Jodrell Pulsar Timing Programs - Making a new template

Data in the form of profiles with accurate start times can come from a variety of soures. Data from the Jodrells filter bank/hardware dedispersers are taken from the VAX as binary files. Their standard processing is detailed in the "General" section. However data in the form of EPN, mel(Parkes) and a few other formats can also be dealt with.

To produce a set of arrival times from profile data, the following steps are taken (usually by scripts).

• Produce a single profile from a set of subints (by combining L and R pols and different frequencies).
• Expand the profile to at least 1 period plus the length of a template.
• convolve the profile with an appropriate template to produce a SAT (site arrival time)
• Use TEMPO to work with SATS and/or
• Convert the SAT to a BAT and use psrtime to work with the set of BATS

• less than 500 MHz
• from 500 MHz to 750 MHz
• from 750 MHz to 1100 MHz
• from 1100 MHz to 1500 MHz
• greater than 1500 MHz

This assumes that you are working with some data from a new discovery!
and the data is "in house". Observations should have been sorted into a directory /psrdata/timing/PSRNAME which will contain nothing but your new data file(s) called Axx.bin.
If the data is from another source, create a directory and copy your data files there and produce a Jodrell formatted bin file - then you can make use of similar processing methods.)

• touch auto to create an empty auto file which enables script processing. (you can always remove this later).
• put the pulsar's ephemeris file in this directory and name it (or copy it to) psrav.eph
• Run the processing script psrav PSRNAME all to force the processing of whatever data files are in the PSRNAME directory. Thsi script will not run completely, since you haven't got any templates yet, but will produce all the default configuration files required for processing.
  The psrav script should get as far as producing an averaged profile from each set of subints in a file called psrav.bin.
• If the pulsar is strong and the ephemeris good, you may be able to use the profiles from each subint to produce a template, otherwise you will probably have to try and correct any drift in arrival times between subints before a profile can be seen.
  
• Start psrprof
• If you have good averaged profiles, use the the data in psrav.bin by typing
  set in1file psrav.bin. Otherwise type
  set in1file Axx.bin where Axx.bin is the raw data file,and then type obey psravedit.dat to configure psrprof to average, dedisp.and baseline channels in each subint.
• If your data file contains observations at different frequencies, you may want to select a particlar frequency range to work on
  selectfreq from XXXX to YYYY where X and Y are in MHz.
• Read and display profiles until you see a clear example
  read in disp in
• copy this profile to the av buffer
  copy inav
• Contine reading and displaying profiles, whenever the profile is "good" ie a reasonable, if noisy, example of the pulse, align this profile with that already stored in the av buffer , and combine them
  align in av average 0.0
• When you reach the end of all your data, see what you've got in the av buffer
  disp av
  If you have a visible pulse there you can continue to use it as the basis of a template. (A better template can always be produced when more data is available and an improved ephemeris gives less smearing of the pulse in each subint).
• copy your profile to the in buffer for the next stage
  copy avin

• If the profile is noisy, use the smooth command (repeatedly) to reduce the noise. (the smooth command convolves the profile with an N bin triangle) eg
  smooth in 3 disp in
• Window in on the pulse plus a few pulse widths. We're aiming to make a template with the pulse flanked on each side by approx. a pulse width of basline, so give yourself this plus a bit extra to start with
  window in pulse 0.0 xx.x disp in where xx.x is the window size in secs.
• flatten the noise from the baseline using the changedata command
  changedata in
  I use the zero command for the baseline, sometimes a little interpolation, and don't worry about the outside edges, thes can be trimmed! (everyone has their own style here :-).
• Run the profile through smooth again if you like.
• window in to a final width window in pulse 0.0 xx.x disp in
• Is it OK?
  If so, create a template
  maketemp in disp a3
  The template is created by normalising the profile (so that the area is 1) and adding a timestamp tothe header to mark the centre of the profile. The new profile is stored in the a3 buffer
• Write the template to a file
  set out1file newtemp.bin write a3 quit

psrprof reads templates.code, if no flag is found, it then searches first for a set of templates in templates.bin which must be a multi channel file with the channels containing a template for each of the 5 freq. ranges. If found, these templates sre used. If not, psrprof looks for profiles in separate files for each freq. band (408temps.bin,610temps.bin,910temps.bin,1420temps.bin, and 1600temps.bin

So.... when you have produced your new template (see above):

• rename the file with the correct name for it's frequency band eg 1420temps.bin
• produce a templates.code file with the line xPPPPPPPPPx12345 where PPPPPPPPP is the pulsarname and change 12345 to show the new template eg if you have only got a template for the 1100MHz to 1500MHZ range, this should be in 1420temps.bin and templates.code should read xPPPPPPPPPx44444 ie use range 4 template for all ranges.

These templates are produced in the same way as for method 1, but examples of the different modes of the pulsar are selected for each template file. (Some work with changetbin can also be used to adjust the profiles).

• comment lines shown by a # in column 1
• Version: 1.0
• Pulsar: 0737-3039 (pulsar name max 12 chars)
• Freq (MHz): 1390.000
• Tau (deg): 0.000000
• Components: 26
• list of components - component number, centre, amplitude,width
  eg
  1 86.0696 0.3066 2.5074
  2 66.4865 0.4654 3.7385
  .
  .
  .
  26 80.0024 0.3053 4.9867