The main changes associated with the release are enumerated below:
- Single flags (CLI options with a single dash) are now reserved for a special functionality that is based on Unix operating systems. They can be combined together to shorten the number of arguments used. An example is shown below. Because this functionality cannot have inputs with the associated flags, these are most limited to boolean type inputs (``-s`` for show, ``-v`` for verbose, ``-k`` for Kepler artefact correction, ``-x`` for turning off the first module and ``-b`` for turning off the second module):
- ``pysyd run --star 1435467 -show -verbose`` can be shortened to pysyd run ``--star 1435467 -sv`` but will do the same exact thing.
- The simplest model (aka flat white-noise term only) has been implemented BUT this has not been tested on null detections yet. I am curious to see if this works as nicely as I hoped it would.
- The metric used for model selection is now the BIC, with an option to use the AIC as well. The ``scipy.chisquare`` function has been removed, which by default should eliminate the issue with the scipy versions.
- The background-corrected PS is now saved to a text file in the same directory as the other output data
- There is a new ``Constants`` class available in ``utils.py`` that contains all of the constants used in any calculations throughout the software (and therefore easily importable)
- The plotting “block” has been turned off, so you no longer have to close out of the figure to continue running the software
- The white noise estimation module has been fixed and does not require the nyquist to be defined. I think this * should * fix the ``x0 infeasible`` error we were seeing, which was because the estimated white noise was a ``nan``.
- CLI options have been further separated into relevant sections so they are easier to know where they are applicable (i.e. ``pysyd run --help`` will output text that is much easier to follow)
- Along that line, many new command line arguments/options have been added, including (but not limited to):
- the width (``--ew``, ``--exwidth``) of the power excess region (this is a fractional value of the width calculated based on numax and the numax/width of the Sun). So by default, this is 1.0 but can be any fractional value (i.e. 0.5, 2.0), which will still remain centered on the estimated numax.
- you can be even more specific and provide the exact bounds to use of this region for the power excess by specifying the upper (``--up``, ``--upperp``) and lower (``--lp``, ``--lowerp``) bound (i.e. not necessarily centered on numax). this is helpful if you have power excess near a strange artefact (or anything), where selecting strict bounds helps reduce the noise in the computed ACF.
- ``--thresh``, ``--threshold`` is the fractional value of the FWHM used in the ACF to find the best dnu. Similar to the excess width option above, it’s 1.0 by default but can be adjusted based on the ACF. An example to justify this would be if the calculated FWHM encapsulates two peaks and it’s latching on to the incorrect peak.
- Some of the modules have been modified but the functionality is still the same. I’ve attempted to break down some of the functions into more intuitive steps, the end goal being a more modular software package.
- The harvey models are now directly sampling in {tau, sigma} space, as opposed to the original {a, b} parametrization. This helped ensure the priors were strictly physical values.
- Due to the numerous upper/lower bounds used throughout the software, the names/keys for these are slightly more descriptive. For example, ``lowerx``/``upperx`` is now ``lower_ex``/``upper_ex`` and same for the background fitting routine, so it’s clear that these are general bounds for the modules. ``Lower_ps``/``upper_ps`` is for defining the region with the power excess (optional), ``lower_ech``/``upper_ech`` is for defining the region in a folded PS (i.e. echelle diagram) for whitening mixed modes from the PS before attempting to estimate dnu (optional). **NOTE: this may require you to either re-run ``pysyd setup`` or to change the keys (i.e. columns) in the ``info/star_info.csv``**.