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History

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[v3.0.4] - 2025-02-13

Summary

  • Updates to the Post-processing tools and documentation.

Fixed

  • Fixed the Post-processing tutorial to show the correct shaded credible regions (not using the outdated shade_root_index syntax).

Changed

  • Posterior predictive error bars were added to the bolometric pulse profile model plot (in _residuals.py).
  • Clarified in the Post-processing tutorial that the set parameter bounds must match those used during sampling.

Attribution

Lucien Mauviard, Christine Kazantsev, Tuomo Salmi

[v3.0.3] - 2025-01-29

Summary

  • _poisson_likelihood_given_background.pyx extension can now handle likelihood computation when the model generates phases with 0 counts, and penalizes situations where data has phase-energy bins with 0 counts but the model does not.

Fixed

  • Fixes likelihood computation crash (for the Poisson extension) when model predicts phase bin with 0 counts. Previously that would result in an attempt to compute log(0).

Changed

  • Added conditions to deal with situations involving data counts or model counts being 0 in any phase-energy bin.

Attribution

Devarshi Choudhury, Tuomo Salmi, Bas Dorsman

[v3.0.2] - 2025-01-17

Summary

  • Everywhere can now be used with time_invariant=True and a numerical atmosphere model. This would silently bug before.

Fixed

  • Fixes silent error resulting in wrong model spectrum when using a numerical atmosphere model with Everywhere.
  • Fixes silent error in likelihood computation when time_invariant=True where likelihood would behave stochastically for fixed parameters.

Changed

  • Only pass the temperature and effective gravity to the _compute_cellParamVecs() in Everywhere.
  • Added a condition on the number of phase bins of the model (more than 2) to interpolate on data bins.

Attribution

Tuomo Salmi, Christine Kazantsev, Lucien Mauviard

[v3.0.1] - 2025-01-16

Summary

  • If the prior.call() returns -np.inf because a parameter value outside the allowed prior (multidimensional) interval, the likelihood will now return random_near_llzero rather than less_than_llzero.

Fixed

  • This fixes a problem that we believe used to be rare but was recently occuring quite frequently, where MultiNest gets stuck in an infinite loop. That means runs were still appearing to be running but were actually stuck in an infinite loop state.

Changed

  • We no longer follow the procedure of point rejection as described in Appendix B.5.3 in Tom Riley's thesis.
  • Instead of outright rejection (in the MultiNest code), points will now be 'weakly' rejected when their loglikelihoods are compared and turn out to be lower than the likelihoods of the current 'good' livepoints.
  • The bulk of the work is in the evaluation of the loglikelihoods, which is still being skipped, so rejection after loglikelihood comparison amounts to negligible extra work.
  • We have done a few tests of sampling and found no noticeable effects on the posteriors that come out on the other end.
  • Just a note, we discussed but will not implement prior limits in the prior.inverse_sample(), since that will be complicated while we do not expect that it speeds us up. One may argue that alternative is a bit cleaner and a more direct way to inform MultiNest not to consider forbidden parameter values.

Deprecated

  • likelihood.less_than_llzero()

Removed

  • likelihood.less_than_llzero()

Attribution

Bas Dorsman, Mariska Hoogkamer, Tuomo Salmi

[v3.0.0] - 2024-12-19

Summary

  • This release upgrades X-PSI to be Cython3 compatible and provides many new features and examples, such as UltraNest sampling, Simulation-Based Inference, and reading data and instrument files that are in FITS format. A few deprecated features were also removed.

Fixed

  • Fixed Python3.12 related syntax warnings when installing X-PSI were fixed by adding 'r' in front of strings that contain a backslash.
  • The default value for image_order_limit in the module generator was set to match what is said in the docstring (i.e. the default being None).

Added

  • Added UltraNest as an example to the modelling tutorial and installation instructions.
  • Added some docstrings to mesh_tools.pyx and effective_gravity_universal.pyx.
  • Added new optional plots for clustering of residuals.
  • Added the possibility to print a user-defined credible level.
  • Data (event list or spectrum) and responses (RMF, ARF, RSP) can now be loaded from FITS files.
  • Added Simulation-Based Inference examples in the documentation, and wrapper class in the utilities.
  • Added a new option star_shape for the Spacetime class to allow pulse calculation and inference with a spherical star (instead of an oblate spheroid).
  • Added background, convergence, and "P-P" plots in the Post-processing tutorial.
  • Multi-mode plotting was made possible in the corner plots (different modes from a MultiNest run done with multimodal=True can be now plotted separately).
  • Added bolometric pulse and blurring of the residuals options in xpsi/PostProcessing/_residual.py.
  • Added a possibility to use a parameter vector instead of a random set of samples in all post-processing functions.
  • Added a chi-squared calculation property to the Signal class.

Changed

  • X-PSI was upgraded to support Cython3 by updating the syntax and the structure of all the Cython files. Installation instructions were also updated. Using Cython3 is now recommended. The code seems to still run also with Cython version 0.29, but its functioning correctly and efficiently is not guaranteed.
  • Residual plotting was updated to fix issues when using a logarithmic scale and including channel 0.
  • Updated the installation instructions for Helios and Snellius, and updated the example job script.
  • The desired precision of credible intervals can now be defined already when loading the runs.
  • The Photosphere class atmosphere setter can now load by default atmosphere table files similar to those of NSX model used in NICER analyses (without the need for writing a CustomPhotosphere for this).
  • Future plans, publications, etc. were updated in the documentation.
  • The counts are not divided by 2 anymore for signal plots when 2 cycles are shown. The label was changed to "counts per cycle" to denote this change.

Removed

  • X-PSI Python 2 documentation (v1.x and earlier) was retired from the main online documentation (but can still be accessed via GitHub).
  • Removed the deprecated is_secondary argument from the HotRegion class. Note that setting ``is_secondary=True`` has now no effect, and will lead to wrong likelihood values if not replacing it with ``is_antiphased=True``.
  • Removed the TwoHotRegions class that nobody was known to be using.

Attribution

Devarshi Choudhury, Bas Dorsman, Denis Gonzalez-Caniulef, Sebastien Guillot, Mariska Hoogkamer, Daniela Huppenkothen, Christine Kazantsev, Yves Kini, Lucien Mauviard-Haag, Evert Rol, Tuomo Salmi, Pierre Stammler, Anna Watts

[v2.2.7] - 2024-07-13

Summary

  • Fixed a bug, introduced in the accretion disk upgrade in version 2.2.5, when calculating the "Elsewhere" signal. IMPORTANT: Do not use X-PSI versions 2.2.5 or 2.2.6 if including the Elsewhere (i.e. rest of star surface) signal into the analysis!! It can lead to faulty results without warnings/errors.

Fixed

  • Fixed a bug in `xpsi/cellmesh/integrator_for_azimuthal_invariance.pyx, by changing the "E_electronrest" input parameter back to the original "E_prime" when calling the intensity evaluation for the "elsewhere" contribution of the hot spot surface. The "E_electronrest" parameter should have likely been there only when having the new Num5D atmosphere activated (although it probably would not have worked correctly even in that case). For other atmospheres, no values were assigned to "E_electronrest", and thus intensities were probably calculated for some random energy values from the computer memory.

Attribution

Tuomo Salmi (T.S.)

[v2.2.6] - 2024-07-11

Summary

  • Added UltraNest as a sampler.

Added

  • Added xpsi.UltranestSampler.py which is a wrapper for the UltraNest package.
  • Added ultranested function to xpsi.Sample.py to select UltraNest as a sampler.

Attribution

Mariska Hoogkamer (M.H.)

[v2.2.5] - 2024-06-17

Summary

  • A new accretion disk implentation and another 5D atmosphere interpolation examples were added.

Attribution

Bas Dorsman Tuomo Salmi

[v2.2.4] - 2024-05-28

Summary

  • Likelihood class was modified to allow inference runs with Everywhere objects without re-writing the Likelihood class.

Fixed

  • Likelihood class was modified so that it can be directly used also for Everywhere objects (and not only for Hotregion objects). (T.S., Y.G., Y.K)

Attribution

Tuomo Salmi (T.S.), Ylvie Gerritsma (Y.G.), Yves Kini (Y.K.)

[v2.2.3] - 2024-05-23

Summary

  • A new parameter for the spin axis position angle was added when modelling polarized X-rays. In addition, polarimetry examples were updated and a few bugs in the module generator were fixed.

Fixed

  • A bug in the module generator was fixed, so that selecting blackbody atmosphere works correctly. (D.C.)
  • A bug in the module generator was fixed, so that not all the parameters are accidentally wrapped. (D.C., L.M.)

Added

  • A new parameter called spin_axis_position_angle was added to the Photosphere class when calculating the pulses using the stokes=True option. This is the angle between the observer north and the projection of the pulsar rotation axis on the plane of the sky, affecting the observed polarization angle and Stokes parameters. (T.S.)
  • An example of using a constant accretion disk background was added in xpsi/examples/examples_modeling_tutorial/TestRun_PolNum_split_1spot.py. (T.S., B.D.)

Attribution

Tuomo Salmi (T.S.), Bas Dorsman (B.D.), Devarshi Choudhury (D.C.), Lucien Mauviard-Haag (L.M.)

[v2.2.2] - 2024-04-26

Summary

  • The default imaging extension has been changed from uniform.pyx to PDT_U.pyx to avoid the need for X-PSI re-installation when computing neutron star images for different nested models. The tutorials have been updated to account for this change when necessary.

Fixed

  • Fixed a bug in photosphere.image() causing the code crash if not providing the sky_map_kwargs argument.
  • Fixed a bug in photosphere.image() causing the code crash if setting reimage=False and trying to plot the skymaps.

Added

  • The Global surface emission -tutorial was added back to the documentation pages since it works now.

Changed

  • The default xpsi/surface_radiation_field/local_variables.pyx extension is now PDT_U.pyx instead of uniform.pyx. The former is a more general version of the latter, and also a more general version of PST_U.pyx and two_spots.pyx. The new default extension can be used to compute neutron star images for all the aforementioned models without re-installing X-PSI. For the simpler models, one can define e.g. the global variable for ceding region size to be zero if no ceding regions exist in the model. The tutorials have been updated to have those variables defined when needed.
  • Example scripts updated to have settings more commonly used in NICER analyses (for compactness limits and multiple imaging orders).

Removed

  • Removed the archived versions of imaging extensions that are not needed anymore.

Attribution

Tuomo Salmi

[v2.2.1] - 2024-04-24

Summary

  • Fixes and updates in the projection tool, post-processing, documentation, and example scripts.

Fixed

  • A bug in the projection tool for PDT-U model was fixed. (T.S., S.V.)

Added

  • Added a keyword argument ci_gap for xpsi/PostProcessing/_corner.py that can be used to adjust the vertical space between the reported credible intervals above the contour plots. (T.S.)

Changed

  • The installation instructions and example job script for Snellius cluster were updated. (T.S., B.D., M.H.)
  • Small updates done on the likelihood check and settings used in the fast example scripts. (B.D.)
  • Post-processing tutorial updated to account for the changes in the imported example modules. (T.S.)

Attribution

Tuomo Salmi (T.S.), Serena Vinciguerra (S.V.), Bas Dorsman (B.D.), Mariska Hoogkamer (M.H.)

[v2.2.0] - 2024-02-06

Summary

  • Modeling polarized X-ray signals has been implemented and examples added for simulating polarized pulses (Stokes parameters) using a couple of different atmosphere options. Support for polarized likelihood calculation has also been included. In addition, new integrators (with and without polarimetry) have been implemented to allow atmosphere interpolations with 5 parameters to be performed in 2 steps.

Added

  • Option to calculate and extract all the Stokes I, Q, and U signals as a function of energy and phase. This can be activated if giving stokes=True as an input parameter (default is stokes=False) when initializing a photosphere object. The computed (photosphere) stokes signals can then be obtained using the signal, signalQ, and signalU functions of the Photosphere class. For using Stokes signals in the likelihood calculation, a separate signal object of the Signal class needs to be created for each Stokes signal so that the type of the signal is specified using a stokes input argument. A list of all the signals can be then given to the likelihood object when initializing it. (T.S.)
  • Polarized alternatives for integrators in xpsi/cellmesh/integratorIQU_..., which include the transportation of polarization angle from the star to the observer using the formalism of Loktev et al. (2020). These are used when setting stokes=True as instructed above. (T.S.)
  • A new "split" integrator in xpsi/cellmesh/, which allows atmosphere interpolations with 5 parameters to be performed in 2 steps: first interpolating 3 parameters that do not vary within the hot region (creating a 2D data set) and then interpolating in 2D for each photon energy and emission angle. This can be activated by giving split=True (default is split=False) input parameter when initializing a hotregion object. Setting split=True will automatically determine also the atmosphere option. (B.D.)
  • New atmosphere options in xpsi/cellmesh/surface_radiation_field/. See the docstring of the HotRegion class for all the options. (B.D., T.S.)
  • Polarization tutorial to the documentation pages. (T.S.)
  • Example scripts for calculating polarized pulses in examples/examples_modeling_tutorial/ using either an analytical polarized burst atmosphere (TestRun_Pol.py) or a numerical 5D atmosphere model (TestRun_PolNum_split_1spot.py or TestRun_PolNum_split_inference.py). (T.S.)
  • Example scripts for combining X-PSI to ixpeobssim for simulating polarized X-ray observations in examples/examples_modeling_tutorial/ixpeobssim/. See instructions in the documentation. (T.S.)

Changed

  • To allow modeling of all Stokes parameters, no error is anymore raised if the data have negative values in xpsi/Data.py. (T.S.)
  • No error is anymore raised in xpsi/Data.py if setting the first and last energy channel to be the same channel. (T.S.)

Attribution

Tuomo Salmi (T.S.), Bas Dorsman (B.D.)

[v2.1.2] - 2024-02-05

Summary

  • Updates and fixes were done to background marginalisation, post-processing, and module generator routines.

Added

  • Added error messages in the background marginalisation if providing a background support that does not fulfill the documented requirements (T.S.).

Fixed

  • Fixed the sometimes incorrect value of the factor (B_for_integrand) that should ensure that the exponent in the likelihood integrand is at some point unity within the integration domain in xpsi/likelihoods/default_background_marginalisation.pyx. This was not always working when the background bounds were based both on the user-given bounds and on the default bounds leading to numerical problems in the integration and unnecessarily bad likelihood values in some example cases. Now B_for_integrand is forced to be within the integration limits (T.S.).
  • Fixed module imports in xpsi/module_generator.py (D.C., T.S.).
  • Fixed the background support upper limit zero replacements to work even when all the highest energy channels have zero background in xpsi/module_generator.py (T.S., S.V.).

Changed

  • Changed xpsi/PostProcessing/_metadata.py so that None can be given as truth value for a parameter, which is not wanted to be shown in a corner plot (T.S., Y.K.).

Attribution

Tuomo Salmi (T.S.), Devarshi Choudhury (D.C.), Serena Vinciguerra (S.V.), Yves Kini (Y.K.)

[v2.1.1] - 2023-11-10

Summary

  • Updates and fixes done to post-processing, synthesise, and module generator routines.

Added

  • An option show_vband added to the CornerPlotter class allowing to choose how many colored vertical bands are shown in the corner plots (Y.K., T.S., S.G).
  • Options xticks and yticks added in xpsi/PostProcessing/_signalplot.py to adjust the axis ticks and tick labels in signal plots for post-processing (T.S.).
  • Examples of the new features added to the Post-processing tutorial (T.S.).

Fixed

  • Displaying the credible intervals for all plotted posteriors fixed to work for multiple models and not only for multiple runs. The argument credible_interval_1d_all_show needs to be True to use this functionality (Y.K., T.S.).
  • Corrected a deprecated version of numpy float in xpsi/PostProcessing/_corner.py (M.H.).
  • Synthesise function in xpsi/Likelihood.py forced to always use the given parameters and produce synthetic data regardless of other settings. (T.S.).
  • Prior probability values prevented from being exactly zero (or negative) for KL-divergence calculation and avoiding thus infinite values for the reported KL-divergence estimates (T.S.).
  • Module generator fixed to work with the current version of X-PSI and tutorial updated (T.S., D.C).

Changed

  • The 1D credible intervals for all the plotted posteriors are now always calculated (and saved if annotate_credible_interval=True), even though not choosing to show all of them in a corner plot (Y.K).

Attribution

Tuomo Salmi (T.S.), Yves Kini (Y.K.), Sebastien Guillot (S.G.), Devarshi Choudhury (D.C.), Mariska Hoogkamer (M.H.)

[v2.1.0] - 2023-09-08

Summary

  • Atmosphere switching implemented without need for re-installing X-PSI for different atmosphere extensions. Note that old scripts using the numerical atmosphere extension need to be slightly modified (see Deprecated below).

Added

  • Atmosphere extension flag atm_ext that can be used to select the wanted atmosphere extension (for an instance of HotRegion, Elsewhere, or Everywhere class). The default option is a blackbody atmosphere, but a numerical atmosphere extension can be switched by setting atm_ext="Num4D".
  • Beaming modification flag beam_opt (an integer) that can be used to select the wanted atmospheric beaming correction model for an instance of HotRegion or Everywhere class (not implemented to Elsewhere currently). The default option is no modification. See the docstring for HotRegion class for other options.
  • Extra atmosphere extension xpsi/surface_radiation_field/hot_user.pyx that can be replaced with a user-modified atmosphere model before (re-)installing X-PSI. This model can then be used by setting atm_ext="user" allowing still the possibility to use the other built-in options without re-installing X-PSI.
  • Options to switch atmosphere extension and beaming option in the surface radiation field tools (xpsi/surface_radiation_field/__init__.pyx).

Changed

  • Documentation, tutorials, and example scripts updated for using the new atmosphere switching (except xpsi/module_generator.py).

Deprecated

  • The previous way of installing X-PSI with different atmosphere extensions has been deprecated. To use the old python scripts (files usually named as `main.py`) to run X-PSI with numerical atmosphere setup, one needs to add `atm_ext="Num4D"` as an input parameter for all the relevant HotRegion/Elsewhere/Everywhere objects.

Removed

  • Archived versions of atmosphere extensions that are not needed anymore.

Attribution

Tuomo Salmi, Bas Dorsman, Sebastien Guillot

[v2.0.3] - 2023-07-11

Summary

  • Updates and bug fixes in post-processing.

Fixed

  • Fixed a bug when defining param_plot_lims in xpsi/PostProcessing/_corner.py caused by tight_gap_fraction being only defined in the customized GetDist version that is not used anymore. That parameter is now defined in X-PSI instead (T.S., Y.K., S.G.).
  • Fixed a bug when combining multiple runs in xpsi/PostProcessing/_runs.py, which caused the combination sometimes fail since PolyChord (instead of MultiNest) default was used for the initial live point likelihoods in dead-birth files. This bug appeared after switching to use a non-customized version of NestCheck (after X-PSI version 2.0.0). Now the newest NestCheck version allows to change this value, and this change is now done within X-PSI. If trying to use an older NestCheck version, an error is raised (T.S., Y.K.).
  • Fixed the hyphens in the file names in xpsi/PostProcessing/_backends.py when reading MultiNest output files with the newest NestCheck version from GitHub, although trying still to read the filenames also with the older syntax to allow older NestCheck versions for other things than combining runs (T.S.).

Added

  • Added a keyword argument in xpsi/PostProcessing/_corner.py to allow user to define the decimal precisions for all the credible intervals printed in the figures (T.S.).
  • Added a photosphere setter in xpsi/Star.py which should allow producing residual and signal plots for models with multiple photosphere objects as explained in https://github.com/xpsi-group/xpsi/issues/304 (Y.K, T.S.).
  • Added minor ticks back to corner plots in xpsi/PostProcessing/_corner.py. Previously, these ticks were produced by the customized older GetDist version (T.S.).

Attribution

Tuomo Salmi, Yves Kini, Sebastien Guillot

[v2.0.2] - 2023-06-09

Summary

  • More numerical problems in likelihood computation were fixed for cases with zero counts. These fixes seem not to have any effect on the current examples, but for data with zero counts at some energy channels, more parameter vectors can now have acceptable likelihoods.

Fixed

  • Several numerical issues in xpsi/likelihoods/default_background_marginalisation.pyx for a given energy channel:
  • Prevented the upper limit of the background from becoming negative if using the semi-bounded option of the background support and having both zero modeled and observed counts at all phases.
  • Prevented the lower limit (and the initial guess) of the background from becoming negative if having zero observed counts at all phases but non-zero modeled counts at some phases.
  • Prevented division by zero when estimating the standard deviation for the background that maximizes the likelihood in the case of zero observed counts at all phases but non-zero modeled counts at some phases.

Attribution

Tuomo Salmi

[v2.0.1] - 2023-04-25

Summary

  • Numerical problems in likelihood computation were fixed for cases with zero counts, preventing also the code from being incorrectly optimized on Intel CPUs when using Intel compilers (producing incorrect GSL integration results and likelihoods). For the tested cases, the effect of these fixes seems non-detectable for the results in the systems where the optimization was already working correctly. In addition, a likelihood check was added as a part of continuous integration tests.

Fixed

  • Treatment of the special cases in the likelihood computation in xpsi/likelihoods/default_background_marginalisation.pyx was changed so that taking the logarithm of zero is not allowed anymore. Previously, that could happen if the modelled counts were zero, but the observed counts were not. In addition, in case they both are zero, we now add 0 (i.e., log(1)) to the log-likelihood, instead of 1 added before. (T.S., E.R., M.H.)

Added

  • Continuous integration test for checking the likelihood (T.S.)

Attribution

Tuomo Salmi, Evert Rol, Martin Heemskerk

[v2.0.0] - 2023-02-16

Summary

  • This major release migrates X-PSI from Python2 (X-PSI v1.2.1 or lower) to Python3 (X-PSI v2.0 and higher), with corresponding updates and improvements to all documentation and tutorials.

Fixed

  • Debugging projection tool

Added

  • Multi-version documentation so that users can view documentation/tutorials for either Python2 or Python3 (with warning on main page)
  • Post-processing - adding names of parameters across diagonal in corner plots
  • Extra yticks options for plotting functions in the tutorials
  • --noopenmp install option for Mac Users
  • Added option to fix the random seed for the synthetic data generation in Python3 version.
  • Added option to plot y-axis in the residuals in a user selected scale (e.g., either log or lin).

Changed

  • Modified all X-PSI routines to work in Python3.
  • General Documentation (Applications, Team and Acknowledgements, Citation, Future pages) updated for both Python2 and Python3 documentation branches.
  • Installation and tutorial pages modified for Python3.
  • Module generator updated for Python3 and documentation added.
  • Projection tool updated for Python3 and documentation added.
  • Github actions modified to work in Python3.
  • Github actions modified to use mamba with install commands on one line to improve speed.
  • Updated references in the documentation and tutorial notebooks.
  • CustomInstrument channel_edges argument now changed to mandatory in tutorial notebooks and examples.
  • X-PSI Postprocessing now supports up-to-date versions of NestCheck and GetDist.
  • Specified the integer types to be always size_t in Cython files in those integer comparisons that raised warnings for different signedness of integers.
  • The JOSS paper has been updated to link to published version.
  • A final Python2 release of X-PSI (v1.2.2) was created in the Python2 branch to match the JOSS publication.

Deprecated

  • The Python2 version of X-PSI (v1.2.2) is now considered deprecated, although documentation and tutorials are still available.

Removed

  • Removed requirement of FFMPEG for Animations in tutorials.
  • Suppressed printf() statements from c code in tutorial notebooks.

Attribution

Devarshi Choudhury, Bas Dorsman, Sebastien Guillot, Daniela Huppenkothen, Yves Kini, Tuomo Salmi, Serena Vinciguerra, Anna Watts

[v1.2.1] - 2022-12-12

Summary

  • Hard upper bound for temperature increased from 7.0 to 7.6, allowed user an option to adjust when the exact likelihood calculation is skipped because of too bright signal, and license information updated.

Changed

  • Strict bounds for temperature changed in xpsi/HotRegion.py, xpsi/Everywhere.py, and xpsi/xpsi/Elsewhere.py to allow analysis for hotter neutron stars.
  • Added mention in xpsi/HotRegion.py, xpsi/Everywhere.py, and xpsi/xpsi/Elsewhere.py that the user should set the parameter bounds to be within the values given in the numerical atmosphere table.
  • Added a new input parameter slim to xpsi/likelihoods/default_background_marginalisation.pyx, which can be used to adjust when the exact likelihood calculation is skipped because of the signal being too bright compared to the data. The default value of this parameter is set to the same value as in the code before (20.0).
  • Made the warning in synthesise function in xpsi/Likelihood.py more accurate.
  • Fetched the prior to likelihood object in examples/examples_fast/Synthetic_data.ipynb to make sure prior bounds are checked when synthesising data.
  • License of X-PSI was changed from MIT to GPLv3.

Attribution

Tuomo Salmi, Yves Kini, Sebastien Guillot, Anna Watts

[v1.2.0] - 2022-12-05

Summary

  • Included a new numerical atmosphere extension in a xpsi/surface_radiation_field/archive/hot/ directory allowing freedom in the predicted atmospheric beaming pattern.

Added

  • xpsi/surface_radiation_field/archive/hot/numerical_fbeam.pyx: New numerical atmosphere extension with additional beaming parameters.
  • examples/examples_modeling_tutorial/TestRun_NumBeam.py: An example run using the new atmosphere extension.
  • examples/examples_modeling_tutorial/modules: Additional modules (e.g. a CustomHotRegion) needed by the new example run.

Changed

  • Setup.py file changed to include the option for installing with new atmosphere extension.
  • Documentation page for "Example script and modules" updated to include the new example.

Attribution

Tuomo Salmi

[v1.1.0] - 2022-11-14

Summary

  • Additional tools included in a xpsi/utilities directory for plotting hot regions on a sphere and performing importance sampling in X-PSI. Documentation for these tools is to be appended later. In addition, the internet documentation compilation was automated using GitHub actions for every merged pull request.

Added

  • xpsi/utilities/ProjectionTool.py: Tool for projecting hot regions.
  • xpsi/utilities/ImportanceSample.py: Tool for calling X-PSI importance sampling.

Changed

  • Setup.py file changed to include the new utilities directory.
  • Documentation is now compiled automatically using .github/workflows/build_docs.yml every time merging a pull request into the main branch.

Attribution

Serena Vinciguerra, Daniela Huppenkothen, Tuomo Salmi, Devarshi Choudhury

[v1.0.0] - 2022-09-26

Summary

  • This major release contains minor bug fixes, improved error messages, as well as improved documentation and tutorials (jupyter notebooks). This release coincided with the submission of an X-PSI article to the Journal of Open Source Software

Fixed

Added

  • A modification of the setup.py with flags (--NumHot and --NumElse) now facilitates switching between surface emission models.
  • The post-processing module has now an option to show the credible intervals of each parameter and run (above the 1D distribution of the corner plot) when multiple runs are plotted in the same figure (but not working for multiple models yet). The appropriate tutorial notebook is also provided.
  • Some unit tests and continuous integration.
  • A tutorial landing page and a link to a dedicated Zenodo repository for large files needed to run the tutorials.

Changed

  • The general documentation has been improved, reorganized and clarified. More details are provided for the installation, locally and on HPC systems.
  • The messages of several possible errors have been clarified and detailed to help the user resolve them.
  • A small modification now allows production runs without importing matplotlib.
  • All tutorials have been updated and improved.

Deprecated

Removed

  • Method fixed_spin of spacetime.py module. A spacetime with fixed spin can be created by specifying a spin frequency value and omitting the spin frequency bounds

Attribution

Devarshi Choudhury, Bas Dorsman, Sebastien Guillot, Daniela Huppenkothen, Yves Kini, Tuomo Salmi, Serena Vinciguerra, Anna Watts

[v0.7.12] - 2022-09-15

Summary

  • Since version 0.7.11. a few changes have been made including updates to the documentation and the handling of numerical problems in ray tracing. The latter fix can potentially have a small effect on the calculated pulse profiles and likelihood values for some parameter vectors, but according to testing that effect is very minor at most.

Fixed

  • Numerical problem in xpsi/cellmesh/rays.pyx for certain paramaters causing sporadic warnings in later computation. This is prevented by allowing small rounding errors when checking if sin_alpha parameter is unity, and in case NaNs still occur, replacing them with zero (T.S.).
  • Comment about returned variables updated to include the best-fitting background limited by the support in xpsi/likelihoods/default_background_marginalisation.pyx (T.S.).
  • The photosphere object validity check in xpsi/Star.py which incorrectly failed if all photosphere parameters were fixed (D.C., Y.K., T.S.).

Added

  • Added more information and warnings about about switching between the blackbody and numerical atmosphere extensions in the documentation for Installation, Surface radiation field tools and (FA)Q pages. Added also a links to the Zenodo publication of Riley+2021 from where the numerical atmosphere data can be obtained (T.S.).
  • Added a new kwargs ("prior_samples_fnames") used in xpsi/PostProcessing/_corner.py to allow user to set the name of file from where the prior samples are read/saved (T.S.).
  • Added comments about the new kwargs (introduced already in version 0.7.11) in the function descriptions used in xpsi/PostProcessing/_corner.py visible also for the documentation (T.S.).
  • Added an option to force update xpsi/Star.py to avoid errors, for example, when all paremeters are fixed and X-PSI thinks otherwise that updating can be skipped (T.S., D.C., Y.K.).
  • Added options allowing the user to truly force update the likelihood in xpsi/Likelihood.py and avoid errors caused by the automatic need-update-checks not working for all the possible cases. Added also an error message suggesting to use those options if the usual "AttributeError: 'CustomSignal' object has no attribute '_loglikelihood'" would be encountered (T.S.).

Changed

Deprecated

Removed

Attribution

  • Tuomo Salmi (T.S.), Devarshi Choudhury (D.C.), and Yves Kini (Y.K.)

[v0.7.11] - 2022-08-22

Summary

  • Since version 0.7.10, a few bugs have been fixed in the module generator, error handling and postprocessing. Also, new error/warning messages are given if trying to use wrong atmosphere extension. In addition, some improvements have also been added to the postprocessing (possibility to e.g. save and read the drawn priors to produce corner plots much faster), without mentioning them in the documentation yet.

Fixed

  • Bug in xpsi/EnsembleSampler.py when initializing walkers. Need to use "self._prior" instead of "prior" (Y.K.).
  • Bug (typo) in xpsi/PostProcessing/_pulse.py when plotting the true signal. Need to use "component" instead of "eomponent" (G.L.).
  • Several bugs (typos) in xpsi/PostProcessing/_spectrum.py when plotting the true signal (T.S., G.L.).
  • Issues with xpsi/PostProcessing/_corner.py not being able to plot the cross hairs for true parameter values in the corner plot if only a subset of model parameters chosen for the figure (T.S., Y.K.).
  • Error handling in xpsi/Signal.py when the number of event data channels does not match the number of the instrument data channels (S.G.).
  • Fixed reference to incident_background in the modeling tutorial (B.D.).
  • Several bug fixes in xpsi/module_generator.py (D.C.).

Added

  • Added a warning message in the blackbody atmosphere extension xpsi/surface_radiation_field/hot.pyx if providing numerical atmosphere data (T.S.).
  • Added an error message in the numerical atmosphere extension xpsi/surface_radiation_field/archive/hot/numerical.pyx before a segmentation fault error caused by not loading the numerical atmosphere data (T.S.).
  • Added a warning when trying to synthetize data in xpsi/Likelihood.py with input parameters outside of the defined prior bounds, finishing without errors but with no data produced (Y.K. & T.S.).
  • Added option for the user to set the line colors for different runs in xpsi/PostProcessing/_corner.py using kwargs (T.S.).
  • Added possibility to save and read the previously drawn prior samples in xpsi/PostProcessing/_corner.py using "force_draw" kwargs (T.S.).
  • Added possibility to plot the priors only for the first run in xpsi/PostProcessing/_corner.py using "priors_identical" kwargs, if known that priors are the same for all runs (T.S.).
  • Saved credible intervals in numerical format that can be accessed after plotting the corner plot (see "val_cred" in xpsi/PostProcessing/_corner.py and xpsi/PostProcessing/_postprocessor.py) (Y.K., T.S.).

Changed

Deprecated

Removed

Attribution

  • Tuomo Salmi (T.S.), Yves Kini (Y.K.), Devarshi Choudhury (D.C.), Bas Dorsman (B.D.), Gwénaël Loyer (G.L.), and Sebastien Guillot (S.G.)

[v0.7.10] - 2022-02-10

Summary

  • Since version 0.7.9, several bugs have been fixed. For example, fixing the double counting of the second component of a dual temperature region when caching turned on. Also, documentation and example scripts have been updated.

Fixed

  • Bug in xpsi/Signal.py when looping over dual temperature components while using caching (D.C., T.S, S.V.).
  • Bug in xpsi/Signal.py merging the new phase-shift parameter to the parameter subspace (T.S. & D.C.).
  • Missing global argument added in xpsi/module_generator.py (D.C.).
  • Documentation and example scripts updated and fixed to work with newest X-PSI versions (S.G.).
  • Bug in xpsi/PostProcessing/_corner.py not showing true values correctly in corner plots for simulated data (T.S. & Y.K.).
  • Corrected the link to the documentation pages when importing X-PSI (D.C. & T.S.).

Added

Changed

Deprecated

Removed

Attribution

  • Devarshi Choudhury (D.C.), Tuomo Salmi (T.S.), Serena Vinciguerra (S.V.), Sebastien Guillot (S.G.), and Yves Kini (Y.K.)

[v0.7.9] - 2021-11-26

Summary

  • New program that automates generation of model modules for common usage patterns, in particular the NICER modelling workflow. The program may be located at xpsi/module_generator.py and executed as python module_generator.py -h to see the usage help.

Fixed

  • The :class:`~.Background` call method body template and fixed the :class:`~.Signal` class to access the correct property of the background instance.
  • Documentation URLs to reference the organisation repository. (D.H.)

Added

  • Functionality to the :class:`~.Data` class method for event handling so that it can load events from file when the energy in eV is given.
  • Optional maximum energy to use for ray-tracing simulations. Useful if there is a background component such as a powerlaw that is jointly modelled with higher-energy event data using a subset of instruments.
  • A phase-shift parameter for each :class:`~.Signal` instance. If there are two or more phase-resolved data-sets, there may be a need to have a phase- shifting parameter for each signal. For phase-summed data sets, the phase- shift can be arbitrarily fixed. Phase-shifts can be derived from other phase-shifts, and one signal's phase-shift can always be fixed as zero and thus locked to the phase shifts of the hot regions.

Attribution

  • Daniela Huppenkothen (D.H.).

[v0.7.8] - 2021-09-22

Fixed

  • Correction in the importance sampling function. If the number of MPI processes is a factor of the number of samples reweighted, a subset of samples, with cardinality equal to the size of the MPU world, was not reweighted but is included for renormalisation with the same weight as the input weight. E.g., if there is one MPI process, then the last sample is not reweighted, so the output weight is equal to the input weight. (S.V.)
  • Correction of the image appearing on the :mod:`~.HotRegion` page. (S.V.)
  • Minor typos corrected. (T.S. & Y.K.)

Changed

  • Updated the :func:`~.tools.synthesise_exposure` and :func:`~.tools.synthesise_given_total_count_number` functions to handle zero background and make sure that the input background memory buffer does not get modified by the synthesis routines. (T.S. & Y.K.)
  • Added a keyword argument to the default background marginalisation function to enable passing of a background signal in the form of a channel-phase interval buffer. The background should already be averaged over phase intervals, having units of counts/s. Useful for phase-dependent backgrounds, or a phase-independent background if the channel-by-channel background variable prior support is restricted.

Added

  • Updates to the project acknowledgements page of the documentation.

Attribution

  • Serena Vinciguerra (S.V.), Yves Kini (Y.K.), and Tuomo Salmi (T.S.).

[v0.7.7] - 2021-06-24

Fixed

  • Bugs in mesh cell allocation routine. These bugs occur for some specific subset of hot regions with both a superseding member region and a ceding member region and both radiate. This bug does not affect any production analyses to date, but was encountered by D.C. when preparing a model with such a hot region for posterior sampling.
  • Importance sampling bug when reweighting the likelihood function.

Added

  • Guidelines to the documentation for dependency citation.
  • Tips for installing X-PSI on a macOS in the documentation (S.V. & D.C.).
  • Some additional lines to install X-PSI on SURFsara's Cartesius (S.V.).
  • Instructions to install X-PSI on SURFsara's Lisa (T.S.).

Attribution

  • With thanks to Devarshi Choudhury (D.C.) for noticing and investigating potentially buggy mesh construction behaviour that was, indeed, buggy.
  • With thanks to Serena Vinciguerra for noticing and investigating potentially buggy importance sampling behaviour that was, indeed, buggy.
  • With thanks to Serena Vinciguerra (S.V.), D.C., and Tuomo Salmi (T.S.) for patches to documentation install instructions.

[v0.7.6] - 2021-05-16

Summary

  • NB: This patch is unfortunately not backwards compatible. This patch has been pushed nevertheless to comply with a NICER collaboration publication which uses X-PSI v0.7 with some features from a development version. The analysis is open-source, so the development features used have been pushed in this patch. The next minor release will officially include these tested features together with documentation.
  • New skymap plotting functionality and an MPI-capable importance sampling method that can handle likelihood function and prior PDF changes. New documentation and examples will be made available in the future.

Changed

  • The extension module for default background marginalisation returns a tuple with an extra element. This is probably backwards incompatible with custom subclasses of the :class:`~.Signal` class.

Added

  • Skymap plotting functionality. Examples will be added to the documentation in a future patch. The most useful feature is plotting a skymap time-series so that the image of the model surface hot regions rotates across and down a static figure. This is useful for papers to summarise an animated figure. This feature is functional but still being tested and developed.
  • An MPI-capable importance sampling method that can handle likelihood function and prior PDF changes. This is useful to save computation time. This feature is being tested and developed.

Fixed

Attribution

  • With thanks to Serena Vinciguerra (S.V.) for testing importance sampling.

[v0.7.5] - 2021-02-10

Fixed

  • Corner-case stability improvements for default background marginalisation.
  • If likelihood function is below :attr:`~.Likelihood.Likelihood.llzero` after evaluation, the parameter vector is included in the prior support as intended.
  • Typo in _precision function in xpsi/PostProcessing/__init__.py. (S.V.)
  • Math typo on the :mod:`~.HotRegion` page. (S.V.)
  • Explanatory text in the multiple-imaging tutorial. (T.S.)

Changed

Added

  • An extension module for calculating hot region local variables from global variables for hot region configurations under the umbrella of the PST-U model introduced in Riley et al. (2019).

Attribution

  • With thanks to Serena Vinciguerra (S.V.) and Tuomo Salmi (T.S.).

[v0.7.4] - 2021-01-26

Fixed

  • Missing packages in setup.py causing errors when importing xpsi.
  • A few typos in the documentation.

Added

  • A few images in the documentation.

Attribution

  • Serena Vinciguerra, Yves Kini, Devarshi Choudhury.

[v0.7.3] - 2020-11-12

Fixed

  • Phase-averaging issue that can sometimes occur due to numerical effects when comparing two numbers that should be the same but can differ by tiny degrees at machine precision level.
  • Some documentation typographic errors.

[v0.7.2] - 2020-11-04

Fixed

  • Error raised while running setup.py for linking rayXpanda with clang compiler.

Attribution

  • Serena Vinciguerra.

[v0.7.1] - 2020-10-01

Fixed

  • An AttributeError raised during runtime linking to the fallback rayXpanda implementation.

Attribution

  • With thanks to Devarshi Choudhury for bug testing.

[v0.7.0] - 2020-09-30

Summary

  • New plotting functionality.
  • Should be backwards compatible, but some small internal tweaks or default behaviour changes could result in small differences in plots that might not even be discernable.

Added

  • Option to specify only the number of phases per cycle when calling :meth:`~.Photosphere.Photosphere.image`, instead of having to supply the phase set.
  • New plot type for animated photon specific intensity skymaps with their associated photon specific flux pulse-profiles and the photon specific flux spectrum that connects the signals at those energies. See the documentation of the :meth:`~.Photosphere.Photosphere.image` method for options, details, and an example.
  • Example plots to the :class:`~.Photosphere.Photosphere` documentation.
  • New helper methods :meth:`~.Photosphere.Photosphere.write_image_data` and :meth:`~.Photosphere.Photosphere.load_image_data` to write ray map data, photon specific intensity image data, and photon specific flux signal data to disk, and then read the data back into memory as attributes so that the data can be reused to accelerate calls to calculate images and generate static and animated plots.
  • Option to :meth:`~.Photosphere.Photosphere._plot_sky_maps`, add_zero_intensity_level, that applies a colormap such that zero intensity corresponds to the lowest colour. In this case a non-radiating part of the stellar surface, and the background sky, have well-defined colour. If lowest colour in the colormap is instead associated with the lowest finite intensity in the skymap panel, then the background sky for instance is assigned the same colour so that the least bright part of the image merges with the background sky colour. The latter choice resolves the variation in the intensity as a function of phase and sky direction better with colour, but the former might give more of an indication of the magnitude of the variation in intensity as a function of phase and sky direction relative to the background sky.

Changed

  • A phase set supplied to :meth:`~.Photosphere.Photosphere.image` can have units of cycles, not radians as was previously the requirement, by setting the phase_in_cycles keyword argument to True if the supplied phase array as units of cycles.
  • The photon specific flux can be calculated with :meth:`~.Photosphere.Photosphere.image` at far more energies than photon specific intensities are cached at, by using the :obj:`cache_energy_indices` keyword to supply and array of integers to index the energy array. This saves memory and means that imaging with an extension module can be executed once to generate both skymaps (which require cached intensities but only typically at a few representative energies) and the photon specific flux (which does not require cached intensities, but typically is computed for a much finer energy array).

Attribution

  • With thanks to Anna Bilous and Serena Vinciguerra for helpful suggestions about the new animated plot type.

[v0.6.3] - 2020-10-01

Fixed

  • An AttributeError raised during runtime linking to the fallback rayXpanda implementation.

Attribution

  • With thanks to Devarshi Choudhury for bug testing.

[v0.6.2] - 2020-09-28

Fixed

Changed

[v0.6.1] - 2020-09-14

Fixed

Changed

Removed

  • An unused prototype extension module.

[v0.6.0] - 2020-09-05

Summary

  • Backwards compatible for most use cases, but possible corner cases.
  • Includes a non-critical, but important patch for animating intensity skymaps, and updates to the environment file for cloning.
  • The new feature is support for higher-order images when invoking an integrator that discretises the surface (with a regular mesh). Secondary images can be very important, whilst tertiary images less so. Quaternary, quinary, and possibly senary images can sometimes be detected and included too, with accuracy that decreases with order. Fortunately, the contribution to the photon specific flux generally decays rapidly with image order beyond the secondary or tertiary images. The computational cost scales almost linearly with order if an appreciable fraction of every iso-latitudinal ring on the surface is multiply-imaged at each order. Note that multiple-imaging manifests entirely naturally when an image-plane is discretised in such away that the regular mesh resolves the stellar limb sufficiently well, where higher-order images get insanely squeezed.

Fixed

  • The memory consumption problem of the animator method in :class:`~.Photosphere.Photosphere`. Now animation should generally require an entirely tracable amount of memory.

Added

  • Multiple-imaging support including an option to specify the maximum image order to iterate up to, with automatic truncation when no image at a given order is detected. If no limit is specified (the default), then images are included as far as they can be detected given the numerical resolution settings, which is typically between quaternary and senary images.
  • A multiple-imaging tutorial.
  • A global switch for changing phase and energy interpolants without recompilation of extensions. To change interpolants, you can use top-level functions :func:`xpsi.set_phase_interpolant` and :func:`xpsi.set_energy_interpolant`. Generally computations are more sensitive to the phase interpolants, of which the options from GSL are: Steffen spline (pre-v0.6 choice), Akima periodic spline, and cubic periodic spline. The default choice is now an Akima periodic spline in an attempt to improve interpolation accuracy of the interpolant at function maxima, where the accuracy is generally most important in the context of likelihood evaluations. Note that in some corner cases, the signal from a hot region is negative in specific flux because there is a correction computed to yield the intended signal from :class:`~.Elsewhere.Elsewhere` when it is partially masked by hot regions. In this case, when using phase interpolant tools from the :mod:`~.tools` and :mod:`~.likelihood` modules it is necessary to use a allow_negative option when calling the tools to specify that a negative interpolant is permitted.
  • Automatic linking of the package rayXpanda for calculation of the inverse of the deflection integral, and it's derivative via a high-order symbolic expansion, for a subset of primary images. The purpose is to mainly as an orthogonal validation of a subset of integrals executed via numerical quadrature and inversion via spline interpolation. The other reason is because to support multiple-imaging with the surface-discretisation integrators this aforementioned interpolation had to change due to non-injectivity of functions when interpolating with respect to the cosine of the deflection angle. However, to calculate the convergence derivative sufficiently accurately, interpolating with respect to the cosine of the deflection seems necessary. Therefore rayXpanda can be linked in, if it is available, for low deflection angles instead of avoid having to allocate additional memory and construct splines specifically for low-deflection primary images. Simple testing suggests there are no valuable speed gains, however, possibly because the high-order expansion and simultaneous evaluation of the polynomial and it's derivate with a nested Horner scheme itself requires a substantial number of floating point operations.
  • A helper method :meth:`~.ParameterSubspace.ParameterSubspace.merge` that merges a set of parameters, or a parameter subspace, or a set of subspaces, into a subspace that has already been instantiated.

Changed

  • Updated the Conda environment.yml file for replication of the development environment. The basic_environment.yml file was also updated in an earlier release in an additional necessary package, wrapt.

Deprecated

  • The repeat, repeat_delay, and ffmpeg_path keyword arguments for the animator method in :class:`~.Photosphere.Photosphere`. These were ultimately not effective. To repeat the animation intrinsically, set the number of cycles, and extrinsically, this can be looped when embedded in another environment.

[v0.5.4] - 2020-09-01

Fixed

  • Bug due to local variable NameError when setting instrument channel energy edges.
  • Bug that prevented a hot region phase parameter from being a fixed or derived variable.

Attribution

  • With thanks to Devarshi Choudhury.

[v0.5.3] - 2020-08-14

Summary

  • Improvement patches. Deliberately backwards incompatible for safety in memory allocation.

Fixed

  • Add try-except block to :attr:`~.Photosphere.Photosphere.global_to_local_file` property so that explicit setting of None by user is not required if file I/O is not needed in the extension module. Actually, None could not be set for the property anyway due to type checking.
  • Bug when declaring that sky maps should be animated and memory freed beforehand.

Added

  • The surface to image-plane ray map is cached in Python process memory so it can be efficiently reused for same spacetime configuration and ray map resolution settings. Explicit support for writing the ray map to disk and loading it is not included, but this should be entirely possible to achieve manually. Backwards compatible except for corner cases, such as not using keyword arguments when calling :meth:`~.Photosphere.Photosphere.image`, or if resolution settings changed between calls to the imager but a ray map otherwise exists in Python process memory and the spacetime configuration has not been changed.
  • A secret keyword argument to :meth:`~.Photosphere.Photosphere.image`, :obj:`_OVERRIDE_MEM_LIM`, which can be used to change an internal hard limit on the intensity cache size. This setting is for safety and designed so that higher memory consumption is deliberate or if something goes awry, it is deemed the responsibilty of the user to have read method docstring carefully. The tutorials will not use this secret keyword, so if the user tries to run them and encounters an exception, they will need to investigate the docstring and either adapt the resolution to their system or take the responsibility of setting the cache size limit for their system to accomodate the resolution settings in the tutorial.
  • Optional argument to :meth:`~.Photosphere.Photosphere.image`, :obj:`single_precision_intensities`, which flags whether or not to cache the intensities in single precision do halve intensity cache memory requirements. The default is to cache in single precision.
  • Verbosity to :meth:`~.Photosphere.Photosphere.image` because execution can take many minutes depending on settings chosen. The verbosity can be deactivated via a keyword argument (see the method docstring).

Changed

  • The usage of the :meth:`~.Photosphere.Photosphere.image` argument :obj:`cache_intensities`. Instead of simply activating intensity caching with boolean, the user must specify a cache size limit that is adhered to. If the required cache size given the resolution settings is larger than the limit, imaging does not proceed. If the cache size limit is zero or equivalent, then imaging safely proceeds without caching the intensities.
  • Intensities are by default cached in single precision to reduce cache memory requirements.

[v0.5.2] - 2020-08-12

Summary

  • Python API: small backwards compatible patches to add useful features.
  • C API: small backwards incompatible patch to support Python API patch.

Added

  • Support for hyperparameters (i.e., parameters of the prior distribution), by making :class:`~.Prior.Prior` inherit from :class:`~.ParameterSubspace.ParameterSubspace`. Custom hyperparameters can then be defined in a subclass initiliser, or otherwise. The hyperparameters are merged into the :class:`~.Likelihood.Likelihood` parameter subspace as mostly normal parameters (with small caveat in the form of property :attr:`~.Parameter.Parameter.is_hyperparameter`) and can have their own prior (the hyperprior) implemented in a :class:`~.Prior.Prior` subclass along with the other free parameters in the model. A tutorial will be delivered in due course. These modifications are backwards compatible.
  • Simple support for transforming from global to local variables (for image- plane calculations) with the help of a file on disk, whose path can be specified dynamically in Python and relayed to the relevant extension where a custom model implemention can do I/O with the file. This is useful if one has a set of files containing precomputed data, but understandably does not want to do filesystem acrobatics or recompile an extension every time the file path changes. Setting the file path dynamically in this way is akin to changing the value of some discrete variable in the mapping between global and local variables. With thanks to Anna Bilous for the suggestion. A tutorial will be delivered when possible.
  • Added :attr:`~.Instrument.Instrument.channel_edges` property, and updated tutorials to reflect this new concrete implementation.

Changed

  • The init_local_variables function signature in the header xpsi/surface_radiation_field/local_variables.pxd, and in the corresponding xpsi/surface_radiation_field/archive/local_variables extensions. You would have to modify a custom extension module manually to match the function signature declared in the header.

Fixed

  • Removed remnant manual Sphinx method signatures; the decorator now preserves the method signature so automated Sphinx doc works on those decorated methods.
  • Updated package docstring to reflect name change.
  • Uses of xpsi.Data.channel_range property to adhere to future deprecation.

[v0.5.1] - 2020-08-07

Fixed

Added

  • Capability to add custom parameters when instantiating :class:`xpsi.Photosphere`, which is useful for calling image plane extensions whilst passing global variables, without having to instantiate surface-discretisation classes and without having to handle global variable values at compile time or from disk for runtime access.

[v0.5.0] - 2020-08-06

Summary

  • The major change is an update and refactoring of the post-processing module to work again with past API changes. (The module was not being kept up to date with previous releases listed below because it wasn't to our knowledge being used by anyone yet, and thus we focussed on other features.) The module has been refactored to be more modular, flexible, and extensible. For instance, posterior signal-plot classes can be added by the user and complex plotting routines can thus be developed, as demonstrated in the concrete classes such as :class:`xpsi.PostProcessing.PulsePlot`. The plot classes have been used to reproduce (with improved functionality and performance) the relevant signal plots from Riley et al. (2019), as demonstrated in the post-processing tutorial notebook and embedded in the class docstrings for reference.
  • Development of online documentation pages, including project organisation pages and a Code of Conduct (please read), and development of docstrings. Note that some snippets of documentation look forward to v1.0 (e.g., release of technical notes in the repo itself).

Fixed

  • The :class:`xpsi.Data` docstring explanations have been improved for clarity, mainly regarding the instrument channel definitions. The explanation is of how the information contained in a :class:`xpsi.Data` instance pertains to the loaded instrument response (sub)matrix.
  • The :class:`xpsi.Instrument` docstrings have also been improved for clarity, explaining the relationship to :class:`xpsi.Data` in more detail.
  • Update extension module for background marginalisation to take distinct phase sets associated with hot regions.
  • The constructor :meth:`xpsi.Spacetime.fixed_spin` inclination upper bound is \pi/2 radians to eliminate degeneracy due to equatorial-reflection symmetry in the default prior on source-receiver geometric configuration.
  • Tweak caching (memoization) so that cache and current vectors are equal at the end of likelihood evaluation routine.
  • Generally clean up naming and docstrings for extension modules. Add return types.
  • Bug was fixed for transforming posterior sample sets and prior samples when parameter orders different in sample files and a prior object due to API updates. Whether this solution is to be long-term is to be decided; more generally need to figure out how to elegantly handle derived parameters that are not needed for likelihood evaluation (those derived parameters are instances of :class:`xpsi.Parameter`) but are of interest for post-processing.
  • Handle param_plot_lims=None correctly in :class:`xpsi.PostProcessing.CornerPlotter`.
  • Checked for unintended mutable defaults package-wide, and fixed as appropriate.
  • Fix bugs in CustomPrior class (:ref:`example_script`; these example modules were not run at the time of translation between past API versions, so only found bugs when making post-processing tutorial for this release).
  • The formatting of annotated credible intervals in :class:`xpsi.PostProcessing.CornerPlotter` has been improved by inferring the largest number of decimal places needed for two non-zero decimal digits, and then formatting the median and quantile differences to this shared decimal precision above the on-diagonal panels. If the numbers cannot be well- represented by this scheme, the user could try a unit transformation.
  • Tried to tweak automated margins for intensity sky map multi-panel plots, so as not to sometimes partially cut an axis label.
  • Bug that prevented animation of sky map frames written to disk because the frames were not cached in memory by reimaging.

Added

  • The :class:`xpsi.Data` is now concrete in implementation, such that in common usage patterns, it does not need to be subclassed.
  • A constructor to :class:`xpsi.Data` to load a phase-folded event list and phase-bin the events in a subset of selected channels.
  • A :meth:`xpsi.Data.channels` property that holds the instrument channels to be checked by a :class:`xpsi.Signal` instance against those declared for the loaded instrument response (sub)matrix. This property as also required by the post-processing module (namely, :class:`xpsi.PostProcessing.ResidualPlot` and the other :class:`xpsi._signalplot.SignalPlot` subclasses).
  • A :meth:`xpsi.Instrument.channels` property that holds the instrument channels to be checked by a :class:`xpsi.Signal` instance against those declared for the event data matrix.
  • Support for multiple instruments operating on the same incident signal due to assumed effective time-invariance of the signal generated during one rotational cycle of the surface radiation field.
  • Module :mod:`xpsi.surface_radiation_field` to call atmosphere extensions directly (without the calls being embedded in integration algorithms), for checking implementation of complicated atmospheres such as those requiring interpolation with respect to a numerical lookup table.
  • Support for the extension module for calculating the local surface radiation field variables to read in numerical model data. An example extension module designed to execute nearest-neighbour lookup amonst an general unstructured array of points of the openness of magnetic field lines has been developed.
  • Add simple energy annotation option to photon specific intensity sky-map panels.
  • State the energy units (keV) that the :class:`xpsi.Instrument` must comply with when energy interval bounds are specified.
  • State the units of variables such as energy and specific intensity in the surface radiation field extension module. These requirements may be found in function body comments.
  • Explain in :class:`xpsi.PostProcessing.CornerPlotter` docstring the order in which posteriors are plotted given the input order.
  • Post-processing switches to overwrite transformed-sample files and combined-run files on disk.
  • Workaround to handle the case where due to API changes, the relationship between sample parameter vectors on disk and the parameter vector in the current API are related not just by reordering, but transformations. This is demonstrated in the post-processing tutorial instead of transforming the original sample files on disk in place, the transformed files written to disk contain both the transformed vector (same number of elements) to match the parameters defined under the current API (the order of the vector can be different between the :class:`xpsi.ParameterSubspace` underlying with a :class:`xpsi.Likelihood` instance and the files on disk containing the transformed samples), and the additional derived parameters.
  • Attempt to free up memory when :meth:`xpsi.Photosphere.images` is no longer needed, but memory-intensive operations need to be performed.
  • Attempt to free memory properly after animating a sky-map phase sequence.

Changed

  • Change (Earth) inclination parameter i to \cos(i) so that the default prior density function is isotropic.
  • The object formerly named xpsi.Pulse has had its name changed to :class:`xpsi.Signal`, and across the package, names that were pulse are apart from potential corner cases or documentation instances of the word, are now signal, because when support joint likelihood functions over multiple instruments, some data sets are phase averaged. Moreover, signal is arguably clearer in meaning than pulse, once it has been established that the signals the package focuses on are pulsed but depending on the instrument, the data we confront the model with has some degree of phase (timing) resolution that might be insufficient for phase-resolved observations.
  • The :class:`xpsi.Data` definition of the last channel has changed to be the index of the last row in the loaded instrument response (sub)matrix, instead of being the index of the last row plus one; this means that the value exposed via a property is last+1.
  • For numerical atmospheres of same number of grid dimensions, improved extension surface_radiation_field/archive/{hot,elsewhere}/numerical.pyx module to infer grid size for memory allocation and interpolation searches (implemented automatic inference of grid size, but hard-coded four-dimensional cubic polynomial interpolation persistent). Different those atmospheres can be loaded simply via a Python subclass without the relevant extension module being recompiled.
  • The :class:`xpsi.Photosphere` class sometimes does no surface discretisation, so allow no hot regions, elsewhere, or everywhere objects; then image-plane discretisation can be accessed without dummy object creation.
  • Tweak :class:`xpsi.SpectrumPlot` settings to print a warning statement that spectrum plot works best with logarithmic spacing, and the user has to shadow class attribute with logspace_y=False.
  • Do not print :class:`xpsi.HotRegion` instance parameter properties upon creation if fixed at boundary value so that the region is fully described by fewer parameters.
  • Merged energy integration extension modules into one.
  • Made phase shift parameters (strictly) unbounded; remember however that for a sensible prior, bound the phase shifts on a unit interval, and thus it is required that phase bounds are specified and finite.
  • In extensions, modified phase shifting so that a shift permitted by unbounded phase parameter does not require many iterations to decrement or increment to unit interval (achieved simply with floor operation).

Deprecated

Removed

  • The ensemble MCMC sample backend for post-processing because we do not expect it to be useful in the immediate future, but requires some non-trivial development work to meld properly with the current post-processing module which is focussed on nested sampling. This functionality will be reintroduced in a future release (refer to :ref:`todo`). The ensemble sampler can still be run, however, and the native backend for accessing sample information on disk is demonstrated in a tutorial notebook. However, the runs cannot be processed for posterior integrals and visualisation using the same tools as available for nested sampling runs.

Attribution

  • With thanks to Sebastien Guillot (testing and feedback), Devarshi Choudhury (testing and feedback), Sam Geen & Bob de Witte (Windows installation advice), and Anna L. Watts (documentation patches and feedback).

[v0.4.1] - 2020-06-03

Fixed

  • Function signatures to match header declarations in atmosphere extensions: xpsi/surface_radiation_field/archive/elsewhere/numerical.pyx to match xpsi/surface_radiation_field/elsewhere_radiation_field.pxd. With thanks to Sebastien Guillot.

[v0.4.0] - 2020-02-14

Summary

  • Mainly new features.
  • Backwards compatible (apart from possible corner cases).

Fixed

  • Removed a spurious geometric factor in the integrator that discretises the surface with a static mesh. This integrator was called by the Elsewhere class. The error when this factor is included is O(1%) at 600 Hz for soft emission from the entire stellar disk, and then scales with spin and energy beyond this. To reproduce the bug, find the commented out / superlum in file xpsi/cellmesh/integrator_for_time_invariance.pyx (line 251) and uncomment it. Then reinstall the package. When this factor is included, the mesh itself is moving in the context of the images subtended by its constituent elements on our sky. We want the mesh to be static so that this integrator can be used for faster calculation of time-invariant signals.
  • Bug in which the prior density factor is incorporated twice if a Likelihood instance held a reference to a Prior object and these are merged into a Posterior object which is fed to the ensemble sampler. If the prior density was flat, this bug will have had no effect on posterior distributions.

Added

  • New features are the simulation of signals from more general surface radiation fields that globally span the stellar surface. This can be done with several types of integrator.
  • The new image-plane discretisation integrator supports imaging of a star, and Python functionality has been added to automate plotting and animation of intensity sky maps.
  • A new tutorial to the documentation to demonstrate these new features and an internal cross-check of distinct integration algorithms.
  • A visual introduction to the documentation pages with some animated sky maps.

[v0.3.6] - 2020-01-24

Fixed

  • Some code snippets in documentation examples of prior implementation with the latest API minor version (v0.3).

Changed

  • Modify the HotRegions class to function with two or more hot region objects.

[v0.3.5] - 2020-01-22

Summary

  • Docstring edits and backwards compatible changes to several class initialisation arguments.

Attribution

  • Based mostly on discussion with and feedback from Devarshi Choudhury.

Fixed

  • Some docs formatting problems.
  • Some corrections to example scripts/modules updated in v0.3.4 to use current API.

Changed

  • The photospheric mode frequency parameter is not converted to an angular frequency until it is used, so the cached value matches the docstring description.

Deprecated

  • The is_secondary argument of the HotRegion class. Use is_antiphased instead to ensure future compatibility.
  • The store argument of the Pulse class. Use cache instead to ensure future compatibility.

[v0.3.4] - 2020-01-20

Summary

  • A few patches including backwards compatible improvements.
  • Various docstring/comment/doc edits.
  • Update docs example model to use v0.3.4 API.

Fixed

  • Ensure consistency between input parameter bounds and values by always requiring dictionaries. Fix applies to Elsewhere and Photosphere. Courtesy Sebastien Guillot.
  • Gravitational mass doc typo fix.

Changed

  • Add input argument checks to Likelihood.check method.
  • Add default hypercube=None to Prior.inverse_sample_and_transform method.
  • If derived parameters found in subspace, assume an update is needed because cache mechanism not in place. (WIP.)

[v0.3.3] - 2020-01-20

Fixed

  • At several places in the Likelihood class, calls were place to self, forgetting that Likelihood overwrites ParameterSubspace.__call__. Now calls are super(Likelihood, self).__call__() to obtain the current parameter vector.

[v0.3.2] - 2020-01-16

Summary

  • Bug fixes. Backwards compatible.
  • When initializing the ensemble-MCMC chains using an nd-ball, the inclusion in the prior support was checked by passing a vector to Prior.__call__ but that code assumed that the parameter vector had already been assigned and can be accessed through the ParameterSubspace. As a result either an exception would be thrown (if parameter objects have no value set) or the support condition would be evaluated for some preset vector that does not change has we iterate through chains.
  • The Likelihood.check method now has a fallback implementation given that the NumPy allclose function in v1.17 does not support Python 2.7.

Attribution

  • Based on testing by Sebastien Guillot.

Fixed

  • The EnsembleSampler so that it does not rely on the CustomPrior.__call__ implementation to handle a vector argument. Chains should now be in prior support from the start and never leave.
  • The Likelihood.check method so that a call to a Likelihood instance updates the parameters with a vector if the physical points are passed for value checking.
  • The Likelihood.check method error error handling and if/else branching has been fixed.
  • Some typographic errors in docs.

Changed

  • The way EnsembleSampler accesses the prior object.

[v0.3.1] - 2019-12-12

Fixed

  • Some docstring and Sphinx-related formatting.

[v0.3.0] - 2019-12-10

Summary

  • Not backwards compatible.
  • The main feature is a more sophisticated backend for handling parameters, parameter subspaces, and the object hierarchy that forms the modelling language. Notably, the parameter objects can be accessed everywhere more readily, with dictionary-like functionality that alleviates the problem of remembering the imposed order of parameters in a vector. Resultantly, there is much more freedom when a user constructs a model and interfaces it with sampling software.
  • Model parameters can either be free, fixed/frozen at some scalar value, or derived deterministically from other model parameters.
  • The docs and tutorials have also been updated to reflect these developments.

Attribution

  • Feedback and ideas for the above development were discussed at an X-PSI workshop in Amsterdam, November 25-29 2019: Sebastien Guillot, Emma van der Wateren, Devarshi Choudhury, Pushpita Das, Anna Bilous, and Anna Watts.

Added

  • A new class xpsi.Parameter of which every model parameter is an instance.

Changed

  • The xpsi.ParameterSubspace class, which has far more sophisticated behaviours as a parameter container. The class, upon initialisation with arguments, also merges parameters and subspaces into a higher-dimensional (sub)space. Most other classes in the modelling language inherit from the xpsi.ParameterSubspace class.
  • The xpsi.TwoHotRegions class is now dedicated to representing antipodally reflection-symmetric configurations only to simplify the choice of which class to use between xpsi.HotRegions and xpsi.TwoHotRegions. However, antipodally reflection-symmetric models can also be constructed using just xpsi.HotRegions because of the new derived parameter support. The may be a minor speed difference: xpsi.TwoHotRegions should be very slightly faster, but it might be imperceptible. Future warning: in the future xpsi.TwoHotRegions might removed altogther for simplication.
  • The xpsi.Photosphere class can be instantiated to encapsulate only a reference to an xpsi.Elsewhere instance, and no xpsi.HotRegion instances. An xpsi.Elsewhere instance can by definition only generate a phase-invariant signal. However, further development is needed to handle this phase-invariant signal efficiently for likelihood functionality, given that operations with respect to phase are not required. Instead likelihood functions would be defined only with respect to energy.

Removed

  • The xpsi.ParameterSpace module. The global model parameter space is also simply an intance of the xpsi.ParameterSubspace class.