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.nc
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