PSRCHIVE user documentation: pcm

Measurement Equation Modeling Example

For this example, suppose that all of the pulsar observations are located in the current working directory and have the extension .ar and that all of your calibrator archives are summarized in the data base, $MYCALS/database.txt.

The simplest way to run pcm is to let it choose the optimal phase bins to use as model constraints. Assuming that calib.TT has been created as described in Section 2.1, run 

pcm -d $MYCALS/database.txt -c calib.TT -s -t2 *.ar
Here, the -s option specifies that the Stokes parameters should be normalized to compensate for temporal flux variations and the -t2 option specifies to use two processing threads (not useful if your machine has only one single-core CPU).

Manaual selection of phase bins

Alternatively, it is also possible to specify the phase bins to be used as constraints. When plotting data to support phase bin selection, be sure to dedisperse and centre the data; e.g. 
psrplot -j "dedisperse, centre 0" -p S -jF calib.TT
Suppose that the Stokes parameters at pulse phases equal to 0.45 and 0.51 look like they will make good constraints. If there are 2048 phase bins, then bin numbers 922 and 1044 are to be used. The command line is: 
pcm -b 922 -b 1044 -d $MYCALS/database.txt *.ar

Alternatively, suppose that you would like to select 8 bins between pulse phases 0.39 and 0.51. The command line is: 

pcm -p 0.39,0.51 -n 8 -d $MYCALS/database.txt *.ar


In the latter example, pcm will begin with something like: 

Pulsar::Archive::Agent::init 
pcm: selecting input states from 0.39 to 0.51
pcm: selecting a maximum of 8 bins
pcm: assuming that System + Hydra A Stokes V = 0
pcm: allowing CAL Stokes Q to vary
pcm: normalizing Stokes parameters by invariant interval
pcm: constructing Calibration::Database from
     /export/home/user/pcm/cals/database.txt
pcm: searching for calibrator observations within 24 hours of midtime
pcm: midtime = 2003-08-29-19:02:00
pcm: adding n2003241194914.pcal
pcm: adding n2003241223100.fcal
pcm: adding n2003241222635.fcal
pcm: set calibrators
pcm: loading archives
pcm: adding phase bin 799
[...]
pcm: adding phase bin 1044
pcm: 8 states
Pulsar::ReceptionCalibrator::load_calibrators 
  loading /export/home/user/pcm/cals/n2003241194914.pcal
Note that pcm begins by loading the calibrators. At this stage, you may see error messages like: 

Pulsar::ReceptionCalibrator::add_calibrator error adding ichan=0
Error::stack
        Calibration::ReceptionModel::add_data
Error::InvalidParam
Error::message
        source_index=0 ipol=3 variance=0.000000 < 0
Or also: 

Pulsar::ReceptionCalibrator::add_data discarding ichan=0 ibin=1044
Unless all of the data are getting discarded, or appear to be corrupted, these error messages may be ignored; pcm can handle and flag a variety of problems in the data.

After the calibrators have been loaded, pcm will output on stderr lines such as: 


Setting 128 channel receiver
Pulsar::ReceptionCalibrator::precalibrate
pcm: loaded archive: n2003200181319.cfb
These mean that pcm is calibrating the input archives with its current best guess of the receiver before adding their data to the best guess of the input polarizations.

After all the data is loaded, pcm will output something like: 


pcm: plotting initial guess of receiver
Pulsar::ReceptionCalibrator::solve information:
  Parallactic angle ranges from -102.621536254883 to 98.1568908691406 degrees
Pulsar::ReceptionCalibrator::solve reference epoch: 52839.945158016725522
pcm: plotting uncalibrated pulsar total stokes
pcm: plotting uncalibrated CAL
pcm: plotting pulsar constraints
pcm: nstate=1
ichan=1 istate=1
pcm: nstate=1
ichan=11 istate=1
pcm: nstate=1
ichan=21 istate=1

[...]
At this stage, pcm creates a number of postscript files: guess.ps and channel_*.ps. In guess.ps is plotted the first guess of the instrumental response and the Stokes parameters of both the calibrator the pulsar. In channel_*.ps are plotted the variations of the observed Stokes parameters as a function of parallactic angle in a selection of up to 13 frequency channels, which are evenly spaced across the band.

Next, pcm will output lines like: 


pcm: solving model
Pulsar::ReceptionCalibrator::solve ichan=0
Pulsar::ReceptionCalibrator::solve failure ichan=0
Error::stack
        Calibration::ReceptionModel::solve
Error::InvalidRange
Error::message
        input source 0 with free parameter(s) not observed

Pulsar::ReceptionCalibrator::solve ichan=1
Calibration::ReceptionModel::solve converged in 53 iterations. 
  chi_sq=785.590026855469/406=1.93495082855225
Pulsar::ReceptionCalibrator::solve ichan=2
Calibration::ReceptionModel::solve converged in 40 iterations.
  chi_sq=739.773132324219/406=1.822101354599
Pulsar::ReceptionCalibrator::solve ichan=3
Calibration::ReceptionModel::solve converged in 30 iterations.
  chi_sq=737.575866699219/406=1.81668937206268

[...]

Pulsar::ReceptionCalibrator::solve ichan=36
Calibration::ReceptionModel::solve converged in 5 iterations.
  chi_sq=593.349975585938/406=1.4614531993866
Pulsar::ReceptionCalibrator::solve ichan=37
Calibration::ReceptionModel::solve converged in 6 iterations.
  chi_sq=626.255004882812/406=1.54250001907349
Pulsar::ReceptionCalibrator::solve ichan=38
Calibration::ReceptionModel::solve converged in 5 iterations.
  chi_sq=614.626037597656/406=1.51385724544525
Note the error message that arises because channel 0 was corrupted in all of the calibrator archives (the PolnCal Stokes parameters are assigned an input source index of zero). Note also that corruption due to aliasing during downconversion causes slower convergence and a larger reduced chi squared near the leading edge of the passband (which corresponds to the lowest values of ichan shown above). On a 1.2 GHz Pentium III, the solution takes approximately:
  • less than a minute with one pulse phase bin
  • about an hour with 16 pulse phase bins
  • about 19 hours with 64 pulse phase bins
  • When all of the frequency channels have been fitted, pcm will output the solution in the FEEDPAR HDU of a PSRFITS file named pcm.fits. It will also over-write channel_*.ps by plotting the same data with the best fit model curves drawn through the data points. It will also output a new file, result.ps, which plots the best-fit model parameters that describe the instrumental response and the Stokes parameters of the flux calibrator and noise diode. pcm then re-calibrates all of the Pulsar, PolnCal, and FluxCalOn files, producing new files with a .calib extension. Finally, the mean of the calibrated pulsar data is output in the file, total.ar and the fscrunched and tscrunched calibrated pulse profile is plotted in calibrated.ps.