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Changelog

Version 1.5.1

Bug fixes

  • Add support to ready HDF5 files created with very old versions of Carpet (< 2012).

Version 1.5.0 (19 June 2024)

General

  • Python 3.12 is now supported, Python 3.8.1 is required for development.
  • total_filesize now errors out when directories are passed.

Features

  • Added experimental support for reading OpenPMD files (with most of the heavy-lifting done by @krishivbhatia). Please, report any issue you might find.

Version 1.4.0 (2 May 2023)

General

  • Minimum version of Python required is now 3.7. kuibit now explicitly follows NEP29.
  • Started gradual typing
  • Now SimDir can be imported directly from kuibit (from kuibit import SimDir)
  • Update logo to high resolution (and vector graphics)

Features

  • Added linear momentum lost by gravitational waves along the x and y directions (starting from a contribution by @konrad-topolski)
  • Added Tree data structure
  • Added effective_amplitude_spectral_density within gw_utils (starting from a contribution by @irrationalnumbers, #27)
  • Added fourth order accuracy in finite differences of grid functions
  • Added copy to gravitational and electromagnetic waves
  • Added crop and cropped to multipole data
  • setup_matplotlib now takes an optional parameter rc_param_file to configure matplotlib using a file
  • Added computation of linear momentum lost by electromagnetic waves
  • Added rotation180_symmetry_undo to undo rotational symmetries in grid data
  • Added cactus_twopunctures to read metadata from TwoPunctures
  • Added local_maxima and local_minima to series
  • Added mean, average, median, std reductions to series and grid data
  • Added ah_available, qlm_available to OneHorizon
  • Added tensor module
  • Added support to surface*.vtk from QuasiLocalMeasures

Support to VTK variables from QuasiLocalMeasures

QuasiLocalMeasures has an option to output its variables on the horizon. Now, kuibit can read and parse them, so it is possible to plot horizon meshes and variables onto the mesh.

New tensor module

kuibit.tensor is a new module to provide high-level interfaces to work with tensorial objects. A Tensor can be built with collections of TimeSeries, FrequencySeries, UniformGridData, HierarchicalGridData, or any other class derived from BaseNumerical. Tensors support all the mathematical operations and inherit the methods from their contained object. At the moment, there are two new subclasses of Tensor that implement additional features for vector calculus. For example, if bh_cen is a Vector with the time evolution of the centroid of an horizon. bh_cen.differentiated().norm() will be a TimeSeries with the magnitude of the coordinate velocity as a function of time (as a TimeSeries).

Currently, the number of specialized methods in Vector and Matrix is not large. Nonetheless, the infrastructure is in place and adding new will be straightforward.

New cactus_twopunctures module

TwoPunctures creates a metadata file that stores important physical information about the initial data. The new module cactus_twopunctures can read this information and present it as a dictionary. If sim is a SimFactory, sim.twopunctures will be a dictionary-like object that has as keys the various quantities saved by TwoPunctures and as values, their values as read from the TwoPunctures.bbh file.

New tree module

kuibit.tree is a new module that can represent tree structures. At the moment, it is main use is to work with timer trees.

New hor_utils module

kuibit.hor_utils is a handy new module that implements common functions needed when working with binary black holes. At the moment, the functions implemented are:

  • compute_separation_vector
  • compute_separation
  • compute_center_of_mass
  • compute_angular_velocity_vector

Bug fixes

  • Fix passing an empty ah_vars to OneHorizon.
  • Fix floating-point comparison in grid_data.
  • Fix optional positional arguments to series._local_extrema.
  • Fix algorithm to compute hash for UniformGrid.
  • Make classes that should not hashed unhashable.
  • GravitationalWaves now find multipole variables that contain psi4 (as opposed to being identically to Psi4)

Detector sensitivity curves

  • Add more updated sensitivity curve for Einstein Telescope (ET-D) (thanks, @bgiacoma, #33).

New/updated examples

Scripts:

  • describe_simdir.py
  • interactive_timertree.py
  • print_available_iteration.py optionally prints the corresponding time
  • plot_charge_phi1.py
  • plot_binary_ah_angular_velocity.py
  • plot_binary_ah_period.py

Version 1.3.6 (5 July 2022)

Bug fixes

  • Fix time incorrectly read in ASCII data (thanks @AuroraDysis, #30)

Version 1.3.5 (14 June 2022)

Bug fixes

  • Fix str representation of multipoles
  • Fix implicit plotting of Series for matplotlib >= 3.5.2
  • Fix test_init in test_cactus_grid_function

Version 1.3.4 (22 April 2022)

General

  • Improvements to documentation and docstrings

Bug fixes

  • Added error in _plot_horizon_on_plane when the horizon cannot be plotted
  • Updated NumPy types (np.int -> int, np.float -> float)
  • Windowing uneven signals is no longer allowed
  • Correctly remove ghost zones for 1-2D HDF5 files
  • Fix deprecation warning for Matplotlib 3.4
  • Fix is_masked after removing a mask (thanks @ekwessel, #28)
  • Fix some information not being propagated by grid_data_utils.merge_uniform_grids.

Breaking changes

  • The merge_refinement_levels function in HierarchicalGridData has been renamed to refinement_levels_merged for consistency. (Imperative methods edit the object in-place)

New examples

Scripts:

  • plot_ah_trajectories.py

Version 1.3.3 (19 November 2021)

Bug fixes

  • Fixed tikzplotlib dependency for Python 3.6

Version 1.3.2 (16 November 2021)

Bug fixes

  • Examples with plot_components_boundaries now respect axes limits
  • Improved support to installing mayavi
  • Python 3.10 is now supported (with exception of numba)
  • Fixed parity in reflection_symmetry_undo

Version 1.3.1 (4 November 2021)

Bug fixes

  • h5py >= 3 is now supported

Version 1.3.0 (28 October 2021)

SimDir can now be cached in pickle files

kuibit tries to do as much lazy-loading as possible. For examples, files are opened only when needed. When analyzing simulations it is useful to save the work done by kuibit to avoid re-doing the same operations over and over. It is now possible to do this using pickle files. SimDir can now be used as a context manager and the progresses can be loaded and saved from files. For example:

with SimDir("path_of_simulation", pickle_file="simdir.pickle") as sim:
    # do operations

In this case, if pickle_file exists, it will be loaded (ignoring all the other arguments passed to SimDir), and it will be kept updated with the additional work done by kuibit. If pickle_file does not exist, the SimDir will be created as usual as a pickle_file will be generated.

It is important to stress that, when using pickles, no consistency check with the current state of the simulation is performed. If the simulation changes (e.g., new checkpoints are added), this will result in errors. In that case, a new pickle file must be produced.

Masked data

Numerical objects now support mask, which can be used to ignore part of the data that satisfy certain conditions (for example, to exclude the atmosphere from GRMHD computations).

Note that it is not possible to perform interpolation with masked data, so several methods will not work.

Note also that we mask only the data, not the independent coordinate (e.g., the time in TimeSeries or the spatial coordinates in the UniformGridData). In case you need masked coordinates too, you can use the mask method to obtain an array of booleans that identifies the valid data.

  • Series, UniformGridData, HierarhicalGridData have a new method is_masked.
  • Series, UniformGridData, HierarhicalGridData have a new method mask that identifies where data is invalid.
  • Series, UniformGridData, HierarhicalGridData have news methods to create masked data (e.g., mask_greater). See complete list in documentation.
  • Series have new methods mask_remove and mask_removed to create objects without masked data.
  • Series have new methods mask_apply and mask_applyed to create objects with a given mask (as the one obtained with the mask method).

General

  • SimDir can be saved to disk with the method save and read with the function load_SimDir. This is useful to work with a simulation that has finished.
  • Examples can now use pickles.
  • New CI workflow: linting.
  • New First Steps documentation page.
  • When a release is published, its documentation is saved to sbozzolo.github.io/kuibit/VERSION

Features

  • time_at_maximum and time_at_minimum in TimeSeries can now take the optional argument absolute.
  • Added x_at_minimum_y and x_at_maximum_y to BaseNumerical.
  • Added coordinates_at_maximum and coordinates_at_minimum for grid data.
  • Added HierarchicalGridData.is_complex().
  • Added tikz_clean_figure to visualize_matplotlib.save, to argparse_helper.add_figure, and to examples. This can be used to reduce the size of output tikz files.
  • Added clear_cache in OneGridFunction.
  • Added plot_contour.
  • Added alias time_found to formation_time in horizons.
  • Added plot_components_boundaries.
  • Added ghost_zones_remove in HierarchicalGridData
  • Added add_grid_structure_to_parser.
  • Added reflection_symmetry_undone.

Breaking changes

  • The ignore parameter in SimDir has been renamed to ignored_dirs.
  • The trim_ends parameter in cactus_waves is now set to False by default.

Bug fixes

  • plot_colorbar does not steal axis focus anymore.
  • The legend in plot_psi4_lm was corrected.
  • visualize_matplotlib.save now correctly supports the figure argument.
  • plot_strain_lm.py no longer crashes when window_args is not provided.
  • HierarchicalGridData now owns the components.
  • Clear OneGridFunction cache in grid_var to avoid death by OOM.
  • Uniform constructor of GridSeries with constructors of other Series.
  • Horizon properties now lead to valid python variable names.

New examples

Examples with --detector-num now also accept --num-detector as alias.

Scripts:

  • picklify.py
  • plot_1d_slice.py
  • plot_grid_expr.py
  • plot_phi_time_averaged.py
  • plot_gw_angular_momentum.py
  • print_grid_point_minmax.py

Version 1.2.0 (1 June 2021)

New module: visualize_matplotlib

The visualize_matplotlib module aims to simplify common visualization tasks with matplotlib. At the moment, it mainly supports visualizing grid data and apparent horizons outlines. The public functions in visualize_matplotlib try to be as general as possible: if you pass some grid objects, they will try to figure out how to plot it. Nonetheless, you should read the documentation and the docstrings of the various functions.

motionpicture

Making movies is a critical step in analyzing a simulation. Now, kuibit comes with motionpicture, a Python tool to assist you animate your data. motionpicture provides all the infrastructure needed to render multiple frames and glue them together, so, all you need to worry is how to render one single frame. Importantly, motionpicture supports parallel rendering, which can dramatically speed up the time needed to produce a video. Check out the grid_var example to see how easy it is to make a movie.

New class: GridSeries

GridSeries is a new class to describe 1D grid data. This class utilizes the same infrastructure used by TimeSeries and FrequencySeries to represent a single-valued function. UniformGridData can be transformed into GridSeries with the method to_GridSeries. The main reason you would want to do this is because GridSeries are leaner and more direct to use.

General

  • Improvements to documentation, docstrings, and tutorials
  • Examples are now automatically packaged and uploaded upon release
  • New YouTube series, Using kuibit

New examples

Scripts:

  • plot_1d_vars.py
  • plot_ah_coordinate_velocity.py
  • plot_ah_found.py
  • plot_ah_radius.py
  • plot_ah_separation.py
  • plot_constraints.py
  • plot_em_energy.py
  • plot_grid_var.py
  • plot_gw_energy.py
  • plot_gw_linear_momentum.py
  • plot_physical_time_per_hour.py
  • plot_phi_lm.py
  • plot_psi4_lm.py
  • plot_strain_lm.py
  • plot_timeseries.py
  • plot_total_luminosity.py
  • print_qlm_properties_at_time.py

Movies:

  • grid_var

Bug fixes

  • Fixed header recognition for carpet-grid.asc (#22)

Features

  • New methods get_apparent_horizon and get_qlm_horizon in HorizonsDir.

Version 1.1.1 (22 April 2021)

Bug fixes

  • Fixed corner in __str__ in UniformGrid
  • Fixed _finest_component_at_point_mapping for some points for which floor and rounding lead to different results.

Version 1.1.0 (18 April 2021)

New module: argparse_helper

The argparse_helper module collects functions to set up arguments for command-line scripts. It comes with options for working with figure, grid data, and horizons. Options can be stored in text files and read passing the path to the -c flag.

Faster HierarchicalGridData

The function that finds the component corresponding to a given point in HierarchicalGridData was significantly sped up by adopting the algorithm used in PostCactus (developed by Wolfgang Kastaun). This new algorithm is significantly faster, but it will not work in case the refinement factors across different levels are not constant integers. In that case (e.g., the refinement boundaries are at 1, 2, and 6), the older algorithm will be used. For large towers of refinement levels and hundreds of MPI processes, the new algorithm is orders of magnitude faster.

Examples

Now kuibit comes with runnable examples. These are production-grade codes that you can immediately use for your simulations. They are a great way to learn about how to use kuibit. The examples included are:

  • print_ah_formation_time.py
  • print_available_iterations.py
  • print_available_timeseries.py
  • save_resampled_grid_data.py

General

  • Releases are now automatically pushed to PyPI.

Features

  • Added method to compute the linear momentum lost by gravitational waves
  • Now the method save in UniformGridData supports .npz files. This is the recommend and fastest way to save a UniformGridData to disk.
  • The function load_UniformGridData can now read .npz files.

Bug fixes

  • Fixed bug that, under certain circumstances, resulted in cactus_grid_function not correctly indexing all the 3D data files
  • Fixed a test that was triggering the wrong error.
  • Fixed a bug that made ra_dec_to_theta_phi depend on the local time

Breaking changes

  • finest_level_component_at_point is now finest_component_at_point and returns directly the component as UniformGridData as opposed to the refinement level and component number.

Version 1.0.0 (11 April 2021)

General

  • Improvements to documentation and docstrings

Features

  • Added nanmax, nanmix, abs_nanmax, abs_nanmin to BaseNumerical
  • Added support for HDF5 grid arrays
  • Added slicing HierarchicalGridData
  • Added shape_time_at_iteration in cactus_horizon
  • Added shape_at_time in cactus_horizon
  • Added shape_outline_at_time in cactus_horizon
  • Added compute_horizons_separation in cactus_horizon
  • Added ignore_symlinks to SimDir

Bug fixes

  • cactus_horizons and cactus_multiploes now remove duplicate iterations

Breaking changes

  • remove_duplicate_iters was renamed to remove_duplicated_iters
  • _derive methods are renamed to_differentiate

Version 1.0.0b0 (11 January 2021)

Initial release