ATNF Spectral Analysis Package User Guide v2.2
Contents
1. O Correct for gain el effects q recalc_azel Tid does not write the elevation q gain_el q opacity 0 05 Seperate data from the 1 1 amp 2 2 and 4 4 transitions g1 q get_scan range 6 scans 0 5 g2 q get_scan range 6 12 scans 6 11 Align data in velocity gi freq_align g2 freq_align Average individual scans al gl average_time a2 g2 average_time Rpfits file only contains a single rest frequency Set both a1 set_restfreqs 23694 4700e6 23722 6336e6 plotter plot a1 plotter set_mode i t al auto_poly_baseline plotter plot a1 smooth gauss 5 33 plotter plot 34 17 Appendix 17 1 Function Summary The scan container scantable copy get_scan S drop_scan set_selection get_selection summary stats stddev get_tsys S get_time get_sourcename get_azimuth get_elevation get_parangle get_unit set_unit get_abcissa get_column_names set_freqframe set_doppler set_dirframe z set_instrument set_feedtype get_fluxunit set_fluxunit create_mask get_restfreqs set_restfreqs flag a container for integrations scans can open asap rpfits sdfits and ms files returns a copy of a scan gets a specific scan out of a scantable by name or number drops a specific scan out of a scantable by number set a new subselection of the data get the current selection ob2. ASAP gt ss scans copy 8 Data Output ASAP can save scantables in a variety of formats suitable for reading into other packages The formats are 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 SDFITS The Single Dish FITS format This format was designed to for interchange between packages but few packages actually can read it ASCII A simple text based format suitable for the user to processing using Perl or Python gnuplot etc MS2 Saves the data in an aips MeasurementSet V2 format You can also access this with the Table browser and other AIPS tools The default output format can be set in the users asaprc file Typical usages are ASAP gt scans save myscans Save in default format ASAP gt scans save myscans overwrite True Overwrite an existing file 16 9 Plotter Scantable spectra can be plotted at any time An asapplotter object is used for plotting meaning multiple plot windows can be active at the same time On start up a default asapplotter object is created called plotter This would normally be used for standard plotting The plotter optionally will run in a
3. 3223 3 9494 CH 701 6811 0441 7 1641 21 CH 724 7709 0456 7 3912 CH 3263 7940 1000 6 3501 CH 3335 4810 1000 6 0304 To load a line catalog then save it in the internal format ASAP gt jpl linecatalog jpl_pruned txt ASAP gt jpl save jpl tbl Later the saved line catalog can reloaded ASAP gt jpl linecatalog jpl tbl NOTE Due to a bug in ipython if you do not del the linecatalog table before quiting asap you will be left with temporary files It is safe to delete these once asap has finished 10 2 Line selection The linecatalog has a number of selection functions to select a range of lines from a larger catalog the JPL catalog has gt 180000 lines for example set_frequency_limits selects on frequency range set_strength limits selects on intensity while set_name selects on molecule name wild cards allowed The summary function lists the currently selected lines ASAP gt jpl linecatalog jpl tbl ASAP gt jpl set_frequency_limits 80 115 GHz Lines for 3mm receiver ASAP gt jpl set_name 0H Select all alcohols ASAP gt jpl set_name OH Select only OH molecules ASAP gt jpl summary ASAP gt jpl reset Selections are accumulative ASAP gt jpl set_frequency_limits 80 115 GHz ASAP gt jpl set_strength_limits 2 10 Select brightest lines ASAP gt jpl summary 10 3 Using Linecatalog The line catalogs can be used for line overlays on the plotter or
4. if each beam has observed the source multiple times you will need to use the selector object multiple times to select a single MX cycle run mx_quotient for each cycle then merge the resulting scan tables back together Example ASAP gt scans scantable mydata rpf ASAP gt q scans mx_quotient ASAP gt plotter plot q The function average_beam averages multiple beam data together This is need if MX mode has been used to make a long integration on a single source E g ASAP gt av q average_beam 13 2 Frequency Switching FILL ME IN 13 3 Disk Based Processing Normally scantables exist entirely in memory during an ASAP session This has the ad vantage of speed but causes limits on the size of the dataset which can be loaded ASAP can use disk based scan tables which cache the bulk of the scantable on disk and require significantly less memory usage This should be used for all MOPS data To use disk based tables you either need to change the default in your asaprc file e g 27 scantable storage disk or use set the rc value while running asap to change this on the fly E g ASAP gt rc scantable storage disk ASAP gt data scantable data rpf Loaded using disk based table ASAP gt rc scantable storage memory Memory tables will be used now Changing the rc value affects the next time the scantable constructor is called NOTE Currently a bug in ipython
5. one reference for multiple sources Auto quotient assumes reference scans have a trailing _R in the source name for data from Parkes and Mopra and a trailing e or w for data from Tidbinbilla This functions has two modes paired the default which assumes matching adjacent pairs of source reference scans and time which finds the closest reference scan in time ASAP gt q s auto_quotient By default the quotient spectra is calculated to preserve continuum emission If you wish to remove the continuum contribution use the preserve argument ASAP gt q s auto_quotient preserve True If this is not sufficient the following alternative method can be used 6 2 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 ASAP gt r scans get_scan _R ASAP gt s scans get_scan _R For Tidbinbilla data ASAP gt r scans get_scan _ ew ASAP gt s scans get_scan _ ew 6 3 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 ASAP gt av q average_time If for some you want
6. situ A correction for the receiver parallactic angle may need to be made generally because of how it is mounted Use 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 25 ASAP gt scans rotate_linpolphase 45 Degrees correct for receiver mounting If the sign of the complex correlation is wrong this can happen depending on the correlator configuration use invert_phase to change take the complex conjugate of the complex correlation term This is always performed in situ ASAP gt scans invert_phase Depending on how the correlator is configured BA may be correlated instead of AB Use swap_linears to correct for this problem ASAP gt scans swap_linears 12 2 Conversion Data can be permanently converted between linear and circular polarisations and stokes ASAP gt stokescans linearscans convert_pol stokes 12 3 Plotting To plot Stokes values a selector object must be created and the set_polarisation function used to select the desired polarisation products The values which can be plotted include a selection of I Q U V I Plinear Pangle V RR LL or XX YY Real XY Imaginary XY Plinear and Pangle are the percentage and position angle of linear polarisation Example ASAP gt selection selector ASAP gt selection set_polarisations I Q U V ASAP plotter set_se
7. to average multiple sets of scantables together you can ASAP gt av average_time q1 q2 q3 11 The default is to use integration time weighting The alternative is to use none variance Tsys weighting Tsys amp integration time or median averaging ASAP gt av average_time q weight tintsys To use variance based weighting you need to supply a mask saying which channel range you want it to calculate the variance from ASAP gt msk scans create_mask 200 400 600 800 ASAP gt av average_time scans mask msk weight var If you have not observed your data with Doppler tracking or run freq_align explicitly you should align the data in frequency before averaging ASAP gt av scans average_time align True Note that if needed you should run gain_el and opacity before you average the data in time 6 6 5 amp 6 7 6 4 Baseline fitting To make a baseline fit you must first create a mask of channels to use in the baseline fit ASAP gt msk scans create_mask 100 400 600 900 ASAP gt scans poly_baseline msk order 1 This will fit a first order polynomial to the selected channels and subtract this polynomial from the full spectra 6 4 1 Auto baselining The function auto_poly_baseline can be used to automatically baseline your data without having to specify channel ranges for the line free data It automatically figures out the line free emission and fits a polynomial baseline to that da
8. 22 7 Only plot the velocity range of interest plotter set_range 30 10 Update the plot with the baselined data plotter plot Look at the various polarisation products selection selector selection set_polarisations RR LL plotter set_selection selection selection set_polarisations I Plinear plotter set_selection selection selection set_polarisations I Q U V plotter set_selection selection Save the plot as postscript plotter save g351_stokes ps Save the process spectra plotscans save g351 asap 16 3 Tidbinbilla The following example is processing of some Tidbinbilla observations of NH3 at 12 mm Tidbinbilla has at the time of observations a single polarisation but can process two IFs simultaneously In the example the first half of the observation was observing the 1 1 and 2 2 transitions simultaneously The second half observed only the 4 4 transition due to bandwidth limitations The data is position switched observing first an reference to 32 the west then the source twice and finally reference to the east Important to note that auto_quotient should be executed using the mode time Load the rpfits file and inspect d scantable 2003 03 16_082048_t0002 rpf print d Make the quotient spectra q d auto_quotient mode time print q del d Plot select in velocity set_freqframe LSRK q set_unit km s
9. 23 75 GHz ASAP gt data scantable data rpf ASAP gt data set_restfreqs jpl If a larger linecatalog is used individual elements can be used Use the summary to get the index number of the rest frequency you wish to use E g ASAP gt jpl summary ASAP gt data set_restfreqs jp1 11 jp1 21 For data with many IFs such as from MOPS the user it is recommended that the user creates their own line cstalog for the data and use this to set the rest frequency for each IF 11 Fitting Currently multicomponent Gaussian function is available This is done by creating a fitting object setting up the fit and actually fitting the data Fitting can either be done on a single scantable selection or on an entire scantable using the auto_fit function If single value fitting is used and the current selection includes multiple spectra beams IFs scans etc then the first spectrum in the scantable will be used for fitting ASAP gt f fitter ASAP gt f set_function gauss 2 Fit two Gaussians 23 ASAP gt f set_scan scans ASAP gt selection selector ASAP gt selection set_polarisations 1 Fit the second polarisation ASAP gt scans set_selection selection ASAP gt scans set_unit km s Make fit in velocity units ASAP gt f fit 1 Run the fit on the second row in the table ASAP gt f plot Show fit in a plot window ASAP gt f get_parameters Return the fit paramaters This auto guesses the initial
10. ATNF Spectral Analysis Package User Guide v2 2 Chris Phillips August 16 2007 1 Introduction ASAP is a single dish spectral line processing package currently being developed by the ATNF It is intended to process data from all ATNF antennas and can probably be used for other antennas if they can produce Single Dish FITS format It is based on the AIPS package This userguide has been updated for the ASAP 2 2 Please report any mistakes you find 2 Installation and Running Currently there are installations running on Linux machines at e Epping use hosts draco or hydra e Narrabri use host kaputar e Parkes use host e Mopra use host minos or kaputar if at Narrabri Or use your own Linux desktop Note ASAP2 2 only runs on ATNF Linux machines which have been updated to Debian Sarge and are using the DEBIANSarge usr local If your favourite machine has not been upgraded send a request to your friendly IT support To start asap log onto one of these Linux hosts and enter gt cd my data directory gt asap This starts ASAP To quit you need to type d control d or type Exit 3 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 3 1 Inte
11. ake a set of kwargs commands These can be used to set colour linewidth fontsize etc These are standard matplotlib settings Common ones include color facecolor edgecolor width linewidth fontsize fontname Sans Helvetica Courier Times etc rotation Text rotation horizontal vertical alpha The alpha transparency on 0 1 scale Examples ASAP gt plotter axhline 6 0 0 2 0 8 color red linewidth 3 ASAP gt plotter text 10 7 CO fontsize 20 10 Line Catalog ASAP can load and manipulate line catlogs to retrieve rest frequencies for set_restfreqs and for line identification in the plotter All line catalogs are loaded into a linecatalog object No line catalogs are built into ASAP the user must load a ASCII based table which can optionally be saved in an internal format either of the users own creation or a standard line catalog such as the JPL line catalog or Lovas The ATNF asap ftp area as copies of the JPL and Lovas catalog in the appropriate format ftp ftp atnf csiro au pub software asap data 10 1 Loading a Line Catalog The ASCII text line catalog must have at least 4 columns The first four columns must contain in order Molecule name frequency in MHz frequency error and intensity any units If the molecule name contains any spaces they must be wrapped in quotes A sample from the JPL line catalog H2D 3955 2551 228 8818 7 1941 H2D 12104 7712 177 1558 6 0769 H2D 45809 2731 118
12. ands to process a specific dataset As an alternative to run scripts without entering ASAP create a script which starts with 28 from asap import lt your code gt And run it with python scriptname 15 2 asapuserfuncs py The file asap asapuserfuncs py is automatically read in when ASAP is started The user can use this to define a set of user functions which are automatically available each time ASAP is used The execfile function can be called from within this file 16 Worked examples In the following section a few examples of end to end processing of some data in ASAP are given 16 1 Mopra The following example is of some dual polarisation position switched data from Mopra The source has been observed multiple times split into a number of separate RPFITS files To make the processing easier the first step is to cat the separate RPFITS files together and load as a whole future versions of ASAP will make this unnecessary get a list of the individual rpfits files in the current directory myfiles list_files Load the data into a scantable data scantable myfiles print data Form the quotient spectra q data auto_quotient print q Look at the spectra plotter plot q Set unit and reference frame q set_unit km s q set_freqframe LSRK Average all scans in time aligning in velocity av q average_time align True plotter plot av 29 Remove the baseline msk a
13. be applied to different IFs To use a mask on such data the selector should be applied to select all IFs with the same number of channels Example Select channel range for baselining ASAP gt scans set_unit channel ASAP gt msk scans create_mask 100 400 600 800 Select velocity range for fitting ASAP gt scans set_unit km s ASAP gt msk scans create_mask 30 10 Sometimes it is more convenient to specify the channels to be excluded rather included You can do this with the invert argument Example ASAP gt scans set_unit channel ASAP gt msk scans create_mask 0 100 900 1023 invert True By default 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 ASAP gt scans set_unit km s ASAP gt msk q create_mask 30 10 row 5 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 ASAP gt scans set_unit channel ASAP gt msk1 q create_mask 0 100 511 511 900 1023 invert True ASAP gt scans set_unit km s ASAP gt msk2 q create_mask 20 10 invert True ASAP gt mask mski and msk2 4 4 Management During processing it is pos
14. ble manipulation While it is very useful to have many independent sources within one scantable it is often inconvenient for data processing The get_scan function can be used to create a new scantable with a selection of scans from a scantable The selection can either be on the source name with simple wildcard matching or set of scan ids Internally this uses the selector object so for more complicated selection the selector should be used directly instead For example ASAP gt ss scans get_scan 10 Get the 11th scan zero based ASAP gt ss scans get_scan range 10 Get the first 10 scans 15 ASAP gt ss scans get_scan range 10 20 Get the next 10 scans ASAP gt ss scans get_scan 2 4 6 8 10 Get a selection of scans ASAP gt ss scans get_scan 345p407 Get a specific source ASAP gt ss scans get_scan 345 Get a few sources ASAP gt r scans get_scan _R Get all reference sources Parkes Mopra ASAP gt s scans get_scan _R Get all program sources Parkes Mopra ASAP gt r scans get_scan ew Get all reference sources Tid ASAP gt s scans get_scan ew Get all program sources Tid One can also apply the inverse of get_scan drop_scan To copy a scantable the following does not work ASAP gt ss scans as this just creates a reference to the original scantable Any changes made to ss are also seen in scans To duplicate a scantable use the copy function
15. colors 0000 blue FFOOFF set_linestyles Change the line styles used for plots Allowable values are line dashed dotted dashdot dashdotdot and dashdashdot Example ASAP gt plotter set_linestyles line dash cotted datshot ASAP gt plotter set_font size 10 set_font Change the font style and size Example ASAP gt plotter set_font weight bold ASAP gt plotter set_font size 10 ASAP gt plotter set_font style italic set_layout Change the multi panel layout i e now many rows and columns ASAP gt plotter set_layout 3 2 19 set_legend Set the position size and optional value of the legend ASAP gt plotter set_legend fontsize 16 ASAP gt plotter set_legend mode 0 ASAP chooses where to put the legend ASAP gt plotter set_legend mode 4 Put legend on lower right ASAP gt plotter set_legend mode 1 No legend ASAP gt plotter set_legend mp RR LL Specify legend labels ASAP gt plotter set_legend mp r 12 CO r 13 CO Latex labels set_title Set the plot title If multiple panels are plotted multiple titles have to be specified ASAP gt plotter set_title G323 12 1 79 ASAP gt plotter set_title Si0 Methanol fontsize 18 9 5 Plotter Annotations The plotter allows various annotations lines arrows text and spans to be added to the plot These annotations are temporary when the plotter is next refreshe
16. d e g plotter plot or plotter set_range the annotations will be removed arrow x y x dx ytdy axhline y xmin xmax avhline x ymin ymax axhspan ymin ymax xmin xmax Draw an arrow from a specified x y position to x dx yt dy The values are in world coordinates Addition argu ments which must be passed are head_width and head_length ASAP gt plotter arrow 40 7 35 0 head width 0 2 head_length 10 Draw a horizontal line at the specified y position in world coordinates between xmin and xmax in relative coordinates i e 0 0 is the left hand edge of the plot while 1 0 is the right side of the plot ASAP gt plotter axhline 6 0 0 2 0 8 Draw a vertical line at the specified x position in world coordi nates between ymin and ymax in relative coordinates i e 0 0 is the left hand edge of the plot while 1 0 is the right side of the plot ASAP gt plotter axvline 50 0 0 1 1 0 Overlay a transparent colour rectangle ymin and ymax are given in world coordinates while xmin and xmax are given in relative coordinates ASAP gt plotter axhspan 2 4 0 25 0 75 20 axvspan xmin xmax Overlay a transparent colour rectangle ymin and ymax are ymin ymax given in relative coordinates while xmin and xmax are given in world coordinates ASAP gt plotter axvspan 50 60 0 2 0 5 text x y str Place the string str at the given x y position in world coor dinates ASAP gt plotter text 10 7 CO These functions all t
17. e plotter Examples ASAP gt selection selector 17 Select second IF ASAP gt selection set_ifs 1 ASAP gt plotter set_selection selection Select first 4 beams ASAP gt selection set_beams 0 1 2 3 ASAP gt plotter set_selection selection Select a few scans ASAP gt selection set_scans 2 4 6 10 ASAP gt plotter set_selection selection Multiple selection ASAP gt selection set_ifs 1 ASAP gt selection set_scans 2 4 6 10 ASAP gt plotter set_selection selection 9 2 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 Home This will unzoom the plots to the original zoom factor 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 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 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 Adjust rectangle with 4 arrows adjust subplot parameters space at edge of plots Save floppy disk Save the plot as a postscr
18. ents A scantable has header information and data a scantable is actually an AIPS Table and it is generally stored in memory when you are manipulating it with ASAP You can save it to disk and then browse it with the AIPS Table browser if you know how to do that The data are stored in columns the length of a column is the number of rows spectra of course Two important columns are those that describe the frequency setup We mention them explicitly here because you need to be able to understand the presentation of the frequency information and possibly how to manipulate it These columns are called FREQ_ID and MOLECULE_ID They contain indices for each IF pointing into tables with all of the frequency and rest frequency information for that integration There are of course many other columns which contain the actual spectra the flags the Tsys the source names and so on There is also a function summary to list a summary of the scantable You will find this very useful Example ASAP gt scans scantable MyData rpf ASAP gt scans summary Brief listing Equivalent to brief summary function call ASAP gt print scan The summary function gives you a scan based summary presenting the scantable as a cascading view of Beams and IFs Note that the output of summary is redirected into your current pager specified by the PAGER environment variable If you find the screen is reset to the original state when summary i
19. er 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 summary function the user can either override this value on reading the data or later E g ASAP gt scans scantable 2004 11 23_1841 P484 rpf unit Jy Or in two steps ASAP gt scans scantable 2004 11 23_1841 P484 rpf ASAP gt scans set_fluxunit Jy 6 6 2 Feed Polarisation The RPFITS files also do not contain any information as to the feed polarisation ASAP will set a default based on the antenna but this will often be wrong the data has been read the default can be changed using the set_feedtype function with an argument of linear or circular E g 13 ASAP gt scans scantable 2004 11 23_1841 P484 rpf ASAP gt scans set_feedtype circular 6 6 3 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 scale only scaless the spectra and not the corresponding Tsys ASAP gt scans scale 1 05 tsys True 6 6 4 Unit Conversion To convert measurements in Kelvin to Jy and vice versa the global function convert flux is needed This converts and scales the data from K to Jy or vice versa depending on what the curre
20. ery directly For power users only set_tsys Select data based on Tsys Also example of user definable query reset Reset the selection to include all spectra Note that all indices are zero based Examples ASAP gt selection selector ASAP gt selection set_ifs 0 ASAP gt scans set_selection selection Create selection object Just select the first IF Apply the selection ASAP gt print scans Will just show the first IF ASAP gt selection set_ifs 0 1 Select the first two IFs ASAP gt selection set_beams 1 3 5 Also select three of the beams ASAP gt scans set_selection selection Apply the selection ASAP gt selection set_name G308 Select by source name ASAP gt selection reset Turn off selection ASAP gt scans set_selection selection Apply the reset selection ASAP gt scans set_selection alternative to reset selection 4 3 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 4 3 1 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 un
21. function arguments Example ASAP gt scans scantable MyData rpf ASAP gt scans se lt TAB gt ASAP gt scans set_in lt TAB gt scans set_cursor scans set_freqframe scans set_selection scans set_doppler scans set_instrument scans set_unit scans set_fluxunit scans set_restfreqs ASAP gt scans set_instrument 3 5 2 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 3 5 3 Variable Names During normal data processing the user will have to create named variables to hold spectra etc These must conform to the normal python syntax specifically they cannot contain special characters such as etc and cannot start with a number but can contain num bers Variable and function names are case sensitive 3 5 4 Unix Interaction Basic unix shell commands pwd 1s 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 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 ASAP gt pwd ASAP gt 1s ASAP gt cd my data directory ASAP gt firefoxk amp 3 6 Help ASAP has built in help for all functions To get a list of functions type ASAP gt commands To get help on specific f
22. function arguments Where out is the name of the returned variable could be a new scantable object or a vector of data or a status return object is the object variable name set by the user function is the name of the member function and arguments is a list of arguments to the function The arguments can be provided either though position or name A mix of the two can be used E g ASAP gt av scans average_time msk weight tsys ASAP gt av scans average_time mask msk weight tsys ASAP gt av scans average_time msk tsys ASAP gt scans poly_baseline mask msk order 0 insitu True ASAP gt scans poly_baseline msk 0 True ASAP gt scans poly_baseline mask insitu True 3 4 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 3 5 Interactive environment ipython has a number of useful interactive features and a few things to be aware of for the new user 3 5 1 String completion Tab completion is enabled for all function names If you type the first few letters of a function name then type lt TAB gt the function name will be auto completed if it is un ambiguous or a list of possibilities will be given Auto completion works for the user object names as well as function names and even file names It does not work for for
23. ge_pol average the polarisations together average_beam average the beams together convert_pol convert to a different polarisation type auto_quotient return the on off quotient with automatic detection of the on off scans closest in time off is selected mx_quotient Form a quotient using MX data off beams scale return a scan scaled by a given factor add return a scan with given value added bin return a scan with binned channels resample return a scan with resampled channels smooth return the spectrally smoothed scan poly_baseline fit a polynomial baseline to all Beams IFs Pols auto_poly_baseline automatically fit a polynomial baseline recalc_azel recalculate azimuth and elevation based on the pointing gain_el apply gain elevation correction opacity apply opacity correction convert_flux convert to and from Jy and Kelvin brightness units freq_align align spectra in frequency frame invert_phase Invert the phase of the cross correlation swap_linears Swap XX and YY rotate_xyphase rotate XY phase of cross correlation rotate_linpolphase rotate the phase of the complex polarization 0 Q iU correlation freq_switch perform frequency switching on the data stats Determine the specified statistic e g min gt max rms etc stddev Determine the standard deviation of the current beam if pol Selection selector a selection object to set a subset of a
24. ger Indices are 0 relative Please note all integer indices in ASAP and iPython are 0 relative 3 2 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 scantable The data container actual spectra and header information selector Allows the user to select a subsection of the data such as a specified or range of beam numbers IFs etc plotter A tool used to plot the spectral line data fitter A tool used to fit functions to the spectral data reader A tool which can be used to read data from disks into a scantable object advanced use There can be many objects of the same type Each object is referred to by a variable name made by the user The name of this variable is not important and can be set to whatever the user prefers i e s and ParkesHOH 20052002 are equivalent However having a simple and consistent naming convention will help you a lot 3 3 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 ASAP gt out object
25. ing software asap 40
26. ipt or png file You can also type g in the plot window to toggle on and off grid lines Typing l turns on and off logarithmic Y axis 9 3 Other control The plotter has a number of functions to describe the layout of the plot These include set_legend set_layout and set title To set the exact velocity or channel range to be plotted use the set_range function To reset to the default value call set_range with no arguments E g ASAP gt scans set_unit km s 18 ASAP gt plotter plot scans ASAP gt plotter set_range 150 50 ASAP gt plotter set_range To reset Both the range of the x and y axis can be set at once if desired ASAP gt plotter set_range 10 30 1 6 6 To save a hardcopy of the current plot use the save function e g ASAP gt plotter save myplot ps ASAP gt plotter save myplot png dpi 80 9 4 Plotter Customisation The plotter allows the user to change most properties such as text size and colour The commands function and help asapplotter list all the possible commands that can be used with the plotter set_colors Change the default colours used for line plotting Colours can be given either by name using the html standard e g red blue or hotpink or hexadecimal code e g for black 000000 If less colours are specified than lines plotted the plotter cycles through the colours Example ASAP gt plotter set_colors red blue green ASAP gt plotter set_
27. it e g km s on the fly This is important for example when you are displaying the data or fitting to it The reference frame is set on file read to the value set in the user asaprc file For units the user has the choice of frequency velocity or channel The 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 set_doppler function and the frequency reference frame can be changed with the set_freqframe function Example usage ASAP gt scans scantable 2004 11 23_1841 P484 rpf Read in the data ASAP gt scans set_freqframe LSRK Use the LSR velocity frame ASAP gt scans set_unit km s Use velocity for plots etc from now on ASAP gt scans set_doppler OPTICAL Use the optical velocity convention ASAP gt scans set_unit MHz Use frequency in MHz from now on 4 3 2 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 set_restfreq to set the rest frequencies for the currently selected data For each integration there is a rest frequency per IF the rest frequencies are just stored as a list with an index into them The
28. ject print info about the scantable contents get specified statistic of the spectra in the scantable get the standard deviation of the spectra in the scantable get the TSys get the timestamps of the integrations get the source names of the scans get the azimuth of the scans get the elevation of the scans get the parallactic angle of the scans get the current unit set the abcissa unit to be used from this point on get the abcissa values and name for a given row time get the names of the columns in the scantable for use with selector set_query set the frame info for the Spectral Axis e g LSRK set the doppler to be used from this point on set the frame for the direction on the sky set the instrument name set the feed type get the brightness flux unit set the brightness flux unit return an mask in the current unit for the given region The specified regions are NOT masked get the current list of rest frequencies set a list of rest frequencies flag selected channels in the data 35 save save the scantable to disk as either ASAP gt SDFITS or ASCITI nbeam nif nchan npol the number of beams IFs Pols Chans nscan the number of scans in the scantable nrow te number of spectra in the scantable history print the history of the scantable get_fit get a fit which has been stored witnh the data average_time return the weighted time average of a scan or a list of scans avera
29. lection selection Select I Q U amp V ASAP gt selection set_polarisations I Q ASAP plotter set_selection selection Select just I amp Q ASAP gt selection set_polarisations RR LL ASAP plotter set_selection selection Select just RR amp LL ASAP gt selection set_polarisations XX YY ASAP plotter set_selection selection Select linears ASAP gt selection set_polarisations I Plinear ASAP plotter set_selection selection Fractional linear 26 ASAP gt selection set_polarisations Pangle ASAP plotter set_selection selection Position angle Scan beam and IF selection are also available in the selector object as describe in section 4 2 13 Specialised Processing 13 1 Multibeam MX mode MX mode is a specific observing approach with a multibeam where a single source is ob served cycling through each beam The scans when the beam is off source is used as a reference for the on source scan The function mx_quotient is used to make a quotient spectrum from an MX cycle This works averaging the off source scans for each beam either a median average or mean and using this as a reference scan in a normal quotient for each beam The final spectrum for each beam is returned on a new scantable contain ing single scan it the scan numbers are re labelled to be the same Note that the current version of mx_quotient only handles a single MX cycle i e
30. lled scantables A scantable holds your data and also provides functions to operate upon it The building block of a scantable is an integration which is a single row of a scantable Each row contains just one spectrum for each beam IF and polarisation For example Parkes OH multibeam data would normally contain 13 beams 1 IF and 2 polarisations Parkes methanol multibeam data would contain 7 beams 2 IFs and 2 polarisations while the Mopra 8 GHz MOPS filterbank will produce one beam many IFs and 2 4 polarisations All of the combinations of Beams IFs an Polarisations are contained in separate rows These rows are grouped in cycles same time stamp A collection of cycles for one source is termed a scan and each scan has a unique numeric identifier the SCANNO A scantable is then a collection of one or more scans If you have scan averaged your data in time i e you have averaged all cycles within a scan then each scan would hold just one averaged integration Many of the functions which work on scantables can either return a new scantable with modified data or change the scantable insitu Which method is used depends on the users preference The default can be changed via the asaprc resource file For example a Mopra scan with a 4s integration time two IFs and dual polarisations has two 2s cycles SCANNO CYCLENO BEAMNO IFNO POLNO 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 oooo ere FE FE O Oe Oe FrOoOOrR FOoOrROF 4 1 2 Cont
31. means temporary files are not cleaned up properly when you exit ASAP If you use disk based scan tables your directory will be left with tmpXXXXX_X directories These can be safely removed if ASAP is not running 14 Scantable Mathematics It is possible to to simple mathematics directly on scantables from the command line using the operators as well as their cousins This works between a scantable and a float Note that it does not work for integers Currently mathematics between two scantables is not available ASAP gt scan2 scanit 2 0 ASAP gt scan 1 05 ASAP gt sum scani scan2 15 Scripting Because ASAP is based on python it easy for the user write their own scripts and functions to process data This is highly recommended as most processing of user data could then be done in a couple of steps using a few simple user defined functions A Python primer is beyond the scope of this userguide See the ASAP home pages for a scripting tutorial or the main python website for comprehensive documentation http www atnf csiro au computing software asap tutorials http svn atnf csiro au trac asap wiki http www python org doc Introduction html http ipython scipy org 15 1 Running scripts The ASAP global function execfile reads the named text file and executes the contained python code This file can either contain function definitions which will be used in subse quent processing or just a set of comm
32. multi panel mode and contain multiple plots per panel The user must tell the plotter how they want the data distributed This is done using the set_mode function The default can be set in the users asaprc file The units and frame etc of the abscissa will be whatever has previously been set by set_unit set_freqframe etc Typical plotter usage would be ASAP gt scans set_unit km s ASAP gt plotter set_mode stacking p panelling t ASAP gt plotter plot scans This will plot multiple polarisation within each plot panel and each scan row in a separate panel Other possibilities include Plot multiple IFs per panel ASAP gt plotter set_mode stacking i panelling t Plot multiple beams per panel ASAP gt plotter set_mode stacking b panelling t Plot one IF per panel time stacked ASAP gt plotter set_mode t i Plot each scan in a seperate panel ASAP gt plotter set_mode t s 9 1 Plot Selection The plotter can plot up to 25 panels and stacked spectra per panel If you have data larger than this or for your own sanity you need to select a subset of this data This is particularly true for multibeam or multi IF data The selector object should be used for this purpose Selection can either be applied to the scantable or directly to the plotter the end result is the same You don t have to reset the scantable selection though if you set the selection on th
33. ns on masks created with scantable create_mask 17 2 ASCII output format 17 3 asaprc settings verbose True False Print verbose output good to disable in scripts insitu True False Apply operations on the input scantable or re turn new one useplotter True False Preload a default plotter plotter gui True False Do we want a GUI or plot to a file plotter stacking Pol Beam IF Default mode for colour stacking Scan Time plotter panelling Pol Beam IF Default mode for panelling Scan Time plotter ganged True False Push panels together to share axislabels plotter decimate True False Decimate the number of points plotted by a factor of nchan 1024 plotter histogram True False Plot spectrum using histogram rather than lines plotter colours Set default colours for plotting plotter colours Set default line styles plotter papersze A4 39 scantable save ASAP SDFITS ASCII MS2 scantable autoaverage True False scantable freqframe LSRK TOPO BARY etc scantable verbosesummary True False scantable storage memory disk 17 4 Installation Default output format when saving Auto averaging on read default frequency frame to set when function scantable set_freqframe is called or the data is imported Control the level of information printed by summary Storage of scantables in memory of via based disk tables Please refer to the asap wiki for instructions on downloading and or building asap from source http www atnf csiro au comput
34. nt 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 ASAP gt scans convert_flux If efficency known ASAP gt scans convert_flux eta 0 48 If telescope diameter known ASAP gt scans convert_flux eta 0 48 d 35 Unknown telescope ASAP gt scans convert_flux jypk 15 Alternative 6 6 5 Gain Elevation and Opacity Corrections As higher frequencies particularly gt 20 GHz it is important to make corrections for atmo spheric opacity and gain elevation effects Note that currently the elevation is not written correctly into Tidbinbilla rpfits files This means that gain elevation and opacity corrections will not work unless these get recalculated ASAP gt scans recalc_azel recalculate az el based on pointing Gain elevation curves for some telescopes and frequencies are known to ASAP currently only for Tidbinbilla at 20 GHz and Parkes at K band In these cases making gain corrections is simple If the gain curve for your data is not known the user can supply either a gain polynomial or text file tabulating gain factors at a range of elevations see help scantable gain el Examples ASAP gt scans gain_el If gain table known ASAP gt scans gain_el poly 3 58788e 1 2 87243e 2 3 219093e 4 14 Opacity corrections can be made with the global function opacity This should work
35. on all telescopes as long as a measurement of the opacity factor was made during the observation ASAP gt scans opacity 0 083 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 6 7 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 freq_align E g ASAP gt scans freq_align ASAP gt av average_time scans A Global freq_align command will be made eventually To average together data taken on different days which are in different scantables each scantable must aligned to a common reference time then the scantables averaged The simplest way of doing this is to allow ASAP to choose the reference time for the first scantable then using this time for the subsequent scantables ASAP gt scansi freq_align Copy the refeference Epoch from the output ASAP gt scans2 freq_align reftime 2004 11 23 18 43 35 ASAP gt scans3 freq_align reftime 2004 11 23 18 43 35 ASAP gt av average_time scans1 scans2 scans3 7 Scanta
36. re are a few ways to set the rest frequencies with this function If you specify just one rest frequency then it is set for all IF Set all IFs ASAP gt scans set_restfreqs freqs 1 667359e9 If set a rest frequency for each IF specify a list of frequencies of length the number of IFs Regardless of the source the rest frequency will be set for each IF to the corresponding value in the provided list Set rest frequency for all IFs ASAP gt scans set_restfreqs freqs 1 6654018e9 1 667359e9 A predetermined line catalog can be used to set the rest frequency See section 10 4 3 3 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 create_mask and this specified the channels to be included in the selection When setting the mask in velocity the conversion from velocity to channels is based on the current selection specified row and selected frequency reference frame Note that for multi IF data with different number of channels per IF a single mask cannot
37. s finished i e the output from summary disappears you may need to set the LESS environment variable to include the X option 4 2 Data Selection ASAP contains flexible data selection Data can be selected based on IF beam polarisation scan number as well as values such as Tsys Advanced users can also make use of the AIPS TAQL language to create selections based on almost any of the values recorded Selection is based on a selector object This object is created and various selection functions applied to it set_ifs set_beams etc The selection object then must be applied to a scantable using the set_selection function A single selection object can be created and setup then applied to multiple scantables Once a selection has been applied all following functions will only see the selected spectra including functions such as summary The selection can then be reset and all spectra are visible Note that if functions such as copy are run on a scantable with active selection only the selected spectra are copied The common selection functions are set_beams Select beams by index number set_ifs Select ifs by index number set_name Select by source name Can contain as a wildcard e g Orion _R set_ifs Select IFs by index number set_polarisation Select by polarisation index or name If polarisation names are given the data will be on the fly onverted for example from linears to Stokes set_query Set qu
38. sa specify a user label for the ordinate specify the multi panel layout rows cols specify a set of colours to use specify a set of linestyles to use if only using one color set general font properties e g plot in historam style set a plotting mask for a specific polarization draw text annotations either in data or relative coordinates draw arrow annotations either in data or relative coordinates draw horizontal vertical lines draw horizontal vertical regions family matplotlib pylab plotting functions access rpfits sdfits files draw arrow annotations either in data or relative coordinates draw horizontal vertical lines draw horizontal vertical regions matplotlib pylab plotting functions access rpfits sdfits files attach reader to a file detach reader from file read in integrations list info about all integrations 38 General commands this command print print details about a variable list_scans list all scantables created bt the user list_files list all files readable by asap default rpf del delete the given variable from memory range create a list of values e g range 3 0 1 2 range 2 5 2 3 4 help print help for one of the listed functions execfile execute an asap script e g execfile myscript list_rcparameters print out a list of possible values to be put into asaprc rc set rc parameters from within asap mask_and mask_or mask_not boolean operatio
39. scantable set_cycles set a list of cycles by index set_beams set a list of beamss by index set_ifs set a list of ifs by index set_polarisations set a list of polarisations by name or by index 36 set_names set a selection by name wildcards allowed set_tsys set a selection by tsys thresholds set_query set a selection by SQL like query e g BEAMNO reset unset all selections merge to selections Math Mainly functions which operate on more than one scantable average_time return the weighted time average of a list of scans quotient return the on off quotient simple_math simple mathematical operations on two scantables 2add sub mul div quotient build quotient of the given on and off scans matched pairs and 1 off n on are valid merge merge a list of scantables Line Catalog linecatalog a linecatalog wrapper taking an ASCII or internal format table summary print a summary of the current selection set_name select a subset by name pattern e g 0H set_strength_limits select a subset by line strength limits set_frequency_limits select a subset by frequency limits reset unset all selections save save the current subset to a table internal format get_row get the name and frequency from a specific row in the table Fitting fitter auto_fit return a scan where the function is applied to all Beams IFs Pols commit ret
40. sible to create a large number of scan tables These all consume memory so it is best to periodically remove unneeded scan tables Use list_scans to print a list of all scantables and del to remove unneeded ones Example ASAP gt list_scans The user created scantables are s scans av s2 ss ASAP gt del s2 ASAP gt del ss 5 Data Input Data can be loaded in one of two ways using the reader object or via the scantable con structor The scantable method is simpler but the reader allows the user more control on what is read 5 1 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 ASAP gt scan scantable 2004 11 23_1841 P484 rpf Don t scan average the data ASAP gt scan scantable 2004 11 23_1841 P484 rpf average False 6 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 asaprc file has not been used to change the insitu default value from True 10 6 1 Auto quotient Quotients can be computed automatically This requires the data to have matching source reference pairs or
41. sys 2 nomtsys selection set_polarisations 0 data set_selection selection data scale xtsystytsys 2 nomtsys The typical ASAP session would be Remind ourself the name of the rpfits files ls Load data from an rpfits file d1665 scantable 2005 10 27_0154 P484 rpf Check what we have just loaded d1665 summary View the data in velocity d1665 set_unit km s d1665 set_freqframe LSRK Correct for the known phase offset in the crosspol data d1665 rotate_xyphase 4 Create a copy of the data and set the rest frequency to the 1667 MHz transition di667 d1665 copy d1667 set_restfreqs 1667 3590 MHz d1667 summary Copy out the scan we wish to process g351_5 d1665 get_scan 351p160 g351_7 d1667 get_scan 351p160 Baseline both msk g351_5 create_mask 30 25 5 0 g351_5 poly_baseline msk order 1 msk g351_7 create_mask 30 25 5 0 g351_7 poly_baseline msk order 1 31 Plot the data The plotter can only plot a single scantable So we must merge the two tables first plotscans merge g351_5 g351_7 plotter plot plotscans Only shows one panel Tell the plotter to stack polarisation and panel scans plotter set_mode p s Correct for the Tsys using our predefined function execfile mypol py Read in the function xyscale xyscale g351_5 23 2 22 7 Execute it on the data xyscale g351_7 23 2
42. ta 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 ASAP gt scans auto_poly_baseline order 2 threshold 5 order is the polynomial order for the fit 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 12 Don t try and fit the edge of the bandpass which is noisier ASAP gt scans auto_poly_baseline edge 500 450 order 3 threshold 3 Only fit a given region around the line ASAP gt scans set_unit km s ASAP gt msk scans create_mask 60 20 ASAP gt scans auto_poly_baseline mask msk order 3 threshold 3 6 5 Average the polarisations If you are just interested in the highest SNR for total intensity you will want to average the parallel polarisations together ASAP gt scans average_pol 6 6 Calibration For most uses calibration happens transparently as the input data contains the Tsys mea surements 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 6 6 1 Brightness Units RPFITS files do not contain any information as to wheth
43. unctions the built in help needs to be given the object and function name E g ASAP gt help scantable get_scan or help scantable get_scan ASAP gt help scantable stats ASAP gt help plotter plot ASAP gt help fitter plot ASAP gt scans scantable mydata asap ASAP gt help scans get_scan Same as above Global functions just need their name ASAP gt help average_time Note that if you just type help the internal ipython help is invoked which is probably not what you want Type d control d to escape from this 3 7 Customisation asaprc ASAP use an asaprc file to control the user s preference of default values for various functions arguments This includes the defaults for arguments such as insitu scantable freqframe and the plotters set_mode values The help on individual functions says which arguments can be set default values from the asaprc file To get a sample contents for the asaprc file use the command list_rcparameters Common values include apply operations on the input scantable or return new one insitu False default output format when saving scantable scantable save ASAP default frequency frame to set when function scantable set_freqframe is called scantable freqframe LSRK auto averaging on read scantable autoaverage True For a complete list of asaprc values see the Appendix 4 Scantables 4 1 Description 4 1 1 Basic Structure ASAP data handling works on objects ca
44. urn a new scan where the fits have been commited fit execute the actual fitting process store_fit store the fit parameters in the data scantable get_chi2 get the Chi 2 set_scan set the scantable to be fit set_function set the fitting function set_parameters set the parameters for the function s and set if they should be held fixed during fitting set_gauss_parameters same as above but specialised for individual gaussian components get_parameters get the fitted parameters plot plot the resulting fit and or components and residual 37 Plotter asapplotter plot plot_lines save set_mode set_selection set_range set_legend set_title set_abcissa set_ordinate set_layout set_colors set_linestyles set_font set_histogram set_mask text arrow axhline axvline axhspan axvspan xyplotter Reading files reader arrow axhline axvline axhspan axvspan xyplotter Reading files reader open close read summary a plotter for asap default plotter is called plotter plot a scantable plot a linecatalog overlay save the plot to a file png ps or eps set the state of the plotter i e what is to be plotted colour stacked and what panelled only plot a selected part of the data set a zoom window xmin xmax ymin ymax specify user labels for the legend indeces specify user labels for the panel indeces specify a user label for the abcis
45. v create_mask 100 130 160 200 av poly_baseline msk 2 Average the two polarisations together iav av average_pol print iav plotter plot iav Set a sensible velocity range on the plot plotter set_range 85 200 Smooth the data a little av smooth gauss 4 plotter plot Fit a guassian to the emission fitter set_function gauss 1 set_scan av fit Hh Fh Fh Fh JF View the fit f plot Get the fit parameters f get_parameters 16 2 Parkes Polarimetry The following example is processing of some Parkes polarimetric observations of OH masers at 1 6 GHz Because digital filters where used in the backend the baselines are stable enough not to require a quotient spectra The 4 MHz bandwidth is wide enough to observe both the 1665 and 1667 MHz OH maser transitions Each source was observed once for about 10 minutes Tsys information was not written to the RPFITS file a nominal 25K values was used so the amplitudes need to be adjusted based on a separate log file A simple user function is used to simplify this contained in a file called mypol py def xyscale data xtsys 1 0 ytsys 1 0 nomtsys 25 0 selection selector selection set_polarisations 0 data set_selection selection data scale xtsys nomtsys 30 selection set_polarisations 1 data set_selection selection data scale ytsys nomtsys selection set_polarisations 0 data set_selection selection data scale xtsystyt
46. 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 ASAP gt f fitter ASAP gt f set_function gauss 2 ASAP gt scans set_unit km s Set the mask in channel units ASAP gt msk s create_mask 1800 2200 ASAP gt scans set_unit km s Make fit in velocity units ASAP gt f set_scan s msk ASAP gt f fit ASAP gt f plot ASAP gt f get_parameters If you wish the initial parameter guesses can be specified and specific parameters can be fixed ASAP gt f fitter ASAP gt f set_function gauss 2 ASAP gt f set_scan s msk ASAP gt f fit Fit using auto estimates Set Peak centre and fwhm for the second gaussian Force the centre to be fixed ASAP gt f set_gauss_parameters 0 4 450 150 0 1 0 component 1 ASAP gt f fit Re run the fit The fitter 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 Plot the residual ASAP gt f plot residual True Plot the first 2 componentsa ASAP gt f plot components 0 1 24 Plot the first and third component plus the model sum ASAP gt f plot components 1 0 2 1 means the compoment sum 11 1 Fit saving One you are happ
47. with set_restfreq 10 3 1 Plotting linecatalog The plotter plot_lines function takes a line catalog as an argument and overlays the lines on the spectrum Currently this only works when plotting in units of frequency Hz GHz etc If a large line catalog has been loaded e g JPL it is highly recommended that you use the selection functions to narrow down the number of lines By default the line 22 catalog overlay is plotted assuming a line velocity of 0 0 This can be set using the doppler argument in km s Each time plot_lines is called the new lines are added to any existing line catalog annotations These are all removed after the next call to plotter plot ASAP gt jpl linecatalog jpl tbl ASAP gt jpl set_frequency_limits 23 24 GHz ASAP gt data set_unit GHz Only works with freq axis currently ASAP gt plotter plot data ASAP gt plotter plot_lines jp1 ASAP gt plotter plot Reset plotter ASAP gt plotter plot_lines jpl doppler 10 location Top On top with 10 km s velocity 10 3 2 Setting Rest Frequencies A linecatalog can be used as an argument for set_restfreqs If a personal line catalog has been used which has the same size as the number of number of IFs or linecatalog selection has been used to reduce the number of entries the line catalog can be used directly as an argument to set_restfreqs e g ASAP gt jpl linecatalog jpl tbl ASAP gt jpl set_frequency_limits 23 66
48. y with your fit it is possible to store it as part of the scantable ASAP gt f store_fit 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 get_fit can be used to retrieve the stored fits Currently the fit parameters are just printed to the screen ASAP gt scans get_fit 4 Print fits for row 4 A fit can also be exported to an ASCII file using the store_fit function Simply give the name of the output file requires as an argument ASAP gt f store_fit myfit txt 12 Polarisation Currently ASAP only supports polarmetric analysis on linearly polarised feeds and the cross polarisation products measured Other cases will be added on an as needed basis Conversions of linears to Stokes or Circular polarisations are done on the fly Leakage cannot be corrected for nor are there routines to calibrate position angle offsets 12 1 Simple 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 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 ASAP gt scans rotate_xyphase 10 5 Degrees Note that if this function is run twice the sum of the two values is applied because it is done in
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