CHANGELOG.md

Change Log / Release Log for openPMD-viewer

1.10.0

• use %matplotlib widget by default by @BenWibking in #407
• BP4 Empty Skip: Inline Comment by @ax3l in #403
• Close #402 Fix deprecated ipython command by @RemiLehe in #410

Full Changelog: https://github.com/openPMD/openPMD-viewer/compare/1.9.0...1.10.0

1.9.0

• When passing t, choose the closest iteration by @RemiLehe in #347
• README: Remove Travis-CI Badges by @ax3l in #369
• Adding attributes to the FieldMetaInformation object by @juliettepech in #372
• Sphinx documentation by @RemiLehe in #303
• Add readthedoc configuration by @RemiLehe in #375
• setup.py: no upper version of openPMD-api by @ax3l in #378
• Docs: correct 'get_mean_gamma' description in tutorials by @IlianCS in #379
• Do not use pyflakes for version 3.7 by @RemiLehe in #385
• Impose that user always passes iteration or t by @RemiLehe in #383
• Docs: Improve tutorials by adding basic analysis functions by @IlianCS in #382
• Improve get_laser_waist by @soerenjalas in #359
• Python 3.8+ by @ax3l in #387
• Update version number and CHANGELOG.md by @RemiLehe in #386
• Add all record attributes to FieldMetaInformation by @AngelFP in #390
• Support complex data in thetaMode geometry by @AngelFP in #389
• fix get_data for weighting in momentum reader by @PrometheusPi in #393
• Simplify names of radial particle components by @AngelFP in #392
• Close #396 warning when reading particle data by @RemiLehe in #398
• Support reading of 'rt' lasy files by @RemiLehe in #371

Full Changelog: https://github.com/openPMD/openPMD-viewer/compare/1.7.0...1.9.0

1.8.0

• The functions get_field and get_particle now require iteration or t to be passed (instead of using a default iteration when none was provided). (See #383)

• The function get_laser_waist is more robust and does not crash when the laser field is 0. (See #359)

• The FieldMEtaInformation object has new attributes time and iteration. (See #372)

• The docstring of get_mean_gamma has been updated (See #379) and the attributes ts.t and ts.iterations are now shown in the tutorials (See #382)

1.7.0

This release includes a few improvements:

• The function get_laser_waist is more robust: it does not automatically assume that the z axis is the last axis of the data. In addition, the user can now specify the laser propagation direction. (The default is z.) (See #345)

• The handling of unitSI is now more robust. (See #363)

1.6.0

This release adds a few features:

• openPMD-viewer can now read complex datasets (See #353)

• Avoid errors in LPA diagnostics in the absence of selected particles (See #358)

1.5.0

This release fixes a few miscellaneous bugs:

• Better 3D reconstruction for theta=None (See #344)

• Better support for ADIOS data (See #355)

• Support for group-based encoding (See #346)

1.4.0

This new release introduces several improvements:

• The changes introduced in 1.3.0 caused a major slowdown when reading certain types of data. This has been fixed in this new release. (See #340 for more details.)

• openPMD-viewer now supports thetaMode geometry with data written using r as the fastest index (as written by e.g. WarpX) in addition to the previously supported data format which used z as the fastest index (as written by e.g. fbpic). (See 337)

• openPMD-viewer will raise an exception if the user asks for an iteration that is not part of the dataset (instead of printing a message and reverting to the first iteration, which can be confusing) (See 336)

1.3.0

This new release introduces preliminary support for MR datasets (see #332).

1.2.0

This new release introduces several bug-fixes and miscellaneous features:

• There is a new function get_energy_spread that returns the energy spread of the beam. This is partially redundant with get_mean_gamma, which is kept for backward compatibility. (see #304 and #317)

• The 3D field reconstruction from ThetaMode data now has an option max_resolution_3d that limits the resolution of the final 3D array. This is added in order to limit the memory footprint of this array. (see #307) The 3D reconstruction is now also more accurate, thanks to the implementation of linear interpolation. (see #311)

• A bug that affected reading ThetaMode data with the openpmd-api backend has been fixed. (see #313)

• A bug that affected get_laser_waist has been fixed: (see #320)

1.1.0

This new release introduces the option to read openPMD files with different backends. In addition to the legacy h5py backend (which can read only HDF5 openPMD file), openPMD-viewer now has the option to use the openpmd-api backend (which can read both HDF5 and ADIOS openPMD files). Because the openpmd-api backend is thus more general, it is selected by default if available (i.e. if installed locally). The user can override the default choice, by passing the backend argument when creating an OpenPMDTimeSeries object, and check which backend has been chosen by inspecting the .backend attribute of this object.

In addition, several smaller changes were introduced in this PR:

• The method get_laser_envelope can now take the argument laser_propagation in order to support lasers that do not propagates along the z axis.
• openPMD-viewer can now properly read groupBased openPMD files (i.e. files that contain several iterations) #301.
• Users can now pass arrays of ID to the ParticleTracker #283

1.0.1

This is a bug-fix release.

• Unreadable files are now skipped (instead of crashing the whole timeseries) ; see #262.

• A bug related to units (microns vs meters) was fixed in get_emittance and get_current (see #276)

• The quick-start notebook (openPMD-visualization) raised a warning saying Notebook validation failed in some cases. This was fixed (see #274)

• When using the option plot=True with Python 2, openPMD-viewer crashed. This is now fixed (see #271).

1.0.0

This version introduces major changes and breaks backward compatibility.

Here is a list of the changes:

• The import statement now uses openpmd_viewer instead of opmd_viewer, e.g.

from openpmd_viewer import OpenPMDTimeSeries

• For consistency, ts.get_particle now return particle positions in meters, instead of microns. For instance, in the code below, x, y, z will be in meters

x, y, z = ts.get_particle(['x', 'y', 'z'], iteration=1000)

• In ts.get_field, slicing can now be done in several directions, and for 1d, 2d, 3d, and circ geometries. As a consequence, this breaks backward compatibility for 3d field: get_field(field=field, coord=coord, iteration=iteration) used to return the central slice along y while it now returns the full 3d field. In addition, the name of the argument of get_field that triggers slicing has been changed from slicing_dir to slice_across (and slicing has been changed to slice_relative_position).
• openPMD-viewer does not rely on Cython anymore. Instead, it uses numba for functions that perform a substantial amount of computation.
• A new function (ts.iterate) was introduced in order to quickly apply a given function to all iterations of a time series. See the docstring of ts.iterate for more information.
• The function get_laser_envelope does not support the argument index anymore (which was effectively used in order to perform slicing). Instead, users should use the argument slicing_dir. In addition, get_laser_envelope now supports the argument plot_range.
• The function get_laser_waist does not support the agument slicing_dir anymore.

0.9.0

This release adds two features:

• Improved calculation of the laser envelope, using the Hilbert transform.
• Reconstruction of full 3D field from a quasi-3D dataset, when passing theta=None.

0.8.2

This is a bug-fix release. It allows the slider to work properly in JupyterLab, by using the %matplotlib widget magic.

0.8.1

This version includes minor improvements to the viewer:

• (Experiemental) support for Windows users
• In the interactive Jupyter GUI, the user can now select the scale of the vertical axis.
• The function get_emittance has more options (including calculation of the slice emttance)
• The default openPMD_notebook now avoids warning messages about matplotlib inline, which used to occur even though %matplotlib notebook was used.

Many thanks to @MaxThevenet and @AngelFP for their contributions to this release!

0.8

This version introduces several improvements to the viewer:

• The ability to read files that contain fields in different geometries (e.g. 3D fields and 2D slices).
• Better support for files that do not contain mesh (or do not contain particles), including support for the openPMD 1.1.0 standard.
• Cloud-In-Cell deposition in histograms.
• Better handling of %matplotlib notebook for newer version of jupyter.

0.7.1

This version adds better support, when the local installation of matplotlib has issues:

• The LpaDiagnostics can now work without matplotlib if needed.
• The MacOSX matplotlib backend is now avoided, since there can be issues when using it in the latest version of Jupyter.

0.7.0

This version improves support for ipywidgets version 7, especially in the layout of the slider.

In addition, with this version of openPMD-viewer, matplotlib is not a strict requirement anymore. This allows lighter installation for users that need openPMD-viewer only as a data reader.

Finally, the calculation of the laser envelope in 2D has been improved (see PR 170). Note that the function wstd (which is not documented in the tutorial, but which some users might still use) has been renamed to w_std.

0.6.0

This version improves the layout of the Jupyter GUI and allows the user to select a particular region of the plots through this GUI.

In addition, support for massless particle (e.g. photons) was added. In this case, the momenta are returned in kg.m.s^-1, instead of using the dimensionless momenta.

0.5.4

This is version 0.5.4 of openPMD-viewer.

It adds support for Python 3.4 (which erroneously dropped in the past).

0.5.3

This is version 0.5.3 of openPMD-viewer.

It corrects some of the issues with the size of boxes and widgets in the interactive slider. In addition, the iteration number is now read from the hdf5 metadata, and not the name of the file.

0.5.2

This is version 0.5.2 of openPMD-viewer.

It fixes some of the installation issues associated with Cython.

0.5.1

This is version 0.5.1 of openPMD-viewer.

It corrects a minor bug in the dependencies of the package.

0.5.0

This is version 0.5.0 of openPMD-viewer.

This new version includes the ParticleTracker object, which allows user to track individual particles across different iterations, provided that their id is stored in the openPMD file. Also, starting with this version, openPMD-viewer now depends on Cython.

For more information on how to use the ParticleTracker, see the tutorial notebook.

0.4.0

This is version 0.4.0 of openPMD-viewer.

This new version includes:

• support for 1D data
• an additional option use_field_mesh when plotting the particle. When set to True, this option uses information from the field mesh to choose the parameters of the particle histograms (esp. the bins). This is useful in order to avoid plotting/binning artifacts (aliasing) when the particles are evenly spaced.

In addition, the module openpmd_viewer now has an attribute __version__.

0.3.3

This is version 0.3.3 of openPMD-viewer.

This version fixed a bug with the executable openPMD_notebook. More precisely, the executable was not installed, when using pip or conda. In addition, it was failing with Python 3.

0.3.2

This is version 0.3.2 of openPMD-viewer. The following changes were introduced:

• The conda recipe in conda_recipe/ was simplified and streamlined.
• The documentation now explains how to install openPMD-viewer with conda, the instructions to release the package was put into a document RELEASING.md.
• A file MANIFEST.in was added, to avoid issues with pip and Python 3.

0.3.1

This is version 0.3.1 of openPMD-viewer. This version introduces minor changes in the way the tests are run in setup.py. The aim of these changes are to prepare a conda release.

0.3.0

This is version 0.3.0 of openPMD-viewer. This version mainly adapts the interactive GUI so that it can be used with the newer version of ipwidgets (ipywidgets 5.0), while still being compatible with previous versions of ipwidgets. A number of other minor changes have been introduced:

• In the method get_particle, the argument species is now optional in the case where there is only one species.
• A number of methods in the LPA addons (LpaDiagnostics class) now have an optional argument plot, which allows to directly plot the data.

0.2.0

This is version 0.2.0 of openPMD-viewer. A number of minor changes and fixes have been made in order to make the package more general and to prepare it for a PyPI release. Here are the main changes:

• Support for the deprecated widget package IPython.html has been dropped. From now on, users need to install the widget package ipywidgets, for the GUI to work.
• The initialization of an OpenPMDTimeSeries object can now be made faster by setting the optional argument check_all_files to False.
• The data reader can now support macroWeighted quantities. As consequence, output files from PIConGPU can now be correctly read.
• The package does not assume anymore that all species contain the same particle quantities. For instance, the package will support a file that contains the positions of ions, and the positions, momenta and weighting of electrons. As part of this, the attribute OpenPMDTimeSeries.avail_ptcl_quantities has been replaced by a dictionary OpenPMDTimeSeries.avail_record_components.
• This release introduces automatic PEP8 verification as part of the automatic tests that are run on Travis CI (see CONTRIBUTING.md).
• The evaluation of the waist and duration of the laser is now based on Gaussian fit of the transverse and longtudinal profile respectively.