Changeset 971

Timestamp:

04/03/06 11:07:03 (18 years ago)

Author:

mar637

Message:

proof read chris' lat version. added some info.

File:

• trunk/doc/userguide.tex (modified) (32 diffs)

trunk/doc/userguide.tex

@@ -62 +62 @@
 
 This starts the ASAP. To quit, you need to type \verb+^+-d
-(control-d).
+(control-d) or type \cmd{\%Exit}.
 
 \section{Interface}
@@ -93 +93 @@
   \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.
+    into a scantable object (advanced use).
 \end{itemize}
 
@@ -126 +126 @@
   ASAP> av = scans.average_time(mask=msk,weight='tsys')
   ASAP> av = scans.average_time(msk,tsys)
-  ASAP> scans.polybaseline(mask=msk, order=0, insitu=True)
-  ASAP> scans.polybaseline(msk,0,True)
-  ASAP> scans.polybaseline(mask, insitu=True)
+  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}
 
@@ -157 +157 @@
   ASAP> scans = scantable('MyData.rpf')
   ASAP> scans.se<TAB>
-scans.set_cursor      scans.set_freqframe   scans.set_unit        scans.setpol
-scans.set_doppler     scans.set_instrument  scans.setbeam
-scans.set_fluxunit    scans.set_restfreqs   scans.setif
   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()
 \end{verbatim}
@@ -209 +210 @@
 
 \begin{verbatim}
-  ASAP> help scantable.get_scan
+  ASAP> help scantable.get_scan # or help(scantable.get_scan)
   ASAP> help scantable.stats
   ASAP> help plotter.plot
@@ -269 +270 @@
 
 The building block of a scantable is an integration, which is a single
-row of a scantable. Each row contains spectra for each beam, IF and
+row of a scantable. Each row contains just one spectrum for each beam, IF and
 polarisation. For example Parkes multibeam data would contain many
 beams, one IF and 2-4 polarisations, while the new Mopra 8-GHz
 filterbank will eventually produce one beam, many IFs, and 2-4
-polarisations.
-
-A collection of sequential integrations (rows) for one source is termed
-a scan (and each scan has a unique numeric identifier, the ScanID). A
+polarisations. All of the combinations of Beams/IFs an Polarisations are
+contained in seperate rows. These rows are grouped in cycles - same time stamp.
+
+A collection of cyclesfor 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, then each scan would  hold just one
-(averaged) integration.
+scan-averaged your data in time, i.e. you have averegaed all cycles within
+a scan, then each scan would hold just one (averaged) integration.
 
 Many of the functions which work on scantables can either return a
@@ -303 +305 @@
 of the frequency information and possibly how to manipulate it.
 
-These columns are called FreqID and RestFreqID.  They contain indices, for
-each IF, pointing into tables with all of the frequency information for that
-integration.   More on these below when we discuss the \cmd{summary} function
-in the next subsection.
+These columns are called FreqID and MoleculeID.  They contain indices, for
+each IF, pointing into tables with all of the frequency and rest-frequency
+information for that integration. More on these below when we discuss
+the \cmd{summary} function in the next subsection.
 
 There are of course many other columns which contain the actual spectra,
-the flags, the Tsys, the source names and so on, but those are a little
-more transparently handled.
+the flags, the Tsys, the source names and so on.
 
 There is also a function \cmd{summary} to list a summary of the scantable.
@@ -320 +321 @@
   ASAP> scans = scantable('MyData.rpf')
   ASAP> scans.summary()                # Brief listing
-  ASAP> scans.summary(verbose=True)    # Include frequency information
 
   # Equivalent to brief summary function call
@@ -326 +326 @@
 \end{verbatim}
 
-Most of what the \cmd{summary} function  prints out is obvious. However,
-it also prints out the FreqIDs and RestFreqIDs to which we alluded above.
-These are the last column of the listing.
-
-The summary function gives you a scan-based summary.  So it lists all of
-the FreqIDs and RestFreqIDs that it encountered for each scan.  If you'd
-like to see what each FreqID actually means, then set the verbose
-argument to True and the frequency table will be listed at the end.
-FreqID of 3 say, refers to the fourth row of the frequency table (ASAP
-is 0-relative). The list of rest frequencies, to which the RestFreqIDs
-refer, is always listed.
+The summary function gives you a scan-based summary, presenting the
+scantable as a cascading view od Beams and IFs.
 
 \subsection{Data Selection}
@@ -344 +335 @@
 IF, beam, polarisation, scan number as well as values such as
 Tsys. Advanced users can also make use of the AIPS++ TAQL language to
-create selections based on almost any of the standard header values.
+create selections based on almost any of the values recorded.
 
 Selection is based on a \cmd{selector} object. This object is created
@@ -369 +360 @@
 \item[\cmd{set\_polarisation}] Select but polarisation index or
 name. If polarisation names are given, the data will be on-the-fly
-converted (for example from linears to Stokes). Not all conversions
-are currently supported.
+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
@@ -418 +408 @@
 (e.g. LSRK), Doppler (e.g. OPTICAL) and unit (e.g. km/s) on-the-fly.
 This is important, for example, when you are displaying the data or
-fitting to it.
+fitting to it. The reference frame is set on file read to the value
+set in the user \cmd{.asaprc} file.
 
 For units, the user has the choice of frequency, velocity or channel.
@@ -573 +564 @@
 \section{Data Input}
 
-\index{Reading data}Data can be loaded in one of two ways; using the reader object or via
-the scantable constructor. The scantable method is simpler but the
-reader allow the user more control on what is read.
+\index{Reading data}Data can be loaded in one of two ways; using the
+reader object or via the scantable constructor. The scantable method
+is simpler but the reader allows the user more control on what is read.
 
 \subsection{Scantable constructor}
@@ -615 +606 @@
   ASAP> r.summary()
   ASAP> scan = r.read()
-  ASAP> s = r.read(range(100)) # To read in the first 100 integrations
   ASAP> del r
 \end{verbatim}
@@ -635 +625 @@
 \begin{verbatim}
   ASAP> q = s.auto_quotient()
+\end{verbatim}
+
+By default the quotient spectra is calculated
+to preserve continuum emission. If you wish to remove the continuum
+contribution, use the \cmd{preserve} argument:
+
+\begin{verbatim}
+ ASAP> q = s.auto_quotient(preserve=True)
 \end{verbatim}
 
@@ -670 +668 @@
 %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. By default the quotient spectra is calculated
-%to preserve continuum emission. If you wish to remove the continuum
-%contribution, use the \cmd{preserve} argument:
-%
-%\begin{verbatim}
-%  ASAP> q = s.quotient(r, preserve=True)
-%\end{verbatim}
+%the same number of rows.
 
 \subsection{Time average separate scans}
@@ -729 +721 @@
 \begin{verbatim}
  ASAP> msk = scans.create_mask([100,400],[600,900])
- ASAP> scans.poly_baseline(msk, 1)
+ ASAP> scans.poly_baseline(msk, order=1)
 \end{verbatim}
 
@@ -766 +758 @@
   # Only fit a given region around the line
   ASAP> scans.set_unit('km/s')
-  ASAP> msk = scans.create_mask((-60,-20))
+  ASAP> msk = scans.create_mask([-60,-20])
   ASAP> scans.auto_poly_baseline(mask=msk,order=3,threshold=3)
 
@@ -799 +791 @@
 
 \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 = scantable('2004-11-23_1841-P484.rpf')
   ASAP> scans.set_fluxunit('Jy)
 \end{verbatim}
@@ -989 +981 @@
   ASAP> scans.save('myscans') # Save in default format
   ASAP> scans.save('myscans', 'FITS') # Save as FITS for exporting into CLASS
-
-  ASAP> scans.save('myscans', stokes=True) # Convert raw polarisations into Stokes
   ASAP> scans.save('myscans', overwrite=True) # Overwrite an existing file
 \end{verbatim}
@@ -1044 +1034 @@
 your own sanity) you need to select a subset of this data. This is
 particularly true for multibeam or multi IF data. The selector object
-should be used for this purpose. Selection can either be applide to
+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
+the selection on the plotter.
 
 Examples:
@@ -1130 +1122 @@
 \begin{verbatim}
   ASAP> plotter.save('myplot.ps')
+  ASAP> plotter.save('myplot.png', dpi=80)
 \end{verbatim}
 
@@ -1140 +1133 @@
 \cmd{auto\_fit} function. If single value fitting is used, and the
 current selection includes multiple spectra (beams, IFs, scans etc)
-then the first spectra in the scantable will be used for fitting.
+then the first spectrum in the scantable will be used for fitting.
 
 \begin{verbatim}
@@ -1147 +1140 @@
  ASAP> f.set_scan(scans)
  ASAP> selection = selector()
- ASAP> selection.set_polarisation(1) # Fit the second polarisation
+ 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
@@ -1230 +1223 @@
 \index{Polarisation}Currently ASAP only supports polarmetric analysis
 on linearly polarised feeds and the cross polarisation products
-measured. Other cases will be added on an as needed basic.
+measured. Other cases will be added on an as needed basis.
 
 Conversions of linears to Stokes or Circular polarisations are done
@@ -1297 +1290 @@
   ASAP> selection = selector()
 
-  ASAP> selection.set_polarisations([``I Q U V''])
+  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
 
 [[MALTE: This does not work]]
 
-  ASAP> selection.set_polarisations([``Pangle'')
+  ASAP> selection.set_polarisations(``Pangle'')
   ASAP  plotter.set_selection(selection);              # Position angle
 
@@ -1339 +1332 @@
 directly on scantables from the command line using the \cmd{+, -, *,
 /} operators as well as their cousins \cmd{+=, -= *=, /=}. This works
-between two scantables or a scantable and a float. (Note that it does
+between a scantable and a float. (Note that it does
 not work for integers).
 
-{\em Currently mathematics between two scan tables is not available }
-
-\begin{verbatim}
+{\em Currently mathematics between two scantables is not available }
+
 %  ASAP> sum = scan1+scan2
+\begin{verbatim}
   ASAP> scan2 = scan1+2.0
   ASAP> scan *= 1.05
@@ -1464 +1457 @@
 
  selection = selector()
- selection.set_polarisation(0)
+ selection.set_polarisations(0)
  data.set_selection(selection)
  data.scale(xtsys/nomtsys)
 
- selection.set_polarisation(1)
+ selection.set_polarisations(1)
  data.set_selection(selection)
  data.scale(ytsys/nomtsys)
 
- selection.set_polarisation(0)
+ selection.set_polarisations(0)
  data.set_selection(selection)
  data.scale((xtsys+ytsys)/(2*nomtsys))
 
- selection.set_polarisation(0)
+ selection.set_polarisations(0)
  data.set_selection(selection)
  data.scale((xtsys+ytsys)/(2*nomtsys))
@@ -1529 +1522 @@
 
 # Correct for the Tsys using our predefined function
-execfile('mypol.py') # Read in the function
+execfile('mypol.py') # Read in the function xyscale
 xyscale(g351_5,23.2,22.7) # Execute it on the data
 xyscale(g351_7,23.2,22.7)
@@ -1591 +1584 @@
 
 # Seperate data from the (1,1)&(2,2) and (4,4) transitions
-g1 = q.get_scan(range(6))     # Rows 0..5
-g2 = q.get_scan(range(6,12))  # Rows 6..11
+g1 = q.get_scan(range(6))     # scans 0..5
+g2 = q.get_scan(range(6,12))  # scans 6..11
 
 # Align data in velocity
@@ -1771 +1764 @@
 \subsection{.asaprc settings}
 \index{.asaprc}
-\asaprc{verbose}{{\bf True}/False}{Print verbose output}
+\asaprc{verbose}{{\bf True}/False}{Print verbose output, good to disable in scripts}
 
 \asaprc{insitu}{{\bf True}/False}{Apply operations on the input
@@ -1808 +1801 @@
 \asaprc{scantable.freqframe}{{\bf LSRK} TOPO BARY etc}{default
 frequency frame to set when function scantable.set\_freqframe is
-called}
-
-\asaprc{scantable.plotter}{{\bf True}/False}{Use internal plotter}
-
-\asaprc{scantable.verbosesummary}{True/{\bf False}}{Control the level
-of information printed by summary}
+called or the data is imported}
 
 \subsection{Installation}