[534] | 1 | \documentclass[11pt]{article} |
---|
| 2 | \usepackage{a4} |
---|
[770] | 3 | \usepackage{calc} |
---|
[534] | 4 | \usepackage[dvips]{graphicx} |
---|
[794] | 5 | \usepackage{makeidx} |
---|
[534] | 6 | |
---|
| 7 | % Adjust the page size |
---|
| 8 | \addtolength{\oddsidemargin}{-0.4in} |
---|
| 9 | \addtolength{\evensidemargin}{+0.4in} |
---|
| 10 | \addtolength{\textwidth}{+0.8in} |
---|
| 11 | |
---|
| 12 | \setlength{\parindent}{0mm} |
---|
| 13 | \setlength{\parskip}{1ex} |
---|
| 14 | |
---|
[770] | 15 | \title{ATNF Spectral Analysis Package\\User Guide } |
---|
[534] | 16 | \author{Chris Phillips} |
---|
| 17 | |
---|
| 18 | \newcommand{\cmd}[1]{{\tt #1}} |
---|
| 19 | |
---|
[770] | 20 | \newcommand{\asaprc}[3]{ |
---|
| 21 | \begin{minipage}[t]{45mm}#1\end{minipage} |
---|
| 22 | \begin{minipage}[t]{30mm}\raggedright #2\end{minipage}\hspace{3mm} |
---|
| 23 | \begin{minipage}[t]{\textwidth-75mm}#3\end{minipage} |
---|
| 24 | } |
---|
| 25 | |
---|
[794] | 26 | \makeindex |
---|
| 27 | |
---|
| 28 | |
---|
[534] | 29 | \begin{document} |
---|
| 30 | |
---|
| 31 | \maketitle |
---|
| 32 | |
---|
| 33 | \section{Introduction} |
---|
| 34 | |
---|
[544] | 35 | ASAP is a single dish spectral line processing package currently being |
---|
| 36 | developed by the ATNF. It is intended to process data from all ATNF |
---|
[770] | 37 | antennas, and can probably be used for other antennas if they can |
---|
[544] | 38 | produce ``Single Dish FITS'' format. It is based on the AIPS++ |
---|
| 39 | package. |
---|
| 40 | |
---|
[953] | 41 | This useeguide is currently being updated for the ASAP 2.0 release |
---|
| 42 | which has a number of significant changes which affect the user |
---|
| 43 | interface. Please report any mistakes you find in this userguide. |
---|
[534] | 44 | |
---|
[544] | 45 | \section{Installation and Running} |
---|
[534] | 46 | |
---|
[738] | 47 | Currently there are installations running on Linux machines at |
---|
[534] | 48 | |
---|
| 49 | \begin{itemize} |
---|
| 50 | \item Epping - use hosts {\tt draco} or {\tt hydra} |
---|
| 51 | \item Narrabri - use host {\tt kaputar} |
---|
[537] | 52 | \item Parkes - use host {\tt bourbon} |
---|
[534] | 53 | \item Mopra - use host {\tt minos} |
---|
| 54 | \end{itemize} |
---|
| 55 | |
---|
[794] | 56 | \index{Running}To start asap log onto one of these Linux hosts and enter |
---|
[534] | 57 | |
---|
| 58 | \begin{verbatim} |
---|
| 59 | > cd /my/data/directory |
---|
[953] | 60 | > asap2 |
---|
[534] | 61 | \end{verbatim} |
---|
| 62 | |
---|
[544] | 63 | This starts the ASAP. To quit, you need to type \verb+^+-d |
---|
| 64 | (control-d). |
---|
[534] | 65 | |
---|
| 66 | \section{Interface} |
---|
| 67 | |
---|
[794] | 68 | \index{Interface}ASAP is written in C++ and python. The user interface uses the |
---|
[534] | 69 | ``ipython'' interactive shell, which is a simple interactive interface |
---|
| 70 | to python. The user does not need to understand python to use this, |
---|
| 71 | but certain aspects python affect what the user can do. The current |
---|
| 72 | interface is object oriented. In the future, we will build a |
---|
| 73 | functional (non object oriented) shell on top of this to ease |
---|
| 74 | interactive use. |
---|
| 75 | |
---|
| 76 | \subsection {Integer Indices are 0-relative} |
---|
| 77 | |
---|
| 78 | Please note, all integer indices in ASAP and iPython are {\bf 0-relative}. |
---|
| 79 | |
---|
| 80 | \subsection{Objects} |
---|
[794] | 81 | \index{objects} |
---|
[534] | 82 | The ASAP interface is based around a number of ``objects'' which the |
---|
| 83 | user deals with. Objects range from the data which have been read from |
---|
| 84 | disk, to tools used for fitting functions to the data. The following |
---|
| 85 | main objects are used : |
---|
| 86 | |
---|
| 87 | \begin{itemize} |
---|
[544] | 88 | \item[\cmd{scantable}] The data container (actual spectra and header |
---|
| 89 | information) |
---|
[953] | 90 | \item[\cmd{selector}] Allows the user to select a subsection of the |
---|
| 91 | data, such as a specified or ramge of beam numbers, IFs, etc. |
---|
| 92 | \item[\cmd{plotter}] A tool used to plot the spectral line data |
---|
[544] | 93 | \item[\cmd{fitter}] A tool used to fit functions to the spectral data |
---|
| 94 | \item[\cmd{reader}] A tool which can be used to read data from disks |
---|
[534] | 95 | into a scantable object. |
---|
| 96 | \end{itemize} |
---|
| 97 | |
---|
[738] | 98 | There can be many objects of the same type. Each object is referred to |
---|
[534] | 99 | by a variable name made by the user. The name of this variable is not |
---|
[770] | 100 | important and can be set to whatever the user prefers (i.e. ``s'' and |
---|
[534] | 101 | ``ParkesHOH-20052002'' are equivalent). However, having a simple and |
---|
| 102 | consistent naming convention will help you a lot. |
---|
| 103 | |
---|
[544] | 104 | \subsection{Member Functions (functions)} |
---|
[534] | 105 | |
---|
[794] | 106 | \index{Functions!member}Following the object oriented approach, |
---|
| 107 | objects have associated ``member functions'' which can either be used |
---|
| 108 | to modify the data in some way or change global properties of the |
---|
| 109 | object. In this document member functions will be referred to simply |
---|
| 110 | as functions. From the command line, the user can execute these |
---|
| 111 | functions using the syntax: |
---|
[534] | 112 | \begin{verbatim} |
---|
| 113 | ASAP> out = object.function(arguments) |
---|
| 114 | \end{verbatim} |
---|
| 115 | |
---|
| 116 | Where \cmd{out} is the name of the returned variable (could be a new |
---|
[544] | 117 | scantable object, or a vector of data, or a status return), |
---|
| 118 | \cmd{object} is the object variable name (set by the user), |
---|
| 119 | \cmd{function} is the name of the member function and \cmd{arguments} |
---|
| 120 | is a list of arguments to the function. The arguments can be provided |
---|
| 121 | either though position or \cmd{name=}. A mix of the two can be used. |
---|
| 122 | E.g. |
---|
[534] | 123 | |
---|
| 124 | \begin{verbatim} |
---|
[953] | 125 | ASAP> av = scans.average_time(msk,weight='tsys') |
---|
| 126 | ASAP> av = scans.average_time(mask=msk,weight='tsys') |
---|
| 127 | ASAP> av = scans.average_time(msk,tsys) |
---|
[544] | 128 | ASAP> scans.polybaseline(mask=msk, order=0, insitu=True) |
---|
[534] | 129 | ASAP> scans.polybaseline(msk,0,True) |
---|
| 130 | ASAP> scans.polybaseline(mask, insitu=True) |
---|
| 131 | \end{verbatim} |
---|
| 132 | |
---|
| 133 | \subsection{Global Functions} |
---|
| 134 | |
---|
[794] | 135 | \index{Functions!global}It does not make sense to implement some functions as member |
---|
[544] | 136 | functions, typically functions which operate on more than one |
---|
| 137 | scantable (e.g. time averaging of many scans). These functions will |
---|
| 138 | always be referred to as global functions. |
---|
[534] | 139 | |
---|
[538] | 140 | \subsection{Interactive environment} |
---|
[534] | 141 | |
---|
[794] | 142 | \index{ipython!environment}ipython has a number of useful interactive |
---|
| 143 | features and a few things to be aware of for the new user. |
---|
[534] | 144 | |
---|
| 145 | \subsubsection{String completion} |
---|
| 146 | |
---|
[794] | 147 | \index{ipython!string completion}Tab completion is enabled for all |
---|
| 148 | function names. If you type the first few letters of a function name, |
---|
| 149 | then type {\tt <TAB>} the function name will be auto completed if it |
---|
| 150 | is un-ambiguous, or a list of possibilities will be |
---|
| 151 | given. Auto-completion works for the user object names as well as |
---|
| 152 | function names. It does not work for filenames, nor for function |
---|
| 153 | arguments. |
---|
[534] | 154 | |
---|
| 155 | Example |
---|
| 156 | \begin{verbatim} |
---|
| 157 | ASAP> scans = scantable('MyData.rpf') |
---|
| 158 | ASAP> scans.se<TAB> |
---|
| 159 | scans.set_cursor scans.set_freqframe scans.set_unit scans.setpol |
---|
[738] | 160 | scans.set_doppler scans.set_instrument scans.setbeam |
---|
| 161 | scans.set_fluxunit scans.set_restfreqs scans.setif |
---|
[534] | 162 | ASAP> scans.set_in<TAB> |
---|
[794] | 163 | ASAP> scans.set_instrument() |
---|
[534] | 164 | \end{verbatim} |
---|
| 165 | |
---|
[544] | 166 | \subsubsection{Leading Spaces} |
---|
| 167 | |
---|
[794] | 168 | \index{ipython!leading space}Python uses leading space to mark blocks |
---|
| 169 | of code. This means that it you start a command line with a space, the |
---|
| 170 | command generally will fail with an syntax error. |
---|
[544] | 171 | |
---|
[770] | 172 | \subsubsection{Variable Names} |
---|
| 173 | |
---|
[794] | 174 | \index{ipython!variable names}During normal data processing, the user |
---|
| 175 | will have to create named variables to hold spectra etc. These must |
---|
| 176 | conform to the normal python syntax, specifically they cannot contain |
---|
| 177 | ``special'' characters such as \@ \$ etc and cannot start with a |
---|
| 178 | number (but can contain numbers). Variable (and function) names are |
---|
| 179 | case sensitive. |
---|
[770] | 180 | |
---|
[534] | 181 | \subsubsection{Unix Interaction} |
---|
| 182 | |
---|
[794] | 183 | \index{ipython!unix interaction}Basic unix shell commands (\cmd{pwd}, |
---|
| 184 | \cmd{ls}, \cmd{cd} etc) can be issued from within ASAP. This allows |
---|
| 185 | the user to do things like look at files in the current directory. The |
---|
| 186 | shell command ``\cmd{cd}'' works within ASAP, allowing the user to |
---|
| 187 | change between data directories. Unix programs cannot be run this way, |
---|
| 188 | but the shell escape ``$!$'' can be used to run arbitrary |
---|
| 189 | programs. E.g. |
---|
[534] | 190 | |
---|
| 191 | \begin{verbatim} |
---|
| 192 | ASAP> pwd |
---|
| 193 | ASAP> ls |
---|
[953] | 194 | ASAP> cd /my/data/directory |
---|
[534] | 195 | ASAP> ! mozilla& |
---|
| 196 | \end{verbatim} |
---|
| 197 | |
---|
| 198 | \subsection{Help} |
---|
| 199 | |
---|
[794] | 200 | \index{Help}ASAP has built in help for all functions. To get a list of |
---|
| 201 | functions type: |
---|
[534] | 202 | |
---|
[538] | 203 | \begin{verbatim} |
---|
[794] | 204 | ASAP> commands() |
---|
[538] | 205 | \end{verbatim} |
---|
| 206 | |
---|
| 207 | To get help on specific functions, the built in help needs to be given |
---|
| 208 | the object and function name. E.g. |
---|
| 209 | |
---|
| 210 | \begin{verbatim} |
---|
| 211 | ASAP> help scantable.get_scan |
---|
| 212 | ASAP> help scantable.stats |
---|
| 213 | ASAP> help plotter.plot |
---|
| 214 | ASAP> help fitter.plot |
---|
| 215 | |
---|
| 216 | ASAP> scans = scantable('mydata.asap') |
---|
| 217 | ASAP> help scans.get_scan # Same as above |
---|
[544] | 218 | \end{verbatim} |
---|
[538] | 219 | |
---|
[544] | 220 | Global functions just need their name |
---|
[538] | 221 | |
---|
[544] | 222 | \begin{verbatim} |
---|
[738] | 223 | ASAP> help average_time |
---|
[538] | 224 | \end{verbatim} |
---|
| 225 | |
---|
| 226 | Note that if you just type \cmd{help} the internal ipython help is |
---|
| 227 | invoked, which is probably {\em not} what you want. Type \verb+^+-d |
---|
| 228 | (control-d) to escape from this. |
---|
| 229 | |
---|
[738] | 230 | \subsection{Customisation - .asaprc} |
---|
[534] | 231 | |
---|
[794] | 232 | \index{.asaprc}ASAP use an \cmd{.asaprc} file to control the user's |
---|
| 233 | preference of default values for various functions arguments. This |
---|
| 234 | includes the defaults for arguments such as \cmd{insitu}, scantable |
---|
| 235 | \cmd{freqframe} and the plotters \cmd{set\_mode} values. The help on |
---|
| 236 | individual functions says which arguments can be set default values |
---|
| 237 | from the \cmd{.asaprc} file. To get a sample contents for the |
---|
| 238 | \cmd{.asaprc} file use then command \cmd{list\_rcparameters}. |
---|
[534] | 239 | |
---|
[538] | 240 | Common values include: |
---|
| 241 | \begin{verbatim} |
---|
| 242 | # apply operations on the input scantable or return new one |
---|
| 243 | insitu : False |
---|
| 244 | |
---|
[738] | 245 | # default output format when saving scantable |
---|
[953] | 246 | scantable.save : ASAP |
---|
[538] | 247 | |
---|
| 248 | # default frequency frame to set when function |
---|
| 249 | # scantable.set_freqframe is called |
---|
[953] | 250 | scantable.freqframe : LSRK |
---|
[538] | 251 | |
---|
| 252 | # auto averaging on read |
---|
| 253 | scantable.autoaverage : True |
---|
| 254 | \end{verbatim} |
---|
| 255 | |
---|
[953] | 256 | For a complete list of \cmd{.asaprc} values, see the Appendix. |
---|
[770] | 257 | |
---|
[534] | 258 | \section{Scantables} |
---|
[794] | 259 | \index{Scantables} |
---|
[534] | 260 | \subsection {Description} |
---|
| 261 | |
---|
| 262 | \subsubsection {Basic Structure} |
---|
| 263 | |
---|
[794] | 264 | \index{Scantable!structure}ASAP data handling works on objects called |
---|
| 265 | scantables. A scantable holds your data, and also provides functions |
---|
| 266 | to operate upon it. |
---|
[534] | 267 | |
---|
[953] | 268 | {\bf [MALTE: Could you please reword this??]} |
---|
| 269 | |
---|
[534] | 270 | The building block of a scantable is an integration, which is a single |
---|
| 271 | row of a scantable. Each row contains spectra for each beam, IF and |
---|
| 272 | polarisation. For example Parkes multibeam data would contain many |
---|
| 273 | beams, one IF and 2-4 polarisations, while the new Mopra 8-GHz |
---|
| 274 | filterbank will eventually produce one beam, many IFs, and 2-4 |
---|
| 275 | polarisations. |
---|
| 276 | |
---|
| 277 | A collection of sequential integrations (rows) for one source is termed |
---|
| 278 | a scan (and each scan has a unique numeric identifier, the ScanID). A |
---|
| 279 | scantable is then a collection of one or more scans. If you have |
---|
| 280 | scan-averaged your data in time, then each scan would hold just one |
---|
| 281 | (averaged) integration. |
---|
| 282 | |
---|
| 283 | Many of the functions which work on scantables can either return a |
---|
| 284 | new scantable with modified data or change the scantable insitu. Which |
---|
| 285 | method is used depends on the users preference. The default can be |
---|
| 286 | changed via the {\tt .asaprc} resource file. |
---|
| 287 | |
---|
| 288 | \subsubsection {Contents} |
---|
| 289 | |
---|
[794] | 290 | \index{Scantable!contents}A scantable has header information and data |
---|
[953] | 291 | (a scantable is actually an AIPS++ Table and it is generally stored in |
---|
| 292 | memory when you are manipulating it with ASAP. You can save it to |
---|
| 293 | disk and then browse it with the AIPS++ Table browser if you know how |
---|
| 294 | to do that !). |
---|
[534] | 295 | |
---|
| 296 | The data are stored in columns (the length of a column is the number of |
---|
[738] | 297 | rows/integrations of course). |
---|
[534] | 298 | |
---|
[953] | 299 | {\bf [MALTE: Is this outdated??]} |
---|
| 300 | |
---|
[534] | 301 | Two important columns are those that describe the frequency setup. We mention |
---|
[538] | 302 | them explicitly here because you need to be able to understand the presentation |
---|
[534] | 303 | of the frequency information and possibly how to manipulate it. |
---|
| 304 | |
---|
| 305 | These columns are called FreqID and RestFreqID. They contain indices, for |
---|
| 306 | each IF, pointing into tables with all of the frequency information for that |
---|
| 307 | integration. More on these below when we discuss the \cmd{summary} function |
---|
| 308 | in the next subsection. |
---|
| 309 | |
---|
| 310 | There are of course many other columns which contain the actual spectra, |
---|
| 311 | the flags, the Tsys, the source names and so on, but those are a little |
---|
| 312 | more transparently handled. |
---|
| 313 | |
---|
| 314 | There is also a function \cmd{summary} to list a summary of the scantable. |
---|
| 315 | You will find this very useful. |
---|
| 316 | |
---|
| 317 | Example: |
---|
| 318 | |
---|
| 319 | \begin{verbatim} |
---|
| 320 | ASAP> scans = scantable('MyData.rpf') |
---|
| 321 | ASAP> scans.summary() # Brief listing |
---|
| 322 | ASAP> scans.summary(verbose=True) # Include frequency information |
---|
[544] | 323 | |
---|
| 324 | # Equivalent to brief summary function call |
---|
[738] | 325 | ASAP> print scan |
---|
[534] | 326 | \end{verbatim} |
---|
| 327 | |
---|
| 328 | Most of what the \cmd{summary} function prints out is obvious. However, |
---|
[738] | 329 | it also prints out the FreqIDs and RestFreqIDs to which we alluded above. |
---|
[534] | 330 | These are the last column of the listing. |
---|
| 331 | |
---|
| 332 | The summary function gives you a scan-based summary. So it lists all of |
---|
| 333 | the FreqIDs and RestFreqIDs that it encountered for each scan. If you'd |
---|
| 334 | like to see what each FreqID actually means, then set the verbose |
---|
[738] | 335 | argument to True and the frequency table will be listed at the end. |
---|
[534] | 336 | FreqID of 3 say, refers to the fourth row of the frequency table (ASAP |
---|
| 337 | is 0-relative). The list of rest frequencies, to which the RestFreqIDs |
---|
| 338 | refer, is always listed. |
---|
| 339 | |
---|
[953] | 340 | \subsection{Data Selection} |
---|
| 341 | \label{sec:selection} |
---|
| 342 | |
---|
| 343 | CHRIS TOFILL IN |
---|
| 344 | |
---|
[544] | 345 | %You can copy one scantable to another with the \cmd{copy} function. |
---|
[534] | 346 | |
---|
[544] | 347 | %Example: |
---|
[534] | 348 | |
---|
[544] | 349 | %\begin{verbatim} |
---|
| 350 | % ASAP> scans = scantable('MyData.rpf') |
---|
| 351 | % ASAP> scan2 = scans.copy() |
---|
| 352 | %\end{verbatim} |
---|
[534] | 353 | |
---|
| 354 | \subsection{State} |
---|
| 355 | |
---|
[794] | 356 | \index{Scantable!state}Each scantable contains "state"; these are |
---|
| 357 | properties applying to all of the data in the scantable. |
---|
[534] | 358 | |
---|
| 359 | Examples are the selection of beam, IF and polarisation, spectral unit |
---|
[770] | 360 | (e.g. km/s), frequency reference frame (e.g. BARY) and velocity Doppler |
---|
[534] | 361 | type (e.g. RADIO). |
---|
| 362 | |
---|
| 363 | \subsubsection{Units, Doppler and Frequency Reference Frame} |
---|
| 364 | |
---|
| 365 | The information describing the frequency setup for each integration |
---|
| 366 | is stored fundamentally in frequency in the reference frame |
---|
[738] | 367 | of observation (E.g. TOPO). |
---|
[534] | 368 | |
---|
[544] | 369 | When required, this is converted to the desired reference frame |
---|
| 370 | (e.g. LSRK), Doppler (e.g. OPTICAL) and unit (e.g. km/s) on-the-fly. |
---|
| 371 | This is important, for example, when you are displaying the data or |
---|
| 372 | fitting to it. |
---|
[534] | 373 | |
---|
| 374 | For units, the user has the choice of frequency, velocity or channel. |
---|
| 375 | The \cmd{set\_unit} function is used to set the current unit for a |
---|
| 376 | scantable. All functions will (where relevant) work with the selected |
---|
| 377 | unit until this changes. This is mainly important for fitting (the fits |
---|
[738] | 378 | can be computed in any of these units), plotting and mask creation. |
---|
[534] | 379 | |
---|
[544] | 380 | The velocity definition can be changed with the \cmd{set\_doppler} |
---|
| 381 | function, and the frequency reference frame can be changed with the |
---|
[534] | 382 | \cmd{set\_freqframe} function. |
---|
| 383 | |
---|
| 384 | Example usage: |
---|
| 385 | |
---|
| 386 | \begin{verbatim} |
---|
| 387 | ASAP> scans = scantable('2004-11-23_1841-P484.rpf') # Read in the data |
---|
| 388 | ASAP> scans.set_freqframe('LSRK') # Use the LSR velocity frame |
---|
| 389 | ASAP> scans.set_unit('km/s') # Use velocity for plots etc from now on |
---|
| 390 | ASAP> scans.set_doppler('OPTICAL') # Use the optical velocity convention |
---|
| 391 | ASAP> scans.set_unit('MHz') # Use frequency in MHz from now on |
---|
| 392 | \end{verbatim} |
---|
| 393 | |
---|
| 394 | |
---|
| 395 | \subsubsection{Rest Frequency} |
---|
| 396 | |
---|
[794] | 397 | \index{Scantable!rest frequency}ASAP reads the line rest frequency |
---|
| 398 | from the RPFITS file when reading the data. The values stored in the |
---|
| 399 | RPFITS file are not always correct and so there is a function |
---|
[953] | 400 | \cmd{set\_restfreq} to set the rest frequencies for the currently |
---|
| 401 | selected data. |
---|
[534] | 402 | |
---|
| 403 | For each integration, there is a rest-frequency per IF (the rest |
---|
| 404 | frequencies are just stored as a list with an index into them). |
---|
| 405 | There are a few ways to set the rest frequencies with this function. |
---|
| 406 | |
---|
[953] | 407 | If you specify just one rest frequency, then it is set for all IF. |
---|
[534] | 408 | |
---|
| 409 | \begin{verbatim} |
---|
[953] | 410 | # Set all IFs |
---|
[738] | 411 | ASAP> scans.set_restfreqs(freqs=1.667359e9) |
---|
[534] | 412 | \end{verbatim} |
---|
| 413 | |
---|
[953] | 414 | If set a rest frequency for each IF, specify a list of frequencies (of |
---|
| 415 | length the number of IFs). Regardless of the source, the rest |
---|
| 416 | frequency will be set for each IF to the corresponding value in the |
---|
| 417 | provided list. |
---|
[534] | 418 | |
---|
| 419 | \begin{verbatim} |
---|
[770] | 420 | # Set rest frequency for all IFs |
---|
| 421 | ASAP> scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,]) |
---|
[538] | 422 | |
---|
[534] | 423 | \end{verbatim} |
---|
| 424 | |
---|
[953] | 425 | {\em Currently this is not implemented} |
---|
| 426 | |
---|
[534] | 427 | In both of the above modes, you can also specify the rest frequencies via |
---|
| 428 | names in a known list rather than by their values. |
---|
| 429 | |
---|
| 430 | Examples: |
---|
| 431 | |
---|
| 432 | \begin{verbatim} |
---|
[953] | 433 | ASAP> scans.set_restfreqs(freqs=['OH1665','OH1667']) |
---|
[534] | 434 | \end{verbatim} |
---|
| 435 | |
---|
| 436 | |
---|
| 437 | \subsubsection{Masks} |
---|
| 438 | |
---|
[794] | 439 | \index{Masks}\index{Scantable!masks}Many tasks (fitting, baseline |
---|
| 440 | subtraction, statistics etc) should only be run on range of |
---|
| 441 | channels. Depending on the current ``unit'' setting this range is set |
---|
| 442 | directly as channels, velocity or frequency ranges. Internally these |
---|
| 443 | are converted into a simple boolean mask for each channel of the |
---|
| 444 | abscissa. This means that if the unit setting is later changed, |
---|
| 445 | previously created mask are still valid. (This is not true for |
---|
| 446 | functions which change the shape or shift the frequency axis). You |
---|
| 447 | create masks with the function \cmd{create\_mask} and this specified |
---|
[534] | 448 | the channels to be included in the selection. |
---|
| 449 | |
---|
| 450 | When setting the mask in velocity, the conversion from velocity |
---|
| 451 | to channels is based on the current cursor setting, selected row and |
---|
[544] | 452 | selected frequency reference frame. |
---|
[534] | 453 | |
---|
| 454 | Example : |
---|
| 455 | \begin{verbatim} |
---|
| 456 | |
---|
| 457 | # Select channel range for baselining |
---|
| 458 | ASAP> scans.set_unit('channels') |
---|
[544] | 459 | ASAP> msk = scans.create_mask([100,400],[600,800]) |
---|
[738] | 460 | |
---|
[534] | 461 | # Select velocity range for fitting |
---|
| 462 | ASAP> scans.set_unit('km/s') |
---|
[544] | 463 | ASAP> msk = scans.create_mask([-30,-10]) |
---|
[534] | 464 | \end{verbatim} |
---|
| 465 | |
---|
[544] | 466 | Sometimes it is more convenient to specify the channels to be |
---|
| 467 | excluded, rather included. You can do this with the ``invert'' |
---|
| 468 | argument. |
---|
[534] | 469 | |
---|
| 470 | Example : |
---|
| 471 | \begin{verbatim} |
---|
| 472 | ASAP> scans.set_unit('channels') |
---|
[738] | 473 | ASAP> msk = scans.create_mask([0,100],[900-1023], invert=True) |
---|
[534] | 474 | \end{verbatim} |
---|
| 475 | |
---|
[544] | 476 | By default \cmd{create\_mask} uses the frequency setup of the first row |
---|
| 477 | to convert velocities into a channel mask. If the rows in the data |
---|
| 478 | cover different velocity ranges, the scantable row to use should be |
---|
| 479 | specified: |
---|
| 480 | |
---|
| 481 | \begin{verbatim} |
---|
| 482 | ASAP> scans.set_unit('km/s') |
---|
| 483 | ASAP> msk = q.create_mask([-30,-10], row=5) |
---|
| 484 | \end{verbatim} |
---|
| 485 | |
---|
[534] | 486 | Because the mask is stored in a simple python variable, the users is |
---|
| 487 | able to combine masks using simple arithmetic. To create a mask |
---|
| 488 | excluding the edge channels, a strong maser feature and a birdie in |
---|
| 489 | the middle of the band: |
---|
| 490 | |
---|
| 491 | \begin{verbatim} |
---|
| 492 | ASAP> scans.set_unit('channels') |
---|
| 493 | ASAP> msk1 = q.create_mask([0,100],[511,511],[900,1023],invert=True) |
---|
| 494 | ASAP> scans.set_unit('km/s') |
---|
| 495 | ASAP> msk2 = q.create_mask([-20,-10],invert=True) |
---|
| 496 | |
---|
| 497 | ASAP> mask = msk1 and msk2 |
---|
| 498 | \end{verbatim} |
---|
| 499 | |
---|
| 500 | |
---|
[953] | 501 | \subsection{Management} |
---|
| 502 | |
---|
| 503 | \index{Scantable!management}During processing it is possible to create |
---|
| 504 | a large number of scan tables. These all consume memory, so it is best |
---|
| 505 | to periodically remove unneeded scan tables. Use \cmd{list\_scans} to |
---|
| 506 | print a list of all scantables and \cmd{del} to remove unneeded ones. |
---|
| 507 | |
---|
| 508 | Example: |
---|
| 509 | |
---|
| 510 | \begin{verbatim} |
---|
| 511 | ASAP> list_scans() |
---|
| 512 | The user created scantables are: |
---|
| 513 | ['s', 'scans', 'av', 's2', 'ss'] |
---|
| 514 | |
---|
| 515 | ASAP> del s2 |
---|
| 516 | ASAP> del ss |
---|
| 517 | \end{verbatim} |
---|
| 518 | |
---|
[534] | 519 | \section{Data Input} |
---|
| 520 | |
---|
[794] | 521 | \index{Reading data}Data can be loaded in one of two ways; using the reader object or via |
---|
[534] | 522 | the scantable constructor. The scantable method is simpler but the |
---|
| 523 | reader allow the user more control on what is read. |
---|
| 524 | |
---|
| 525 | \subsection{Scantable constructor} |
---|
| 526 | |
---|
[794] | 527 | \index{Scantable constructor}\index{Scantable!constructor}This loads |
---|
| 528 | all of the data from filename into the scantable object scans and |
---|
| 529 | averages all the data within a scan (i.e. the resulting scantable |
---|
[534] | 530 | will have one row per scan). The recognised input file formats are |
---|
| 531 | RPFITS, SDFITS (singledish fits), ASAP's scantable format and aips++ |
---|
[738] | 532 | MeasurementSet2 format. |
---|
[534] | 533 | |
---|
| 534 | Example usage: |
---|
| 535 | |
---|
| 536 | \begin{verbatim} |
---|
| 537 | ASAP> scan = scantable('2004-11-23_1841-P484.rpf') |
---|
[544] | 538 | |
---|
| 539 | # Don't scan average the data |
---|
| 540 | ASAP> scan = scantable('2004-11-23_1841-P484.rpf', average=False) |
---|
[534] | 541 | \end{verbatim} |
---|
| 542 | |
---|
| 543 | |
---|
| 544 | \subsection{Reader object} |
---|
| 545 | |
---|
[794] | 546 | \index{Reader object}\index{Scantable!reader object}For more control |
---|
| 547 | when reading data into ASAP, the reader object should be used. This |
---|
[953] | 548 | has the option of only reading in a range of integrations, only a |
---|
| 549 | specified beam or IF and does not perform any scan averaging of the |
---|
| 550 | data, allowing analysis of the individual integrations. Note that due |
---|
| 551 | to limitation of the RPFITS library, only one reader object can be |
---|
| 552 | open at one time reading RPFITS files. To read multiple RPFITS files, |
---|
| 553 | the old reader must be destroyed before the new file is opened. |
---|
| 554 | However, multiple readers can be created and attached to SDFITS files. |
---|
[534] | 555 | |
---|
| 556 | |
---|
| 557 | Example usage: |
---|
| 558 | |
---|
| 559 | \begin{verbatim} |
---|
| 560 | ASAP> r = reader('2003-03-16_082048_t0002.rpf') |
---|
[794] | 561 | ASAP> r.summary() |
---|
[534] | 562 | ASAP> scan = r.read() |
---|
| 563 | ASAP> s = r.read(range(100)) # To read in the first 100 integrations |
---|
| 564 | ASAP> del r |
---|
| 565 | \end{verbatim} |
---|
| 566 | |
---|
| 567 | \section{Basic Processing} |
---|
| 568 | |
---|
| 569 | In the following section, a simple data reduction to form a quotient |
---|
[544] | 570 | spectrum of a single source is followed. It has been assume that the |
---|
| 571 | \cmd{.asaprc} file has {\em not} been used to change the \cmd{insitu} |
---|
| 572 | default value from \cmd{True}. |
---|
[534] | 573 | |
---|
[738] | 574 | \subsection{Auto quotient} |
---|
[794] | 575 | \index{Auto quotient}Quotients can be computed ``automatically''. This |
---|
| 576 | requires the data to have matching source/reference pairs or one |
---|
| 577 | reference for multiple sources. Auto quotient assumes reference scans |
---|
| 578 | have a trailing ``\_R'' in the source name for data from Parkes and |
---|
| 579 | Mopra, and a trailing ``e'' or ``w'' for data fro, Tidbinbilla. |
---|
[534] | 580 | |
---|
[738] | 581 | \begin{verbatim} |
---|
| 582 | ASAP> q = s.auto_quotient() |
---|
| 583 | \end{verbatim} |
---|
| 584 | |
---|
[953] | 585 | %If this is not sufficient the following alternative method can be used. |
---|
| 586 | % |
---|
| 587 | %\subsection{Separate reference and source observations} |
---|
| 588 | % |
---|
| 589 | %\index{Quotient spectra}Most data from ATNF observatories |
---|
| 590 | %distinguishes on and off source data using the file name. This makes |
---|
| 591 | %it easy to create two scantables with the source and reference |
---|
| 592 | %data. As long as there was exactly one reference observation for each |
---|
| 593 | %on source observation for following method will work. |
---|
| 594 | % |
---|
| 595 | %For Mopra and Parkes data: |
---|
| 596 | %\begin{verbatim} |
---|
| 597 | % ASAP> r = scans.get_scan('*_R') |
---|
| 598 | % ASAP> s = scans.get_scan('*_S') |
---|
| 599 | %\end{verbatim} |
---|
| 600 | % |
---|
| 601 | %For Tidbinbilla data |
---|
| 602 | %\begin{verbatim} |
---|
| 603 | % ASAP> r = scans.get_scan('*_[ew]') |
---|
| 604 | % ASAP> s = scans.get_scan('*_[^ew]') |
---|
| 605 | %\end{verbatim} |
---|
| 606 | % |
---|
| 607 | %\subsection{Make the quotient spectra} |
---|
| 608 | % |
---|
| 609 | %Use the quotient function |
---|
| 610 | % |
---|
| 611 | %\begin{verbatim} |
---|
| 612 | % ASAP> q = s.quotient(r) |
---|
| 613 | %\end{verbatim} |
---|
| 614 | % |
---|
| 615 | %This uses the rows in scantable \cmd{r} as reference spectra for the |
---|
| 616 | %rows in scantable \cmd{s}. Scantable \cmd{r} must have either 1 row |
---|
| 617 | %(which is applied to all rows in \cmd{s}) or both scantables must have |
---|
| 618 | %the same number of rows. By default the quotient spectra is calculated |
---|
| 619 | %to preserve continuum emission. If you wish to remove the continuum |
---|
| 620 | %contribution, use the \cmd{preserve} argument: |
---|
| 621 | % |
---|
| 622 | %\begin{verbatim} |
---|
| 623 | % ASAP> q = s.quotient(r, preserve=True) |
---|
| 624 | %\end{verbatim} |
---|
[738] | 625 | |
---|
[534] | 626 | \subsection{Time average separate scans} |
---|
| 627 | |
---|
[794] | 628 | \index{Time average}If you have observed the source with multiple |
---|
| 629 | source/reference cycles you will want to scan-average the quotient |
---|
| 630 | spectra together. |
---|
[534] | 631 | |
---|
| 632 | \begin{verbatim} |
---|
[953] | 633 | ASAP> av = q.average_time() |
---|
[534] | 634 | \end{verbatim} |
---|
| 635 | |
---|
[544] | 636 | If for some you want to average multiple sets of scantables together |
---|
| 637 | you can: |
---|
[534] | 638 | |
---|
| 639 | \begin{verbatim} |
---|
| 640 | ASAP> av = average_time(q1, q2, q3) |
---|
| 641 | \end{verbatim} |
---|
| 642 | |
---|
[544] | 643 | The default is to use integration time weighting. The alternative is |
---|
[770] | 644 | to use none, variance, Tsys weighting or Tsys \& integration time. |
---|
[534] | 645 | |
---|
[544] | 646 | \begin{verbatim} |
---|
| 647 | ASAP> av = average_time(q, weight='tintsys') |
---|
| 648 | \end{verbatim} |
---|
| 649 | |
---|
[534] | 650 | To use variance based weighting, you need to supply a mask saying which |
---|
| 651 | channel range you want it to calculate the variance from. |
---|
| 652 | |
---|
| 653 | \begin{verbatim} |
---|
[544] | 654 | ASAP> msk = scans.create_mask([200,400],[600,800]) |
---|
| 655 | ASAP> av = average_time(scans, mask=msk, weight='var') |
---|
[534] | 656 | \end{verbatim} |
---|
| 657 | |
---|
[953] | 658 | If you have not observed your data with Doppler tracking (or run |
---|
| 659 | \cmd{freq\_align} explicitally) you should align the data in frequency |
---|
| 660 | before averaging. |
---|
[794] | 661 | |
---|
[953] | 662 | \begin{verbatim} |
---|
| 663 | ASAP> av = scans.average_time(align=True) |
---|
| 664 | \end{verbatim} |
---|
| 665 | |
---|
| 666 | Note that, if needed, you should run \cmd{gain\_el} and \cmd{opacity} |
---|
| 667 | before you average the data in time (\S \ref{sec:gainel} \& |
---|
| 668 | \ref{sec:freqalign}). |
---|
| 669 | |
---|
[534] | 670 | \subsection{Baseline fitting} |
---|
| 671 | |
---|
[794] | 672 | \index{Baseline fitting}To make a baseline fit, you must first create |
---|
| 673 | a mask of channels to use in the baseline fit. |
---|
[534] | 674 | |
---|
| 675 | \begin{verbatim} |
---|
| 676 | ASAP> msk = scans.create_mask([100,400],[600,900]) |
---|
[738] | 677 | ASAP> scans.poly_baseline(msk, 1) |
---|
[534] | 678 | \end{verbatim} |
---|
| 679 | |
---|
| 680 | This will fit a first order polynomial to the selected channels and subtract |
---|
| 681 | this polynomial from the full spectra. |
---|
| 682 | |
---|
| 683 | \subsubsection{Auto-baselining} |
---|
| 684 | |
---|
[794] | 685 | \index{Auto-baseline}The function \cmd{auto\_poly\_baseline} can be used to automatically |
---|
[770] | 686 | baseline your data without having to specify channel ranges for the |
---|
| 687 | line free data. It automatically figures out the line-free emission |
---|
| 688 | and fits a polynomial baseline to that data. The user can use masks to |
---|
| 689 | fix the range of channels or velocity range for the fit as well as |
---|
| 690 | mark the band edge as invalid. |
---|
[534] | 691 | |
---|
| 692 | Simple example |
---|
| 693 | |
---|
| 694 | \begin{verbatim} |
---|
| 695 | ASAP> scans.auto_poly_baseline(order=2,threshold=5) |
---|
| 696 | \end{verbatim} |
---|
| 697 | |
---|
| 698 | \cmd{order} is the polynomial order for the fit. \cmd{threshold} is |
---|
| 699 | the SNR threshold to use to deliminate line emission from |
---|
[548] | 700 | signal. Generally the value of threshold is not too critical, however |
---|
| 701 | making this too large will compromise the fit (as it will include |
---|
| 702 | strong line features) and making it too small will mean it cannot find |
---|
| 703 | enough line free channels. |
---|
[534] | 704 | |
---|
[548] | 705 | |
---|
[534] | 706 | Other examples: |
---|
| 707 | |
---|
| 708 | \begin{verbatim} |
---|
| 709 | # Don't try and fit the edge of the bandpass which is noisier |
---|
| 710 | ASAP> scans.auto_poly_baseline(edge=(500,450),order=3,threshold=3) |
---|
| 711 | |
---|
| 712 | # Only fit a given region around the line |
---|
| 713 | ASAP> scans.set_unit('km/s') |
---|
| 714 | ASAP> msk = scans.create_mask((-60,-20)) |
---|
| 715 | ASAP> scans.auto_poly_baseline(mask=msk,order=3,threshold=3) |
---|
| 716 | |
---|
| 717 | \end{verbatim} |
---|
| 718 | |
---|
| 719 | \subsection{Average the polarisations} |
---|
| 720 | |
---|
[794] | 721 | \index{average\_pol}If you are just interested in the highest SNR for total intensity you |
---|
[534] | 722 | will want to average the parallel polarisations together. |
---|
| 723 | |
---|
| 724 | \begin{verbatim} |
---|
| 725 | ASAP> scans.average_pol() |
---|
| 726 | \end{verbatim} |
---|
| 727 | |
---|
| 728 | \subsection{Calibration} |
---|
| 729 | |
---|
[794] | 730 | \index{Calibration}For most uses, calibration happens transparently as the input data |
---|
[534] | 731 | contains the Tsys measurements taken during observations. The nominal |
---|
| 732 | ``Tsys'' values may be in Kelvin or Jansky. The user may wish to |
---|
| 733 | supply a Tsys correction or apply gain-elevation and opacity |
---|
| 734 | corrections. |
---|
| 735 | |
---|
| 736 | \subsubsection{Brightness Units} |
---|
| 737 | |
---|
[794] | 738 | \index{Brightness Units}RPFITS files do not contain any information as |
---|
| 739 | to whether the telescope calibration was in units of Kelvin or |
---|
| 740 | Janskys. On reading the data a default value is set depending on the |
---|
| 741 | telescope and frequency of observation. If this default is incorrect |
---|
| 742 | (you can see it in the listing from the \cmd{summary} function) the |
---|
| 743 | user can either override this value on reading the data or later. |
---|
| 744 | E.g: |
---|
[534] | 745 | |
---|
| 746 | \begin{verbatim} |
---|
| 747 | ASAP> scans = scantable(('2004-11-23_1841-P484.rpf', unit='Jy') |
---|
| 748 | # Or in two steps |
---|
| 749 | ASAP> scans = scantable(('2004-11-23_1841-P484.rpf') |
---|
| 750 | ASAP> scans.set_fluxunit('Jy) |
---|
| 751 | \end{verbatim} |
---|
| 752 | |
---|
| 753 | \subsubsection{Tsys scaling} |
---|
| 754 | |
---|
[794] | 755 | \index{Tsys scaling}Sometime the nominal Tsys measurement at the |
---|
| 756 | telescope is wrong due to an incorrect noise diode calibration. This |
---|
| 757 | can easily be corrected for with the scale function. By default, |
---|
| 758 | \cmd{scale} only scans the spectra and not the corresponding Tsys. |
---|
[534] | 759 | |
---|
| 760 | \begin{verbatim} |
---|
[738] | 761 | ASAP> scans.scale(1.05, tsys=True) |
---|
[534] | 762 | \end{verbatim} |
---|
| 763 | |
---|
| 764 | \subsubsection{Unit Conversion} |
---|
| 765 | |
---|
[794] | 766 | \index{Unit conversion}To convert measurements in Kelvin to Jy (and |
---|
| 767 | vice versa) the global function \cmd{convert\_flux} is needed. This |
---|
| 768 | converts and scales the data from K to Jy or vice-versa depending on |
---|
| 769 | what the current brightness unit is set to. The function knows the |
---|
| 770 | basic parameters for some frequencies and telescopes, but the user may |
---|
| 771 | need to supply the aperture efficiency, telescope diameter or the Jy/K |
---|
| 772 | factor. |
---|
[534] | 773 | |
---|
| 774 | \begin{verbatim} |
---|
[794] | 775 | ASAP> scans.convert_flux() # If efficency known |
---|
[534] | 776 | ASAP> scans.convert_flux(eta=0.48) # If telescope diameter known |
---|
| 777 | ASAP> scans.convert_flux(eta=0.48,d=35) # Unknown telescope |
---|
| 778 | ASAP> scans.convert_flux(jypk=15) # Alternative |
---|
| 779 | \end{verbatim} |
---|
| 780 | |
---|
| 781 | \subsubsection{Gain-Elevation and Opacity Corrections} |
---|
[794] | 782 | \label{sec:gainel} |
---|
[534] | 783 | |
---|
[794] | 784 | \index{Gain-elevation}As higher frequencies (particularly $>$20~GHz) |
---|
| 785 | it is important to make corrections for atmospheric opacity and |
---|
| 786 | gain-elevation effects. |
---|
[534] | 787 | |
---|
[794] | 788 | Note that currently the elevation is not written correctly into |
---|
[770] | 789 | Tidbinbilla rpfits files. This means that gain-elevation and opacity |
---|
[794] | 790 | corrections will not work unless these get recalculated. |
---|
[770] | 791 | |
---|
[794] | 792 | \begin{verbatim} |
---|
| 793 | ASAP> scans.recalc_azel() # recalculate az/el based on pointing |
---|
| 794 | \end{verbatim} |
---|
| 795 | |
---|
[544] | 796 | Gain-elevation curves for some telescopes and frequencies are known to |
---|
[794] | 797 | ASAP (currently only for Tidbinbilla at 20~GHz). In these cases |
---|
| 798 | making gain-corrections is simple. If the gain curve for your data is |
---|
| 799 | not known, the user can supply either a gain polynomial or text file |
---|
[534] | 800 | tabulating gain factors at a range of elevations (see \cmd{help |
---|
[544] | 801 | scantable.gain\_el}). |
---|
[534] | 802 | |
---|
| 803 | Examples: |
---|
| 804 | |
---|
| 805 | \begin{verbatim} |
---|
| 806 | ASAP> scans.gain_el() # If gain table known |
---|
| 807 | ASAP> scans.gain_el(poly=[3.58788e-1,2.87243e-2,-3.219093e-4]) |
---|
| 808 | \end{verbatim} |
---|
| 809 | |
---|
[794] | 810 | \index{Opacity}Opacity corrections can be made with the global |
---|
| 811 | function \cmd{opacity}. This should work on all telescopes as long as |
---|
| 812 | a measurement of the opacity factor was made during the observation. |
---|
[534] | 813 | |
---|
| 814 | \begin{verbatim} |
---|
| 815 | ASAP> scans.opacity(0.083) |
---|
| 816 | \end{verbatim} |
---|
| 817 | |
---|
| 818 | Note that at 3~mm Mopra uses a paddle wheel for Tsys calibration, |
---|
| 819 | which takes opacity effects into account (to first order). ASAP |
---|
[544] | 820 | opacity corrections should not be used for Mopra 3-mm data. |
---|
[534] | 821 | |
---|
| 822 | \subsection{Frequency Frame Alignment} |
---|
[794] | 823 | \label{sec:freqalign} |
---|
[534] | 824 | |
---|
[794] | 825 | \index{Frequency alignment}\index{Velicity alignment}When time |
---|
| 826 | averaging a series of scans together, it is possible that the velocity |
---|
| 827 | scales are not exactly aligned. This may be for many reasons such as |
---|
| 828 | not Doppler tracking the observations, errors in the Doppler tracking |
---|
| 829 | etc. This mostly affects very long integrations or integrations |
---|
| 830 | averaged together from different days. Before averaging such data |
---|
| 831 | together, they should be frequency aligned using \cmd{freq\_align}. |
---|
[534] | 832 | |
---|
| 833 | E.g.: |
---|
| 834 | |
---|
| 835 | \begin{verbatim} |
---|
| 836 | ASAP> scans.freq_align() |
---|
| 837 | ASAP> av = average_time(scans) |
---|
| 838 | \end{verbatim} |
---|
| 839 | |
---|
[953] | 840 | {\em A Global freq\_align command will be made eventually} |
---|
[534] | 841 | |
---|
| 842 | To average together data taken on different days, which are in |
---|
| 843 | different scantables, each scantable must aligned to a common |
---|
| 844 | reference time then the scantables averaged. The simplest way of |
---|
| 845 | doing this is to allow ASAP to choose the reference time for the first |
---|
[738] | 846 | scantable then using this time for the subsequent scantables. |
---|
[534] | 847 | |
---|
| 848 | \begin{verbatim} |
---|
| 849 | ASAP> scans1.freq_align() # Copy the refeference Epoch from the output |
---|
| 850 | ASAP> scans2.freq_align(reftime='2004/11/23/18:43:35') |
---|
| 851 | ASAP> scans3.freq_align(reftime='2004/11/23/18:43:35') |
---|
| 852 | ASAP> av = average_time(scans1, scans2, scans3) |
---|
| 853 | \end{verbatim} |
---|
| 854 | |
---|
| 855 | \section{Scantable manipulation} |
---|
| 856 | |
---|
[794] | 857 | \index{Scantable!manipulation}While it is very useful to have many |
---|
| 858 | independent sources within one scantable, it is often inconvenient for |
---|
| 859 | data processing. The \cmd{get\_scan} function can be used to create a |
---|
| 860 | new scantable with a selection of scans from a scantable. The |
---|
| 861 | selection can either be on the source name, with simple wildcard |
---|
[953] | 862 | matching or set of scan ids. Internally this uses the selector object, |
---|
| 863 | so for more complicated selection the selector should be used directly |
---|
| 864 | instead. |
---|
[534] | 865 | |
---|
| 866 | For example: |
---|
| 867 | |
---|
| 868 | \begin{verbatim} |
---|
| 869 | ASAP> ss = scans.get_scan(10) # Get the 11th scan (zero based) |
---|
| 870 | ASAP> ss = scans.get_scan(range(10)) # Get the first 10 scans |
---|
[538] | 871 | ASAP> ss = scans.get_scan(range(10,20)) # Get the next 10 scans |
---|
[534] | 872 | ASAP> ss = scans.get_scan([2,4,6,8,10]) # Get a selection of scans |
---|
| 873 | |
---|
| 874 | ASAP> ss = scans.get_scan('345p407') # Get a specific source |
---|
| 875 | ASAP> ss = scans.get_scan('345*') # Get a few sources |
---|
| 876 | |
---|
| 877 | ASAP> r = scans.get_scan('*_R') # Get all reference sources (Parkes/Mopra) |
---|
| 878 | ASAP> s = scans.get_scan('*_S') # Get all program sources (Parkes/Mopra) |
---|
[953] | 879 | ASAP> r = scans.get_scan('*[ew]') # Get all reference sources (Tid) |
---|
| 880 | ASAP> s = scans.get_scan('*[^ew]') # Get all program sources (Tid) |
---|
[534] | 881 | |
---|
| 882 | \end{verbatim} |
---|
| 883 | |
---|
| 884 | To copy a scantable the following does not work: |
---|
| 885 | |
---|
| 886 | \begin{verbatim} |
---|
| 887 | ASAP> ss = scans |
---|
| 888 | \end{verbatim} |
---|
| 889 | |
---|
[544] | 890 | as this just creates a reference to the original scantable. Any |
---|
| 891 | changes made to \cmd{ss} are also seen in \cmd{scans}. To duplicate a |
---|
[534] | 892 | scantable, use the copy function. |
---|
| 893 | |
---|
| 894 | \begin{verbatim} |
---|
[794] | 895 | ASAP> ss = scans.copy() |
---|
[534] | 896 | \end{verbatim} |
---|
| 897 | |
---|
| 898 | \section{Data Output} |
---|
| 899 | |
---|
[794] | 900 | \index{Scantable!save}\index{Saving data}ASAP can save scantables in a |
---|
| 901 | variety of formats, suitable for reading into other packages. The |
---|
| 902 | formats are: |
---|
[534] | 903 | |
---|
[953] | 904 | {\em Currently only raw ASAP output is available. Other formats will be added soon} |
---|
| 905 | |
---|
[534] | 906 | \begin{itemize} |
---|
| 907 | \item[ASAP] This is the internal format used for ASAP. It is the only |
---|
[544] | 908 | format that allows the user to restore the data, fits etc. without |
---|
| 909 | loosing any information. As mentioned before, the ASAP scantable is |
---|
| 910 | an AIPS++ Table (a memory-based table). This function just converts |
---|
| 911 | it to a disk-based Table. You can the access that Table with the |
---|
| 912 | AIPS++ Table browser or any other AIPS++ tool. |
---|
[534] | 913 | |
---|
[544] | 914 | \item[SDFITS] The Single Dish FITS format. This format was designed to |
---|
| 915 | for interchange between packages, but few packages actually can read |
---|
| 916 | it. |
---|
[534] | 917 | |
---|
| 918 | \item[FITS] This uses simple ``image'' fits to save the data, each row |
---|
[544] | 919 | being written to a separate fits file. This format is suitable for |
---|
| 920 | importing the data into CLASS. |
---|
[534] | 921 | |
---|
| 922 | \item[ASCII] A simple text based format suitable for the user to |
---|
| 923 | processing using Perl or, Python, gnuplot etc. |
---|
| 924 | |
---|
| 925 | \item[MS2] Saves the data in an aips++ MeasurementSet V2 format. |
---|
| 926 | You can also access this with the Table browser and other AIPS++ |
---|
| 927 | tools. |
---|
| 928 | |
---|
| 929 | \end{itemize} |
---|
| 930 | |
---|
[738] | 931 | The default output format can be set in the users {\tt .asaprc} file. |
---|
[534] | 932 | Typical usages are: |
---|
| 933 | |
---|
| 934 | \begin{verbatim} |
---|
| 935 | ASAP> scans.save('myscans') # Save in default format |
---|
| 936 | ASAP> scans.save('myscans', 'FITS') # Save as FITS for exporting into CLASS |
---|
| 937 | |
---|
| 938 | ASAP> scans.save('myscans', stokes=True) # Convert raw polarisations into Stokes |
---|
| 939 | ASAP> scans.save('myscans', overwrite=True) # Overwrite an existing file |
---|
| 940 | \end{verbatim} |
---|
| 941 | |
---|
| 942 | |
---|
| 943 | \section{Plotter} |
---|
| 944 | |
---|
[794] | 945 | \index{Plotter}Scantable spectra can be plotted at any time. An asapplotter object is |
---|
[534] | 946 | used for plotting, meaning multiple plot windows can be active at the |
---|
| 947 | same time. On start up a default asapplotter object is created called |
---|
| 948 | ``plotter''. This would normally be used for standard plotting. |
---|
| 949 | |
---|
[538] | 950 | The plotter, optionally, will run in a multipanel mode and contain |
---|
[534] | 951 | multiple plots per panel. The user must tell the plotter how they want |
---|
| 952 | the data distributed. This is done using the set\_mode function. The |
---|
| 953 | default can be set in the users {\tt .asaprc} file. The units (and frame |
---|
[538] | 954 | etc) of the abscissa will be whatever has previously been set by |
---|
| 955 | \cmd{set\_unit}, \cmd{set\_freqframe} etc. |
---|
[534] | 956 | |
---|
| 957 | Typical plotter usage would be: |
---|
| 958 | |
---|
| 959 | \begin{verbatim} |
---|
| 960 | ASAP> scans.set_unit('km/s') |
---|
| 961 | ASAP> plotter.set_mode(stacking='p',panelling='t') |
---|
| 962 | ASAP> plotter.plot(scans) |
---|
| 963 | \end{verbatim} |
---|
| 964 | |
---|
| 965 | This will plot multiple polarisation within each plot panel and each |
---|
[544] | 966 | scan row in a separate panel. |
---|
[534] | 967 | |
---|
[538] | 968 | Other possibilities include: |
---|
[534] | 969 | |
---|
| 970 | \begin{verbatim} |
---|
| 971 | # Plot multiple IFs per panel |
---|
| 972 | ASAP> plotter.set_mode(stacking='i',panelling='t') |
---|
[538] | 973 | |
---|
| 974 | # Plot multiple beams per panel |
---|
| 975 | ASAP> plotter.set_mode(stacking='b',panelling='t') |
---|
| 976 | |
---|
| 977 | # Plot one IF per panel, time stacked |
---|
| 978 | ASAP> plotter.set_mode('t', 'i') |
---|
| 979 | |
---|
| 980 | # Plot each scan in a seperate panel |
---|
| 981 | ASAP> plotter.set_mode('t', 's') |
---|
| 982 | |
---|
[534] | 983 | \end{verbatim} |
---|
| 984 | |
---|
[538] | 985 | \subsection{Plot Selection} |
---|
| 986 | \label{sec:plotter_cursor} |
---|
| 987 | |
---|
[794] | 988 | \index{Plotter!selection}The plotter can plot up to 25 panels and |
---|
| 989 | stacked spectra per panel. If you have data larger than this (or for |
---|
| 990 | your own sanity) you need to select a subset of this data. This is |
---|
[953] | 991 | particularly true for multibeam or multi IF data. The selector object |
---|
| 992 | should be used for this purpose. Selection can either be applide to |
---|
| 993 | the scantable or directly to the plotter, the end result is the same. |
---|
[538] | 994 | |
---|
| 995 | Examples: |
---|
| 996 | |
---|
| 997 | \begin{verbatim} |
---|
[953] | 998 | ASAP> selection = selector() |
---|
[538] | 999 | # Select second IF |
---|
[953] | 1000 | ASAP> selection.set_if(1) |
---|
| 1001 | ASAP> plotter.set_selection(selection) |
---|
[538] | 1002 | |
---|
| 1003 | # Select first 4 beams |
---|
[953] | 1004 | ASAP> selection.set_beam([0,1,2,3]) |
---|
| 1005 | ASAP> plotter.set_selection(selection) |
---|
[538] | 1006 | |
---|
[953] | 1007 | # Select a few scans |
---|
| 1008 | ASAP> selection.set_scans([2,4,6,10]) |
---|
| 1009 | ASAP> plotter.set_selection(selection) |
---|
[538] | 1010 | |
---|
| 1011 | # Multiple selection |
---|
[953] | 1012 | ASAP> selection.set_if(1) |
---|
| 1013 | ASAP> selection.set_scans([2,4,6,10]) |
---|
| 1014 | ASAP> plotter.set_selection(selection) |
---|
| 1015 | |
---|
[538] | 1016 | \end{verbatim} |
---|
| 1017 | |
---|
[544] | 1018 | \subsection{Plot Control} |
---|
| 1019 | |
---|
[794] | 1020 | \index{Plotter!control}The plotter window has a row of buttons on the |
---|
| 1021 | lower left. These can be used to control the plotter (mostly for |
---|
| 1022 | zooming the individual plots). From left to right: |
---|
[534] | 1023 | |
---|
| 1024 | \begin{itemize} |
---|
| 1025 | |
---|
| 1026 | \item[Home] This will unzoom the plots to the original zoom factor |
---|
| 1027 | |
---|
| 1028 | \item[Plot history] (left and right arrow). The plotter keeps a |
---|
| 1029 | history of zoom settings. The left arrow sets the plot zoom to the |
---|
| 1030 | previous value. The right arrow returns back again. This allows you, |
---|
| 1031 | for example, to zoom in on one feature then return the plot to how it |
---|
| 1032 | was previously. |
---|
| 1033 | |
---|
| 1034 | \item[Pan] (The Cross) This sets the cursor to pan, or scroll mode |
---|
[953] | 1035 | allowing you to shift the plot within the window. Useful when |
---|
| 1036 | zoomed in on a feature. |
---|
[534] | 1037 | |
---|
| 1038 | \item[Zoom] (the letter with the magnifying glass) lets you draw a |
---|
[953] | 1039 | rectangle around a region of interest then zooms in on that |
---|
| 1040 | region. Use the plot history to unzoom again. |
---|
[534] | 1041 | |
---|
[953] | 1042 | \item[Adjust] (rectangle with 4 arrows) adjust subplot paramaters |
---|
| 1043 | (space at edge of plots) |
---|
| 1044 | |
---|
[534] | 1045 | \item[Save] (floppy disk). Save the plot as a postscript or .png file |
---|
| 1046 | |
---|
[794] | 1047 | You can also type ``g'' in the plot window to toggle on and off grid |
---|
| 1048 | lines. Typing 'l' turns on and off logarithmic Y-axis. |
---|
| 1049 | |
---|
[534] | 1050 | \end{itemize} |
---|
| 1051 | |
---|
| 1052 | \subsection{Other control} |
---|
| 1053 | |
---|
| 1054 | The plotter has a number of functions to describe the layout of the |
---|
| 1055 | plot. These include \cmd{set\_legend}, \cmd{set\_layout} and \cmd{set\_title}. |
---|
| 1056 | |
---|
| 1057 | To set the exact velocity or channel range to be plotted use the |
---|
| 1058 | \cmd{set\_range} function. To reset to the default value, call |
---|
| 1059 | \cmd{set\_range} with no arguments. E.g. |
---|
| 1060 | |
---|
| 1061 | \begin{verbatim} |
---|
| 1062 | ASAP> scans.set_unit('km/s') |
---|
| 1063 | ASAP> plotter.plot(scans) |
---|
| 1064 | ASAP> plotter.set_range(-150,-50) |
---|
[544] | 1065 | ASAP> plotter.set_range() # To reset |
---|
[534] | 1066 | \end{verbatim} |
---|
| 1067 | |
---|
[544] | 1068 | Both the range of the ``x'' and ``y'' axis can be set at once, if desired: |
---|
| 1069 | |
---|
| 1070 | \begin{verbatim} |
---|
| 1071 | ASAP> plotter.set_range(-10,30,-1,6.6) |
---|
| 1072 | \end{verbatim} |
---|
| 1073 | |
---|
[738] | 1074 | To save a hardcopy of the current plot, use the save function, e.g. |
---|
[534] | 1075 | |
---|
| 1076 | \begin{verbatim} |
---|
| 1077 | ASAP> plotter.save('myplot.ps') |
---|
| 1078 | \end{verbatim} |
---|
| 1079 | |
---|
| 1080 | \section{Fitting} |
---|
| 1081 | |
---|
[794] | 1082 | \index{Fitting}Currently multicomponent Gaussian function is |
---|
| 1083 | available. This is done by creating a fitting object, setting up the |
---|
| 1084 | fit and actually fitting the data. Fitting can either be done on a |
---|
| 1085 | single scantable row/cursor selection or on an entire scantable using |
---|
| 1086 | the \cmd{auto\_fit} function. |
---|
[534] | 1087 | |
---|
| 1088 | \begin{verbatim} |
---|
| 1089 | ASAP> f = fitter() |
---|
| 1090 | ASAP> f.set_function(gauss=2) # Fit two Gaussians |
---|
| 1091 | ASAP> f.set_scan(scans) |
---|
| 1092 | ASAP> scans.set_cursor(0,0,1) # Fit the second polarisation |
---|
| 1093 | ASAP> scans.set_unit('km/s') # Make fit in velocity units |
---|
| 1094 | ASAP> f.fit(1) # Run the fit on the second row in the table |
---|
| 1095 | ASAP> f.plot() # Show fit in a plot window |
---|
| 1096 | ASAP> f.get_parameters() # Return the fit paramaters |
---|
| 1097 | \end{verbatim} |
---|
| 1098 | |
---|
| 1099 | This auto-guesses the initial values of the fit and works well for data |
---|
| 1100 | without extra confusing features. Note that the fit is performed in |
---|
| 1101 | whatever unit the abscissa is set to. |
---|
| 1102 | |
---|
| 1103 | If you want to confine the fitting to a smaller range (e.g. to avoid |
---|
| 1104 | band edge effects or RFI you must set a mask. |
---|
| 1105 | |
---|
| 1106 | \begin{verbatim} |
---|
| 1107 | ASAP> f = fitter() |
---|
| 1108 | ASAP> f.set_function(gauss=2) |
---|
| 1109 | ASAP> scans.set_unit('km/s') # Set the mask in channel units |
---|
| 1110 | ASAP> msk = s.create_mask([1800,2200]) |
---|
| 1111 | ASAP> scans.set_unit('km/s') # Make fit in velocity units |
---|
| 1112 | ASAP> f.set_scan(s,msk) |
---|
| 1113 | ASAP> f.fit() |
---|
| 1114 | ASAP> f.plot() |
---|
| 1115 | ASAP> f.get_parameters() |
---|
| 1116 | \end{verbatim} |
---|
| 1117 | |
---|
[544] | 1118 | If you wish, the initial parameter guesses can be specified and |
---|
| 1119 | specific parameters can be fixed: |
---|
[534] | 1120 | |
---|
| 1121 | \begin{verbatim} |
---|
| 1122 | ASAP> f = fitter() |
---|
| 1123 | ASAP> f.set_function(gauss=2) |
---|
| 1124 | ASAP> f.set_scan(s,msk) |
---|
| 1125 | ASAP> f.fit() # Fit using auto-estimates |
---|
[738] | 1126 | # Set Peak, centre and fwhm for the second gaussian. |
---|
[534] | 1127 | # Force the centre to be fixed |
---|
| 1128 | ASAP> f.set_gauss_parameters(0.4,450,150,0,1,0,component=1) |
---|
| 1129 | ASAP> f.fit() # Re-run the fit |
---|
| 1130 | \end{verbatim} |
---|
| 1131 | |
---|
| 1132 | The fitter \cmd{plot} function has a number of options to either view |
---|
| 1133 | the fit residuals or the individual components (by default it plots |
---|
| 1134 | the sum of the model components). |
---|
| 1135 | |
---|
| 1136 | Examples: |
---|
| 1137 | |
---|
| 1138 | \begin{verbatim} |
---|
| 1139 | # Plot the residual |
---|
[738] | 1140 | ASAP> f.plot(residual=True) |
---|
[534] | 1141 | |
---|
| 1142 | # Plot the first 2 componentsa |
---|
[738] | 1143 | ASAP> f.plot(components=[0,1]) |
---|
[534] | 1144 | |
---|
| 1145 | # Plot the first and third component plus the model sum |
---|
| 1146 | ASAP> f.plot(components=[-1,0,2]) # -1 means the compoment sum |
---|
| 1147 | \end{verbatim} |
---|
| 1148 | |
---|
[544] | 1149 | \subsection{Fit saving} |
---|
| 1150 | |
---|
[794] | 1151 | \index{Fitter!Fit saving}One you are happy with your fit, it is |
---|
| 1152 | possible to store it as part of the scantable. |
---|
[544] | 1153 | |
---|
| 1154 | \begin{verbatim} |
---|
| 1155 | ASAP> f.storefit() |
---|
| 1156 | \end{verbatim} |
---|
| 1157 | |
---|
| 1158 | This will be saved to disk with the data, if the ``ASAP'' file format |
---|
| 1159 | is selected. Multiple fits to the same data can be stored in the |
---|
[738] | 1160 | scantable. |
---|
[544] | 1161 | |
---|
| 1162 | The scantable function \cmd{get\_fit} can be used to retrieve the |
---|
| 1163 | stored fits. Currently the fit parameters are just printed to the |
---|
| 1164 | screen. |
---|
| 1165 | |
---|
| 1166 | \begin{verbatim} |
---|
| 1167 | ASAP> scans.get_fit(4) # Print fits for row 4 |
---|
| 1168 | \end{verbatim} |
---|
| 1169 | |
---|
[534] | 1170 | \section{Polarisation} |
---|
| 1171 | |
---|
[794] | 1172 | \index{Polarisation}Currently ASAP only supports polarmetric analysis |
---|
| 1173 | on linearly polarised feeds and the cross polarisation products |
---|
| 1174 | measured. Other cases will be added on an as needed basic. |
---|
[534] | 1175 | |
---|
[538] | 1176 | Conversions of linears to Stokes or Circular polarisations are done |
---|
[544] | 1177 | ``on-the-fly''. Leakage cannot be corrected for nor are these routines |
---|
[738] | 1178 | able to calibrate position angle offsets. |
---|
[534] | 1179 | |
---|
[538] | 1180 | \subsection{Simple Calibration} |
---|
| 1181 | |
---|
[794] | 1182 | \index{Polarisation!calibration}It is possible that there is a phase |
---|
| 1183 | offset between polarisation which will effect the phase of the cross |
---|
| 1184 | polarisation correlation, and so give rise to spurious |
---|
| 1185 | polarisation. \cmd{rotate\_xyphase} can be used to correct for this |
---|
| 1186 | error. At this point, the user must know how to determine the size of |
---|
| 1187 | the phase offset themselves. |
---|
[538] | 1188 | |
---|
| 1189 | \begin{verbatim} |
---|
[546] | 1190 | ASAP> scans.rotate_xyphase(10.5) # Degrees |
---|
[538] | 1191 | \end{verbatim} |
---|
| 1192 | |
---|
| 1193 | Note that if this function is run twice, the sum of the two values is |
---|
[546] | 1194 | applied because it is done in-situ. |
---|
[538] | 1195 | |
---|
[546] | 1196 | A correction for the receiver parallactic angle may need to be made, |
---|
[953] | 1197 | generally because of how it is mounted. Use \cmd{rotate\_linpolphase} |
---|
| 1198 | to correct the position angle. Running this function twice results in |
---|
| 1199 | the sum of the corrections being applied because it is applied |
---|
| 1200 | in-situ. |
---|
[538] | 1201 | |
---|
| 1202 | \begin{verbatim} |
---|
[953] | 1203 | ASAP> scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting |
---|
| 1204 | \end{verbatim} |
---|
[538] | 1205 | |
---|
[953] | 1206 | If the sign of the complex correlation is wrong (this can happen |
---|
| 1207 | depending on the correlator configuration), use \cmd{invert\_phase} to |
---|
| 1208 | change take the complex conjugate of the complex correlation |
---|
| 1209 | term. This is always performed in-situ. |
---|
| 1210 | |
---|
| 1211 | \begin{verbatim} |
---|
| 1212 | ASAP> scans.invert_phase() |
---|
[538] | 1213 | \end{verbatim} |
---|
| 1214 | |
---|
[953] | 1215 | Depending on how the correlator is configured, ``BA'' may be |
---|
| 1216 | correlated insead of ``AB''. Use \cmd{swap\_linears} to correct for |
---|
| 1217 | this problem: |
---|
| 1218 | |
---|
| 1219 | \begin{verbatim} |
---|
| 1220 | ASAP> scans.swap_linears() |
---|
| 1221 | \end{verbatim} |
---|
| 1222 | |
---|
[538] | 1223 | \subsection{Plotting} |
---|
| 1224 | \label{sec:polplot} |
---|
| 1225 | |
---|
[953] | 1226 | \index{Polarisation!plotting}To plot Stokes values, a selector object |
---|
| 1227 | must be created and the set\_polarisation function used to select the |
---|
| 1228 | desired polarisation products. |
---|
| 1229 | |
---|
| 1230 | The values which can be plotted include a selection of [I,Q,U,V], [I, |
---|
| 1231 | Plinear, Pangle, V], [RR, LL] or [XX, YY, Real(XY), |
---|
[794] | 1232 | Imaginary(XY)]. (Plinear and Pangle are the percentage and position |
---|
| 1233 | angle of linear polarisation). Conversion to circular polarisations |
---|
| 1234 | are currently not available. |
---|
[538] | 1235 | |
---|
| 1236 | Example: |
---|
| 1237 | |
---|
| 1238 | \begin{verbatim} |
---|
[953] | 1239 | ASAP> selection = selector() |
---|
| 1240 | |
---|
| 1241 | ASAP> selection.set_polarisations([``I'', ``Q'', ``U'', ``V'']) |
---|
| 1242 | ASAP plotter.set_selection(selection); # Select I, Q, U \& V |
---|
| 1243 | |
---|
| 1244 | ASAP> selection.set_polarisations([``I'', ``Q'') |
---|
| 1245 | ASAP plotter.set_selection(selection); # Select just I \& Q |
---|
| 1246 | |
---|
| 1247 | ASAP> selection.set_polarisations([``RR'', ``LL'') |
---|
| 1248 | ASAP plotter.set_selection(selection); # Select just RR \& LL |
---|
| 1249 | |
---|
| 1250 | ASAP> selection.set_polarisations([``XX'', ``YY'') |
---|
| 1251 | ASAP plotter.set_selection(selection); # Select linears |
---|
| 1252 | |
---|
| 1253 | ASAP> selection.set_polarisations([``I'', ``Plinear'') |
---|
| 1254 | ASAP plotter.set_selection(selection); # Select linears |
---|
| 1255 | |
---|
[538] | 1256 | \end{verbatim} |
---|
| 1257 | |
---|
[953] | 1258 | Scan, beam and IF selection are also available in the selector object as |
---|
| 1259 | describe in section~\ref{sec:selection}. |
---|
[538] | 1260 | |
---|
| 1261 | \subsection{Saving} |
---|
| 1262 | |
---|
[794] | 1263 | \index{Polarisation!saving}When saving data using the \cmd{save} |
---|
| 1264 | function, the \cmd{stokes} argument can be used to save the data as |
---|
| 1265 | Stoke values when saving in FITS format. |
---|
[538] | 1266 | |
---|
| 1267 | Example: |
---|
| 1268 | |
---|
| 1269 | \begin{verbatim} |
---|
| 1270 | ASAP> scans.save('myscan.sdfits', 'SDFITS', stokes=True) |
---|
| 1271 | \end{verbatim} |
---|
| 1272 | |
---|
[534] | 1273 | |
---|
[770] | 1274 | \section{Scantable Mathematics} |
---|
| 1275 | |
---|
[794] | 1276 | \index{Scantable!maths}It is possible to to simple mathematics |
---|
| 1277 | directly on scantables from the command line using the \cmd{+, -, *, |
---|
| 1278 | /} operators as well as their cousins \cmd{+=, -= *=, /=}. This works |
---|
| 1279 | between two scantables or a scantable and a float. (Note that it does |
---|
| 1280 | not work for integers). |
---|
[770] | 1281 | |
---|
[534] | 1282 | \begin{verbatim} |
---|
[770] | 1283 | ASAP> sum = scan1+scan2 |
---|
| 1284 | ASAP> scan2 = scan1+2.0 |
---|
| 1285 | ASAP> scan *= 1.05 |
---|
| 1286 | \end{verbatim} |
---|
| 1287 | |
---|
| 1288 | \section{Scripting} |
---|
| 1289 | |
---|
[794] | 1290 | \index{Scripting}Because asap is based on python, it easy for the user |
---|
| 1291 | write their own scripts and functions to process data. This is highly |
---|
| 1292 | recommended as most processing of user data could then be done in a |
---|
| 1293 | couple of steps using a few simple user defined functions. A Python |
---|
| 1294 | primer is beyond the scope of this userguide. See the asap home pages |
---|
| 1295 | for a scripting tutorial or the main python website for comprehensive |
---|
| 1296 | documentation. |
---|
[770] | 1297 | |
---|
| 1298 | \hspace{1cm} http://www.atnf.csiro.au/computing/software/asap/tutorials |
---|
[953] | 1299 | |
---|
[770] | 1300 | \hspace{1cm} http://www.python.org/doc/Introduction.html |
---|
| 1301 | |
---|
| 1302 | \subsection{Running scripts} |
---|
| 1303 | |
---|
| 1304 | The asap global function \cmd{execfile} reads the named text file and |
---|
| 1305 | executes the contained python code. This file can either contain |
---|
| 1306 | function definitions which will be used in subsequent processing or |
---|
| 1307 | just a set of commands to process a specific dataset. |
---|
| 1308 | |
---|
| 1309 | \subsection{asapuserfuncs.py} |
---|
| 1310 | |
---|
| 1311 | The file $\sim$/.asap/asapuserfuncs.py is automatically read in when |
---|
| 1312 | asap is started. The user can use this to define a set of user |
---|
| 1313 | functions which are automatically available each time asap is |
---|
| 1314 | used. The \cmd{execfile} function can be called from within this file. |
---|
| 1315 | |
---|
| 1316 | \section{Worked examples} |
---|
| 1317 | |
---|
| 1318 | In the following section a few examples of end-to-end processing of |
---|
[794] | 1319 | some data in asap are given. |
---|
[770] | 1320 | |
---|
| 1321 | \subsection{Mopra} |
---|
[794] | 1322 | \index{Mopra} |
---|
[770] | 1323 | |
---|
[794] | 1324 | The following example is of some dual polarisation, position switched |
---|
| 1325 | data from Mopra. The source has been observed mulitple times split |
---|
| 1326 | into a number of seperate rpfits files. To make the processing easier, |
---|
| 1327 | the first step is to \cmd{cat} the seeprate rpfits files together and |
---|
| 1328 | load as a whole (future versions of asap will make this unnecessary). |
---|
| 1329 | |
---|
| 1330 | |
---|
| 1331 | \begin{verbatim} |
---|
| 1332 | # Concatenate the individual rpfits files together before loading |
---|
| 1333 | !cat 2005-06*.rpf > data.rpf |
---|
| 1334 | |
---|
| 1335 | # Load the data into a scantable |
---|
| 1336 | data = scantable('data.rpf') |
---|
| 1337 | print data |
---|
| 1338 | |
---|
| 1339 | # Form the quotient spectra |
---|
| 1340 | q = data.auto_quotient() |
---|
| 1341 | print q |
---|
| 1342 | |
---|
| 1343 | # Look at the spectra |
---|
| 1344 | plotter.plot(q) |
---|
| 1345 | |
---|
| 1346 | # Velocity align the data before averaging |
---|
| 1347 | q.set_unit('km/s') |
---|
| 1348 | q.set_freqframe('LSRK') |
---|
| 1349 | q.freq_align() |
---|
| 1350 | |
---|
| 1351 | # Average all scans in time |
---|
| 1352 | av = q.average_time() |
---|
| 1353 | plotter.plot(av) |
---|
| 1354 | |
---|
| 1355 | # Remove the baseline |
---|
| 1356 | msk = av.create_mask([100,130],[160,200]) |
---|
| 1357 | av.poly_baseline(msk,2) |
---|
| 1358 | |
---|
| 1359 | # Average the two polarisations together |
---|
| 1360 | iav = av.average_pol() |
---|
| 1361 | print iav |
---|
| 1362 | plotter.plot(iav) |
---|
| 1363 | |
---|
| 1364 | # Set a sensible velocity range on the plot |
---|
| 1365 | plotter.set_range(85,200) |
---|
| 1366 | |
---|
| 1367 | # Smooth the data a little |
---|
| 1368 | av.smooth('gauss',4) |
---|
| 1369 | plotter.plot() |
---|
| 1370 | |
---|
| 1371 | # Fit a guassian to the emission |
---|
| 1372 | f = fitter() |
---|
| 1373 | f.set_function(gauss=1) |
---|
| 1374 | f.set_scan(av) |
---|
| 1375 | f.fit() |
---|
| 1376 | |
---|
| 1377 | # View the fit |
---|
| 1378 | f.plot() |
---|
| 1379 | |
---|
| 1380 | # Get the fit parameters |
---|
| 1381 | f.get_parameters() |
---|
| 1382 | |
---|
| 1383 | \end{verbatim} |
---|
| 1384 | |
---|
| 1385 | |
---|
[770] | 1386 | \subsection{Parkes Polarimetry} |
---|
| 1387 | |
---|
[794] | 1388 | \index{Parkes}\index{Polarisation}The following example is processing |
---|
| 1389 | of some Parkes polarmetric observations of OH masers at |
---|
| 1390 | 1.6~GHz. Because digital filters where used in the backend, the |
---|
| 1391 | baselines are stable enough not to require a quotient spectra. The |
---|
| 1392 | 4~MHz bandwidth is wide enough to observe both the 1665 and 1667~MHz |
---|
| 1393 | OH maser transitions. Each source was observed once for about 10 |
---|
| 1394 | minutes. Tsys information was not written to the rpfits file (a |
---|
| 1395 | nominal 25K values was used), so the amplitudes need to be adjusted |
---|
| 1396 | based on a separate log file. A simple user function is used to |
---|
| 1397 | simplify this, contained in a file called mypol.py: |
---|
[770] | 1398 | |
---|
| 1399 | \begin{verbatim} |
---|
| 1400 | def xyscale(data,xtsys=1.0,ytsys=1.0,nomtsys=25.0) : |
---|
| 1401 | |
---|
| 1402 | data.set_cursor(pol=0) |
---|
| 1403 | data.scale(xtsys/nomtsys,allaxes=False) |
---|
| 1404 | |
---|
| 1405 | data.set_cursor(pol=1) |
---|
| 1406 | data.scale(ytsys/nomtsys,allaxes=False) |
---|
| 1407 | |
---|
| 1408 | data.set_cursor(pol=2) |
---|
| 1409 | data.scale((xtsys+ytsys)/(2*nomtsys),allaxes=False) |
---|
| 1410 | |
---|
| 1411 | data.set_cursor(pol=3) |
---|
| 1412 | data.scale((xtsys+ytsys)/(2*nomtsys),allaxes=False) |
---|
| 1413 | \end{verbatim} |
---|
| 1414 | |
---|
| 1415 | The typical asap session would be |
---|
| 1416 | |
---|
| 1417 | \begin{verbatim} |
---|
[794] | 1418 | |
---|
[770] | 1419 | # Remind ourself the name of the rpfits files |
---|
[794] | 1420 | ls |
---|
[770] | 1421 | |
---|
| 1422 | # Load data from an rpfits file |
---|
| 1423 | d1665 = scantable('2005-10-27_0154-P484.rpf') |
---|
| 1424 | |
---|
| 1425 | # Check what we have just loaded |
---|
| 1426 | d1665.summary |
---|
| 1427 | |
---|
| 1428 | # View the data in velocity |
---|
| 1429 | d1665.set_unit('km/s') |
---|
| 1430 | d1665.set_freqframe('LSRK') |
---|
| 1431 | |
---|
| 1432 | # Correct for the known phase offset in the crosspol data |
---|
| 1433 | d1665.rotate_xyphase(-4) |
---|
| 1434 | |
---|
[794] | 1435 | # Create a copy of the data and set the rest frequency to the 1667 MHz |
---|
[770] | 1436 | # transition |
---|
| 1437 | d1667 = d1665.copy() |
---|
| 1438 | d1667.set_restfreqs(lines=['OH1667']) |
---|
| 1439 | d1667.summary |
---|
| 1440 | |
---|
| 1441 | # Copy out the scan we wish to process |
---|
| 1442 | g351_5 = d1665.get_scan('351p160') |
---|
| 1443 | g351_7 = d1667.get_scan('351p160') |
---|
| 1444 | |
---|
| 1445 | # Plot the data |
---|
| 1446 | plotter.plot(g351_5,g351_7) # Only shows one panel |
---|
| 1447 | |
---|
| 1448 | # Tell the plotter to stack polarisation and panel scans |
---|
| 1449 | plotter.set_mode('p','s') |
---|
| 1450 | |
---|
| 1451 | # Correct for the Tsys using our predefined function |
---|
| 1452 | execfile('mypol.py') # Read in the function |
---|
| 1453 | xyscale(g351_5,23.2,22.7) # Execute it on the data |
---|
| 1454 | xyscale(g351_7,23.2,22.7) |
---|
| 1455 | |
---|
| 1456 | # Only plot the velocity range of interest |
---|
| 1457 | plotter.set_range(-30,10) |
---|
| 1458 | |
---|
| 1459 | # Baseline the data |
---|
| 1460 | msk = g351_5.create_mask([-20,-15],[0,5]) |
---|
| 1461 | g351_5.poly_baseline(msk,1) |
---|
| 1462 | msk = g351_7.create_mask([-20,-15],[0,5]) |
---|
| 1463 | g351_7.poly_baseline(msk,1) |
---|
| 1464 | |
---|
| 1465 | # Update the plot with the baselined data |
---|
| 1466 | plotter.plot() |
---|
| 1467 | |
---|
| 1468 | # Look at the various polarisation products |
---|
| 1469 | plotter.set_cursor(pol='RR LL') |
---|
| 1470 | plotter.set_cursor(pol='I Plinear') |
---|
| 1471 | plotter.set_cursor(pol='I Q U V') |
---|
| 1472 | |
---|
| 1473 | # Save the plot as postscript |
---|
| 1474 | plotter.save('g361_stokes.ps') |
---|
| 1475 | |
---|
| 1476 | # Save the process spectra |
---|
| 1477 | g351_5.save('junk5.asap') |
---|
| 1478 | g351_7.save('junk7.asap') |
---|
| 1479 | |
---|
| 1480 | \end{verbatim} |
---|
| 1481 | |
---|
| 1482 | \subsection{Tidbinbilla} |
---|
| 1483 | |
---|
[794] | 1484 | \index{Tidbinbilla}The following example is processing of some |
---|
| 1485 | Tidbinbilla observations of NH$_3$ at 12~mm. Tidbinbilla has (at the |
---|
| 1486 | time of observations) a single polarisation, but can process two IFs |
---|
| 1487 | simultaneously. In the example, the first half of the observation was |
---|
| 1488 | observing the (1,1) and (2,2) transitions simultaneously). The second |
---|
| 1489 | half observed only the (4,4) transition due to bandwidth |
---|
| 1490 | limitations. The data is position switched, observing first an |
---|
| 1491 | reference to the west, then the source twice and finally reference to |
---|
| 1492 | the east. |
---|
[770] | 1493 | |
---|
| 1494 | \begin{verbatim} |
---|
| 1495 | |
---|
| 1496 | # Load the rpfits file and inspect |
---|
| 1497 | d = scantable('2003-03-16_082048_t0002.rpf') |
---|
| 1498 | print d |
---|
| 1499 | |
---|
| 1500 | # Make the quotient spectra |
---|
| 1501 | q = d.auto_quotient() |
---|
| 1502 | print q |
---|
| 1503 | |
---|
| 1504 | # Plot/select in velocity |
---|
| 1505 | q.set_freqframe('LSRK') |
---|
| 1506 | q.set_unit('km/s') |
---|
| 1507 | |
---|
| 1508 | # Seperate data from the (1,1)&(2,2) and (4,4) transitions |
---|
| 1509 | g1 = q.get_scan(range(6)) # Rows 0..5 |
---|
| 1510 | g2 = q.get_scan(range(6,12)) # Rows 6..11 |
---|
| 1511 | |
---|
[794] | 1512 | # Align data in velocity |
---|
[770] | 1513 | g1.freq_align(perif=True) |
---|
| 1514 | g2.freq_align(perif=True) |
---|
| 1515 | |
---|
| 1516 | # Average individual scans |
---|
| 1517 | a1 = g1.average_time() |
---|
| 1518 | a2 = g2.average_time() |
---|
| 1519 | |
---|
| 1520 | # Rpfits file only contrains a single rest frequency. Set both |
---|
| 1521 | a1.set_restfreqs(freqs= [23694.4700e6,23722.6336e6]) |
---|
| 1522 | |
---|
| 1523 | plotter.plot(a1,a2) |
---|
| 1524 | plotter.set_mode('i','s') |
---|
| 1525 | |
---|
| 1526 | a1.auto_poly_baseline() |
---|
| 1527 | a2.auto_poly_baseline() |
---|
| 1528 | |
---|
| 1529 | plotter.plot() |
---|
| 1530 | |
---|
| 1531 | a1.smooth('gauss',5) |
---|
| 1532 | a2.smooth('gauss',5) |
---|
| 1533 | plotter.plot() |
---|
| 1534 | |
---|
| 1535 | \end{verbatim} |
---|
| 1536 | |
---|
| 1537 | \newpage |
---|
| 1538 | |
---|
| 1539 | \section{Appendix} |
---|
| 1540 | |
---|
| 1541 | \subsection{Function Summary} |
---|
| 1542 | |
---|
[794] | 1543 | \index{Functions!summary}% |
---|
[770] | 1544 | \begin{verbatim} |
---|
[738] | 1545 | [The scan container] |
---|
[534] | 1546 | scantable - a container for integrations/scans |
---|
| 1547 | (can open asap/rpfits/sdfits and ms files) |
---|
| 1548 | copy - returns a copy of a scan |
---|
| 1549 | get_scan - gets a specific scan out of a scantable |
---|
| 1550 | summary - print info about the scantable contents |
---|
| 1551 | set_cursor - set a specific Beam/IF/Pol 'cursor' for |
---|
| 1552 | further use |
---|
| 1553 | get_cursor - print out the current cursor position |
---|
| 1554 | stats - get specified statistic of the spectra in |
---|
| 1555 | the scantable |
---|
| 1556 | stddev - get the standard deviation of the spectra |
---|
| 1557 | in the scantable |
---|
| 1558 | get_tsys - get the TSys |
---|
| 1559 | get_time - get the timestamps of the integrations |
---|
[794] | 1560 | get_azimuth - get the azimuth of the scans |
---|
| 1561 | get_elevation - get the elevation of the scans |
---|
| 1562 | get_parangle - get the parallactic angle of the scans |
---|
[534] | 1563 | get_unit - get the currnt unit |
---|
| 1564 | set_unit - set the abcissa unit to be used from this |
---|
| 1565 | point on |
---|
| 1566 | get_abcissa - get the abcissa values and name for a given |
---|
| 1567 | row (time) |
---|
| 1568 | set_freqframe - set the frame info for the Spectral Axis |
---|
| 1569 | (e.g. 'LSRK') |
---|
| 1570 | set_doppler - set the doppler to be used from this point on |
---|
| 1571 | set_instrument - set the instrument name |
---|
| 1572 | get_fluxunit - get the brightness flux unit |
---|
| 1573 | set_fluxunit - set the brightness flux unit |
---|
| 1574 | create_mask - return an mask in the current unit |
---|
| 1575 | for the given region. The specified regions |
---|
| 1576 | are NOT masked |
---|
| 1577 | get_restfreqs - get the current list of rest frequencies |
---|
| 1578 | set_restfreqs - set a list of rest frequencies |
---|
| 1579 | lines - print list of known spectral lines |
---|
| 1580 | flag_spectrum - flag a whole Beam/IF/Pol |
---|
| 1581 | save - save the scantable to disk as either 'ASAP' |
---|
| 1582 | or 'SDFITS' |
---|
| 1583 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
---|
| 1584 | history - print the history of the scantable |
---|
[544] | 1585 | get_fit - get a fit which has been stored witnh the data |
---|
[738] | 1586 | average_time - return the (weighted) time average of a scan |
---|
[534] | 1587 | or a list of scans |
---|
| 1588 | average_pol - average the polarisations together. |
---|
| 1589 | The dimension won't be reduced and |
---|
| 1590 | all polarisations will contain the |
---|
| 1591 | averaged spectrum. |
---|
[738] | 1592 | auto_quotient - return the on/off quotient with |
---|
| 1593 | automatic detection of the on/off scans |
---|
[534] | 1594 | quotient - return the on/off quotient |
---|
| 1595 | scale - return a scan scaled by a given factor |
---|
[738] | 1596 | add - return a scan with given value added |
---|
[534] | 1597 | bin - return a scan with binned channels |
---|
| 1598 | resample - return a scan with resampled channels |
---|
| 1599 | smooth - return the spectrally smoothed scan |
---|
| 1600 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
---|
[738] | 1601 | auto_poly_baseline - automatically fit a polynomial baseline |
---|
[794] | 1602 | recalc_azel - recalculate azimuth and elevation based on |
---|
| 1603 | the pointing |
---|
[534] | 1604 | gain_el - apply gain-elevation correction |
---|
| 1605 | opacity - apply opacity correction |
---|
| 1606 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
| 1607 | units |
---|
| 1608 | freq_align - align spectra in frequency frame |
---|
| 1609 | rotate_xyphase - rotate XY phase of cross correlation |
---|
| 1610 | rotate_linpolphase - rotate the phase of the complex |
---|
| 1611 | polarization O=Q+iU correlation |
---|
| 1612 | [Math] Mainly functions which operate on more than one scantable |
---|
| 1613 | |
---|
[738] | 1614 | average_time - return the (weighted) time average |
---|
[534] | 1615 | of a list of scans |
---|
| 1616 | quotient - return the on/off quotient |
---|
[544] | 1617 | simple_math - simple mathematical operations on two scantables, |
---|
| 1618 | 'add', 'sub', 'mul', 'div' |
---|
[534] | 1619 | [Fitting] |
---|
| 1620 | fitter |
---|
| 1621 | auto_fit - return a scan where the function is |
---|
| 1622 | applied to all Beams/IFs/Pols. |
---|
| 1623 | commit - return a new scan where the fits have been |
---|
| 1624 | commited. |
---|
| 1625 | fit - execute the actual fitting process |
---|
[544] | 1626 | store_fit - store the fit paramaters in the data (scantable) |
---|
[534] | 1627 | get_chi2 - get the Chi^2 |
---|
| 1628 | set_scan - set the scantable to be fit |
---|
| 1629 | set_function - set the fitting function |
---|
| 1630 | set_parameters - set the parameters for the function(s), and |
---|
| 1631 | set if they should be held fixed during fitting |
---|
[544] | 1632 | set_gauss_parameters - same as above but specialised for individual |
---|
| 1633 | gaussian components |
---|
[534] | 1634 | get_parameters - get the fitted parameters |
---|
| 1635 | plot - plot the resulting fit and/or components and |
---|
| 1636 | residual |
---|
| 1637 | [Plotter] |
---|
| 1638 | asapplotter - a plotter for asap, default plotter is |
---|
| 1639 | called 'plotter' |
---|
| 1640 | plot - plot a (list of) scantable |
---|
| 1641 | save - save the plot to a file ('png' ,'ps' or 'eps') |
---|
| 1642 | set_mode - set the state of the plotter, i.e. |
---|
| 1643 | what is to be plotted 'colour stacked' |
---|
| 1644 | and what 'panelled' |
---|
[544] | 1645 | set_cursor - only plot a selected part of the data |
---|
| 1646 | set_range - set a 'zoom' window |
---|
[534] | 1647 | set_legend - specify user labels for the legend indeces |
---|
| 1648 | set_title - specify user labels for the panel indeces |
---|
| 1649 | set_ordinate - specify a user label for the ordinate |
---|
| 1650 | set_abcissa - specify a user label for the abcissa |
---|
| 1651 | set_layout - specify the multi-panel layout (rows,cols) |
---|
[738] | 1652 | |
---|
[534] | 1653 | [Reading files] |
---|
| 1654 | reader - access rpfits/sdfits files |
---|
| 1655 | read - read in integrations |
---|
| 1656 | summary - list info about all integrations |
---|
| 1657 | |
---|
| 1658 | [General] |
---|
| 1659 | commands - this command |
---|
| 1660 | print - print details about a variable |
---|
| 1661 | list_scans - list all scantables created bt the user |
---|
| 1662 | del - delete the given variable from memory |
---|
| 1663 | range - create a list of values, e.g. |
---|
| 1664 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
| 1665 | help - print help for one of the listed functions |
---|
[538] | 1666 | execfile - execute an asap script, e.g. execfile('myscript') |
---|
[544] | 1667 | list_rcparameters - print out a list of possible values to be |
---|
[770] | 1668 | put into \$HOME/.asaprc |
---|
[534] | 1669 | mask_and,mask_or, |
---|
| 1670 | mask_not - boolean operations on masks created with |
---|
| 1671 | scantable.create_mask |
---|
[738] | 1672 | |
---|
[534] | 1673 | Note: |
---|
| 1674 | How to use this with help: |
---|
| 1675 | # function 'summary' |
---|
| 1676 | [xxx] is just a category |
---|
[544] | 1677 | Every 'sub-level' in this list should be replaces by a '.' Period when |
---|
[738] | 1678 | using help |
---|
[534] | 1679 | Example: |
---|
| 1680 | ASAP> help scantable # to get info on ths scantable |
---|
| 1681 | ASAP> help scantable.summary # to get help on the scantable's |
---|
| 1682 | ASAP> help average_time |
---|
[544] | 1683 | |
---|
[534] | 1684 | \end{verbatim} |
---|
| 1685 | |
---|
| 1686 | \subsection{ASCII output format} |
---|
| 1687 | |
---|
| 1688 | \subsection{.asaprc settings} |
---|
[794] | 1689 | \index{.asaprc} |
---|
[770] | 1690 | \asaprc{verbose}{{\bf True}/False}{Print verbose output} |
---|
| 1691 | |
---|
| 1692 | \asaprc{insitu}{{\bf True}/False}{Apply operations on the input |
---|
| 1693 | scantable or return new one} |
---|
| 1694 | |
---|
| 1695 | % plotting |
---|
| 1696 | |
---|
| 1697 | \asaprc{useplotter}{{\bf True}/False}{Preload a default plotter} |
---|
| 1698 | |
---|
| 1699 | \asaprc{plotter.gui}{{\bf True}/False}{Do we want a GUI or plot to a |
---|
| 1700 | file} |
---|
| 1701 | |
---|
| 1702 | \asaprc{plotter.stacking}{{\bf Pol} Beam IF Scan Time}{Default mode for |
---|
| 1703 | colour stacking} |
---|
| 1704 | |
---|
| 1705 | \asaprc{plotter.panelling}{Pol Beam IF {\bf Scan} Time}{Default mode |
---|
| 1706 | for panelling} |
---|
| 1707 | |
---|
| 1708 | \asaprc{plotter.ganged}{{\bf True}/False}{Push panels together, to |
---|
| 1709 | share axislabels} |
---|
| 1710 | |
---|
| 1711 | \asaprc{plotter.decimate}{True/{\bf False}}{Decimate the number of |
---|
| 1712 | points plotted by a factor of nchan/1024} |
---|
| 1713 | |
---|
| 1714 | % default colours/linestyles |
---|
| 1715 | %\asaprc{plotter.colours}{.}{.} |
---|
| 1716 | %\asaprc{plotter.linestyles{.}{.} |
---|
| 1717 | |
---|
| 1718 | % scantable |
---|
| 1719 | \asaprc{scantable.save}{{\bf ASAP} SDFITS FITS ASCII MS2}{Default output |
---|
[794] | 1720 | format when saving} |
---|
[770] | 1721 | |
---|
| 1722 | \asaprc{scantable.autoaverage}{{\bf True}/False}{Auto averaging on |
---|
| 1723 | read} |
---|
| 1724 | |
---|
| 1725 | \asaprc{scantable.freqframe}{{\bf LSRK} TOPO BARY etc}{default |
---|
| 1726 | frequency frame to set when function scantable.set\_freqframe is |
---|
| 1727 | called} |
---|
| 1728 | |
---|
| 1729 | \asaprc{scantable.allaxes}{{\bf True}/False}{Apply action to all axes |
---|
| 1730 | not just the cursor location} |
---|
| 1731 | |
---|
| 1732 | \asaprc{scantable.plotter}{{\bf True}/False}{Use internal plotter} |
---|
| 1733 | |
---|
| 1734 | \asaprc{scantable.verbosesummary}{True/{\bf False}}{Control the level |
---|
| 1735 | of information printed by summary} |
---|
| 1736 | |
---|
[953] | 1737 | \subsection{Installation} |
---|
| 1738 | |
---|
| 1739 | \index{Installation}ASAP depends on a number of third-party libraries which you must |
---|
| 1740 | have installed before attempting to build ASAP. These are: |
---|
| 1741 | |
---|
| 1742 | \begin{itemize} |
---|
| 1743 | \item AIPS++ |
---|
| 1744 | \item Boost |
---|
| 1745 | \item Matplotlib |
---|
| 1746 | \item python/ipython |
---|
| 1747 | \end{itemize} |
---|
| 1748 | |
---|
| 1749 | Debian Linux is currently supported and we intend also |
---|
| 1750 | to support other popular Linux flavours, Solaris and Mac. |
---|
| 1751 | |
---|
| 1752 | Of the dependencies, AIPS++ is the most complex to install. |
---|
| 1753 | |
---|
[794] | 1754 | \printindex |
---|
| 1755 | |
---|
[534] | 1756 | \end{document} |
---|
[770] | 1757 | |
---|