psradd -I 300 *.$file-extension the output files of which have .it extensions. Use of the -E <psr.eph> argument tells psradd to load a new ephemeris if required.

The solution from pcm can now be used for calibration. First, the solution must be added to the calibrator database; e.g.

cp pcm.fits /path to/pcm_<date>.fits
cd /path to
pac -wp . -u fits -u $file-extension
cd -

Then run pac using the -S command-line option that enables the calibration technique described in section 2.1 of Ord, van Straten, Hotan & Bailes (2004); eg:

pac -d /path to/database.txt -e new.calib -S *.it where pac outputs the fully calibrated files with extension ‘.new.calib’ (-e).

Finally, create a new fully calibrated archive for viewing with pav or psrplot (see ‘Viewing archives’ below) eg:

To list available plot types use psrplot -P. To list plot options for a specific plot type use psrplot -C <plot-type>, or psrplot -A <plot-type> for more common options.

Some psrplot examples:

Overlaying multiple plots can be achieved using both the -F and -c arguments, for example:

psrplot -p D -j FTp -F -c “x:win=(0,1),y:win=(0,1)” fileA fileB

Timing

In the presence of a parameter (.par) file for the chosen pulsar, run TEMPO or TEMPO2 on the .tim files. Alternatively, use GUIs such as PSRCHIVE’s RHYTHM.

In the presence of a parameter (.par) file for the chosen pulsar, run TEMPO or TEMPO2 on the .tim files. Alternatively, use GUIs such as RHYTHM here PSRCHIVE or TEMPOTK.

In the presence of a parameter (.par) file for the chosen pulsar, run TEMPO or TEMPO2 on the .tim files. Alternatively, use GUIs such as or TEMPOTK.

pas -r <reference_profile> -a *.std

Run pat on the calibrated 300 second subints and output to a .tim file eg:

pat -a /path/to/refernce_profile *.calibP > pulsar.tim

d) Fit the TOAs to the timing model

In the presence of a parameter (.par) file for the chosen pulsar, run TEMPO or TEMPO2 on the .tim files. Alternatively, use GUIs such as RHYTHM or TEMPOTK.

In order to produce pulse time of arrival estimates (TOAs), a template profile needs to be created and a fudicial point chosen on that profile, for each frequency of observation. These templates or standards (stds) are then aligned so that toas can be combined from different frequencies.

Choose one of the stds created above as the reference profile, and align the others to it either individually (-r) or automatically (-a) eg:

@@pas -r <reference profile> -a *.std

This leaves all stds aligned in phase with your reference profile.

c) Create the TOAs

a) Create the stds.

Then run pas on the archive for each frequency eg.:

pas 300sec.ar At this point, pas enters interactive mode, offering a number of fine tuning options. With the crosshairs over the plot, centre © and smoooth the profile (m), and save (s) the file.

b) Align the templates

Choose one of the stds created above as the reference profile, and align the others to it either individually (pas -r) or automatically

Then run pas on the archive:

pas 300sec.ar

Timing (work in progress!!)

In order to produce pulse time of arrival estimates (toas), a template profile needs to be created and a fudicial point chosen on that profile, for each frequency of observation. These templates or standards (stds) are then aligned so that toas can be combined from different frequencies.

The first step is to create the stds.

Using 300 second calibrated integrations, scrunch them (-j FTp) and add them into one archive eg:

psradd -f 300sec.ar -j FTp *.calibP

Produce ASCII output for external analysis

pdv can print output as ascii textfiles, that can then be manipulated using awk as you see fit, and sent to external plotting packages. For example,

Increase throughput with scripts

psrsh is a scripting tool designed to allow repetitive processing of multiple archives. For example the following script, if included in a shell for-loop, will load each archive, perform some preprocessing and then unload with new file extensions, leaving the originals untouched:

#!/usr/bin/env psrsh

#zap band edges
zap edge 0.05

#scrunch frequency channels and subints
FT

#centre maximum intensity of profile
centre max

#unload with new extension
unload ext=new
 

Increase throughput with scripts

psrsh is a scripting tool designed to allow repetitive processing of multiple archives. For example the following script, if included in a shell for-loop, will load each archive, perform some preprocessing and then unload with new file extensions, leaving the originals untouched:

#!/usr/bin/env psrsh #zap band edges zap edge 0.05 #scrunch frequency channels and subints FT #centre maximum intensity of profile centre max #unload with new extension unload ext=new

psrtxt -m -b 100 <archive> returns the max and min values in bin 100 (-b) and the relevant channels, pols and subints the values occurred in.

psrtxt -m -b 100 <archive> returns the max and min values in bin 100 (-b) and the relevant channels, pols and subints the values occurred in.

pdv prints out as ascii, useful for external analysis. Textfiles can then be manipulated using awk as you see fit, and sent to external plotting packages. For example,

pdv -NK archive > file.txt prints the S/N

2) psrtxt

psrtxt can output single channels, bins, pols or subints to ascii text.

A useful option is to find max and min values in the data eg:

@@

pdv prints out as ascii, useful for external analysis. Textfiles can then be manipulated using awk as you see fit. For example,

pdv -K -f -n 20 archive > file.txt prints mean flux and pulse width (both W10 and W50) (-f) of channel 20 (-n), and hashes the header lines (-K).

pdv -NK archive > file.txt prints the S/N

pdv prints out as ascii, useful for external analysis. For example,

pdv -K -f -n 20 archive > file.txt prints mean flux and pulse width (both W10 and W50) (-f) of channel 20 (-n), and hashes the header lines (-K). The textfile can then be manipulated using awk as you wish.

pdv -FTZKt archive > file.txt scrunches frequency and time (-FTp), hashes the header lines and prints the pulse profile, stokes parameters and polarisation angle as ascii (-t).

Timing

Produce ASCII output

1) pdv

pdmp also outputs two ascii files, pdmp.per and pdmp.posn. These can be passed to an external plotting package such as gnuplot, and in the case of a millisecond pulsar in a binary orbit such as 0437–4715, plotting period change with time for example, can demonstrate the doppler effect on the signal as the pulsar orbits its companion.

To include a period offset in the search, use the -po option:

Timing

pdmp <archive> -g archive.ps/ps Here the output is a postcript file (-g DEVICE).

To plot the DM/period output only, use the -k option:

To include a period offset, use the -po option:

pdmp -po <> <archive>

Optimisation

pdmp searches for the best period and DM, and S/N at that period/DM of a given archive, eg:

@@pdmp <archive>

Using 0437–4715 as an example, you could then refine the DM search by decreasing the DM range (-dr) and step (-ds), eg:

pdmp -dr 5 -ds 0.01 <archive>

To plot only the DM/period output:

pdmp -k 0 0 <archive>

vap -nc bw * returns the bandwidth (bw) without headers (-n) of all the files in the current directory. Type vap -H for a full list of parameters able to be queried.

Archives may be combined with or without preprocessing using psradd, for example

RFI mitigation

Archive analysis

Analysis of pulsar archives can be done either by dedicated software in the PSRCHIVE suite itself such as pdmp for parameter optimisation and pat for timing, or by running external scripts on the ascii output from PSRCHIVE’s pdv or psrtxt.

psradd -I 300 -E <.eph> <archive> creates 5 minute integrations (-I 300) using the supplied ephemeris (-E). The addition of the -j option allows preprocessing before integration.

Supposing you wanted to tweak the folding period of an archive but leave the original unchanged, use pam with the - -period option eg.

Archives may be combined with or without preprocessing using psradd, or split using psrsplit, for example

@@psradd

One can check a file’s attributes using psrstat. A polarization calibration is marked ‘PolnCal’, a flux calibrator is marked ‘FluxCal-On’ or ‘FluxCal-Off’, and a pulsar observation type marked ‘Pulsar’.

For example,

psrstat m2009100020946.fb produces the following output for this particular polarization calibration file:

Other useful tools for querying attributes are vap, psredit and vip.

vip -a <file> returns the pointing attributes of a particular file, such as RA, DEC, LST etc

1) To check the subints, create a frequency-scrunched archive and run pazi:

2) To check for bad channels first create a time-scrunched archive, then run pazi:

3) Corrupt phase bins can be zapped either interactively or manually. In interactive mode, pazi allows checking and removal of bins by use of the ‘b’ option, and as above, bins can be removed individually or in blocks, with the use of ‘p’ printing the command plus a list of bins removed.

RFI Mitigation

Use pazi the interactive version of paz the zapper to check for and remove bad subints, channels or bins.

Here, paz zero-weights subint 20 (-w), and flags channels (-z) at the edges of the band (119 120 121 122 123 124 125 126 127 0 1 2 3 4 5 6 7 8 9 10) and outputs the new archive ‘<archive>.pazi’

Bins can be zapped either interactively or manually. In interactive mode, pazi allows checking and removal of bins by use of the ‘b’ option, and as above, bins can be removed individually or in blocks, with the use of ‘p’ printing the command plus a list of bins removed.

Any bad subints can now be zapped by right-clicking the mouse, or to remove a block of subints for example, left-click at one end of the block, move the cursor to the other end of the block and press ‘z’. By default the subints are not removed but zero-weighted (paz -w) to conserve the temporal signature of the archive. A useful option is ‘p’ which prints the command used, listing the subints that are zero-weighted. Left click the mouse twice to zoom in, and at any time use ‘u’ to undo any changes if required.

To check the subints, create a frequency-scrunched archive and run pazi:

pam -e Fscrunched -F <archive>.ar

pazi <archive>.Fscrunched enters into interactive mode with a cross as a cursor on the time/phase graphic, movable by mouse.

pav -Y <archive>.pazi

To check for bad channels first create a time-scrunched archive, then run pazi:

pam -e Tscrunched -T <archive>.ar

pazi <archive>.Tscrunched

With the cursor on the time/phase graphic, press ‘f’ to switch to the frequency/phase graphic.

Any bad channels can now be zapped using the methods described above. Similarly, ‘p’ prints the command and lists the channels that pazi removes.

Press ‘s’ to save the file, and ‘q’ to quit.

As above, the saved file can be checked and viewed with pav eg:

pav -G <archive>.pazi

Alternatively, after checking the subints and channels above but not saving the changes, run paz on the unscrunched archive using the output from the ‘p’ option above to automate the procedure, for example:

paz -w “20” -z “119 120 121 122 123 124 125 126 127 0 1 2 3 4 5 6 7 8 9 10” -e pazi <archive>.ar

Her, paz zero-weights subint 20 (-w), and flags channels (-z) at the edges of the band (119 120 121 122 123 124 125 126 127 0 1 2 3 4 5 6 7 8 9 10) and outputs the new archive ‘<archive>.pazi’

The saved file can be checked and viewed with pav eg:

pav -TG <archive>.pazi (frequency/phase) or

pav -FY <archive>.pazi (subint/phase)

During interactive sessions with pazi, left click the mouse twice to zoom in on subint or channel. At any time use ‘u’ to undo any changes if required.

To zap subints:

pazi <archive>.ar enters into interactive mode with a cross as a cursor on the time/phase graphic, movable by mouse.

To zap channels:

To zoom in on a particular, left click the mouse twice. At any time use ‘u’ to undo if required.

Use pazi the interactive version of paz the zapper to check for and remove bad subints or channels.

First, create a phase-aligned archive from individual sub-integrations eg.

To zap subints, frequency scrunch the archive, and run pazi on the new archive:

pam -e Fscrunched -F <archive>.ar

pazi <archive>.Fscrunched enters into interactive mode with a cross as a cursor on the time/phase graphic, movable by mouse.

Any bad subints can now be zapped by right-clicking the mouse, or to remove a block of subints for example, left-click at one end of the block, move the cursor to the other end of the block and press ‘z’. By default the subints are not removed but zero-weighted (paz -w) to conserve the temporal signature of the archive. A useful option is ‘p’ which prints the command used, listing the subints that are zero-weighted.

To zoom in on a particular, left click the mouse twice. At any time use ‘u’ to undo if required.

To zap channels, time scrunch the archive and write out to a new file:

Use pazi to check for and remove any RFI:

pazi <archive>.Tscrunched

With the cursor on the time/phase graphic, press ‘f’ to switch to the frequency/phase graphic.

Any bad channels can now be zapped using the methods described above. Similarly, ‘p’ prints the command and lists the channels that pazi removes.

Create a phase-aligned archive from individual sub-integrations eg.

Time scrunch the archive and write out to a new file:

Use pazi the interactive zapper to check for and remove RFI:

Any bad channels can now be zapped by right-clicking the mouse, or to remove a block of channels for example at the edges of the band, left-click at one end of the block, move the cursor to the other end of the block and press ‘z’. A useful option is ‘p’ which prints the command and therefore the channels that pazi removes.

pav -G <archive>.pazi

pazi <archive>.Tscrunched enters into interactive mode (a cross appears, movable by mouse).

Press ‘f’ to switch to the frequency/phase graphic.

pav -G <archive>.pazi

pazi <archive>.Tscrunched enters into interactive mode (a cross appears, movable by mouse). Press ‘f’ to switch to the frequency/phase graphic.

Any bad channels can now be zapped by right-clicking the mouse, or to remove a block of channels, left-click at one end of the block, move the cursor to the other end of the block and press ‘z’. A useful option is ‘p’ which prints the command and therefore the channels that pazi removes.

When happy with the outcome, press ‘s’ to save the file (default is to <archive>.pazi), and ‘q’ to quit.

The saved file can be checked and viewed with pav eg:

pav -G <archive>.Tscrunched.pazi

RFI Mitigation (Incomplete!!)

Create phase-aligned archive from individual subints eg.

psradd -f <archive>.ar *.fb

Time scrunch the archive and write out to new file:

pam -e Tscrunched -T <archive>.ar

Use interactive zapper to check for and remove RFI:

pazi <archive>.Tscrunched enters into interactive mode (a cross appears, movable by mouse). Press ‘f’ to switch to frequency/phase graphic.

Any bad channels can now be zapped by right-clicking the mouse, or left-clicking with ‘z’ to remove a block of channels. A useful option is ‘p’ which prints the command and therefore the channels that pazi removes.

Assuming the archives are free of problematic RFI (See ‘RFI Mitigation’ below), they can be calibrated for flux and polarisation, again by applying pac but this time with reference to the calibrator summary file created above. By default, pac uses the ‘SingleAxis’ calibration model, but use of this model assumes that the two receptors are orthogonally polarised, that the reference source is 100% polarised, and that both receptors receive the signal in phase.

Assuming the archives are free of problematic RFI (See below), they can be calibrated for flux and polarisation, again by applying pac but this time with reference to the calibrator summary file created above. By default, pac uses the ‘SingleAxis’ calibration model, but use of this model assumes that the two receptors are orthogonally polarised, that the reference source is 100% polarised, and that both receptors receive the signal in phase.

Assuming the archives are free of problematic RFI (See RFI Mitigation below), they can be calibrated for flux and polarisation, again by applying pac but this time with reference to the calibrator summary file created above. By default, pac uses the ‘SingleAxis’ calibration model, but use of this model assumes that the two receptors are orthogonally polarised, that the reference source is 100% polarised, and that both receptors receive the signal in phase.

RFI Mitigation

Supposing you wanted to tweak the folding period of an archive but leave the original unchanged, use pam with the —period option eg.

pam -e new -FTp - -period <arg> <archive>

Supposing you wanted to tweak the folding period of an archive, use pam with the —period option eg.

pam -e new -FTp —period <arg> <archive>

Or

psredit -c type,name,dm <archive> returns the observation type, name and dispersion measure of an archive

Calibration

pam allows you to conduct pre-processing on an archive, for example

pam -m -SFT <archive> scrunches in time and frequency (FT), transforming to Stokes parameters (S) and overwrites the archive (-m) while,

pam -e new -SFT <archive> creates the new archive (-e), leaving the original untouched.

Other useful tools for querying attributes are vap and psredit.

psredit -c type,name,dm <archive> returns the observation type, name and dispersion measure

psredit allows you to change a file parameter (-c), for example to change the bandwidth (bw) sign to positive (sometimes the CPSR2 output might have been set incorrectly) and output to a new archive (-e) with no change to the original:

psredit -c bw=64 -e new <archive>

psrplot -p D -j FTp <archive> scrunches frequency channels, sub-integrations and polarizations (-j FTp), and produces a single plot of total flux (-p D), eg. for checking the performance of the linear noise diode cal square wave.

psradd -I 300 $file-extension the output files of which have .it extensions. Use of the -E <psr.eph> argument tells psradd to load a new ephemeris if required.

PSRCHIVE facilitates many levels of archive manipulation, from changing file parameters to full pre-processing and output of new archives. Here are just a few examples.

pav -G <archive>, plots pulse amplitude and phase with frequency (G); addition of the -d (dedisperse) option corrects for the dispersion delay of the interstellar medium, illustrated by the frequency-dependent phase sweep across the band

For example,

psrplot -N1×3 -jFT -c ch=2 -p o -p s -p Y <archive>, preprocesses by scrunching frequency and integrations (-jFT), and plots an array of 3 plots one on top of the other (-N1×3), polarisation angle (-p o), stokes parameters (-p s) and subint/phase with amplitude (-p Y). Character height (ch) is set to double the default using the -c argument (-c ch=2).

Zooming in on the data is possible by including eg. -c ‘x:range=(0.5,0.7)’, which plots the xrange from 0.5–0.7

psradd -T -o total.calibP *.calibP creates a Tscrunched archive (-T) ‘total.calibP’ (-o)

Then run pcm on the uncalibrated *.it archives:

pcm -d /path to/database.txt -c total.calibP -s -t2 -D result *.it where pcm automatically chooses the best phase bins from the calibrated archive (-c), intrinsic signal fluctuations are compensated for (-s), a diagnostic report is printed (-D result), and the process is split between two processor cores (-t2) since it is quite computationally intensive. The output from pcm is the calibrator solution ‘pcm.fits’, and can be viewed with pacv.

The solution from pcm can now be used in the calibration process by re-running pac using the ‘Receptor’ model option eg:

pac -d /path to/database.txt -e new.calib -A pcm.fits -S *.it where pac utilises the pcm output for instrument response (-A), and the complete Reception model (-S), and outputs recalibrated files with extension ‘.new.calib’ (-e).

Finally, create a new recalibrated archive for viewing with pav or psrplot (see ‘Viewing archives’ below) eg:

psradd -T -o total.calibP.new *.new.calibP

pcm -d /path to/database.txt -c total.calibP -s -t2 -D result *.it where pcm automatically chooses the best phase bins from the calibrated archive (-c), intrinsic signal fluctuations are compensated for (-s), a diagnostic report is printed (-D result), and the process is split between two processor cores (-t2) since it is quite computationally intensive. The output from pcm is the calibrator solution ‘pcm.fits’.

This can now be used in the calibration process by re-running pac using the ‘Receptor’ model option eg:

pac -d /path to/database.txt -A pcm.fits -S *.it where pac utilises the pcm output for instrument response (-A), and the complete Reception model (-S). In this case the *.calibP files from preliminary running of pac are overwritten as new re-calibrated *.calibP files.

In order to acquire a more accurate instrument response, use of the ‘Reception’ calibration model is required. Firstly, pcm is used to produce a calibrator solution by choosing the most suitable phase bins in the integrated pulse profile created by psradd, for example:

Say the output of pac above are .calibP files, then

psradd -T -o total.calibP *.calibP creates a Tscrunched archive

Then run pcm on the uncalibrated *.it archives

pcm -d /path to/database.txt -c total.calibP -s -t2 -D result *.it where pcm automatically chooses the best phase bins from the calibrated archive (-c), intrinsic signal fluctuations are compensated for (-s), a diagnostic report is printed (-D result), and the process is split between two processor cores (-t2) since it is quite computationally intensive

The output from @@pcm

Gather all cal files into a single directory, and make this directory the working directory.

pac -wp . -u $file-extension where pac searches in the local directory (-p .) for files with extension $file-extension (-u), and writes to a new database.txt file (-w)

Next, determine the system temperature and flux density of the reference source using fluxcal eg:

Here, fluxcal appends database.txt with flux calibration solutions, but keeps a copy of the original as database.txt.bkp

The output files are given .calib extension if both flux and pol calibration were possible, and .calibP if only pol calibration was possible; use of the -P argument with pac, calibrates for polarization only.

In order to acquire a more accurate instrument response, use of the ‘Reception’ model is required.

pav -X - -publn - -ch 0.8 <archive> produces a black and white publication plot (- -publn) with a set character height (- -ch 0.8), of the cal and system amplitude and phase as a function of frequency channel (X)

pav -X —publn —ch 0.8 <archive> produces a black and white publication plot (—publn) with a set character height (—ch 0.8), of the cal and system amplitude and phase as a function of frequency channel (X)

One can check a file’s attributes using psrstat. For example, a polarization calibration is marked ‘PolnCal’, a flux calibrator is marked ‘FluxCal-On’ or ‘FluxCal-Off’, and a pulsar observation type marked ‘Pulsar’.

psrstat m2009100020946.fb produces the following output for this particular calibration file, in this case a polarization calibration:

Gather all cal files into a single directory.

Next, determine system temperature and flux density of reference source using fluxcal eg:

Graphical display of the calibrator archive is possible with pacv, psrplot and pav, utilising the PGPLOT graphics package, for example

pacv -P <archive>.fluxcal produces a publication quality plot of a flux calibrator archive, showing system and noise diode cal equivalent flux densities with frequency, of both polarizations. When applied to a HYDRA cal file, say a ‘FluxCal-Off’ pointing (ie. a pointing taken one full beam width north or south of HYDRA), pacv will display the calibrator solution of the instrument response in terms of absolute gain, differential gain and differential phase

pav -TX <archive> scrunches all sub-integrations (-T), and plots the cal and system amplitude and phase as a function of frequency channel (X)

A typical data set will generally contain files from a stable reference flux calibrator eg. HYDRA A taken once per day, files from a 100% linearly polarized reference source (CAL - an amplitude modulated linear noise diode signal), taken before and after each observation, and the observation files from the pulsar itself. Before starting any analysis, it is worth getting to know the file attributes.

First, gather all cal files into a single directory.

Create a database summary file (default output is database.txt) of all the calibrators eg:

pacv -n cpu <archive> plots uncalibrated on-pulse total and polarized flux (-n cpu) with frequency; for calibrated use -n cpc; to view system parameters (ie. off-pulse) use -n spu and -n spc

pacv -n csu <archive> plots uncalibrated on-pulse Stokes parameters (-n csu) with frequency; for calibrated use -n csc; likewise to view system parameters use -n ssu and -n ssc

psrplot -p D -j FTp <archive> scrunches frequency channels, sub-integrations and polarizations (-j FTp), and produces a single plot of total flux, eg. for checking the performance of the linear noise diode cal square wave.

The next step is to make the pulsar observations directory the working directory and use psradd to create 5 minute integrations (-I 300), prior to calibration eg:

psradd -I 300 $file-extension the output files of which have .it extensions

pacv -P <archive>.fluxcal produces a publication quality plot of a flux calibrator archive, showing system and noise diode cal equivalent flux densities with frequency, of both polarisations. When applied to a HYDRA cal file, say a ‘FluxCal-Off’ pointing (ie. a pointing taken one full beam width north or south of HYDRA), pacv will display the receiver response in terms of absolute gain, differential gain and differential phase

pacv -n cpu <archive> plots uncalibrated on-pulse total and polarized flux (-n cpu) with frequency

pacv -n csu <archive> plots uncalibrated on-pulse Stokes parameters (-n csu) with frequency

psrplot -p D -j FTp n2009098132037.fb scrunches frequency channels, sub-integrations and polarizations (-j FTp), and produces a single plot of total flux, eg. for checking the performance of the linear noise diode cal square wave.

Calibration (Work in progress…not complete!)

1) pav

2) psrplot

1)pav

2)psrplot

1)@pav@

2)@psrplot@

pav

psrplot

psrplot -p D n2009098132037.fb produces a single plot of flux, eg. the square wave of the linear noise diode cal.

The next step is to make the pulsar observations directory the working directory and use psradd to create 5 minute integrations (-I 300) and Tscrunch the archive when time to the next archive is > than 30 seconds (-G), prior to calibration eg:

Other options for pav include the ability to zoom in on a specific range of phase (-z), frequency (-k), sub-integration (-y) and position angle (-l).

pav -FT -SC -g 1/xs <archive>, scrunches all frequency channels and sub-integrations (-FT), and plots centred polarization parameters I, L, V and PA (-SC) on PGPLOT window no. 1 (-g 1/xs); addition of - -plot_qu displays the stokes parameters I, Q, U, V and PA, and addition of - -ld displays pulse phase in degrees

pav -FTp -DC <archive>, scrunches all frequency channels, sub-integrations and pols (-FTp), and plots the centred (-C) integrated pulse profile (-D)

pav -FT -SC <archive>, scrunches all frequency channels and sub-integrations (-FT), and plots centred polarization parameters I, L, V and PA (-SC); addition of - -plot_qu displays the stokes parameters I, Q, U, V and PA, and addition of - -ld displays pulse phase in degrees

pav -FTp -DC <archive>, scrunches all frequency channels, sub-integrations and pols (-FTp), and plots the centred © integrated pulse profile (-D)

pav -FY <archive>, scrunches all frequency channels (-F), and plots sub-integrations with pulse phase (Y)

pav -TG <archive>, scrunches sub-integrations (-T), and plots pulse amplitude and phase with frequency (G); addition of the -d (dedisperse) option corrects for the dispersion delay of the interstellar medium, illustrated by the frequency-dependent phase sweep across the band

pav -FT -SC <archive>, scrunches all frequency channels and sub-integrations (-FT), and plots centred polarization parameters I, L, V and PA (-SC); addition of —plot_qu displays the stokes parameters I, Q, U, V and PA, and addition of —ld displays pulse phase in degrees

pav -TG archive.calibP, scrunches sub-integrations (-T), and plots pulse amplitude and phase with frequency (G); addition of the -d (dedisperse) option corrects for the dispersion delay of the interstellar medium, illustrated by the frequency-dependent phase sweep across the band

pav -FTp -DC archive.calibP, scrunches all frequency channels, sub-integrations and pols (-FTp), and plots the centred integrated pulse profile (-DC)

pav -FY archive.calibP, scrunches all frequency channels (-F), and plots sub-integrations with pulse phase (Y)

pav -TG archive.calibP, scrunches sub-integrations (-T), and plots pulse amplitude and phase with frequency (G)

pav -FTp -DC archive.calibP, scrunches all frequency channels, integrations and pols (-FTp), and plots the centred integrated pulse profile (-DC)

pav -N 1,2 -g 1/xs -FT -DC -SC archive.calibP, scrunches all frequency channels and integrations (-FT), then plots the centred integrated pulse profile (-DC) above (-N 1,2) a plot of the polarization parameters (-SC), on PGPLOT window no. 1 (-g 1/xs)

For example,

pav -FT -DC archive.calibP, scrunches all frequency channels and integrations (-FT), and plots the centred integrated pulse profile (-DC) of a calibrated archive pav -N 1,2 -g 1/xs -FT -DC -SC archive.calibP, scrunches all frequency channels and integrations (-FT), and plots the centred integrated pulse profile above a plot of the polarization parameters, on PGPLOT window no. 1

Set up calibrator summary file

Calibrator graphical display

Graphical display of the calibrator archive is possible with pacv and psrplot, utilising the PGPLOT graphics package, for example

pacv -P m2009099074221.fluxcal produces a publication quality plot of a flux calibrator archive, showing system and noise diode cal equivalent flux densities with frequency, of both polarisations. When applied to a HYDRA cal file, say a ‘FluxCal-Off’ pointing (ie. a pointing taken one full beam width north or south of HYDRA), pacv will display the receiver response in terms of absolute gain, differential gain and differential phase

and,

psrplot -p D n2009098132037.fb produces a single plot of the square wave flux, in this case for the linear noise diode cal.

Calibrate the pulsar archives

The next step is to make the pulsar observations directory the working directory and create 5 minute integrations prior to calibration using psradd eg:

pacv -P m2009099074221.fluxcal produces a publication quality plot of a flux calibrator archive, showing system and noise diode cal equivalent flux densities with frequency, of both polarisations. When applied to a HYDRA cal file, say a ‘FluxCal-Off’ pointing (ie. a pointing taken one full beam width north or south of HYDRA), pacv will display the receiver response in terms of absolute gain, differential gain and differential phase.

Viewing of the calibrator archives is possible with pacv, for example

pacv -P m2009099074221.fluxcal produces a publication quality plot of a flux calibrator archive, showing system and noise diode cal equivalent flux densities with frequency, of both polarisations.

So now the .it archives can be calibrated for flux and polarisation, again by applying pac but this time with reference to the calibrator summary file created above. By default, pac uses the ‘SingleAxis’ calibration model, but use of this model assumes that the two receptors are orthogonally polarised, that the reference source is 100% polarised, and that both receptors receive the signal in phase.

Viewing archives

The PSRCHIVE suite offers two archive viewing and plotting routines, namely pav and psrplot. Both utilise the PGPLOT graphics package and can produce publication quality plots.

pav can graphically display the content of an archive, and also allows preprocessing of the archive before displaying it, but without any change to the archive’s content.

For example,

So now the .it archives can be calibrated for flux and polarisation, again by applying pac but this time with reference to the calibrator summary file created above. By default, pac uses the ‘SingleAxis’ calibration model, but use of this model assumes the two receptors are orthogonally polarised, that the reference source is 100% polarised, and that both receptors receive the signal in phase.

Archive manipulation

Then make the pulsar observations directory the working directory and create 5 minute integrations prior to calibration using psradd eg:

So now the .it archives can be calibrated for flux and polarisation, again by applying pac but this time with reference to the calibrator summary file created above eg:

pac -d /path to/database.txt *.it

The output files are given .calib extension if both flux and pol calibration were possible, and .calibP if only pol calibration was possible.

The new calibrated archives can now be viewed with pav eg:

psradd -I 300 -G 30 $file-extension the output files of which have .it extensions

psradd -I 290 -G 30 $file-extension the output files of which have .it extensions.

pac -wp . -u $file-extension

Next determine system temperature and flux density of reference source using fluxcal eg:

fluxcal -d database.txt -c $prefix/share/fluxcal.cfg where fluxcal.cfg contains the standard candle information

Then make the pulsar observations directory the working directory and create 5 minute integrations using psradd eg:

@@

Once familiar with the file attributes, it is a good idea to sort the observation files according to frequency and/or bandwidth, in preparation for downstream analysis. This becomes important during archive creation to avoid frequency/bandwidth mismatch errors.

First, gather all cal files into a single directory $cals.

Create a database summary file of all the calibrators eg:

@@pac -wp . -u $file-extension

Calibration

One can check a file’s attributes using psrstat. For example, a polarisation calibration is marked ‘PolnCal’, a flux calibrator is marked ‘FluxCal-On’ or ‘FluxCal-Off’, and a pulsar observation type marked ‘Pulsar’.

psrstat m2009100020946.fb produces the following output for this particular calibration file, in this case a polarisation calibration:

file Name of the file m2009100020946.fb

coord Source coordinates 04:37:00.000–47:35:00.00 freq Centre frequency (MHz) 1341

length Observation duration (s) 4.718762

A typical data set will generally contain files from a stable reference flux calibrator eg. HYDRA, files from an amplitude modulated linear noise diode, and the observation files from the pulsar itself. Before starting any analysis, it is worth getting to know the file attributes.

One can check a file’s attributes using psrstat. For example, a calibration observation type is marked ‘PolnCal’ and a pulsar observation type marked ‘Pulsar’.

etc…

etc…

Another useful tool for querying attributes is vap.

For example:

One can check a file’s attributes using psrstat. For example, a polarisation calibration observation type is marked ‘PolnCal’ and a pulsar observation type marked ‘Pulsar’.

Once familiar with the file attributes, it is a good idea to sort the observation files according to frequency and/or bandwidth, in preparation for downstream analysis. This becomes important during archive creation to avoid frequency/bandwidth mismatch errors. In addition, all cal files should be placed in a single directory.

A typical data set will generally contain flux calibration files from a bright radio source eg. HYDRA, polarisation calibration files from injection of the noise diode signal, and the observation files from the pulsar itself. Before starting any analysis, it is worth getting to know your files.

One can check a file’s attributes using psrstat. For example, a polarisation calibration type is marked ‘Polncal’ and a pulsar observation marked ‘Pulsar’.

psrstat n2009098131726.fb produces the following output for this particular calibration file:

Once familiar with the file attributes, it is a good idea to sort the observation files according to frequency and/or bandwidth, and place all the cal files in one directory, in preparation for downstream analysis.

Another tool for querying attributes is vap eg.

vap -nc bw * returns the bandwidth (bw) without headers (-n) of all the files in the current directory

For the purpose of this demonstration, I will be using data from PSR J0437–4715 collected at Parkes in 2009.

psrstat n2009098131726.fb

file Name of the file n2009098131726.fb

coord Source coordinates 09:18:06.000–11:05:45.00 freq Centre frequency (MHz) 685 bw Bandwidth (MHz) 64

Similarly,

psrstat m2009097074500.fb produces the following output for a Pulsar file:

Typical data - querying attributes

For the purpose of this demonstartion, I will be using data from PSR J0437–4715 collected at Parkes in 2009. A typical data set will generally contain flux calibration files from a bright radio source eg. HYDRA, polarisation calibration files from the noise diode, and the observation files from the pulsar itself. Before starting any analysis, it is worth getting to know your files.

One can check a file’s attributes using psrstat. A calibration type is marked ‘Polncal’ and a pulsar observation marked ‘Pulsar’, for example:

One can check a file’s properties using psrstat. A calibration type is marked ‘Polncal’ and a pulsar observation marked ‘Pulsar’, for example:

Similarly,

psrstat m2009097074500.fb produces the following output for a Pulsar file:

Attribute Name   Description                                 Value
------------------------------------------------------------------
file             Name of the file                            m2009097074500.fb
nbin             Number of pulse phase bins                  1024
nchan            Number of frequency channels                128
npol             Number of polarizations                     4
nsubint          Number of sub-integrations                  1
type             Observation type                            Pulsar
site             Telescope name                              7
name             Source name                                 0437-4715
coord            Source coordinates                          04:37:15.815-47:15:08.63
freq             Centre frequency (MHz)                      3256
bw               Bandwidth (MHz)                             64
dm               Dispersion measure (pc/cm^3)                2.64397811889648
rm               Rotation measure (rad/m^2)                  0
dmc              Dispersion corrected                        0
rmc              Faraday Rotation corrected                  0
polc             Polarization calibrated                     0
scale            Data units                                  FluxDensity
state            Data state                                  Coherence
length           Observation duration (s)                    13.1076740000001

Below is a portion of the output for this particular calibration file:

[=

[=

Typical data

I will be using data from PSR J0437–4715 for this example. A typical data set will generally contain flux calibration files from a bright radio source eg. HYDRA, and the observation files from the pulsar itself.

One can check a file’s properties using psrstat, for example:

psrstat HYDRA/m2009099074540.fb

This is a portion of the output for a calibration file:

Attribute Name Description Value ------------------------------------------------------------------ file Name of the file HYDRA/m2009099074540.fb nbin Number of pulse phase bins 1024 nchan Number of frequency channels 128 npol Number of polarizations 4 nsubint Number of sub-integrations 1 type Observation type PolnCal site Telescope name 7 name Source name CAL coord Source coordinates 09:18:06.000-13:05:45.00 freq Centre frequency (MHz) 1341 bw Bandwidth (MHz) -64 dm Dispersion measure (pc/cm^3) 0 rm Rotation measure (rad/m^2) 0 dmc Dispersion corrected 0 rmc Faraday Rotation corrected 0 polc Polarization calibrated 0 scale Data units FluxDensity state Data state Coherence length Observation duration (s) 16.7778240000001

Alternatively, psrsh can print file type eg.

$ psrsh psrsh> load m2009099074540.fb ok psrsh> edit type type=PolnCal

Using Tempo2

Work with PSRCHIVE to analyse Parkes CPSR2 data

Typical data

Search for new pulsars with Sigproc and PulsarHunter

If you know the pulsar period, but don’t have the exact values (e.g. you have done an FFT or looked the period up in a catalogue, you might want to do optimisation, therefore use PDM or PulsarHunter

PulsarHunter - an alternate way to optimise (works on a range of different data types).

Timing at the ATNF principally uses the PSRCHIVE software from Swinburne.

• pdmp *.ar do a period and frequency optimisation on the .ar file

Given a set of .ar archives (and frequency and time ‘scrunched’ .FT files) one can use all the psrchive commands to make the toas and view the profiles. Useful commands are:

• pam -FT -e FT *.ar makes ‘.FT’s from the ‘.ar’s. Use -E *.eph to use a new ephemeris
• pav -D -N2,2 *.FT displays the folded profiles 2 by 2.
• pas x.FT To make a standard template from x.FT
• pat -s x.std *.FT Creates tempo format TOAs from the FTs using standard template x.std
• pat -s x.std -f tempo2 *.FT Creates tempo2 format TOAs from the FTs using standard template x.std

Search for new pulsars with Sigproc and PulasrHunter

see Search With Sigproc.

Create Time of Arrival measurements from observations

Before timing of a pulsar can commence, one must generate time of arrival measurements from the observations. How this is done varies depending on the telescope/hardware that is used.

At Parkes/Epping

Timing at the ATNF principally uses the PSRCHIVE software from Swinburne.

Given .ar archive files (If the data is already in the epping archive)

Given a set of .ar archives

To make the .ar archive files (for fresh data, straight from the telescope)

Creating these files depends on the hardware system used.

At Jodrell Bank

At Arecebo

Fit TOAs

Using Tempo

Using PSRTime

Using Tempo2

How to find a specific pointing

How to get a pointing from the archives

Looking at the results (2001 A.Faulkner reprocessing)

A quick way to check what is in a beam is to look at the processed results. This data is currently only available at JBO.

The results are stored in the results directories in

dcore15_1/PMSURV/results and dcore14_1/PMSURV/results

The data is subdivided into tape, pointing and beams. Each results directory contains the following files:

• .ph files (one per candidate from standard search)
• .aph files (one per candidate from accel search)
• a .ascu file which contains bookkeeping info (I have no idea what this is, please explain ~mkeith)
• .pulse_best and .pulse_stats which are single pulse search output (I have no idea how to read this format ~mkeith)
• a ‘long’ dir which contains a number of .lph files and ffa files that are long period search candidates. (Sorry, no idea what these contain either ~mkeith)
• a .sp file (I have no idea what this is ~mkeith)
• a dir with the name of the pointing, that contains the phase acceleration candidates (See Presto for information on the phase acceleration search). Note that for some reason not all beams have this…

The .ph files and .aph files are the most useful, as they have the actual candidates. Most of the other files are not described here, but it would be useful if someone with knowledge of these could fill this in.

The .ph files and the .aph files are almost identical, but they have some subtle differences. The files are in a binary format with no markings to identify the components. They can be read by Reaper, vph (the .ph/.aph viewing software) and JReaper.

To best understand the uses of these files, and the way they were produced, it would be advisable to read Andrew Faulkner’s PhD thesis.

Work with Parkes Multibeam Pulsar Survey Data

Looking at the results

This gives you a postscript output as well as a .phcf file. The .phcf (PularHunter Candidate File) stores all the info about the data in a format described in PHCFFormat. This can be viewed with ph-view-phcf, which starts an Xwindow with the plots in.

Note that pulsarhunter is pretty new, so it is not as tested as PDM. Although it is generally more flexible than PDM, it is still being developed so more features will appear/disappear in future.

Search for new Pulsars

Once you have filterbanked the data:

filterbank infile.dat > outfile.fil

you can use the generic sigproc search methodology.

PMsurv data can also be searched with PMMinifind

To search for new pulsars with Sigproc and PulasrHunter

see Search With Sigproc.

@@filterbank [infile].dat | dedisperse -d [dm] -s 4 → [infile].sub ph-tune [infile].sub [outfile] …options…

PDM - for when you want to optimise (only works for Parkes Filterbank data)

and follow the options… unfortunately it’s a bit picky about what you say to it.

Here is a typical conversation:

>$ pdm

Input data file: PT0279_0461
Telescope site: PARKES    

 File extn (3 char max): mjk
 Graphics device (n for none): /vps
 Nkill, (chk(j),j=1,nkill): 0
 Write plot data to file? (y/n) [y]: 
 Write dedispersed data to file? (y/n) [n]: 
 Write profile file? (y/n) [y]: 
 Period (p), frequency (f), baryctr P (b) or catalogue (c)? [c]: p
 Folding centre period (ms)? : 123.4567
 Half-range of period scan (ms) or negative Nsub? : -256
 Centre DM? : 345
 Nr of bands for DM search? : 6
 Range factor for DM search (max nr samples/chan)? : 1

 Block length (sec):   0.256
 Nr of blocks to skip?         : 0
 Nr of blocks to read? (0=all) : 1
 Tsub array overflow - nsub decreased
 Nsub too small - set to 3
 2048 256 0 2

 1mjk  RAA:  15:52:41.4  DecA: -56:49:02.  Gl:  325.850  Gb:   -2.240  Date: 061
  UT:  19:35:22.0  LST:  11:41:10

 EOF reached at nsub =   0

Using these options will cause it to at least produce a plot (which may be called pgplot.ps, although it may also be [infile].ps). Try playing around with these options to find what you want (At least change the period and dm!).

PularHunter - an alternate way to optimise (works on a range of different data types).

PulsarHunter is best combined with sigproc to perform the initial dedispersion steps.

If you have Sigproc and PulsarHunter installed, then you can do a PDM style optimisation with the command:

ph-pdm infile ] [[outfile [dm] -period [period]

Note that ph-pdm is a script that does the following:

@@filterbank infile.dat | dedisperse -d [dm] -s 4 → infile.sub ph-tune infile.sub outfile …options…

That is, it uses sigproc to make a sub-banded time-series with 4 sub bands (i.e. 4 dedispersed frequency channels) and then runs ph-tune. Therefore you can use any option that ph-tune takes (try ph-tune with no args to see a list of options).

The data for the PM survey is in the SCAMP data format, and can be extracted by the sc_td software ((I think) it can also be used directly by Presto).

In general the following seems to work (although there are many more options of sc_td you might want to try):

sc_td -d d -A -b [beam number] -K [tape name] [file name]

Where: [beam number] is the ordinal number of the beam you want to extract (1–13, not 1-D), [tape name] is the name of the tape (so that it can be looked up in kill.chans) and [file name] is the name of the file you want to process.

This will provide you with a [file name][beam name]1.dat and the same .hdr. For example you might get

PM0042_001B1.dat
PM0042_001B1.hdr

Note that if you are using an older version of sc_td, you might have to remove the -K switch and you might get mangled file names (in particular with the wrong pointing number), but the right file should have been extracted. Also don’t panic if it reaches 2051 blocks (for a full PM file) and throws some error about end of file, this is just the way of sc_td, your files have been extracted ok!

What can I do with .dat/.hdr files?

So you have some .dat/.hdr files. Well… you can now process them, but the way you do this depends on what software you want to use.

Here we will use PDM, PulsarHunter and Sigproc for some examples, but you might want to use PMMinifind or Presto.

Folding the data with a known period and DM

Lets suppose you want to fold the data up in time and frequency with a known period and dispersion measure. It may be that you know the period and DM exactly (i.e. you have already optimised the period on this data, or have a good ephemeris), then you can just fold the data. If you know the pulsar period, but don’t have the exact values (e.g. you have done an FFT or looked the period up in a catalogue, you might want to do optimisation, therefore use PDM or PulasrHunter

Sigproc filterbank, dedisperse and fold - For when you know exactly the period and DM

So, firstly check if you have Sigproc installed. Assuming it is, you can perform the following steps (Assuming your file is called PMXXXX_XXXX1.dat):

filterbank PMXXXX_XXXX1.dat > PMXXXX_XXXX1.fil This converts the .dat and .hdr into a sigproc generic raw data format.

dedisperse PMXXXX_XXXX1.fil -d [dm] > PMXXXX_XXXX1.tim This dedispersed the data at a dm of [dm] and places the single channel time series into PMXXXX_XXX1.tim.

fold PMXXXX_XXXX1.tim -p [period] | profile This will make a nice ascii profile of the plot. Of course you probably want something more useful, so either pipe the output from fold into a file and then read it into your favourite plotting package, or perhaps make an EPNFormat file:

fold PMXXXX_XXXX1.tim -p [period] -epn > PMXXXX_XXXX1.epn

Check the fold help for more (type ‘fold -h’) output options.

PDM for when you want to optimise (only works for Parkes Filterbank data)

PDM is the standard PMsurv folder. It has been tried and tested over the years and is considered to be relyable.

to use, simply type:

pdm

and follow the options…

PularHunter an alternate way to optimise (works on a range of different data types).

The files are typically indexed by tape name, then by pointing, for example:

is pointing 1 on tape PM0042

Dealing with the data

The data for the PM survey is in the SCAMP data format, and can be extracted by the sc_td software.

This is a work in progress, but please add to it as you see fit.

How to get a pointing from the archives

This can be achieved by using a file called pmobs.db.

Firstly, if logged into Parkes (say, Perseus), the command:

will print all files from that tape (it’s just a glorified grep, but saves some typing!).

How to get a pointing from the archives

Currently there is no online mechanism for extracting files from the archive, although this is planned.

Therefore you need to find a local copy of the PM survey. At JBO this is (or should be soon!) at:

/remote/dcore[8–15]_1/PMSURV/

The files are typicaly indexed by tape name, then by pointing, for example:

PM0042/PM0042_001

is pointing 1 on tape PM0042

It’s a bit of a botch job however, so care should be taken to ensure that it makes sense. It is configured in /psr at JBO, however it will be made available shortly as part of the PSRUtils Package. To use:

gridid [gl] [gb]

Note that this only works for PMsurv and PASurv observations (and anything else that uses PMsurv grid ids). This will return other results though, for example from the MMB survey (which will be bogus as their grid ids are different), so watch out!

This can be achived by using a file called pmobs.db.

Please see the page on pmobs.db for more details.

The important fact here is that the grid id and the tape label and pointing number are in the same line of the file. Therefore by ‘grep’ing for the grid ID, one can determine the tapes and pointings to look at.

Of course, this is not as easy as it appears, as pmobs.db only has the grid id for the central beam, and the observation you want may be in a different beam. Therefore 13 greps are required to check each of the possible centre beams for different arrangements of the reciever.

It is important to note that the grid id cannot ever tell you which beam to extract from the file, as the beam numbers are from the receiver which is at an unknown orientation to the sky.

On the positive side, there is several tools to help you with this…

Firstly, if logged into parkes (say, perseus), the command:

tape_list [tape name]

will print all files from that tape (it’s just a gloified grep, but saves some typing!). Since it is powered by grep, one can just write a source id instead of a tape name (say the grid number) and it will return all observations of that source.

Alternately, if you have a Gl and Gb, and want to find the grid id and search the pmobs.db, the tool ‘gridid’ has been created to do that. It’s a bit of a botch job however, so care should be taken to ensure that it makes sense.

It is configured in /psr at JBO, however it will be made available shortly as part of the PSRUtils Package.

This can be achived by using a file called pmobs.db.

Please see the page on pmobs.db for more details.