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<p>1 new commit in yt:</p>
<p><a href="https://bitbucket.org/yt_analysis/yt/commits/58f3b309fa30/">https://bitbucket.org/yt_analysis/yt/commits/58f3b309fa30/</a> Changeset: 58f3b309fa30 Branch: yt User: ngoldbaum Date: 2016-04-06 18:26:34+00:00 Summary: Merged in chummels/yt (pull request #2045)</p>
<p>Updating the absorption spectrum documentation. Affected #: 1 file</p>
<p>diff -r 47bf935396cbd394791ae4c838d48f3e3a453c92 -r 58f3b309fa309c38f23f5a6aecbbedc608b2629d doc/source/analyzing/analysis_modules/absorption_spectrum.rst --- a/doc/source/analyzing/analysis_modules/absorption_spectrum.rst +++ b/doc/source/analyzing/analysis_modules/absorption_spectrum.rst @@ -1,48 +1,91 @@</p>
<pre>.. _absorption_spectrum:
</pre>
<p>-Absorption Spectrum -=================== +Creating Absorption Spectra +===========================</p>
<pre>.. sectionauthor:: Britton Smith <brittonsmith@gmail.com>
</pre>
<p>-Absorption line spectra, such as shown below, can be made with data created -by the (:ref:`light-ray-generator`). For each element of the ray, column -densities are calculated multiplying the number density within a grid cell -with the path length of the ray through the cell. Line profiles are -generated using a voigt profile based on the temperature field. The lines -are then shifted according to the redshift recorded by the light ray tool -and (optionally) the peculiar velocity of gas along the ray. Inclusion of the -peculiar velocity requires setting ``use_peculiar_velocity`` to True in the call to -:meth:`~yt.analysis_modules.cosmological_observation.light_ray.light_ray.LightRay.make_light_ray`. +Absorption line spectra are spectra generated using bright background sources +to illuminate tenuous foreground material and are primarily used in studies +of the circumgalactic medium and intergalactic medium. These spectra can +be created using the +:class:`~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum` +and +:class:`~yt.analysis_modules.cosmological_observation.light_ray.light_ray.LightRay` +analysis modules.</p>
<p>-The spectrum generator will output a file containing the wavelength and -normalized flux. It will also output a text file listing all important lines. +The +:class:`~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum` class +and its workhorse method +:meth:`~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum.make_spectrum` +return two arrays, one with wavelengths, the other with the normalized +flux values at each of the wavelength values. It can also output a text file +listing all important lines. + +For example, here is an absorption spectrum for the wavelength range from 900 +to 1800 Angstroms made with a light ray extending from z = 0 to z = 0.4:</p>
<pre>.. image:: _images/spectrum_full.png
:width: 500
</pre>
<p>-An absorption spectrum for the wavelength range from 900 to 1800 Angstroms -made with a light ray extending from z = 0 to z = 0.4. +And a zoom-in on the 1425-1450 Angstrom window:</p>
<pre>.. image:: _images/spectrum_zoom.png
:width: 500
</pre>
<p>-A zoom-in of the above spectrum. +Method for Creating Absorption Spectra +--------------------------------------</p>
<p>-Creating an Absorption Spectrum -------------------------------- +Once a +:class:`~yt.analysis_modules.cosmological_observation.light_ray.light_ray.LightRay` +has been created traversing a dataset using the :ref:`light-ray-generator`, +a series of arrays store the various fields of the gas parcels (represented +as cells) intersected along the ray. +:class:`~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum` +steps through each element of the +:class:`~yt.analysis_modules.cosmological_observation.light_ray.light_ray.LightRay`'s +arrays and calculates the column density for desired ion by multiplying its +number density with the path length through the cell. Using these column +densities along with temperatures to calculate thermal broadening, voigt +profiles are deposited on to a featureless background spectrum. By default, +the peculiar velocity of the gas is included as a doppler redshift in addition +to any cosmological redshift of the data dump itself.</p>
<p>-To instantiate an AbsorptionSpectrum object, the arguments required are the -minimum and maximum wavelengths, and the number of wavelength bins. +Subgrid Deposition +^^^^^^^^^^^^^^^^^^ + +For features not resolved (i.e. possessing narrower width than the spectral +resolution), +:class:`~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum` +performs subgrid deposition. The subgrid deposition algorithm creates a number +of smaller virtual bins, by default the width of the virtual bins is 1/10th +the width of the spectral feature. The Voigt profile is then deposited +into these virtual bins where it is resolved, and then these virtual bins +are numerically integrated back to the resolution of the original spectral bin +size, yielding accurate equivalent widths values. +:class:`~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum` +informs the user how many spectral features are deposited in this fashion. + +Tutorial on Creating an Absorption Spectrum +------------------------------------------- + +Initializing `AbsorptionSpectrum` Class +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +To instantiate an +:class:`~yt.analysis_modules.absorption_spectrum.absorption_spectrum.AbsorptionSpectrum` +object, the arguments required are the +minimum and maximum wavelengths (assumed to be in Angstroms), and the number +of wavelength bins to span this range (including the endpoints)</p>
<pre>.. code-block:: python
from yt.analysis_modules.absorption_spectrum.api import AbsorptionSpectrum
</pre>
<ul><li><p>sp = AbsorptionSpectrum(900.0, 1800.0, 10000)</p></li></ul>
<p>+ sp = AbsorptionSpectrum(900.0, 1800.0, 10001)</p>
<pre>Adding Features to the Spectrum</pre>
<p>-------------------------------- +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^</p>
<pre>Absorption lines and continuum features can then be added to the spectrum.
To add a line, you must know some properties of the line: the rest wavelength,</pre>
<p>@@ -67,8 +110,8 @@</p>
<pre>field from the ray data to use to calculate the column density. The
``label_threshold`` keyword tells the spectrum generator to add all lines
above a column density of 10 :superscript:`10` cm :superscript:`-2` to the</pre>
<p>-text line list. If None is provided, as is the default, no lines of this -type will be added to the text list. +text line list output at the end. If None is provided, as is the default, +no lines of this type will be added to the text list.</p>
<pre>Continuum features with optical depths that follow a power law can also be
added. Like adding lines, you must specify details like the wavelength</pre>
<p>@@ -86,7 +129,7 @@</p>
<pre> sp.add_continuum(my_label, field, wavelength, normalization, index)
Making the Spectrum</pre>
<p>-------------------- +^^^^^^^^^^^^^^^^^^^</p>
<pre>Once all the lines and continuum are added, it is time to make a spectrum out
of some light ray data.</pre>
<p>@@ -95,12 +138,12 @@</p>
<pre>wavelength, flux = sp.make_spectrum('lightray.h5',
output_file='spectrum.fits',</pre>
<ul><li><p>line_list_file='lines.txt',</p></li>
<li><p>use_peculiar_velocity=True)</p></li></ul>
<p>+ line_list_file='lines.txt')</p>
<pre>A spectrum will be made using the specified ray data and the wavelength and</pre>
<p>-flux arrays will also be returned. If ``use_peculiar_velocity`` is set to -False, the lines will only be shifted according to the redshift. +flux arrays will also be returned. If you set the optional +``use_peculiar_velocity`` keyword to False, the lines will not incorporate +doppler redshifts to shift the deposition of the line features.</p>
<pre>Three output file formats are supported for writing out the spectrum: fits,
hdf5, and ascii. The file format used is based on the extension provided</pre>
<p>@@ -112,15 +155,16 @@</p>
<pre>Generating Spectra in Parallel
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
</pre>
<p>-The spectrum generator can be run in parallel simply by following the procedures -laid out in :ref:`parallel-computation` for running yt scripts in parallel. -Spectrum generation is parallelized using a multi-level strategy where each -absorption line is deposited by a different processor. If the number of available -processors is greater than the number of lines, then the deposition of -individual lines will be divided over multiple processors. +The `AbsorptionSpectrum` analysis module can be run in parallel simply by +following the procedures laid out in :ref:`parallel-computation` for running +yt scripts in parallel. Spectrum generation is parallelized using a multi-level +strategy where each absorption line is deposited by a different processor. +If the number of available processors is greater than the number of lines, +then the deposition of individual lines will be divided over multiple +processors.</p>
<p>-Fitting an Absorption Spectrum ------------------------------- +Fitting Absorption Spectra +==========================</p>
<pre>.. sectionauthor:: Hilary Egan <hilary.egan@colorado.edu></pre>
<p>Repository URL: <a href="https://bitbucket.org/yt_analysis/yt/">https://bitbucket.org/yt_analysis/yt/</a></p>
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