- Added project status documentation.
- Bumped the minimum version of astropy to 5.0.
- Fixed ADAPT map reading with sunpy >= 4.0.
Fixed imports so pfsspy does not depend on sympy
as a runtime dependency.
(sympy
is still needed for the analytic
module however).
pfsspy now depends on Python >= 3.8, and is officially supported with Python 3.10
A host of new examples comparing pfsspy results to analytic solutions have been added to the example gallery.
- Updated the sunpy package requirement to include all packages needed to use sunpy maps.
- Any traced field line points that are out of bounds in latitude (ie. have a latitude > 90 deg) are now filtered out. This was previously only an issue for very low tracing step sizes.
- Fixed compatibility of map validity checks with sunpy 3.1.
- Updated this changelog to make it clear that pfsspy 1.0.0 depends on sunpy >= 3.0.
pfsspy now depends on python >= 3.7, sunpy >=3, and now does not depend on Matplotlib.
- The
max_steps
argument to pfsspy.tracers.FortranTracer now defaults to'auto'
and automatically sets the maximum number of steps to four times the number of steps that are needed to span radially from the solar to source surface.max_steps
can still be manually specified as a number if more or less steps are desired. - ~pfsspy.fieldline.FieldLines now has a
__len__
method, meaning one can now don_field_lines = len(my_field_lines)
. - Added :func:`pfsspy.utils.roll_map` to roll a map in the longitude direction. This is particularly helpful to modify GONG maps so they have a common longitude axis.
- Added the pfsspy.analytic sub-module that provides functions to sample analytic solutions to the PFSS equations.
- :func:`pfsspy.utils.carr_cea_wcs_header` now works with versions of sunpy >= 2.0.
- GONG synoptic maps now automatically have their observer information corrected (by assuming an Earth observer) when loaded by sunpy.map.Map.
- The plot settings of input maps are no longer modified in place.
- The interpretation of the
step_size
to pfsspy.tracers.FortranTracer has been corrected so that it is the step size relative to the radial cell size. A step size of 0.01 specified in pfsspy<1.0 is approximately equivalent to a step size of 1 in pfsspy 1.0, so you will need to adjust any custom step sizes accordingly. - Any points on field lines that are out of bounds (ie. below the solar surface or above the source surface) are now removed by the ~pfsspy.tracing.FortranTracer.
- :func:`pfsspy.pfss` no longer warns if the mean of the input data is non-zero, and silently ignores the monopole component.
- Saving and load PFSS solutions is no longer possible. This was poorly tested, and possibly broken. If you have interest in saving and loading being added as a new feature to pfsspy, please open a new issue at https://github.com/dstansby/pfsspy/issues.
Two bugs have been fixed in pfsspy.utils.carr_cea_wcs_header:
- The reference pixel was previously one pixel too large in both longitude and latitude.
- The longitude coordinate was previously erroneously translated by one degree.
Both of these are now fixed.
This release improves documentation and handling of HMI maps. In particular:
- The HMI map downloading example has been updated to use the polar filled data product, which does not have any data missing at the poles.
- :func:`pfsspy.utils.fix_hmi_meta` has been added to fix metadata issues in HMI maps. This modifies the metadata of a HMI map to make it FITS compliant, allowing it to be used with pfsspy.
This release adds citation information to the documentation.
This release contains the source for the accepted JOSS paper describing pfsspy.
This release includes several small fixes in response to a review of pfsspy for the Journal of Open Source Software. Thanks to Matthieu Ancellin and Simon Birrer for their helpful feedback!
- A permanent code of conduct file has been added to the repository.
- Information on how to contribute to pfsspy has been added to the docs.
- The example showing the performance of different magnetic field tracers has been fixed.
- The docs are now clearer about optional dependencies that can increase performance.
- The GONG example data has been updated due to updated data on the remote GONG server.
- Fixed some messages in errors raised by functions in pfsspy.utils.
- The pfsspy.utils module has been added, and contains various tools for loading and working with synoptic maps.
- pfsspy.Output has a new ~pfsspy.Output.bunit property, which returns the ~astropy.units.Unit of the input map.
- Added :meth:`pfsspy.Output.get_bvec`, to sample the magnetic field solution at arbitrary coordinates.
- Added the pfsspy.fieldline.FieldLine.b_along_fline property, to sample the magnetic field along a traced field line.
- Added a guide to the numerical methods used by pfsspy.
- The
.al
property of pfsspy.Output is now private, as it is not intended for user access. If you really want to access it, use._al
(but this is now private API and there is no guarantee it will stay or return the same thing in the future). - A ValueError is now raised if any of the input data to pfsspy.Input is non-finite or NaN. Previously the PFSS computation would run fine, but the output would consist entirely of NaNs.
- The monopole term is now ignored in the PFSS calculation. Previously a non-zero (but small) monopole term would cause floating point precision issues, leading to a very noisy result. Now the monopole term is explicitly removed from the calculation. If your input has a non-zero mean value, pfsspy will issue a warning about this.
- The data downloaded by the examples is now automatically downloaded and cached with sunpy.data.manager. This means the files used for running the examples will be downloaded and stored in your sunpy data directory if they are required.
- The observer coordinate information in GONG maps is now automatically set to the location of Earth at the time in the map header.
- The
date-obs
FITS keyword in GONG maps is now correctly populated.
- Improved descriptions in the AIA overplotting example.
- Fixed the 'date-obs' keyword in GONG metadata. Previously this just stored the date and not the time; now both the date and time are properly stored.
- Drastically sped up the calculation of source surface and solar surface magnetic field footpoints.
- Fixed a bug in the GONG synoptic map source where a map failed to load once it had already been loaded once.
- Fixed some calculations in
pfsspy.carr_cea_wcs_header
, and clarified in the docstring that the input shape must be in[nlon, nlat]
order. - Added validation to pfsspy.Input to check that the inputted map covers the whole solar surface.
- Removed ghost cells from pfsspy.Output.bc. This changes the shape of the returned arrays by one along some axes.
- Corrected the shape of pfsspy.Output.bg in the docstring.
- Added an example showing how to load ADAPT ensemble maps into a ~sunpy.map.CompositeMap
- Sped up field line expansion factor calculations.
This release largely sees a transition to leveraging Sunpy Map objects. As such, the following changes have been made:
pfsspy.Input now must take a sunpy.map.GenericMap as an
input boundary condition (as opposed to a numpy array). To convert a numpy array
to a ~sunpy.map.GenericMap, the helper function
pfsspy.carr_cea_wcs_header
can be used:
map_date = datetime(...) br = np.array(...) header = pfsspy.carr_cea_wcs_header(map_date, br.shape) m = sunpy.map.Map((br, header)) pfss_input = pfsspy.Input(m, ...)
pfsspy.Output.source_surface_br now returns a ~sunpy.map.GenericMap
instead of an array. To get the data array use source_surface_br.data
.
The new pfsspy.Output.source_surface_pils returns the coordinates of the polarity inversion lines on the source surface.
In favour of directly using the plotting functionality built into SunPy, the following plotting functionality has been removed:
pfsspy.Input.plot_input
. Instead ~pfsspy.Input has a new ~pfsspy.Input.map property, which returns a SunPy map, which can easily be plotted using sunpy.map.GenericMap.plot.pfsspy.Output.plot_source_surface
. A map of B_{r} on the source surface can now be obtained using pfsspy.Output.source_surface_br, which again returns a SunPy map.pfsspy.Output.plot_pil
. The coordinates of the polarity inversion lines on the source surface can now be obtained using pfsspy.Output.source_surface_pils, which can then be plotted usingax.plot_coord(pil[0])
etc. See the examples section for an example.
In order to make specifying seeds easier, they must now be a ~astropy.coordinates.SkyCoord object. The coordinates are internally transformed to the Carrington frame of the PFSS solution, and then traced.
This should make specifying coordinates easier, as lon/lat/r coordinates can be created using:
seeds = astropy.coordinates.SkyCoord(lon, lat, r, frame=output.coordinate_frame)
To convert from the old x, y, z array used for seeds, do:
r, lat, lon = pfsspy.coords.cart2sph r = r * astropy.constants.R_sun lat = (lat - np.pi / 2) * u.rad lon = lon * u.rad seeds = astropy.coordinates.SkyCoord(lon, lat, r, frame=output.coordinate_frame)
Note that the latitude must be in the range [-\pi/2, \pi/2].
pfsspy now comes with built in sunpy map sources for GONG and ADAPT synoptic
maps, which automatically fix some non-compliant FITS header values. To use
these, just import pfsspy
and load the .FITS files as normal with sunpy.
pfsspy.tracing.Tracer no longer has a transform_seeds
helper method, which
has been replaced by ~pfsspy.tracing.Tracer.coords_to_xyz and
pfsspy.tracing.Tracer.xyz_to_coords
. These new methods convert
between ~astropy.coordinates.SkyCoord objects, and Cartesian xyz coordinates
of the internal magnetic field grid.
- Improved the error thrown when trying to use
:class`pfsspy.tracing.FotranTracer` without the
streamtracer
module installed. - Fixed some layout issues in the documentation.
- Fix a bug where :class`pfsspy.tracing.FotranTracer` would overwrite the magnetic field values in an ~pfsspy.Output each time it was used.
- Reduced the default step size for the ~pfsspy.tracing.FortranTracer from 0.1 to 0.01 to give more resolved field lines by default.
:mod:`pfsspy.tracing` contains a new tracer, ~pfsspy.tracing.FortranTracer. This requires and uses the streamtracer package which does streamline tracing rapidly in python-wrapped fortran code. For large numbers of field lines this results in an ~50x speedup compared to the ~pfsspy.tracing.PythonTracer.
Changing existing code to use the new tracer is as easy as swapping out
tracer = pfsspy.tracer.PythonTracer()
for
tracer = pfsspy.tracer.FortranTracer()
. If you notice any issues with the
new tracer, please report them at https://github.com/dstansby/pfsspy/issues.
pfsspy.FieldLines
andpfsspy.FieldLine
have moved to pfsspy.fieldline.FieldLines and pfsspy.fieldline.FieldLine.- ~pfsspy.fieldline.FieldLines no longer has
source_surface_feet
andsolar_feet
properties. Instead these have moved to the new pfsspy.fieldline.OpenFieldLines class. All the open field lines can be accessed from a ~pfsspy.fieldline.FieldLines instance using the new ~pfsspy.fieldline.FieldLines.open_field_lines property.
- pfsspy.Output.bg is now returned as a 4D array instead of three 3D arrays. The final index now indexes the vector components; see the docstring for more information.
- Fixed a bug in
pfsspy.FieldLine.is_open
, where some open field lines were incorrectly calculated to be closed.
- Fixed a bug that incorrectly set closed line field polarities to -1 or 1 (instead of the correct value of zero).
FieldLine.footpoints
has been removed in favour of the newpfsspy.FieldLine.solar_footpoint
andpfsspy.FieldLine.source_surface_footpoint
. These each return a single footpoint. For a closed field line, see the API docs for further details on this.pfsspy.FieldLines
has been added, as a convenience class to store a collection of field lines. This means convenience attributes such aspfsspy.FieldLines.source_surface_feet
can be used, and their values are cached greatly speeding up repeated use.
The API for doing magnetic field tracing has changed. The new :mod:`pfsspy.tracing` module contains ~pfsspy.tracing.Tracer classes that are used to perform the tracing. Code needs to be changed from:
fline = output.trace(x0)
to:
tracer = pfsspy.tracing.PythonTracer() tracer.trace(x0, output) flines = tracer.xs
Additionally
x0
can be a 2D array that contains multiple seed points to trace, taking advantage of the parallelism of some solvers.The
pfsspy.FieldLine
class no longer inherits from ~astropy.coordinates.SkyCoord, but the ~astropy.coordinates.SkyCoord coordinates are now stored inpfsspy.FieldLine.coords
attribute.pfsspy.FieldLine.expansion_factor
now returnsnp.nan
instead ofNone
if the field line is closed.pfsspy.FieldLine
now has a~pfsspy.FieldLine.footpoints
attribute that returns the footpoint(s) of the field line.
- pfsspy.Input and pfsspy.Output now take the optional keyword argument dtime, which stores the datetime on which the magnetic field measurements were made. This is then propagated to the obstime attribute of computed field lines, allowing them to be transformed in to coordinate systems other than Carrington frames.
pfsspy.FieldLine
no longer overrrides the SkyCoord__init__
; this should not matter to users, as FieldLine objects are constructed internally by calling pfsspy.Output.trace
Output.plot_source_surface
now accepts keyword arguments that are given to Matplotlib to control the plotting of the source surface.
- Added more explanatory comments to the examples
- Corrected the dipole solution calculation
- Added
pfsspy.coords.sph2cart
to transform from spherical to cartesian coordinates.
pfsspy.Output.plot_pil
now accepts keyword arguments that are given to Matplotlib to control the style of the contour.pfsspy.FieldLine.expansion_factor
is now cached, and is only calculated once if accessed multiple times.