Changeset 538 for trunk

Timestamp:

03/08/05 11:51:55 (20 years ago)

Author:

phi196

Message:

Updates

File:

• trunk/doc/cookbook.tex (modified) (24 diffs)

trunk/doc/cookbook.tex

@@ -1 +1 @@
 %% TODO
-%% Help doco
-%% .asaprc
 %% Intro
-%% Plotter options - pol etc
 %% Fit saving
 
@@ -54 +51 @@
 \end{verbatim}
 
-This starts the asap. To quit, you need to type  \verb+^+-d (control-d).
+This starts the asap. To quit, you need to type \verb+^+-d (control-d).
 
 \section{Interface}
@@ -99 +96 @@
 some way or change global properties of the object. In this document
 member functions will be referred to simply as functions. From the
-command line, the user can excute these functions using the syntax:
+command line, the user can execute these functions using the syntax:
 \begin{verbatim}
   ASAP> out = object.function(arguments)
@@ -105 +102 @@
 
 Where \cmd{out} is the name of the returned variable (could be a new
-scantable object, or a vector of data, or a status retrn),  \cmd{object} is the
+scantable object, or a vector of data, or a status return),  \cmd{object} is the
 object variable name (set by the user), \cmd{function} is the name of
 the member function and \cmd{arguments} is a list of arguments to the
@@ -123 +120 @@
 
 Some functions do not make sense to be implemented as member
-functions, typically fuctions which operate on more than one scantable
+functions, typically functions which operate on more than one scantable
 (e.g. time averaging of many scans). These functions will always be
-refered to as global functions.
-
-\subsection{Interactive enviroment}
+referred to as global functions.
+
+\subsection{Interactive environment}
 
 ipython has a number of useful interactive features and a few things to be aware
@@ -136 +133 @@
 Tab completion is enabled for all function names. If you type the
 first few letters of a function name, then type <TAB> the function
-name will be auto completed if it is un-ambigious, or a list of
+name will be auto completed if it is un-ambiguous, or a list of
 possibilities will be given. Auto-completion works for the user
 object names as well as function names. It does not work for filenames,
@@ -169 +166 @@
 \subsection{Help}
 
-Help me...
+ASAP has built in help for all functions. To get a list of functions type:
+
+\begin{verbatim}
+  ASAP> commands
+\end{verbatim}
+
+To get help on specific functions, the built in help needs to be given
+the object and function name. E.g.
+
+\begin{verbatim}
+  ASAP> 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 average_time # Global functions just need their name
+
+\end{verbatim}
+
+Note that if you just type \cmd{help} the internal ipython help is
+invoked, which is probably {\em not} what you want. Type \verb+^+-d
+(control-d) to escape from this.
 
 \subsection{.asaprc}
 
+ASAP use a \cmd{.asaprc} file to control the users preferences of
+default values for various functions arguments. This includes the
+defaults for aguments such as \cmd{insitu}, scantable \cmd{freqframe}
+and the plotters \cmd{set\_mode} values. The help on individual
+functons says which agruments can be set default values from the
+\cmd{.asaprc} file. To get a sample contents for the \cmd{.asaprc}
+file use then command \cmd{list\_rcparameters}.
+
+Common values include:
+\begin{verbatim}
+  # apply operations on the input scantable or return new one
+  insitu                     : False
+
+  # default ouput format when saving scantable
+  scantable.save             : 'ASAP'
+
+
+  # default frequency frame to set when function
+  # scantable.set_freqframe is called
+  scantable.freqframe        : 'LSRK'
+
+  # auto averaging on read
+  scantable.autoaverage      : True
+\end{verbatim}
 
 \section{Scantables}
@@ -213 +258 @@
 
 Two important columns are those that describe the frequency setup.  We mention
-them explicitly here because you need to be able to undertand the presentation
+them explicitly here because you need to be able to understand the presentation
 of the frequency information and possibly how to manipulate it.
 
@@ -276 +321 @@
 \end{verbatim}
 
-
-
 \subsection{State}
-
 
 Each scantable contains "state"; these are properties  applying to all
@@ -285 +327 @@
 
 Examples are the selection of beam, IF and polarisation,  spectral unit
-(e.g. $km/s$) frequency reference frame (e.g. BARY) and velocity doppler
+(e.g. $km/s$) frequency reference frame (e.g. BARY) and velocity Doppler
 type (e.g. RADIO).
-
-
 
 \subsubsection{Units, Doppler and Frequency Reference Frame}
@@ -306 +346 @@
 can be computed in any of these units), plotting and mask creation. 
 
-The velocity doppler can be changed with the \cmd{set\_doppler}
+The velocity Doppler can be changed with the \cmd{set\_doppler}
 function, and the frequency reference frame can be changed with the 
 \cmd{set\_freqframe} function.
@@ -335 +375 @@
 
 \begin{verbatim}
-  ASAP> scans.set_restfreqs(freqs=1.667359e9, source='NGC253', theif=0)   # Selected for specified source/IF
-  ASAP> scans.set_restfreqs(freqs=1.667359e9)                             # Selected for all sources and IFs
+  # Select for specified source/IF
+  ASAP> scans.set_restfreqs(freqs=1.667359e9, source='NGC253', theif=0)   
+
+  # Select for all sources and IFs
+  ASAP> scans.set_restfreqs(freqs=1.667359e9)                             
 \end{verbatim}
 
@@ -348 +391 @@
 
 \begin{verbatim}
-  ASAP> scans.set_restfreqs(freqs=1.667359e9, source='NGC253', theif=0)   # Selected for specified source/IF
-  ASAP> scans.set_restfreqs(freqs=1.667359e9)                             # Selected for all sources and IFs
+  # Select for specified source/IF
+  ASAP> scans.set_restfreqs(freqs=1.667359e9, source='NGC253', theif=0)   
+
+  # Select for all sources and IFs
+  ASAP> scans.set_restfreqs(freqs=1.667359e9)                             
 \end{verbatim}
 
@@ -390 +436 @@
 Most functions work on all rows of a scan table. Exceptions are the
 fitter and plotter. If you wish to only operate on a selected set of
-scantable rows, usw the \cmd{get_scan} function to copy the rows into
+scantable rows, use the \cmd{get\_scan} function to copy the rows into
 a new scantable.
 
@@ -501 +547 @@
 
 In the following section, a simple data reduction to form a quotient
-spectrum of a single source is followed. Variations of this approach
-are given later.
+spectrum of a single source is followed. In the following it has been
+assume that the \cmd{.asaprc} file has been used to set \cmd{insitu}
+to a default value or \cmd{True}.
 
 %\subsection{Editing}
@@ -770 +817 @@
   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
 
@@ -839 +887 @@
 
 
-
 \section{Plotter}
 
@@ -847 +894 @@
 ``plotter''. This would normally be used for standard plotting.
 
-The plotter, optionally, will run in a mulipanel mode and contain
+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
 default can be set in the users {\tt .asaprc} file. The units (and frame
-etc) of the abcissa will be whatever has previously been set by
-set\_unit, set\_freqframe etc.
+etc) of the abscissa will be whatever has previously been set by
+\cmd{set\_unit}, \cmd{set\_freqframe} etc.
 
 Typical plotter usage would be:
@@ -865 +912 @@
 scanrow in a separate panel.
 
-Other possbilities include:
+Other possibilities include:
 
 \begin{verbatim}
   # Plot multiple IFs per panel
   ASAP> plotter.set_mode(stacking='i',panelling='t')
-  more????
+
+  # Plot multiple beams per panel
+  ASAP> plotter.set_mode(stacking='b',panelling='t')
+
+  # Plot one IF per panel, time stacked
+  ASAP> plotter.set_mode('t', 'i')
+
+  # Plot each scan in a seperate panel
+  ASAP> plotter.set_mode('t', 's')
+
+\end{verbatim}
+
+\subsection{Plot Selection}
+\label{sec:plotter_cursor}
+
+The plotter can plot up to 25 panels and stacked spectra per
+panel. If you have data larger than this (or for your own sanity) you
+need to select a subset of this data. This is particularly true for
+multibeam or multi IF data. The plotter \cmd{set\_cursor} function is
+used to select a subset of the data. The arguments \cmd{row},
+\cmd{beam} and \cmd{IF} all accept a vector if indices corresponding
+to tow, beam or IF selection. Only the selected data will be plotted.
+So select on polarisation, see section~\ref{sec:polplot}.
+
+Examples:
+
+\begin{verbatim}
+  # Select second IF
+  ASAP> plotter.set_cursor(IF=[1])
+
+  # Select first 4 beams
+  ASAP> plotter.set_cursor(beam=[0,1,2,3])
+
+  # Select a few rows
+  ASAP> plotter.set_cursor(row=[2,4,6,10])
+
+  # Multiple selection
+  ASAP> plotter.set_cursor(IF=[1], beam=[0,2], row=range(10))
 \end{verbatim}
 
@@ -900 +984 @@
 
 \end{itemize}
+
+\subsection{Plot selection}
 
 \subsection{Other control}
@@ -989 +1075 @@
   # Plot the first and third component plus the model sum
   ASAP> f.plot(components=[-1,0,2])  # -1 means the compoment sum
-
 \end{verbatim}
 
@@ -998 +1083 @@
 cases will be added on an as needed basic.
 
-But how do you actually do it...
+Conversions of linears to Stokes or Circular polarisations are done
+``on-the-fly''. Leakage cannot be corrected for nor are there routines
+able to calibrate position angle offsets. 
+
+\subsection{Simple Calibration}
+
+{\em Currently the receiver position angle is not stored in the rpfits
+file. This serverly hampers correct handling of polarimetry.}
+
+It is possible that there is a phase offset between polarisation which
+will effect the phase of the cross polarisation
+correlation. \cmd{rotate\_xyphase} can be used to correct for this
+error. The user must know how to determine the size of the phase
+offset.
+
+\begin{verbatim}
+  ASAP> scans.rotate_xyphase(10.5)
+\end{verbatim}
+
+Note that if this function is run twice, the sum of the two values is
+applied.
+
+A correction for the receiver paralactic angle may need to be made,
+either because of how it is mounted or if paralactifiying had to track
+at 90 degrees rather than 0. Use \cmd{rotate\_linpolphase} to correct
+the position angle. Running this function twice results in the sum of
+the corrections being applied.
+
+\begin{verbatim}
+  ASAP> scans.rotate_linpolphase(-20) # Correct for receiver mounting
+
+  # Receiver was tracking 90 degrees rather than 0
+  ASAP> scans.rotate_linpolphase(90)  
+\end{verbatim}
+
+\subsection{Plotting}
+\label{sec:polplot}
+
+To plot stokes values, the plotter \cmd{set\_cursor} function should
+be called first using the \cmd{pol} argument. The values which can be
+plotted include a selection of [I,Q,U,V], [I, Plinear, Pangle, V] or
+[XX, YY, Real(XY), Imaginary(XY)]. (Plinear and Pangle are the
+percentage and position angle of linear polarisation). Conversion to
+circular polarisations are currently not available.
+
+Example:
+
+\begin{verbatim}
+  ASAP> plotter.set_cursor(pol=[``I'',''Q'']
+  ASAP> plotter.set_cursor(pol=[``XX'',''YY'']
+  ASAP> plotter.set_cursor(pol=[``I'',''Plinear'']
+\end{verbatim}
+
+Row, beam and IF selection are also available in \cmd{set\_cursor} as
+describe in section~\ref{sec:plotter_cursor}.
+
+\subsection{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{Function Summary}
@@ -1113 +1264 @@
                               range(3) = [0,1,2], range(2,5) = [2,3,4]
         help                - print help for one of the listed functions
-        execfile            - execute an asap script, e.g. execfile('myscript')        list_rcparameters   - print out a list of possible values to be
-                              put into $HOME/.asaprc
+        execfile            - execute an asap script, e.g. execfile('myscript')
+        list_rcparameters   - print out a list of possible values to be
+                              put into \$HOME/.asaprc
         mask_and,mask_or,
         mask_not            - boolean operations on masks created with
@@ -1128 +1280 @@
             ASAP> help scantable.summary # to get help on the scantable's
             ASAP> help average_time
-
-
-\end{verbatim}
-
-\section{Scripting}
-
-Malte to add something
+\end{verbatim}
+
+%\section{Scripting}
+
+%Malte to add something
 
 \section{Appendix}
 
 \subsection{Installation}
-
 
 ASAP depends on a number of third-party libraries which you must