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+ ' + + '' + + _("Hide Search Matches") + + "
" + ) + ); + }, + + /** + * helper function to hide the search marks again + */ + hideSearchWords: () => { + document + .querySelectorAll("#searchbox .highlight-link") + .forEach((el) => el.remove()); + document + .querySelectorAll("span.highlighted") + .forEach((el) => el.classList.remove("highlighted")); + localStorage.removeItem("sphinx_highlight_terms") + }, + + initEscapeListener: () => { + // only install a listener if it is really needed + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; + if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { + SphinxHighlight.hideSearchWords(); + event.preventDefault(); + } + }); + }, +}; + +_ready(() => { + /* Do not call highlightSearchWords() when we are on the search page. + * It will highlight words from the *previous* search query. + */ + if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); + SphinxHighlight.initEscapeListener(); +}); diff --git a/docs/build/html/contributing.html b/docs/build/html/contributing.html new file mode 100644 index 0000000..1e3d336 --- /dev/null +++ b/docs/build/html/contributing.html @@ -0,0 +1,248 @@ + + + + + + +
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+ Contributing
+Contributions are welcome, and they are greatly appreciated! Every little bit +helps, and credit will always be given.
+You can contribute in many ways:
+Types of Contributions
+Report Bugs
+Report bugs at https://github.com/JohannesBuchner/snowline/issues.
+If you are reporting a bug, please include:
+-
+
Your operating system name and version.
+Any details about your local setup that might be helpful in troubleshooting.
+Detailed steps to reproduce the bug.
+
Fix Bugs
+Look through the GitHub issues for bugs. Anything tagged with “bug” and “help +wanted” is open to whoever wants to implement it.
+Implement Features
+Look through the GitHub issues for features. Anything tagged with “enhancement” +and “help wanted” is open to whoever wants to implement it.
+Write Documentation
+snowline could always use more documentation, whether as part of the +official snowline docs, in docstrings, or even on the web in blog posts, +articles, and such.
+Submit Feedback
+The best way to send feedback is to file an issue at https://github.com/JohannesBuchner/snowline/issues.
+If you are proposing a feature:
+-
+
Explain in detail how it would work.
+Keep the scope as narrow as possible, to make it easier to implement.
+Remember that this is a volunteer-driven project, and that contributions +are welcome :)
+
Get Started!
+Ready to contribute? Here’s how to set up snowline for local development.
+-
+
Fork the snowline repo on GitHub.
+Clone your fork locally:
+++$ git clone git@github.com:JohannesBuchner/snowline.git +
+Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
+++$ mkvirtualenv snowline +$ cd snowline/ +$ python setup.py develop +
+Create a branch for local development:
+++$ git checkout -b name-of-your-bugfix-or-feature +
Now you can make your changes locally.
+
+When you’re done making changes, check that your changes pass flake8 and the +tests, including testing other Python versions with tox:
+++$ flake8 snowline tests +$ python setup.py test # or pytest +$ tox +
To get flake8 and tox, just pip install them into your virtualenv.
+
+Commit your changes and push your branch to GitHub:
+++$ git add . +$ git commit -m "Your detailed description of your changes." +$ git push origin name-of-your-bugfix-or-feature +
+Submit a pull request through the GitHub website.
+
Pull Request Guidelines
+Before you submit a pull request, check that it meets these guidelines:
+-
+
The pull request should include tests.
+If the pull request adds functionality, the docs should be updated. Put +your new functionality into a function with a docstring, and add the +feature to the list in README.rst.
+The pull request should work for Python 2.7, 3.5, 3.6 and 3.7, and for PyPy. Check +https://travis-ci.org/JohannesBuchner/snowline/pull_requests +and make sure that the tests pass for all supported Python versions.
+
Tips
+To run a subset of tests:
+$ pytest tests.test_snowline
+Deploying
+A reminder for the maintainers on how to deploy. +Make sure all your changes are committed (including an entry in HISTORY.rst). +Then run:
+$ bump2version patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+Travis will then deploy to PyPI if tests pass.
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+ Index
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+ Welcome to LightRayRider’s documentation!
+
+
+Contents:
+ +LightRayRider
+A fast library for calculating intersections of a line with many spheres or inhomogeneous material.
+Introduction
+
+Technically speaking, the library performs three-dimensional line integrals +through various geometric bodies, such as millions of spheres of various sizes, +three-dimensional uniform grids, and arbitrary density fields approximated by their +point densities and voronoi tesselation.
+In astrophysics, a point source can be obscured by a gas distribution along the line-of-sight. +For hydrodynamic simulations which produce such a gas distribution, this code can compute +the total density along a arbitrary ray. The output is a column density, +also known as N_H if hydrogen gas is irradiated.
+
+
+Line/Sphere cutting
+Input:
+-
+
Points in space representing sphere centres.
+Sphere radii and densities.
+One or more arbitrary lines from the origin.
+
Output:
+-
+
This computes the total length / column density cut.
+From distance 0 or another chosen minimal distance (or multiple).
+
Method:
+-
+
Simple quadratic equations.
+
Voronoi cutting
+Input:
+-
+
Points in space.
+Densities.
+One or more arbitrary lines from the origin
+
Output:
+-
+
This computes the total length along the line, +where every point on the line is assigned the density from the +nearest point (Voronoi segmentation).
+From distance 0 or another chosen minimal distance (or multiple).
+
Method:
+-
+
Segmentation of the line where points become equi-distant. +Performs approximately linearly with number of points.
+
Grid cutting
+Input:
+-
+
3D Grid with densities at each location
+One or more arbitrary lines from a point
+
Output:
+-
+
This computes the total length along the line, +where every point on the line is assigned the density from the +grid cell it passes through.
+From distance 0 or another chosen minimal distance (or multiple).
+
Method:
+-
+
Finding intersections of the cell borders (planes) with the lines, and +checking which cell to consider next.
+
Usage
+Compile the c library first with:
+$ make
+To use from Python, use raytrace.py:
+from raytrace import *
+You can find the declaration of how to call these functions in raytrace.py. +Basically, you pass the coordinates of your gas particles, the associated +densities and the starting point and direction of your raytracing.
+Example usage is demonstrated in irradiate.py. This was used for Illustris and +EAGLE particle in the associated paper. +There are additional unit test examples in test/.
+Parallel processing
+LightRayRider supports multiple processors through OpenMP. +Set the variable OMP_NUM_THREADS to the number of processors you want to use, +and the parallel library ray-parallel.so will be loaded.
+License and Acknowledgements
+If you use this code, please cite “Galaxy gas as obscurer: II. Separating the galaxy-scale and +nuclear obscurers of Active Galactic Nuclei”, by Buchner & Bauer (2017), https://arxiv.org/abs/1610.09380
+Bibcode:
+@ARTICLE{2017MNRAS.465.4348B,
+ author = {{Buchner}, J. and {Bauer}, F.~E.},
+ title = "{Galaxy gas as obscurer - II. Separating the galaxy-scale and nuclear obscurers of active galactic nuclei}",
+ journal = {\mnras},
+archivePrefix = "arXiv",
+ eprint = {1610.09380},
+ primaryClass = "astro-ph.HE",
+ keywords = {dust, extinction, ISM: general, galaxies: active, galaxies: general, galaxies: ISM, X-rays: ISM},
+ year = 2017,
+ month = mar,
+ volume = 465,
+ pages = {4348-4362},
+ doi = {10.1093/mnras/stw2955},
+ adsurl = {http://adsabs.harvard.edu/abs/2017MNRAS.465.4348B},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+The code is licensed under AGPLv3 (see LICENSE file).
+Indices and tables
+-
+
- +
- +
- +
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+ Installation
+Stable release
+To install lightrayrider, run this command in your terminal:
+$ python -m pip install lightrayrider
+This is the preferred method to install lightrayrider, as it will always install the most recent stable release.
+If you don’t have pip installed, this Python installation guide can guide +you through the process.
+From sources
+The sources for lightrayrider can be downloaded from the Github repo.
+You can either clone the public repository:
+$ git clone git://github.com/JohannesBuchner/lightrayrider
+Or download the tarball:
+$ curl -OJL https://github.com/JohannesBuchner/lightrayrider/tarball/master
+Once you have a copy of the source, you can install it with:
+$ python setup.py install
+
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+ Frequently Asked Questions
+ +How can I add a question here?
+See Contributing for how to report bugs and ask questions. (hint: open a github issue)
+How should I cite LightRayRider?
+Please cite Buchner & Bauer (2017), http://adsabs.harvard.edu/abs/2017MNRAS.465.4348B
+They describe the underlying techniques.
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+ lightrayrider package
+Submodules
+lightrayrider.parallel module
+This file is part of LightRayRider, a fast column density computation tool.
+-
+
- +lightrayrider.parallel.py_cone_raytrace_finite(thetas, rhos, x, y, z, a, b, c, d) +
Perform ray tracing through a sphere/cone cuts.
+Sphere radius is 1, each cone angle defines a region of a certain density.
+This function raytraces from the starting coordinates in the direction +given and compute the column density of the intersecting segments. +Then it will go along the ray in the positive direction until the +column density d is reached. The coordinates of that point are stored into +(x, y, z).
+-
+
- Parameters: +
cones (regarding the)
+
+
-
+
- thetas: array
the opening angles of the cones
+
+- rhos: array
density of the cones. For conversion from length to column density.
+
+- x: array
ray start coordinate, x component
+
+- y: array
ray start coordinate, y component
+
+- z: array
ray start coordinate, z component
+
+- a: array
ray direction, x component
+
+- b: array
ray direction, y component
+
+- c: array
ray direction, z component
+
+- d: array
column density where the ray should terminate.
+
+
-
+
- Returns: +
t – end position in multiples of the direction vector. -1 if infinite. +Of shape len(x).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.parallel.py_grid_raytrace(rho, x, y, z, a, b, c) +
Ray tracing on a grid.
+-
+
- Parameters: +
-
+
rho (array) – 3D cube of densities (in units of 1e22/cm^2). For conversion from length to column density. +Must be same size in each axis.
+lenrho (int) – length of rho.
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+
+- Returns: +
NHout – column density from the origin to infinity. shape is len(a).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.parallel.py_grid_raytrace_finite(rho, x, y, z, a, b, c, NHmax) +
Ray tracing on a grid.
+-
+
- Parameters: +
-
+
rho (array) – 3D cube of densities (in units of 1e22/cm^2). For conversion from length to column density. +Must be same size in each axis.
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+NHmax (array) – column density where the ray should terminate.
+
+- Returns: +
t – end position in multiples of the direction vector. -1 if infinite. +Of shape len(x).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.parallel.py_grid_raytrace_finite_flat(rho_flat, lenrho, x, y, z, a, b, c, NHmax) +
Ray tracing on a grid.
+-
+
- Parameters: +
-
+
rho_flat (array) – flattened 3D cube of densities. For conversion from length to column density.
+lenrho (int) – length of each 3D cube axis
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+NHmax (array) – column density where the ray should terminate.
+
+- Returns: +
t – end position in multiples of the direction vector. -1 if infinite. +Of shape len(x).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.parallel.py_grid_raytrace_flat(rho_flat, lenrho, x, y, z, a, b, c) +
Ray tracing on a grid.
+-
+
- Parameters: +
-
+
rho_flat (array) – flattened 3D cube of densities. For conversion from length to column density.
+lenrho (int) – length of the original rho cube in each axis.
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+
+- Returns: +
NHout – column density from the origin to infinity. shape is len(a).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.parallel.py_sphere_raytrace(xx, yy, zz, RR, rho, a, b, c, mindistances) +
Perform ray tracing using sphere intersections.
+-
+
- Parameters: +
-
+
xx (array) – sphere x coordinates
+yy (array) – sphere y coordinates
+zz (array) – sphere z coordinates
+RR (array) – sphere radii
+rho (array) – sphere densities (in units of 1e22/cm^2). For conversion from length to column density.
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+mindistances (array) – distance from the origin for each subtotal to consider.
+
+- Returns: +
NHout – column density from the origin to infinity. shape is (len(mindistances), len(a)).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.parallel.py_sphere_raytrace_count_between(xx, yy, zz, RR, a, b, c) +
Count number of spheres lying (partially or completely) between point a,b,c and origin.
+Stops counting at 1.
+-
+
- Parameters: +
-
+
xx (array) – sphere x coordinates
+yy (array) – sphere y coordinates
+zz (array) – sphere z coordinates
+RR (array) – sphere radii
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+
+- Returns: +
n – number of spheres
+
+- Return type: +
int
+
+
-
+
- +lightrayrider.parallel.py_sphere_raytrace_finite(xx, yy, zz, RR, rho, x, y, z, a, b, c, NHmax) +
Perform ray tracing using sphere intersections.
+-
+
- Parameters: +
-
+
xx (array) – sphere x coordinates
+yy (array) – sphere y coordinates
+zz (array) – sphere z coordinates
+RR (array) – sphere radii
+rho (array) – sphere densities (in units of 1e22/cm^2). For conversion from length to column density.
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+NHmax (array) – column density where the ray should terminate.
+
+- Returns: +
t – end position in multiples of the direction vector. -1 if infinite. +Of shape len(x).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.parallel.py_sphere_sphere_collisions(xx, yy, zz, RR, kstop) +
Marks the first kstop non-intersecting spheres.
+-
+
- Parameters: +
-
+
xx (array) – sphere x coordinates
+yy (array) – sphere y coordinates
+zz (array) – sphere z coordinates
+RR (array) – sphere radii
+k (int) – number of spheres desired
+
+- Returns: +
-
+
NHout (array) – 1 if collides with another sphere of lower index, +2 if okay.
+Parameters regarding the spheres
+
+
-
+
- +lightrayrider.parallel.py_voronoi_raytrace(xx, yy, zz, RR, rho, a, b, c, mindistances) +
Ray tracing using nearest point density.
+-
+
- Parameters: +
-
+
xx (array) – x coordinates
+yy (array) – y coordinates
+zz (array) – z coordinates
+RR (array) – radii
+rho (array) – sphere densities. For conversion from length to column density.
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+mindistances (array) – distance from the origin for each subtotal to consider.
+
+- Returns: +
NHout – column density from the origin to infinity. shape is (len(mindistances), len(a)).
+
+- Return type: +
array
+
+
lightrayrider.raytrace module
+This file is part of LightRayRider, a fast column density computation tool.
+-
+
- +lightrayrider.raytrace.py_cone_raytrace_finite(thetas, rhos, x, y, z, a, b, c, d) +
Perform ray tracing through a sphere/cone cuts.
+Sphere radius is 1, each cone angle defines a region of a certain density.
+This function raytraces from the starting coordinates in the direction +given and compute the column density of the intersecting segments. +Then it will go along the ray in the positive direction until the +column density d is reached. The coordinates of that point are stored into +(x, y, z).
+-
+
- Parameters: +
cones (regarding the)
+
+
-
+
- thetas: array
the opening angles of the cones
+
+- rhos: array
density of the cones. For conversion from length to column density.
+
+- x: array
ray start coordinate, x component
+
+- y: array
ray start coordinate, y component
+
+- z: array
ray start coordinate, z component
+
+- a: array
ray direction, x component
+
+- b: array
ray direction, y component
+
+- c: array
ray direction, z component
+
+- d: array
column density where the ray should terminate.
+
+
-
+
- Returns: +
t – end position in multiples of the direction vector. -1 if infinite. +Of shape len(x).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.raytrace.py_grid_raytrace(rho, x, y, z, a, b, c) +
Ray tracing on a grid.
+-
+
- Parameters: +
-
+
rho (array) – 3D cube of densities (in units of 1e22/cm^2). For conversion from length to column density. +Must be same size in each axis.
+lenrho (int) – length of rho.
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+
+- Returns: +
NHout – column density from the origin to infinity. shape is len(a).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.raytrace.py_grid_raytrace_finite(rho, x, y, z, a, b, c, NHmax) +
Ray tracing on a grid.
+-
+
- Parameters: +
-
+
rho (array) – 3D cube of densities (in units of 1e22/cm^2). For conversion from length to column density. +Must be same size in each axis.
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+NHmax (array) – column density where the ray should terminate.
+
+- Returns: +
t – end position in multiples of the direction vector. -1 if infinite. +Of shape len(x).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.raytrace.py_grid_raytrace_finite_flat(rho_flat, lenrho, x, y, z, a, b, c, NHmax) +
Ray tracing on a grid.
+-
+
- Parameters: +
-
+
rho_flat (array) – flattened 3D cube of densities. For conversion from length to column density.
+lenrho (int) – length of each 3D cube axis
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+NHmax (array) – column density where the ray should terminate.
+
+- Returns: +
t – end position in multiples of the direction vector. -1 if infinite. +Of shape len(x).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.raytrace.py_grid_raytrace_flat(rho_flat, lenrho, x, y, z, a, b, c) +
Ray tracing on a grid.
+-
+
- Parameters: +
-
+
rho_flat (array) – flattened 3D cube of densities. For conversion from length to column density.
+lenrho (int) – length of the original rho cube in each axis.
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+
+- Returns: +
NHout – column density from the origin to infinity. shape is len(a).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.raytrace.py_sphere_raytrace(xx, yy, zz, RR, rho, a, b, c, mindistances) +
Perform ray tracing using sphere intersections.
+-
+
- Parameters: +
-
+
xx (array) – sphere x coordinates
+yy (array) – sphere y coordinates
+zz (array) – sphere z coordinates
+RR (array) – sphere radii
+rho (array) – sphere densities (in units of 1e22/cm^2). For conversion from length to column density.
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+mindistances (array) – distance from the origin for each subtotal to consider.
+
+- Returns: +
NHout – column density from the origin to infinity. shape is (len(mindistances), len(a)).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.raytrace.py_sphere_raytrace_count_between(xx, yy, zz, RR, a, b, c) +
Count number of spheres lying (partially or completely) between point a,b,c and origin.
+Stops counting at 1.
+-
+
- Parameters: +
-
+
xx (array) – sphere x coordinates
+yy (array) – sphere y coordinates
+zz (array) – sphere z coordinates
+RR (array) – sphere radii
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+
+- Returns: +
n – number of spheres
+
+- Return type: +
int
+
+
-
+
- +lightrayrider.raytrace.py_sphere_raytrace_finite(xx, yy, zz, RR, rho, x, y, z, a, b, c, NHmax) +
Perform ray tracing using sphere intersections.
+-
+
- Parameters: +
-
+
xx (array) – sphere x coordinates
+yy (array) – sphere y coordinates
+zz (array) – sphere z coordinates
+RR (array) – sphere radii
+rho (array) – sphere densities (in units of 1e22/cm^2). For conversion from length to column density.
+x (array) – ray start coordinate, x component
+y (array) – ray start coordinate, y component
+z (array) – ray start coordinate, z component
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+NHmax (array) – column density where the ray should terminate.
+
+- Returns: +
t – end position in multiples of the direction vector. -1 if infinite. +Of shape len(x).
+
+- Return type: +
array
+
+
-
+
- +lightrayrider.raytrace.py_sphere_sphere_collisions(xx, yy, zz, RR, kstop) +
Marks the first kstop non-intersecting spheres.
+-
+
- Parameters: +
-
+
xx (array) – sphere x coordinates
+yy (array) – sphere y coordinates
+zz (array) – sphere z coordinates
+RR (array) – sphere radii
+k (int) – number of spheres desired
+
+- Returns: +
-
+
NHout (array) – 1 if collides with another sphere of lower index, +2 if okay.
+Parameters regarding the spheres
+
+
-
+
- +lightrayrider.raytrace.py_voronoi_raytrace(xx, yy, zz, RR, rho, a, b, c, mindistances) +
Ray tracing using nearest point density.
+-
+
- Parameters: +
-
+
xx (array) – x coordinates
+yy (array) – y coordinates
+zz (array) – z coordinates
+RR (array) – radii
+rho (array) – sphere densities. For conversion from length to column density.
+a (array) – ray direction, x component
+b (array) – ray direction, y component
+c (array) – ray direction, z component
+mindistances (array) – distance from the origin for each subtotal to consider.
+
+- Returns: +
NHout – column density from the origin to infinity. shape is (len(mindistances), len(a)).
+
+- Return type: +
array
+
+
Module contents
+LightRayRider is a tiny fast library to compute column densities along a ray.
+Supported geometries:
+-
+
Uniform density grids.
+Spheres of varying size, density and position.
+Co-centred cones of varying opening angles and density.
+
+
+
+
+
+
+
+
+
+
+
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+ +
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+ Python Module Index
+ +
+ l
+
+
+ | + l | ||
| + |
+ lightrayrider | + |
| + |
+ lightrayrider.parallel | + |
| + |
+ lightrayrider.raytrace | + |
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+ LightRayRider
+A fast library for calculating intersections of a line with many spheres or inhomogeneous material.
+Introduction
+
+Technically speaking, the library performs three-dimensional line integrals +through various geometric bodies, such as millions of spheres of various sizes, +three-dimensional uniform grids, and arbitrary density fields approximated by their +point densities and voronoi tesselation.
+In astrophysics, a point source can be obscured by a gas distribution along the line-of-sight. +For hydrodynamic simulations which produce such a gas distribution, this code can compute +the total density along a arbitrary ray. The output is a column density, +also known as N_H if hydrogen gas is irradiated.
+
+
+Line/Sphere cutting
+Input:
+-
+
Points in space representing sphere centres.
+Sphere radii and densities.
+One or more arbitrary lines from the origin.
+
Output:
+-
+
This computes the total length / column density cut.
+From distance 0 or another chosen minimal distance (or multiple).
+
Method:
+-
+
Simple quadratic equations.
+
Voronoi cutting
+Input:
+-
+
Points in space.
+Densities.
+One or more arbitrary lines from the origin
+
Output:
+-
+
This computes the total length along the line, +where every point on the line is assigned the density from the +nearest point (Voronoi segmentation).
+From distance 0 or another chosen minimal distance (or multiple).
+
Method:
+-
+
Segmentation of the line where points become equi-distant. +Performs approximately linearly with number of points.
+
Grid cutting
+Input:
+-
+
3D Grid with densities at each location
+One or more arbitrary lines from a point
+
Output:
+-
+
This computes the total length along the line, +where every point on the line is assigned the density from the +grid cell it passes through.
+From distance 0 or another chosen minimal distance (or multiple).
+
Method:
+-
+
Finding intersections of the cell borders (planes) with the lines, and +checking which cell to consider next.
+
Usage
+Compile the c library first with:
+$ make
+To use from Python, use raytrace.py:
+from raytrace import *
+You can find the declaration of how to call these functions in raytrace.py. +Basically, you pass the coordinates of your gas particles, the associated +densities and the starting point and direction of your raytracing.
+Example usage is demonstrated in irradiate.py. This was used for Illustris and +EAGLE particle in the associated paper. +There are additional unit test examples in test/.
+Parallel processing
+LightRayRider supports multiple processors through OpenMP. +Set the variable OMP_NUM_THREADS to the number of processors you want to use, +and the parallel library ray-parallel.so will be loaded.
+License and Acknowledgements
+If you use this code, please cite “Galaxy gas as obscurer: II. Separating the galaxy-scale and +nuclear obscurers of Active Galactic Nuclei”, by Buchner & Bauer (2017), https://arxiv.org/abs/1610.09380
+Bibcode:
+@ARTICLE{2017MNRAS.465.4348B,
+ author = {{Buchner}, J. and {Bauer}, F.~E.},
+ title = "{Galaxy gas as obscurer - II. Separating the galaxy-scale and nuclear obscurers of active galactic nuclei}",
+ journal = {\mnras},
+archivePrefix = "arXiv",
+ eprint = {1610.09380},
+ primaryClass = "astro-ph.HE",
+ keywords = {dust, extinction, ISM: general, galaxies: active, galaxies: general, galaxies: ISM, X-rays: ISM},
+ year = 2017,
+ month = mar,
+ volume = 465,
+ pages = {4348-4362},
+ doi = {10.1093/mnras/stw2955},
+ adsurl = {http://adsabs.harvard.edu/abs/2017MNRAS.465.4348B},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+The code is licensed under AGPLv3 (see LICENSE file).
+
+
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+
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@@ -0,0 +1 @@
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