\documentclass[11pt]{article} \usepackage{a4} \usepackage[dvips]{graphicx} % 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\\Cookbook } \author{Chris Phillips} \newcommand{\cmd}[1]{{\tt #1}} \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 antnnas if they can produce ``Single Dish FITS'' format. It is based on the AIPS++ package. %\section{Documentation Standards} %In most of the examples in this document, it has been assumed that the \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 bourbon} \item Mopra - use host {\tt minos} \end{itemize} To start asap log onto one of these Linux hosts and enter \begin{verbatim} > cd /my/data/directory > asap \end{verbatim} This starts the ASAP. To quit, you need to type \verb+^+-d (control-d). \section{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. In the future, we will build a functional (non object oriented) shell on top of this to ease interactive use. \subsection {Integer Indices are 0-relative} Please note, all integer indices in ASAP and iPython are {\bf 0-relative}. \subsection{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{itemize} \item[\cmd{scantable}] The data container (actual spectra and header information) \item[\cmd{fitter}] A tool used to fit functions to the spectral data \item[\cmd{plotter}] A tool used to plot the spectral line data \item[\cmd{reader}] A tool which can be used to read data from disks into a scantable object. \end{itemize} 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 (ie ``s'' and ``ParkesHOH-20052002'' are equivalent). However, having a simple and consistent naming convention will help you a lot. \subsection{Member Functions (functions)} 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(msk,weight='tsys') ASAP> av = scans(mask=msk,weight='tsys') ASAP> av = scans(msk,True) ASAP> scans.polybaseline(mask=msk, order=0, insitu=True) ASAP> scans.polybaseline(msk,0,True) ASAP> scans.polybaseline(mask, insitu=True) \end{verbatim} \subsection{Global Functions} 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} ipython has a number of useful interactive features and a few things to be aware of for the new user. \subsubsection{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. It does not work for filenames, nor for function arguments. Example \begin{verbatim} ASAP> scans = scantable('MyData.rpf') ASAP> scans.se scans.set_cursor scans.set_freqframe scans.set_unit scans.setpol scans.set_doppler scans.set_instrument scans.setbeam scans.set_fluxunit scans.set_restfreqs scans.setif ASAP> scans.set_in ASAP> scans.set_instrument \end{verbatim} \subsubsection{Leading Spaces} 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{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> ! mozilla& \end{verbatim} \subsection{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 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{.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 then command \cmd{list\_rcparameters}. Common values include: \begin{verbatim} # apply operations on the input scantable or return new one insitu : False # default ouput format when saving scantable scantable.save : 'ASAP' # default frequency frame to set when function # scantable.set_freqframe is called scantable.freqframe : 'LSRK' # auto averaging on read scantable.autoaverage : True \end{verbatim} \section{Scantables} \subsection {Description} \subsubsection {Basic 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 spectra for each beam, IF and polarisation. For example Parkes multibeam data would contain many beams, one IF and 2-4 polarisations, while the new Mopra 8-GHz filterbank will eventually produce one beam, many IFs, and 2-4 polarisations. A collection of sequential integrations (rows) for one source is termed a scan (and each scan has a unique numeric identifier, the ScanID). A scantable is then a collection of one or more scans. If you have scan-averaged your data in time, then each scan would hold just one (averaged) integration. 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. \subsubsection {Contents} A scantable has header information and data (a scantable is actually an AIPS++ Table and it is stored in Memory when you are manipulating it with ASAP. You can store 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/integrations 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 FreqID and RestFreqID. They contain indices, for each IF, pointing into tables with all of the frequency information for that integration. More on these below when we discuss the \cmd{summary} function in the next subsection. There are of course many other columns which contain the actual spectra, the flags, the Tsys, the source names and so on, but those are a little more transparently handled. \subsection{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} 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 ASAP> scans.summary(verbose=True) # Include frequency information # Equivalent to brief summary function call ASAP> print scan \end{verbatim} Most of what the \cmd{summary} function prints out is obvious. However, it also prints out the FreqIDs and RestFreqIDs to which we alluded above. These are the last column of the listing. The summary function gives you a scan-based summary. So it lists all of the FreqIDs and RestFreqIDs that it encountered for each scan. If you'd like to see what each FreqID actually means, then set the verbose argument to True and the frequency table will be listed at the end. FreqID of 3 say, refers to the fourth row of the frequency table (ASAP is 0-relative). The list of rest frequencies, to which the RestFreqIDs refer, is always listed. %You can copy one scantable to another with the \cmd{copy} function. %Example: %\begin{verbatim} % ASAP> scans = scantable('MyData.rpf') % ASAP> scan2 = scans.copy() %\end{verbatim} \subsection{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. 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} 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 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 selected for the specified source and IF and added to the list of rest frequencies. \begin{verbatim} # Select for specified source/IF ASAP> scans.set_restfreqs(freqs=1.667359e9, source='NGC253', theif=0) # Select for all sources and IFs ASAP> scans.set_restfreqs(freqs=1.667359e9) \end{verbatim} If you specify a list of frequencies, then it must be 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. The internally stored list of rest frequencies will be replaced by this list. \begin{verbatim} # Select for specified source/IF ASAP> scans.set_restfreqs(freqs=1.667359e9, source='NGC253', theif=0) # Select for all sources and IFs ASAP> scans.set_restfreqs(freqs=1.667359e9) \end{verbatim} In both of the above modes, you can also specify the rest frequencies via names in a known list rather than by their values. Examples: \begin{verbatim} ASAP> scans.lines() # Print list of known lines ASAP> scans.set_restfreqs(lines=['OH1665','OH1667']) \end{verbatim} \subsection{Data Selection} Data selection is currently fairly limited. This will be improved in the future. \subsubsection{Cursor} Generally the user will want to run functions on all rows in a scantable. This allows very fast reduction of data. There are situations when functions should only operate on specific elements of the spectra. This is handled by the scantable cursor, which allows the user to select a single beam, IF and polarisation combination. Example : \begin{verbatim} ASAP> scans.set_cursor(0,2,1) # beam, IF, pol ASAP> scans.smooth(allaxes=F) # in situ by default or .aipsrc \end{verbatim} \subsubsection{Row number} Most functions work on all rows of a scan table. Exceptions are the fitter and plotter. If you wish to only operate on a selected set of scantable rows, use the \cmd{get\_scan} function to copy the rows into a new scantable. \subsubsection{Allaxes} Many functions have an \cmd{allaxes} option which controls whether the function will operate on all elements within a scantable row, or just those selected with the current cursor. The default is taken from the users {\tt .asaprc} file. \subsubsection{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 cursor setting, selected row and selected frequency reference frame. Example : \begin{verbatim} # Select channel range for baselining ASAP> scans.set_unit('channels') 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('channels') 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('channels') 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} \section{Data Input} Data can be loaded in one of two ways; using the reader object or via the scantable constructor. The scantable method is simpler but the reader allow the user more control on what is read. \subsection{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} 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 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> s = r.read(range(100)) # To read in the first 100 integrations 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{Editing} %How and when? \subsection{Separate reference and source observations} 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('*_S') \end{verbatim} For Tidbinbilla data \begin{verbatim} ASAP> r = scans.get_scan('*_[ew]') ASAP> s = scans.get_scan('*_[^ew]') \end{verbatim} \subsection{Make the quotient spectra} Use the quotient function \begin{verbatim} ASAP> q = s.quotient(r) \end{verbatim} This uses the rows in scantable \cmd{r} as reference spectra for the rows in scantable \cmd{s}. Scantable \cmd{r} must have either 1 row (which is applied to all rows in \cmd{s}) or both scantables must have the same number of rows. By default the quotient spectra is calculated to preserve continuum emission. If you wish to remove the continuum contribution, use the \cmd{preserve} argument: \begin{verbatim} ASAP> q = s.quotient(r, preserve=True) \end{verbatim} \subsection{Time average separate scans} 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 = average_time(q) \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 or Tsys \& integration time. \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} \subsection{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, 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} The function \cmd{auto\_poly\_baseline} can be used to automatically baseline your data with out 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} 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} 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} RPFITS files to 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{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 scans the spectra and not the corresponding Tsys. \begin{verbatim} ASAP> scans.scale(1.05, tsys=True) \end{verbatim} \subsubsection{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} As higher frequencies (particularly $>$20~GHz) it is important to make corrections for atmospheric opacity and gain-elevation effects. Gain-elevation curves for some telescopes and frequencies are known to ASAP (currently only for Tidbinbilla at 20~GHz). 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} 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} 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} \cmd{freq\_align} has two modes of operations controlled by the \cmd{perif} argument. By default it will align each source and freqid separately. This is needed for scan tables containing multiple sources. However if scan-based Doppler tracking has been made at the observatory, each row will have a different freqid. In these cases run with \cmd{perif=True} and all rows of a source will be aligned to the same frame. In general \cmd{perif=True} will be needed for most observations as Doppler tracking of some form is made at Parkes, Tid and Mopra. \begin{verbatim} ASAP> scans.freq_align(perif=True) \end{verbatim} 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} 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. 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('*_S') # 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} 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} 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. This format 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', 'FITS') # Save as FITS for exporting into CLASS ASAP> scans.save('myscans', stokes=True) # Convert raw polarisations into Stokes ASAP> scans.save('myscans', overwrite=True) # Overwrite an existing file \end{verbatim} \section{Plotter} Scantable spectra can be plotter 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 multipanel mode and contain multiple plots per panel. The user must tell the plotter how they want the data distributed. This is done using the set\_mode function. The default can be set in the users {\tt .asaprc} file. The units (and frame etc) of the 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} The plotter can plot up to 25 panels and stacked spectra per panel. If you have data larger than this (or for your own sanity) you need to select a subset of this data. This is particularly true for multibeam or multi IF data. The plotter \cmd{set\_cursor} function is used to select a subset of the data. The arguments \cmd{row}, \cmd{beam} and \cmd{IF} all accept a vector of indices corresponding to row, beam or IF selection. Only the selected data will be plotted. To select on polarisation, see section~\ref{sec:polplot}. Examples: \begin{verbatim} # Select second IF ASAP> plotter.set_cursor(IF=[1]) # Select first 4 beams ASAP> plotter.set_cursor(beam=[0,1,2,3]) # Select a few rows ASAP> plotter.set_cursor(row=[2,4,6,10]) # Multiple selection ASAP> plotter.set_cursor(IF=[1], beam=[0,2], row=range(10)) \end{verbatim} Note that the plotter cursor selection is independent of the scantable cursor. \subsection{Plot 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{itemize} \item[Home] This will unzoom the plots to the original zoom factor \item[Plot history] (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. \item[Pan] (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. \item[Zoom] (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. \item[Save] (floppy disk). Save the plot as a postscript or .png file \end{itemize} \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') \end{verbatim} \section{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 row/cursor selection or on an entire scantable using the \cmd{auto\_fit} function. \begin{verbatim} ASAP> f = fitter() ASAP> f.set_function(gauss=2) # Fit two Gaussians ASAP> f.set_scan(scans) ASAP> scans.set_cursor(0,0,1) # Fit the second polarisation 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} One you are happy with your fit, it is possible to store it as part of the scantable. \begin{verbatim} ASAP> f.storefit() \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} \section{Polarisation} Currently ASAP only supports polarmetric analysis on linearly polarised feeds and the cross polarisation products measured. Other cases will be added on an as needed basic. Conversions of linears to Stokes or Circular polarisations are done ``on-the-fly''. Leakage cannot be corrected for nor are these routines able to calibrate position angle offsets. \subsection{Simple Calibration} {\em Currently the receiver position angle is not stored in the RPFITS file. This severely hampers correct handling of polarimetry. In the future we aim to define a general framework and populate the RPFITS files with the data required for transparent polarimetric 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, either because of how it is mounted or if parallactifiying had to track at 90 degrees rather than 0. Use \cmd{rotate\_linpolphase} to correct the position angle. Running this function twice results in the sum of the corrections being applied because it is applied in-situ. \begin{verbatim} ASAP> scans.rotate_linpolphase(-20) # Degrees; correct for receiver mounting # Receiver was tracking 90 degrees rather than 0 ASAP> scans.rotate_linpolphase(90) \end{verbatim} \subsection{Plotting} \label{sec:polplot} To plot Stokes values, the plotter \cmd{set\_cursor} function should be called first using the \cmd{pol} argument. The values which can be plotted include a selection of [I,Q,U,V], [I, Plinear, Pangle, V], [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. Example: \begin{verbatim} ASAP> plotter.set_cursor(pol=[``I'',''Q''] ASAP> plotter.set_cursor(pol=[``RR'',''LL''] ASAP> plotter.set_cursor(pol=[``XX'',''YY''] ASAP> plotter.set_cursor(pol=[``I'',''Plinear''] \end{verbatim} Row, beam and IF selection are also available in \cmd{set\_cursor} as describe in section~\ref{sec:plotter_cursor}. \subsection{Saving} When saving data using the \cmd{save} function, the \cmd{stokes} argument can be used to save the data as Stoke values when saving in FITS format. Example: \begin{verbatim} ASAP> scans.save('myscan.sdfits', 'SDFITS', stokes=True) \end{verbatim} \section{Function Summary} \begin{verbatim} 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 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 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_unit - get the currnt 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) 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_instrument - set the instrument name 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 lines - print list of known spectral lines flag_spectrum - flag a whole Beam/IF/Pol save - save the scantable to disk as either 'ASAP' or 'SDFITS' nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans 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. The dimension won't be reduced and all polarisations will contain the averaged spectrum. quotient - return the on/off quotient 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 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 rotate_xyphase - rotate XY phase of cross correlation rotate_linpolphase - rotate the phase of the complex polarization O=Q+iU correlation [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' [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 paramaters 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 (list of) 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_legend - specify user labels for the legend indeces set_title - specify user labels for the panel indeces 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) [Reading files] reader - access rpfits/sdfits files 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 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 file mask_and,mask_or, mask_not - boolean operations on masks created with scantable.create_mask Note: How to use this with help: # function 'summary' [xxx] is just a category Every 'sub-level' in this list should be replaces by a '.' Period when using help Example: ASAP> help scantable # to get info on ths scantable ASAP> help scantable.summary # to get help on the scantable's ASAP> help average_time \end{verbatim} \section{Scantable Mathematics} 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 two scantables or a scantable and a float. (Note that it does not work for integers). \begin{verbatim} ASAP> sum = scan1+scan2 ASAP> scan2 = scan1+2.0 ASAP> scan *= 1.05 \end{verbatim} %\section{Scripting} %Malte to add something \section{Appendix} \subsection{Installation} ASAP depends on a number of third-party libraries which you must have installed before attempting to build ASAP. These are: \begin{itemize} \item AIPS++ \item Boost \item Matplotlib \item ipython/python \end{itemize} Debian Linux is currently supported and we intend also to support other popular Linux flavours, Solaris and Mac. Of the dependencies, AIPS++ is the most complex to install. \subsection{ASCII output format} \subsection{.asaprc settings} \end{document}