Changeset 1265

Timestamp:

09/11/06 23:16:06 (18 years ago)

Author:

phi196

Message:

Release 2.1 updates

File:

• branches/Release2.1/doc/userguide.tex (modified) (16 diffs)

branches/Release2.1/doc/userguide.tex

@@ -67 +67 @@
 updated to Debian Sarge and are using the ``DEBIANsarge''
 /usr/local. If your favourite machine has not been upgraded, send a
-request your your friendly IT support.}
+request your your friendly IT support. At the time of writing asap 2.1
+does not run on hydra, bourbon or kaputar.}
 
 \index{Running}To start asap log onto one of these Linux hosts and enter
@@ -1265 +1266 @@
 }
 
-
-
 These functions all take a set of \cmd{kwargs} commands. These can be
 used to set colour, linewidth fontsize etc. These are standard
@@ -1290 +1289 @@
 \index{Linecatalog}ASAP can load and manipulate line catlogs to
 retrieve rest frequencies for \cmd{set\_restfreqs} and for line
-identification in the plotter. No line catalogs are built into ASAP,
-the user must load a ASCII based table (which can optionally be saved
-in an internal format) either of the users own creation or a standard
-line catalog such as the JPL line catalog or Lovas. The ATNF asap ftp
-area as copies of the JPL and Lovas catalog in the appropriate
-format. All line catalogs are loaded into a ``linecatalog'' object.
+identification in the plotter. All line catalogs are loaded into a ``linecatalog'' object.
+
+No line catalogs are built into ASAP, the user must load a ASCII based
+table (which can optionally be saved in an internal format) either of
+the users own creation or a standard line catalog such as the JPL line
+catalog or Lovas. The ATNF asap ftp area as copies of the JPL and
+Lovas catalog in the appropriate format
+(\cmd{ftp://ftp.atnf.csiro.au/pub/software/asap/data})
 
 \subsection{Loading a Line Catalog}
 
-\index{Linecatalog|loading}The ASCII text line catalog must have at
+\index{Linecatalog!loading}The ASCII text line catalog must have at
 least 4 columns. The first four columns must contain (in order):
 Molecule name, frequency in MHz, frequency error and ``intensity''
@@ -1330 +1331 @@
 \end{verbatim}
 
+{\em NOTE:} Due to a bug in ipython, if you do not \cmd{del} the
+linecatalog table before quiting asap, you will be left with temporary
+files. It is safe to delete these once asap has finished.
+
 \subsection{Line selection}
 
-\index{Linecatalog|line selection}The linecatalog has a number of
+\index{Linecatalog!line selection}The linecatalog has a number of
 selection functions to select a range of lines from a larger catalog
 (the JPL catalog has $>$180000 lines for
@@ -1359 +1364 @@
 \subsubsection{Plotting linecatalog}
 
-\index{Linecatalog|plotting}
+\index{Linecatalog!plotting}
 
 The plotter \cmd{plot\_lines} function takes a line catalog as an
@@ -1385 +1390 @@
 \subsubsection{Setting Rest Frequencies}
 
-\index{Linecatalog|set_restfreq}
+\index{Linecatalog!set\_restfreq}A linecatalog can be used as an
+argument for \cmd{set\_restfreqs}. If a personal line catalog has been
+used (which has the same size as the number of number of IFs) or
+linecatalog selection has been used to reduce the number of entries,
+the line catalog can be used directly as an argument to
+\cmd{set\_restfreqs}, e.g.:
+\begin{verbatim}
+  ASAP>jpl = linecatalog('jpl.tbl')
+  ASAP>jpl.set_frequency_limits(23.66,23.75,'GHz')
+  ASAP>data = scantable('data.rpf')
+  ASAP>data.set_restfreqs(jpl)
+\end{verbatim}
+
+If a larger linecatalog is used, individual elements can be used. Use
+the \cmd{summary} to get the index number of the rest frequency you
+wish to use. E.g.:
+
+\begin{verbatim}
+  ASAP>jpl.summary()
+  ASAP>data.set_restfreqs([jpl[11],[jpl[21]])
+\end{verbatim}
+
+
+
 
 \section{Fitting}
@@ -1645 +1673 @@
 
 \subsection{Disk Based Processing}
-\index{Scantable|disk based}
-
-Normally scantables exisit entirely in memory during an ASAP
-session. This has the adtantage of speed, but causes limits on the
+\index{Scantable!disk based}
+
+Normally scantables exist entirely in memory during an ASAP
+session. This has the advantage of speed, but causes limits on the
 size of the dataset which can be loaded. ASAP can use ``disk based''
 scan tables which cache the bulk of the scantable on disk and require
-significantely less memory usage.
+significantly less memory usage.
 
 To use disk based tables you either need to change the default in your
@@ -1672 +1700 @@
 {\bf NOTE: } Currently a bug in ipython means temporary files are not
 cleaned up properly when you exit ASAP. If you use disk based scan
-tables your directory will be left with 'tabXXXXX_X' directories. These can
+tables your directory will be left with 'tabXXXXX\_X' directories. These can
 be safely removed if ASAP is not running.
 
@@ -1791 +1819 @@
 
 \index{Parkes}\index{Polarisation}The following example is processing
-of some Parkes polarmetric observations of OH masers at
+of some Parkes polarimetric observations of OH masers at
 1.6~GHz. Because digital filters where used in the backend, the
 baselines are stable enough not to require a quotient spectra. The
@@ -1967 +1995 @@
 \index{Functions!summary}%
 \begin{verbatim}
-
-    [The scan container]
+   [The scan container]
         scantable           - a container for integrations/scans
                               (can open asap/rpfits/sdfits and ms files)
@@ -1994 +2021 @@
             get_abcissa     - get the abcissa values and name for a given
                               row (time)
+            get_column_names - get the names of the columns in the scantable
+                               for use with selector.set_query
             set_freqframe   - set the frame info for the Spectral Axis
                               (e.g. 'LSRK')
@@ -2008 +2037 @@
             set_restfreqs   - set a list of rest frequencies
             flag            - flag selected channels in the data
-            lag_flag        - flag specified frequency in the data
             save            - save the scantable to disk as either 'ASAP',
                               'SDFITS' or 'ASCII'
@@ -2051 +2079 @@
      [Selection]
          selector              - a selection object to set a subset of a scantable
-            set_scans          - set (a list of) scans by index
-            set_cycles         - set (a list of) cycles by index
+           set_cycles         - set (a list of) cycles by index
             set_beams          - set (a list of) beamss by index
             set_ifs            - set (a list of) ifs by index
@@ -2059 +2086 @@
             set_names          - set a selection by name (wildcards allowed)
             set_tsys           - set a selection by tsys thresholds
+            set_query          - set a selection by SQL-like query, e.g. BEAMNO==1
             reset              - unset all selections
             +                  - merge to selections
@@ -2129 +2157 @@
             arrow           - draw arrow annotations either in data or relative
                               coordinates
-            set_abcissa     - specify a user label for the abcissa
-            set_ordinate    - specify a user label for the ordinate
-            set_layout      - specify the multi-panel layout (rows,cols)
-            set_colors      - specify a set of colours to use
-            set_linestyles  - specify a set of linestyles to use if only
-                              using one color
-            set_font        - set general font properties, e.g. 'family'
-            set_histogram   - plot in historam style
-            set_mask        - set a plotting mask for a specific polarization
-            text            - draw text annotations either in data or relative
-                              coordinates
+            axhline,axvline - draw horizontal/vertical lines
+            axhspan,axvspan - draw horizontal/vertical regions
+
+        xyplotter           - matplotlib/pylab plotting functions
+
+    [Reading files]
+        reader              - access rpfits/sdfits files
             arrow           - draw arrow annotations either in data or relative
                               coordinates
@@ -2201 +2225 @@
 histogram rather than lines.}
 
-{\em MALTE TO FIX}
-
 \asaprc{plotter.colours}{}{Set default colours for plotting}