History¶
For a brief overview of the history and state-of-the-art in spectral timing, and for more information about the design and capabilities of Stingray, please refer to Huppenkothen et al. (2019).
Stingray originated during the 2016 workshop The X-ray Spectral-Timing Revolution: a group of X-ray astronomers and developers decided to agree on a common platform to develop a new software package. At that time, there were a number of official software packages for X-ray spectral fitting (XSPEC, ISIS, Sherpa, …), but such a widely used and standard software package did not exist for X-ray timing, that was mostly the domain of custom, proprietary software. Our goals were to merge existing efforts towards a timing package in Python, following the best guidelines for modern open-source programming, thereby providing the basis for developing spectral-timing analysis tools. We needed to provide an easily accessible scripting interface, a GUI, and an API for experienced coders. Stingray’s ultimate goal is to provide the community with a package that eases the learning curve for advanced spectral-timing techniques, with a correct statistical framework.
Further spectral-timing functionality, in particularly command line scripts based on the API defined within Stingray, is available in the package HENDRICS. A graphical user interface is under development as part of the project DAVE.
Previous projects merged to Stingray¶
Daniela Huppenkothen’s original Stingray
Matteo Bachetti’s MaLTPyNT
Abigail Stevens’ RXTE power spectra code and phase-resolved spectroscopy code
Simone Migliari’s and Paul Balm’s X-ray data exploration GUI commissioned by ESA
Changelog¶
v2.1 (2024-05-29)¶
New Features¶
Bug Fixes¶
Internal Changes¶
v2.0 (2024-03-13)¶
New Features¶
Power colors à la Heil et al. 2015 (#780)
Calculate colors and intensities on a segment-by-segment basis in event lists (#781)
A function to randomize data in small bad time intervals (#782)
The Lomb Scargle Fourier Transform (fast and slow versions) and the corresponding
LombScargleCrossspectrum
andLombScarglePowerspectrum
(#737)A JAX implementation of the Gaussian Process tool by Hubener et al for QPO detection and parameter analysis. (#739)
Extend join operation for events to arbitrary array attributes, not just pi and energy (#742)
Allow the creation of empty light curves. (#745)
Make StingrayTimeseries into a generalized light curve, with a less strict naming but implementing much of the underlying computing useful for Lightcurve as well. (#754)
Our fast implementation of histograms is now safer (failing safely to the equivalent numpy histogram functions), more consistent (ranges moved to range, for consistency with numpy), and accept complex weights as well! (#764)
Bug Fixes¶
When rms is low, the calculation in compute_rms often gave
NaN
. We now check for this situation and give 0 with an uncertainty as a result. (#736)Eliminates deprecated call to
enable_deprecations_as_warnings
, and contextually, changes the code to be much more robust in catching harmful warnings. (#738)Changes Crossspectrum.plot() function to plot the actual real and imaginary parts instead of their absolute values. (#747)
Make commits marked as [docs only] skip all CI but the docs build (#749)
Update tstart and tseg when using Lightcurve.truncate() (#753)
Changed list comprehension to generator expression to reduce memory usage. (#756)
Fix a bug with segment sizes not exact multiples of dt when dealing with light curves (#760)
Fix a bug when light curve segments contain complex values (#760)
Crossspectrum had “real” as default value. This meant that, for example, lags could not be calculated. Now the default value is “all”, as it should be. (#762)
Fix plotting of spectra, avoiding the plot of imaginary parts of real numbers (#763)
Various bugfixes in
gti.py
, and a new function to interpret the mix of multiple GTIs. (#774)Fixed subcs duplication by adding a check in the for loop that copies the attributes from table’s meta items. (#776)
Various bug fixes in DynamicalPowerspectrum, on event loading and time rebinning (#779)
Fix issue with the Poisson noise calculation in lag spectra, that produced NaN errors under some conditions (#789)
Fix rms computation and error bars (#792)
Fix issue with
Powerspectrum
of a single light curve (#663)Fix nphots estimate in accelsearch, that lead to an underestimation of the power of candidates (#807)
Breaking Changes¶
Internal Changes¶
v1.1.2 (2023-05-25)¶
New Features¶
Phase Dispersion Minimization as a method to search for periodic signals in data is now implemented in the
stingray.pulse
submodule. To use it, you can use thephase_dispersion_search
function instingray.pulse.search
. The accompanying statistical tests are located in thestingray.stats
module, underphase_dispersion_probability
,phase_dispersion_logprobability
andphase_dispersion_detection_level
. (#716)Add is_sorted function, to test if an array is sorted. (#723)
Check if invalid data are inside GTIs, and warn or raise exception accordingly (#730)
Bug Fixes¶
The method apply_gtis of the class Lightcurve is applied to all the attributes of the class Lightcurve. This works for both inplace=True and inplace=False (#712)
Avoid allocation of an unneeded square matrix to improve memory management in
_als
(fix Issue 724) (#725)Fix Issue #726 – Loading events without fmt keyword crashes (#727)
Documentation¶
Reordered information about contributions with new
black
andtowncrier
procedures (#721)
Internal Changes¶
Added stingray’s logo in the documentation’s favicon and top bar. (#707)
Improved contributing workflow by appending
black
codestyle configuration topyproject.toml
and ignoring PEP-8 non-compliantE203
,W503
inflake8
. (#715)Added a scrollbar to sidebarwrapper (#718)
Simplify numba mocking code, and possibly improve code coverage estimate (#731)
v1.1.1 (2022-10-10)¶
Bug fixes¶
Fixed
white_noise_offset
incompute_rms
to 2.0, as it should beFixed a bug that produced a crash when calculating the rms in spectra corrected through the FAD technique
Fixed a bug that eliminated the imaginary part from cross spectra corrected with the FAD
Fixed a bug that considered contiguous GTIs as non-continuous (due to very small differences between stop and start of the next GTI) by allowing a small tolerance
v1.1 (2022-10-02)¶
Bug fixes¶
IMPORTANT: Fixed sign of time lags, which were calculated using the interest band as the reference.
Fixed an issue when the fractional exposure in FITS light curves is slightly >1 (as sometimes happens in NICER data)
New¶
Implemented the
bexvar
variability estimation method for light curves.
Improvements¶
A less confusing default value of segment_size in Z searches
v1.0 (2022-03-29)¶
TL,DR: these things will break your code with v1.0:
Python version < 3.8
The
gtis
keyword inpulse/pulsar.py
(it is nowgti
, without the ‘s’)
New¶
Dropped support to Python < 3.8
Multi-taper periodogram, including a Lomb-Scargle implementation for non-uniformly sampled data
Create count-rate spectrum when calculating spectral-timing products
Make modlation upper limit in
(Averaged)Powerspectrum
work with any normalization (internally converts to Leahy for the calculation)Implement Gardner-Done normalization (1 for perfect correlation, -1 for perfect anticorrelation) for
Auto/Crosscorrelation
New infrastructure for converting
EventList
andLightCurve
objects into AstropyTimeSeries
New infrastructure for converting most Stingray classes into Astropy
Table
objects, Xarray and Pandas data frames.Save and load of most Stingray classes to/from many different file formats (
pickle
,ECSV
,HDF5
,FITS
, and all formats compatible with Astropy Table)Accept input
EventList
inDynamicalPowerSpectrum
New
stingray.fourier
module containing the basic timing products, usable onnumpy
arrays, and centralizes fft importNew methods in
Crossspectrum
andPowerspectrum
to load data from specific inputs:from_events
,from_lightcurve
,from_time_array
,from_lc_list
(from_time_array
was also tested using memory-mapped event lists as inputs: useful in very large datasets)New and improved spectral timing methods:
ComplexCovarianceSpectrum
,CovarianceSpectrum
,LagSpectrum
,RmsSpectrum
Some deprecated features are now removed
PSDLogLikelihood
now also works with a log-rebinned PDS
Improvements¶
Performance on large data sets is VASTLY improved
Lots of performance improvements in the
AveragedCrossspectrum
andAveragedPowerspectrum
classesStandardized use of new fast psd/cs algorithm, with
legacy
still available as an alternative option to specifyReading calibrated photon energy from event files by default
In
pulse/pulsar.py
, methods use the keywordgti
instead ofgtis
(for consistency with the rest of Stingray)Moved
CovarianceSpectrum` to ``VarEnergySpectrum
and reuse part of the machineryImproved error bars on cross-spectral and spectral timing methods
Measure absolute rms in
RmsEnergySpectrum
Friendlier
pyfftw
warningsStreamline PDS/CrossSp production, adding
from_events
,from_lc
,from_lc_iterable
, andfrom_time_array
(to input a numpy array) methodsPDS/CrossSp initially store the unnormalized power, and convert it on the fly when requested, to any normalization
Bug fixes¶
Fixed error bars and
err_dist
for sliced (iterated) light curves and power spectraFixed a bug in how the start time when applying GTIs (now using the minimum value of the GTI array, instead of half a time bin below the minimum value)
Fixed a bug in which all simulator errors were incorrectly non-zero
Fixed coherence uncertainty
Documented a Windows-specific issue when large count rate light curves are defined as integer arrays (Windows users should use
float
or specifyint-64
)If the variance of the lightcurve is zero, the code will fail to implement Leahy normalization
The value of the
PLEPHEM
header keyword is forced to be a string, in the rare cases that it’s a numberand more!
v1.0beta was released on 2022-02-25.
v0.3 (2021-05-31)¶
Lots of performance improvements
Faster simulations
Averaged Power spectra and Cross spectra now handle Gaussian light curves correctly
Fixes in rebin functions
New statistical functions for signal detection in power spectra and pulsar search periodograms
Much improved FTOOL-compatible mission support
New implementation of the FFTFIT method to calculate pulsar times of arrival
H-test for pulsar searches
Z^2_n search adapted to binned and normally distribute pulse profiles
Large data processing (e.g. from NICER) allowed
Rebinning function now accepts unevenly sampled data
New saving and loading from/to Astropy Tables and Timeseries
Improved I/O to ascii, hdf5 and other formats
Rehaul of documentation
v0.2 (2020-06-17)¶
Added Citation info
Fixed various normalization bugs in Powerspectrum
Speedup of lightcurve creation and handling
Made code compatible with Python 3.6, and dropped support to Python 2.7
Test speedups
Dead time models and Fourier Amplitude Difference correction
Roundtrip of LightCurve to lightkurve objects
Fourier-domain accelerated search for pulsars
Adapt package to APE-17
Periodograms now also accept event lists (instead of just light curves)
Allow transparent MJDREF change in event lists and light curves
v0.1.3 (2019-06-11)¶
Bug fixes
v0.1.2¶
Bug fixes
v0.1.1¶
Bug fixes
v0.1 (2019-05-29)¶
Initial release.
Presentations¶
Members of the Stingray team have given a number of presentations which introduce Stingray. These include: