\documentclass[11pt]{article} \usepackage{a4} \usepackage{calc} \usepackage[dvips]{graphicx} \usepackage{makeidx} % Adjust the page size \addtolength{\oddsidemargin}{-0.4in} \addtolength{\evensidemargin}{+0.4in} \addtolength{\textwidth}{+0.8in} \setlength{\parindent}{0mm} \setlength{\parskip}{1ex} \title{ATNF Spectral Analysis Package\\User Guide v2.3 } \author{Chris Phillips} \newcommand{\cmd}[1]{{\tt #1}} \newcommand{\asaprc}[3]{ \begin{minipage}[t]{45mm}#1\end{minipage} \begin{minipage}[t]{30mm}\raggedright #2\end{minipage}\hspace{3mm} \begin{minipage}[t]{\textwidth-75mm}#3\end{minipage} } \newcommand{\commanddef}[3]{ \begin{minipage}[t]{27mm}\tt #1\end{minipage}\hspace{3mm} \begin{minipage}[t]{\textwidth-30mm}#2 \\ \tt #3\end{minipage} } \newcommand{\bigcommanddef}[3]{ \begin{minipage}[t]{45mm}\tt #1\end{minipage}\hspace{3mm} \begin{minipage}[t]{\textwidth-47mm}#2 \\ \tt #3\end{minipage} } \makeindex \begin{document} \maketitle \section{Introduction} ASAP is a single dish spectral line processing package currently being developed by the ATNF. It is intended to process data from all ATNF antennas, and can probably be used for other antennas if they can produce ``Single Dish FITS'' format. It is based on the AIPS++ package. This userguide has been updated for the ASAP 2.3. Please report any mistakes you find. \section{Installation and Running} Currently there are installations running on Linux machines at \begin{itemize} \item Epping - use hosts {\tt draco} or {\tt hydra} \item Narrabri - use host {\tt kaputar} \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. ASAP2.2 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.} \index{Running}To start asap log onto one of these Linux hosts and enter \begin{verbatim} > cd /my/data/directory > asap \end{verbatim} This starts ASAP. To quit, you need to type \verb+^+-d (control-d) or type \cmd{\%Exit}. \section{Interface} \index{Interface}ASAP is written in C++ and python. The user interface uses the ``ipython'' interactive shell, which is a simple interactive interface to python. The user does not need to understand python to use this, but certain aspects python affect what the user can do. The current interface is object oriented. \subsection {Integer Indices are 0-relative} Please note, all integer indices in ASAP and iPython are {\bf 0-relative}. \subsection{Objects} \index{objects} The ASAP interface is based around a number of ``objects'' which the user deals with. Objects range from the data which have been read from disk, to tools used for fitting functions to the data. The following main objects are used : \begin{tabular}{ll} \cmd{scantable} & \parbox[t]{0.7\textwidth}{The data container (actual spectra and header information)} \\ \cmd{selector} & \parbox[t]{0.80\textwidth}{Allows the user to select a subsection of the data, such as a specified or range of beam numbers, IFs, etc.} \\ \cmd{plotter} & A tool used to plot the spectral line data \\ \cmd{fitter} & A tool used to fit functions to the spectral data \\ \cmd{reader} & \parbox[t]{0.8\textwidth}{A tool which can be used to read data from disks into a scantable object (advanced use).}\\ \end{tabular} There can be many objects of the same type. Each object is referred to by a variable name made by the user. The name of this variable is not important and can be set to whatever the user prefers (i.e. ``s'' and ``ParkesHOH-20052002'' are equivalent). However, having a simple and consistent naming convention will help you a lot. \subsection{Member Functions (functions)} \index{Functions!member}Following the object oriented approach, objects have associated ``member functions'' which can either be used to modify the data in 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 execute these functions using the syntax: \begin{verbatim} ASAP>out = object.function(arguments) \end{verbatim} Where \cmd{out} is the name of the returned variable (could be a new 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 function. The arguments can be provided either though position or \cmd{name=}. A mix of the two can be used. E.g. \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) \end{verbatim} \subsection{Global Functions} \index{Functions!global}It does not make sense to implement some functions as member functions, typically functions which operate on more than one scantable (e.g. time averaging of many scans). These functions will always be referred to as global functions. \subsection{Interactive environment} \index{ipython!environment}ipython has a number of useful interactive features and a few things to be aware of for the new user. \subsubsection{String completion} \index{ipython!string completion}Tab completion is enabled for all function names. If you type the first few letters of a function name, then type {\tt } the function 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 and even file names It does not work for for function arguments. Example \begin{verbatim} ASAP>scans = scantable('MyData.rpf') ASAP>scans.se ASAP>scans.set_in 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} \subsubsection{Leading Spaces} \index{ipython!leading space}Python uses leading space to mark blocks of code. This means that it you start a command line with a space, the command generally will fail with an syntax error. \subsubsection{Variable Names} \index{ipython!variable names}During normal data processing, the user will have to create named variables to hold spectra etc. These must conform to the normal python syntax, specifically they cannot contain ``special'' characters such as \@ \$ etc and cannot start with a number (but can contain numbers). Variable (and function) names are case sensitive. \subsubsection{Unix Interaction} \index{ipython!unix interaction}Basic unix shell commands (\cmd{pwd}, \cmd{ls}, \cmd{cd} etc) can be issued from within ASAP. This allows the user to do things like look at files in the current directory. The shell command ``\cmd{cd}'' works within ASAP, allowing the user to change between data directories. Unix programs cannot be run this way, but the shell escape ``$!$'' can be used to run arbitrary programs. E.g. \begin{verbatim} ASAP>pwd ASAP>ls ASAP>cd /my/data/directory ASAP>! firefox& \end{verbatim} \subsection{Help} \index{Help}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 # 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} Global functions just need their name \begin{verbatim} ASAP>help average_time \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{Customisation - .asaprc} \index{.asaprc}ASAP use an \cmd{.asaprc} file to control the user's preference of default values for various functions arguments. This includes the defaults for arguments such as \cmd{insitu}, scantable \cmd{freqframe} and the plotters \cmd{set\_mode} values. The help on individual functions says which arguments can be set default values from the \cmd{.asaprc} file. To get a sample contents for the \cmd{.asaprc} file use the command \cmd{list\_rcparameters}. Common values include: \begin{verbatim} # apply operations on the input scantable or return new one insitu : False # default output 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} For a complete list of \cmd{.asaprc} values, see the Appendix. \section{Scantables} \index{Scantables} \subsection {Description} \subsubsection {Basic Structure} \index{Scantable!structure}ASAP data handling works on objects called scantables. A scantable holds your data, and also provides functions to operate upon it. 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 polarisation. For example Parkes OH-multibeam data would 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 MOPS filterbank will produce one beam, many IFs, and 2-4 polarisations. All of the combinations of Beams/IFs an Polarisations are 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 averaged 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 new scantable with modified data or change the scantable insitu. Which 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 integration 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} \index{Scantable!contents}A scantable has header information and data (a scantable is actually an AIPS++ Table and it is generally stored in memory when you are manipulating it with ASAP. You can save it to disk and then browse it with the AIPS++ Table browser if you know how to do that !). The data are stored in columns (the length of a column is the number of rows/spectra of course). Two important columns are those that describe the frequency setup. We mention them explicitly here because you need to be able to understand the presentation of the frequency information and possibly how to manipulate it. 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. There are of course many other columns which contain the actual spectra, the flags, the Tsys, the source names and so on. There is also a function \cmd{summary} to list a summary of the scantable. You will find this very useful. Example: \begin{verbatim} ASAP>scans = scantable('MyData.rpf') ASAP>scans.summary() # Brief listing # Equivalent to brief summary function call ASAP>print scans \end{verbatim} The summary function gives you a scan-based summary, presenting the scantable as a cascading view of Beams and IFs. Note that the output 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 (i.e. the output from summary disappears), you may need to set the \$LESS environment variable to include the \cmd{-X} option. \subsection{Data Selection} \label{sec:selection} ASAP contains flexible data selection. Data can be selected based on 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 values recorded. Selection is based on a \cmd{selector} object. This object is created and various selection functions applied to it (\cmd{set\_ifs}, \cmd{set\_beams} etc). The selection object then must be applied to a scantable using the \cmd{set\_selection} function. A single selection object can be created and setup then applied to multiple scantables. Once a selection has been applied, all following functions will only ``see'' the selected spectra (including functions such as \cmd{summary}). The selection can then be reset and all spectra are visible. Note that if functions such as \cmd{copy} are run on a scantable with active selection, only the selected spectra are copied. The common selection functions are: \begin{tabular}{ll} \cmd{set\_beams} & Select beams by index number \\ \cmd{set\_ifs} & Select ifs by index number \\ \cmd{set\_name} & Select by source name. Can contain ``*'' as a wildcard, e.g. ``Orion*\_R''. \\ \cmd{set\_ifs} & Select IFs by index number \\ \cmd{set\_polarisation} & \parbox[t]{0.73\textwidth}{Select by polarisation index or name. If polarisation names are given, the data will be on-the-fly onverted (for example from linears to Stokes). }\\ \cmd{set\_query} & Set query directly. For power users only! \\ \cmd{set\_tsys} & Select data based on Tsys. Also example of user definable query. \\ \cmd{reset} & Reset the selection to include all spectra. \\ \end{tabular} Note that all indices are zero based. Examples: \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>scans.set_selection() # alternative to reset selection \end{verbatim} \subsection{State} \index{Scantable!state}Each scantable contains "state"; these are properties applying to all of the data in the scantable. Examples are the selection of beam, IF and polarisation, spectral unit (e.g. km/s), frequency reference frame (e.g. BARY) and velocity Doppler type (e.g. RADIO). \subsubsection{Units, Doppler and Frequency Reference Frame} The information describing the frequency setup for each integration is stored fundamentally in frequency in the reference frame of observation (E.g. TOPO). When required, this is converted to the desired reference frame (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. 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. The \cmd{set\_unit} function is used to set the current unit for a scantable. All functions will (where relevant) work with the selected unit until this changes. This is mainly important for fitting (the fits can be computed in any of these units), plotting and mask creation. The velocity definition can be changed with the \cmd{set\_doppler} function, and the frequency reference frame can be changed with the \cmd{set\_freqframe} function. Example usage: \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 \end{verbatim} \subsubsection{Rest Frequency} \index{Scantable!rest frequency}ASAP reads the line rest frequency from the RPFITS file when reading the data. The values stored in the RPFITS file are not always correct and so there is a function \cmd{set\_restfreq} to set the rest frequencies for the currently selected data. For each integration, there is a rest-frequency per IF (the rest frequencies are just stored as a list with an index into them). There are a few ways to set the rest frequencies with this function. If you specify just one rest frequency, then it is set for all IF. \begin{verbatim} # Set all IFs ASAP>scans.set_restfreqs(freqs=1.667359e9) \end{verbatim} If set a rest frequency for each IF, specify a list of frequencies (of length the number of IFs). Regardless of the source, the rest frequency will be set for each IF to the corresponding value in the provided list. \begin{verbatim} # Set rest frequency for all IFs ASAP>scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,]) \end{verbatim} A predetermined ``line catalog'' can be used to set the rest frequency. See section \S \ref{sec:linecat}. \subsubsection{Masks} \index{Masks}\index{Scantable!masks} Many tasks (fitting, baseline subtraction, statistics etc) should only be run on range of channels. Depending on the current ``unit'' setting this range is set directly as channels, velocity or frequency ranges. Internally these are converted into a simple boolean mask for each channel of the abscissa. This means that if the unit setting is later changed, previously created mask are still valid. (This is not true for functions which change the shape or shift the frequency axis). You create masks with the function \cmd{create\_mask} and this specified the channels to be included in the selection. When setting the mask in velocity, the conversion from velocity to channels is based on the current selection, specified row and selected frequency reference frame. Note that for multi IF data with different number of channels per IF a single mask cannot be applied to different IFs. To use a mask on such data the selector should be applied to select all IFs with the same number of channels. Example : \begin{verbatim} # Select channel range for baselining ASAP>scans.set_unit('channel') 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]) \end{verbatim} Sometimes it is more convenient to specify the channels to be excluded, rather included. You can do this with the ``invert'' argument. Example : \begin{verbatim} ASAP>scans.set_unit('channel') ASAP>msk = scans.create_mask([0,100],[900-1023], invert=True) \end{verbatim} By default \cmd{create\_mask} uses the frequency setup of the first row to convert velocities into a channel mask. If the rows in the data cover different velocity ranges, the scantable row to use should be specified: \begin{verbatim} ASAP>scans.set_unit('km/s') ASAP>msk = q.create_mask([-30,-10], row=5) \end{verbatim} Because the mask is stored in a simple python variable, the users is able to combine masks using simple arithmetic. To create a mask excluding the edge channels, a strong maser feature and a birdie in the middle of the band: \begin{verbatim} ASAP>scans.set_unit('channel') 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} \subsection{Management} \index{Scantable!management}During processing it is possible to create a large number of scan tables. These all consume memory, so it is best to periodically remove unneeded scan tables. Use \cmd{list\_scans} to print a list of all scantables and \cmd{del} to remove unneeded ones. Example: \begin{verbatim} ASAP>list_scans() The user created scantables are: ['s', 'scans', 'av', 's2', 'ss'] ASAP>del s2 ASAP>del ss \end{verbatim} \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 allows the user more control on what is read. \subsection{Scantable constructor} \index{Scantable constructor}\index{Scantable!constructor}This loads all of the data from filename into the scantable object scans and averages all the data within a scan (i.e. the resulting scantable will have one row per scan). The recognised input file formats are RPFITS, SDFITS (singledish fits), ASAP's scantable format and aips++ MeasurementSet2 format. Example usage: \begin{verbatim} 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) \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} In the following section, a simple data reduction to form a quotient spectrum of a single source is followed. It has been assume that the \cmd{.asaprc} file has {\em not} been used to change the \cmd{insitu} default value from \cmd{True}. \subsection{Auto quotient} \index{Auto quotient}Quotients can be computed ``automatically''. This requires the data to have matching source/reference pairs or one reference for multiple sources. Auto quotient assumes reference scans 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 default), which assumes matching adjacent pairs of source/reference scans and \cmd{time}, which finds the closest reference scan in time. \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} If this is not sufficient the following alternative method can be used. \subsection{Separate reference and source observations} \index{Quotient spectra}Most data from ATNF observatories distinguishes on and off source data using the file name. This makes it easy to create two scantables with the source and reference data. As long as there was exactly one reference observation for each on source observation for following method will work. For Mopra and Parkes data: \begin{verbatim} ASAP>r = scans.get_scan('*_R') ASAP>s = scans.get_scan('*^_R') \end{verbatim} For Tidbinbilla data \begin{verbatim} ASAP>r = scans.get_scan('*_[ew]') ASAP>s = scans.get_scan('*_[^ew]') \end{verbatim} \subsection{Time average separate scans} \index{Time average}If you have observed the source with multiple source/reference cycles you will want to scan-average the quotient spectra together. \begin{verbatim} ASAP>av = q.average_time() \end{verbatim} If for some you want to average multiple sets of scantables together you can: \begin{verbatim} ASAP>av = average_time(q1, q2, q3) \end{verbatim} The default is to use integration time weighting. The alternative is to use none, variance, Tsys weighting, Tsys \& integration time or median averaging. \begin{verbatim} ASAP>av = average_time(q, weight='tintsys') \end{verbatim} To use variance based weighting, you need to supply a mask saying which channel range you want it to calculate the variance from. \begin{verbatim} 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} explicitly) you should align the data in frequency before averaging. \begin{verbatim} ASAP>av = scans.average_time(align=True) \end{verbatim} Note that, if needed, you should run \cmd{gain\_el} and \cmd{opacity} before you average the data in time (\S \ref{sec:gainel} \& \ref{sec:freqalign}). \subsection{Baseline fitting} \index{Baseline fitting}To make a baseline fit, you must first create a mask of channels to use in the baseline fit. \begin{verbatim} ASAP>msk = scans.create_mask([100,400],[600,900]) ASAP>scans.poly_baseline(msk, order=1) \end{verbatim} This will fit a first order polynomial to the selected channels and subtract this polynomial from the full spectra. \subsubsection{Auto-baselining} \index{Auto-baseline}The function \cmd{auto\_poly\_baseline} can be used to automatically baseline your data without having to specify channel ranges for the line free data. It automatically figures out the line-free emission and fits a polynomial baseline to that data. The user can use masks to fix the range of channels or velocity range for the fit as well as mark the band edge as invalid. Simple example \begin{verbatim} ASAP>scans.auto_poly_baseline(order=2,threshold=5) \end{verbatim} \cmd{order} is the polynomial order for the fit. \cmd{threshold} is the SNR threshold to use to deliminate line emission from signal. Generally the value of threshold is not too critical, however making this too large will compromise the fit (as it will include strong line features) and making it too small will mean it cannot find enough line free channels. Other examples: \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) # 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) \end{verbatim} \subsection{Average the polarisations} \index{average\_pol}If you are just interested in the highest SNR for total intensity you will want to average the parallel polarisations together. \begin{verbatim} ASAP>scans.average_pol() \end{verbatim} \subsection{Calibration} \index{Calibration}For most uses, calibration happens transparently as the input data contains the Tsys measurements taken during observations. The nominal ``Tsys'' values may be in Kelvin or Jansky. The user may wish to supply a Tsys correction or apply gain-elevation and opacity corrections. \subsubsection{Brightness Units} \index{Brightness Units}RPFITS files do not contain any information as to whether the telescope calibration was in units of Kelvin or Janskys. On reading the data a default value is set depending on the telescope and frequency of observation. If this default is incorrect (you can see it in the listing from the \cmd{summary} function) the user can either override this value on reading the data or later. E.g: \begin{verbatim} 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') \end{verbatim} \subsubsection{Feed Polarisation} \index{Brightness Units}The RPFITS files also do not contain any information as to the feed polarisation. ASAP will set a default based on the antenna, but this will often be wrong the data has been read, the default can be changed using the \cmd{set\_feedtype} function with an argument of \cmd{'linear'} or \cmd{'circular'}. E.g: \begin{verbatim} ASAP>scans = scantable('2004-11-23_1841-P484.rpf') ASAP>scans.set_feedtype('circular') \end{verbatim} \subsubsection{Tsys scaling} \index{Tsys scaling}Sometime the nominal Tsys measurement at the 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 scaless the spectra and not the corresponding Tsys. \begin{verbatim} ASAP>scans.scale(1.05, tsys=True) \end{verbatim} \subsubsection{Unit Conversion} \index{Unit conversion}To convert measurements in Kelvin to Jy (and vice versa) the global function \cmd{convert\_flux} is needed. This converts and scales the data from K to Jy or vice-versa depending on what the current brightness unit is set to. The function knows the basic parameters for some frequencies and telescopes, but the user may need to supply the aperture efficiency, telescope diameter or the Jy/K factor. \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 \end{verbatim} \subsubsection{Gain-Elevation and Opacity Corrections} \label{sec:gainel} \index{Gain-elevation}As higher frequencies (particularly $>$20~GHz) it is important to make corrections for atmospheric opacity and gain-elevation effects. Note that currently the elevation is not written correctly into Tidbinbilla rpfits files. This means that gain-elevation and opacity corrections will not work unless these get recalculated. \begin{verbatim} ASAP>scans.recalc_azel() # recalculate az/el # based on pointing \end{verbatim} Gain-elevation curves for some telescopes and frequencies are known to ASAP (currently only for Tidbinbilla at 20~GHz and Parkes at K-band). In these cases making gain-corrections is simple. If the gain curve for your data is not known, the user can supply either a gain polynomial or text file tabulating gain factors at a range of elevations (see \cmd{help scantable.gain\_el}). Examples: \begin{verbatim} ASAP>scans.gain_el() # If gain table known ASAP>scans.gain_el(poly=[3.58788e-1,2.87243e-2,-3.219093e-4]) \end{verbatim} \index{Opacity}Opacity corrections can be made with the global function \cmd{opacity}. This should work on all telescopes as long as a measurement of the opacity factor was made during the observation. \begin{verbatim} ASAP>scans.opacity(0.083) \end{verbatim} Note that at 3~mm Mopra uses a paddle wheel for Tsys calibration, which takes opacity effects into account (to first order). ASAP opacity corrections should not be used for Mopra 3-mm data. \subsection{Frequency Frame Alignment} \label{sec:freqalign} \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 not Doppler tracking the observations, errors in the Doppler tracking etc. This mostly affects very long integrations or integrations averaged together from different days. Before averaging such data together, they should be frequency aligned using \cmd{freq\_align}. E.g.: \begin{verbatim} ASAP>scans.freq_align() ASAP>av = average_time(scans) \end{verbatim} {\em A Global freq\_align command will be made eventually} To average together data taken on different days, which are in different scantables, each scantable must aligned to a common reference time then the scantables averaged. The simplest way of doing this is to allow ASAP to choose the reference time for the first scantable then using this time for the subsequent scantables. \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) \end{verbatim} \section{Scantable manipulation} \index{Scantable!manipulation}While it is very useful to have many independent sources within one scantable, it is often inconvenient for data processing. The \cmd{get\_scan} function can be used to create a new scantable with a selection of scans from a scantable. The selection can either be on the source name, with simple wildcard matching or set of scan ids. Internally this uses the selector object, so for more complicated selection the selector should be used directly instead. For example: \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('*^_R') # 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} One can also apply the inverse of \cmd{get\_scan} \cmd{drop\_scan} To copy a scantable the following does not work: \begin{verbatim} ASAP>ss = scans \end{verbatim} as this just creates a reference to the original scantable. Any changes made to \cmd{ss} are also seen in \cmd{scans}. To duplicate a scantable, use the copy function. \begin{verbatim} ASAP>ss = scans.copy() \end{verbatim} \section{Data Output} \index{Scantable!save}\index{Saving data}ASAP can save scantables in a variety of formats, suitable for reading into other packages. The formats are: \begin{itemize} \item[ASAP] This is the internal format used for ASAP. It is the only format that allows the user to restore the data, fits etc. without loosing any information. As mentioned before, the ASAP scantable is an AIPS++ Table (a memory-based table). This function just converts it to a disk-based Table. You can the access that Table with the AIPS++ Table browser or any other AIPS++ tool. \item[SDFITS] The Single Dish FITS format. This format was designed to for interchange between packages, but few packages actually can read it. \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 processing using Perl or, Python, gnuplot etc. \item[MS2] Saves the data in an aips++ MeasurementSet V2 format. You can also access this with the Table browser and other AIPS++ tools. \end{itemize} The default output format can be set in the users {\tt .asaprc} file. Typical usages are: \begin{verbatim} ASAP>scans.save('myscans') # Save in default format 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 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 default can be set in the users {\tt .asaprc} file. The units (and frame etc) of the abscissa will be whatever has previously been set by \cmd{set\_unit}, \cmd{set\_freqframe} etc. Typical plotter usage would be: \begin{verbatim} ASAP>scans.set_unit('km/s') ASAP>plotter.set_mode(stacking='p', panelling='t') ASAP>plotter.plot(scans) \end{verbatim} This will plot multiple polarisation within each plot panel and each scan row in a separate panel. Other possibilities include: \begin{verbatim} # Plot multiple IFs per panel ASAP>plotter.set_mode(stacking='i', panelling='t') # 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} \index{Plotter!selection}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 selector object 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 selection though, if you set the selection on the plotter. Examples: \begin{verbatim} ASAP>selection = selector() # Select second IF 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) # Select a few scans 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) \end{verbatim} \subsection{Plot Control} \index{Plotter!control}The plotter window has a row of buttons on the lower left. These can be used to control the plotter (mostly for zooming the individual plots). From left to right: \begin{tabular}{ll} Home & This will unzoom the plots to the original zoom factor \\ Plot history & \parbox[t]{0.8\textwidth}{(left and right arrow) The plotter keeps a history of zoom settings. The left arrow sets the plot zoom to the previous value. The right arrow returns back again. This allows you, for example, to zoom in on one feature then return the plot to how it was previously. }\\ Pan & \parbox[t]{0.8\textwidth}{(The Cross) This sets the cursor to pan, or scroll mode allowing you to shift the plot within the window. Useful when zoomed in on a feature. }\\ Zoom & \parbox[t]{0.8\textwidth}{(the letter with the magnifying glass) lets you draw a rectangle around a region of interest then zooms in on that region. Use the plot history to unzoom again.}\\ Adjust & \parbox[t]{0.8\textwidth}{(rectangle with 4 arrows) adjust subplot parameters (space at edge of plots)}\\ Save & \parbox[t]{0.8\textwidth}{(floppy disk). Save the plot as a postscript or .png file}\\ \end{tabular} You can also type ``g'' in the plot window to toggle on and off grid lines. Typing 'l' turns on and off logarithmic Y-axis. \subsection{Other control} The plotter has a number of functions to describe the layout of the plot. These include \cmd{set\_legend}, \cmd{set\_layout} and \cmd{set\_title}. To set the exact velocity or channel range to be plotted use the \cmd{set\_range} function. To reset to the default value, call \cmd{set\_range} with no arguments. E.g. \begin{verbatim} ASAP>scans.set_unit('km/s') ASAP>plotter.plot(scans) ASAP>plotter.set_range(-150,-50) ASAP>plotter.set_range() # To reset \end{verbatim} Both the range of the ``x'' and ``y'' axis can be set at once, if desired: \begin{verbatim} ASAP>plotter.set_range(-10,30,-1,6.6) \end{verbatim} To save a hardcopy of the current plot, use the save function, e.g. \begin{verbatim} ASAP>plotter.save('myplot.ps') ASAP>plotter.save('myplot.png', dpi=80) \end{verbatim} \subsection{Plotter Customisation} The plotter allows the user to change most properties such as text size and colour. The \cmd{commands} function and {\cmd help\ asapplotter} list all the possible commands that can be used with the plotter. \commanddef{set\_colors}{Change the default colours used for line plotting. Colours can be given either by name, using the html standard (e.g. red, blue or hotpink), or hexadecimal code (e.g. for black \#000000). If less colours are specified than lines plotted , the plotter cycles through the colours. Example:} {ASAP> plotter.set\_colors('red blue green')\\ ASAP> plotter.set\_colors(`\#0000 blue \#FF00FF')\\ } \commanddef{set\_linestyles}{Change the line styles used for 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)\\ } \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')\\ } \commanddef{set\_layout}{Change the multi-panel layout, i.e. now many rows and columns}{ 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 } \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)\\ } \subsection{Plotter Annotations} 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 (e.g. \cmd{plotter.plot} or \cmd{plotter.set\_range}) the annotations will be removed. \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. Addition arguments which must be passed are {\cmd head\_width} and \cmd{head\_length}}{ ASAP>plotter.arrow(-40,7,35,0,head\_width=0.2, head\_length=10) } \bigcommanddef{axhline(y, xmin, xmax)}{Draw a horizontal line at the 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) } \bigcommanddef{avhline(x, ymin, ymax)}{Draw a vertical line at the 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) } \bigcommanddef{axhspan(ymin, ymax, \\ \hspace*{20mm}xmin, xmax)}{Overlay a transparent colour rectangle. \cmd{ymin} 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) } \bigcommanddef{axvspan(xmin, xmax, \\ \hspace*{20mm} ymin, ymax)}{Overlay a transparent colour rectangle. \cmd{ymin} 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) } \bigcommanddef{text(x, y, str)}{Place the string \cmd{str} at the given \cmd{(x,y)} position in world coordinates.}{ ASAP>plotter.text(-10,7,"CO") } These functions all take a set of \cmd{kwargs} commands. These can be used to set colour, linewidth fontsize etc. These are standard matplotlib settings. Common ones include: \begin{tabular}{ll} \tt color, facecolor, edgecolor \\ \tt width, linewidth \\ \tt fontsize \\ \tt fontname & Sans, Helvetica, Courier, Times etc\\ \tt rotation & Text rotation (horizontal, vertical) \\ \tt alpha & The alpha transparency on 0-1 scale\\ \end{tabular} 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} \section{Line Catalog} \label{sec:linecat} \index{Linecatalog}ASAP can load and manipulate line catlogs to retrieve rest frequencies for \cmd{set\_restfreqs} and for line identification in the plotter. All line catalogs are loaded into a ``linecatalog'' object. 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: \hspace{1cm}\cmd{ftp://ftp.atnf.csiro.au/pub/software/asap/data} \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} {\em NOTE:} Due to a bug in ipython, if you do not \cmd{del} the linecatalog table before quiting asap, you will be left with temporary files. It is safe to delete these once asap has finished. \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). The \cmd{summary} function lists the currently selected lines. \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}A linecatalog can be used as an argument for \cmd{set\_restfreqs}. If a personal line catalog has been used (which has the same size as the number of number of IFs) or linecatalog selection has been used to reduce the number of entries, the line catalog can be used directly as an argument to \cmd{set\_restfreqs}, e.g.: \begin{verbatim} ASAP>jpl = linecatalog('jpl.tbl') ASAP>jpl.set_frequency_limits(23.66,23.75,'GHz') ASAP>data = scantable('data.rpf') ASAP>data.set_restfreqs(jpl) \end{verbatim} If a larger linecatalog is used, individual elements can be used. Use the \cmd{summary} to get the index number of the rest frequency you wish to use. E.g.: \begin{verbatim} ASAP>jpl.summary() ASAP>data.set_restfreqs([jpl[11],[jpl[21]]) \end{verbatim} 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. \section{Fitting} \index{Fitting}Currently multicomponent Gaussian function is available. This is done by creating a fitting object, setting up the fit and actually fitting the data. Fitting can either be done on a single scantable selection or on an entire scantable using the \cmd{auto\_fit} function. If single value fitting is used, and the current selection includes multiple spectra (beams, IFs, scans etc) then the first spectrum in the scantable will be used for fitting. \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 \end{verbatim} This auto-guesses the initial values of the fit and works well for data without extra confusing features. Note that the fit is performed in whatever unit the abscissa is set to. If you want to confine the fitting to a smaller range (e.g. to avoid band edge effects or RFI you must set a mask. \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() \end{verbatim} If you wish, the initial parameter guesses can be specified and specific parameters can be fixed: \begin{verbatim} 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 \end{verbatim} The fitter \cmd{plot} function has a number of options to either view the fit residuals or the individual components (by default it plots the sum of the model components). Examples: \begin{verbatim} # Plot the residual ASAP>f.plot(residual=True) # Plot the first 2 componentsa 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 \end{verbatim} \subsection{Fit saving} \index{Fitter!Fit saving}One you are happy with your fit, it is possible to store it as part of the scantable. \begin{verbatim} ASAP>f.store_fit() \end{verbatim} This will be saved to disk with the data, if the ``ASAP'' file format is selected. Multiple fits to the same data can be stored in the scantable. The scantable function \cmd{get\_fit} can be used to retrieve the stored fits. Currently the fit parameters are just printed to the screen. \begin{verbatim} 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} \section{Polarisation} \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 basis. Conversions of linears to Stokes or Circular polarisations are done ``on-the-fly''. Leakage cannot be corrected for nor are there routines to calibrate position angle offsets. \subsection{Simple Calibration} \index{Polarisation!calibration}It is possible that there is a phase offset between polarisation which will effect the phase of the cross polarisation correlation, and so give rise to spurious polarisation. \cmd{rotate\_xyphase} can be used to correct for this error. At this point, the user must know how to determine the size of the phase offset themselves. \begin{verbatim} ASAP>scans.rotate_xyphase(10.5) # Degrees \end{verbatim} Note that if this function is run twice, the sum of the two values is applied because it is done in-situ. A correction for the receiver parallactic angle may need to be made, generally because of how it is mounted. Use \cmd{rotate\_linpolphase} to correct the position angle. Running this function twice results in the sum of the corrections being applied because it is applied in-situ. \begin{verbatim} ASAP>scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting \end{verbatim} If the sign of the complex correlation is wrong (this can happen depending on the correlator configuration), use \cmd{invert\_phase} to change take the complex conjugate of the complex correlation term. This is always performed in-situ. \begin{verbatim} ASAP>scans.invert_phase() \end{verbatim} Depending on how the correlator is configured, ``BA'' may be correlated instead of ``AB''. Use \cmd{swap\_linears} to correct for this problem: \begin{verbatim} ASAP>scans.swap_linears() \end{verbatim} \subsection{Conversion} \label{sec:polconv} Data can be permanently converted between linear and circular polarisations and stokes. \begin{verbatim} ASAP>stokescans = linearscans.convert_pol("stokes") \end{verbatim} \subsection{Plotting} \label{sec:polplot} \index{Polarisation!plotting}To plot Stokes values, a selector object must be created and the set\_polarisation function used to select the desired polarisation products. The values which can be plotted include a selection of [I,Q,U,V], [I, Plinear, Pangle, V], [RR, LL] or [XX, YY, Real(XY), Imaginary(XY)]. (Plinear and Pangle are the percentage and position angle of linear polarisation). Example: \begin{verbatim} 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 plotter.set_selection(selection); # Select just I \& Q ASAP>selection.set_polarisations(``RR LL'') ASAP plotter.set_selection(selection); # Select just RR \& LL ASAP>selection.set_polarisations(``XX YY'') ASAP plotter.set_selection(selection); # Select linears ASAP>selection.set_polarisations(``I Plinear'') ASAP plotter.set_selection(selection); # Fractional linear ASAP>selection.set_polarisations(``Pangle'') ASAP plotter.set_selection(selection); # Position angle \end{verbatim} Scan, beam and IF selection are also available in the selector object as describe in section~\ref{sec:selection}. \section{Specialised Processing} \subsection{Multibeam MX mode} 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 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'' scans for each beam (either a median average or mean) and using this as a reference scan in a normal quotient (for each beam). The final spectrum for each beam is returned on a new scantable containing 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, 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 resulting scan tables back together. Example: \begin{verbatim} ASAP>scans = scantable('mydata.rpf') ASAP>q = scans.mx_quotient() ASAP>plotter.plot(q) \end{verbatim} The function \cmd{average\_beam} averages multiple beam data together. This is need if MX mode has been used to make a long integration on a single source. E.g. \begin{verbatim} ASAP>av = q.average_beam() \end{verbatim} \subsection{Frequency Switching} {\em FILL ME IN} \subsection{Disk Based Processing} \index{Scantable!disk based} Normally scantables exist entirely in memory during an ASAP session. This has the advantage of speed, but causes limits on the 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. This should be used for all MOPS data! To use disk based tables you either need to change the default in your \cmd{.asaprc} file, e.g. \begin{verbatim} scantable.storage : disk \end{verbatim} or use set the ``\cmd{rc}'' value while running asap to change this on-the-fly. E.g. \begin{verbatim} ASAP>rc('scantable',storage='disk') ASAP>data = scantable('data.rpf') # Loaded using disk based table ASAP>rc('scantable',storage='memory') # Memory tables will be used now \end{verbatim} Changing the ``\cmd{rc}'' value affects the next time the \cmd{scantable} constructor is called. {\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 'tmpXXXXX\_X' directories. These can be safely removed if ASAP is not running. \section{Scantable Mathematics} \index{Scantable!maths}It is possible to to simple mathematics directly on scantables from the command line using the \cmd{+, -, *, /} operators as well as their cousins \cmd{+=, -= *=, /=}. This works between a scantable and a float. (Note that it does not work for integers). {\em Currently mathematics between two scantables is not available } \begin{verbatim} ASAP>scan2 = scan1+2.0 ASAP>scan *= 1.05 ASAP>sum = scan1+scan2 \end{verbatim} \section{Scripting} \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 for a scripting tutorial or the main python website for comprehensive documentation. \hspace{1cm} http://www.atnf.csiro.au/computing/software/asap/tutorials \hspace{1cm} http://svn.atnf.csiro.au/trac/asap/wiki \hspace{1cm} http://www.python.org/doc/Introduction.html \hspace{1cm} http:/ipython.scipy.org \subsection{Running scripts} 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 just a set of commands to process a specific dataset. As an alternative to run scripts without entering ASAP, create a script which starts with. \begin{verbatim} from asap import * \end{verbatim} And run it with \cmd{python scriptname}. \subsection{asapuserfuncs.py} 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 used. The \cmd{execfile} function can be called from within this file. \section{Worked examples} In the following section a few examples of end-to-end processing of some data in ASAP are given. \subsection{Mopra} \index{Mopra} The following example is of some dual polarisation, position switched 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). \begin{verbatim} # get a list of the individual rpfits files in the current directory myfiles = list_files() # Load the data into a scantable data = scantable(myfiles) print data # Form the quotient spectra q = data.auto_quotient() print q # Look at the spectra plotter.plot(q) # Set unit and reference frame q.set_unit('km/s') q.set_freqframe('LSRK') # Average all scans in time, aligning in velocity av = q.average_time(align=True) plotter.plot(av) # Remove the baseline msk = av.create_mask([100,130],[160,200]) av.poly_baseline(msk,2) # Average the two polarisations together iav = av.average_pol() print iav plotter.plot(iav) # Set a sensible velocity range on the plot plotter.set_range(85,200) # Smooth the data a little av.smooth('gauss',4) plotter.plot() # Fit a guassian to the emission f = fitter() f.set_function(gauss=1) f.set_scan(av) f.fit() # View the fit f.plot() # Get the fit parameters f.get_parameters() \end{verbatim} \subsection{Parkes Polarimetry} \index{Parkes}\index{Polarisation}The following example is processing of some Parkes polarimetric observations of OH masers at 1.6~GHz. Because digital filters where used in the backend, the baselines are stable enough not to require a quotient spectra. The 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 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 simplify this, contained in a file called mypol.py: \begin{verbatim} def xyscale(data,xtsys=1.0,ytsys=1.0,nomtsys=25.0) : selection = selector() selection.set_polarisations(0) data.set_selection(selection) data.scale(xtsys/nomtsys) selection.set_polarisations(1) data.set_selection(selection) data.scale(ytsys/nomtsys) selection.set_polarisations(0) data.set_selection(selection) data.scale((xtsys+ytsys)/(2*nomtsys)) selection.set_polarisations(0) data.set_selection(selection) data.scale((xtsys+ytsys)/(2*nomtsys)) \end{verbatim} The typical ASAP session would be \begin{verbatim} # Remind ourself the name of the rpfits files ls # Load data from an rpfits file d1665 = scantable('2005-10-27_0154-P484.rpf') # Check what we have just loaded d1665.summary() # View the data in velocity d1665.set_unit('km/s') d1665.set_freqframe('LSRK') # Correct for the known phase offset in the crosspol data d1665.rotate_xyphase(-4) # Create a copy of the data and set the rest frequency to the 1667 MHz # transition d1667 = d1665.copy() d1667.set_restfreqs([1667.3590], 'MHz') d1667.summary() # Copy out the scan we wish to process g351_5 = d1665.get_scan('351p160') g351_7 = d1667.get_scan('351p160') # Baseline both msk = g351_5.create_mask([-30,-25],[-5,0]) g351_5.poly_baseline(msk,order=1) msk = g351_7.create_mask([-30,-25],[-5,0]) g351_7.poly_baseline(msk,order=1) # Plot the data. The plotter can only plot a single scantable # So we must merge the two tables first plotscans = merge(g351_5, g351_7) plotter.plot(plotscans) # Only shows one panel # Tell the plotter to stack polarisation and panel scans plotter.set_mode('p','s') # Correct for the Tsys using our predefined 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) # Only plot the velocity range of interest plotter.set_range(-30,10) # Update the plot with the baselined data plotter.plot() # Look at the various polarisation products selection = selector() selection.set_polarisations(``RR LL'') plotter.set_selection(selection) selection.set_polarisations(``I Plinear'') plotter.set_selection(selection) selection.set_polarisations(``I Q U V'') plotter.set_selection(selection) # Save the plot as postscript plotter.save('g351_stokes.ps') # Save the process spectra plotscans.save('g351.asap') \end{verbatim} \subsection{Tidbinbilla} \index{Tidbinbilla}The following example is processing of some Tidbinbilla observations of NH$_3$ at 12~mm. Tidbinbilla has (at the time of observations) a single polarisation, but can process two IFs simultaneously. In the example, the first half of the observation was observing the (1,1) and (2,2) transitions simultaneously). The second half observed only the (4,4) transition due to bandwidth limitations. The data is position switched, observing first an reference to the west, then the source twice and finally reference to the east. Important to note, that \cmd{auto\_quotient} should be executed using the \cmd{mode} `time'. \begin{verbatim} # Load the rpfits file and inspect d = scantable('2003-03-16_082048_t0002.rpf') print d # Make the quotient spectra q = d.auto_quotient(mode='time') print q del d # Plot/select in velocity q.set_freqframe('LSRK') q.set_unit('km/s') # Correct for gain/el effects q.recalc_azel() # Tid does not write the elevation q.gain_el() q.opacity(0.05) # Seperate data from the (1,1)&(2,2) and (4,4) transitions g1 = q.get_scan(range(6)) # scans 0..5 g2 = q.get_scan(range(6,12)) # scans 6..11 # Align data in velocity g1.freq_align() g2.freq_align() # Average individual scans a1 = g1.average_time() a2 = g2.average_time() # Rpfits file only contains a single rest frequency. Set both a1.set_restfreqs([23694.4700e6,23722.6336e6]) plotter.plot(a1) plotter.set_mode('i','t') a1.auto_poly_baseline() plotter.plot() a1.smooth('gauss',5) plotter.plot() \end{verbatim} \newpage \section{Appendix} \subsection{Function Summary} \index{Functions!summary}% \begin{verbatim} [The scan container] scantable - a container for integrations/scans (can open asap/rpfits/sdfits and ms files) copy - returns a copy of a scan get_scan - gets a specific scan out of a scantable (by name or number) drop_scan - drops a specific scan out of a scantable (by number) set_selection - set a new subselection of the data get_selection - get the current selection object summary - print info about the scantable contents stats - get specified statistic of the spectra in the scantable stddev - get the standard deviation of the spectra in the scantable 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 current unit set_unit - set the abcissa unit to be used from this point on get_abcissa - get the abcissa values and name for a given row (time) get_column_names - get the names of the columns in the scantable for use with selector.set_query set_freqframe - set the frame info for the Spectral Axis (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 set_feedtype - set the feed type get_fluxunit - get the brightness flux unit set_fluxunit - set the brightness flux unit create_mask - return an mask in the current unit for the given region. The specified regions are NOT masked get_restfreqs - get the current list of rest frequencies set_restfreqs - set a list of rest frequencies flag - flag selected channels in the data save - save the scantable to disk as either 'ASAP', 'SDFITS' or 'ASCII' 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 average_time - return the (weighted) time average of a scan or a list of scans average_pol - average the polarisations together. average_beam - average the beams together. convert_pol - convert to a different polarisation type auto_quotient - return the on/off quotient with automatic detection of the on/off scans (closest in time off is selected) mx_quotient - Form a quotient using MX data (off beams) scale, *, / - return a scan scaled by a given factor add, +, - - return a scan with given value added bin - return a scan with binned channels resample - return a scan with resampled channels smooth - return the spectrally smoothed scan poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols auto_poly_baseline - automatically fit a polynomial baseline recalc_azel - recalculate azimuth and elevation based on the pointing gain_el - apply gain-elevation correction opacity - apply opacity correction convert_flux - convert to and from Jy and Kelvin brightness units freq_align - align spectra in frequency frame invert_phase - Invert the phase of the cross-correlation swap_linears - Swap XX and YY rotate_xyphase - rotate XY phase of cross correlation 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 [Selection] selector - a selection object to set a subset of a scantable set_cycles - set (a list of) cycles by index set_beams - set (a list of) beamss by index set_ifs - set (a list of) ifs by index set_polarisations - set (a list of) polarisations by name or by index set_names - set a selection by name (wildcards allowed) set_tsys - set a selection by tsys thresholds set_query - set a selection by SQL-like query, e.g. BEAMNO==1 reset - unset all selections + - merge to selections [Math] Mainly functions which operate on more than one scantable average_time - return the (weighted) time average of a list of scans quotient - return the on/off quotient simple_math - simple mathematical operations on two scantables, 'add', 'sub', 'mul', 'div' quotient - build quotient of the given on and off scans (matched pairs and 1 off/n on are valid) merge - merge a list of scantables [Line Catalog] linecatalog - a linecatalog wrapper, taking an ASCII or internal format table summary - print a summary of the current selection set_name - select a subset by name pattern, e.g. '*OH*' set_strength_limits - select a subset by line strength limits set_frequency_limits - select a subset by frequency limits reset - unset all selections save - save the current subset to a table (internal format) get_row - get the name and frequency from a specific row in the table [Fitting] fitter auto_fit - return a scan where the function is applied to all Beams/IFs/Pols. commit - return a new scan where the fits have been commited. fit - execute the actual fitting process store_fit - store the fit parameters in the data (scantable) get_chi2 - get the Chi^2 set_scan - set the scantable to be fit set_function - set the fitting function set_parameters - set the parameters for the function(s), and set if they should be held fixed during fitting set_gauss_parameters - same as above but specialised for individual gaussian components get_parameters - get the fitted parameters plot - plot the resulting fit and/or components and residual [Plotter] asapplotter - a plotter for asap, default plotter is called 'plotter' plot - plot a scantable plot_lines - plot a linecatalog overlay 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_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_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_font - set general font properties, e.g. 'family' set_histogram - plot in historam style set_mask - set a plotting mask for a specific polarization text - draw text annotations either in data or relative coordinates arrow - draw arrow annotations either in data or relative coordinates axhline,axvline - draw horizontal/vertical lines axhspan,axvspan - draw horizontal/vertical regions xyplotter - matplotlib/pylab plotting functions [Reading files] reader - access rpfits/sdfits files arrow - draw arrow annotations either in data or relative coordinates axhline,axvline - draw horizontal/vertical lines axhspan,axvspan - draw horizontal/vertical regions xyplotter - matplotlib/pylab plotting functions [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 [General] commands - this command 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. 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 .asaprc rc - set rc parameters from within asap mask_and,mask_or, mask_not - boolean operations on masks created with scantable.create_mask \end{verbatim} \subsection{ASCII output format} \subsection{.asaprc settings} \index{.asaprc} \asaprc{verbose}{{\bf True}/False}{Print verbose output, good to disable in scripts} \asaprc{insitu}{{\bf True}/False}{Apply operations on the input scantable or return new one} \asaprc{useplotter}{{\bf True}/False}{Preload a default plotter} \asaprc{plotter.gui}{{\bf True}/False}{Do we want a GUI or plot to a file} \asaprc{plotter.stacking}{{\bf Pol} Beam IF Scan Time}{Default mode for colour stacking} \asaprc{plotter.panelling}{Pol Beam IF {\bf Scan} Time}{Default mode for panelling} \asaprc{plotter.ganged}{{\bf True}/False}{Push panels together, to share axislabels} \asaprc{plotter.decimate}{True/{\bf False}}{Decimate the number of points plotted by a factor of nchan/1024} \asaprc{plotter.histogram}{True/{\bf False}}{Plot spectrum using histogram rather than lines.} \asaprc{plotter.colours}{}{Set default colours for plotting} \asaprc{plotter.colours}{}{Set default line styles} \asaprc{plotter.papersze}{{\bf A4}}{} % scantable \asaprc{scantable.save}{{\bf ASAP} SDFITS ASCII MS2}{Default output format when saving} \asaprc{scantable.autoaverage}{{\bf True}/False}{Auto averaging on read} \asaprc{scantable.freqframe}{{\bf LSRK} TOPO BARY etc}{default frequency frame to set when function scantable.set\_freqframe is called or the data is imported} \asaprc{scantable.verbosesummary}{True/{\bf False}}{Control the level of information printed by summary} \asaprc{scantable.storage}{{\bf memory}/disk}{Storage of scantables in memory of via based disk tables} \subsection{Installation} \index{Installation} Please refer to the asap wiki for instructions on downloading and/or building asap from source. \hspace{1cm}\cmd{http://www.atnf.csiro.au/computing/software/asap/} \printindex \end{document}