Changes in trunk/doc/userguide.tex [1347:1217]

File:

• trunk/doc/userguide.tex (modified) (100 diffs)

trunk/doc/userguide.tex

@@ -48 +48 @@
 package.
 
-This userguide has been updated for the ASAP 2.1. Please report any
+This userguide is being updated for the ASAP 2.1. Please report any
 mistakes you find.
 
@@ -65 +65 @@
 
 {\em Note. ASAP2.1 only runs on ATNF Linux machines which have been
-updated to Debian Sarge and are using the ``DEBIANSarge''
+updated to Debian Sarge and are using the ``DEBIANsarge''
 /usr/local. If your favourite machine has not been upgraded, send a
-request to your friendly IT support. At the time of writing asap 2.1
-does not run on hydra, bourbon or kaputar.}
+request your your friendly IT support.}
 
 \index{Running}To start asap log onto one of these Linux hosts and enter
@@ -77 +76 @@
 \end{verbatim}
 
-This starts ASAP. To quit, you need to type \verb+^+-d (control-d) or
-type \cmd{\%Exit}.
+This starts the ASAP. To quit, you need to type \verb+^+-d
+(control-d) or type \cmd{\%Exit}.
 
 \section{Interface}
@@ -99 +98 @@
 main objects are used :
 
-\begin{tabular}{ll}
-
-\cmd{scantable} & \parbox[t]{0.7\textwidth}{The data container (actual
-  spectra and header information)} \\
-\cmd{selector} & \parbox[t]{0.80\textwidth}{Allows the user to select
-  a subsection of the data, such as a specified or range of beam
-  numbers, IFs, etc.} \\
-\cmd{plotter} & A tool used to plot the spectral line data \\
-\cmd{fitter} & A tool used to fit functions to the spectral data \\
-\cmd{reader} & \parbox[t]{0.8\textwidth}{A tool which can be used to
-    read data from disks into a scantable object (advanced use).}\\
-\end{tabular}
+\begin{itemize}
+  \item[\cmd{scantable}] The data container (actual spectra and header
+    information)
+  \item[\cmd{selector}] Allows the user to select a subsection of the
+    data, such as a specified or range of beam numbers, IFs, etc.
+  \item[\cmd{plotter}] A tool used to plot the spectral line data
+  \item[\cmd{fitter}] A tool used to fit functions to the spectral data
+  \item[\cmd{reader}] A tool which can be used to read data from disks
+    into a scantable object (advanced use).
+\end{itemize}
 
 There can be many objects of the same type. Each object is referred to
@@ -127 +124 @@
 functions using the syntax:
 \begin{verbatim}
-  ASAP>out = object.function(arguments)
+  ASAP> out = object.function(arguments)
 \end{verbatim}
 
@@ -139 +136 @@
 
 \begin{verbatim}
-  ASAP>av = scans.average_time(msk,weight='tsys')
-  ASAP>av = scans.average_time(mask=msk,weight='tsys')
-  ASAP>av = scans.average_time(msk,tsys)
-  ASAP>scans.poly_baseline(mask=msk, order=0, insitu=True)
-  ASAP>scans.poly_baseline(msk,0,True)
-  ASAP>scans.poly_baseline(mask, insitu=True)
+  ASAP> av = scans.average_time(msk,weight='tsys')
+  ASAP> av = scans.average_time(mask=msk,weight='tsys')
+  ASAP> av = scans.average_time(msk,tsys)
+  ASAP> scans.poly_baseline(mask=msk, order=0, insitu=True)
+  ASAP> scans.poly_baseline(msk,0,True)
+  ASAP> scans.poly_baseline(mask, insitu=True)
 \end{verbatim}
 
@@ -171 +168 @@
 Example
 \begin{verbatim}
-  ASAP>scans = scantable('MyData.rpf')
-  ASAP>scans.se<TAB>
-  ASAP>scans.set_in<TAB>
+  ASAP> scans = scantable('MyData.rpf')
+  ASAP> scans.se<TAB>
+  ASAP> scans.set_in<TAB>
 scans.set_cursor      scans.set_freqframe   scans.set_selection
 scans.set_doppler     scans.set_instrument  scans.set_unit
 scans.set_fluxunit    scans.set_restfreqs
 
-  ASAP>scans.set_instrument()
+  ASAP> scans.set_instrument()
 \end{verbatim}
 
@@ -207 +204 @@
 
 \begin{verbatim}
-  ASAP>pwd
-  ASAP>ls
-  ASAP>cd /my/data/directory
-  ASAP>! mozilla&
+  ASAP> pwd
+  ASAP> ls
+  ASAP> cd /my/data/directory
+  ASAP> ! mozilla&
 \end{verbatim}
 
@@ -219 +216 @@
 
 \begin{verbatim}
-  ASAP>commands()
+  ASAP> commands()
 \end{verbatim}
 
@@ -226 +223 @@
 
 \begin{verbatim}
-  ASAP>help scantable.get_scan # or help(scantable.get_scan)
-  ASAP>help scantable.stats
-  ASAP>help plotter.plot
-  ASAP>help fitter.plot
-
-  ASAP>scans = scantable('mydata.asap')
-  ASAP>help scans.get_scan # Same as above
+  ASAP> help scantable.get_scan # or help(scantable.get_scan)
+  ASAP> help scantable.stats
+  ASAP> help plotter.plot
+  ASAP> help fitter.plot
+
+  ASAP> scans = scantable('mydata.asap')
+  ASAP> help scans.get_scan # Same as above
 \end{verbatim}
 
@@ -238 +235 @@
 
 \begin{verbatim}
-  ASAP>help average_time
+  ASAP> help average_time
 \end{verbatim}
 
@@ -288 +285 @@
 normally contain 13 beams, 1 IF and 2 polarisations, Parkes
 methanol-multibeam data would contain 7 beams, 2 IFs and 2
-polarisations while the Mopra 8-GHz MOPS filterbank will produce one
+polarisations while the Mopra 8-GHz MOPDS filterbank will produce one
 beam, many IFs, and 2-4 polarisations.
 
 All of the combinations of Beams/IFs an Polarisations are
-contained in separate rows. These rows are grouped in cycles (same time stamp).
+contained in seperate rows. These rows are grouped in cycles (same time stamp).
 
 A collection of cycles for one source is termed a scan (and each scan
 has a unique numeric identifier, the SCANNO). A scantable is then a
 collection of one or more scans. If you have scan-averaged your data
-in time, i.e. you have averaged all cycles within a scan, then each
+in time, i.e. you have averegaed all cycles within a scan, then each
 scan would hold just one (averaged) integration.
 
@@ -305 +302 @@
 changed via the {\tt .asaprc} resource file.
 
-For example a Mopra scan with a  4s integration time, two IFs and
+For example a Mopra scan with a  4s intergration time, two IFs and
 dual polarisations has two (2s) cycles.
 \begin{verbatim}
@@ -348 +345 @@
 
 \begin{verbatim}
-  ASAP>scans = scantable('MyData.rpf')
-  ASAP>scans.summary()                # Brief listing
+  ASAP> scans = scantable('MyData.rpf')
+  ASAP> scans.summary()                # Brief listing
 
   # Equivalent to brief summary function call
-  ASAP>print scan
+  ASAP> print scan
 \end{verbatim}
 
@@ -359 +356 @@
 of summary is redirected into your current pager specified by the
 \$PAGER environment variable. If you find the screen is reset to the
-original state when summary is finished (i.e. the output from summary
+original state when summary is finished (ie the output from summary
 disappears), you may need to set the \$LESS environment variable to
 include the \cmd{-X} option.
@@ -385 +382 @@
 The common selection functions are:
 
-\begin{tabular}{ll}
-
-\cmd{set\_beams} & Select beams by index number \\
-\cmd{set\_ifs} & Select ifs by index number \\
-\cmd{set\_name} & Select by source name. Can contain ``*'' as a
-wildcard, e.g. ``Orion*\_R''. \\
-\cmd{set\_ifs} & Select IFs by index number \\
-
-\cmd{set\_polarisation} & \parbox[t]{0.73\textwidth}{Select by
-polarisation index or name. If polarisation names are given, the data
-will be on-the-fly onverted (for example from linears to Stokes). }\\
-
-\cmd{set\_query} & Set query directly. For power users only! \\
-\cmd{set\_tsys} & Select data based on Tsys. Also example of user
-definable query. \\
-\cmd{reset} & Reset the selection to include all spectra. \\
-
-\end{tabular}
+\begin{itemize}
+
+\item[\cmd{set\_beams}] Select beams by index number
+\item[\cmd{set\_ifs}] Select ifs by index number
+\item[\cmd{set\_name}] Select by source name. Can contain ``*'' as a
+wildcard, e.g. ``Orion*\_R''.
+\item[\cmd{set\_ifs}] Select IFs by index number
+\item[\cmd{set\_polarisation}] Select by polarisation index or
+name. If polarisation names are given, the data will be on-the-fly
+converted (for example from linears to Stokes).
+\item[\cmd{set\_query}] Set query directly. For power users only!
+\item[\cmd{set\_tsys}] Select data based on Tsys. Also example of user
+definable query.
+\item[\cmd{reset}] Reset the selection to include all spectra.
+
 
 Note that all indices are zero based.
@@ -409 +403 @@
 
 \begin{verbatim}
-  ASAP>selection = selector()         # Create selection object
-  ASAP>selection.set_ifs(0)           # Just select the first IF
-  ASAP>scans.set_selection(selection) # Apply the selection
-  ASAP>print scans                    # Will just show the first IF
-
-  ASAP>selection.set_ifs([0,1])       # Select the first two IFs
-  ASAP>selection.set_beams([1,3,5])   # Also select three of the beams
-  ASAP>scans.set_selection(selection) # Apply the selection
-
-  ASAP>selection.set_name('G308*')     # Select by source name
-
-  ASAP>selection.reset()              # Turn off selection
-  ASAP>scans.set_selection(selection) # Apply the reset selection
-
-\end{verbatim}
+  ASAP> selection = selector()         # Create selection object
+  ASAP> selection.set_ifs(0)           # Just select the first IF
+  ASAP> scans.set_selection(selection) # Apply the selection
+  ASAP> print scans                    # Will just show the first IF
+
+  ASAP> selection.set_ifs([0,1])       # Select the first two IFs
+  ASAP> selection.set_beams([1,3,5])   # Also select three of the beams
+  ASAP> scans.set_selection(selection) # Apply the selection
+
+  ASAP> selection.set_name('G308*')     # Select by source name
+
+  ASAP> selection.reset()              # Turn off selection
+  ASAP> scans.set_selection(selection) # Apply the reset selection
+
+\end{verbatim}
+
+\end{itemize}
 
 \subsection{State}
@@ -459 +455 @@
 
 \begin{verbatim}
-  ASAP>scans = scantable('2004-11-23_1841-P484.rpf') # Read in the data
-  ASAP>scans.set_freqframe('LSRK')  # Use the LSR velocity frame
-  ASAP>scans.set_unit('km/s')        # Use velocity for plots etc from now on
-  ASAP>scans.set_doppler('OPTICAL')  # Use the optical velocity convention
-  ASAP>scans.set_unit('MHz')         # Use frequency in MHz from now on
+  ASAP> scans = scantable('2004-11-23_1841-P484.rpf') # Read in the data
+  ASAP> scans.set_freqframe('LSRK')  # Use the LSR velocity frame
+  ASAP> scans.set_unit('km/s')        # Use velocity for plots etc from now on
+  ASAP> scans.set_doppler('OPTICAL')  # Use the optical velocity convention
+  ASAP> scans.set_unit('MHz')         # Use frequency in MHz from now on
 \end{verbatim}
 
@@ -483 +479 @@
 \begin{verbatim}
   # Set all IFs
-  ASAP>scans.set_restfreqs(freqs=1.667359e9)
+  ASAP> scans.set_restfreqs(freqs=1.667359e9)
 \end{verbatim}
 
@@ -493 +489 @@
 \begin{verbatim}
   # Set rest frequency for all IFs
-  ASAP>scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,])
-
-\end{verbatim}
-
-A predetermined ``line catalog'' can be used to set the rest
-frequency. See section \S \ref{sec:linecat}.
-
+  ASAP> scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,])
+
+\end{verbatim}
+
+{\em Currently the following is not implemented
+
+In both of the above modes, you can also specify the rest frequencies via
+names in a known list rather than by their values.
+
+Examples:
+
+\begin{verbatim}
+  ASAP> scans.set_restfreqs(freqs=['OH1665','OH1667'])
+\end{verbatim}
+}
 
 \subsubsection{Masks}
@@ -528 +532 @@
 
   # Select channel range for baselining
-  ASAP>scans.set_unit('channels')
-  ASAP>msk = scans.create_mask([100,400],[600,800])
+  ASAP> scans.set_unit('channels')
+  ASAP> msk = scans.create_mask([100,400],[600,800])
 
   # Select velocity range for fitting
-  ASAP>scans.set_unit('km/s')
-  ASAP>msk = scans.create_mask([-30,-10])
+  ASAP> scans.set_unit('km/s')
+  ASAP> msk = scans.create_mask([-30,-10])
 \end{verbatim}
 
@@ -542 +546 @@
 Example :
 \begin{verbatim}
-  ASAP>scans.set_unit('channels')
-  ASAP>msk = scans.create_mask([0,100],[900-1023], invert=True)
+  ASAP> scans.set_unit('channels')
+  ASAP> msk = scans.create_mask([0,100],[900-1023], invert=True)
 \end{verbatim}
 
@@ -552 +556 @@
 
 \begin{verbatim}
-  ASAP>scans.set_unit('km/s')
-  ASAP>msk = q.create_mask([-30,-10], row=5)
+  ASAP> scans.set_unit('km/s')
+  ASAP> msk = q.create_mask([-30,-10], row=5)
 \end{verbatim}
 
@@ -562 +566 @@
 
 \begin{verbatim}
-  ASAP>scans.set_unit('channels')
-  ASAP>msk1 = q.create_mask([0,100],[511,511],[900,1023],invert=True)
-  ASAP>scans.set_unit('km/s')
-  ASAP>msk2 = q.create_mask([-20,-10],invert=True)
-
-  ASAP>mask = msk1 and msk2
+  ASAP> scans.set_unit('channels')
+  ASAP> msk1 = q.create_mask([0,100],[511,511],[900,1023],invert=True)
+  ASAP> scans.set_unit('km/s')
+  ASAP> msk2 = q.create_mask([-20,-10],invert=True)
+
+  ASAP> mask = msk1 and msk2
 \end{verbatim}
 
@@ -581 +585 @@
 
 \begin{verbatim}
-  ASAP>list_scans()
+  ASAP> list_scans()
   The user created scantables are:
   ['s', 'scans', 'av', 's2', 'ss']
 
-  ASAP>del s2
-  ASAP>del ss
+  ASAP> del s2
+  ASAP> del ss
 \end{verbatim}
 
@@ -607 +611 @@
 
 \begin{verbatim}
-  ASAP>scan = scantable('2004-11-23_1841-P484.rpf')
+  ASAP> scan = scantable('2004-11-23_1841-P484.rpf')
 
   # Don't scan average the data
-  ASAP>scan = scantable('2004-11-23_1841-P484.rpf', average=False)
+  ASAP> scan = scantable('2004-11-23_1841-P484.rpf', average=False)
 \end{verbatim}
 
@@ -630 +634 @@
 
 \begin{verbatim}
-  ASAP>r = reader('2003-03-16_082048_t0002.rpf')
-  ASAP>r.summary()
-  ASAP>scan = r.read()
-  ASAP>del r
+  ASAP> r = reader('2003-03-16_082048_t0002.rpf')
+  ASAP> r.summary()
+  ASAP> scan = r.read()
+  ASAP> del r
 \end{verbatim}
 
@@ -648 +652 @@
 reference for multiple sources. Auto quotient assumes reference scans
 have a trailing ``\_R'' in the source name for data from Parkes and
-Mopra, and a trailing ``e'' or ``w'' for data from Tidbinbilla.
-This functions has two \cmd{mode}s. \cmd{paired} (the deafault), which assumes
-matching adjacent pairs of source/reference scans and \cmd{time}, which finds
-the closest reference scan in time.
-
-\begin{verbatim}
-  ASAP>q = s.auto_quotient()
+Mopra, and a trailing ``e'' or ``w'' for data fro, Tidbinbilla.
+
+\begin{verbatim}
+  ASAP> q = s.auto_quotient()
 \end{verbatim}
 
@@ -662 +663 @@
 
 \begin{verbatim}
- ASAP>q = s.auto_quotient(preserve=True)
+ ASAP> q = s.auto_quotient(preserve=True)
 \end{verbatim}
 
@@ -677 +678 @@
 For Mopra and Parkes data:
 \begin{verbatim}
-  ASAP>r = scans.get_scan('*_R')
-  ASAP>s = scans.get_scan('*^_R')
+  ASAP> r = scans.get_scan('*_R')
+  ASAP> s = scans.get_scan('*_S')
 \end{verbatim}
 
 For Tidbinbilla data
 \begin{verbatim}
-  ASAP>r = scans.get_scan('*_[ew]')
-  ASAP>s = scans.get_scan('*_[^ew]')
-\end{verbatim}
+  ASAP> r = scans.get_scan('*_[ew]')
+  ASAP> s = scans.get_scan('*_[^ew]')
+\end{verbatim}
+
+\subsection{Make the quotient spectra}
+
+Use the quotient function
+
+\begin{verbatim}
+  ASAP> q = s.quotient(r)
+\end{verbatim}
+
+This uses the rows in scantable \cmd{r} as reference spectra for the
+rows in scantable \cmd{s}. Scantable \cmd{r} must have either 1 row
+(which is applied to all rows in \cmd{s}) or both scantables must have
+the same number of rows.
 
 \subsection{Time average separate scans}
@@ -694 +708 @@
 
 \begin{verbatim}
- ASAP>av = q.average_time()
+ ASAP> av = q.average_time()
 \end{verbatim}
 
@@ -701 +715 @@
 
 \begin{verbatim}
- ASAP>av = average_time(q1, q2, q3)
+ ASAP> av = average_time(q1, q2, q3)
 \end{verbatim}
 
@@ -709 +723 @@
 
 \begin{verbatim}
- ASAP>av = average_time(q, weight='tintsys')
+ ASAP> av = average_time(q, weight='tintsys')
 \end{verbatim}
 
@@ -716 +730 @@
 
 \begin{verbatim}
- ASAP>msk = scans.create_mask([200,400],[600,800])
- ASAP>av = average_time(scans, mask=msk, weight='var')
+ ASAP> msk = scans.create_mask([200,400],[600,800])
+ ASAP> av = average_time(scans, mask=msk, weight='var')
 \end{verbatim}
 
 If you have not observed your data with Doppler tracking (or run
-\cmd{freq\_align} explicitly) you should align the data in frequency
+\cmd{freq\_align} explicitally) you should align the data in frequency
 before averaging.
 
 \begin{verbatim}
- ASAP>av = scans.average_time(align=True)
+ ASAP> av = scans.average_time(align=True)
 \end{verbatim}
 
@@ -738 +752 @@
 
 \begin{verbatim}
- ASAP>msk = scans.create_mask([100,400],[600,900])
- ASAP>scans.poly_baseline(msk, order=1)
+ ASAP> msk = scans.create_mask([100,400],[600,900])
+ ASAP> scans.poly_baseline(msk, order=1)
 \end{verbatim}
 
@@ -757 +771 @@
 
 \begin{verbatim}
-  ASAP>scans.auto_poly_baseline(order=2,threshold=5)
+  ASAP> scans.auto_poly_baseline(order=2,threshold=5)
 \end{verbatim}
 
@@ -772 +786 @@
 \begin{verbatim}
   # Don't try and fit the edge of the bandpass which is noisier
-  ASAP>scans.auto_poly_baseline(edge=(500,450),order=3,threshold=3)
+  ASAP> scans.auto_poly_baseline(edge=(500,450),order=3,threshold=3)
 
   # Only fit a given region around the line
-  ASAP>scans.set_unit('km/s')
-  ASAP>msk = scans.create_mask([-60,-20])
-  ASAP>scans.auto_poly_baseline(mask=msk,order=3,threshold=3)
+  ASAP> scans.set_unit('km/s')
+  ASAP> msk = scans.create_mask([-60,-20])
+  ASAP> scans.auto_poly_baseline(mask=msk,order=3,threshold=3)
 
 \end{verbatim}
@@ -787 +801 @@
 
 \begin{verbatim}
- ASAP>scans.average_pol()
+ ASAP> scans.average_pol()
 \end{verbatim}
 
@@ -809 +823 @@
 
 \begin{verbatim}
-  ASAP>scans = scantable('2004-11-23_1841-P484.rpf', unit='Jy')
+  ASAP> scans = scantable('2004-11-23_1841-P484.rpf', unit='Jy')
   # Or in two steps
-  ASAP>scans = scantable('2004-11-23_1841-P484.rpf')
-  ASAP>scans.set_fluxunit('Jy')
+  ASAP> scans = scantable('2004-11-23_1841-P484.rpf')
+  ASAP> scans.set_fluxunit('Jy')
 \end{verbatim}
 
@@ -826 +840 @@
 
 \begin{verbatim}
-  ASAP>scans = scantable('2004-11-23_1841-P484.rpf')
-  ASAP>scans.set_feedtype('circular')
+  ASAP> scans = scantable('2004-11-23_1841-P484.rpf')
+  ASAP> scans.set_feedtype('circular')
 \end{verbatim}
 
@@ -838 +852 @@
 
 \begin{verbatim}
-  ASAP>scans.scale(1.05, tsys=True)
+  ASAP> scans.scale(1.05, tsys=True)
 \end{verbatim}
 
@@ -852 +866 @@
 
 \begin{verbatim}
-  ASAP>scans.convert_flux()               # If efficency known
-  ASAP>scans.convert_flux(eta=0.48)       # If telescope diameter known
-  ASAP>scans.convert_flux(eta=0.48,d=35)  # Unknown telescope
-  ASAP>scans.convert_flux(jypk=15)        # Alternative
+  ASAP> scans.convert_flux()               # If efficency known
+  ASAP> scans.convert_flux(eta=0.48)       # If telescope diameter known
+  ASAP> scans.convert_flux(eta=0.48,d=35)  # Unknown telescope
+  ASAP> scans.convert_flux(jypk=15)        # Alternative
 \end{verbatim}
 
@@ -870 +884 @@
 
 \begin{verbatim}
-  ASAP>scans.recalc_azel()                # recalculate az/el 
-                                                                  # based on pointing
+  ASAP> scans.recalc_azel()                # recalculate az/el based on pointing
 \end{verbatim}
 
 Gain-elevation curves for some telescopes and frequencies are known to
-ASAP (currently only for Tidbinbilla at 20~GHz and Parkes at K-band). 
-In these cases making gain-corrections is simple.  If the gain curve for your
-data is not known, the user can supply either a gain polynomial or text file
+ASAP (currently only for Tidbinbilla at 20~GHz).  In these cases
+making gain-corrections is simple.  If the gain curve for your data is
+not known, the user can supply either a gain polynomial or text file
 tabulating gain factors at a range of elevations (see \cmd{help
 scantable.gain\_el}).
@@ -884 +897 @@
 
 \begin{verbatim}
-  ASAP>scans.gain_el()   # If gain table known
-  ASAP>scans.gain_el(poly=[3.58788e-1,2.87243e-2,-3.219093e-4])
+  ASAP> scans.gain_el()   # If gain table known
+  ASAP> scans.gain_el(poly=[3.58788e-1,2.87243e-2,-3.219093e-4])
 \end{verbatim}
 
@@ -893 +906 @@
 
 \begin{verbatim}
-  ASAP>scans.opacity(0.083)
+  ASAP> scans.opacity(0.083)
 \end{verbatim}
 
@@ -903 +916 @@
 \label{sec:freqalign}
 
-\index{Frequency alignment}\index{Velocity alignment}When time
+\index{Frequency alignment}\index{Velicity alignment}When time
 averaging a series of scans together, it is possible that the velocity
 scales are not exactly aligned.  This may be for many reasons such as
@@ -914 +927 @@
 
 \begin{verbatim}
-  ASAP>scans.freq_align()
-  ASAP>av = average_time(scans)
+  ASAP> scans.freq_align()
+  ASAP> av = average_time(scans)
 \end{verbatim}
 
@@ -927 +940 @@
 
 \begin{verbatim}
-  ASAP>scans1.freq_align() # Copy the refeference Epoch from the output
-  ASAP>scans2.freq_align(reftime='2004/11/23/18:43:35')
-  ASAP>scans3.freq_align(reftime='2004/11/23/18:43:35')
-  ASAP>av = average_time(scans1, scans2, scans3)
+  ASAP> scans1.freq_align() # Copy the refeference Epoch from the output
+  ASAP> scans2.freq_align(reftime='2004/11/23/18:43:35')
+  ASAP> scans3.freq_align(reftime='2004/11/23/18:43:35')
+  ASAP> av = average_time(scans1, scans2, scans3)
 \end{verbatim}
 
@@ -947 +960 @@
 
 \begin{verbatim}
-  ASAP>ss = scans.get_scan(10) # Get the 11th scan (zero based)
-  ASAP>ss = scans.get_scan(range(10)) # Get the first 10 scans
-  ASAP>ss = scans.get_scan(range(10,20)) # Get the next 10 scans
-  ASAP>ss = scans.get_scan([2,4,6,8,10]) # Get a selection of scans
-
-  ASAP>ss = scans.get_scan('345p407') # Get a specific source
-  ASAP>ss = scans.get_scan('345*')    # Get a few sources
-
-  ASAP>r = scans.get_scan('*_R') # Get all reference sources (Parkes/Mopra)
-  ASAP>s = scans.get_scan('*^_R') # Get all program sources (Parkes/Mopra)
-  ASAP>r = scans.get_scan('*[ew]')  # Get all reference sources (Tid)
-  ASAP>s = scans.get_scan('*[^ew]') # Get all program sources (Tid)
+  ASAP> ss = scans.get_scan(10) # Get the 11th scan (zero based)
+  ASAP> ss = scans.get_scan(range(10)) # Get the first 10 scans
+  ASAP> ss = scans.get_scan(range(10,20)) # Get the next 10 scans
+  ASAP> ss = scans.get_scan([2,4,6,8,10]) # Get a selection of scans
+
+  ASAP> ss = scans.get_scan('345p407') # Get a specific source
+  ASAP> ss = scans.get_scan('345*')    # Get a few sources
+
+  ASAP> r = scans.get_scan('*_R') # Get all reference sources (Parkes/Mopra)
+  ASAP> s = scans.get_scan('*_S') # Get all program sources (Parkes/Mopra)
+  ASAP> r = scans.get_scan('*[ew]')  # Get all reference sources (Tid)
+  ASAP> s = scans.get_scan('*[^ew]') # Get all program sources (Tid)
 
 \end{verbatim}
@@ -965 +978 @@
 
 \begin{verbatim}
-  ASAP>ss = scans
+  ASAP> ss = scans
 \end{verbatim}
 
@@ -973 +986 @@
 
 \begin{verbatim}
-  ASAP>ss = scans.copy()
+  ASAP> ss = scans.copy()
 \end{verbatim}
 
@@ -1011 +1024 @@
 
 \begin{verbatim}
-  ASAP>scans.save('myscans') # Save in default format
-  ASAP>scans.save('myscans', overwrite=True) # Overwrite an existing file
+  ASAP> scans.save('myscans') # Save in default format
+  ASAP> scans.save('myscans', 'FITS') # Save as FITS for exporting into CLASS
+  ASAP> scans.save('myscans', overwrite=True) # Overwrite an existing file
 \end{verbatim}
 
 \section{Plotter}
 
-\index{Plotter}Scantable spectra can be plotted at any time. An
-asapplotter object is used for plotting, meaning multiple plot windows
-can be active at the same time. On start up a default asapplotter
-object is created called ``plotter''. This would normally be used for
-standard plotting.
-
-The plotter, optionally, will run in a multi-panel mode and contain
+\index{Plotter}Scantable spectra can be plotted at any time. An asapplotter object is
+used for plotting, meaning multiple plot windows can be active at the
+same time. On start up a default asapplotter object is created called
+``plotter''. This would normally be used for standard plotting.
+
+The plotter, optionally, will run in a multipanel mode and contain
 multiple plots per panel. The user must tell the plotter how they want
 the data distributed. This is done using the set\_mode function. The
@@ -1033 +1046 @@
 
 \begin{verbatim}
-  ASAP>scans.set_unit('km/s')
-  ASAP>plotter.set_mode(stacking='p', panelling='t')
-  ASAP>plotter.plot(scans)
+  ASAP> scans.set_unit('km/s')
+  ASAP> plotter.set_mode(stacking='p',panelling='t')
+  ASAP> plotter.plot(scans)
 \end{verbatim}
 
@@ -1045 +1058 @@
 \begin{verbatim}
   # Plot multiple IFs per panel
-  ASAP>plotter.set_mode(stacking='i', panelling='t')
+  ASAP> plotter.set_mode(stacking='i',panelling='t')
 
   # Plot multiple beams per panel
-  ASAP>plotter.set_mode(stacking='b', panelling='t')
+  ASAP> plotter.set_mode(stacking='b',panelling='t')
 
   # Plot one IF per panel, time stacked
-  ASAP>plotter.set_mode('t', 'i')
+  ASAP> plotter.set_mode('t', 'i')
 
   # Plot each scan in a seperate panel
-  ASAP>plotter.set_mode('t', 's')
+  ASAP> plotter.set_mode('t', 's')
 
 \end{verbatim}
@@ -1067 +1080 @@
 should be used for this purpose. Selection can either be applied to
 the scantable or directly to the plotter, the end result is the same.
-You don't have to reset the scantable selection though, if you set
+You don't have to reset the scantable slection though, if you set
 the selection on the plotter.
 
@@ -1073 +1086 @@
 
 \begin{verbatim}
-  ASAP>selection = selector()
+  ASAP> selection = selector()
   # Select second IF
-  ASAP>selection.set_ifs(1)
-  ASAP>plotter.set_selection(selection)
+  ASAP> selection.set_ifs(1)
+  ASAP> plotter.set_selection(selection)
 
   # Select first 4 beams
-  ASAP>selection.set_beams([0,1,2,3])
-  ASAP>plotter.set_selection(selection)
+  ASAP> selection.set_beams([0,1,2,3])
+  ASAP> plotter.set_selection(selection)
 
   # Select a few scans
-  ASAP>selection.set_scans([2,4,6,10])
-  ASAP>plotter.set_selection(selection)
+  ASAP> selection.set_scans([2,4,6,10])
+  ASAP> plotter.set_selection(selection)
 
   # Multiple selection
-  ASAP>selection.set_ifs(1)
-  ASAP>selection.set_scans([2,4,6,10])
-  ASAP>plotter.set_selection(selection)
+  ASAP> selection.set_ifs(1)
+  ASAP> selection.set_scans([2,4,6,10])
+  ASAP> plotter.set_selection(selection)
 
 \end{verbatim}
@@ -1099 +1112 @@
 zooming the individual plots). From left to right:
 
-\begin{tabular}{ll}
-
-Home & This will unzoom the plots to the original zoom factor \\
-
-Plot history & \parbox[t]{0.8\textwidth}{(left and right arrow) The
-plotter keeps a history of zoom settings. The left arrow sets the plot
-zoom to the previous value. The right arrow returns back again. This
-allows you, for example, to zoom in on one feature then return the
-plot to how it was previously. }\\
-
-Pan & \parbox[t]{0.8\textwidth}{(The Cross) This sets the cursor to
-  pan, or scroll mode allowing you to shift the plot within the
-  window. Useful when zoomed in on a feature. }\\
-
-Zoom & \parbox[t]{0.8\textwidth}{(the letter with the magnifying
-  glass) lets you draw a rectangle around a region of interest then
-  zooms in on that region. Use the plot history to unzoom again.}\\
-
-Adjust & \parbox[t]{0.8\textwidth}{(rectangle with 4 arrows) adjust
-  subplot parameters (space at edge of plots)}\\
-
-Save & \parbox[t]{0.8\textwidth}{(floppy disk). Save the plot as a
-postscript or .png file}\\
-
-\end{tabular}
+\begin{itemize}
+
+\item[Home] This will unzoom the plots to the original zoom factor
+
+\item[Plot history] (left and right arrow). The plotter keeps a
+history of zoom settings. The left arrow sets the plot zoom to the
+previous value. The right arrow returns back again. This allows you,
+for example, to zoom in on one feature then return the plot to how it
+was previously.
+
+\item[Pan] (The Cross) This sets the cursor to pan, or scroll mode
+  allowing you to shift the plot within the window. Useful when
+  zoomed in on a feature.
+
+\item[Zoom] (the letter with the magnifying glass) lets you draw a
+  rectangle around a region of interest then zooms in on that
+  region. Use the plot history to unzoom again.
+
+\item[Adjust] (rectangle with 4 arrows) adjust subplot paramaters
+  (space at edge of plots)
+
+\item[Save] (floppy disk). Save the plot as a postscript or .png file
 
 You can also type ``g'' in the plot window to toggle on and off grid
 lines. Typing 'l' turns on and off logarithmic Y-axis.
+
+\end{itemize}
 
 \subsection{Other control}
@@ -1138 +1150 @@
 
 \begin{verbatim}
-  ASAP>scans.set_unit('km/s')
-  ASAP>plotter.plot(scans)
-  ASAP>plotter.set_range(-150,-50)
-  ASAP>plotter.set_range() # To reset
+  ASAP> scans.set_unit('km/s')
+  ASAP> plotter.plot(scans)
+  ASAP> plotter.set_range(-150,-50)
+  ASAP> plotter.set_range() # To reset
 \end{verbatim}
 
@@ -1147 +1159 @@
 
 \begin{verbatim}
-  ASAP>plotter.set_range(-10,30,-1,6.6)
+  ASAP> plotter.set_range(-10,30,-1,6.6)
 \end{verbatim}
 
@@ -1153 +1165 @@
 
 \begin{verbatim}
-  ASAP>plotter.save('myplot.ps')
-  ASAP>plotter.save('myplot.png', dpi=80)
+  ASAP> plotter.save('myplot.ps')
+  ASAP> plotter.save('myplot.png', dpi=80)
 \end{verbatim}
 
@@ -1160 +1172 @@
 
 The plotter allows the user to change most properties such as text
-size and colour. The \cmd{commands} function and {\cmd help\
+size and colour. The \cmd{commands} funcation and {\cmd help\
 asapplotter} list all the possible commands that can be used with the
 plotter.
@@ -1175 +1187 @@
 plots. Allowable values are 'line', 'dashed', 'dotted', 'dashdot', 
 'dashdotdot' and 'dashdashdot. Example: }{
-  ASAP>plotter.set\_linestyles('line dash cotted datshot.)\\
-  ASAP>plotter.set\_font(size=10)\\
+  ASAP> plotter.set\_linestyles('line dash cotted datshot.)\\
+  ASAP> plotter.set\_font(size=10)\\
 }
 
 \commanddef{set\_font}{Change the font style and size. Example}{
-  ASAP>plotter.set\_font(weight='bold')\\
-  ASAP>plotter.set\_font(size=10)\\
-  ASAP>plotter.set\_font(style='italic')\\
+  ASAP> plotter.set\_font(weight='bold')\\
+  ASAP> plotter.set\_font(size=10)\\
+  ASAP> plotter.set\_font(style='italic')\\
 }
 
-\commanddef{set\_layout}{Change the multi-panel layout, i.e. now many
+\commanddef{set\_layout}{Change the multi-panel layout, ie now many
   rows and columns}{
-  ASAP>plotter.set\_layout(3,2)
+  ASAP> plotter.set\_layout(3,2)
 }
 
 \commanddef{set\_legend}{Set the position, size and optional value of the legend}{
-  ASAP>plotter.set\_legend(fontsize=16)\\
-  ASAP>plotter.set\_legend(mode=0)  \# ASAP chooses where to put the legend\\
-  ASAP>plotter.set\_legend(mode=4)  \# Put legend on lower right\\
-  ASAP>plotter.set\_legend(mode=-1) \# No legend\\
-  ASAP>plotter.set\_legend(mp=['RR','LL']) \# Specify legend labels\\
-  ASAP>plotter.set\_legend(mp=[r'\$\^\{12\}CO\$',r'\$\^\{13\}CO\$']) \# Latex labels
+  ASAP> plotter.set\_legend(fontsize=16)\\
+  ASAP> plotter.set\_legend(mode=0)  \# ASAP chooses where to put the legend\\
+  ASAP> plotter.set\_legend(mode=4)  \# Put legend on lower right\\
+  ASAP> plotter.set\_legend(mode=-1) \# No legend\\
+  ASAP> plotter.set\_legend(mp=['RR','LL']) \# Specify legend labels\\
+  ASAP> plotter.set\_legend(mp=[r'\$\^\{12\}CO\$',r'\$\^\{13\}CO\$']) \# Latex labels
 }
 
 \commanddef{set\_title}{Set the plot title. If multiple panels are
   plotted, multiple titles have to be specified}{
-  ASAP>plotter.set\_title(`G323.12$-$1.79`)\\
-  ASAP>plotter.set\_title([`SiO`, 'Methanol'], fontsize=18)\\
+  ASAP> plotter.set\_title(`G323.12$-$1.79`)\\
+  ASAP> plotter.set\_title([`SiO`, 'Methanol'], fontsize=18)\\
 }
 
 \subsection{Plotter Annotations}
 
-The plotter allows various annotations (lines, arrows, text and
+The plotter allows various annontations (lines, arrows, text and
 ``spans'') to be added to the plot. These annotations are
 ``temporary'', when the plotter is next refreshed
@@ -1213 +1225 @@
 will be removed. 
 
-\bigcommanddef{arrow(x,y,x+dx,y+dy)}{Draw an arrow from a specified
+\bigcommanddef{arrow(x,y,x+dx,y+dy)}{Draw an arrow from a specifed
 \cmd{(x,y)} position to \cmd{(x+dx, y+dy)}. The values are in world
-coordinates. Addition arguments which must be passed are {\cmd head\_width} and \cmd{head\_length}}{
-  ASAP>plotter.arrow(-40,7,35,0,head\_width=0.2, head\_length=10)
+coordinates. \em {HOW TO SET ARROW HEAD??}}{
+  ASAP> plotter.arrow(-40,7,35,0)
 }
 
 \bigcommanddef{axhline(y, xmin, xmax)}{Draw a horizontal line at the
-specified \cmd{y} position (in world coordinates) between xmin and xmax
-(in relative coordinates, i.e. 0.0 is the left hand edge of the plot
-while 1.0 is the right side of the plot).}{
- ASAP>plotter.axhline(6.0,0.2,0.8)
+specifed \cmd{y} position (in world coordinates) between xmin and xmax
+(in relative coordinates, ie 0.0 is the left hand edge of the plot
+while 1.0 is the right side of the plot.}{
+ ASAP> plotter.axhline(6.0,0.2,0.8)
 }
 
 \bigcommanddef{avhline(x, ymin, ymax)}{Draw a vertical line at the
-specified \cmd{x} position (in world coordinates) between \cmd{ymin}
-and \cmd{ymax} (in relative coordinates, i.e. 0.0 is the left hand edge
+specifed \cmd{x} position (in world coordinates) between \cmd{ymin}
+and \cmd{ymax} (in relative coordinates, ie 0.0 is the left hand edge
 of the plot while 1.0 is the right side of the plot).}{
- ASAP>plotter.axvline(-50.0,0.1,1.0)
+ ASAP> plotter.axvline(-50.0,0.1,1.0)
 }
 
 \bigcommanddef{axhspan(ymin, ymax, \\ \hspace*{20mm}xmin,
  xmax)}{Overlay a transparent colour rectangle. \cmd{ymin} and
- \cmd{ymax} are given in world coordinates while \cmd{xmin} and
+ \cmd{ymax} are given in world coordnates while \cmd{xmin} and
  \cmd{xmax} are given in relative coordinates}{ 
-ASAP>plotter.axhspan(2,4,0.25,0.75) 
+ASAP> plotter.axhspan(2,4,0.25,0.75) 
 }
 
 \bigcommanddef{axvspan(xmin, xmax, \\ \hspace*{20mm} ymin,
  ymax)}{Overlay a transparent colour rectangle. \cmd{ymin} and
- \cmd{ymax} are given in relative coordinates while \cmd{xmin} and
+ \cmd{ymax} are given in relative coordnates while \cmd{xmin} and
  \cmd{xmax} are given in world coordinates}{ 
-ASAP>plotter.axvspan(-50,60,0.2,0.5) 
+ASAP> plotter.axvspan(-50,60,0.2,0.5) 
 }
 
@@ -1252 +1264 @@
 }
 
+
+
 These functions all take a set of \cmd{kwargs} commands. These can be
 used to set colour, linewidth fontsize etc. These are standard
@@ -1257 +1271 @@
 
 \begin{tabular}{ll}
- \tt color, facecolor, edgecolor \\
- \tt width, linewidth \\
+ \tt color  \\
+ \tt linewidth \\
  \tt fontsize \\
  \tt fontname & Sans, Helvetica, Courier, Times etc\\
@@ -1267 +1281 @@
 Examples: 
 \begin{verbatim}
-  ASAP>plotter.axhline(6.0,0.2,0.8, color='red', linewidth=3)
-  ASAP>plotter.text(-10,7,"CO", fontsize=20)
-\end{verbatim}
-
-\section{Line Catalog}
-\label{sec:linecat}
-\index{Linecatalog}ASAP can load and manipulate line catlogs to
-retrieve rest frequencies for \cmd{set\_restfreqs} and for line
-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:
-
-\hspace{1cm}\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
-least 4 columns. The first four columns must contain (in order):
-Molecule name, frequency in MHz, frequency error and ``intensity''
-(any units). If the molecule name contains any spaces, they must be
-wrapped in quotes \verb+""+.
-
-A sample from the JPL line catalog:
-
-\begin{verbatim}
-     H2D+    3955.2551 228.8818  -7.1941  
-     H2D+   12104.7712 177.1558  -6.0769  
-     H2D+   45809.2731 118.3223  -3.9494  
-     CH       701.6811    .0441  -7.1641  
-     CH       724.7709    .0456  -7.3912  
-     CH      3263.7940    .1000  -6.3501  
-     CH      3335.4810    .1000  -6.0304  
-\end{verbatim}
-
-To load a line catalog then save it in the internal format:
-
-\begin{verbatim}
-  ASAP>jpl = linecatalog('jpl_pruned.txt')
-  ASAP>jpl.save('jpl.tbl')
-\end{verbatim}
-
-Later the saved line catalog can reloaded:
-
-\begin{verbatim}
-  ASAP>jpl = linecatalog('jpl.tbl')
-\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
-selection functions to select a range of lines from a larger catalog
-(the JPL catalog has $>$180000 lines for
-example). \cmd{set\_frequency\_limits} selects on frequency range,
-\cmd{set\_strength\_limits} selects on intensity while \cmd{set\_name}
-selects on molecule name (wild cards allowed). The \cmd{summary}
-function lists the currently selected lines.
-
-\begin{verbatim}
-  ASAP>jpl = linecatalog('jpl.tbl')
-  ASAP>jpl.set_frequency_limits(80,115,'GHz') # Lines for 3mm receiver
-  ASAP>jpl.set_name('*OH')                    # Select all alcohols
-  ASAP>jpl.set_name('OH')                     # Select only OH molecules
-  ASAP>jpl.summary()
-
-  ASAP>jpl.reset()                            # Selections are accumulative
-  ASAP>jpl.set_frequency_limits(80,115,'GHz') 
-  ASAP>jpl.set_strength_limits(-2,10)         # Select brightest lines
-  ASAP>jpl.summary() 
-\end{verbatim}
-
-\subsection{Using Linecatalog}
-
-The line catalogs can be used for line overlays on the plotter or with
-\cmd{set\_restfreq}.
-
-\subsubsection{Plotting linecatalog}
-
-\index{Linecatalog!plotting}
-
-The plotter \cmd{plot\_lines} function takes a line catalog as an
-argument and overlays the lines on the spectrum. {\em Currently this
-only works when plotting in units of frequency (Hz, GHz etc).} If a
-large line catalog has been loaded (e.g. JPL) it is highly recommended
-that you use the selection functions to narrow down the number of
-lines.  By default the line catalog overlay is plotted assuming a line
-velocity of 0.0. This can be set using the \cmd{doppler} argument (in
-km/s). Each time \cmd{plot\_lines} is called the new lines are added
-to any existing line catalog annotations. These are all removed after
-the next call to \cmd{plotter.plot()}.
-
-\begin{verbatim}
-  ASAP>jpl = linecatalog('jpl.tbl')
-  ASAP>jpl.set_frequency_limits(23,24,'GHz')
-  ASAP>data.set_unit('GHz')            # Only works with freq axis currently
-  ASAP>plotter.plot(data)
-  ASAP>plotter.plot_lines(jpl)
-
-  ASAP>plotter.plot()                  # Reset plotter
-  ASAP>plotter.plot_lines(jpl,doppler=-10,location='Top') 
-                             # On top with -10 km/s velocity
-\end{verbatim}
-
-\subsubsection{Setting Rest Frequencies}
-
-\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}
-
-For data with many IFs, such as from MOPS, the user it is recommended
-that the user creates their own line cstalog for the data and use this
-to set the rest frequency for each IF.
+  ASAP> plotter.axhline(6.0,0.2,0.8, color='red', linewidth=3)
+  ASAP> plotter.text(-10,7,"CO", fontsize=20)
+\end{verbatim}
 
 \section{Fitting}
@@ -1417 +1296 @@
 
 \begin{verbatim}
- ASAP>f = fitter()
- ASAP>f.set_function(gauss=2) # Fit two Gaussians
- ASAP>f.set_scan(scans)
- ASAP>selection = selector()
- ASAP>selection.set_polarisations(1) # Fit the second polarisation
- ASAP>scans.set_selection(selection)
- ASAP>scans.set_unit('km/s')  # Make fit in velocity units
- ASAP>f.fit(1)                # Run the fit on the second row in the table
- ASAP>f.plot()                # Show fit in a plot window
- ASAP>f.get_parameters()      # Return the fit paramaters
+ ASAP> f = fitter()
+ ASAP> f.set_function(gauss=2) # Fit two Gaussians
+ ASAP> f.set_scan(scans)
+ ASAP> selection = selector()
+ ASAP> selection.set_polarisations(1) # Fit the second polarisation
+ ASAP> scans.set_selection(selection)
+ ASAP> scans.set_unit('km/s')  # Make fit in velocity units
+ ASAP> f.fit(1)                # Run the fit on the second row in the table
+ ASAP> f.plot()                # Show fit in a plot window
+ ASAP> f.get_parameters()      # Return the fit paramaters
 \end{verbatim}
 
@@ -1437 +1316 @@
 
 \begin{verbatim}
-  ASAP>f = fitter()
-  ASAP>f.set_function(gauss=2)
-  ASAP>scans.set_unit('km/s')  # Set the mask in channel units
-  ASAP>msk = s.create_mask([1800,2200])
-  ASAP>scans.set_unit('km/s')  # Make fit in velocity units
-  ASAP>f.set_scan(s,msk)
-  ASAP>f.fit()
-  ASAP>f.plot()
-  ASAP>f.get_parameters()
+  ASAP> f = fitter()
+  ASAP> f.set_function(gauss=2)
+  ASAP> scans.set_unit('km/s')  # Set the mask in channel units
+  ASAP> msk = s.create_mask([1800,2200])
+  ASAP> scans.set_unit('km/s')  # Make fit in velocity units
+  ASAP> f.set_scan(s,msk)
+  ASAP> f.fit()
+  ASAP> f.plot()
+  ASAP> f.get_parameters()
 \end{verbatim}
 
@@ -1452 +1331 @@
 
 \begin{verbatim}
-  ASAP>f = fitter()
-  ASAP>f.set_function(gauss=2)
-  ASAP>f.set_scan(s,msk)
-  ASAP>f.fit() # Fit using auto-estimates
+  ASAP> f = fitter()
+  ASAP> f.set_function(gauss=2)
+  ASAP> f.set_scan(s,msk)
+  ASAP> f.fit() # Fit using auto-estimates
   # Set Peak, centre and fwhm for the second gaussian.
   # Force the centre to be fixed
-  ASAP>f.set_gauss_parameters(0.4,450,150,0,1,0,component=1)
-  ASAP>f.fit() # Re-run the fit
+  ASAP> f.set_gauss_parameters(0.4,450,150,0,1,0,component=1)
+  ASAP> f.fit() # Re-run the fit
 \end{verbatim}
 
@@ -1470 +1349 @@
 \begin{verbatim}
   # Plot the residual
-  ASAP>f.plot(residual=True)
+  ASAP> f.plot(residual=True)
 
   # Plot the first 2 componentsa
-  ASAP>f.plot(components=[0,1])
+  ASAP> f.plot(components=[0,1])
 
   # Plot the first and third component plus the model sum
-  ASAP>f.plot(components=[-1,0,2])  # -1 means the compoment sum
+  ASAP> f.plot(components=[-1,0,2])  # -1 means the compoment sum
 \end{verbatim}
 
@@ -1485 +1364 @@
 
 \begin{verbatim}
-  ASAP>f.store_fit()
+  ASAP> f.storefit()
 \end{verbatim}
 
@@ -1497 +1376 @@
 
 \begin{verbatim}
-  ASAP>scans.get_fit(4) # Print fits for row 4
-\end{verbatim}
-
-A fit can also be exported to an ASCII file using the \cmd{store\_fit}
-function. Simply give the name of the output file requires as an
-argument.
-
-\begin{verbatim}
-  ASAP>f.store_fit('myfit.txt')
+  ASAP> scans.get_fit(4) # Print fits for row 4
 \end{verbatim}
 
@@ -1528 +1399 @@
 
 \begin{verbatim}
-  ASAP>scans.rotate_xyphase(10.5)            # Degrees
+  ASAP> scans.rotate_xyphase(10.5)            # Degrees
 \end{verbatim}
 
@@ -1541 +1412 @@
 
 \begin{verbatim}
-  ASAP>scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting
+  ASAP> scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting
 \end{verbatim}
 
@@ -1550 +1421 @@
 
 \begin{verbatim}
-  ASAP>scans.invert_phase()
+  ASAP> scans.invert_phase()
 \end{verbatim}
 
 Depending on how the correlator is configured, ``BA'' may be
-correlated instead of ``AB''. Use \cmd{swap\_linears} to correct for
+correlated insead of ``AB''. Use \cmd{swap\_linears} to correct for
 this problem:
 
 \begin{verbatim}
-  ASAP>scans.swap_linears()
+  ASAP> scans.swap_linears()
 \end{verbatim}
 
@@ -1568 +1439 @@
 
 \begin{verbatim}
-  ASAP>stokescans = linearscans.convert_pol("stokes")
+  ASAP> stokescans = linearscans.convert_pol("stokes")
 \end{verbatim}
 
@@ -1587 +1458 @@
 
 \begin{verbatim}
-  ASAP>selection = selector()
-
-  ASAP>selection.set_polarisations(``I Q U V'')
+  ASAP> selection = selector()
+
+  ASAP> selection.set_polarisations(``I Q U V'')
   ASAP  plotter.set_selection(selection);              # Select I, Q, U \& V
 
-  ASAP>selection.set_polarisations(``I Q'')
+  ASAP> selection.set_polarisations(``I Q'')
   ASAP  plotter.set_selection(selection);              # Select just I \& Q
 
-  ASAP>selection.set_polarisations(``RR LL'')
+  ASAP> selection.set_polarisations(``RR LL'')
   ASAP  plotter.set_selection(selection);              # Select just RR \& LL
 
-  ASAP>selection.set_polarisations(``XX YY'')
+  ASAP> selection.set_polarisations(``XX YY'')
   ASAP  plotter.set_selection(selection);              # Select linears
 
-  ASAP>selection.set_polarisations(``I Plinear'')
+  ASAP> selection.set_polarisations(``I Plinear'')
   ASAP  plotter.set_selection(selection);              # Fractional linear
 
-  ASAP>selection.set_polarisations(``Pangle'')
+  ASAP> selection.set_polarisations(``Pangle'')
   ASAP  plotter.set_selection(selection);              # Position angle
 
@@ -1612 +1483 @@
 describe in section~\ref{sec:selection}.
 
+\subsection{Saving}
+
+\index{Polarisation!saving}When saving data using the \cmd{save}
+function, the \cmd{stokes} argument can be used to save the data as
+Stoke values when saving in FITS format.
+
+Example:
+
+\begin{verbatim}
+  ASAP> scans.save('myscan.sdfits', 'SDFITS', stokes=True)
+\end{verbatim}
+
 \section{Specialised Processing}
 
@@ -1618 +1501 @@
 MX mode is a specific observing approach with a multibeam where a
 single source is observed cycling through each beam. The scans when
-the beam is off source is used as a reference for the on-source
+the beam is off source is used as a reference for the onsource
 scan. The function \cmd{mx\_quotient} is used to make a quotient
 spectrum from an MX cycle. This works averaging the ``off-source''
@@ -1626 +1509 @@
 single scan (it the scan numbers are re-labelled to be the same). Note
 that the current version of \cmd{mx\_quotient} only handles a single
-MX cycle, i.e. if each beam has observed the source multiple times you
+MX cycle, ie if each beam has observed the source multiple times you
 will need to use the selector object multiple times to select a single
 MX cycle, run \cmd{mx\_quotient} for each cycle then merge the
@@ -1634 +1517 @@
 
 \begin{verbatim}
-  ASAP>scans = scantable('mydata.rpf')
-  ASAP>q = scans.mx_quotient()
-  ASAP>plotter.plot(q)
+  ASAP> scans = scantable('mydata.rpf')
+  ASAP> q = scans.mx_quotient()
+  ASAP> plotter.plot(q)
 \end{verbatim}
 
@@ -1644 +1527 @@
 
 \begin{verbatim}
-  ASAP>av = q.average_beam()
+  ASAP> av = q.average_beam()
 \end{verbatim}
 
@@ -1650 +1533 @@
 
 {\em FILL ME IN}
-
-\subsection{Disk Based Processing}
-\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
-significantly less memory usage.
-
-To use disk based tables you either need to change the default in your
-\cmd{.asaprc} file, e.g.
-\begin{verbatim}
-   scantable.storage          : disk
-\end{verbatim}
-
-or use set the ``\cmd{rc}'' value while running asap to change this
-on-the-fly. E.g.
-\begin{verbatim}
-  ASAP>rc('scantable',storage='disk')
-  ASAP>data = scantable('data.rpf')     # Loaded using disk based table
-  ASAP>rc('scantable',storage='memory') # Memory tables will be used now
-\end{verbatim}
-
-Changing the ``\cmd{rc}'' value affects the next time the
-\cmd{scantable} constructor is called.
-
-{\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
-be safely removed if ASAP is not running.
 
 \section{Scantable Mathematics}
@@ -1692 +1544 @@
 {\em Currently mathematics between two scantables is not available }
 
-%  ASAP>sum = scan1+scan2
-\begin{verbatim}
-  ASAP>scan2 = scan1+2.0
-  ASAP>scan *= 1.05
+%  ASAP> sum = scan1+scan2
+\begin{verbatim}
+  ASAP> scan2 = scan1+2.0
+  ASAP> scan *= 1.05
 \end{verbatim}
 
 \section{Scripting}
 
-\index{Scripting}Because ASAP is based on python, it easy for the user
+\index{Scripting}Because asap is based on python, it easy for the user
 write their own scripts and functions to process data. This is highly
 recommended as most processing of user data could then be done in a
 couple of steps using a few simple user defined functions. A Python
-primer is beyond the scope of this userguide. See the ASAP home pages
+primer is beyond the scope of this userguide. See the asap home pages
 for a scripting tutorial or the main python website for comprehensive
 documentation.
@@ -1710 +1562 @@
 \hspace{1cm} http://www.atnf.csiro.au/computing/software/asap/tutorials
 
-\hspace{1cm} http://svn.atnf.csiro.au/trac/asap/wiki
-
 \hspace{1cm} http://www.python.org/doc/Introduction.html
 
 \subsection{Running scripts}
 
-The ASAP global function \cmd{execfile} reads the named text file and
+The asap global function \cmd{execfile} reads the named text file and
 executes the contained python code. This file can either contain
 function definitions which will be used in subsequent processing or
 just a set of commands to process a specific dataset.
 
-As an alternative to run scripts without entering ASAP, create a script which
-starts with.
-
-\begin{verbatim}
-from asap import *
-
-<your code>
-\end{verbatim}
-
-And run it with \cmd{python scriptname}.
-
 \subsection{asapuserfuncs.py}
 
 The file $\sim$/.asap/asapuserfuncs.py is automatically read in when
-ASAP is started. The user can use this to define a set of user
-functions which are automatically available each time ASAP is
+asap is started. The user can use this to define a set of user
+functions which are automatically available each time asap is
 used. The \cmd{execfile} function can be called from within this file.
 
@@ -1742 +1581 @@
 
 In the following section a few examples of end-to-end processing of
-some data in ASAP are given.
+some data in asap are given.
 
 \subsection{Mopra}
@@ -1748 +1587 @@
 
 The following example is of some dual polarisation, position switched
-data from Mopra. The source has been observed multiple times split
-into a number of separate RPFITS files. To make the processing easier,
-the first step is to \cmd{cat} the separate RPFITS files together and
-load as a whole (future versions of ASAP will make this unnecessary).
+data from Mopra. The source has been observed mulitple times split
+into a number of seperate rpfits files. To make the processing easier,
+the first step is to \cmd{cat} the seeprate rpfits files together and
+load as a whole (future versions of asap will make this unnecessary).
 
 
@@ -1811 +1650 @@
 
 \index{Parkes}\index{Polarisation}The following example is processing
-of some Parkes polarimetric observations of OH masers at
+of some Parkes polarmetric 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
 4~MHz bandwidth is wide enough to observe both the 1665 and 1667~MHz
 OH maser transitions. Each source was observed once for about 10
-minutes. Tsys information was not written to the RPFITS file (a
+minutes. Tsys information was not written to the rpfits file (a
 nominal 25K values was used), so the amplitudes need to be adjusted
 based on a separate log file. A simple user function is used to
@@ -1842 +1681 @@
 \end{verbatim}
 
-The typical ASAP session would be
+The typical asap session would be
 
 \begin{verbatim}
@@ -1927 +1766 @@
 limitations. The data is position switched, observing first an
 reference to the west, then the source twice and finally reference to
-the east. Important to note, that \cmd{auto\_quotient} should be executed 
-using the \cmd{mode} `time'.
+the east.
 
 \begin{verbatim}
@@ -1937 +1775 @@
 
 # Make the quotient spectra
-q = d.auto_quotient(mode='time')
+q = d.auto_quotient()
 print q
 
@@ -1988 +1826 @@
 \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)
@@ -2014 +1853 @@
             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')
@@ -2030 +1867 @@
             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'
@@ -2072 +1910 @@
      [Selection]
          selector              - a selection object to set a subset of a scantable
-           set_cycles         - set (a list of) cycles by index
+            set_scans          - set (a list of) scans 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
@@ -2079 +1918 @@
             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
@@ -2150 +1988 @@
             arrow           - draw arrow 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
+            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
             arrow           - draw arrow annotations either in data or relative
                               coordinates
@@ -2218 +2060 @@
 histogram rather than lines.}
 
+{\em MALTE TO FIX}
+
 \asaprc{plotter.colours}{}{Set default colours for plotting}
 
@@ -2225 +2069 @@
 
 % scantable
-\asaprc{scantable.save}{{\bf ASAP} SDFITS ASCII MS2}{Default output
+\asaprc{scantable.save}{{\bf ASAP} SDFITS FITS ASCII MS2}{Default output
 format when saving}
 
@@ -2243 +2087 @@
 \subsection{Installation}
 
-\index{Installation}
-
-Please refer to the asap wiki for instructions on downloading and/or
-building asap from source.
-
-\hspace{1cm}\cmd{http://www.atnf.csiro.au/computing/software/asap/}
+\index{Installation}ASAP depends on a number of third-party libraries which you must
+have installed before attempting to build ASAP. These are:
+
+\begin{itemize}
+\item AIPS++
+\item Boost
+\item Matplotlib
+\item python/ipython
+\end{itemize}
+
+Debian Linux is currently supported and we intend also
+to support other popular Linux flavours, Solaris and Mac.
+
+Of the dependencies, AIPS++ is the most complex to install.
 
 \printindex