Command line interface

HEN2xspec

usage: HEN2xspec [-h] [--flx2xsp] [--loglevel LOGLEVEL] [--debug] files [files ...]

Save a frequency spectrum in a qdp file that can be read by flx2xsp and produce a XSpec-compatible spectrumfile

positional arguments:
  files                List of files

options:
  -h, --help           show this help message and exit
  --flx2xsp            Also call flx2xsp at the end
  --loglevel LOGLEVEL  use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug              set DEBUG logging level

HENaccelsearch

usage: HENaccelsearch [-h] [--outfile OUTFILE] [--emin EMIN] [--emax EMAX] [--fmin FMIN] [--fmax FMAX] [--nproc NPROC] [--zmax ZMAX] [--delta-z DELTA_Z] [--interbin]
                      [--pad-to-double] [--detrend DETREND] [--deorbit-par DEORBIT_PAR] [--red-noise-filter] [--loglevel LOGLEVEL] [--debug]
                      fname

Run the accelerated search on pulsar data.

positional arguments:
  fname                 Input file name

options:
  -h, --help            show this help message and exit
  --outfile OUTFILE     Output file name
  --emin EMIN           Minimum energy (or PI if uncalibrated) to plot
  --emax EMAX           Maximum energy (or PI if uncalibrated) to plot
  --fmin FMIN           Minimum frequency to search, in Hz
  --fmax FMAX           Maximum frequency to search, in Hz
  --nproc NPROC         Number of processors to use
  --zmax ZMAX           Maximum acceleration (in spectral bins)
  --delta-z DELTA_Z     Fdot step for search (1 is the default resolution)
  --interbin            Use interbinning
  --pad-to-double       Pad to the double of bins (sort-of interbinning)
  --detrend DETREND     Detrending timescale
  --deorbit-par DEORBIT_PAR
                        Parameter file in TEMPO2/PINT format
  --red-noise-filter    Correct FFT for red noise (use with caution)
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENbaseline

usage: HENbaseline [-h] [-o OUT] [--loglevel LOGLEVEL] [--debug] [-p ASYMMETRY] [-l LAM] files [files ...]

Subtract a baseline from the lightcurve using the Asymmetric Least Squares algorithm. The two parameters p and lambda control the asymmetry and smoothness of the baseline. See
below for details.

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  -o OUT, --out OUT     Output file
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               use DEBUG logging level
  -p ASYMMETRY, --asymmetry ASYMMETRY
                        "asymmetry" parameter. Smaller values make the baseline more "horizontal". Typically 0.001 < p < 0.1, but not necessarily.
  -l LAM, --lam LAM     lambda, or "smoothness", parameter. Larger values make the baseline stiffer. Typically 1e2 < lam < 1e9

HENbinary

usage: HENbinary [-h] [-l MAX_LENGTH] [-b BINTIME] [-e ENERGY_INTERVAL ENERGY_INTERVAL] [-p DEORBIT_PAR] [--nproc NPROC] [--loglevel LOGLEVEL] [--debug] files [files ...]

Save light curves in a format readable to PRESTO

positional arguments:
  files                 List of input light curves

options:
  -h, --help            show this help message and exit
  -l MAX_LENGTH, --max-length MAX_LENGTH
                        Maximum length of light curves (split otherwise)
  -b BINTIME, --bintime BINTIME
                        Bin time
  -e ENERGY_INTERVAL ENERGY_INTERVAL, --energy-interval ENERGY_INTERVAL ENERGY_INTERVAL
                        Energy interval used for filtering
  -p DEORBIT_PAR, --deorbit-par DEORBIT_PAR
                        Deorbit data with this parameter file (requires PINT installed)
  --nproc NPROC         Number of processors to use
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENcalibrate

usage: HENcalibrate [-h] [-r RMF] [--rough] [-o] [--nproc NPROC] [--loglevel LOGLEVEL] [--debug] files [files ...]

Calibrate clean event files by associating the correct energy to each PI channel. Uses either a specified rmf file or (for NuSTAR only) an rmf file from the CALDB

positional arguments:
  files                List of files

options:
  -h, --help           show this help message and exit
  -r RMF, --rmf RMF    rmf file used for calibration. Not working with XMM data
  --rough              Rough calibration, without rmf file (only for NuSTAR, XMM, and NICER). Only for compatibility purposes. This is done automatically by HENreadevents
  -o, --overwrite      Overwrite; default: no
  --nproc NPROC        Number of processors to use
  --loglevel LOGLEVEL  use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug              set DEBUG logging level

HENcolors

usage: HENcolors [-h] -e ENERGIES ENERGIES ENERGIES ENERGIES [-b BINTIME] [--use-pi] [-o OUTFILE] [--loglevel LOGLEVEL] [--debug] files [files ...]

Calculate color light curves

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  -e ENERGIES ENERGIES ENERGIES ENERGIES, --energies ENERGIES ENERGIES ENERGIES ENERGIES
                        The energy boundaries in keV used to calculate the color. E.g. -e 2 3 4 6 means that the color will be calculated as 4.-6./2.-3. keV. If --use-pi is
                        specified, these are interpreted as PI channels
  -b BINTIME, --bintime BINTIME
                        Bin time
  --use-pi              Use the PI channel instead of energies
  -o OUTFILE, --outfile OUTFILE
                        Output file
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENcreategti

usage: HENcreategti [-h] [-f FILTER] [-c] [--overwrite] [-a APPLY_GTI] [-l MINIMUM_LENGTH] [--safe-interval SAFE_INTERVAL SAFE_INTERVAL] [--loglevel LOGLEVEL] [--debug]
                    files [files ...]

Create GTI files from a filter expression, or applies previously created GTIs to a file

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  -f FILTER, --filter FILTER
                        Filter expression, that has to be a valid Python boolean operation on a data variable contained in the files
  -c, --create-only     If specified, creates GTIs withouth applyingthem to files (Default: False)
  --overwrite           Overwrite original file (Default: False)
  -a APPLY_GTI, --apply-gti APPLY_GTI
                        Apply a GTI from this file to input files
  -l MINIMUM_LENGTH, --minimum-length MINIMUM_LENGTH
                        Minimum length of GTIs (below this length, they will be discarded)
  --safe-interval SAFE_INTERVAL SAFE_INTERVAL
                        Interval at start and stop of GTIs used for filtering
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENdeorbit

usage: HENdeorbit [-h] [-p DEORBIT_PAR] [--loglevel LOGLEVEL] [--debug] files [files ...]

Deorbit the event arrival times

positional arguments:
  files                 Input event file

options:
  -h, --help            show this help message and exit
  -p DEORBIT_PAR, --deorbit-par DEORBIT_PAR
                        Deorbit data with this parameter file (requires PINT installed)
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENdumpdyn

usage: HENdumpdyn [-h] [--noplot] files [files ...]

Dump dynamical (cross) power spectra. This script is being reimplemented. Please be patient :)

positional arguments:
  files       List of files in any valid HENDRICS format for PDS or CPDS

options:
  -h, --help  show this help message and exit
  --noplot    plot results

HENefsearch

usage: HENefsearch [-h] -f FMIN -F FMAX [--emin EMIN] [--emax EMAX] [--mean-fdot MEAN_FDOT] [--mean-fddot MEAN_FDDOT] [--fdotmin FDOTMIN] [--fdotmax FDOTMAX] [--dynstep DYNSTEP]
                   [--npfact NPFACT] [--n-transient-intervals N_TRANSIENT_INTERVALS] [-n NBIN] [--segment-size SEGMENT_SIZE] [--step STEP] [--oversample OVERSAMPLE] [--fast]
                   [--ffa] [--transient] [--expocorr] [--find-candidates] [--conflevel CONFLEVEL] [--fit-candidates] [--curve CURVE] [--fit-frequency FIT_FREQUENCY] [-N N]
                   [-p DEORBIT_PAR] [--loglevel LOGLEVEL] [--debug]
                   files [files ...]

Search for pulsars using the epoch folding or the Z_n^2 algorithm

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  -f FMIN, --fmin FMIN  Minimum frequency to fold
  -F FMAX, --fmax FMAX  Maximum frequency to fold
  --emin EMIN           Minimum energy (or PI if uncalibrated) to plot
  --emax EMAX           Maximum energy (or PI if uncalibrated) to plot
  --mean-fdot MEAN_FDOT
                        Mean fdot to fold (only useful when using --fast)
  --mean-fddot MEAN_FDDOT
                        Mean fddot to fold (only useful when using --fast)
  --fdotmin FDOTMIN     Minimum fdot to fold
  --fdotmax FDOTMAX     Maximum fdot to fold
  --dynstep DYNSTEP     Dynamical EF step
  --npfact NPFACT       Size of search parameter space
  --n-transient-intervals N_TRANSIENT_INTERVALS
                        Number of transient intervals to investigate
  -n NBIN, --nbin NBIN  Number of phase bins of the profile
  --segment-size SEGMENT_SIZE
                        Size of the event list segment to use (default None, implying the whole observation)
  --step STEP           Step size of the frequency axis. Defaults to 1/oversample/observ.length.
  --oversample OVERSAMPLE
                        Oversampling factor - frequency resolution improvement w.r.t. the standard FFT's 1/observ.length.
  --fast                Use a faster folding algorithm. It automatically searches for the first spin derivative using an optimized step.This option ignores expocorr, fdotmin/max,
                        segment-size, and step
  --ffa                 Use *the* Fast Folding Algorithm by Staelin+69. No accelerated search allowed at the moment. Only recommended to search for slow pulsars.
  --transient           Look for transient emission (produces an animated GIF with the dynamic Z search)
  --expocorr            Correct for the exposure of the profile bins. This method is *much* slower, but it is useful for very slow pulsars, where data gaps due to occultation or
                        SAA passages can significantly alter the exposure of different profile bins.
  --find-candidates     Find pulsation candidates using thresholding
  --conflevel CONFLEVEL
                        percent confidence level for thresholding [0-100).
  --fit-candidates      Fit the candidate peaks in the periodogram
  --curve CURVE         Kind of curve to use (sinc or Gaussian)
  --fit-frequency FIT_FREQUENCY
                        Force the candidate frequency to FIT_FREQUENCY
  -N N                  The number of harmonics to use in the search (the 'N' in Z^2_N; only relevant to Z search!)
  -p DEORBIT_PAR, --deorbit-par DEORBIT_PAR
                        Deorbit data with this parameter file (requires PINT installed)
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENexcvar

usage: HENexcvar [-h] [-c CHUNK_LENGTH] [--fraction-step FRACTION_STEP] [--norm NORM] [--loglevel LOGLEVEL] [--debug] files [files ...]

Calculate excess variance in light curve chunks

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  -c CHUNK_LENGTH, --chunk-length CHUNK_LENGTH
                        Length in seconds of the light curve chunks
  --fraction-step FRACTION_STEP
                        If the step is not a full chunk_length but less,this indicates the ratio between step step and `chunk_length`
  --norm NORM           Choose between fvar, excvar and norm_excvar normalization, referring to Fvar, excess variance, and normalized excess variance respectively (see Vaughan et
                        al. 2003 for details).
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENexposure

usage: HENexposure [-h] [-o OUTROOT] [--plot] [--loglevel LOGLEVEL] [--debug] lcfile uffile

Create exposure light curve based on unfiltered event files.

positional arguments:
  lcfile                Light curve file (HENDRICS format)
  uffile                Unfiltered event file (FITS)

options:
  -h, --help            show this help message and exit
  -o OUTROOT, --outroot OUTROOT
                        Root of output file names
  --plot                Plot on window
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENfake

usage: HENfake [-h] [-e EVENT_LIST] [-l LC] [-c CTRATE] [-o OUTNAME] [-i INSTRUMENT] [-m MISSION] [--tstart TSTART] [--tstop TSTOP] [--mjdref MJDREF]
               [--deadtime DEADTIME [DEADTIME ...]] [--loglevel LOGLEVEL] [--debug]

Create an event file in FITS format from an event list, or simulating it. If input event list is not specified, generates the events randomly

options:
  -h, --help            show this help message and exit
  -e EVENT_LIST, --event-list EVENT_LIST
                        File containing event list
  -l LC, --lc LC        File containing light curve
  -c CTRATE, --ctrate CTRATE
                        Count rate for simulated events
  -o OUTNAME, --outname OUTNAME
                        Output file name
  -i INSTRUMENT, --instrument INSTRUMENT
                        Instrument name
  -m MISSION, --mission MISSION
                        Mission name
  --tstart TSTART       Start time of the observation (s from MJDREF)
  --tstop TSTOP         End time of the observation (s from MJDREF)
  --mjdref MJDREF       Reference MJD
  --deadtime DEADTIME [DEADTIME ...]
                        Dead time magnitude. Can be specified as a single number, or two. In this last case, the second value is used as sigma of the dead time distribution
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENfiltevents

usage: HENfiltevents [-h] [--emin EMIN] [--emax EMAX] [--loglevel LOGLEVEL] [--debug] [--test] files [files ...]

Filter events

positional arguments:
  files                Input event files

options:
  -h, --help           show this help message and exit
  --emin EMIN          Minimum energy (or PI if uncalibrated) to plot
  --emax EMAX          Maximum energy (or PI if uncalibrated) to plot
  --loglevel LOGLEVEL  use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug              set DEBUG logging level
  --test               Only used for tests

HENfold

usage: HENfold [-h] [-f FREQ] [--fdot FDOT] [--fddot FDDOT] [--tref TREF] [-n NBIN] [--nebin NEBIN] [--emin EMIN] [--emax EMAX] [--out-file-root OUT_FILE_ROOT] [--pepoch PEPOCH]
               [--norm NORM] [--colormap COLORMAP] [-p DEORBIT_PAR] [--loglevel LOGLEVEL] [--debug] [--test]
               file

Plot a folded profile

positional arguments:
  file                  Input event file

options:
  -h, --help            show this help message and exit
  -f FREQ, --freq FREQ  Initial frequency to fold
  --fdot FDOT           Initial fdot
  --fddot FDDOT         Initial fddot
  --tref TREF           Reference time (same unit as time array)
  -n NBIN, --nbin NBIN  Number of phase bins (X axis) of the profile
  --nebin NEBIN         Number of energy bins (Y axis) of the profile
  --emin EMIN           Minimum energy (or PI if uncalibrated) to plot
  --emax EMAX           Maximum energy (or PI if uncalibrated) to plot
  --out-file-root OUT_FILE_ROOT
                        Root of the output files (plots and csv tables)
  --pepoch PEPOCH       Reference epoch for timing parameters (MJD)
  --norm NORM           Normalization for the dynamical phase plot. Can be: 'to1' (each profile normalized from 0 to 1); 'std' (subtract the mean and divide by the standard
                        deviation); 'sub' (just subtract the mean of each profile); 'ratios' (divide by the average profile, to highlight changes). Prepending 'median' to any of
                        those options uses the median in place of the mean. Appending '_smooth' smooths the 2d array with a Gaussian filter. E.g. mediansub_smooth subtracts the
                        median and smooths the imagedefault None
  --colormap COLORMAP   Change the color map of the image. Any matplotlib colormap is valid
  -p DEORBIT_PAR, --deorbit-par DEORBIT_PAR
                        Deorbit data with this parameter file (requires PINT installed)
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level
  --test                Only used for tests

HENfspec

usage: HENfspec [-h] [-b BINTIME] [-r REBIN] [-f FFTLEN] [-k KIND] [--norm NORM] [--noclobber] [-o OUTROOT] [--back BACK] [--save-dyn] [--ignore-instr] [--ignore-gtis]
                [--save-all] [--save-lcs] [--no-auxil] [--test] [--emin EMIN] [--emax EMAX] [--lombscargle] [--loglevel LOGLEVEL] [--debug]
                files [files ...]

Create frequency spectra (PDS, CPDS, cospectrum) starting from well-defined input ligthcurves

positional arguments:
  files                 List of light curve files

options:
  -h, --help            show this help message and exit
  -b BINTIME, --bintime BINTIME
                        Light curve bin time; if negative, interpreted as negative power of 2. Default: 2^-10, or keep input lc bin time (whatever is larger)
  -r REBIN, --rebin REBIN
                        (C)PDS rebinning to apply. Default: none
  -f FFTLEN, --fftlen FFTLEN
                        Length of FFTs. Default: 512 s
  -k KIND, --kind KIND  Spectra to calculate, as comma-separated list (Accepted: PDS and CPDS; Default: "PDS,CPDS")
  --norm NORM           Normalization to use (Accepted: leahy and rms; Default: "leahy")
  --noclobber           Do not overwrite existing files
  -o OUTROOT, --outroot OUTROOT
                        Root of output file names for CPDS only
  --back BACK           Estimated background (non-source) count rate
  --save-dyn            save dynamical power spectrum
  --ignore-instr        Ignore instrument names in channels
  --ignore-gtis         Ignore GTIs. USE AT YOUR OWN RISK
  --save-all            Save all information contained in spectra, including light curves and dynamical spectra.
  --save-lcs            Save all information contained in spectra, including light curves.
  --no-auxil            Do not save auxiliary spectra (e.g. pds1 and pds2 of cross spectrum)
  --test                Only to be used in testing
  --emin EMIN           Minimum energy (or PI if uncalibrated) to plot
  --emax EMAX           Maximum energy (or PI if uncalibrated) to plot
  --lombscargle         Use Lomb-Scargle periodogram or cross spectrum (will ignore segment_size)
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENjoinevents

usage: HENjoinevents [-h] [-o OUTPUT] [--ignore-instr] files [files ...]

Read a cleaned event files and saves the relevant information in a standard format

positional arguments:
  files                 Files to join

options:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        Name of output file
  --ignore-instr        Ignore instrument names in channels

HENlags

usage: HENlags [-h] [--loglevel LOGLEVEL] [--debug] files [files ...]

Read timelags from cross spectrum results and save them to a qdp file

positional arguments:
  files                List of files

options:
  -h, --help           show this help message and exit
  --loglevel LOGLEVEL  use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug              set DEBUG logging level

HENlcurve

usage: HENlcurve [-h] [-b BINTIME] [--safe-interval SAFE_INTERVAL SAFE_INTERVAL] [-e ENERGY_INTERVAL ENERGY_INTERVAL] [--pi-interval PI_INTERVAL PI_INTERVAL] [-s] [-j] [-g]
                 [--minlen MINLEN] [--ignore-gtis] [-d OUTDIR] [--noclobber] [--fits-input] [--txt-input] [--weight-on WEIGHT_ON] [-p DEORBIT_PAR] [-o OUTFILE]
                 [--loglevel LOGLEVEL] [--debug] [--nproc NPROC]
                 files [files ...]

Create lightcurves starting from event files. It is possible to specify energy or channel filtering options

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  -b BINTIME, --bintime BINTIME
                        Bin time; if negative, negative power of 2
  --safe-interval SAFE_INTERVAL SAFE_INTERVAL
                        Interval at start and stop of GTIs used for filtering
  -e ENERGY_INTERVAL ENERGY_INTERVAL, --energy-interval ENERGY_INTERVAL ENERGY_INTERVAL
                        Energy interval used for filtering
  --pi-interval PI_INTERVAL PI_INTERVAL
                        PI interval used for filtering
  -s, --scrunch         Create scrunched light curve (single channel)
  -j, --join            Create joint light curve (multiple channels)
  -g, --gti-split       Split light curve by GTI
  --minlen MINLEN       Minimum length of acceptable GTIs (default:4)
  --ignore-gtis         Ignore GTIs
  -d OUTDIR, --outdir OUTDIR
                        Output directory
  --noclobber           Do not overwrite existing files
  --fits-input          Input files are light curves in FITS format
  --txt-input           Input files are light curves in txt format
  --weight-on WEIGHT_ON
                        Use a given attribute of the event list as weights for the light curve
  -p DEORBIT_PAR, --deorbit-par DEORBIT_PAR
                        Deorbit data with this parameter file (requires PINT installed)
  -o OUTFILE, --outfile OUTFILE
                        Output file
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level
  --nproc NPROC         Number of processors to use

HENmodel

usage: HENmodel [-h] [-m MODELFILE] [--fitmethod FITMETHOD] [--frequency-interval FREQUENCY_INTERVAL [FREQUENCY_INTERVAL ...]] [--loglevel LOGLEVEL] [--debug] files [files ...]

Fit frequency spectra (PDS, CPDS, cospectrum) with user-defined models

positional arguments:
  files                 List of light curve files

options:
  -h, --help            show this help message and exit
  -m MODELFILE, --modelfile MODELFILE
                        File containing an Astropy model with or without constraints
  --fitmethod FITMETHOD
                        Any scipy-compatible fit method
  --frequency-interval FREQUENCY_INTERVAL [FREQUENCY_INTERVAL ...]
                        Select frequency interval(s) to fit. Must be an even number of frequencies in Hz, like "--frequency-interval 0 2" or "--frequency-interval 0 2 5 10",
                        meaning that the spectrum will be fitted between 0 and 2 Hz, or using the intervals 0-2 Hz and 5-10 Hz.
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENphaseogram

usage: HENphaseogram [-h] [-f FREQ] [--fdot FDOT] [--fddot FDDOT] [--periodogram PERIODOGRAM] [-n NBIN] [--ntimes NTIMES] [--binary]
                     [--binary-parameters BINARY_PARAMETERS BINARY_PARAMETERS BINARY_PARAMETERS] [--emin EMIN] [--emax EMAX] [--plot-only] [--get-toa] [--pepoch PEPOCH]
                     [--norm NORM] [--colormap COLORMAP] [-p DEORBIT_PAR] [--test] [--loglevel LOGLEVEL] [--debug]
                     file

Plot an interactive phaseogram

positional arguments:
  file                  Input event file

options:
  -h, --help            show this help message and exit
  -f FREQ, --freq FREQ  Initial frequency to fold
  --fdot FDOT           Initial fdot
  --fddot FDDOT         Initial fddot
  --periodogram PERIODOGRAM
                        Periodogram file
  -n NBIN, --nbin NBIN  Number of phase bins (X axis) of the profile
  --ntimes NTIMES       Number of time bins (Y axis) of the phaseogram
  --binary              Interact on binary parameters instead of frequency derivatives
  --binary-parameters BINARY_PARAMETERS BINARY_PARAMETERS BINARY_PARAMETERS
                        Initial values for binary parameters
  --emin EMIN           Minimum energy (or PI if uncalibrated) to plot
  --emax EMAX           Maximum energy (or PI if uncalibrated) to plot
  --plot-only           Only plot the phaseogram
  --get-toa             Only calculate TOAs
  --pepoch PEPOCH       Reference epoch for timing parameters (MJD)
  --norm NORM           Normalization for the dynamical phase plot. Can be: 'to1' (each profile normalized from 0 to 1); 'std' (subtract the mean and divide by the standard
                        deviation); 'sub' (just subtract the mean of each profile); 'ratios' (divide by the average profile, to highlight changes). Prepending 'median' to any of
                        those options uses the median in place of the mean. Appending '_smooth' smooths the 2d array with a Gaussian filter. E.g. mediansub_smooth subtracts the
                        median and smooths the imagedefault None
  --colormap COLORMAP   Change the color map of the image. Any matplotlib colormap is valid
  -p DEORBIT_PAR, --deorbit-par DEORBIT_PAR
                        Deorbit data with this parameter file (requires PINT installed)
  --test                Only used for tests
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENphasetag

usage: HENphasetag [-h] [--parfile PARFILE] [-f FREQS [FREQS ...]] [-n NBIN] [--plot] [--tomax] [--test] [--refTOA PULSE_REF_TIME] [--pepoch PEPOCH] file

positional arguments:
  file                  Event file

options:
  -h, --help            show this help message and exit
  --parfile PARFILE     Parameter file
  -f FREQS [FREQS ...], --freqs FREQS [FREQS ...]
                        Frequency derivatives
  -n NBIN, --nbin NBIN  Nbin
  --plot                Plot profile
  --tomax               Refer phase to pulse max
  --test                Only for unit tests! Do not use
  --refTOA PULSE_REF_TIME
                        Reference TOA in MJD (overrides --tomax) for reference pulse phase
  --pepoch PEPOCH       Reference time for timing solution

HENplot

usage: HENplot [-h] [--noplot] [--CCD] [--HID] [--figname FIGNAME] [-o OUTFILE] [--xlog] [--ylog] [--xlin] [--ylin] [--white-sub] [--fromstart] [--axes AXES AXES]
               files [files ...]

Plot the content of HENDRICS light curves and frequency spectra

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  --noplot              Only create images, do not plot
  --CCD                 This is a color-color diagram. In this case, the list of files is expected to be given as soft0.nc, hard0.nc, soft1.nc, hard1.nc, ...
  --HID                 This is a hardness-intensity diagram. In this case, the list of files is expected to be given as color0.nc, intensity0.nc, color1.nc, intensity1.nc, ...
  --figname FIGNAME     Figure name
  -o OUTFILE, --outfile OUTFILE
                        Output data file in QDP format
  --xlog                Use logarithmic X axis
  --ylog                Use logarithmic Y axis
  --xlin                Use linear X axis
  --ylin                Use linear Y axis
  --white-sub           Subtract Poisson noise (only applies to PDS)
  --fromstart           Times are measured from the start of the observation (only relevant for light curves)
  --axes AXES AXES      Plot two variables contained in the file

HENpowercolors

usage: HENpowercolors [-h] [-f FREQUENCY_EDGES FREQUENCY_EDGES FREQUENCY_EDGES FREQUENCY_EDGES FREQUENCY_EDGES] [-r REBIN] [-s SEGMENT_SIZE] [--poisson-noise POISSON_NOISE]
                      [-b BINTIME] [--cross] [-o OUTFILE] [--loglevel LOGLEVEL] [--debug]
                      files [files ...]

Calculate color light curves

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  -f FREQUENCY_EDGES FREQUENCY_EDGES FREQUENCY_EDGES FREQUENCY_EDGES FREQUENCY_EDGES, --frequency-edges FREQUENCY_EDGES FREQUENCY_EDGES FREQUENCY_EDGES FREQUENCY_EDGES FREQUENCY_EDGES
                        Five frequency edges in Hz, delimiting four frequency ranges used to calculate the power colors
  -r REBIN, --rebin REBIN
                        Dynamical power spectrum rebinning (how many nearby segments to average before calculating the colors) to apply. Default: 5
  -s SEGMENT_SIZE, --segment-size SEGMENT_SIZE
                        Length of FFTs. Default: 512 s
  --poisson-noise POISSON_NOISE
                        Poisson noise level of the periodograms. Default: 2 for powerspectrum, 0 for crossspectrum
  -b BINTIME, --bintime BINTIME
                        Light curve bin time; if negative, interpreted as negative power of 2. Default: 2^-10, or keep input lc bin time (whatever is larger)
  --cross               Use cross spectrum from pairs of files
  -o OUTFILE, --outfile OUTFILE
                        Output file
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENreadevents

usage: HENreadevents [-h] [--noclobber] [-g] [--discard-calibration] [-l LENGTH_SPLIT] [--min-length MIN_LENGTH] [--gti-string GTI_STRING] [--randomize-by RANDOMIZE_BY]
                     [--fill-small-gaps FILL_SMALL_GAPS] [--additional ADDITIONAL [ADDITIONAL ...]] [-o OUTFILE] [--loglevel LOGLEVEL] [--debug] [--nproc NPROC]
                     files [files ...]

Read a cleaned event files and saves the relevant information in a standard format

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  --noclobber           Do not overwrite existing event files
  -g, --gti-split       Split event list by GTI
  --discard-calibration
                        Discard automatic calibration (if any)
  -l LENGTH_SPLIT, --length-split LENGTH_SPLIT
                        Split event list by length
  --min-length MIN_LENGTH
                        Minimum length of GTIs to consider
  --gti-string GTI_STRING
                        GTI string
  --randomize-by RANDOMIZE_BY
                        Randomize event arrival times by this amount (e.g. it might be the 0.073-s frame time in XMM)
  --fill-small-gaps FILL_SMALL_GAPS
                        Fill gaps between GTIs with random data, if shorter than this amount
  --additional ADDITIONAL [ADDITIONAL ...]
                        Additional columns to be read from the FITS file
  -o OUTFILE, --outfile OUTFILE
                        Output file
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level
  --nproc NPROC         Number of processors to use

HENreadfile

usage: HENreadfile [-h] [--print-header] files [files ...]

Print the content of HENDRICS files

positional arguments:
  files           List of files

options:
  -h, --help      show this help message and exit
  --print-header  Print the full FITS header if present in the meta data.

HENrebin

usage: HENrebin [-h] [-r REBIN] [--loglevel LOGLEVEL] [--debug] files [files ...]

Rebin light curves and frequency spectra.

positional arguments:
  files                 List of light curve files

options:
  -h, --help            show this help message and exit
  -r REBIN, --rebin REBIN
                        Rebinning to apply. Only if the quantity to rebin is a (C)PDS, it is possible to specify a non-integer rebin factor, in which case it is interpreted as a
                        geometrical binning factor
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENscramble

usage: HENscramble [-h] [--smooth-kind {smooth,flat,pulsed}] [--deadtime DEADTIME] [--dt DT] [--pulsed-fraction PULSED_FRACTION] [-f FREQUENCY] [--outfile OUTFILE]
                   [-p DEORBIT_PAR] [-e ENERGY_INTERVAL ENERGY_INTERVAL] [--loglevel LOGLEVEL] [--debug]
                   fname

Scramble the events inside an event list, maintaining the same energies and GTIs

positional arguments:
  fname                 File containing input event list

options:
  -h, --help            show this help message and exit
  --smooth-kind {smooth,flat,pulsed}
                        Special testing value
  --deadtime DEADTIME   Dead time magnitude. Can be specified as a single number, or two. In this last case, the second value is used as sigma of the dead time distribution
  --dt DT               Time resolution of smoothed light curve
  --pulsed-fraction PULSED_FRACTION
                        Pulsed fraction of simulated pulsations
  -f FREQUENCY, --frequency FREQUENCY
                        Pulsed fraction of simulated pulsations
  --outfile OUTFILE     Output file name
  -p DEORBIT_PAR, --deorbit-par DEORBIT_PAR
                        Deorbit data with this parameter file (requires PINT installed)
  -e ENERGY_INTERVAL ENERGY_INTERVAL, --energy-interval ENERGY_INTERVAL ENERGY_INTERVAL
                        Energy interval used for filtering
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENscrunchlc

usage: HENscrunchlc [-h] [-o OUT] [--loglevel LOGLEVEL] [--debug] files [files ...]

Sum lightcurves from different instruments or energy ranges

positional arguments:
  files                List of files

options:
  -h, --help           show this help message and exit
  -o OUT, --out OUT    Output file
  --loglevel LOGLEVEL  use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug              use DEBUG logging level

HENsplitevents

usage: HENsplitevents [-h] [-l LENGTH_SPLIT] [--overlap OVERLAP] [--split-at-mjd SPLIT_AT_MJD] fname

Reads a cleaned event files and splits the file into overlapping multiple chunks of fixed length

positional arguments:
  fname                 File 1

options:
  -h, --help            show this help message and exit
  -l LENGTH_SPLIT, --length-split LENGTH_SPLIT
                        Split event list by GTI
  --overlap OVERLAP     Overlap factor. 0 for no overlap, 0.5 for half-interval overlap, and so on.
  --split-at-mjd SPLIT_AT_MJD
                        Split at this MJD

HENsumfspec

usage: HENsumfspec [-h] [-o OUTNAME] files [files ...]

Sum (C)PDSs contained in different files

positional arguments:
  files                 List of light curve files

options:
  -h, --help            show this help message and exit
  -o OUTNAME, --outname OUTNAME
                        Output file name for summed (C)PDS. Default: tot_(c)pds.p

HENvarenergy

usage: HENvarenergy [-h] [-f FREQ_INTERVAL FREQ_INTERVAL] [--energy-values ENERGY_VALUES ENERGY_VALUES ENERGY_VALUES ENERGY_VALUES] [--segment-size SEGMENT_SIZE]
                    [--ref-band REF_BAND REF_BAND] [--rms] [--covariance] [--use-pi] [--cross-instr] [--lag] [--count] [--label LABEL] [--norm NORM] [--format FORMAT] [-b BINTIME]
                    [--loglevel LOGLEVEL] [--debug]
                    files [files ...]

Calculates variability-energy spectra

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  -f FREQ_INTERVAL FREQ_INTERVAL, --freq-interval FREQ_INTERVAL FREQ_INTERVAL
                        Frequence interval
  --energy-values ENERGY_VALUES ENERGY_VALUES ENERGY_VALUES ENERGY_VALUES
                        Choose Emin, Emax, number of intervals,interval spacing, lin or log
  --segment-size SEGMENT_SIZE
                        Length of the light curve intervals to be averaged
  --ref-band REF_BAND REF_BAND
                        Reference band when relevant
  --rms                 Calculate rms
  --covariance          Calculate covariance spectrum
  --use-pi              Energy intervals are specified as PI channels
  --cross-instr         Use data files in pairs, for example with thereference band from one and the subbands from the other (useful in NuSTAR and multiple-detector missions)
  --lag                 Calculate lag-energy
  --count               Calculate lag-energy
  --label LABEL         Additional label to be added to file names
  --norm NORM           When relevant, the normalization of the spectrum. One of ['abs', 'frac', 'rms', 'leahy', 'none']
  --format FORMAT       Output format for the table. Can be ECSV, QDP, or any other format accepted by astropy
  -b BINTIME, --bintime BINTIME
                        Bin time
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENz2vspf

usage: HENz2vspf [-h] [--ntrial NTRIAL] [--outfile OUTFILE] [--show-z-values SHOW_Z_VALUES [SHOW_Z_VALUES ...]] [--emin EMIN] [--emax EMAX] [-N N] [--loglevel LOGLEVEL] [--debug]
                 fname

Get Z2 vs pulsed fraction for a given observation. Takes the original event list, scrambles the event arrival time, adds a pulsation with random pulsed fraction, and takes the
maximum value of Z2 in a small interval around the pulsation. Does this ntrial times, and plots.

positional arguments:
  fname                 Input file name

options:
  -h, --help            show this help message and exit
  --ntrial NTRIAL       Number of trial values for the pulsed fraction
  --outfile OUTFILE     Output table file name
  --show-z-values SHOW_Z_VALUES [SHOW_Z_VALUES ...]
                        Show these Z values in the plot
  --emin EMIN           Minimum energy (or PI if uncalibrated) to plot
  --emax EMAX           Maximum energy (or PI if uncalibrated) to plot
  -N N                  The N in Z^2_N
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level

HENzsearch

usage: HENzsearch [-h] -f FMIN -F FMAX [--emin EMIN] [--emax EMAX] [--mean-fdot MEAN_FDOT] [--mean-fddot MEAN_FDDOT] [--fdotmin FDOTMIN] [--fdotmax FDOTMAX] [--dynstep DYNSTEP]
                  [--npfact NPFACT] [--n-transient-intervals N_TRANSIENT_INTERVALS] [-n NBIN] [--segment-size SEGMENT_SIZE] [--step STEP] [--oversample OVERSAMPLE] [--fast]
                  [--ffa] [--transient] [--expocorr] [--find-candidates] [--conflevel CONFLEVEL] [--fit-candidates] [--curve CURVE] [--fit-frequency FIT_FREQUENCY] [-N N]
                  [-p DEORBIT_PAR] [--loglevel LOGLEVEL] [--debug]
                  files [files ...]

Search for pulsars using the epoch folding or the Z_n^2 algorithm

positional arguments:
  files                 List of files

options:
  -h, --help            show this help message and exit
  -f FMIN, --fmin FMIN  Minimum frequency to fold
  -F FMAX, --fmax FMAX  Maximum frequency to fold
  --emin EMIN           Minimum energy (or PI if uncalibrated) to plot
  --emax EMAX           Maximum energy (or PI if uncalibrated) to plot
  --mean-fdot MEAN_FDOT
                        Mean fdot to fold (only useful when using --fast)
  --mean-fddot MEAN_FDDOT
                        Mean fddot to fold (only useful when using --fast)
  --fdotmin FDOTMIN     Minimum fdot to fold
  --fdotmax FDOTMAX     Maximum fdot to fold
  --dynstep DYNSTEP     Dynamical EF step
  --npfact NPFACT       Size of search parameter space
  --n-transient-intervals N_TRANSIENT_INTERVALS
                        Number of transient intervals to investigate
  -n NBIN, --nbin NBIN  Number of phase bins of the profile
  --segment-size SEGMENT_SIZE
                        Size of the event list segment to use (default None, implying the whole observation)
  --step STEP           Step size of the frequency axis. Defaults to 1/oversample/observ.length.
  --oversample OVERSAMPLE
                        Oversampling factor - frequency resolution improvement w.r.t. the standard FFT's 1/observ.length.
  --fast                Use a faster folding algorithm. It automatically searches for the first spin derivative using an optimized step.This option ignores expocorr, fdotmin/max,
                        segment-size, and step
  --ffa                 Use *the* Fast Folding Algorithm by Staelin+69. No accelerated search allowed at the moment. Only recommended to search for slow pulsars.
  --transient           Look for transient emission (produces an animated GIF with the dynamic Z search)
  --expocorr            Correct for the exposure of the profile bins. This method is *much* slower, but it is useful for very slow pulsars, where data gaps due to occultation or
                        SAA passages can significantly alter the exposure of different profile bins.
  --find-candidates     Find pulsation candidates using thresholding
  --conflevel CONFLEVEL
                        percent confidence level for thresholding [0-100).
  --fit-candidates      Fit the candidate peaks in the periodogram
  --curve CURVE         Kind of curve to use (sinc or Gaussian)
  --fit-frequency FIT_FREQUENCY
                        Force the candidate frequency to FIT_FREQUENCY
  -N N                  The number of harmonics to use in the search (the 'N' in Z^2_N; only relevant to Z search!)
  -p DEORBIT_PAR, --deorbit-par DEORBIT_PAR
                        Deorbit data with this parameter file (requires PINT installed)
  --loglevel LOGLEVEL   use given logging level (one between INFO, WARNING, ERROR, CRITICAL, DEBUG; default:WARNING)
  --debug               set DEBUG logging level