Index: tags/Release2.1.0b/doc/userguide.tex
===================================================================
--- tags/Release2.1.0b/doc/userguide.tex	(revision 1242)
+++ tags/Release2.1.0b/doc/userguide.tex	(revision 1243)
@@ -124,5 +124,5 @@
 functions using the syntax:
 \begin{verbatim}
-  ASAP> out = object.function(arguments)
+  ASAP>out = object.function(arguments)
 \end{verbatim}
 
@@ -136,10 +136,10 @@
 
 \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}
 
@@ -168,12 +168,12 @@
 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}
 
@@ -204,8 +204,8 @@
 
 \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}
 
@@ -216,5 +216,5 @@
 
 \begin{verbatim}
-  ASAP> commands()
+  ASAP>commands()
 \end{verbatim}
 
@@ -223,11 +223,11 @@
 
 \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}
 
@@ -235,5 +235,5 @@
 
 \begin{verbatim}
-  ASAP> help average_time
+  ASAP>help average_time
 \end{verbatim}
 
@@ -285,14 +285,14 @@
 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 MOPDS filterbank will produce one
+polarisations while the Mopra 8-GHz MOPS filterbank will produce one
 beam, many IFs, and 2-4 polarisations.
 
 All of the combinations of Beams/IFs an Polarisations are
-contained in seperate rows. These rows are grouped in cycles (same time stamp).
+contained in separate 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 averegaed all cycles within a scan, then each
+in time, i.e. you have averaged all cycles within a scan, then each
 scan would hold just one (averaged) integration.
 
@@ -302,5 +302,5 @@
 changed via the {\tt .asaprc} resource file.
 
-For example a Mopra scan with a  4s intergration time, two IFs and
+For example a Mopra scan with a  4s integration time, two IFs and
 dual polarisations has two (2s) cycles.
 \begin{verbatim}
@@ -345,9 +345,9 @@
 
 \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}
 
@@ -356,5 +356,5 @@
 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 (ie the output from summary
+original state when summary is finished (i.e. the output from summary
 disappears), you may need to set the \$LESS environment variable to
 include the \cmd{-X} option.
@@ -403,17 +403,17 @@
 
 \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
+  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}
@@ -455,9 +455,9 @@
 
 \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}
 
@@ -479,5 +479,5 @@
 \begin{verbatim}
   # Set all IFs
-  ASAP> scans.set_restfreqs(freqs=1.667359e9)
+  ASAP>scans.set_restfreqs(freqs=1.667359e9)
 \end{verbatim}
 
@@ -489,5 +489,5 @@
 \begin{verbatim}
   # Set rest frequency for all IFs
-  ASAP> scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,])
+  ASAP>scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,])
 
 \end{verbatim}
@@ -501,5 +501,5 @@
 
 \begin{verbatim}
-  ASAP> scans.set_restfreqs(freqs=['OH1665','OH1667'])
+  ASAP>scans.set_restfreqs(freqs=['OH1665','OH1667'])
 \end{verbatim}
 }
@@ -532,10 +532,10 @@
 
   # 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}
 
@@ -546,6 +546,6 @@
 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}
 
@@ -556,6 +556,6 @@
 
 \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}
 
@@ -566,10 +566,10 @@
 
 \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}
 
@@ -585,10 +585,10 @@
 
 \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}
 
@@ -611,8 +611,8 @@
 
 \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}
 
@@ -634,8 +634,8 @@
 
 \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}
 
@@ -655,5 +655,5 @@
 
 \begin{verbatim}
-  ASAP> q = s.auto_quotient()
+  ASAP>q = s.auto_quotient()
 \end{verbatim}
 
@@ -663,5 +663,5 @@
 
 \begin{verbatim}
- ASAP> q = s.auto_quotient(preserve=True)
+ ASAP>q = s.auto_quotient(preserve=True)
 \end{verbatim}
 
@@ -678,12 +678,12 @@
 For Mopra and Parkes data:
 \begin{verbatim}
-  ASAP> r = scans.get_scan('*_R')
-  ASAP> s = scans.get_scan('*_S')
+  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]')
+  ASAP>r = scans.get_scan('*_[ew]')
+  ASAP>s = scans.get_scan('*_[^ew]')
 \end{verbatim}
 
@@ -693,5 +693,5 @@
 
 \begin{verbatim}
-  ASAP> q = s.quotient(r)
+  ASAP>q = s.quotient(r)
 \end{verbatim}
 
@@ -708,5 +708,5 @@
 
 \begin{verbatim}
- ASAP> av = q.average_time()
+ ASAP>av = q.average_time()
 \end{verbatim}
 
@@ -715,5 +715,5 @@
 
 \begin{verbatim}
- ASAP> av = average_time(q1, q2, q3)
+ ASAP>av = average_time(q1, q2, q3)
 \end{verbatim}
 
@@ -723,5 +723,5 @@
 
 \begin{verbatim}
- ASAP> av = average_time(q, weight='tintsys')
+ ASAP>av = average_time(q, weight='tintsys')
 \end{verbatim}
 
@@ -730,14 +730,14 @@
 
 \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} explicitally) you should align the data in frequency
+\cmd{freq\_align} explicitly) 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}
 
@@ -752,6 +752,6 @@
 
 \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}
 
@@ -771,5 +771,5 @@
 
 \begin{verbatim}
-  ASAP> scans.auto_poly_baseline(order=2,threshold=5)
+  ASAP>scans.auto_poly_baseline(order=2,threshold=5)
 \end{verbatim}
 
@@ -786,10 +786,10 @@
 \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}
@@ -801,5 +801,5 @@
 
 \begin{verbatim}
- ASAP> scans.average_pol()
+ ASAP>scans.average_pol()
 \end{verbatim}
 
@@ -823,8 +823,8 @@
 
 \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}
 
@@ -840,6 +840,6 @@
 
 \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}
 
@@ -852,5 +852,5 @@
 
 \begin{verbatim}
-  ASAP> scans.scale(1.05, tsys=True)
+  ASAP>scans.scale(1.05, tsys=True)
 \end{verbatim}
 
@@ -866,8 +866,8 @@
 
 \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}
 
@@ -884,5 +884,5 @@
 
 \begin{verbatim}
-  ASAP> scans.recalc_azel()                # recalculate az/el based on pointing
+  ASAP>scans.recalc_azel()                # recalculate az/el based on pointing
 \end{verbatim}
 
@@ -897,6 +897,6 @@
 
 \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}
 
@@ -906,5 +906,5 @@
 
 \begin{verbatim}
-  ASAP> scans.opacity(0.083)
+  ASAP>scans.opacity(0.083)
 \end{verbatim}
 
@@ -916,5 +916,5 @@
 \label{sec:freqalign}
 
-\index{Frequency alignment}\index{Velicity alignment}When time
+\index{Frequency alignment}\index{Velocity 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
@@ -927,6 +927,6 @@
 
 \begin{verbatim}
-  ASAP> scans.freq_align()
-  ASAP> av = average_time(scans)
+  ASAP>scans.freq_align()
+  ASAP>av = average_time(scans)
 \end{verbatim}
 
@@ -940,8 +940,8 @@
 
 \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}
 
@@ -960,16 +960,16 @@
 
 \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('*_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)
+  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}
@@ -978,5 +978,5 @@
 
 \begin{verbatim}
-  ASAP> ss = scans
+  ASAP>ss = scans
 \end{verbatim}
 
@@ -986,5 +986,5 @@
 
 \begin{verbatim}
-  ASAP> ss = scans.copy()
+  ASAP>ss = scans.copy()
 \end{verbatim}
 
@@ -1024,17 +1024,18 @@
 
 \begin{verbatim}
-  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
+  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 multipanel 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 multi-panel 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
@@ -1046,7 +1047,7 @@
 
 \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}
 
@@ -1058,14 +1059,14 @@
 \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}
@@ -1080,5 +1081,5 @@
 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 slection though, if you set
+You don't have to reset the scantable selection though, if you set
 the selection on the plotter.
 
@@ -1086,21 +1087,21 @@
 
 \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}
@@ -1130,5 +1131,5 @@
   region. Use the plot history to unzoom again.
 
-\item[Adjust] (rectangle with 4 arrows) adjust subplot paramaters
+\item[Adjust] (rectangle with 4 arrows) adjust subplot parameters
   (space at edge of plots)
 
@@ -1150,8 +1151,8 @@
 
 \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}
 
@@ -1159,5 +1160,5 @@
 
 \begin{verbatim}
-  ASAP> plotter.set_range(-10,30,-1,6.6)
+  ASAP>plotter.set_range(-10,30,-1,6.6)
 \end{verbatim}
 
@@ -1165,6 +1166,6 @@
 
 \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}
 
@@ -1172,5 +1173,5 @@
 
 The plotter allows the user to change most properties such as text
-size and colour. The \cmd{commands} funcation and {\cmd help\
+size and colour. The \cmd{commands} function and {\cmd help\
 asapplotter} list all the possible commands that can be used with the
 plotter.
@@ -1187,37 +1188,37 @@
 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, ie now many
+\commanddef{set\_layout}{Change the multi-panel layout, i.e. 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 annontations (lines, arrows, text and
+The plotter allows various annotations (lines, arrows, text and
 ``spans'') to be added to the plot. These annotations are
 ``temporary'', when the plotter is next refreshed
@@ -1225,36 +1226,36 @@
 will be removed. 
 
-\bigcommanddef{arrow(x,y,x+dx,y+dy)}{Draw an arrow from a specifed
+\bigcommanddef{arrow(x,y,x+dx,y+dy)}{Draw an arrow from a specified
 \cmd{(x,y)} position to \cmd{(x+dx, y+dy)}. The values are in world
 coordinates. \em {HOW TO SET ARROW HEAD??}}{
-  ASAP> plotter.arrow(-40,7,35,0)
+  ASAP>plotter.arrow(-40,7,35,0)
 }
 
 \bigcommanddef{axhline(y, xmin, xmax)}{Draw a horizontal line at the
-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
+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)
+ ASAP>plotter.axhline(6.0,0.2,0.8)
 }
 
 \bigcommanddef{avhline(x, ymin, ymax)}{Draw a vertical line at the
-specifed \cmd{x} position (in world coordinates) between \cmd{ymin}
-and \cmd{ymax} (in relative coordinates, ie 0.0 is the left hand edge
+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
 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 coordnates while \cmd{xmin} and
+ \cmd{ymax} are given in world coordinates 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 coordnates while \cmd{xmin} and
+ \cmd{ymax} are given in relative coordinates 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) 
 }
 
@@ -1281,7 +1282,108 @@
 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}
+  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}
+
+\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.
+
+\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}
+
+\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).
+
+\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}
 
 \section{Fitting}
@@ -1296,14 +1398,14 @@
 
 \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}
 
@@ -1316,13 +1418,13 @@
 
 \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}
 
@@ -1331,12 +1433,12 @@
 
 \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}
 
@@ -1349,11 +1451,11 @@
 \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}
 
@@ -1364,5 +1466,5 @@
 
 \begin{verbatim}
-  ASAP> f.storefit()
+  ASAP>f.store_fit()
 \end{verbatim}
 
@@ -1376,5 +1478,13 @@
 
 \begin{verbatim}
-  ASAP> scans.get_fit(4) # Print fits for row 4
+  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')
 \end{verbatim}
 
@@ -1399,5 +1509,5 @@
 
 \begin{verbatim}
-  ASAP> scans.rotate_xyphase(10.5)            # Degrees
+  ASAP>scans.rotate_xyphase(10.5)            # Degrees
 \end{verbatim}
 
@@ -1412,5 +1522,5 @@
 
 \begin{verbatim}
-  ASAP> scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting
+  ASAP>scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting
 \end{verbatim}
 
@@ -1421,13 +1531,13 @@
 
 \begin{verbatim}
-  ASAP> scans.invert_phase()
+  ASAP>scans.invert_phase()
 \end{verbatim}
 
 Depending on how the correlator is configured, ``BA'' may be
-correlated insead of ``AB''. Use \cmd{swap\_linears} to correct for
+correlated instead of ``AB''. Use \cmd{swap\_linears} to correct for
 this problem:
 
 \begin{verbatim}
-  ASAP> scans.swap_linears()
+  ASAP>scans.swap_linears()
 \end{verbatim}
 
@@ -1439,5 +1549,5 @@
 
 \begin{verbatim}
-  ASAP> stokescans = linearscans.convert_pol("stokes")
+  ASAP>stokescans = linearscans.convert_pol("stokes")
 \end{verbatim}
 
@@ -1458,22 +1568,22 @@
 
 \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
 
@@ -1492,5 +1602,5 @@
 
 \begin{verbatim}
-  ASAP> scans.save('myscan.sdfits', 'SDFITS', stokes=True)
+  ASAP>scans.save('myscan.sdfits', 'SDFITS', stokes=True)
 \end{verbatim}
 
@@ -1501,5 +1611,5 @@
 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 onsource
+the beam is off source is used as a reference for the on-source
 scan. The function \cmd{mx\_quotient} is used to make a quotient
 spectrum from an MX cycle. This works averaging the ``off-source''
@@ -1509,5 +1619,5 @@
 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, ie if each beam has observed the source multiple times you
+MX cycle, i.e. 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
@@ -1517,7 +1627,7 @@
 
 \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}
 
@@ -1527,5 +1637,5 @@
 
 \begin{verbatim}
-  ASAP> av = q.average_beam()
+  ASAP>av = q.average_beam()
 \end{verbatim}
 
@@ -1533,4 +1643,17 @@
 
 {\em FILL ME IN}
+
+\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
+size of the dataset which can be loaded. ASAP can use ``disk based''
+scan tables which
+
+{\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 'tmp*' directories. These can
+be safely removed if ASAP is not running.
 
 \section{Scantable Mathematics}
@@ -1544,17 +1667,17 @@
 {\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.
@@ -1566,5 +1689,5 @@
 \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
@@ -1574,6 +1697,6 @@
 
 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.
 
@@ -1581,5 +1704,5 @@
 
 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}
@@ -1587,8 +1710,8 @@
 
 The following example is of some dual polarisation, position switched
-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).
+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).
 
 
@@ -1655,5 +1778,5 @@
 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
@@ -1681,5 +1804,5 @@
 \end{verbatim}
 
-The typical asap session would be
+The typical ASAP session would be
 
 \begin{verbatim}
