Marxs

Latest version: v2.0

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2.0

-----------------

New Features
^^^^^^^^^^^^

- `marxs.simulator.Parallel` and `marxs.simulator.Sequence` now have a
``first_of_class_top_level`` method to help find certain subelements. [222]

- Added `marxs.design.tolerancing.run_tolerances_for_energies2` is similar to
`marxs.design.tolerancing.run_tolerances_for_energies`, but with a
simplified interface. [222]

- Output columns from optical elements can now be `None` (they will be ignored)
or specify the datatype and other Column meta information. [226]

- To avoid probabilities <0 or >1, values assigned to this column are now
tested and a ``ValueError`` may be raised. [230]

- Added a new class ``CaptureResAeff_CCDgap`` that selects photons differently for
calculation of the effective area and resolving power to account for chip gaps. [235]

- Add direct X3D visualization backend to avoid the need for Mayavi. [238]
- Add several missions under development that were previously developed in separate
repros. As it turn out, keeping the code separate lead to significant parallel
work that can be simplified by keeping all of them in marxs itself. However, those
mission are less fleshed out then marxs itself, less documented and less tested. [237]
- Add ``CircularMeshGrid`` as a new way to place gratings on the Rowlandtorus. Adapted from
previous Lynx code. [237]
- Add various helper functions that previously lived in separate repros. [237]
- Add methods to fit the LSF to generate a Chandra-style LSFPARM file. [237]
- Include code for several missions (Athena, Arcus, Lynx, AXIS) into marxs.
This code had been previously developed separately, since none of it is really ready for
public consumption (e.g. the Lynx concept has been rejected, Arcus is under continuous redefinition).
However, given how few people except me currently use MARXS, "practicality beats purity"
and I'm now including this into marxs. Note that the mission code generally is not documented
in the docs and not tested as well.
It's simply either not interesting enough for general users (but needed to
replicate some of my SPIE proceedings so Moritz Guenther wants it publicly available)
or evolving too fast to write good docs and tests (e.g. the Arcus effective area
changes every time the coating or layout changes, tests that check Aeff are
thus more checks on the CALDB than on the code). [240]
- A number of updates that were developed for those individual missions and are
now included into marxs proper, e.g.: A class to make certain plots that display
the performance loss for misalignments and utilities to run tolerancing etc. [240]
- Add new functions to `marxs.design.rowland` to construct Rowland tori in a
double tilted Rowland torus design. [245]
- Add more options to ``PerfectLens`` to account for non-perfect reflectivity and
the option to have the optical axis offset from the geometrical center of the element. [248]
- Add method to create archive files of X3D files. [251]

API Changes
^^^^^^^^^^^
- For all classes that place elements on the Rowland torus, the API has been
standardized. That means changes to almost all of them. In particular:

- ``rowland.RectangularGrid`` replaces ``RowlandTorusArray`` and ``LinearCCDArray``.
Inputs are specified the y and z ranges now instead of Rowland circle
:math:`$\phi` coordinates that are hard to visualize since it's measure from the
center of the Rowland circle and the origin of :math:`$\phi=0` depends on the
rotation of the torus. ``rowland.RectangularGrid`` can be used for 1D or 2D
arrangements and thus ``d_element`` must always be two numbers for dimension in
both directions.
- All classes now use a minimizer instead of a brackets root finder. So, instead
of a bracketing interval, they now need a ``guess_distance`` where the minimization
starts.

- ``load_table2d`` has been replaced by ``marxs.utils.tablerows_to_2d``, which performs
the same reformatting of a table, but does not read it in. [237]
- ``marxs.missions.mitsnl.InterpolateEfficiencyTable`` now takes a table, instead of a
filename as parameter. [237]
- `effectivearea_from_photonlist` now requires a unit for the input of the effective area. [237]
- ``CaptureResAeff_CCDgap`` and ``CaptureResAeff`` are moved to
``marxs.analysis.gratings``. [237]
- ``plot_wiggle`` and ``load_and_plot`` are now summarized in the class to make it
easier to derive from them. [237]

- Rename files that had a class of the same name, because this confuses the Sphinx autosummary
extension. The following files have been renamed: `marxs.missions.chandra.chandra` to
`marxs.missions.chandra.chandra_global`, `marxs.source.source` to `marxs.source.basesources`,
and `marxs.optics.baffle` to `marxs.optics.baffles`. Users that follow the recommended practice
of importing from the higher level such as `from marxs.optics import Baffle` should not notice
any difference. [424]

- The unit of photon energy is now set to keV. [252]

- ``CCDRedistNormal`` now inherits from an optical element and takes the sigma for redistribution
as a keyword argument. [252]

Bug fixes
^^^^^^^^^

- `marxs.missions.mitsnl.catsupportbars` no longer throws an exception if
no photon hit a facet before. [221]

- To avoid probabilities <0 or >1, the default interpolation for MIT grating
efficiency tables is now linear. [229]

- Fig bug in ``design_tilted_torus``. The equations implemented previously
implicitly assumed 2 * alpha = beta. [250]

Other changes and additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^

- Previously, MARXS only contained modules for currently operating missions.
However, in practice, it's mostly used to simulate proposed missions. Thus,
we changed the policy to include simulation code for proposed missions here.
That code may not be of general use, but it simplifies the workflow for
developers considerably and serve example on how to build your own
instrument from the building blocks provided by the main marxs modules. [237]

- Updates of CI and simplify _astropy_init and conftest for new Python and
astropy verisons. [236]

1.2

-----------------

New Features
^^^^^^^^^^^^
- Unit milimeter on ``"pos"`` and ``"dir"`` columns of photonlist. [169]

- Add method `marxs.simulator.Parallel.move_center` to change the ``pos4d``
value of a `marxs.simulator.Parallel` and adjust position of elements at
the same time. [169]

- Refactor `marxs.analysis.analysis.find_best_detector_position` to allow
for more general objective functions. [171]

- Update plotting for `marxs.optics.aperture.CircleAperture` to give more
flexibility in plotting the inner part of a ring-like aperture. This is
needed for models or stacked, rind-like apertures. [180]

- Add new module `marxs.design.tolerancing` to estimate alignment tolerances.
[186]

- Add class `marxs.optics.RandomGaussianScatter`. [192]

- The column names for blaze and order written by
`marxs.optics.FlatGrating` can now be configured. [195]

- Add a number of helper functions (incl. plotting) to
`marxs.design.tolerancing`. [199]

- Add a module to simulate CAT gratings manufactures in MIT's SNL. [202]

- Make MIT SNL grating specification more flexible. [210]


API Changes
^^^^^^^^^^^

- Sources now require input for flux, energy, and polarization as astropy
quantities. Any table-like input must not be a astropy `QTable` and flux and
polarization values are *densities* not per-bin. [218]

- The geometry of a class is now defined as a separate object from the new
`marxs.math.geometry` module. Before, the geometry was backed into the
optical components itself which led to significant code duplication. The new
scheme allows to make e.g. cylindrical and flat gratings with the same
gratings objects. However, not all geometries work with all objects and there
is currently no way to check automatically - the user has to use caution or
check the code. [182]

- Geometry objects provide item access like this
``detector.geometry['center']`` instead of a function interface with
``(...)``. [182]

- Remove ``utils.MergeIdentical`` merge strategy since it is not longer used
after 189. [191]

- `~astropy.units.Quantity` is used in more places, and thus
the base classes need to accept quantities as output from
"specific_process_photons". This change requires some care and thus
is done gradually only where needed at this point. [202]

- `~marxs.optics.RandomGaussianScatter` can be initialized without setting
scatter, provided that its already defined a class level variable (e.g.
for subclasses). [202]

- `~marxs.optics.RandomGaussianScatter` and `~marxs.optics.Scatter` now expect
angular quantities instead of plain floats. [216]


Bug fixes
^^^^^^^^^

- `marxs.analysis.gratings.resolvingpower_per_order` has been updated to ignore
photons with probability 0. [162]

- An index mix-up in `marxs.simulator.ParallelCalculated.calculate_elempos` introduced
unintended zoom and shear in the elements. [164]

- [159] left behind an undefined ``filterfunc``. This is fixed and a
regression test added. [165]

- `marxs.analysis.analysis.find_best_detector_position` will now change the
detector position always along an axis perpendicular to the detector plane.
[171]

- `marxs.optics.scatter.RadialMirrorScatter` now works with
``inplanescatter=0`` which is useful for parameters studies. [174]

- Plot only "half-box" for elements such as mirrors where the optical
interaction occurs on a surface. [178]

- With `marxs.optics.MultiAperture` photons would always be sorted by aperture
number. To fix this, apertures now behave more like other optical elements
and use ``process_photons``. [189]

- `marxs.optics.FlatStack` now inherits from `marxs.simulator.BaseContainer`.
[196]

- Fix bug in distributions generated by `marxs.source.SphericalDiskSource`. [202]

- Objects now fail to generate when zoom is set to 0. [217]

Other changes and additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^
- Examples are now written for numpy >= 1.14 (which changed some printing
formats). [182]

1.1

-----------------

New Features
^^^^^^^^^^^^
- Add ability to plot cylinders in Mayavi (for support struts) [147]

- Add shape `"None"` (as a string) to avoid plotting an object [157]

API Changes
^^^^^^^^^^^
- Remove ``marxs.source.LabPointSource``, which was just a special case of
`~marxs.source.LabPointSourceCone`. Instead, set the default values of the
later so that it reproduces the behaviour of the former. [144]

- `~marxs.optics.multiLayerMirror.MultiLayerEfficiency` and
`~marxs.optics.multiLayerMirror.MultiLayerMirror` now
expect all parameters as keyword arguments for consistency with the other
elements in MARXS. [144]

- ``marxs.visualization.utils.format_saved_positions`` is now a method of
`~marxs.simulator.KeepCol` with the new name ``format_positions()`` and
the ``atol`` keyword can be switched off.
Additionally, `~marxs.simulator.KeepCol` now has a ``__array__`` method.
This makes the function useful for columns that
are not positions, but e.g. polarization vectors.
On the other hand, the ``plot_rays`` functions do not accept
`~marxs.simulator.KeepCol` objects directly as input any longer.
[149, 152]

- According to the docs, a pointing could be initialized with either a
`~astropy.coordinates.SkyCoord` or a tuple that would initialize the
`~astropy.coordinates.SkyCoord`. The later option was broken and has
been removed entirely. [151]

- Remove parameter ``filterfunc`` from `~marxs.analysis.gratings.resolvingpower_from_photonlist` and `~marxs.analysis.analysis.detected_fraction`.
Instead, the photon list can be filtered before calling these functions
just as easily. [159]

Bug fixes
^^^^^^^^^
- Added missing keywords in display dict for some objects and fixed exception
when plotting things that are not objects. Discovered and fixed as part of
[147].

- Polarization after reflection from a mirror used to just parallel transport
the vector and calculate the probability of the photon based on s and p
polarization. This needs to be applied to the outgoing polarization vector,
too. [148]

- Plotting of Rowland Torus failed in Mayavi due to typo. [154]


Other changes and additions
^^^^^^^^^^^^^^^^^^^^^^^^^^^
- Improve Documentation [146]

- Docs: Add polarization example [153]

- Docs: Add example to calculate flux from normalized spectrum [160]

- Add experiemental data for comparison to the polarization example [158]

1.0

-----------------
This is the first release intended to use. The Change log will begin starting
with this release.

0.1

--------------------------
This release was not intended to be used, but the verisioning scheme in the
development branch required a tagged commit.

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