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