Disk Based Processing}
    1647 \index{Scantable|disk based}
    1648 
    1649 Normally scantables exisit entirely in memory during an ASAP
    1650 session. This has the adtantage of speed, but causes limits on the
     1675\index{Scantable!disk based}
     1676
     1677Normally scantables exist entirely in memory during an ASAP
     1678session. This has the advantage of speed, but causes limits on the
    16511679size of the dataset which can be loaded. ASAP can use ``disk based''
    16521680scan tables which cache the bulk of the scantable on disk and require
    1653 significantely less memory usage.
     1681significantly less memory usage.
    16541682
    16551683To use disk based tables you either need to change the default in your
     
    16721700{\bf NOTE: } Currently a bug in ipython means temporary files are not
    16731701cleaned up properly when you exit ASAP. If you use disk based scan
    1674 tables your directory will be left with 'tabXXXXX_X' directories. These can
     1702tables your directory will be left with 'tabXXXXX\_X' directories. These can
    16751703be safely removed if ASAP is not running.
    16761704
     
    17911819
    17921820\index{Parkes}\index{Polarisation}The following example is processing
    1793 of some Parkes polarmetric observations of OH masers at
     1821of some Parkes polarimetric observations of OH masers at
    179418221.6~GHz. Because digital filters where used in the backend, the
    17951823baselines are stable enough not to require a quotient spectra. The
     
    19671995\index{Functions!summary}%
    19681996\begin{verbatim}
    1969 
    1970     [The scan container]
     1997   [The scan container]
    19711998        scantable           - a container for integrations/scans
    19721999                              (can open asap/rpfits/sdfits and ms files)
     
    19942021            get_abcissa     - get the abcissa values and name for a given
    19952022                              row (time)
     2023            get_column_names - get the names of the columns in the scantable
     2024                               for use with selector.set_query
    19962025            set_freqframe   - set the frame info for the Spectral Axis
    19972026                              (e.g. 'LSRK')
     
    20082037            set_restfreqs   - set a list of rest frequencies
    20092038            flag            - flag selected channels in the data
    2010             lag_flag        - flag specified frequency in the data
    20112039            save            - save the scantable to disk as either 'ASAP',
    20122040                              'SDFITS' or 'ASCII'
     
    20512079     [Selection]
    20522080         selector              - a selection object to set a subset of a scantable
    2053             set_scans          - set (a list of) scans by index
    2054             set_cycles         - set (a list of) cycles by index
     2081           set_cycles         - set (a list of) cycles by index
    20552082            set_beams          - set (a list of) beamss by index
    20562083            set_ifs            - set (a list of) ifs by index
     
    20592086            set_names          - set a selection by name (wildcards allowed)
    20602087            set_tsys           - set a selection by tsys thresholds
     2088            set_query          - set a selection by SQL-like query, e.g. BEAMNO==1
    20612089            reset              - unset all selections
    20622090            +                  - merge to selections
     
    21292157            arrow           - draw arrow annotations either in data or relative
    21302158                              coordinates
    2131             set_abcissa     - specify a user label for the abcissa
    2132             set_ordinate    - specify a user label for the ordinate
    2133             set_layout      - specify the multi-panel layout (rows,cols)
    2134             set_colors      - specify a set of colours to use
    2135             set_linestyles  - specify a set of linestyles to use if only
    2136                               using one color
    2137             set_font        - set general font properties, e.g. 'family'
    2138             set_histogram   - plot in historam style
    2139             set_mask        - set a plotting mask for a specific polarization
    2140             text            - draw text annotations either in data or relative
    2141                               coordinates
     2159            axhline,axvline - draw horizontal/vertical lines
     2160            axhspan,axvspan - draw horizontal/vertical regions
     2161
     2162        xyplotter           - matplotlib/pylab plotting functions
     2163
     2164    [Reading files]
     2165        reader              - access rpfits/sdfits files
    21422166            arrow           - draw arrow annotations either in data or relative
    21432167                              coordinates
     
    22012225histogram rather than lines.}
    22022226
    2203 {\em MALTE TO FIX}
    2204 
    22052227\asaprc{plotter.colours}{}{Set default colours for plotting}
    22062228
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