vcstools scripts

The following scripts are provided as part of the vcstools package:

RVM_fit.py

A script that performs a least squares fit to the Rotating Vector Model

usage: RVM_fit.py [-h] --archive ARCHIVE [--outfile OUTFILE]
                  [--phase_ranges PHASE_RANGES [PHASE_RANGES ...]] [-L LOGLVL]

optional arguments:
  -h, --help            show this help message and exit
  --archive ARCHIVE     The pathname of the archive (.ar) file to attempt to
                        fit (default: None)
  --outfile OUTFILE     The pathname of the file to write the ouput to. If
                        None, will not write. Note: file outputs are in
                        radians (default: None)
  --phase_ranges PHASE_RANGES [PHASE_RANGES ...]
                        The phase range(s) to fit the RM to. If unsupplied,
                        will find the on-pulse and fit that range. Supports
                        multiple ranges. eg. 0.1 0.15 0.55 0.62 will fit
                        values from 0.1 to 0.15 and from 0.55 to 0.62.
                        (default: None)
  -L LOGLVL, --loglvl LOGLVL
                        Logger verbostity level (default: INFO)

calibrate_vcs.py

Script for creating RTS configuration files and submitting relevant jobs in the VCS pulsar pipeline

usage: calibrate_vcs.py [-h] -o OBSID -O CAL_OBSID -m METAFITS -s SRCLIST
                        [--gpubox_dir GPUBOX_DIR]
                        [--rts_output_dir RTS_OUTPUT_DIR]
                        [--beam_model {ANALYTIC,FEE2016}]
                        [--n_vis_grp N_VIS_GRP] [--offline]
                        [--vcstools_version VCSTOOLS_VERSION] [--nosubmit]
                        [-L {DEBUG,INFO,WARNING}] [-V]

optional arguments:
  -h, --help            show this help message and exit
  -o OBSID, --obsid OBSID
                        Observation ID of target (default: None)
  -O CAL_OBSID, --cal_obsid CAL_OBSID
                        Calibrator observation ID for the target observation.
                        Can be the same as --obs if using in-beam visibilities
                        (default: None)
  -m METAFITS, --metafits METAFITS
                        Path to the relevant calibration observation metafits
                        file (default: None)
  -s SRCLIST, --srclist SRCLIST
                        Path to the desired source list (default: None)
  --gpubox_dir GPUBOX_DIR
                        Where the *_gpubox*.fits files are located (ONLY USE
                        IF YOU WANT THE NON-STANDARD LOCATIONS.) (default:
                        None)
  --rts_output_dir RTS_OUTPUT_DIR
                        Parent directory where you want the /rts directory and
                        /batch directory to be created (ONLY USE IF YOU WANT
                        THE NON-STANDARD LOCATIONS.) (default: None)
  --beam_model {ANALYTIC,FEE2016}
                        Which beam model to use to create the calibration
                        solution (default: FEE2016)
  --n_vis_grp N_VIS_GRP
                        The number of visbility groups for the RTS to
                        construct. This changes with the MWA configuration
                        (i.e. long baselines require more visibility groups to
                        combat decorrelation) (default: 6)
  --offline             Tell the RTS to read calibrator data in the offline
                        correlated data format (default: False)
  --vcstools_version VCSTOOLS_VERSION
                        The version of vcstools to use. Only relevant for
                        offline correlation (default: master)
  --nosubmit            Write jobs scripts but DO NOT submit to the queue
                        (default: True)
  -L {DEBUG,INFO,WARNING}, --loglvl {DEBUG,INFO,WARNING}
                        Logger verbosity level. Default: INFO (default: INFO)
  -V, --version         Print version and quit (default: False)

checks.py

scripts to check sanity of downloads and recombine.

usage: checks.py [-h] [-m {download,recombine}]
                 [-d {11,15,16,raw,ics,tar_ics}] [-o OBS ID] [-b start]
                 [-e stop] [-a] [-i time increment] [-s SIZE] [-S SIZE_ICS]
                 [-w WORK_DIR] [-V] [-L {DEBUG,INFO,WARNING}]

optional arguments:
  -h, --help            show this help message and exit
  -m {download,recombine}, --mode {download,recombine}
                        Mode you want to run: download, recombine
  -d {11,15,16,raw,ics,tar_ics}, --data_type {11,15,16,raw,ics,tar_ics}
                        Only necessary when checking downloads. Types refer to
                        those as definded in voltdownload.py: 11 = Raw, 15 =
                        ICS only, 16 = ICS and tarballs of recombined data.
  -o OBS ID, --obs OBS ID
                        Observation ID you want to process [no default]
  -b start, --begin start
                        gps time of first file to check on [default=None]
  -e stop, --end stop   gps time of last file to check on [default=None]
  -a, --all             Perform on entire observation span. Use instead of -b
                        & -e. [default=False]
  -i time increment, --increment time increment
                        Effectively the number of seconds to ckeck for
                        starting at start time [default=None]
  -s SIZE, --size SIZE  The files size in bytes that you expect all files to
                        have. Per default will figure this out from files on
                        he archiveWe expect 253440000 (download raw),
                        327680000 (recombined, not ics), 7865368576 (tarballs)
  -S SIZE_ICS, --size_ics SIZE_ICS
                        Size in bytes thatyou expect the ics files to have.
                        Default = 30720000
  -w WORK_DIR, --work_dir WORK_DIR
                        Directory to check the files in. Default is
                        /astro/mwavcs/vcs/[obsID]/[raw,combined]
  -V, --version         Print version and quit
  -L {DEBUG,INFO,WARNING}, --loglvl {DEBUG,INFO,WARNING}
                        Logger verbosity level. Default: INFO

cleanup.py

Tool for cleaning up after processing MWA Pulsar Data on Galaxy

usage: cleanup.py [-h] [-o OBS] [--raw] [--beamformed] [-V]
                  [-L {DEBUG,INFO,WARNING}]

optional arguments:
  -h, --help            show this help message and exit
  -o OBS, --obs OBS     Observation ID you want to process [no default]
  --raw                 Add this option if you want to remove the raw and/or
                        recombined files for an observation
  --beamformed          Add this option if you want to remove the recombined
                        files for an observation
  -V, --version         Print version and quit
  -L {DEBUG,INFO,WARNING}, --loglvl {DEBUG,INFO,WARNING}
                        Logger verbosity level. Default: INFO

combine_calibrations.py

If there is no calibration observation with the correct channels, use this script to combine the result of two calibration solutions to make a new calibration solution with all the required frequency channels.

usage: combine_calibrations.py [-h] [-o OBSID] [-c1 CAL1] [-c2 CAL2]
                               [--out_dir OUT_DIR] [-V]
                               [-L {DEBUG,INFO,WARNING}]

optional arguments:
  -h, --help            show this help message and exit
  -o OBSID, --obsid OBSID
                        Observation ID you want to process
  -c1 CAL1, --cal1 CAL1
                        The first calibration observation ID you want to
                        combine
  -c2 CAL2, --cal2 CAL2
                        The second calibration observation ID you want to
                        combine
  --out_dir OUT_DIR     The output directory of the combined solution. Default
                        is /astro/mwavcs/vcs/[obsid]/cal/[cal1]_[cal2]/rts
  -V, --version         Print version and quit
  -L {DEBUG,INFO,WARNING}, --loglvl {DEBUG,INFO,WARNING}
                        Logger verbosity level. Default: INFO

create_ics_psrfits.py

positional arguments: obsID Observation ID for which to create the incoherent sum PSRFITS

usage: create_ics_psrfits.py [-h] [-b BASE_DIR] [-l {DEBUG,INFO,WARNING}] [-V]
                             obsID

optional arguments:
  -h, --help            show this help message and exit
  -b BASE_DIR, --base_dir BASE_DIR
                        Base directory to look and then create the PSRFITS. In
                        the directory provided, there MUST exist a 'combined'
                        subfolder. An additional subfolder named 'ics' will be
                        created as a result of the incoherent sum creation.
                        Default is /group/mwavcs/vcs/[obsID]
  -l {DEBUG,INFO,WARNING}, --loglvl {DEBUG,INFO,WARNING}
                        Desired logging verbosity level
  -V, --version         Print version and quit

find_pulsar_in_obs.py

This code is used to list the sources within the beam of observations IDs or using –obs_for_source list all the observations for each source. The sources can be input serval ways: using a list of pulsar names (–pulsar), using a complete catalogue file of pulsars (–dl_PSRCAT) or RRATs (–RRAT and –dl_RRAT), using a compatable catalogue (–in_cat with the help of –names and –coordstype) or using a RA and DEC coordinate (–coords). The observation IDs can be input (–obsid) or gathered from a directory (–FITS_dir). The default is to search all observation IDs from http://mwa- metadata01.pawsey.org.au/metadata/ that have voltages and list every known pulsar from PSRCAT in each observation ID.

usage: find_pulsar_in_obs.py [-h] [--obs_for_source] [-b BEAM] [-m MIN_POWER]
                             [--sn_est] [--flux_est] [--plot_est]
                             [--output OUTPUT] [-L {DEBUG,INFO,WARNING}] [-V]
                             [-p [PULSAR [PULSAR ...]]] [--max_dm MAX_DM]
                             [--source_type SOURCE_TYPE] [--in_cat IN_CAT]
                             [-c [COORDS [COORDS ...]]] [--FITS_dir FITS_DIR]
                             [-o [OBSID [OBSID ...]]] [--min_time MIN_TIME]
                             [--freq_chan FREQ_CHAN] [--contig] [--all_volt]
                             [--cal_check]

optional arguments:
  -h, --help            show this help message and exit
  --obs_for_source      Instead of listing all the sources in each observation
                        it will list all of the observations for each source.
                        For increased efficiency it will only search OBSIDs
                        within the primary beam. (default: False)
  -b BEAM, --beam BEAM  Decides the beam approximation that will be used.
                        Options: "analytic" the analytic beam model (2012
                        model, fast and reasonably accurate), "advanced" the
                        advanced beam model (2014 model, fast and slighty more
                        accurate) or "full_EE" the full EE model (2016 model,
                        slow but accurate). " Default: "analytic" (default:
                        analytic)
  -m MIN_POWER, --min_power MIN_POWER
                        The minimum fraction of the zenith normalised power
                        that a source needs to have to be recorded. Default
                        0.3 (default: 0.3)
  --sn_est              Make a expected signal to noise calculation using the
                        flux densities from the ANTF pulsar catalogue and
                        include them in the output file. Default: False.
                        (default: False)
  --flux_est            Make a expected flux density calculation using the
                        flux densities from the ANTF pulsar catalogue and
                        include them in the output file. Default: False.
                        (default: False)
  --plot_est            If used, will output flux estimation plots while
                        sn_est arg is true. Default: False. (default: False)
  --output OUTPUT       Chooses a file for all the text files to be output to.
                        The default is your current directory (default: ./)
  -L {DEBUG,INFO,WARNING}, --loglvl {DEBUG,INFO,WARNING}
                        Logger verbosity level. Default: INFO (default: INFO)
  -V, --version         Print version and quit (default: False)
  --min_time MIN_TIME   The minimum observation duration to include in output
                        files. Default 0 (default: 0)
  --freq_chan FREQ_CHAN
                        Only use observations that include this frequency
                        channel. (default: None)
  --contig              Only use observations that have contiguous frequency
                        channels. (default: False)

mwa_metadb_utils.py

Returns information on an input Obs ID

usage: mwa_metadb_utils.py [-h] [-c] obsid

positional arguments:
  obsid           Input Observation ID

pabeam.py

Script to calculate the array factor required to model the tied-array beam for the MWA. This is an MPI-based simulation code and will use all available processes when run (i.e. there is no user choice in how many to use)

usage: pabeam.py [-h] [-o OBSID] [--metafits METAFITS] [-f FREQ [FREQ ...]]
                 [--flagged_tiles FLAGGED_TILES [FLAGGED_TILES ...]]
                 [--delays DELAYS [DELAYS ...]] [-e EFFICIENCY] [--coplanar]
                 [-p TARGET] [-b BEGIN] [-d DURATION] [-s STEP]
                 [--grid_res GRID_RES GRID_RES] [--az AZ AZ] [--za ZA ZA]
                 [--ra_dec_projection] [--ra_dec_res RA_DEC_RES RA_DEC_RES]
                 [--ra_radius RA_RADIUS] [--dec_radius DEC_RADIUS]
                 [--out_dir OUT_DIR] [--out_name OUT_NAME] [--write]
                 [--beam_model BEAM_MODEL] [--ord_version] [--no_delays]
                 [-L {DEBUG,INFO,WARNING,ERROR}]

optional arguments:
  -h, --help            show this help message and exit

process_vcs.py

process_vcs.py is a script for processing the MWA VCS data on Galaxy in steps. It can download data from the archive, call on recombine to form course channels, run the offline correlator, make tile re-ordered and bit promoted PFB files or for a coherent beam for a given pointing.

usage: process_vcs.py [-h] [-d PARALLEL_DL] [-j UNTAR_JOBS] [-k]
                      [--ft_res FREQ RES,TIME RES FREQ RES,TIME RES]
                      [-p [POINTINGS [POINTINGS ...]]]
                      [--pointing_file POINTING_FILE] [--DI_dir DI_DIR]
                      [--bf_out_format {psrfits,vdif,both}] [--incoh] [--sum]
                      [--flagged_tiles FLAGGED_TILES] [--cal_type CAL_TYPE]
                      [-E EXECPATH] [--ipfb_filter {LSQ12,MIRROR}]
                      [--beam_version {ANALYTIC,FEE2016}]
                      [-m {download,download_ics,download_cal,recombine,correlate,beamform}]
                      [-o OBS ID] [--cal_obs CALIBRATOR OBS ID] [-b BEGIN]
                      [-e END] [-a] [--all_avail] [-i INCREMENT] [-s] [-w DIR]
                      [-c NCOARSE_CHAN] [-n NFINE_CHAN] [--mail] [-L LOGLVL]
                      [-V] [--vcstools_version VCSTOOLS_VERSION] [--nice NICE]

optional arguments:
  -h, --help            show this help message and exit
  -m {download,download_ics,download_cal,recombine,correlate,beamform}, --mode {download,download_ics,download_cal,recombine,correlate,beamform}
                        Mode you want to run. ['download', 'download_ics',
                        'download_cal', 'recombine', 'correlate', 'beamform']
                        (default: None)
  -o OBS ID, --obs OBS ID
                        Observation ID you want to process [no default]
                        (default: None)
  --cal_obs CALIBRATOR OBS ID, -O CALIBRATOR OBS ID
                        Only required in 'download_cal' mode.Observation ID of
                        calibrator you want to process. In case of in-beam
                        calibration should be the same as input to -o (obsID).
                        [no default] (default: None)
  -b BEGIN, --begin BEGIN
                        First GPS time to process [no default] (default: None)
  -e END, --end END     Last GPS time to process [no default] (default: None)
  -a, --all             Perform on entire observation span. Use instead of -b
                        & -e. (default: False)
  --all_avail           Uses all of the available combined files available
                        (does not check for gaps). [default=False] (default:
                        False)
  -i INCREMENT, --increment INCREMENT
                        Increment in seconds (how much we process at once)
                        (default: 64)
  -s                    Single step (only process one increment and this is it
                        (False == do them all) (default: False)
  -w DIR, --work_dir DIR
                        Base directory you want run things in. USE WITH
                        CAUTION! Per default raw data will will be downloaded
                        into /astro/mwavcs/vcs/[obsID] and data products will
                        be in /group/mwavcs/vcs/[obsID]. If set, this will
                        create a folder for the Obs. ID if it doesn't exist
                        (default: None)
  -c NCOARSE_CHAN, --ncoarse_chan NCOARSE_CHAN
                        Coarse channel count (how many to process) (default:
                        24)
  -n NFINE_CHAN, --nfine_chan NFINE_CHAN
                        Number of fine channels per coarse channel (default:
                        128)
  --mail                Enables e-mail notification about start, end, and fail
                        of jobs. Currently only implemented for beamformer
                        mode. (default: False)
  -L LOGLVL, --loglvl LOGLVL
                        Logger verbosity level. Default: INFO (default: INFO)
  -V, --version         Print version and quit (default: False)
  --vcstools_version VCSTOOLS_VERSION
                        VCSTools version to load in jobs (i.e. on the queues)
                        (default: master)
  --nice NICE           Reduces your priority of Slurm Jobs. (default: 0)

prof_estimate.py

A utility file for calculating a variety of pulse profile properties

usage: prof_estimate.py [-h] [--bestprof BESTPROF] [--ascii ASCII]
                        [--archive ARCHIVE] [--max_N MAX_N]
                        [--min_comp_len MIN_COMP_LEN]
                        [--clip_type {regular,noisy,verbose}]
                        [--plot_name PLOT_NAME] [-L LOGLVL]

optional arguments:
  -h, --help            show this help message and exit

recombine.py

Combines raw VCS data

usage: recombine.py [-h] -o OBSID -s START -d DURATION [-w DATA_DIR]
                    [-p OUTPUT_BASE_DIR] [-e RECOMBINE_COMMAND]
                    [-L {DEBUG,INFO,WARNING,ERROR}] [-V]

optional arguments:
  -h, --help            show this help message and exit
  -o OBSID, --obsid OBSID
                        Input Observation ID.
  -s START, --start START
                        First GPS second of data to recombine.
  -d DURATION, --duration DURATION
                        Seconds of data to recomine
  -w DATA_DIR, --data_dir DATA_DIR
                        Directory containing the raw data
  -p OUTPUT_BASE_DIR, --output_base_dir OUTPUT_BASE_DIR
                        The base directory to put the recombined data. Eg
                        /astro/mwavcs/vcs/<obsid>.
  -e RECOMBINE_COMMAND, --recombine_command RECOMBINE_COMMAND
                        the filename of the recombine function. Default:
                        recombine
  -L {DEBUG,INFO,WARNING,ERROR}, --loglvl {DEBUG,INFO,WARNING,ERROR}
                        Logger verbosity level. Default: INFO
  -V, --version         Print version and quit

rename_corr_output.py

Script to rename the files that are produced by the offline correlator to the convention assumed by Andr Offringa’s tools.

usage: rename_corr_output.py [-h] -o OBS ID -b start [-e stop] [-n n_secs]
                             [-w WORKDIR] [-V]

optional arguments:
  -h, --help            show this help message and exit
  -o OBS ID, --obs OBS ID
                        Observation ID you want to process [no default]
  -b start, --begin start
                        Time string of first file that needs renaming.
                        Format=YYYYMMDDHHMMSS. [default=None]
  -e stop, --end stop   Time string of last file that needs renaming.
                        Format=YYYYMMDDHHMMSS. [default=None]
  -n n_secs, --nsec n_secs
                        Number of seconds that need renaming. Maximal
                        100.[default=100]
  -w WORKDIR, --workdir WORKDIR
                        Directory that contains the output files of the
                        offline Correlator. Default is
                        /astro/mwavcs/vcs/<obsID/vis.
  -V, --version         Print version and quit

reorder_chans.py

Print the coarse channel sequence as in gpubox/subband order. Make sure you have *_metafits_ppds.fits

usage: reorder_chans.py [-h] -o OBSID [-m MFITS] [-V]

optional arguments:
  -h, --help            show this help message and exit
  -o OBSID, --obsid OBSID
                        Observation ID of target
  -m MFITS, --mfits MFITS
                        Please provide the path of the *_metafits_ppds.fits if
                        it is not
                        /astro/mwavcs/vcs/[OBID]/*_metafits_ppds.fits
  -V, --version         Print version and quit

rm_synthesis.py

A script that performs the RM synthesis technique

usage: rm_synthesis.py [-h] -a ARCHIVE
                       [--phase_ranges PHASE_RANGES [PHASE_RANGES ...]]
                       [--phi_steps PHI_STEPS]
                       [--phi_range PHI_RANGE [PHI_RANGE ...]]
                       [--force_single] [--label LABEL] [--write] [--plot_rm]
                       [--plot_gfit] [--keep_QUV] [--cliptype CLIPTYPE]
                       [-d WORK_DIR] [-L {DEBUG,INFO,WARNING,ERROR}]

optional arguments:
  -h, --help            show this help message and exit

rts2ao.py

rts2ao.py is a tool for converting an RTS solution to an Offringa-style solution.

usage: rts2ao.py [-h] [-d DIR] [-m METAFITS] [-r RTS_GLOB] [-o OUTFILE]
                 [-L {DEBUG,INFO,WARNING}] [-V]

optional arguments:
  -h, --help            show this help message and exit
  -d DIR, --dir DIR     Directory containing RTS solution files (DI_Jones...)
                        (default: ./)
  -m METAFITS, --metafits METAFITS
                        Metafits file from which to determine antenna and
                        channel order (default: None)
  -r RTS_GLOB, --rts_glob RTS_GLOB
                        Filename globbing pattern for the RTS direction
                        independent solution files (default:
                        DI_JonesMatrices_node[0-9]*.dat)
  -o OUTFILE, --outfile OUTFILE
                        Name of the file to write (default:
                        calibration_solution.bin)
  -L {DEBUG,INFO,WARNING}, --loglvl {DEBUG,INFO,WARNING}
                        Logger verbosity level. Default: INFO (default: INFO)
  -V, --version         Print version and quit (default: False)

sn_flux_est.py

.. _splice-wrapper.py-label:

splice_wrapper.py

Wraps the splice_psrfits.sh script to automate it. Should be run from the foulder containing the files.

usage: splice_wrapper.py [-h] [-o OBSERVATION] [-i] [-d] [-w WORK_DIR]
                         [-c CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS]

optional arguments:
  -h, --help            show this help message and exit
  -o OBSERVATION, --observation OBSERVATION
                        The observation ID to be used.
  -i, --incoh           Use this check if there are and incoh files from the
                        beamformer.
  -d, --delete          This will cause the script to remove the unspliced
                        files if splice_psrfits.sh succeeds (error code of 0).
  -w WORK_DIR, --work_dir WORK_DIR
                        Working directory of the vcs files.
  -c CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS, --channels CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS CHANNELS
                        A list of the observations channel IDs for example "-c
                        109 110 111 112 113 114 115 116 117 118 119 120 121
                        122 123 124 125 126 127 128 129 130 131 132". If this
                        option is not used a metadata call will be used to
                        find the channel IDs.

submit_to_database.py

This code is used to submit pulsar detections and observation calibrations to the MWA Pulsar Database. It can calculate all need values (flux density, width, scattering) for each detection and submit them to the pulsar database without having to manually input them. It can also submit diagnostic files such as pulse profiles and calibrations. This code assumes that the observation is coherent and correlated using the RTS so please use –incoh and –andre if your observation is incoherent or correlated using Andre’s Tools respectively.

usage: submit_to_database.py [-h] [-o OBSID] [-O CALID] [-p PULSAR] [--incoh]
                             [--andre] [--sefd_file SEFD_FILE] [--simple_sefd]
                             [--vcstools_version VCSTOOLS_VERSION]
                             [-L {DEBUG,INFO,WARNING}] [-V] [-b BESTPROF]
                             [--ascii ASCII] [--dont_upload]
                             [--pointing POINTING] [--start START]
                             [--stop STOP] [--trcvr TRCVR]
                             [--cal_dir_to_tar CAL_DIR_TO_TAR]
                             [--srclist SRCLIST] [-c CALIBRATION] [-a ARCHIVE]
                             [--single_pulse_series SINGLE_PULSE_SERIES]
                             [--ppps PPPS] [-i IPPD] [-w WATERFALL]

A common use case is to simply upload a calibration file (this can be done before a detection is uploaded)
> submit_to_database.py --cal_dir_to_tar <calibration directory> --srclist <srclist> -o <obs ID> -O <calibrator obs ID>
Another is to record a pulsar detection and its paramters, such as flux density and pulse width, to the database. To do this the bestprof file is needed
> submit_to_database.py -b <bestprof file location>
Diagnostic files (see Upload Options) such as PRESTO plots can be uploaded using:
> submit_to_database.py  -o <obs ID> -O <calibrator obs ID> -p <pulsar> --ppps <PRESTO prepfold output post script file location>
The diagnostic files can be created using the Dspsr Calculation Options (not robustly tested).

zapchan.py

Output the correctly formated MWA band edge channels and user-defined channels to remove for aliasing/RFI excision. If no options are given, returns an empty string.

usage: zapchan.py [-h] [-N Nchan] [-C Nchan Nchan] [-Z] [-n Nedge] [-m]
                  [-z chan [chan ...]] [-r] [-p filename]
                  [-L {DEBUG,INFO,WARNING}] [-V]

optional arguments:
  -h, --help            show this help message and exit
  -N Nchan, --nchans Nchan
                        TOTAL number of frequency channels in data set.
                        Assumes 128 fine channels per coarse channel.
                        (default: None)
  -C Nchan Nchan, --n_coarse_fine Nchan Nchan
                        Number of coarse channels followed by the number of
                        fine channels per coarse channel. This options
                        overrides --nchans. (default: None)
  -Z, --zapedges        Zap the fine channel edges of the coarse channels.
                        (default: False)
  -n Nedge, --nzap Nedge
                        Number of edge channels to remove from each side of a
                        coarse channel. If given, but --zapedges is not then
                        this argument is ignored. (default: 20)
  -m, --middle          Flag the center fine channels for each coarse channel?
                        (default: False)
  -z chan [chan ...]    Individual channels to zap (default: None)
  -r, --rfifind         Output to screen the edge channels in a format
                        readable by the PRESTO rfifind routine (default:
                        False)
  -p filename, --paz filename
                        Output channels for PSRCHIVE paz routine into the
                        given file, using paz's '-k filename' option (default:
                        None)
  -L {DEBUG,INFO,WARNING}, --loglvl {DEBUG,INFO,WARNING}
                        Logger verbosity level. Default: WARNING (default:
                        WARNING)
  -V, --version         Print version and quit (default: False)