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kbwestfall committed Jul 31, 2024
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8 changes: 8 additions & 0 deletions doc/api/pypeit.scripts.extract_datacube.rst
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pypeit.scripts.extract\_datacube module
=======================================

.. automodule:: pypeit.scripts.extract_datacube
:members:
:private-members:
:undoc-members:
:show-inheritance:
1 change: 1 addition & 0 deletions doc/api/pypeit.scripts.rst
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Expand Up @@ -26,6 +26,7 @@ Submodules
pypeit.scripts.compare_sky
pypeit.scripts.compile_wvarxiv
pypeit.scripts.edge_inspector
pypeit.scripts.extract_datacube
pypeit.scripts.flux_calib
pypeit.scripts.flux_setup
pypeit.scripts.identify
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8 changes: 4 additions & 4 deletions doc/coadd3d.rst
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Expand Up @@ -155,7 +155,7 @@ There are several recommended steps of the coadd3d process that can be run separ
pypeit_sensfunc spec1d_StandardStarName.fits -o sens_StandardStarName.fits
For further details, see :doc:`_sensitivity_function`.
For further details, see :ref:`sensitivity_function`.

#. Step 4 - Generate a datacube of the science exposures. This is done by running the following command:

Expand All @@ -164,7 +164,7 @@ There are several recommended steps of the coadd3d process that can be run separ
pypeit_coadd_datacube ScienceName.coadd3d -o
Note that you will need to specify the sensitivity function file using the ``sensfile`` option in the
:doc:`coadd3d_file` file. For further details, see :ref:`coadd3d_fluxing`.
:ref:`coadd3d_file` file. For further details, see :ref:`coadd3d_fluxing`.

Combination options
===================
Expand Down Expand Up @@ -239,7 +239,7 @@ If you would like to flux calibrate your datacube, you need to
produce your standard star datacube first. Then extract the spectrum
of the standard star using the ``pypeit_extract_datacube`` script. This
will produce a ``spec1d`` file that you will need to use to generate a
sensitivity function in the usual way (see :doc:`_sensitivity_function`).
sensitivity function in the usual way (see :ref:`sensitivity_function`).
Then, when generating the datacube of the science frame you must include
the name of the sensitivity function in your ``coadd3d`` file as follows:

Expand Down Expand Up @@ -289,7 +289,7 @@ then you can specify the ``skysub_frame`` in the ``spec2d`` block of the
above. If you have dedicated sky frames, then it is generally
recommended to reduce these frames as if they are regular science
frames, but add the following keyword arguments at the top of your
:doc:`coadd3d_file`:
:ref:`coadd3d_file`:

.. code-block:: ini
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29 changes: 29 additions & 0 deletions doc/help/pypeit_extract_datacube.rst
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.. code-block:: console
$ pypeit_extract_datacube -h
usage: pypeit_extract_datacube [-h] [-e EXT_FILE] [-s SAVE] [-o]
[-b BOXCAR_RADIUS] [-v VERBOSITY]
file
Read in a datacube, extract a spectrum of a point source,and save it as a spec1d
file.
positional arguments:
file spec3d.fits DataCube file
options:
-h, --help show this help message and exit
-e EXT_FILE, --ext_file EXT_FILE
Configuration file with extraction parameters (default:
None)
-s SAVE, --save SAVE Output spec1d filename (default: None)
-o, --overwrite Overwrite any existing files/directories (default:
False)
-b BOXCAR_RADIUS, --boxcar_radius BOXCAR_RADIUS
Radius of the circular boxcar (in arcseconds) to use for
the extraction. (default: None)
-v VERBOSITY, --verbosity VERBOSITY
Verbosity level between 0 [none] and 2 [all]. Default:
1. Level 2 writes a log with filename
extract_datacube_YYYYMMDD-HHMM.log (default: 1)
12 changes: 7 additions & 5 deletions doc/help/pypeit_sensfunc.rst
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Expand Up @@ -62,11 +62,13 @@
-s SENS_FILE, --sens_file SENS_FILE
Configuration file with sensitivity function parameters
-f FLATFILE, --flatfile FLATFILE
Use the flat file for computing the sensitivity
function. Note that it is not possible to set
--flatfile and simultaneously use a .sens file with the
--sens_file option. If you are using a .sens file, set
the flatfile there via e.g.:
Use a flat calibration file to compute the blaze
function when generating the sensitivity function. This
is helpful to account for small scale undulations in the
sensitivity function. Note that it is not possible to
set --flatfile and simultaneously use a .sens file with
the --sens_file option. If you are using a .sens file,
set the flatfile there via e.g.:
[sensfunc]
flatfile = Calibrations/Flat_A_0_DET01.fits
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1 change: 1 addition & 0 deletions doc/include/class_datamodel_pypeitimage.rst
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Expand Up @@ -10,6 +10,7 @@ Attribute Type
``det_img`` `numpy.ndarray`_ `numpy.integer`_ If a detector mosaic, this image provides the detector that contributed to each pixel.
``detector`` :class:`~pypeit.images.detector_container.DetectorContainer`, :class:`~pypeit.images.mosaic.Mosaic` The detector (see :class:`~pypeit.images.detector_container.DetectorContainer`) or mosaic (see :class:`~pypeit.images.mosaic.Mosaic`) parameters
``exptime`` int, float Effective exposure time (s)
``filename`` str Filename for the image
``fullmask`` :class:`~pypeit.images.imagebitmask.ImageBitMaskArray` Image mask
``image`` `numpy.ndarray`_ `numpy.floating`_ Primary image data
``img_scale`` `numpy.ndarray`_ `numpy.floating`_ Image count scaling applied (e.g., 1/flat-field)
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10 changes: 5 additions & 5 deletions doc/include/keck_deimos.sorted.rst
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Expand Up @@ -12,17 +12,17 @@
filename | frametype | ra | dec | target | dispname | decker | binning | mjd | airmass | exptime | dispangle | amp | filter1 | lampstat01 | dateobs | utc | frameno | calib
DE.20170527.06713.fits | arc,tilt | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.077631 | 1.41291034 | 1.0 | 8099.98291016 | SINGLE:B | OG550 | Kr Xe Ar Ne | 2017-05-27 | 01:51:53.87 | 30 | 0
d0527_0030.fits.gz | arc,tilt | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.077631 | 1.41291034 | 1.0 | 8099.98291016 | SINGLE:B | OG550 | Kr Xe Ar Ne | 2017-05-27 | 01:51:53.87 | 30 | 0
DE.20170527.06790.fits | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.07851 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | Qz | 2017-05-27 | 01:53:10.93 | 31 | 0
d0527_0031.fits.gz | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.07851 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | Qz | 2017-05-27 | 01:53:10.93 | 31 | 0
d0527_0032.fits.gz | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.079356 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | Qz | 2017-05-27 | 01:54:24.03 | 32 | 0
DE.20170527.06790.fits | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.07851 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | Qz | 2017-05-27 | 01:53:10.93 | 31 | 0
DE.20170527.06864.fits | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.079356 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | Qz | 2017-05-27 | 01:54:24.03 | 32 | 0
DE.20170527.06936.fits | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.080211 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | Qz | 2017-05-27 | 01:55:36.93 | 33 | 0
d0527_0032.fits.gz | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.079356 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | Qz | 2017-05-27 | 01:54:24.03 | 32 | 0
d0527_0033.fits.gz | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.080211 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | Qz | 2017-05-27 | 01:55:36.93 | 33 | 0
DE.20170527.06936.fits | pixelflat,illumflat,trace | 57.99999999999999 | 45.0 | DOME PHLAT | 830G | LongMirr | 1,1 | 57900.080211 | 1.41291034 | 4.0 | 8099.98291016 | SINGLE:B | OG550 | Qz | 2017-05-27 | 01:55:36.93 | 33 | 0
DE.20170527.37601.fits | science | 261.0363749999999 | 19.028166666666667 | P261_OFF | 830G | LongMirr | 1,1 | 57900.435131 | 1.03078874 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 10:26:41.61 | 80 | 0
DE.20170527.38872.fits | science | 261.0363749999999 | 19.028166666666667 | P261_OFF | 830G | LongMirr | 1,1 | 57900.449842 | 1.01267696 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 10:47:52.92 | 81 | 0
d0527_0081.fits.gz | science | 261.0363749999999 | 19.028166666666667 | P261_OFF | 830G | LongMirr | 1,1 | 57900.449842 | 1.01267696 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 10:47:52.92 | 81 | 0
d0527_0083.fits.gz | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.483427 | 1.00093023 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 11:36:15.35 | 83 | 0
DE.20170527.38872.fits | science | 261.0363749999999 | 19.028166666666667 | P261_OFF | 830G | LongMirr | 1,1 | 57900.449842 | 1.01267696 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 10:47:52.92 | 81 | 0
DE.20170527.41775.fits | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.483427 | 1.00093023 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 11:36:15.35 | 83 | 0
d0527_0083.fits.gz | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.483427 | 1.00093023 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 11:36:15.35 | 83 | 0
DE.20170527.43045.fits | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.498135 | 1.00838805 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 11:57:25.35 | 84 | 0
DE.20170527.44316.fits | science | 261.0362916666666 | 19.028888888888886 | P261_OFF | 830G | LongMirr | 1,1 | 57900.512854 | 1.02377681 | 1200.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 12:18:36.71 | 85 | 0
DE.20170527.53184.fits | science | 349.99316666666664 | -5.16575 | Feige 110 | 830G | LongMirr | 1,1 | 57900.615484 | 1.42505162 | 45.0 | 8099.98291016 | SINGLE:B | OG550 | Off | 2017-05-27 | 14:46:24.88 | 93 | 0
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