Changeset 1011 for trunk

Timestamp:

04/11/06 13:20:44 (19 years ago)

Author:

mar637

Message:

some more updates for asap2 - Ticket #9

File:

• trunk/doc/userguide.tex (modified) (27 diffs)

trunk/doc/userguide.tex

@@ -13 +13 @@
 \setlength{\parskip}{1ex}
 
-\title{ATNF Spectral Analysis Package\\User Guide }
+\title{ATNF Spectral Analysis Package\\User Guide  v2.0beta }
 \author{Chris Phillips}
 
@@ -39 +39 @@
 package.
 
-This useeguide is currently being updated for the ASAP 2.0 release
+This userguide is currently being updated for the ASAP 2.0 release
 which has a number of significant changes which affect the user
 interface. Please report any mistakes you find in this userguide.
@@ -267 +267 @@
 to operate upon it.
 
-{\bf [MALTE: Could you please reword this??]}
-
 The building block of a scantable is an integration, which is a single
 row of a scantable. Each row contains just one spectrum for each beam, IF and
@@ -275 +273 @@
 filterbank will eventually 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.
-
-A collection of cyclesfor one source is termed
-a scan (and each scan has a unique numeric identifier, the ScanNo). A
+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 averegaed all cycles within
@@ -287 +285 @@
 method is used depends on the users preference. The default can be
 changed via the {\tt .asaprc} resource file.
+
+For example a Mopra scan with a  4s intergration time, two IFs and
+dual polarisations has two (2s) cycles.
+
+\begin{verbatim}
+SCANNO  CYCLENO BEAMNO IFNO POLNO
+0       0       0      0    0
+0       0       0      0    1
+0       0       0      1    0
+0       0       0      1    1
+0       1       0      0    0
+0       1       0      0    1
+0       1       0      1    0
+0       1       0      1    1
+
+\end{verbatim}
+
 
 \subsubsection {Contents}
@@ -297 +312 @@
 
 The data are stored in columns (the length of a column is the number of
-rows/integrations of course).
-
-{\bf [MALTE: Is this outdated??]}
+rows/spectra of course).
+
 
 Two important columns are those that describe the frequency setup.  We mention
@@ -305 +319 @@
 of the frequency information and possibly how to manipulate it.
 
-These columns are called FreqID and MoleculeID.  They contain indices, for
+These columns are called FREQ\_ID and MOLECULE\_ID.  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
@@ -948 +962 @@
 formats are:
 
-{\em Currently only raw ASAP output is available. Other formats will be added soon}
-
 \begin{itemize}
 \item[ASAP] This is the internal format used for ASAP. It is the only
@@ -1272 +1284 @@
 \end{verbatim}
 
+\subsection{Conversion}
+\label{sec:polconv}
+Data can be converted between linear and circular polarisations and stokes.
+
+\begin{verbatim}
+  ASAP> stokescans = linearscans.convert_pol("stokes")
+\end{verbatim}
+
+
 \subsection{Plotting}
 \label{sec:polplot}
@@ -1282 +1303 @@
 Plinear, Pangle, V], [RR, LL] 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.
+angle of linear polarisation).
 
 Example:
@@ -1304 +1324 @@
   ASAP> selection.set_polarisations(``I Plinear'')
   ASAP  plotter.set_selection(selection);              # Fractional linear
-
-[[MALTE: This does not work]]
 
   ASAP> selection.set_polarisations(``Pangle'')
@@ -1387 +1405 @@
 
 \begin{verbatim}
-# Concatenate the individual rpfits files together before loading
-!cat 2005-06*.rpf > data.rpf
+# get a list of the individual rpfits files in the current directory
+myfiles = list_files()
 
 # Load the data into a scantable
-data = scantable('data.rpf')
+data = scantable(myfiles)
 print data
 
@@ -1401 +1419 @@
 plotter.plot(q)
 
-# Set reference frame
+# Set unit and reference frame
 q.set_unit('km/s')
 q.set_freqframe('LSRK')
@@ -1485 +1503 @@
 
 # Check what we have just loaded
-d1665.summary
+d1665.summary()
 
 # View the data in velocity
@@ -1595 +1613 @@
 a2 = g2.average_time()
 
-# Rpfits file only contrains a single rest frequency. Set both
+# Rpfits file only contains a single rest frequency. Set both
 a1.set_restfreqs([23694.4700e6,23722.6336e6])
 
 plotter.plot(a1)
-plotter.set_mode('i','s')
+plotter.set_mode('i','t')
 
 a1.auto_poly_baseline()
@@ -1619 +1637 @@
 \index{Functions!summary}%
 \begin{verbatim}
+ASAP> commands()
     [The scan container]
         scantable           - a container for integrations/scans
@@ -1624 +1643 @@
             copy            - returns a copy of a scan
             get_scan        - gets a specific scan out of a scantable
+                              (by name or number)
+            set_selection   - set a new subselection of the data
+            get_selection   - get the current selection object
             summary         - print info about the scantable contents
-            set_cursor      - set a specific Beam/IF/Pol 'cursor' for
-                              further use
-            get_cursor      - print out the current cursor position
             stats           - get specified statistic of the spectra in
                               the scantable
@@ -1634 +1653 @@
             get_tsys        - get the TSys
             get_time        - get the timestamps of the integrations
+            get_sourcename  - get the source names of the scans
             get_azimuth     - get the azimuth of the scans
             get_elevation   - get the elevation of the scans
             get_parangle    - get the parallactic angle of the scans
-            get_unit        - get the currnt unit
+            get_unit        - get the current unit
             set_unit        - set the abcissa unit to be used from this
                               point on
@@ -1645 +1665 @@
                               (e.g. 'LSRK')
             set_doppler     - set the doppler to be used from this point on
+            set_dirframe    - set the frame for the direction on the sky
             set_instrument  - set the instrument name
             get_fluxunit    - get the brightness flux unit
@@ -1653 +1674 @@
             get_restfreqs   - get the current list of rest frequencies
             set_restfreqs   - set a list of rest frequencies
-            lines           - print list of known spectral lines
-            flag_spectrum   - flag a whole Beam/IF/Pol
+            flag_spectrum   - flag data
             save            - save the scantable to disk as either 'ASAP'
                               or 'SDFITS'
             nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans
+            nscan           - the number of scans in the scantable
+            nrow            - te number of spectra in the scantable
             history         - print the history of the scantable
             get_fit         - get a fit which has been stored witnh the data
@@ -1666 +1688 @@
                               all polarisations will contain the
                               averaged spectrum.
+            convert_pol     - convert to a different polarisation type
             auto_quotient   - return the on/off quotient with
                               automatic detection of the on/off scans
-            quotient        - return the on/off quotient
+                              (matched pairs and 1 off - n on)
             scale           - return a scan scaled by a given factor
             add             - return a scan with given value added
@@ -1686 +1709 @@
             rotate_linpolphase - rotate the phase of the complex
                                  polarization O=Q+iU correlation
+            freq_switch     - perform frequency switching on the data
+            stats           - Determine the specified statistic, e.g. 'min'
+                              'max', 'rms' etc.
+            stddev          - Determine the standard deviation of the current
+                              beam/if/pol
+
      [Math] Mainly functions which operate on more than one scantable
 
@@ -1700 +1729 @@
                               commited.
             fit             - execute the actual fitting process
-            store_fit       - store the fit paramaters in the data (scantable)
+            store_fit       - store the fit parameters in the data (scantable)
             get_chi2        - get the Chi^2
             set_scan        - set the scantable to be fit
@@ -1714 +1743 @@
         asapplotter         - a plotter for asap, default plotter is
                               called 'plotter'
-            plot            - plot a (list of) scantable
+            plot            - plot a scantable
             save            - save the plot to a file ('png' ,'ps' or 'eps')
             set_mode        - set the state of the plotter, i.e.
                               what is to be plotted 'colour stacked'
                               and what 'panelled'
-            set_cursor      - only plot a selected part of the data
-            set_range       - set a 'zoom' window
+            set_selection   - only plot a selected part of the data
+            set_range       - set a 'zoom' window [xmin,xmax,ymin,ymax]
             set_legend      - specify user labels for the legend indeces
             set_title       - specify user labels for the panel indeces
+            set_abcissa     - specify a user label for the abcissa
             set_ordinate    - specify a user label for the ordinate
-            set_abcissa     - specify a user label for the abcissa
             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_mask        - set a plotting mask for a specific polarization
 
     [Reading files]
         reader              - access rpfits/sdfits files
+            open            - attach reader to a file
+            close           - detach reader from file
             read            - read in integrations
             summary         - list info about all integrations
@@ -1736 +1771 @@
         print               - print details about a variable
         list_scans          - list all scantables created bt the user
+        list_files          - list all files readable by asap (default rpf)
         del                 - delete the given variable from memory
         range               - create a list of values, e.g.
@@ -1742 +1778 @@
         execfile            - execute an asap script, e.g. execfile('myscript')
         list_rcparameters   - print out a list of possible values to be
-                              put into \$HOME/.asaprc
+                              put into $HOME/.asaprc
         mask_and,mask_or,
         mask_not            - boolean operations on masks created with
@@ -1758 +1794 @@
             ASAP> help average_time
 
+
 \end{verbatim}