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Merge pull request #6 from LowellObservatory/doc_bug_fixes
Flesh out the documentation and fix bugs
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‎.github/workflows/documentation.yaml

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with:
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# we want to find git tags to pass version to sphinx
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fetch-depth: 0
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- uses: actions/setup-python@v3
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- uses: actions/setup-python@v4
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with:
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python-version: '3.11'
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- name: Install dependencies
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run: |
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pip install sphinx sphinx_rtd_theme sphinx-automodapi .[dev]

‎README.rst

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.. |License| image:: https://img.shields.io/github/license/LowellObservatory/LDTObserverTools
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:target: https://github.com/LowellObservatory/LDTObserverTools/blob/main/LICENSE
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.. |astropy| image:: https://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat
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.. |astropy| image:: https://img.shields.io/badge/powered%20by-AstroPy-blue.svg?style=flat
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:target: https://www.astropy.org/
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.. |forks| image:: https://img.shields.io/github/forks/LowellObservatory/LDTObserverTools?style=social
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:target: https://github.com/LowellObservatory/LDTObserverTools
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:target: https://github.com/LowellObservatory/LDTObserverTools/forks
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.. |issues| image:: https://img.shields.io/github/issues/LowellObservatory/LDTObserverTools?style=social
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:target: https://github.com/LowellObservatory/LDTObserverTools
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.. |issues| image:: https://img.shields.io/github/issues/LowellObservatory/LDTObserverTools?style=badge
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:target: https://github.com/LowellObservatory/LDTObserverTools/issues
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.. |pulls| image:: https://img.shields.io/github/issues-pr/LowellObservatory/LDTObserverTools?style=badge
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:target: https://github.com/LowellObservatory/LDTObserverTools/pulls
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.. |stars| image:: https://img.shields.io/github/stars/LowellObservatory/LDTObserverTools?style=social
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:target: https://github.com/LowellObservatory/LDTObserverTools
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:target: https://github.com/LowellObservatory/LDTObserverTools/stargazers
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.. |watch| image:: https://img.shields.io/github/watchers/LowellObservatory/LDTObserverTools?style=social
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:target: https://github.com/LowellObservatory/LDTObserverTools
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:target: https://github.com/LowellObservatory/LDTObserverTools/watchers
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.. |github| image:: https://img.shields.io/badge/GitHub-LDTObserverTools-brightgreen
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:target: https://github.com/LowellObservatory/LDTObserverTools
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.. |language| image:: https://img.shields.io/github/languages/top/LowellObservatory/LDTObserverTools
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:target: https://github.com/LowellObservatory/LDTObserverTools
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.. image:: https://raw.githubusercontent.com/LowellObservatory/LDTObserverTools/main/doc/_static/obstools_logo.png
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:target: https://github.com/LowellObservatory/LDTObserverTools
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:width: 500
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|github| |astropy| |License|
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|language| |issues| |pulls|
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The LDTObserverTools package is a collection of command-line and GUI tools
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for observers at the Lowell Discovery Telescope (LDT) in Happy Jack, AZ.
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occur. This mitigates any possible dependency conflicts with other packages
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you use.
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The recommended method of setting up a new envrionment is with ``conda``:
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The recommended method of setting up a new environment is with ``conda``:
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.. code-block:: console
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Optional Dependencies
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^^^^^^^^^^^^^^^^^^^^^
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There are no optional dependencies at this time.
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.. There are no optional dependencies at this time.
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.. Some of the instrument-specific routines in this package require additional dependencies
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.. that are not otherwise needed by the majority of the routines herein.
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Some of the instrument-specific routines in this package require additional dependencies
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that are not otherwise needed by the majority of the routines herein.
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.. - If you are using the ``deveny_pickup_cleaner`` routine, you will need the
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.. spectroscopic data reduction pipeline PypeIt for the iterative cleaning of
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.. the pickup noise. It can be installed by including it in the optional
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.. dependencies, `e.g.`:
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- If you are using the ``scrub_deveny_pickup`` tool, you will need the
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spectroscopic data reduction pipeline `PypeIt <https://pypeit.readthedocs.io/en/release/>`_
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for the iterative cleaning of the pickup noise. It can be installed by
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including it in the optional dependencies, *e.g.*:
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.. .. code-block:: console
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.. code-block:: console
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.. pip install "obstools[pypeit] @ git+https://github.com/LowellObservatory/LDTObserverTools"
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pip install "obstools[pypeit] @ git+https://github.com/LowellObservatory/LDTObserverTools"

‎doc/api/obstools.etc_calc.rst

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‎doc/api/obstools.lmi_etc.rst

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obstools.lmi\_etc module
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========================
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.. automodule:: obstools.lmi_etc
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:members:
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:private-members:
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:undoc-members:
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:show-inheritance:

‎doc/api/obstools.rst

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obstools.deveny_collfocus
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obstools.deveny_grangle
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obstools.dfocus
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obstools.etc_calc
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obstools.fix_ldt_header
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obstools.lmi_etc
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obstools.neocp_ephem
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obstools.scrub_deveny_pickup
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obstools.utils

‎doc/conf.py

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"sphinx.ext.mathjax",
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"sphinx.ext.ifconfig",
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"sphinx.ext.viewcode",
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"sphinx_subfigure",
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# "sphinx.ext.autosectionlabel",
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]
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# Example configuration for intersphinx: refer to the Python standard library.
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intersphinx_mapping = {
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"python": ("https://docs.python.org/3/", None),
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"astropy": ("https://docs.astropy.org/en/stable/", None),
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"attrs": ("https://www.attrs.org/en/stable/", None),
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"astropy": ("https://docs.astropy.org/en/stable/", None),
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"ccdproc": ("https://ccdproc.readthedocs.io/en/stable/", None),
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"matplotlib": ("https://matplotlib.org/stable/", None),
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"numpy": ("https://numpy.org/doc/stable/", None),
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"sphinx": ("https://www.sphinx-doc.org/en/master/", None),
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"scipy": ("https://docs.scipy.org/doc/scipy/", None),
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"pypeit": ("https://pypeit.readthedocs.io/en/release/", None),
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"stomp": ("https://jasonrbriggs.github.io/stomp.py/", None),
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}

‎doc/deveny_collfocus.rst

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.. include:: include/links.rst
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.. |nbsp| unicode:: 0xA0
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:trim:
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.. _deveny_collfocus:
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=================================
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DeVeny Collimator Focus Estimator
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=================================
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\end{aligned}
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where :math:`T_{\rm m}` is the mount temperature and tilt is the grating tilt
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angle. This equation is coded into the GUI tool.
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angle. The RMS of the fit is :math:`\sim 0.6` |nbsp| mm. This equation is coded into
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the GUI tool.
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Unlike other focus procedures at LDT, the DeVeny LOUI focus sequence script
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does not take the *expected* focus value, but rather one end of the range,
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.. include:: help/deveny_collfocus.rst
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When the application launches, a GUI window will appear:
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When the application launches, a GUI window will appear as in
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:numref:`collfocus_startup`.
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.. image:: figures/deveny_collfocus_startup.png
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.. _collfocus_startup:
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.. figure:: figures/deveny_collfocus_startup.png
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:class: with-shadow
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:alt: GUI at startup
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-- The ``deveny_collfocus`` GUI at startup.
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When you click "Compute", the bottom half of the GUI is populated with the
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estimated focus value from the equation above and values to enter into the
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DeVeny LOUI focus sequence tab.
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DeVeny LOUI focus sequence tab. See :numref:`collfocus_values`.
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.. image:: figures/deveny_collfocus_values.png
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.. _collfocus_values:
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.. figure:: figures/deveny_collfocus_values.png
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:class: with-shadow
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:alt: GUI after clicking "Compute"
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-- The ``deveny_collfocus`` GUI after clicking "Compute". The estimated
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focus value (with uncertainty) is printed, along with suggested values for
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use with the LOUI Focus Sequence tab.
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Observers should note that the lower limit on the collimator focus motorized
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‎doc/deveny_grangle.rst

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.. include:: include/links.rst
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.. |nbsp| unicode:: 0xA0
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:trim:
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.. _deveny_grangle:
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===============================
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DeVeny Grating Angle Calculator
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===============================
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Overview
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========
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- ``deveny_grangle``: Compute the desired grating angle based on selected
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grating and desired central wavelength. This routine comes with two interfaces.
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The default GUI features a dropdown menu for grating selection and contains error
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checking on the input for central wavelength. There is a ``MAX_GUI`` option for
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computing central wavelength given the grating angle in addition to the standard
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GUI features. Also included is a command-line interface, identical to the old
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IDL function. Online help is available with the ``-h`` option.
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[`Completed: 2021-01-26`]
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.. _grateq:
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The Grating Equation
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^^^^^^^^^^^^^^^^^^^^
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The angles at which the diffracted light reflects off the grating are given
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by the grating equation:
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.. math::
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\begin{equation}
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m\lambda = d(\sin \theta _{i}-\sin \theta _{m})~,
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\end{equation}
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where :math:`d` is the spacing between adjacent grooves on the grating,
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:math:`\theta_{i} = \theta_{\rm grangle} + 10^{\circ}` is the incident angle,
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and :math:`\theta_{m} = 55^{\circ} - \theta_{i}` is the outgoing angle for light
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with wavelength :math:`\lambda` diffracting into order :math:`m` (see the
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DeVeny user manual for a description of the physical layout of the
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spectrograph). The DeVeny gratings are typically operated in
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1\ :superscript:`st`\ order (:math:`m = 1`), although use of :math:`m=2` would
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possible with the proper short-pass order-blocking filters to remove
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1\ :superscript:`st`\ -order light.
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This tool computes the necessary tilt :math:`\theta_{\rm grangle}` by
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numerically solving the equation below for a given grating. The computation
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uses the groove density (in g/mm) in place of :math:`d`, and finds
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:math:`\theta_{\rm grangle}` for a specified 1\ :superscript:`st`\ -order
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central wavelength (:math:`\lambda_c`) in Angstroms on the spectral CCD.
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.. math::
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\begin{equation}
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\lambda_c~({\rm \mathring{A}}) = \frac{\sin(\theta_{\rm grangle} +10^{\circ}) - \sin(45^{\circ} - \theta_{\rm grangle})}{ {\rm groove~density~(g/mm)} }\times 10^7
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\end{equation}
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Usage
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.. include:: help/deveny_grangle.rst
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In its default mode, the tool launches a GUI window as in
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:numref:`grangle_startup`.
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.. _grangle_startup:
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.. figure:: figures/deveny_grangle_startup.png
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:class: with-shadow
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:alt: GUI at startup
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-- The ``deveny_collfocus`` GUI at startup.
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Select your grating from the dropdown menu (this selects the groove density),
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and enter your desired central wavelength (in angstroms). When you click
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"Compute", the bottom half of the GUI is populated with the needed grating tilt
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value from the equation above and the computed slit demagnification value (see
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the DeVeny user manual for a brief discussion of grating physics). See
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:numref:`grangle_values`.
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.. _grangle_values:
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.. figure:: figures/deveny_grangle_values.png
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:class: with-shadow
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:alt: GUI after clicking "Compute"
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-- The ``deveny_grangle`` GUI after clicking "Compute". The needed grating
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tilt angle and computed slit demagnification values have been populated.
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There are two optional modes for running this tool:
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* ``--cli``: A command-line version of this tool, which looks and functions
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identical to the old IDL routine with the same name.
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* ``--max``: The GUI will have the option to compute the central wavelength
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from :math:`\theta_{\rm grangle}` in addition to the forward calculation
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done in the default mode.

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