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doc fixes
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@kbwestfall
kbwestfall committed Aug 1, 2023
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8 changes: 0 additions & 8 deletions doc/api/pypeit.scripts.ql_multislit.rst
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1 change: 0 additions & 1 deletion doc/api/pypeit.scripts.rst
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Expand Up @@ -35,7 +35,6 @@ Submodules
pypeit.scripts.parse_slits
pypeit.scripts.qa_html
pypeit.scripts.ql
pypeit.scripts.ql_multislit
pypeit.scripts.run_pypeit
pypeit.scripts.scriptbase
pypeit.scripts.sensfunc
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2 changes: 1 addition & 1 deletion doc/calibrations/image_proc.rst
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Expand Up @@ -198,7 +198,7 @@ in our documentation as ``(nspec,nspat)``. The operations required to
flip/transpose the image arrays to match the PypeIt convention are dictated by
instrument-specific :class:`~pypeit.images.detector_container.DetectorContainer`
parameters and performed by
:func:`~pypeit.spectrograph.spectrographs.Spectrograph.orient_image`. Image
:func:`~pypeit.spectrographs.spectrograph.Spectrograph.orient_image`. Image
orientation will be performed if the ``orient`` parameter is true.

.. warning::
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2 changes: 1 addition & 1 deletion doc/calibrations/tilt.rst
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Expand Up @@ -58,7 +58,7 @@ Current TiltImage Data Model
============================

Internally, the image is held in
:class:`pypeit.tiltimage.TiltImage`
:class:`pypeit.images.buildimage.tiltimage.TiltImage`
which subclasses from :class:`pypeit.images.pypeitimage.PypeItImage` and
:class:`pypeit.datamodel.DataContainer`.

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9 changes: 8 additions & 1 deletion doc/conf.py
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Expand Up @@ -120,9 +120,16 @@

# When nit-picking, ignore these warnings:
nitpick_ignore = [ ('py:class', 'optional'),
('py:class', 'iterable'),
('py:class', 'ndarray'),
('py:class', 'dict-like'),
('py:class', 'array-like'),
('py:class', 'table-like'),
('py:class', 'float-like'),
('py:class', 'scalar-like'),
('py:class', 'default') ]
('py:class', 'default'),
('py:class', 'callable'),
]

# The reST default role (used for this markup: `text`) to use for all
# documents.
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3 changes: 1 addition & 2 deletions doc/fluxing.rst
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Expand Up @@ -589,6 +589,5 @@ FluxSpec Class
==============

The guts of the flux algorithms are guided by the
:class:`~pypeit.fluxcalibrate.FluxCalibrate`
class.
:func:`~pypeit.fluxcalibrate.apply_flux_calib` class.

78 changes: 0 additions & 78 deletions doc/help/pypeit_ql_multislit.rst
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2 changes: 1 addition & 1 deletion doc/include/bitmaskarray_usage.rst
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Expand Up @@ -38,7 +38,7 @@ You can access the bit flag names using:
Bit access
++++++++++

You can flag bits using :func:`~pypeit.bitmaskarray.BitMaskArray.turn_on`. For
You can flag bits using :func:`~pypeit.images.bitmaskarray.BitMaskArray.turn_on`. For
example, the following code flags the center column of the image as being
part of the detector bad-pixel mask:

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32 changes: 16 additions & 16 deletions doc/include/class_datamodel_wavetilts.rst
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@@ -1,19 +1,19 @@

**Version**: 1.2.0

==================== ============================ ================= ==============================================================================================================================
Attribute Type Array Type Description
==================== ============================ ================= ==============================================================================================================================
``PYP_SPEC`` str PypeIt spectrograph name
``bpmtilts`` `numpy.ndarray`_ `numpy.integer`_ Bad pixel mask for tilt solutions. Keys are taken from SlitTraceSetBitmask
``coeffs`` `numpy.ndarray`_ `numpy.floating`_ 2D coefficents for the fit on the initial slits. One set per slit/order (3D array).
``func2d`` str Function used for the 2D fit
``nslit`` int Total number of slits. This can include masked slits
``slits_filename`` str Path to SlitTraceSet file. This helps to find the Slits calibration file when running pypeit_chk_tilts()
``spat_flexure`` float Flexure shift from the input TiltImage
``spat_id`` `numpy.ndarray`_ `numpy.integer`_ Slit spat_id
``spat_order`` `numpy.ndarray`_ `numpy.integer`_ Order for spatial fit (nslit)
``spec_order`` `numpy.ndarray`_ `numpy.integer`_ Order for spectral fit (nslit)
``tilt_traces`` `astropy.table.table.Table`_ Table with the positions of the traced and fitted tilts for all the slits. see :func:`make_tbl_tilt_traces` for more details.
``tiltimg_filename`` str Path to Tiltimg file. This helps to find Tiltimg file when running pypeit_chk_tilts()
==================== ============================ ================= ==============================================================================================================================
==================== ============================ ================= ===============================================================================================================================================================
Attribute Type Array Type Description
==================== ============================ ================= ===============================================================================================================================================================
``PYP_SPEC`` str PypeIt spectrograph name
``bpmtilts`` `numpy.ndarray`_ `numpy.integer`_ Bad pixel mask for tilt solutions. Keys are taken from SlitTraceSetBitmask
``coeffs`` `numpy.ndarray`_ `numpy.floating`_ 2D coefficents for the fit on the initial slits. One set per slit/order (3D array).
``func2d`` str Function used for the 2D fit
``nslit`` int Total number of slits. This can include masked slits
``slits_filename`` str Path to SlitTraceSet file. This helps to find the Slits calibration file when running pypeit_chk_tilts()
``spat_flexure`` float Flexure shift from the input TiltImage
``spat_id`` `numpy.ndarray`_ `numpy.integer`_ Slit spat_id
``spat_order`` `numpy.ndarray`_ `numpy.integer`_ Order for spatial fit (nslit)
``spec_order`` `numpy.ndarray`_ `numpy.integer`_ Order for spectral fit (nslit)
``tilt_traces`` `astropy.table.table.Table`_ Table with the positions of the traced and fitted tilts for all the slits. see :func:`~pypeit.wavetilts.BuildWaveTilts.make_tbl_tilt_traces` for more details.
``tiltimg_filename`` str Path to Tiltimg file. This helps to find Tiltimg file when running pypeit_chk_tilts()
==================== ============================ ================= ===============================================================================================================================================================
10 changes: 9 additions & 1 deletion doc/include/links.rst
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Expand Up @@ -13,6 +13,7 @@
.. _str.splitlines: https://docs.python.org/3/library/stdtypes.html#str.splitlines
.. _textwrap.wrap: https://docs.python.org/3/library/textwrap.html#textwrap.wrap
.. _Path: https://docs.python.org/3/library/pathlib.html
.. _io.TextIOWrapper: https://docs.python.org/3/library/io.html#io.TextIOWrapper

.. numpy
.. _numpy: https://numpy.org/
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.. _matplotlib: https://matplotlib.org/
.. _matplotlib.pyplot.imshow: http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.imshow
.. _matplotlib.axes.Axes: https://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes
.. _matplotlib.backend_bases.Event: https://matplotlib.org/stable/api/backend_bases_api.html#matplotlib.backend_bases.Event

.. configobj
.. _configobj: http://configobj.readthedocs.io/en/latest/

.. astropy
.. _astropy.io.fits: http://docs.astropy.org/en/stable/io/fits/index.html
.. _astropy.io.fits.getheader: https://docs.astropy.org/en/stable/io/fits/api/files.html#astropy.io.fits.getheader
.. _astropy.io.fits.open: http://docs.astropy.org/en/stable/io/fits/api/files.html#astropy.io.fits.open
.. _astropy.io.fits.HDUList: http://docs.astropy.org/en/stable/io/fits/api/hdulists.html
.. _astropy.io.fits.HDUList.writeto: http://docs.astropy.org/en/stable/io/fits/api/hdulists.html#astropy.io.fits.HDUList.writeto
Expand All @@ -73,19 +76,21 @@
.. _astropy.table.Table.read: https://docs.astropy.org/en/stable/api/astropy.table.Table.html#astropy.table.Table.read
.. _astropy.table.Table.remove_rows: https://docs.astropy.org/en/stable/api/astropy.table.Table.html#astropy.table.Table.remove_rows
.. _astropy.table.Row: https://docs.astropy.org/en/stable/api/astropy.table.Row.html
.. _astropy.wcs.wcs.WCS: http://docs.astropy.org/en/stable/api/astropy.wcs.WCS.html
.. _astropy.wcs.WCS: http://docs.astropy.org/en/stable/api/astropy.wcs.WCS.html
.. _astropy.modeling: http://docs.astropy.org/en/stable/modeling/index.html
.. _astropy.modeling.polynomial.Legendre1D: http://docs.astropy.org/en/stable/api/astropy.modeling.polynomial.Legendre1D.html
.. _astropy.modeling.models.CompoundModel: http://docs.astropy.org/en/stable/modeling/compound-models.html
.. _astropy.modeling.FittableModel: http://docs.astropy.org/en/stable/api/astropy.modeling.FittableModel.html
.. _astropy.cosmology.FlatLambdaCDM: http://docs.astropy.org/en/stable/api/astropy.cosmology.FlatLambdaCDM.html#flatlambdacdm
.. _astropy.constants: http://docs.astropy.org/en/stable/constants/index.html
.. _astropy.time.Time: https://docs.astropy.org/en/stable/time/
.. _astropy.coordinates.Angle: https://docs.astropy.org/en/stable/api/astropy.coordinates.Angle.html
.. _astropy.coordinates.SkyCoord: https://docs.astropy.org/en/stable/api/astropy.coordinates.SkyCoord.html
.. _astropy.coordinates.EarthLocation: https://docs.astropy.org/en/stable/api/astropy.coordinates.EarthLocation.html
.. _astropy.coordinates.SkyCoord.radial_velocity_correction: https://docs.astropy.org/en/stable/api/astropy.coordinates.SkyCoord.html#astropy.coordinates.SkyCoord.radial_velocity_correction
.. _astropy.stats.SigmaClip: https://docs.astropy.org/en/stable/api/astropy.stats.SigmaClip.html
.. _astropy.stats.sigma_clipped_stats: https://docs.astropy.org/en/stable/api/astropy.stats.sigma_clipped_stats.html
.. _astropy.units.Unit: https://docs.astropy.org/en/stable/api/astropy.units.Unit.html
.. _astropy.units.Quantity: https://docs.astropy.org/en/stable/api/astropy.units.Quantity.html

.. scikit
Expand Down Expand Up @@ -122,11 +127,14 @@
.. _bottleneck: https://bottleneck.readthedocs.io/en/latest/
.. _specutils: https://specutils.readthedocs.io/en/stable/
.. _specutils.Spectrum1D: https://specutils.readthedocs.io/en/stable/api/specutils.Spectrum1D.html
.. _specutils.SpectrumList: https://specutils.readthedocs.io/en/stable/api/specutils.SpectrumList.html
.. _jdaviz: https://jdaviz.readthedocs.io/en/latest/
.. _jupyter notebook: https://jupyter.org/
.. _ppxf: https://pypi.org/project/ppxf/

.. ginga
.. _ginga: https://ginga.readthedocs.io/en/stable/
.. _ginga.RemoteClient: https://ginga.readthedocs.io/en/stable/manual/plugins_global/rc.html
.. _AstroImage: https://ginga.readthedocs.io/en/stable/dev_manual/image_wrappers.html#astroimage
.. _ginga GlobalPlugin: https://ginga.readthedocs.io/en/stable/dev_manual/developers.html#writing-a-global-plugin

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