Changeset 1757 for branches/alma/doc

Timestamp:

06/09/10 19:03:06 (15 years ago)

Author:

Kana Sugimoto

Message:

New Development: Yes

JIRA Issue: Yes (CAS-2211)

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: ASAP 3.0.0 interface changes

Test Programs:

Put in Release Notes: Yes

Module(s): all the CASA sd tools and tasks are affected.

Description: Merged ATNF-ASAP 3.0.0 developments to CASA (alma) branch.

Note you also need to update casa/code/atnf.

Location:

branches/alma

Files:

• . (modified) (2 props)
• doc/CHANGELOG (modified) (2 diffs)
• doc/userguide.tex (modified) (22 diffs)

branches/alma/doc/CHANGELOG

@@ -2 +2 @@
 =========
 
-Release 2.2.1 [2007-??-??]
+Release 3.0.0 [2010-05-06]
 
-* source direction for Hobart data - Ticket #109
-* added running median to scantable.(smooth(kernel='rmedian') 
+* BEWARE: added asap2to3 which converts '.asap' files from version 2 to 
+          version 3
+* Ticket #183 Added scantable.get_weather
+* Ticket #181 Added work-around for casacore bug in saving tables with
+              selection
+* Ticket #178 Added opacity_model based on  miriad's atmospheric model
+* Ticket #177 Added function skydip to determine opacities.
+* Ticket #172 Fixed non-working scantable.resample
+* Ticket #155 Better output filenames. Ignore non-existsing 
+              beams/pols/ifs/scans
+* Ticket #157 numpy >= 1.1 support
+* Ticket #158 fixed plotter.set_font
+* Ticket #160 Aspect ratio of plotter is customisable now
+* Ticket #163 fixed for scantable.set_sourcetype
+* Ticket #164 Upgrade note in wiki FAQ
+* Ticket #165 Handle non-parallactified polarimtery data (if supported in 
+              rpfits)
+* Ticket #167 Added running polynomial filter to scantable.smooth
+* Ticket #168 Data exported via scantable.save now contains correct frequency
+              or velocity information
+* Ticket #169 Simplified selection of data
+* Ticket #46  Interactive lag flagging
+* Ticket #170 Provided access to frequency coordinate information via
+              scantable.get_coordinate
+* Added OS X 10.5 Disk image installer
+* Added support for OS X 10.6
+* Interactive plotting annotations via optional argument interactive=True
+* Interactive creation of masks on the plotter - plotter.create_mask
+* Tidy up date range in asapplotter.plotazel/plotpointings
+* support for gcc-4.4
+
+Release 2.3.1 [2009-03-25]
+
+* Ticket #154 Flagged data wasn't hnoured in fitting
+* Ticket #153 plotter.plot_lines fixed for matplotlib >= 0.98
+* Ticket #90  Support integer values for frequencies/errors/intensities
+
+Release 2.3.0 [2009-03-13]
+
+* Ticket #150 fix in casacore for frequency frame conversions
+* Ticket #151 added rc parameter and function set_sourcetype to identify
+              on/off scans
+* Ticket #78/#112 Resolved the issue with random errors occuring under linux
+                  for large
+   data files, which corrupted the identifaction of off scans
+* Ticket #149 Fixed the bug causing spectral line search to go into an
+              infinite loop in some rare circumstances
+* Ticket #110 Added export to CLASS readable FITS files
+   scantable.save("myfile.fits", "CLASS")
+* Ticket #142 Fix of the frequency alignment for long observations
+* Ticket #133 allow supression of history in the scantable via rc parameters
+* Ticket #109 source direction for Hobart data
+* Ticket #115 added running median to scantable.(smooth(kernel='rmedian')
+* Ticket #148 opacity correction wasn't applied to TSYS
+* Ticket #135 quotient detection failure for specific source names
+* Ticket #140 NaN values not handled - added scantable.flag_nans to ensure
+              that the NaN are flagged
+* added python iterator access to scantable rows
+* made functions available to directly manipulate spectra 
+  scantable.get/set_spectrum
+* upgrade to support ipython >= 0.8.1
+* support gcc-4.3
+* use scons >= 1.1.0
+* update to latest livedata I/O functions
+* add WCS info to the exported text files
+
 
 Release 2.2.0 [2007-05-02]
@@ -28 +92 @@
 * fix for Ticket #88 - numpy masks
 * better TAB completion for ipython (handles quotes, don't list private members)
-* Fix for Ticket #81 = scanatble.stats output as list 
+* Fix for Ticket #81 = scanatble.stats output as list
 * ticket #64 - speed up of auto_poly_baseline
 * fix for ticket #89 - export of IF sub-selections

branches/alma/doc/userguide.tex

@@ -13 +13 @@
 \setlength{\parskip}{1ex}
 
-\title{ATNF Spectral Analysis Package\\User Guide v2.1\\DRAFT }
+\title{ATNF Spectral Analysis Package\\User Guide v2.3 }
 \author{Chris Phillips}
 
@@ -48 +48 @@
 package.
 
-This userguide has been updated for the ASAP 2.1. Please report any
+This userguide has been updated for the ASAP 2.3. Please report any
 mistakes you find.
 
@@ -58 +58 @@
 \item Epping - use hosts {\tt draco} or {\tt hydra}
 \item Narrabri - use host {\tt kaputar}
-\item Parkes - use host {\tt bourbon}
-\item Mopra - use host {\tt minos}
+\item Parkes - use host {\tt ?}
+\item Mopra - use host {\tt minos} or {\tt kaputar} if at Narrabri
 \end{itemize}
 
 Or use your own Linux desktop.
 
-{\em Note. ASAP2.1 only runs on ATNF Linux machines which have been
+{\em Note. ASAP2.2 only runs on ATNF Linux machines which have been
 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 to your friendly IT support.}
 
 \index{Running}To start asap log onto one of these Linux hosts and enter
@@ -166 +165 @@
 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, nor for function
+function names and even file names It does not work for for function
 arguments.
 
@@ -210 +209 @@
   ASAP>ls
   ASAP>cd /my/data/directory
-  ASAP>! mozilla&
+  ASAP>! firefox&
 \end{verbatim}
 
@@ -352 +351 @@
 
   # Equivalent to brief summary function call
-  ASAP>print scan
+  ASAP>print scans
 \end{verbatim}
 
@@ -422 +421 @@
   ASAP>selection.reset()              # Turn off selection
   ASAP>scans.set_selection(selection) # Apply the reset selection
+  ASAP>scans.set_selection() # alternative to reset selection
 
 \end{verbatim}
@@ -460 +460 @@
 \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_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
@@ -528 +528 @@
 
   # Select channel range for baselining
-  ASAP>scans.set_unit('channels')
+  ASAP>scans.set_unit('channel')
   ASAP>msk = scans.create_mask([100,400],[600,800])
 
@@ -542 +542 @@
 Example :
 \begin{verbatim}
-  ASAP>scans.set_unit('channels')
+  ASAP>scans.set_unit('channel')
   ASAP>msk = scans.create_mask([0,100],[900-1023], invert=True)
 \end{verbatim}
@@ -562 +562 @@
 
 \begin{verbatim}
-  ASAP>scans.set_unit('channels')
+  ASAP>scans.set_unit('channel')
   ASAP>msk1 = q.create_mask([0,100],[511,511],[900,1023],invert=True)
   ASAP>scans.set_unit('km/s')
@@ -614 +614 @@
 
 
-\subsection{Reader object}
-
-\index{Reader object}\index{Scantable!reader object}For more control
-when reading data into ASAP, the reader object should be used.  This
-has the option of only reading in a range of integrations, only a
-specified beam or IF and does not perform any scan averaging of the
-data, allowing analysis of the individual integrations.  Note that due
-to limitation of the RPFITS library, only one reader object can be
-open at one time reading RPFITS files.  To read multiple RPFITS files,
-the old reader must be destroyed before the new file is opened.
-However, multiple readers can be created and attached to SDFITS files.
-
-
-Example usage:
-
-\begin{verbatim}
-  ASAP>r = reader('2003-03-16_082048_t0002.rpf')
-  ASAP>r.summary()
-  ASAP>scan = r.read()
-  ASAP>del r
-\end{verbatim}
+%\subsection{Reader object}
+
+%\index{Reader object}\index{Scantable!reader object}For more control
+%when reading data into ASAP, the reader object should be used.  This
+%has the option of only reading in a range of integrations, only a
+%specified beam or IF and does not perform any scan averaging of the
+%data, allowing analysis of the individual integrations.  Note that due
+%to limitation of the RPFITS library, only one reader object can be
+%open at one time reading RPFITS files.  To read multiple RPFITS files,
+%the old reader must be destroyed before the new file is opened.
+%However, multiple readers can be created and attached to SDFITS files.
+%
+%
+%Example usage:
+%
+%\begin{verbatim}
+%  ASAP>r = reader('2003-03-16_082048_t0002.rpf')
+%  ASAP>r.summary()
+%  ASAP>scan = r.read()
+%  ASAP>del r
+%\end{verbatim}
 
 \section{Basic Processing}
@@ -649 +649 @@
 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
+This functions has two \cmd{mode}s. \cmd{paired} (the default), which assumes
 matching adjacent pairs of source/reference scans and \cmd{time}, which finds
 the closest reference scan in time.
@@ -835 +835 @@
 telescope is wrong due to an incorrect noise diode calibration. This
 can easily be corrected for with the scale function. By default,
-\cmd{scale} only scans the spectra and not the corresponding Tsys.
+\cmd{scale} only scaless the spectra and not the corresponding Tsys.
 
 \begin{verbatim}
@@ -871 +871 @@
 \begin{verbatim}
   ASAP>scans.recalc_azel()                # recalculate az/el 
-                                                                  # based on pointing
+                                          # based on pointing
 \end{verbatim}
 
@@ -962 +962 @@
 \end{verbatim}
 
+One can also apply the inverse of \cmd{get\_scan} \cmd{drop\_scan}
+
 To copy a scantable the following does not work:
 
@@ -994 +996 @@
   it.
 
-%\item[FITS] This uses simple ``image'' fits to save the data, each row
-%  being written to a separate fits file. This format is suitable for
-%  importing the data into CLASS.
+\item[FITS] This uses simple ``image'' fits to save the data, each row
+  being written to a separate fits file.
+
+\item[CLASS] This uses simple ``image'' fits to save the data, each row
+  being written to a separate fits file. This format has modification so it 
+  is suitable for importing the data into CLASS.
 
 \item[ASCII] A simple text based format suitable for the user to
@@ -1402 +1407 @@
 \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
+For data with many IFs, such as from MOPS, it is recommended
+that users creates their own line catalog table for the data and use this
 to set the rest frequency for each IF.
 
@@ -1658 +1663 @@
 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.
+significantly less memory usage. This should be used for all MOPS data!
 
 To use disk based tables you either need to change the default in your
@@ -1679 +1684 @@
 {\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
+tables your directory will be left with 'tmpXXXXX\_X' directories. These can
 be safely removed if ASAP is not running.
 
@@ -1692 +1697 @@
 {\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
 \end{verbatim}
 
@@ -1713 +1718 @@
 
 \hspace{1cm} http://www.python.org/doc/Introduction.html
+
+\hspace{1cm} http:/ipython.scipy.org
 
 \subsection{Running scripts}