[Yt-svn] yt-commit r458 - in trunk/doc: build/doctrees build/doctrees/extending build/doctrees/modules/lagos build/doctrees/tutorial build/html build/html/_sources build/html/_sources/extending build/html/_sources/modules/lagos build/html/_sources/tutorial build/html/_static build/html/cookbook build/html/extending build/html/modules/lagos build/html/modules/raven build/html/modules/reason build/html/tutorial source source/modules/lagos source/tutorial
mturk at wrangler.dreamhost.com
mturk at wrangler.dreamhost.com
Sat May 10 23:00:29 PDT 2008
Author: mturk
Date: Sat May 10 23:00:13 2008
New Revision: 458
URL: http://yt.spacepope.org/changeset/458
Log:
Another update of the current doc tree. Very few changes; mainly just
outlining the API docs.
Added:
trunk/doc/build/doctrees/extending/analyzing_in_parallel.doctree (contents, props changed)
trunk/doc/build/doctrees/extending/creating_datatypes.doctree (contents, props changed)
trunk/doc/build/doctrees/extending/creating_derived_fields.doctree (contents, props changed)
trunk/doc/build/doctrees/extending/creating_derived_quantities.doctree (contents, props changed)
trunk/doc/build/doctrees/extending/plugin_file.doctree (contents, props changed)
trunk/doc/build/doctrees/extending/running_fortran_routines.doctree (contents, props changed)
trunk/doc/build/doctrees/extending/using_the_interpreter.doctree (contents, props changed)
trunk/doc/build/doctrees/extending/writing_scripts.doctree (contents, props changed)
trunk/doc/build/doctrees/modules/lagos/contours.doctree (contents, props changed)
trunk/doc/build/doctrees/modules/lagos/outputandhierarchy.doctree (contents, props changed)
trunk/doc/build/doctrees/modules/lagos/profiles.doctree (contents, props changed)
trunk/doc/build/html/_sources/extending/analyzing_in_parallel.txt
trunk/doc/build/html/_sources/extending/creating_datatypes.txt
trunk/doc/build/html/_sources/extending/creating_derived_fields.txt
trunk/doc/build/html/_sources/extending/creating_derived_quantities.txt
trunk/doc/build/html/_sources/extending/plugin_file.txt
trunk/doc/build/html/_sources/extending/running_fortran_routines.txt
trunk/doc/build/html/_sources/extending/using_the_interpreter.txt
trunk/doc/build/html/_sources/extending/writing_scripts.txt
trunk/doc/build/html/_sources/modules/lagos/contours.txt
trunk/doc/build/html/_sources/modules/lagos/outputandhierarchy.txt
trunk/doc/build/html/_sources/modules/lagos/profiles.txt
trunk/doc/build/html/extending/analyzing_in_parallel.html
trunk/doc/build/html/extending/creating_datatypes.html
trunk/doc/build/html/extending/creating_derived_fields.html
trunk/doc/build/html/extending/creating_derived_quantities.html
trunk/doc/build/html/extending/plugin_file.html
trunk/doc/build/html/extending/running_fortran_routines.html
trunk/doc/build/html/extending/using_the_interpreter.html
trunk/doc/build/html/extending/writing_scripts.html
trunk/doc/build/html/modules/lagos/contours.html
trunk/doc/build/html/modules/lagos/outputandhierarchy.html
trunk/doc/build/html/modules/lagos/profiles.html
Modified:
trunk/doc/build/doctrees/environment.pickle
trunk/doc/build/doctrees/extending/index.doctree
trunk/doc/build/doctrees/faq.doctree
trunk/doc/build/doctrees/modules/lagos/basedatatypes.doctree
trunk/doc/build/doctrees/modules/lagos/index.doctree
trunk/doc/build/doctrees/tutorial/advanced_objects.doctree
trunk/doc/build/doctrees/tutorial/automated_plotting.doctree
trunk/doc/build/doctrees/tutorial/basic_objects.doctree
trunk/doc/build/doctrees/tutorial/getting_started.doctree
trunk/doc/build/html/_sources/extending/index.txt
trunk/doc/build/html/_sources/faq.txt
trunk/doc/build/html/_sources/modules/lagos/basedatatypes.txt
trunk/doc/build/html/_sources/modules/lagos/index.txt
trunk/doc/build/html/_sources/tutorial/basic_objects.txt
trunk/doc/build/html/_static/sphinxdoc.css
trunk/doc/build/html/cookbook/index.html
trunk/doc/build/html/extending/index.html
trunk/doc/build/html/faq.html
trunk/doc/build/html/genindex.html
trunk/doc/build/html/index.html
trunk/doc/build/html/intro.html
trunk/doc/build/html/modindex.html
trunk/doc/build/html/modules/lagos/basedatatypes.html
trunk/doc/build/html/modules/lagos/index.html
trunk/doc/build/html/modules/raven/index.html
trunk/doc/build/html/modules/reason/index.html
trunk/doc/build/html/search.html
trunk/doc/build/html/searchindex.json
trunk/doc/build/html/tutorial/advanced_objects.html
trunk/doc/build/html/tutorial/automated_plotting.html
trunk/doc/build/html/tutorial/basic_objects.html
trunk/doc/build/html/tutorial/derived_fields.html
trunk/doc/build/html/tutorial/derived_quantities.html
trunk/doc/build/html/tutorial/example_script.html
trunk/doc/build/html/tutorial/getting_started.html
trunk/doc/build/html/tutorial/index.html
trunk/doc/build/html/tutorial/profiles.html
trunk/doc/build/html/tutorial/projections.html
trunk/doc/source/conf.py
trunk/doc/source/modules/lagos/basedatatypes.rst
trunk/doc/source/modules/lagos/index.rst
trunk/doc/source/modules/lagos/outputandhierarchy.rst
trunk/doc/source/tutorial/basic_objects.rst
Modified: trunk/doc/build/doctrees/environment.pickle
==============================================================================
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Added: trunk/doc/build/doctrees/extending/analyzing_in_parallel.doctree
==============================================================================
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Added: trunk/doc/build/doctrees/extending/creating_datatypes.doctree
==============================================================================
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Added: trunk/doc/build/doctrees/extending/creating_derived_fields.doctree
==============================================================================
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Added: trunk/doc/build/doctrees/extending/creating_derived_quantities.doctree
==============================================================================
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Modified: trunk/doc/build/doctrees/extending/index.doctree
==============================================================================
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Added: trunk/doc/build/doctrees/extending/plugin_file.doctree
==============================================================================
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Added: trunk/doc/build/doctrees/extending/running_fortran_routines.doctree
==============================================================================
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Added: trunk/doc/build/doctrees/extending/using_the_interpreter.doctree
==============================================================================
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Added: trunk/doc/build/doctrees/extending/writing_scripts.doctree
==============================================================================
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Modified: trunk/doc/build/doctrees/faq.doctree
==============================================================================
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Modified: trunk/doc/build/doctrees/modules/lagos/basedatatypes.doctree
==============================================================================
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Added: trunk/doc/build/doctrees/modules/lagos/contours.doctree
==============================================================================
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Modified: trunk/doc/build/doctrees/modules/lagos/index.doctree
==============================================================================
Binary files. No diff available.
Added: trunk/doc/build/doctrees/modules/lagos/outputandhierarchy.doctree
==============================================================================
Binary file. No diff available.
Added: trunk/doc/build/doctrees/modules/lagos/profiles.doctree
==============================================================================
Binary file. No diff available.
Modified: trunk/doc/build/doctrees/tutorial/advanced_objects.doctree
==============================================================================
Binary files. No diff available.
Modified: trunk/doc/build/doctrees/tutorial/automated_plotting.doctree
==============================================================================
Binary files. No diff available.
Modified: trunk/doc/build/doctrees/tutorial/basic_objects.doctree
==============================================================================
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Modified: trunk/doc/build/doctrees/tutorial/getting_started.doctree
==============================================================================
Binary files. No diff available.
Added: trunk/doc/build/html/_sources/extending/analyzing_in_parallel.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/extending/analyzing_in_parallel.txt Sat May 10 23:00:13 2008
@@ -0,0 +1,2 @@
+Analyzing in Parallel
+=====================
Added: trunk/doc/build/html/_sources/extending/creating_datatypes.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/extending/creating_datatypes.txt Sat May 10 23:00:13 2008
@@ -0,0 +1,2 @@
+Creating Datatypes
+==================
Added: trunk/doc/build/html/_sources/extending/creating_derived_fields.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/extending/creating_derived_fields.txt Sat May 10 23:00:13 2008
@@ -0,0 +1,2 @@
+Creating Derived Fields
+=======================
Added: trunk/doc/build/html/_sources/extending/creating_derived_quantities.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/extending/creating_derived_quantities.txt Sat May 10 23:00:13 2008
@@ -0,0 +1,2 @@
+Creating Derived Quantities
+===========================
Modified: trunk/doc/build/html/_sources/extending/index.txt
==============================================================================
--- trunk/doc/build/html/_sources/extending/index.txt (original)
+++ trunk/doc/build/html/_sources/extending/index.txt Sat May 10 23:00:13 2008
@@ -1,23 +1,16 @@
Extending yt
============
-Writing Scripts
----------------
+yt has been designed to be flexible, with several entry points.
-Dealing with the Interpreter
-----------------------------
+.. toctree::
+ :maxdepth: 2
-Creating Datatypes
-------------------
-
-Creating Derived Quantities
----------------------------
-
-Creating Derived Fields
------------------------
-
-Analyzing in Parallel
----------------------
-
-Running Fortran Routines
-------------------------
+ writing_scripts
+ using_the_interpreter
+ plugin_file
+ creating_datatypes
+ creating_derived_quantities
+ creating_derived_fields
+ analyzing_in_parallel
+ running_fortran_routines
Added: trunk/doc/build/html/_sources/extending/plugin_file.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/extending/plugin_file.txt Sat May 10 23:00:13 2008
@@ -0,0 +1,2 @@
+The Plugin File
+===============
Added: trunk/doc/build/html/_sources/extending/running_fortran_routines.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/extending/running_fortran_routines.txt Sat May 10 23:00:13 2008
@@ -0,0 +1,2 @@
+Running Fortran Routines
+========================
Added: trunk/doc/build/html/_sources/extending/using_the_interpreter.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/extending/using_the_interpreter.txt Sat May 10 23:00:13 2008
@@ -0,0 +1,2 @@
+Using the Interpreter
+=====================
Added: trunk/doc/build/html/_sources/extending/writing_scripts.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/extending/writing_scripts.txt Sat May 10 23:00:13 2008
@@ -0,0 +1,2 @@
+Writing Scripts
+===============
Modified: trunk/doc/build/html/_sources/faq.txt
==============================================================================
--- trunk/doc/build/html/_sources/faq.txt (original)
+++ trunk/doc/build/html/_sources/faq.txt Sat May 10 23:00:13 2008
@@ -44,6 +44,26 @@
Additionally, if you use yt in a paper, I'd love it if you'd drop me a line to
let me know.
+What are all these .yt files?
+-----------------------------
+
+By default, yt attempts to serialize a couple pieces of data that help speed it
+up in future invocations. Specifically, the entire contents of the hierarchy,
+the parent-child relationships between the grids, and any projections of the
+entire volume that are made.
+
+The numbers that make up the filenames are taken from one of two places. If
+your Enzo outputs the "CurrentTimeIdentifier" parameter, that is the number that it
+uses. (This is a string of digits representing the number of seconds since the
+epoch.) If that is unavailable, the creation time of the file as reported by
+the file system is used.
+
+This can cause problems. Ticket #91 on the bug tracker records some of these.
+If you are creating multiple parameter files per second, this can lead to
+incorrect hierarchies, and thus incorrect behavior, inside your analysis. In
+such cases, it is recommended that the parameter 'serialize' in the section
+'lagos' of your configuration file is set to 'False'.
+
How can I help?
---------------
@@ -62,6 +82,15 @@
files, and either send an email to the ``yt-users`` mailing list (subscribe
first!) or attach them to a ticket at `<http://yt.spacepope.org/>`_.
+.. _axis-specification:
+
+How do I specify an axis?
+-------------------------
+
+For now, axes are specified by integers -- 0,1,2 for x,y,z. In the next
+version, this will probably change, and allow for string-identification as
+well.
+
Where can I go for support?
---------------------------
Modified: trunk/doc/build/html/_sources/modules/lagos/basedatatypes.txt
==============================================================================
--- trunk/doc/build/html/_sources/modules/lagos/basedatatypes.txt (original)
+++ trunk/doc/build/html/_sources/modules/lagos/basedatatypes.txt Sat May 10 23:00:13 2008
@@ -1,15 +1,84 @@
-:mod:`lagos.BaseDataTypes` -- Data Types
-===========================================
+Data Containers
+===============
-.. module:: lagos.BaseDataTypes
- :synopsis: Generate containers to hold AMR data
-.. moduleauthor:: Matthew Turk <mturk at stanford.edu>
+yt provides a number of data containers, defined such that they satisfy a
+logical need. Each of these provides only the finest-resolution cells, unless
+an option is available to restrict the levels from which they draw, as is the
+case with :class:`~yt.lagos.EnzoCoveringGrid`.
+
+Each of these implements the same primary protocol - all data values can be
+access dictionary-style:
+
+.. code-block:: python
+
+ >>> object["Density"]
+ >>> object["Density"].max()
+
+And so on. For more information, see the
+:ref:`the tutorial topic <basic_objects>` on basic objects.
+
+.. currentmodule:: yt.lagos
+
+Base Containers
+---------------
+
+.. autoclass:: yt.lagos.FakeGridForParticles
+ :members:
.. autoclass:: yt.lagos.EnzoData
:members:
+.. autoclass:: yt.lagos.Enzo1DData
+ :members:
+ :inherited-members:
+
+.. autoclass:: yt.lagos.Enzo2DData
+ :members:
+ :inherited-members:
+
.. autoclass:: yt.lagos.Enzo3DData
:members:
+ :inherited-members:
+
+1D Data Containers
+------------------
+
+Each of these inherits from :class:`~yt.lagos.Enzo1DData`, and so has all the
+member functions defined there.
+
+.. autoclass:: yt.lagos.EnzoOrthoRayBase
+ :members:
+
+2D Data Containers
+------------------
+
+.. autoclass:: yt.lagos.EnzoSliceBase
+ :members:
+
+.. autoclass:: yt.lagos.EnzoCuttingPlaneBase
+ :members:
+
+.. autoclass:: yt.lagos.EnzoProjBase
+ :members:
+
+3D Data Containers
+------------------
.. autoclass:: yt.lagos.EnzoSphereBase
:members:
+
+.. autoclass:: yt.lagos.EnzoRegionBase
+ :members:
+
+.. autoclass:: yt.lagos.EnzoCylinderBase
+ :members:
+
+.. autoclass:: yt.lagos.EnzoGridCollection
+ :members:
+
+.. autoclass:: yt.lagos.EnzoCoveringGrid
+ :members:
+
+.. autoclass:: yt.lagos.ExtractedRegionBase
+ :members:
+
Added: trunk/doc/build/html/_sources/modules/lagos/contours.txt
==============================================================================
Modified: trunk/doc/build/html/_sources/modules/lagos/index.txt
==============================================================================
--- trunk/doc/build/html/_sources/modules/lagos/index.txt (original)
+++ trunk/doc/build/html/_sources/modules/lagos/index.txt Sat May 10 23:00:13 2008
@@ -1,9 +1,17 @@
.. _lagos:
-yt.lagos
-======================
+yt.lagos - Data Handling and Analysis
+=====================================
+
+.. module:: yt.lagos
+ :synopsis: The data handling done with Enzo data
+.. moduleauthor:: Matthew Turk <mturk at stanford.edu>
+
.. toctree::
:maxdepth: 2
+ outputandhierarchy
basedatatypes
+ contours
+ profiles
Added: trunk/doc/build/html/_sources/modules/lagos/outputandhierarchy.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/modules/lagos/outputandhierarchy.txt Sat May 10 23:00:13 2008
@@ -0,0 +1,11 @@
+Native Enzo Data Structures
+===========================
+
+.. autoclass:: yt.lagos.EnzoStaticOutput
+ :members:
+
+.. autoclass:: yt.lagos.EnzoHierarchy
+ :members:
+
+.. autoclass:: yt.lagos.EnzoGridBase
+ :members:
Added: trunk/doc/build/html/_sources/modules/lagos/profiles.txt
==============================================================================
Modified: trunk/doc/build/html/_sources/tutorial/basic_objects.txt
==============================================================================
--- trunk/doc/build/html/_sources/tutorial/basic_objects.txt (original)
+++ trunk/doc/build/html/_sources/tutorial/basic_objects.txt Sat May 10 23:00:13 2008
@@ -1,3 +1,5 @@
+.. _basic_objects:
+
Basic Objects
=============
Modified: trunk/doc/build/html/_static/sphinxdoc.css
==============================================================================
--- trunk/doc/build/html/_static/sphinxdoc.css (original)
+++ trunk/doc/build/html/_static/sphinxdoc.css Sat May 10 23:00:13 2008
@@ -195,12 +195,11 @@
div.body {
margin: 0;
- padding: 0;
+ padding: 0.5em 20px 20px 20px;
}
div.bodywrapper {
margin: 0 240px 0 0;
- padding: 0.5em 20px 20px 20px;
border-right: 1px solid #ccc;
}
@@ -243,6 +242,10 @@
margin: 0.8em 0 0.5em 0;
}
+p.rubric {
+ font-weight: bold;
+}
+
h1 {
margin: 0;
padding: 0.7em 0 0.3em 0;
Modified: trunk/doc/build/html/cookbook/index.html
==============================================================================
--- trunk/doc/build/html/cookbook/index.html (original)
+++ trunk/doc/build/html/cookbook/index.html Sat May 10 23:00:13 2008
@@ -58,7 +58,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -81,7 +81,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Added: trunk/doc/build/html/extending/analyzing_in_parallel.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/extending/analyzing_in_parallel.html Sat May 10 23:00:13 2008
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Analyzing in Parallel — yt v0.3 documentation</title>
+ <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0.3'
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/interface.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="contents" title="Global table of contents" href="../contents.html" />
+ <link rel="index" title="Global index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" />
+ <link rel="top" title="yt v0.3 documentation" href="../index.html" />
+ <link rel="up" title="Extending yt" href="index.html" />
+ <link rel="next" title="Running Fortran Routines" href="running_fortran_routines.html" />
+ <link rel="prev" title="Creating Derived Fields" href="creating_derived_fields.html" />
+ </head>
+ <body>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="running_fortran_routines.html" title="Running Fortran Routines" accesskey="N">next</a> |</li>
+ <li class="right"><a href="creating_derived_fields.html" title="Creating Derived Fields" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body">
+
+
+ <div class="section">
+<h1 id="analyzing-in-parallel">Analyzing in Parallel<a class="headerlink" href="#analyzing-in-parallel" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="creating_derived_fields.html" title="previous chapter">Creating Derived Fields</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="running_fortran_routines.html" title="next chapter">Running Fortran Routines</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/extending/analyzing_in_parallel.txt">Show Source</a></li>
+ </ul>
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="running_fortran_routines.html" title="Running Fortran Routines" accesskey="N">next</a> |</li>
+ <li class="right"><a href="creating_derived_fields.html" title="Creating Derived Fields" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2008, Matthew Turk.
+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Added: trunk/doc/build/html/extending/creating_datatypes.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/extending/creating_datatypes.html Sat May 10 23:00:13 2008
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Creating Datatypes — yt v0.3 documentation</title>
+ <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0.3'
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/interface.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="contents" title="Global table of contents" href="../contents.html" />
+ <link rel="index" title="Global index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" />
+ <link rel="top" title="yt v0.3 documentation" href="../index.html" />
+ <link rel="up" title="Extending yt" href="index.html" />
+ <link rel="next" title="Creating Derived Quantities" href="creating_derived_quantities.html" />
+ <link rel="prev" title="The Plugin File" href="plugin_file.html" />
+ </head>
+ <body>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="creating_derived_quantities.html" title="Creating Derived Quantities" accesskey="N">next</a> |</li>
+ <li class="right"><a href="plugin_file.html" title="The Plugin File" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body">
+
+
+ <div class="section">
+<h1 id="creating-datatypes">Creating Datatypes<a class="headerlink" href="#creating-datatypes" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="plugin_file.html" title="previous chapter">The Plugin File</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="creating_derived_quantities.html" title="next chapter">Creating Derived Quantities</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/extending/creating_datatypes.txt">Show Source</a></li>
+ </ul>
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="creating_derived_quantities.html" title="Creating Derived Quantities" accesskey="N">next</a> |</li>
+ <li class="right"><a href="plugin_file.html" title="The Plugin File" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2008, Matthew Turk.
+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Added: trunk/doc/build/html/extending/creating_derived_fields.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/extending/creating_derived_fields.html Sat May 10 23:00:13 2008
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Creating Derived Fields — yt v0.3 documentation</title>
+ <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0.3'
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/interface.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="contents" title="Global table of contents" href="../contents.html" />
+ <link rel="index" title="Global index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" />
+ <link rel="top" title="yt v0.3 documentation" href="../index.html" />
+ <link rel="up" title="Extending yt" href="index.html" />
+ <link rel="next" title="Analyzing in Parallel" href="analyzing_in_parallel.html" />
+ <link rel="prev" title="Creating Derived Quantities" href="creating_derived_quantities.html" />
+ </head>
+ <body>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="analyzing_in_parallel.html" title="Analyzing in Parallel" accesskey="N">next</a> |</li>
+ <li class="right"><a href="creating_derived_quantities.html" title="Creating Derived Quantities" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body">
+
+
+ <div class="section">
+<h1 id="creating-derived-fields">Creating Derived Fields<a class="headerlink" href="#creating-derived-fields" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="creating_derived_quantities.html" title="previous chapter">Creating Derived Quantities</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="analyzing_in_parallel.html" title="next chapter">Analyzing in Parallel</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/extending/creating_derived_fields.txt">Show Source</a></li>
+ </ul>
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="analyzing_in_parallel.html" title="Analyzing in Parallel" accesskey="N">next</a> |</li>
+ <li class="right"><a href="creating_derived_quantities.html" title="Creating Derived Quantities" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2008, Matthew Turk.
+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Added: trunk/doc/build/html/extending/creating_derived_quantities.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/extending/creating_derived_quantities.html Sat May 10 23:00:13 2008
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Creating Derived Quantities — yt v0.3 documentation</title>
+ <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0.3'
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/interface.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="contents" title="Global table of contents" href="../contents.html" />
+ <link rel="index" title="Global index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" />
+ <link rel="top" title="yt v0.3 documentation" href="../index.html" />
+ <link rel="up" title="Extending yt" href="index.html" />
+ <link rel="next" title="Creating Derived Fields" href="creating_derived_fields.html" />
+ <link rel="prev" title="Creating Datatypes" href="creating_datatypes.html" />
+ </head>
+ <body>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="creating_derived_fields.html" title="Creating Derived Fields" accesskey="N">next</a> |</li>
+ <li class="right"><a href="creating_datatypes.html" title="Creating Datatypes" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body">
+
+
+ <div class="section">
+<h1 id="creating-derived-quantities">Creating Derived Quantities<a class="headerlink" href="#creating-derived-quantities" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="creating_datatypes.html" title="previous chapter">Creating Datatypes</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="creating_derived_fields.html" title="next chapter">Creating Derived Fields</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/extending/creating_derived_quantities.txt">Show Source</a></li>
+ </ul>
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="creating_derived_fields.html" title="Creating Derived Fields" accesskey="N">next</a> |</li>
+ <li class="right"><a href="creating_datatypes.html" title="Creating Datatypes" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2008, Matthew Turk.
+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Modified: trunk/doc/build/html/extending/index.html
==============================================================================
--- trunk/doc/build/html/extending/index.html (original)
+++ trunk/doc/build/html/extending/index.html Sat May 10 23:00:13 2008
@@ -41,27 +41,31 @@
<div class="section">
<h1 id="extending-yt">Extending yt<a class="headerlink" href="#extending-yt" title="Permalink to this headline">¶</a></h1>
-<div class="section">
-<h2 id="writing-scripts">Writing Scripts<a class="headerlink" href="#writing-scripts" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section">
-<h2 id="dealing-with-the-interpreter">Dealing with the Interpreter<a class="headerlink" href="#dealing-with-the-interpreter" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section">
-<h2 id="creating-datatypes">Creating Datatypes<a class="headerlink" href="#creating-datatypes" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section">
-<h2 id="creating-derived-quantities">Creating Derived Quantities<a class="headerlink" href="#creating-derived-quantities" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section">
-<h2 id="creating-derived-fields">Creating Derived Fields<a class="headerlink" href="#creating-derived-fields" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section">
-<h2 id="analyzing-in-parallel">Analyzing in Parallel<a class="headerlink" href="#analyzing-in-parallel" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section">
-<h2 id="running-fortran-routines">Running Fortran Routines<a class="headerlink" href="#running-fortran-routines" title="Permalink to this headline">¶</a></h2>
-</div>
+<p>yt has been designed to be flexible, with several entry points.</p>
+<ul>
+<li><a class="reference" href="writing_scripts.html">Writing Scripts</a></li>
+</ul>
+<ul>
+<li><a class="reference" href="using_the_interpreter.html">Using the Interpreter</a></li>
+</ul>
+<ul>
+<li><a class="reference" href="plugin_file.html">The Plugin File</a></li>
+</ul>
+<ul>
+<li><a class="reference" href="creating_datatypes.html">Creating Datatypes</a></li>
+</ul>
+<ul>
+<li><a class="reference" href="creating_derived_quantities.html">Creating Derived Quantities</a></li>
+</ul>
+<ul>
+<li><a class="reference" href="creating_derived_fields.html">Creating Derived Fields</a></li>
+</ul>
+<ul>
+<li><a class="reference" href="analyzing_in_parallel.html">Analyzing in Parallel</a></li>
+</ul>
+<ul>
+<li><a class="reference" href="running_fortran_routines.html">Running Fortran Routines</a></li>
+</ul>
</div>
@@ -70,20 +74,6 @@
</div>
<div class="sidebar">
<div class="sidebarwrapper">
- <h3>Table Of Contents</h3>
- <ul>
-<li><a class="reference" href="">Extending yt</a><ul>
-<li><a class="reference" href="#writing-scripts">Writing Scripts</a></li>
-<li><a class="reference" href="#dealing-with-the-interpreter">Dealing with the Interpreter</a></li>
-<li><a class="reference" href="#creating-datatypes">Creating Datatypes</a></li>
-<li><a class="reference" href="#creating-derived-quantities">Creating Derived Quantities</a></li>
-<li><a class="reference" href="#creating-derived-fields">Creating Derived Fields</a></li>
-<li><a class="reference" href="#analyzing-in-parallel">Analyzing in Parallel</a></li>
-<li><a class="reference" href="#running-fortran-routines">Running Fortran Routines</a></li>
-</ul>
-</li>
-</ul>
-
<h4>Next topic</h4>
<p class="topless"><a href="../faq.html" title="next chapter">FAQ</a></p>
<h3>This Page</h3>
@@ -92,7 +82,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -114,7 +104,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Added: trunk/doc/build/html/extending/plugin_file.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/extending/plugin_file.html Sat May 10 23:00:13 2008
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>The Plugin File — yt v0.3 documentation</title>
+ <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0.3'
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/interface.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="contents" title="Global table of contents" href="../contents.html" />
+ <link rel="index" title="Global index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" />
+ <link rel="top" title="yt v0.3 documentation" href="../index.html" />
+ <link rel="up" title="Extending yt" href="index.html" />
+ <link rel="next" title="Creating Datatypes" href="creating_datatypes.html" />
+ <link rel="prev" title="Using the Interpreter" href="using_the_interpreter.html" />
+ </head>
+ <body>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="creating_datatypes.html" title="Creating Datatypes" accesskey="N">next</a> |</li>
+ <li class="right"><a href="using_the_interpreter.html" title="Using the Interpreter" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body">
+
+
+ <div class="section">
+<h1 id="the-plugin-file">The Plugin File<a class="headerlink" href="#the-plugin-file" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="using_the_interpreter.html" title="previous chapter">Using the Interpreter</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="creating_datatypes.html" title="next chapter">Creating Datatypes</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/extending/plugin_file.txt">Show Source</a></li>
+ </ul>
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="creating_datatypes.html" title="Creating Datatypes" accesskey="N">next</a> |</li>
+ <li class="right"><a href="using_the_interpreter.html" title="Using the Interpreter" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2008, Matthew Turk.
+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Added: trunk/doc/build/html/extending/running_fortran_routines.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/extending/running_fortran_routines.html Sat May 10 23:00:13 2008
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Running Fortran Routines — yt v0.3 documentation</title>
+ <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0.3'
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/interface.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="contents" title="Global table of contents" href="../contents.html" />
+ <link rel="index" title="Global index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" />
+ <link rel="top" title="yt v0.3 documentation" href="../index.html" />
+ <link rel="up" title="Extending yt" href="index.html" />
+ <link rel="next" title="Extending yt" href="index.html" />
+ <link rel="prev" title="Analyzing in Parallel" href="analyzing_in_parallel.html" />
+ </head>
+ <body>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
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+ <div class="section">
+<h1 id="running-fortran-routines">Running Fortran Routines<a class="headerlink" href="#running-fortran-routines" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="analyzing_in_parallel.html" title="previous chapter">Analyzing in Parallel</a></p>
+ <h4>Next topic</h4>
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+ <h3>This Page</h3>
+ <ul class="this-page-menu">
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+ </ul>
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+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div>
+ </div>
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+ </div>
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+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
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+ </ul>
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+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Added: trunk/doc/build/html/extending/using_the_interpreter.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/extending/using_the_interpreter.html Sat May 10 23:00:13 2008
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Using the Interpreter — yt v0.3 documentation</title>
+ <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0.3'
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/interface.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="contents" title="Global table of contents" href="../contents.html" />
+ <link rel="index" title="Global index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" />
+ <link rel="top" title="yt v0.3 documentation" href="../index.html" />
+ <link rel="up" title="Extending yt" href="index.html" />
+ <link rel="next" title="The Plugin File" href="plugin_file.html" />
+ <link rel="prev" title="Writing Scripts" href="writing_scripts.html" />
+ </head>
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+ <li class="right"><a href="plugin_file.html" title="The Plugin File" accesskey="N">next</a> |</li>
+ <li class="right"><a href="writing_scripts.html" title="Writing Scripts" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
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+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
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+ <div class="body">
+
+
+ <div class="section">
+<h1 id="using-the-interpreter">Using the Interpreter<a class="headerlink" href="#using-the-interpreter" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="writing_scripts.html" title="previous chapter">Writing Scripts</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="plugin_file.html" title="next chapter">The Plugin File</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/extending/using_the_interpreter.txt">Show Source</a></li>
+ </ul>
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="plugin_file.html" title="The Plugin File" accesskey="N">next</a> |</li>
+ <li class="right"><a href="writing_scripts.html" title="Writing Scripts" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
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+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2008, Matthew Turk.
+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Added: trunk/doc/build/html/extending/writing_scripts.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/extending/writing_scripts.html Sat May 10 23:00:13 2008
@@ -0,0 +1,93 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Writing Scripts — yt v0.3 documentation</title>
+ <link rel="stylesheet" href="../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../',
+ VERSION: '0.3'
+ };
+ </script>
+ <script type="text/javascript" src="../_static/jquery.js"></script>
+ <script type="text/javascript" src="../_static/interface.js"></script>
+ <script type="text/javascript" src="../_static/doctools.js"></script>
+ <link rel="contents" title="Global table of contents" href="../contents.html" />
+ <link rel="index" title="Global index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" />
+ <link rel="top" title="yt v0.3 documentation" href="../index.html" />
+ <link rel="up" title="Extending yt" href="index.html" />
+ <link rel="next" title="Using the Interpreter" href="using_the_interpreter.html" />
+ <link rel="prev" title="Extending yt" href="index.html" />
+ </head>
+ <body>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="using_the_interpreter.html" title="Using the Interpreter" accesskey="N">next</a> |</li>
+ <li class="right"><a href="index.html" title="Extending yt" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="document">
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+ <div class="bodywrapper">
+ <div class="body">
+
+
+ <div class="section">
+<h1 id="writing-scripts">Writing Scripts<a class="headerlink" href="#writing-scripts" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="index.html" title="previous chapter">Extending yt</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="using_the_interpreter.html" title="next chapter">Using the Interpreter</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/extending/writing_scripts.txt">Show Source</a></li>
+ </ul>
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="using_the_interpreter.html" title="Using the Interpreter" accesskey="N">next</a> |</li>
+ <li class="right"><a href="index.html" title="Extending yt" accesskey="P">previous</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
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+
+ <li><a href="index.html" accesskey="U">Extending yt</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2008, Matthew Turk.
+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Modified: trunk/doc/build/html/faq.html
==============================================================================
--- trunk/doc/build/html/faq.html (original)
+++ trunk/doc/build/html/faq.html Sat May 10 23:00:13 2008
@@ -81,6 +81,23 @@
let me know.</p>
</div>
<div class="section">
+<h2 id="what-are-all-these-yt-files">What are all these .yt files?<a class="headerlink" href="#what-are-all-these-yt-files" title="Permalink to this headline">¶</a></h2>
+<p>By default, yt attempts to serialize a couple pieces of data that help speed it
+up in future invocations. Specifically, the entire contents of the hierarchy,
+the parent-child relationships between the grids, and any projections of the
+entire volume that are made.</p>
+<p>The numbers that make up the filenames are taken from one of two places. If
+your Enzo outputs the “CurrentTimeIdentifier” parameter, that is the number that it
+uses. (This is a string of digits representing the number of seconds since the
+epoch.) If that is unavailable, the creation time of the file as reported by
+the file system is used.</p>
+<p>This can cause problems. Ticket #91 on the bug tracker records some of these.
+If you are creating multiple parameter files per second, this can lead to
+incorrect hierarchies, and thus incorrect behavior, inside your analysis. In
+such cases, it is recommended that the parameter ‘serialize’ in the section
+‘lagos’ of your configuration file is set to ‘False’.</p>
+</div>
+<div class="section">
<h2 id="how-can-i-help">How can I help?<a class="headerlink" href="#how-can-i-help" title="Permalink to this headline">¶</a></h2>
<p>If you find a bug, report it. If you do something cool, write it up. If you
find a place to improve the code, send in a patch.</p>
@@ -96,6 +113,12 @@
first!) or attach them to a ticket at <a class="reference" href="http://yt.spacepope.org/">http://yt.spacepope.org/</a>.</p>
</div>
<div class="section">
+<h2 id="how-do-i-specify-an-axis"><span id="axis-specification"></span>How do I specify an axis?<a class="headerlink" href="#how-do-i-specify-an-axis" title="Permalink to this headline">¶</a></h2>
+<p>For now, axes are specified by integers – 0,1,2 for x,y,z. In the next
+version, this will probably change, and allow for string-identification as
+well.</p>
+</div>
+<div class="section">
<h2 id="where-can-i-go-for-support">Where can I go for support?<a class="headerlink" href="#where-can-i-go-for-support" title="Permalink to this headline">¶</a></h2>
<p>I’ve set up a <tt class="docutils literal"><span class="pre">yt-users</span></tt> mailing list. There’s more information about it
at the <a class="reference" href="http://yt.spacepope.org">yt homepage</a>.</p>
@@ -115,8 +138,10 @@
<li><a class="reference" href="#where-can-i-learn-more-about-python">Where can I learn more about Python?</a></li>
<li><a class="reference" href="#what-s-up-with-the-names">What’s up with the names?</a></li>
<li><a class="reference" href="#are-there-any-restrictions-on-my-use-of-yt">Are there any restrictions on my use of yt?</a></li>
+<li><a class="reference" href="#what-are-all-these-yt-files">What are all these .yt files?</a></li>
<li><a class="reference" href="#how-can-i-help">How can I help?</a></li>
<li><a class="reference" href="#something-has-gone-wrong-what-do-i-do">Something has gone wrong. What do I do?</a></li>
+<li><a class="reference" href="#how-do-i-specify-an-axis">How do I specify an axis?</a></li>
<li><a class="reference" href="#where-can-i-go-for-support">Where can I go for support?</a></li>
</ul>
</li>
@@ -132,7 +157,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -155,7 +180,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/genindex.html
==============================================================================
--- trunk/doc/build/html/genindex.html (original)
+++ trunk/doc/build/html/genindex.html Sat May 10 23:00:13 2008
@@ -39,7 +39,7 @@
<h1 id="index">Index</h1>
- <a href="#Symbols"><strong>Symbols</strong></a> | <a href="#C"><strong>C</strong></a> | <a href="#D"><strong>D</strong></a> | <a href="#E"><strong>E</strong></a> | <a href="#G"><strong>G</strong></a> | <a href="#H"><strong>H</strong></a> | <a href="#I"><strong>I</strong></a> | <a href="#L"><strong>L</strong></a> | <a href="#P"><strong>P</strong></a> | <a href="#R"><strong>R</strong></a> | <a href="#S"><strong>S</strong></a>
+ <a href="#Symbols"><strong>Symbols</strong></a> | <a href="#C"><strong>C</strong></a> | <a href="#D"><strong>D</strong></a> | <a href="#E"><strong>E</strong></a> | <a href="#F"><strong>F</strong></a> | <a href="#G"><strong>G</strong></a> | <a href="#H"><strong>H</strong></a> | <a href="#I"><strong>I</strong></a> | <a href="#P"><strong>P</strong></a> | <a href="#R"><strong>R</strong></a> | <a href="#S"><strong>S</strong></a> | <a href="#Y"><strong>Y</strong></a>
<hr />
@@ -50,14 +50,14 @@
<dt>2ddata</dt>
<dd><dl>
- <dt><a href="tutorial/advanced_objects.html#index-18">Cutting Plane</a></dt>
- <dt><a href="tutorial/basic_objects.html#index-37">Slices</a></dt>
+ <dt><a href="tutorial/advanced_objects.html#index-38">Cutting Plane</a></dt>
+ <dt><a href="tutorial/basic_objects.html#index-50">Slices</a></dt>
</dl></dd>
<dt>3ddata</dt>
<dd><dl>
- <dt><a href="tutorial/advanced_objects.html#index-19">Extracted Regions</a></dt>
- <dt><a href="tutorial/advanced_objects.html#index-20">GridCollection</a></dt>
- <dt><a href="tutorial/getting_started.html#index-23">grid</a></dt>
+ <dt><a href="tutorial/advanced_objects.html#index-39">Extracted Regions</a></dt>
+ <dt><a href="tutorial/advanced_objects.html#index-40">GridCollection</a></dt>
+ <dt><a href="tutorial/getting_started.html#index-48">grid</a></dt>
</dl></dd></dl></td><td width="33%" valign="top"><dl>
</dl></td></tr></table>
@@ -65,114 +65,181 @@
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.Enzo3DData.clear_data">clear_data() (lagos.BaseDataTypes.Enzo3DData method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoGridBase.clear_all">clear_all() (EnzoGridBase method)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo1DData.clear_data">clear_data() (yt.lagos.Enzo1DData method)</a></dt>
<dd><dl>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoData.clear_data">(lagos.BaseDataTypes.EnzoData method)</a></dt>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.clear_data">(lagos.BaseDataTypes.EnzoSphereBase method)</a></dt>
- </dl></dd></dl></td><td width="33%" valign="top"><dl>
-<dt><a href="tutorial/advanced_objects.html#index-18">Cutting Plane</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.clear_data">(yt.lagos.Enzo2DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.clear_data">(yt.lagos.Enzo3DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData.clear_data">(yt.lagos.EnzoData method)</a></dt>
+ </dl></dd>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoGridBase.clear_derived_quantities">clear_derived_quantities() (EnzoGridBase method)</a></dt></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo1DData.convert">convert() (yt.lagos.Enzo1DData method)</a></dt>
+ <dd><dl>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.convert">(yt.lagos.Enzo2DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.convert">(yt.lagos.Enzo3DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData.convert">(yt.lagos.EnzoData method)</a></dt>
+ </dl></dd>
+<dt><a href="tutorial/advanced_objects.html#index-38">Cutting Plane</a></dt>
</dl></td></tr></table>
<h2 id="D">D</h2>
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="tutorial/basic_objects.html#index-36">derivedfield</a></dt></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="tutorial/basic_objects.html#index-49">derivedfield</a></dt></dl></td><td width="33%" valign="top"><dl>
</dl></td></tr></table>
<h2 id="E">E</h2>
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.Enzo3DData">Enzo3DData (class in lagos.BaseDataTypes)</a></dt>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoData">EnzoData (class in lagos.BaseDataTypes)</a></dt>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase">EnzoSphereBase (class in lagos.BaseDataTypes)</a></dt>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.Enzo3DData.extract_connected_sets">extract_connected_sets() (lagos.BaseDataTypes.Enzo3DData method)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo1DData">Enzo1DData (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData">Enzo2DData (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData">Enzo3DData (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoCoveringGrid">EnzoCoveringGrid (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoCuttingPlaneBase">EnzoCuttingPlaneBase (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoCylinderBase">EnzoCylinderBase (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData">EnzoData (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoGridBase">EnzoGridBase (class in None)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoGridCollection">EnzoGridCollection (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy">EnzoHierarchy (class in None)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoOrthoRayBase">EnzoOrthoRayBase (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoProjBase">EnzoProjBase (class in yt.lagos)</a></dt></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoRegionBase">EnzoRegionBase (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoSliceBase">EnzoSliceBase (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoSphereBase">EnzoSphereBase (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoStaticOutput">EnzoStaticOutput (class in None)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.export_amira">export_amira() (EnzoHierarchy method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.export_boxes_pv">export_boxes_pv() (EnzoHierarchy method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.export_particles_pb">export_particles_pb() (EnzoHierarchy method)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.extract_connected_sets">extract_connected_sets() (yt.lagos.Enzo3DData method)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.extract_region">extract_region() (yt.lagos.Enzo3DData method)</a></dt>
+<dt><a href="tutorial/advanced_objects.html#index-39">Extracted Regions</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.ExtractedRegionBase">ExtractedRegionBase (class in yt.lagos)</a></dt>
+</dl></td></tr></table>
+
+<h2 id="F">F</h2>
+<table width="100%" class="indextable"><tr><td width="33%" valign="top">
+<dl>
+
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.FakeGridForParticles">FakeGridForParticles (class in yt.lagos)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoGridBase.find_max">find_max() (EnzoGridBase method)</a></dt>
<dd><dl>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.extract_connected_sets">(lagos.BaseDataTypes.EnzoSphereBase method)</a></dt>
- </dl></dd></dl></td><td width="33%" valign="top"><dl>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.Enzo3DData.extract_region">extract_region() (lagos.BaseDataTypes.Enzo3DData method)</a></dt>
+ <dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.find_max">(EnzoHierarchy method)</a></dt>
+ </dl></dd>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoGridBase.find_min">find_min() (EnzoGridBase method)</a></dt>
<dd><dl>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.extract_region">(lagos.BaseDataTypes.EnzoSphereBase method)</a></dt>
+ <dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.find_min">(EnzoHierarchy method)</a></dt>
</dl></dd>
-<dt><a href="tutorial/advanced_objects.html#index-19">Extracted Regions</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.find_point">find_point() (EnzoHierarchy method)</a></dt></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.find_ray_grids">find_ray_grids() (EnzoHierarchy method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.find_slice_grids">find_slice_grids() (EnzoHierarchy method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.find_sphere_grids">find_sphere_grids() (EnzoHierarchy method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.findMax">findMax() (EnzoHierarchy method)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoCoveringGrid.flush_data">flush_data() (yt.lagos.EnzoCoveringGrid method)</a></dt>
</dl></td></tr></table>
<h2 id="G">G</h2>
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.Enzo3DData.get_field_parameter">get_field_parameter() (lagos.BaseDataTypes.Enzo3DData method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.get_box_grids">get_box_grids() (EnzoHierarchy method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoGridBase.get_data">get_data() (EnzoGridBase method)</a></dt>
<dd><dl>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoData.get_field_parameter">(lagos.BaseDataTypes.EnzoData method)</a></dt>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.get_field_parameter">(lagos.BaseDataTypes.EnzoSphereBase method)</a></dt>
- </dl></dd></dl></td><td width="33%" valign="top"><dl>
-<dt><a href="tutorial/getting_started.html#index-23">Grid</a></dt>
-<dt><a href="tutorial/advanced_objects.html#index-20">GridCollection</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.get_data">(yt.lagos.Enzo2DData method)</a></dt>
+ </dl></dd>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoGridBase.get_enzo_grid">get_enzo_grid() (EnzoGridBase method)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo1DData.get_field_parameter">get_field_parameter() (yt.lagos.Enzo1DData method)</a></dt>
+ <dd><dl>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.get_field_parameter">(yt.lagos.Enzo2DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.get_field_parameter">(yt.lagos.Enzo3DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData.get_field_parameter">(yt.lagos.EnzoData method)</a></dt>
+ </dl></dd></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoGridBase.get_position">get_position() (EnzoGridBase method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.get_smallest_dx">get_smallest_dx() (EnzoHierarchy method)</a></dt>
+<dt><a href="tutorial/getting_started.html#index-48">Grid</a></dt>
+<dt><a href="tutorial/advanced_objects.html#index-40">GridCollection</a></dt>
</dl></td></tr></table>
<h2 id="H">H</h2>
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="tutorial/getting_started.html#index-22">hierarchy</a></dt></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo1DData.has_field_parameter">has_field_parameter() (yt.lagos.Enzo1DData method)</a></dt>
+ <dd><dl>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.has_field_parameter">(yt.lagos.Enzo2DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.has_field_parameter">(yt.lagos.Enzo3DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData.has_field_parameter">(yt.lagos.EnzoData method)</a></dt>
+ </dl></dd>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo1DData.has_key">has_key() (yt.lagos.Enzo1DData method)</a></dt>
+ <dd><dl>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.has_key">(yt.lagos.Enzo2DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.has_key">(yt.lagos.Enzo3DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData.has_key">(yt.lagos.EnzoData method)</a></dt>
+ </dl></dd></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="tutorial/getting_started.html#index-47">hierarchy</a></dt>
</dl></td></tr></table>
<h2 id="I">I</h2>
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="tutorial/basic_objects.html#index-36">indices</a></dt></dl></td><td width="33%" valign="top"><dl>
-</dl></td></tr></table>
-
-<h2 id="L">L</h2>
-<table width="100%" class="indextable"><tr><td width="33%" valign="top">
-<dl>
-
-<dt><a href="modules/lagos/basedatatypes.html#module-lagos.BaseDataTypes">lagos.BaseDataTypes (module)</a></dt></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="tutorial/basic_objects.html#index-49">indices</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.initialize_enzo_interface">initialize_enzo_interface() (EnzoHierarchy method)</a></dt></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.interpolate_discretize">interpolate_discretize() (yt.lagos.Enzo2DData method)</a></dt>
</dl></td></tr></table>
<h2 id="P">P</h2>
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.Enzo3DData.paint_grids">paint_grids() (lagos.BaseDataTypes.Enzo3DData method)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.paint_grids">paint_grids() (yt.lagos.Enzo3DData method)</a></dt>
+<dt><a href="tutorial/automated_plotting.html#index-42">PlotCollections</a></dt>
<dd><dl>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.paint_grids">(lagos.BaseDataTypes.EnzoSphereBase method)</a></dt>
+ <dt><a href="tutorial/automated_plotting.html#index-43">Adding Plots</a></dt>
</dl></dd>
-<dt><a href="tutorial/automated_plotting.html#index-34">PlotCollections</a></dt>
+<dt><a href="tutorial/automated_plotting.html#index-41">Plotting</a></dt>
<dd><dl>
- <dt><a href="tutorial/automated_plotting.html#index-35">Adding Plots</a></dt>
+ <dt><a href="tutorial/automated_plotting.html#index-43">Adding plots to PlotCollections</a></dt>
+ <dt><a href="tutorial/automated_plotting.html#index-42">PlotCollections</a></dt>
</dl></dd></dl></td><td width="33%" valign="top"><dl>
-<dt><a href="tutorial/automated_plotting.html#index-33">Plotting</a></dt>
- <dd><dl>
- <dt><a href="tutorial/automated_plotting.html#index-35">Adding plots to PlotCollections</a></dt>
- <dt><a href="tutorial/automated_plotting.html#index-34">PlotCollections</a></dt>
- </dl></dd>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.print_stats">print_stats() (EnzoHierarchy method)</a></dt>
</dl></td></tr></table>
<h2 id="R">R</h2>
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="tutorial/automated_plotting.html#index-34">Raven</a>, <a href="tutorial/automated_plotting.html#index-35">[Link]</a></dt></dl></td><td width="33%" valign="top"><dl>
+<dt><a href="tutorial/automated_plotting.html#index-42">Raven</a>, <a href="tutorial/automated_plotting.html#index-43">[Link]</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoSliceBase.reslice">reslice() (yt.lagos.EnzoSliceBase method)</a></dt></dl></td><td width="33%" valign="top"><dl>
</dl></td></tr></table>
<h2 id="S">S</h2>
<table width="100%" class="indextable"><tr><td width="33%" valign="top">
<dl>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.Enzo3DData.select_grids">select_grids() (lagos.BaseDataTypes.Enzo3DData method)</a></dt>
+<dt><a href="modules/lagos/outputandhierarchy.html#EnzoHierarchy.save_data">save_data() (EnzoHierarchy method)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo1DData.select_grids">select_grids() (yt.lagos.Enzo1DData method)</a></dt>
<dd><dl>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.select_grids">(lagos.BaseDataTypes.EnzoSphereBase method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.select_grids">(yt.lagos.Enzo2DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.select_grids">(yt.lagos.Enzo3DData method)</a></dt>
</dl></dd>
-<dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.Enzo3DData.set_field_parameter">set_field_parameter() (lagos.BaseDataTypes.Enzo3DData method)</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo1DData.set_field_parameter">set_field_parameter() (yt.lagos.Enzo1DData method)</a></dt>
<dd><dl>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoData.set_field_parameter">(lagos.BaseDataTypes.EnzoData method)</a></dt>
- <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.set_field_parameter">(lagos.BaseDataTypes.EnzoSphereBase method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo2DData.set_field_parameter">(yt.lagos.Enzo2DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.Enzo3DData.set_field_parameter">(yt.lagos.Enzo3DData method)</a></dt>
+ <dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoData.set_field_parameter">(yt.lagos.EnzoData method)</a></dt>
</dl></dd></dl></td><td width="33%" valign="top"><dl>
-<dt><a href="tutorial/basic_objects.html#index-37">Slices</a></dt>
-<dt><a href="tutorial/getting_started.html#index-21">Starting yt</a></dt>
+<dt><a href="modules/lagos/basedatatypes.html#yt.lagos.EnzoSliceBase.shift">shift() (yt.lagos.EnzoSliceBase method)</a></dt>
+<dt><a href="tutorial/basic_objects.html#index-50">Slices</a></dt>
+<dt><a href="tutorial/getting_started.html#index-46">Starting yt</a></dt>
+</dl></td></tr></table>
+
+<h2 id="Y">Y</h2>
+<table width="100%" class="indextable"><tr><td width="33%" valign="top">
+<dl>
+
+<dt><a href="modules/lagos/index.html#module-yt.lagos">yt.lagos (module)</a></dt></dl></td><td width="33%" valign="top"><dl>
</dl></td></tr></table>
@@ -184,7 +251,7 @@
<div class="sidebarwrapper">
<h3>Quick search</h3>
<form class="search" action="search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -205,7 +272,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/index.html
==============================================================================
--- trunk/doc/build/html/index.html (original)
+++ trunk/doc/build/html/index.html Sat May 10 23:00:13 2008
@@ -69,13 +69,14 @@
</ul>
<ul>
<li><a class="reference" href="extending/index.html">Extending yt</a><ul>
-<li><a class="reference" href="extending/index.html#writing-scripts">Writing Scripts</a></li>
-<li><a class="reference" href="extending/index.html#dealing-with-the-interpreter">Dealing with the Interpreter</a></li>
-<li><a class="reference" href="extending/index.html#creating-datatypes">Creating Datatypes</a></li>
-<li><a class="reference" href="extending/index.html#creating-derived-quantities">Creating Derived Quantities</a></li>
-<li><a class="reference" href="extending/index.html#creating-derived-fields">Creating Derived Fields</a></li>
-<li><a class="reference" href="extending/index.html#analyzing-in-parallel">Analyzing in Parallel</a></li>
-<li><a class="reference" href="extending/index.html#running-fortran-routines">Running Fortran Routines</a></li>
+<li><a class="reference" href="extending/writing_scripts.html">Writing Scripts</a></li>
+<li><a class="reference" href="extending/using_the_interpreter.html">Using the Interpreter</a></li>
+<li><a class="reference" href="extending/plugin_file.html">The Plugin File</a></li>
+<li><a class="reference" href="extending/creating_datatypes.html">Creating Datatypes</a></li>
+<li><a class="reference" href="extending/creating_derived_quantities.html">Creating Derived Quantities</a></li>
+<li><a class="reference" href="extending/creating_derived_fields.html">Creating Derived Fields</a></li>
+<li><a class="reference" href="extending/analyzing_in_parallel.html">Analyzing in Parallel</a></li>
+<li><a class="reference" href="extending/running_fortran_routines.html">Running Fortran Routines</a></li>
</ul>
</li>
</ul>
@@ -85,15 +86,18 @@
<li><a class="reference" href="faq.html#where-can-i-learn-more-about-python">Where can I learn more about Python?</a></li>
<li><a class="reference" href="faq.html#what-s-up-with-the-names">What’s up with the names?</a></li>
<li><a class="reference" href="faq.html#are-there-any-restrictions-on-my-use-of-yt">Are there any restrictions on my use of yt?</a></li>
+<li><a class="reference" href="faq.html#what-are-all-these-yt-files">What are all these .yt files?</a></li>
<li><a class="reference" href="faq.html#how-can-i-help">How can I help?</a></li>
<li><a class="reference" href="faq.html#something-has-gone-wrong-what-do-i-do">Something has gone wrong. What do I do?</a></li>
+<li><a class="reference" href="faq.html#how-do-i-specify-an-axis">How do I specify an axis?</a></li>
<li><a class="reference" href="faq.html#where-can-i-go-for-support">Where can I go for support?</a></li>
</ul>
</li>
</ul>
<ul>
-<li><a class="reference" href="modules/lagos/index.html">yt.lagos</a><ul>
-<li><a class="reference" href="modules/lagos/basedatatypes.html"><tt class="docutils literal"><span class="pre">lagos.BaseDataTypes</span></tt> – Data Types</a></li>
+<li><a class="reference" href="modules/lagos/index.html">yt.lagos - Data Handling and Analysis</a><ul>
+<li><a class="reference" href="modules/lagos/outputandhierarchy.html">Native Enzo Data Structures</a></li>
+<li><a class="reference" href="modules/lagos/basedatatypes.html">Data Containers</a></li>
</ul>
</li>
</ul>
@@ -131,7 +135,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -152,7 +156,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/intro.html
==============================================================================
--- trunk/doc/build/html/intro.html (original)
+++ trunk/doc/build/html/intro.html Sat May 10 23:00:13 2008
@@ -149,7 +149,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -172,7 +172,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/modindex.html
==============================================================================
--- trunk/doc/build/html/modindex.html (original)
+++ trunk/doc/build/html/modindex.html Sat May 10 23:00:13 2008
@@ -42,16 +42,16 @@
<table width="100%" class="indextable" cellspacing="0" cellpadding="2"><tr class="pcap"><td></td><td> </td><td></td></tr>
- <tr class="cap"><td></td><td><strong>L</strong></td><td></td></tr><tr>
+ <tr class="cap"><td></td><td><strong>Y</strong></td><td></td></tr><tr>
<td><img src="_static/minus.png" id="toggle-1"
class="toggler" style="display: none" /></td>
<td>
- <tt class="xref">lagos</tt></td><td>
+ <tt class="xref">yt</tt></td><td>
<em></em></td></tr><tr class="cg-1">
<td></td>
<td>
- <a href="modules/lagos/basedatatypes.html#module-lagos.BaseDataTypes"><tt class="xref">lagos.BaseDataTypes</tt></a></td><td>
- <em>Generate containers to hold AMR data</em></td></tr>
+ <a href="modules/lagos/index.html#module-yt.lagos"><tt class="xref">yt.lagos</tt></a></td><td>
+ <em>The data handling done with Enzo data</em></td></tr>
</table>
@@ -62,7 +62,7 @@
<div class="sidebarwrapper">
<h3>Quick search</h3>
<form class="search" action="search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -83,7 +83,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/modules/lagos/basedatatypes.html
==============================================================================
--- trunk/doc/build/html/modules/lagos/basedatatypes.html (original)
+++ trunk/doc/build/html/modules/lagos/basedatatypes.html Sat May 10 23:00:13 2008
@@ -2,7 +2,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>lagos.BaseDataTypes – Data Types — yt v0.3 documentation</title>
+ <title>Data Containers — yt v0.3 documentation</title>
<link rel="stylesheet" href="../../_static/default.css" type="text/css" />
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
@@ -18,9 +18,8 @@
<link rel="index" title="Global index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
<link rel="top" title="yt v0.3 documentation" href="../../index.html" />
- <link rel="up" title="yt.lagos" href="index.html" />
- <link rel="next" title="yt.lagos" href="index.html" />
- <link rel="prev" title="yt.lagos" href="index.html" />
+ <link rel="up" title="yt.lagos - Data Handling and Analysis" href="index.html" />
+ <link rel="prev" title="Native Enzo Data Structures" href="outputandhierarchy.html" />
</head>
<body>
<div class="related">
@@ -28,13 +27,12 @@
<ul>
<li class="right" style="margin-right: 10px"><a href="../../genindex.html" title="General Index" accesskey="I">index</a></li>
<li class="right"><a href="../../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
- <li class="right"><a href="index.html" title="yt.lagos" accesskey="N">next</a> |</li>
- <li class="right"><a href="index.html" title="yt.lagos" accesskey="P">previous</a> |</li>
+ <li class="right"><a href="outputandhierarchy.html" title="Native Enzo Data Structures" accesskey="P">previous</a> |</li>
<li><a href="http://yt.spacepope.org/">yt</a> »</li>
<li><a href="../../index.html">yt v0.3 documentation</a> »</li>
- <li><a href="index.html" accesskey="U">yt.lagos</a> »</li>
+ <li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
</ul>
</div>
<div class="document">
@@ -44,154 +42,368 @@
<div class="section">
-<h1 id="module-lagos.BaseDataTypes"><tt class="xref docutils literal"><span class="pre">lagos.BaseDataTypes</span></tt> – Data Types<a class="headerlink" href="#module-lagos.BaseDataTypes" title="Permalink to this headline">¶</a></h1>
+<h1 id="data-containers">Data Containers<a class="headerlink" href="#data-containers" title="Permalink to this headline">¶</a></h1>
+<p>yt provides a number of data containers, defined such that they satisfy a
+logical need. Each of these provides only the finest-resolution cells, unless
+an option is available to restrict the levels from which they draw, as is the
+case with <a title="yt.lagos.EnzoCoveringGrid" class="reference" href="#yt.lagos.EnzoCoveringGrid"><tt class="xref docutils literal"><span class="pre">EnzoCoveringGrid</span></tt></a>.</p>
+<p>Each of these implements the same primary protocol - all data values can be
+access dictionary-style:</p>
+<div class="highlight"><pre><span class="gp">>>> </span><span class="nb">object</span><span class="p">[</span><span class="s">"Density"</span><span class="p">]</span>
+<span class="gp">>>> </span><span class="nb">object</span><span class="p">[</span><span class="s">"Density"</span><span class="p">]</span><span class="o">.</span><span class="n">max</span><span class="p">()</span>
+</pre></div>
+<p>And so on. For more information, see the
+<a class="reference" href="../../tutorial/basic_objects.html#basic-objects"><em>the tutorial topic</em></a> on basic objects.</p>
+<div class="section">
+<h2 id="base-containers">Base Containers<a class="headerlink" href="#base-containers" title="Permalink to this headline">¶</a></h2>
<dl class="class">
-<dt id="lagos.BaseDataTypes.EnzoData">
-<!--#lagos.BaseDataTypes.EnzoData#-->class <tt class="descclassname">lagos.BaseDataTypes.</tt><tt class="descname">EnzoData</tt><big>(</big><em>pf</em>, <em>fields</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoData" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.FakeGridForParticles">
+<!--#yt.lagos.FakeGridForParticles#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">FakeGridForParticles</tt><big>(</big><em>grid</em><big>)</big><a class="headerlink" href="#yt.lagos.FakeGridForParticles" title="Permalink to this definition">¶</a></dt>
+<dd>Mock up a grid to insert particle positions and radii
+into for purposes of confinement in an <a title="yt.lagos.Enzo3DData" class="reference" href="#yt.lagos.Enzo3DData"><tt class="xref docutils literal"><span class="pre">Enzo3DData</span></tt></a>.</dd></dl>
+
+<dl class="class">
+<dt id="yt.lagos.EnzoData">
+<!--#yt.lagos.EnzoData#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoData</tt><big>(</big><em>pf</em>, <em>fields</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoData" title="Permalink to this definition">¶</a></dt>
<dd><p>Generic EnzoData container. By itself, will attempt to
generate field, read fields (method defined by derived classes)
and deal with passing back and forth field parameters.</p>
+<p>Typically this is never called directly, but only due to inheritance.
+It associates a <tt class="xref docutils literal"><span class="pre">EnzoStaticOutput</span></tt> with the class,
+sets its initial set of fields, and the remainder of the arguments
+are passed as field_parameters.</p>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoData.clear_data">
-<!--#lagos.BaseDataTypes.EnzoData.clear_data#--><tt class="descname">clear_data</tt><big>(</big><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoData.clear_data" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.EnzoData.clear_data">
+<!--#yt.lagos.EnzoData.clear_data#--><tt class="descname">clear_data</tt><big>(</big><big>)</big><a class="headerlink" href="#yt.lagos.EnzoData.clear_data" title="Permalink to this definition">¶</a></dt>
<dd>Clears out all data from the EnzoData instance, freeing memory.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoData.get_field_parameter">
-<!--#lagos.BaseDataTypes.EnzoData.get_field_parameter#--><tt class="descname">get_field_parameter</tt><big>(</big><em>name</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoData.get_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.EnzoData.convert">
+<!--#yt.lagos.EnzoData.convert#--><tt class="descname">convert</tt><big>(</big><em>datatype</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoData.convert" title="Permalink to this definition">¶</a></dt>
+<dd>This will attempt to convert a given unit to cgs from code units.
+It either returns the multiplicative factor or throws a KeyError.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.EnzoData.get_field_parameter">
+<!--#yt.lagos.EnzoData.get_field_parameter#--><tt class="descname">get_field_parameter</tt><big>(</big><em>name</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoData.get_field_parameter" title="Permalink to this definition">¶</a></dt>
<dd>This is typically only used by derived field functions, but
it returns parameters used to generate fields.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoData.set_field_parameter">
-<!--#lagos.BaseDataTypes.EnzoData.set_field_parameter#--><tt class="descname">set_field_parameter</tt><big>(</big><em>name</em>, <em>val</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoData.set_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.EnzoData.has_field_parameter">
+<!--#yt.lagos.EnzoData.has_field_parameter#--><tt class="descname">has_field_parameter</tt><big>(</big><em>name</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoData.has_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dd>Checks if a field parameter is set.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.EnzoData.has_key">
+<!--#yt.lagos.EnzoData.has_key#--><tt class="descname">has_key</tt><big>(</big><em>key</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoData.has_key" title="Permalink to this definition">¶</a></dt>
+<dd>Checks if a data field already exists.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.EnzoData.set_field_parameter">
+<!--#yt.lagos.EnzoData.set_field_parameter#--><tt class="descname">set_field_parameter</tt><big>(</big><em>name</em>, <em>val</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoData.set_field_parameter" title="Permalink to this definition">¶</a></dt>
<dd>Here we set up dictionaries that get passed up and down and ultimately
to derived fields.</dd></dl>
</dd></dl>
<dl class="class">
-<dt id="lagos.BaseDataTypes.Enzo3DData">
-<!--#lagos.BaseDataTypes.Enzo3DData#-->class <tt class="descclassname">lagos.BaseDataTypes.</tt><tt class="descname">Enzo3DData</tt><big>(</big><em>center</em>, <em>fields</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.Enzo3DData" title="Permalink to this definition">¶</a></dt>
-<dd><p>Class describing a cluster of data points, not necessarily sharing any
-particular attribute.</p>
-<dl class="method">
-<dt id="lagos.BaseDataTypes.Enzo3DData.clear_data">
-<!--#lagos.BaseDataTypes.Enzo3DData.clear_data#--><tt class="descname">clear_data</tt><big>(</big><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.Enzo3DData.clear_data" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.Enzo1DData">
+<!--#yt.lagos.Enzo1DData#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">Enzo1DData</tt><big>(</big><em>pf</em>, <em>fields</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo1DData" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="method">
+<dt id="yt.lagos.Enzo1DData.clear_data">
+<!--#yt.lagos.Enzo1DData.clear_data#--><tt class="descname">clear_data</tt><big>(</big><big>)</big><a class="headerlink" href="#yt.lagos.Enzo1DData.clear_data" title="Permalink to this definition">¶</a></dt>
<dd>Clears out all data from the EnzoData instance, freeing memory.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.Enzo3DData.extract_connected_sets">
-<!--#lagos.BaseDataTypes.Enzo3DData.extract_connected_sets#--><tt class="descname">extract_connected_sets</tt><big>(</big><em>field</em>, <em>num_levels</em>, <em>min_val</em>, <em>max_val</em>, <em>log_space=True</em>, <em>cumulative=True</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.Enzo3DData.extract_connected_sets" title="Permalink to this definition">¶</a></dt>
-<dd>This function will create a set of contour objects, defined
-by having connected cell structures, which can then be
-studied and used to ‘paint’ their source grids, thus enabling
-them to be plotted.</dd></dl>
+<dt id="yt.lagos.Enzo1DData.convert">
+<!--#yt.lagos.Enzo1DData.convert#--><tt class="descname">convert</tt><big>(</big><em>datatype</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo1DData.convert" title="Permalink to this definition">¶</a></dt>
+<dd>This will attempt to convert a given unit to cgs from code units.
+It either returns the multiplicative factor or throws a KeyError.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo1DData.get_field_parameter">
+<!--#yt.lagos.Enzo1DData.get_field_parameter#--><tt class="descname">get_field_parameter</tt><big>(</big><em>name</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo1DData.get_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dd>This is typically only used by derived field functions, but
+it returns parameters used to generate fields.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo1DData.has_field_parameter">
+<!--#yt.lagos.Enzo1DData.has_field_parameter#--><tt class="descname">has_field_parameter</tt><big>(</big><em>name</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo1DData.has_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dd>Checks if a field parameter is set.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo1DData.has_key">
+<!--#yt.lagos.Enzo1DData.has_key#--><tt class="descname">has_key</tt><big>(</big><em>key</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo1DData.has_key" title="Permalink to this definition">¶</a></dt>
+<dd>Checks if a data field already exists.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo1DData.select_grids">
+<!--#yt.lagos.Enzo1DData.select_grids#--><tt class="descname">select_grids</tt><big>(</big><em>level</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo1DData.select_grids" title="Permalink to this definition">¶</a></dt>
+<dd>Return all grids on a given level.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.Enzo3DData.extract_region">
-<!--#lagos.BaseDataTypes.Enzo3DData.extract_region#--><tt class="descname">extract_region</tt><big>(</big><em>indices</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.Enzo3DData.extract_region" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return an ExtractedRegion where the points contained in it are defined
-as the points in <em>this</em> data object with the given indices</p>
-<p>@param indices: The indices of the points to keep
-@type indices: The return value of a numpy.where call</p>
+<dt id="yt.lagos.Enzo1DData.set_field_parameter">
+<!--#yt.lagos.Enzo1DData.set_field_parameter#--><tt class="descname">set_field_parameter</tt><big>(</big><em>name</em>, <em>val</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo1DData.set_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dd>Here we set up dictionaries that get passed up and down and ultimately
+to derived fields.</dd></dl>
+
</dd></dl>
+<dl class="class">
+<dt id="yt.lagos.Enzo2DData">
+<!--#yt.lagos.Enzo2DData#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">Enzo2DData</tt><big>(</big><em>axis</em>, <em>fields</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData" title="Permalink to this definition">¶</a></dt>
+<dd><p>Class to represent a set of <a title="yt.lagos.EnzoData" class="reference" href="#yt.lagos.EnzoData"><tt class="xref docutils literal"><span class="pre">EnzoData</span></tt></a> that’s 2-D in nature, and
+thus does not have as many actions as the 3-D data types.</p>
+<p>Prepares the Enzo2DData, normal to <em>axis</em>. If <em>axis</em> is 4, we are not
+aligned with any axis.</p>
+<dl class="method">
+<dt id="yt.lagos.Enzo2DData.clear_data">
+<!--#yt.lagos.Enzo2DData.clear_data#--><tt class="descname">clear_data</tt><big>(</big><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData.clear_data" title="Permalink to this definition">¶</a></dt>
+<dd>Clears out all data from the EnzoData instance, freeing memory.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo2DData.convert">
+<!--#yt.lagos.Enzo2DData.convert#--><tt class="descname">convert</tt><big>(</big><em>datatype</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData.convert" title="Permalink to this definition">¶</a></dt>
+<dd>This will attempt to convert a given unit to cgs from code units.
+It either returns the multiplicative factor or throws a KeyError.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo2DData.get_data">
+<!--#yt.lagos.Enzo2DData.get_data#--><tt class="descname">get_data</tt><big>(</big><em>fields=None</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData.get_data" title="Permalink to this definition">¶</a></dt>
+<dd>Iterates over the list of fields and generates/reads them all.</dd></dl>
+
<dl class="method">
-<dt id="lagos.BaseDataTypes.Enzo3DData.get_field_parameter">
-<!--#lagos.BaseDataTypes.Enzo3DData.get_field_parameter#--><tt class="descname">get_field_parameter</tt><big>(</big><em>name</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.Enzo3DData.get_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.Enzo2DData.get_field_parameter">
+<!--#yt.lagos.Enzo2DData.get_field_parameter#--><tt class="descname">get_field_parameter</tt><big>(</big><em>name</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData.get_field_parameter" title="Permalink to this definition">¶</a></dt>
<dd>This is typically only used by derived field functions, but
it returns parameters used to generate fields.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.Enzo3DData.paint_grids">
-<!--#lagos.BaseDataTypes.Enzo3DData.paint_grids#--><tt class="descname">paint_grids</tt><big>(</big><em>field</em>, <em>value</em>, <em>default_value=None</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.Enzo3DData.paint_grids" title="Permalink to this definition">¶</a></dt>
-<dd><p>This function paints every cell in our dataset with a given value.
-If default_value is given, the other values for the given in every grid
-are discarded and replaced with default_value. Otherwise, the field is
-mandated to ‘know how to exist’ in the grid.</p>
-<p>@note: This only paints the cells <em>in the dataset</em>, so cells in grids
-with children are left untouched.
-@param field: The field to paint
-@param value: The value to paint
-@keyword default_value: The value to use for all other cells. If ‘None’
-then no value is used, and the grid is left untouched except in our cells.</p>
-</dd></dl>
+<dt id="yt.lagos.Enzo2DData.has_field_parameter">
+<!--#yt.lagos.Enzo2DData.has_field_parameter#--><tt class="descname">has_field_parameter</tt><big>(</big><em>name</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData.has_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dd>Checks if a field parameter is set.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.Enzo3DData.select_grids">
-<!--#lagos.BaseDataTypes.Enzo3DData.select_grids#--><tt class="descname">select_grids</tt><big>(</big><em>level</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.Enzo3DData.select_grids" title="Permalink to this definition">¶</a></dt>
-<dd>Select all grids on a given level.</dd></dl>
+<dt id="yt.lagos.Enzo2DData.has_key">
+<!--#yt.lagos.Enzo2DData.has_key#--><tt class="descname">has_key</tt><big>(</big><em>key</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData.has_key" title="Permalink to this definition">¶</a></dt>
+<dd>Checks if a data field already exists.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.Enzo3DData.set_field_parameter">
-<!--#lagos.BaseDataTypes.Enzo3DData.set_field_parameter#--><tt class="descname">set_field_parameter</tt><big>(</big><em>name</em>, <em>val</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.Enzo3DData.set_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.Enzo2DData.interpolate_discretize">
+<!--#yt.lagos.Enzo2DData.interpolate_discretize#--><tt class="descname">interpolate_discretize</tt><big>(</big><em>LE</em>, <em>RE</em>, <em>field</em>, <em>side</em>, <em>log_spacing=True</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData.interpolate_discretize" title="Permalink to this definition">¶</a></dt>
+<dd>This returns a uniform grid of points between <em>LE</em> and <em>RE</em>,
+interpolated using the nearest neighbor method, with <em>side</em> points on a
+side.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo2DData.select_grids">
+<!--#yt.lagos.Enzo2DData.select_grids#--><tt class="descname">select_grids</tt><big>(</big><em>level</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData.select_grids" title="Permalink to this definition">¶</a></dt>
+<dd>Return all grids on a given level.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo2DData.set_field_parameter">
+<!--#yt.lagos.Enzo2DData.set_field_parameter#--><tt class="descname">set_field_parameter</tt><big>(</big><em>name</em>, <em>val</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo2DData.set_field_parameter" title="Permalink to this definition">¶</a></dt>
<dd>Here we set up dictionaries that get passed up and down and ultimately
to derived fields.</dd></dl>
</dd></dl>
<dl class="class">
-<dt id="lagos.BaseDataTypes.EnzoSphereBase">
-<!--#lagos.BaseDataTypes.EnzoSphereBase#-->class <tt class="descclassname">lagos.BaseDataTypes.</tt><tt class="descname">EnzoSphereBase</tt><big>(</big><em>center</em>, <em>radius</em>, <em>fields=None</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoSphereBase" title="Permalink to this definition">¶</a></dt>
-<dd><p>A sphere of points</p>
+<dt id="yt.lagos.Enzo3DData">
+<!--#yt.lagos.Enzo3DData#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">Enzo3DData</tt><big>(</big><em>center</em>, <em>fields</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData" title="Permalink to this definition">¶</a></dt>
+<dd><p>Class describing a cluster of data points, not necessarily sharing any
+particular attribute.</p>
+<p>Returns an instance of Enzo3DData, or prepares one. Usually only
+used as a base class. Note that <em>center</em> is supplied, but only used
+for fields and quantities that require it.</p>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoSphereBase.clear_data">
-<!--#lagos.BaseDataTypes.EnzoSphereBase.clear_data#--><tt class="descname">clear_data</tt><big>(</big><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoSphereBase.clear_data" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.Enzo3DData.clear_data">
+<!--#yt.lagos.Enzo3DData.clear_data#--><tt class="descname">clear_data</tt><big>(</big><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.clear_data" title="Permalink to this definition">¶</a></dt>
<dd>Clears out all data from the EnzoData instance, freeing memory.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoSphereBase.extract_connected_sets">
-<!--#lagos.BaseDataTypes.EnzoSphereBase.extract_connected_sets#--><tt class="descname">extract_connected_sets</tt><big>(</big><em>field</em>, <em>num_levels</em>, <em>min_val</em>, <em>max_val</em>, <em>log_space=True</em>, <em>cumulative=True</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoSphereBase.extract_connected_sets" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.Enzo3DData.convert">
+<!--#yt.lagos.Enzo3DData.convert#--><tt class="descname">convert</tt><big>(</big><em>datatype</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.convert" title="Permalink to this definition">¶</a></dt>
+<dd>This will attempt to convert a given unit to cgs from code units.
+It either returns the multiplicative factor or throws a KeyError.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo3DData.extract_connected_sets">
+<!--#yt.lagos.Enzo3DData.extract_connected_sets#--><tt class="descname">extract_connected_sets</tt><big>(</big><em>field</em>, <em>num_levels</em>, <em>min_val</em>, <em>max_val</em>, <em>log_space=True</em>, <em>cumulative=True</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.extract_connected_sets" title="Permalink to this definition">¶</a></dt>
<dd>This function will create a set of contour objects, defined
by having connected cell structures, which can then be
studied and used to ‘paint’ their source grids, thus enabling
them to be plotted.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoSphereBase.extract_region">
-<!--#lagos.BaseDataTypes.EnzoSphereBase.extract_region#--><tt class="descname">extract_region</tt><big>(</big><em>indices</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoSphereBase.extract_region" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return an ExtractedRegion where the points contained in it are defined
-as the points in <em>this</em> data object with the given indices</p>
-<p>@param indices: The indices of the points to keep
-@type indices: The return value of a numpy.where call</p>
-</dd></dl>
+<dt id="yt.lagos.Enzo3DData.extract_region">
+<!--#yt.lagos.Enzo3DData.extract_region#--><tt class="descname">extract_region</tt><big>(</big><em>indices</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.extract_region" title="Permalink to this definition">¶</a></dt>
+<dd>Return an ExtractedRegion where the points contained in it are defined
+as the points in <cite>this</cite> data object with the given <em>indices</em>.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoSphereBase.get_field_parameter">
-<!--#lagos.BaseDataTypes.EnzoSphereBase.get_field_parameter#--><tt class="descname">get_field_parameter</tt><big>(</big><em>name</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoSphereBase.get_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.Enzo3DData.get_field_parameter">
+<!--#yt.lagos.Enzo3DData.get_field_parameter#--><tt class="descname">get_field_parameter</tt><big>(</big><em>name</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.get_field_parameter" title="Permalink to this definition">¶</a></dt>
<dd>This is typically only used by derived field functions, but
it returns parameters used to generate fields.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoSphereBase.paint_grids">
-<!--#lagos.BaseDataTypes.EnzoSphereBase.paint_grids#--><tt class="descname">paint_grids</tt><big>(</big><em>field</em>, <em>value</em>, <em>default_value=None</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoSphereBase.paint_grids" title="Permalink to this definition">¶</a></dt>
-<dd><p>This function paints every cell in our dataset with a given value.
+<dt id="yt.lagos.Enzo3DData.has_field_parameter">
+<!--#yt.lagos.Enzo3DData.has_field_parameter#--><tt class="descname">has_field_parameter</tt><big>(</big><em>name</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.has_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dd>Checks if a field parameter is set.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo3DData.has_key">
+<!--#yt.lagos.Enzo3DData.has_key#--><tt class="descname">has_key</tt><big>(</big><em>key</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.has_key" title="Permalink to this definition">¶</a></dt>
+<dd>Checks if a data field already exists.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.Enzo3DData.paint_grids">
+<!--#yt.lagos.Enzo3DData.paint_grids#--><tt class="descname">paint_grids</tt><big>(</big><em>field</em>, <em>value</em>, <em>default_value=None</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.paint_grids" title="Permalink to this definition">¶</a></dt>
+<dd><p>This function paints every cell in our dataset with a given <em>value</em>.
If default_value is given, the other values for the given in every grid
-are discarded and replaced with default_value. Otherwise, the field is
+are discarded and replaced with <em>default_value</em>. Otherwise, the field is
mandated to ‘know how to exist’ in the grid.</p>
-<p>@note: This only paints the cells <em>in the dataset</em>, so cells in grids
-with children are left untouched.
-@param field: The field to paint
-@param value: The value to paint
-@keyword default_value: The value to use for all other cells. If ‘None’
-then no value is used, and the grid is left untouched except in our cells.</p>
+<p>Note that this only paints the cells <em>in the dataset</em>, so cells in grids
+with child cells are left untouched.</p>
</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoSphereBase.select_grids">
-<!--#lagos.BaseDataTypes.EnzoSphereBase.select_grids#--><tt class="descname">select_grids</tt><big>(</big><em>level</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoSphereBase.select_grids" title="Permalink to this definition">¶</a></dt>
-<dd>Select all grids on a given level.</dd></dl>
+<dt id="yt.lagos.Enzo3DData.select_grids">
+<!--#yt.lagos.Enzo3DData.select_grids#--><tt class="descname">select_grids</tt><big>(</big><em>level</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.select_grids" title="Permalink to this definition">¶</a></dt>
+<dd>Return all grids on a given level.</dd></dl>
<dl class="method">
-<dt id="lagos.BaseDataTypes.EnzoSphereBase.set_field_parameter">
-<!--#lagos.BaseDataTypes.EnzoSphereBase.set_field_parameter#--><tt class="descname">set_field_parameter</tt><big>(</big><em>name</em>, <em>val</em><big>)</big><a class="headerlink" href="#lagos.BaseDataTypes.EnzoSphereBase.set_field_parameter" title="Permalink to this definition">¶</a></dt>
+<dt id="yt.lagos.Enzo3DData.set_field_parameter">
+<!--#yt.lagos.Enzo3DData.set_field_parameter#--><tt class="descname">set_field_parameter</tt><big>(</big><em>name</em>, <em>val</em><big>)</big><a class="headerlink" href="#yt.lagos.Enzo3DData.set_field_parameter" title="Permalink to this definition">¶</a></dt>
<dd>Here we set up dictionaries that get passed up and down and ultimately
to derived fields.</dd></dl>
</dd></dl>
</div>
+<div class="section">
+<h2 id="d-data-containers">1D Data Containers<a class="headerlink" href="#d-data-containers" title="Permalink to this headline">¶</a></h2>
+<p>Each of these inherits from <a title="yt.lagos.Enzo1DData" class="reference" href="#yt.lagos.Enzo1DData"><tt class="xref docutils literal"><span class="pre">Enzo1DData</span></tt></a>, and so has all the
+member functions defined there.</p>
+<dl class="class">
+<dt id="yt.lagos.EnzoOrthoRayBase">
+<!--#yt.lagos.EnzoOrthoRayBase#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoOrthoRayBase</tt><big>(</big><em>axis</em>, <em>coords</em>, <em>fields=None</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoOrthoRayBase" title="Permalink to this definition">¶</a></dt>
+<dd>Dimensionality is reduced to one, and an ordered list of points at an
+(x,y) tuple along <em>axis</em> are available.</dd></dl>
+
+</div>
+<div class="section">
+<h2 id="id1">2D Data Containers<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
+<dl class="class">
+<dt id="yt.lagos.EnzoSliceBase">
+<!--#yt.lagos.EnzoSliceBase#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoSliceBase</tt><big>(</big><em>axis</em>, <em>coord</em>, <em>fields=None</em>, <em>center=None</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoSliceBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>EnzoSlice is an orthogonal slice through the data, taking all the points
+at the finest resolution available and then indexing them. It is more
+appropriately thought of as a slice ‘operator’ than an object,
+however, as its field and coordinate can both change.</p>
+<p>Slice along <em>axis</em><a class="reference" href="../../faq.html#axis-specification"><em>How do I specify an axis?</em></a>, at the coordinate <em>coord</em>.
+Optionally supply fields.</p>
+<dl class="method">
+<dt id="yt.lagos.EnzoSliceBase.reslice">
+<!--#yt.lagos.EnzoSliceBase.reslice#--><tt class="descname">reslice</tt><big>(</big><em>coord</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoSliceBase.reslice" title="Permalink to this definition">¶</a></dt>
+<dd>Change the entire dataset, clearing out the current data and slicing at
+a new location. Not terribly useful except for in-place plot changes.</dd></dl>
+
+<dl class="method">
+<dt id="yt.lagos.EnzoSliceBase.shift">
+<!--#yt.lagos.EnzoSliceBase.shift#--><tt class="descname">shift</tt><big>(</big><em>val</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoSliceBase.shift" title="Permalink to this definition">¶</a></dt>
+<dd>Moves the slice coordinate up by either a floating point value, or an
+integer number of indices of the finest grid.</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="yt.lagos.EnzoCuttingPlaneBase">
+<!--#yt.lagos.EnzoCuttingPlaneBase#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoCuttingPlaneBase</tt><big>(</big><em>normal</em>, <em>center</em>, <em>fields=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoCuttingPlaneBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>EnzoCuttingPlane is an oblique plane through the data,
+defined by a normal vector and a coordinate. It attempts to guess
+an ‘up’ vector, which cannot be overridden, and then it pixelizes
+the appropriate data onto the plane without interpolation.</p>
+<p>The Cutting Plane slices at an oblique angle, where we use
+the <em>normal</em> vector and the <em>center</em> to define the viewing plane.
+The ‘up’ direction is guessed at automatically.</p>
+</dd></dl>
+
+<dl class="class">
+<dt id="yt.lagos.EnzoProjBase">
+<!--#yt.lagos.EnzoProjBase#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoProjBase</tt><big>(</big><em>axis</em>, <em>field</em>, <em>weight_field=None</em>, <em>max_level=None</em>, <em>center=None</em>, <em>pf=None</em>, <em>source=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoProjBase" title="Permalink to this definition">¶</a></dt>
+<dd>EnzoProj is a projection of a <em>field</em> along an <em>axis</em>. The field
+can have an associated <em>weight_field</em>, in which case the values are
+multiplied by a weight before being summed, and then divided by the sum
+of that weight.</dd></dl>
+
+</div>
+<div class="section">
+<h2 id="id2">3D Data Containers<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h2>
+<dl class="class">
+<dt id="yt.lagos.EnzoSphereBase">
+<!--#yt.lagos.EnzoSphereBase#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoSphereBase</tt><big>(</big><em>center</em>, <em>radius</em>, <em>fields=None</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoSphereBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>A sphere of points</p>
+<p>The most famous of all the data objects, we define it via a
+<em>center</em> and a <em>radius</em>.</p>
+</dd></dl>
+
+<dl class="class">
+<dt id="yt.lagos.EnzoRegionBase">
+<!--#yt.lagos.EnzoRegionBase#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoRegionBase</tt><big>(</big><em>center</em>, <em>left_edge</em>, <em>right_edge</em>, <em>fields=None</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoRegionBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>EnzoRegions are rectangular prisms of data.</p>
+<p>We create an object with a set of three <em>left_edge</em> coordinates,
+three <em>right_edge</em> coordinates, and a <em>center</em> that need not be the
+center.</p>
+</dd></dl>
+
+<dl class="class">
+<dt id="yt.lagos.EnzoCylinderBase">
+<!--#yt.lagos.EnzoCylinderBase#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoCylinderBase</tt><big>(</big><em>center</em>, <em>normal</em>, <em>radius</em>, <em>height</em>, <em>fields=None</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoCylinderBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>We can define a cylinder (or disk) to act as a data object.</p>
+<p>By providing a <em>center</em>, a <em>normal</em>, a <em>radius</em> and a <em>height</em> we
+can define a cylinder of any proportion. Only cells whose centers are
+within the cylinder will be selected.</p>
+</dd></dl>
+
+<dl class="class">
+<dt id="yt.lagos.EnzoGridCollection">
+<!--#yt.lagos.EnzoGridCollection#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoGridCollection</tt><big>(</big><em>center</em>, <em>grid_list</em>, <em>fields=None</em>, <em>connection_pool=True</em>, <em>pf=None</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoGridCollection" title="Permalink to this definition">¶</a></dt>
+<dd><p>An arbitrary selection of grids, within which we accept all points.</p>
+<p>By selecting an arbitrary <em>grid_list</em>, we can act on those grids.
+Child cells are not returned.</p>
+</dd></dl>
+
+<dl class="class">
+<dt id="yt.lagos.EnzoCoveringGrid">
+<!--#yt.lagos.EnzoCoveringGrid#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">EnzoCoveringGrid</tt><big>(</big><em>level</em>, <em>left_edge</em>, <em>right_edge</em>, <em>dims</em>, <em>fields=None</em>, <em>pf=None</em>, <em>num_ghost_zones=0</em>, <em>use_pbar=True</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoCoveringGrid" title="Permalink to this definition">¶</a></dt>
+<dd><p>Covering grids represent fixed-resolution data over a given region.
+In order to achieve this goal – for instance in order to obtain ghost
+zones – grids up to and including the indicated level are included.
+No interpolation is done (as that would affect the ‘power’ on small
+scales) on the input data.</p>
+<p>The data object returned will consider grids up to <em>level</em> in
+generating fixed resolution data between <em>left_edge</em> and <em>right_edge</em>
+that is <em>dims</em> (3-values) on a side.</p>
+<dl class="method">
+<dt id="yt.lagos.EnzoCoveringGrid.flush_data">
+<!--#yt.lagos.EnzoCoveringGrid.flush_data#--><tt class="descname">flush_data</tt><big>(</big><em>field=None</em><big>)</big><a class="headerlink" href="#yt.lagos.EnzoCoveringGrid.flush_data" title="Permalink to this definition">¶</a></dt>
+<dd>Any modifications made to the data in this object are pushed back
+to the originating grids, except the cells where those grids are both
+below the current level <cite>and</cite> have child cells.</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="yt.lagos.ExtractedRegionBase">
+<!--#yt.lagos.ExtractedRegionBase#-->class <tt class="descclassname">yt.lagos.</tt><tt class="descname">ExtractedRegionBase</tt><big>(</big><em>base_region</em>, <em>indices</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#yt.lagos.ExtractedRegionBase" title="Permalink to this definition">¶</a></dt>
+<dd>ExtractedRegions are arbitrarily defined containers of data, useful
+for things like selection along a baryon field.</dd></dl>
+
+</div>
+</div>
</div>
@@ -199,17 +411,26 @@
</div>
<div class="sidebar">
<div class="sidebarwrapper">
+ <h3>Table Of Contents</h3>
+ <ul>
+<li><a class="reference" href="">Data Containers</a><ul>
+<li><a class="reference" href="#base-containers">Base Containers</a></li>
+<li><a class="reference" href="#d-data-containers">1D Data Containers</a></li>
+<li><a class="reference" href="#id1">2D Data Containers</a></li>
+<li><a class="reference" href="#id2">3D Data Containers</a></li>
+</ul>
+</li>
+</ul>
+
<h4>Previous topic</h4>
- <p class="topless"><a href="index.html" title="previous chapter">yt.lagos</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="index.html" title="next chapter">yt.lagos</a></p>
+ <p class="topless"><a href="outputandhierarchy.html" title="previous chapter">Native Enzo Data Structures</a></p>
<h3>This Page</h3>
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@@ -222,18 +443,17 @@
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- <li><a href="index.html" accesskey="U">yt.lagos</a> »</li>
+ <li><a href="index.html" accesskey="U">yt.lagos - Data Handling and Analysis</a> »</li>
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- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
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--- trunk/doc/build/html/modules/lagos/index.html (original)
+++ trunk/doc/build/html/modules/lagos/index.html Sat May 10 23:00:13 2008
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-<h1 id="yt-lagos"><span id="lagos"></span>yt.lagos<a class="headerlink" href="#yt-lagos" title="Permalink to this headline">¶</a></h1>
+<h1 id="module-yt.lagos"><span id="lagos"></span>yt.lagos - Data Handling and Analysis<a class="headerlink" href="#module-yt.lagos" title="Permalink to this headline">¶</a></h1>
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+<li><a class="reference" href="outputandhierarchy.html">Native Enzo Data Structures</a></li>
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+<h1 id="native-enzo-data-structures">Native Enzo Data Structures<a class="headerlink" href="#native-enzo-data-structures" title="Permalink to this headline">¶</a></h1>
+<dl class="class">
+<dt id="EnzoStaticOutput">
+<!--#EnzoStaticOutput#-->class <tt class="descname">EnzoStaticOutput</tt><big>(</big><em>filename</em>, <em>data_style=None</em><big>)</big><a class="headerlink" href="#EnzoStaticOutput" title="Permalink to this definition">¶</a></dt>
+<dd><p>This class is a stripped down class that simply reads and parses, without
+looking at the hierarchy.</p>
+<dl class="docutils">
+<dt>@todo: Move some of the parameters to the EnzoRun?</dt>
+<dd>Maybe it is just more appropriate to think of time series data and
+single-time data?</dd>
+</dl>
+<p>@param filename: The filename of the parameterfile we want to load
+@type filename: String</p>
+</dd></dl>
+
+<dl class="class">
+<dt id="EnzoHierarchy">
+<!--#EnzoHierarchy#-->class <tt class="descname">EnzoHierarchy</tt><big>(</big><em>pf</em>, <em>data_style=None</em><big>)</big><a class="headerlink" href="#EnzoHierarchy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Class for handling Enzo timestep outputs</p>
+<p>@param pf: The OutputFile we’re instantiating from
+@type pf: L{EnzoOutput}
+@keyword data_style: The type of Enzo Output we’re going to read from –</p>
+<div class="system-message">
+<p class="system-message-title">System Message: ERROR/3 (<tt class="docutils"><docstring of yt.lagos.EnzoHierarchy></tt>, line 7)</p>
+Unexpected indentation.</div>
+<blockquote>
+4 : hdf4, 5 : hdf5, 6 : packed HDF5</blockquote>
+<div class="system-message">
+<p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">/Users/matthewturk/Development/yt/trunk/doc/source/modules/lagos/outputandhierarchy.rst</tt>, line 19)</p>
+Block quote ends without a blank line; unexpected unindent.</div>
+<p>@type data_style: int</p>
+<dl class="method">
+<dt id="EnzoHierarchy.export_amira">
+<!--#EnzoHierarchy.export_amira#--><tt class="descname">export_amira</tt><big>(</big><em>basename</em>, <em>fields</em>, <em>a5basename</em>, <em>timestep</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.export_amira" title="Permalink to this definition">¶</a></dt>
+<dd>Exports the grid structure in partiview text format.</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.export_boxes_pv">
+<!--#EnzoHierarchy.export_boxes_pv#--><tt class="descname">export_boxes_pv</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.export_boxes_pv" title="Permalink to this definition">¶</a></dt>
+<dd><p>Exports the grid structure in partiview text format.</p>
+<p>@arg filename: File to export to.
+@type filename: String</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.export_particles_pb">
+<!--#EnzoHierarchy.export_particles_pb#--><tt class="descname">export_particles_pb</tt><big>(</big><em>filename</em>, <em>filter=1</em>, <em>indexboundary=0</em>, <em>fields=None</em>, <em>scale=1.0</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.export_particles_pb" title="Permalink to this definition">¶</a></dt>
+<dd><p>Exports all the star particles, or a subset, to a pb file for viewing in
+partiview</p>
+<p>@param filename: filename of the .pb file to create
+@type filename: string
+@keyword filter: the particle type you want to get (assumes 1)
+@type filter: integer
+@keyword fields: the fields you want to snag. If not supplied, it just</p>
+<div class="system-message">
+<p class="system-message-title">System Message: ERROR/3 (<tt class="docutils"><docstring of yt.lagos.EnzoHierarchy.export_particles_pb></tt>, line 10)</p>
+Unexpected indentation.</div>
+<blockquote>
+grabs the position and index.</blockquote>
+<div class="system-message">
+<p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">/Users/matthewturk/Development/yt/trunk/doc/source/modules/lagos/outputandhierarchy.rst</tt>, line 46)</p>
+Block quote ends without a blank line; unexpected unindent.</div>
+<dl class="docutils">
+<dt>@keyword indexboundary: for those who want to discriminate the</dt>
+<dd>particles with particle index</dd>
+</dl>
+<div class="system-message">
+<p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">/Users/matthewturk/Development/yt/trunk/doc/source/modules/lagos/outputandhierarchy.rst</tt>, line 48)</p>
+Definition list ends without a blank line; unexpected unindent.</div>
+<p>@type indexboundary: integer
+@keyword scale: the factor to multiply the position by (defaults to 1.0)
+@type scale: float</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.findMax">
+<!--#EnzoHierarchy.findMax#--><tt class="descname">findMax</tt><big>(</big><em>field</em>, <em>finestLevels=1</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.findMax" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns value, center of location of maximum for a given field</p>
+<p>Arguments:
+@param field: field (derived or otherwise) of which to look for maximum
+@keyword finestLevels: whether or not to search NUMTOCHECK finest levels
+@type finestLevels: boolean</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.find_max">
+<!--#EnzoHierarchy.find_max#--><tt class="descname">find_max</tt><big>(</big><em>field</em>, <em>finestLevels=1</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.find_max" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns value, center of location of maximum for a given field</p>
+<p>Arguments:
+@param field: field (derived or otherwise) of which to look for maximum
+@keyword finestLevels: whether or not to search NUMTOCHECK finest levels
+@type finestLevels: boolean</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.find_min">
+<!--#EnzoHierarchy.find_min#--><tt class="descname">find_min</tt><big>(</big><em>field</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.find_min" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns value, center of location of minimum for a given field</p>
+<p>Arguments:
+@param field: field (derived or otherwise) of which to look for maximum</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.find_point">
+<!--#EnzoHierarchy.find_point#--><tt class="descname">find_point</tt><big>(</big><em>coord</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.find_point" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the objects, indices of grids containing a point</p>
+<p>@param coord: three floats
+@type coord: tuple of floats</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.find_ray_grids">
+<!--#EnzoHierarchy.find_ray_grids#--><tt class="descname">find_ray_grids</tt><big>(</big><em>coord</em>, <em>axis</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.find_ray_grids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the objects, indices of grids that a ray intersects</p>
+<p>@param coord: the ray endpoint
+@type coord: tuple of floats
+@param axis: the axis the ray travels parallel to
+@type axis: integer</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.find_slice_grids">
+<!--#EnzoHierarchy.find_slice_grids#--><tt class="descname">find_slice_grids</tt><big>(</big><em>coord</em>, <em>axis</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.find_slice_grids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the objects, indices of grids that a slice intersects</p>
+<p>@param coord: three floats
+@type coord: tuple of floats
+@param axis: the axis the slice is through
+@type axis: integer</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.find_sphere_grids">
+<!--#EnzoHierarchy.find_sphere_grids#--><tt class="descname">find_sphere_grids</tt><big>(</big><em>center</em>, <em>radius</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.find_sphere_grids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns objects, indices of grids within a sphere</p>
+<p>@param center: coordinate of center
+@type center: tuple of floats
+@param radius: the radius of the sphere in code units!</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.get_box_grids">
+<!--#EnzoHierarchy.get_box_grids#--><tt class="descname">get_box_grids</tt><big>(</big><em>leftEdge</em>, <em>rightEdge</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.get_box_grids" title="Permalink to this definition">¶</a></dt>
+<dd><p>Gets back all the grids between a left edge and right edge</p>
+<p>@param leftEdge: the left edge
+@type leftEdge: array
+@param rightEdge: the right edge
+@type rightEdge: array</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.get_smallest_dx">
+<!--#EnzoHierarchy.get_smallest_dx#--><tt class="descname">get_smallest_dx</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzoHierarchy.get_smallest_dx" title="Permalink to this definition">¶</a></dt>
+<dd>Returns (in code units) the smallest dx in the simulation.</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.initialize_enzo_interface">
+<!--#EnzoHierarchy.initialize_enzo_interface#--><tt class="descname">initialize_enzo_interface</tt><big>(</big><em>idt_val=0.0</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.initialize_enzo_interface" title="Permalink to this definition">¶</a></dt>
+<dd><p>Here we start up the SWIG interface, grabbing what we need from it.</p>
+<dl class="docutils">
+<dt>@keyword idt_val: the initialdt fed to ReadParameterFile (doesn’t need</dt>
+<dd>to be set)</dd>
+</dl>
+<div class="system-message">
+<p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">/Users/matthewturk/Development/yt/trunk/doc/source/modules/lagos/outputandhierarchy.rst</tt>, line 139)</p>
+Definition list ends without a blank line; unexpected unindent.</div>
+<p>@type idt_val: float</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.print_stats">
+<!--#EnzoHierarchy.print_stats#--><tt class="descname">print_stats</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzoHierarchy.print_stats" title="Permalink to this definition">¶</a></dt>
+<dd>Prints out relevant information about the simulation</dd></dl>
+
+<dl class="method">
+<dt id="EnzoHierarchy.save_data">
+<!--#EnzoHierarchy.save_data#--><tt class="descname">save_data</tt><big>(</big><em>array</em>, <em>node</em>, <em>name</em><big>)</big><a class="headerlink" href="#EnzoHierarchy.save_data" title="Permalink to this definition">¶</a></dt>
+<dd>Arbitrary numpy data will be saved to the region in the datafile
+described by node and name.
+@arg array: The data to be saved.
+@type array: NumPy array
+@arg node: The HDF5 node to save to
+@type node: String
+@arg name: Name of the array in the file
+@type name: String</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="EnzoGridBase">
+<!--#EnzoGridBase#-->class <tt class="descname">EnzoGridBase</tt><big>(</big><em>id</em>, <em>filename=None</em>, <em>hierarchy=None</em><big>)</big><a class="headerlink" href="#EnzoGridBase" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an instance of EnzoGrid</p>
+<p>@param hierarchy: EnzoHierarchy, parent hierarchy
+@type hierarchy: L{EnzoHierarchy<EnzoHierarchy>}
+@param id: grid ID (NOT index, which is ID-1)
+@type id: int
+@keyword filename: filename holding grid data
+@type filename: string</p>
+<dl class="method">
+<dt id="EnzoGridBase.clear_all">
+<!--#EnzoGridBase.clear_all#--><tt class="descname">clear_all</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzoGridBase.clear_all" title="Permalink to this definition">¶</a></dt>
+<dd>Clears all datafields from memory.</dd></dl>
+
+<dl class="method">
+<dt id="EnzoGridBase.clear_derived_quantities">
+<!--#EnzoGridBase.clear_derived_quantities#--><tt class="descname">clear_derived_quantities</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzoGridBase.clear_derived_quantities" title="Permalink to this definition">¶</a></dt>
+<dd>Clears coordinates, child_indices, child_mask.</dd></dl>
+
+<dl class="method">
+<dt id="EnzoGridBase.find_max">
+<!--#EnzoGridBase.find_max#--><tt class="descname">find_max</tt><big>(</big><em>field</em><big>)</big><a class="headerlink" href="#EnzoGridBase.find_max" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns value, coordinate of maximum value in this gird</p>
+<p>@param field: field to check
+@type field: string</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoGridBase.find_min">
+<!--#EnzoGridBase.find_min#--><tt class="descname">find_min</tt><big>(</big><em>field</em><big>)</big><a class="headerlink" href="#EnzoGridBase.find_min" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns value, coordinate of minimum value in this gird</p>
+<p>@param field: field to check
+@type field: string</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="EnzoGridBase.get_data">
+<!--#EnzoGridBase.get_data#--><tt class="descname">get_data</tt><big>(</big><em>field</em><big>)</big><a class="headerlink" href="#EnzoGridBase.get_data" title="Permalink to this definition">¶</a></dt>
+<dd>Returns a field or set of fields for a key or set of keys</dd></dl>
+
+<dl class="method">
+<dt id="EnzoGridBase.get_enzo_grid">
+<!--#EnzoGridBase.get_enzo_grid#--><tt class="descname">get_enzo_grid</tt><big>(</big><big>)</big><a class="headerlink" href="#EnzoGridBase.get_enzo_grid" title="Permalink to this definition">¶</a></dt>
+<dd>This attempts to get an instance of this particular grid from the SWIG
+interface. Note that it first checks to see if the ParameterFile has
+been instantiated.</dd></dl>
+
+<dl class="method">
+<dt id="EnzoGridBase.get_position">
+<!--#EnzoGridBase.get_position#--><tt class="descname">get_position</tt><big>(</big><em>coord</em><big>)</big><a class="headerlink" href="#EnzoGridBase.get_position" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns position of a coordinate</p>
+<p>@param coord: position to check
+@type coord: array of floats</p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Previous topic</h4>
+ <p class="topless"><a href="index.html" title="previous chapter">yt.lagos</a></p>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="basedatatypes.html" title="next chapter">Data Containers</a></p>
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../../_sources/modules/lagos/outputandhierarchy.txt">Show Source</a></li>
+ </ul>
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+ <form class="search" action="../../search.html" method="get">
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+ <input type="hidden" name="area" value="default" />
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+ © Copyright 2008, Matthew Turk.
+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Added: trunk/doc/build/html/modules/lagos/profiles.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/modules/lagos/profiles.html Sat May 10 23:00:13 2008
@@ -0,0 +1,85 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title> — yt v0.3 documentation</title>
+ <link rel="stylesheet" href="../../_static/default.css" type="text/css" />
+ <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: '../../',
+ VERSION: '0.3'
+ };
+ </script>
+ <script type="text/javascript" src="../../_static/jquery.js"></script>
+ <script type="text/javascript" src="../../_static/interface.js"></script>
+ <script type="text/javascript" src="../../_static/doctools.js"></script>
+ <link rel="contents" title="Global table of contents" href="../../contents.html" />
+ <link rel="index" title="Global index" href="../../genindex.html" />
+ <link rel="search" title="Search" href="../../search.html" />
+ <link rel="top" title="yt v0.3 documentation" href="../../index.html" />
+ <link rel="up" title="yt.lagos" href="index.html" />
+ <link rel="next" title="yt.lagos" href="index.html" />
+ </head>
+ <body>
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+ <h3>Navigation</h3>
+ <ul>
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+ <li class="right"><a href="index.html" title="yt.lagos" accesskey="N">next</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">yt.lagos</a> »</li>
+ </ul>
+ </div>
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
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+ </div>
+ <div class="sidebar">
+ <div class="sidebarwrapper">
+ <h4>Next topic</h4>
+ <p class="topless"><a href="index.html" title="next chapter">yt.lagos</a></p>
+ <h3>This Page</h3>
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+ <li><a href="../../_sources/modules/lagos/profiles.txt">Show Source</a></li>
+ </ul>
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+ <form class="search" action="../../search.html" method="get">
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+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="related">
+ <h3>Navigation</h3>
+ <ul>
+ <li class="right" style="margin-right: 10px"><a href="../../genindex.html" title="General Index" accesskey="I">index</a></li>
+ <li class="right"><a href="../../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
+ <li class="right"><a href="index.html" title="yt.lagos" accesskey="N">next</a> |</li>
+ <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+
+ <li><a href="../../index.html">yt v0.3 documentation</a> »</li>
+
+ <li><a href="index.html" accesskey="U">yt.lagos</a> »</li>
+ </ul>
+ </div>
+ <div class="footer">
+ © Copyright 2008, Matthew Turk.
+ Last updated on May 09, 2008.
+ </div>
+ </body>
+</html>
\ No newline at end of file
Modified: trunk/doc/build/html/modules/raven/index.html
==============================================================================
--- trunk/doc/build/html/modules/raven/index.html (original)
+++ trunk/doc/build/html/modules/raven/index.html Sat May 10 23:00:13 2008
@@ -54,7 +54,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -76,7 +76,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/modules/reason/index.html
==============================================================================
--- trunk/doc/build/html/modules/reason/index.html (original)
+++ trunk/doc/build/html/modules/reason/index.html Sat May 10 23:00:13 2008
@@ -54,7 +54,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -76,7 +76,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/search.html
==============================================================================
--- trunk/doc/build/html/search.html (original)
+++ trunk/doc/build/html/search.html Sat May 10 23:00:13 2008
@@ -76,7 +76,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/searchindex.json
==============================================================================
--- trunk/doc/build/html/searchindex.json (original)
+++ trunk/doc/build/html/searchindex.json Sat May 10 23:00:13 2008
@@ -1 +1 @@
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\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/advanced_objects.html
==============================================================================
--- trunk/doc/build/html/tutorial/advanced_objects.html (original)
+++ trunk/doc/build/html/tutorial/advanced_objects.html Sat May 10 23:00:13 2008
@@ -51,7 +51,7 @@
profile them, all of that, right from the command line like you would a sphere
or a region.</p>
<div class="section">
-<h2 id="cutting-plane"><span id="index-18"></span>Cutting Plane<a class="headerlink" href="#cutting-plane" title="Permalink to this headline">¶</a></h2>
+<h2 id="cutting-plane"><span id="index-38"></span>Cutting Plane<a class="headerlink" href="#cutting-plane" title="Permalink to this headline">¶</a></h2>
<p>The first of these is the cutting plane. Let’s say you’re doing some
collapse-based problem, where you end up with a vector that describes the
angular momentum. By feeding this vector into the cutting plane object, you can
@@ -70,7 +70,7 @@
and then used to define the transformed coordinate system.</p>
</div>
<div class="section">
-<h2 id="extracted-regions"><span id="index-19"></span>Extracted Regions<a class="headerlink" href="#extracted-regions" title="Permalink to this headline">¶</a></h2>
+<h2 id="extracted-regions"><span id="index-39"></span>Extracted Regions<a class="headerlink" href="#extracted-regions" title="Permalink to this headline">¶</a></h2>
<p>One of the other interesting data types is mostly only useful for profiles in
one and two dimensions. By whatever criteria you like, you can extract a subset
of any 3D data object. What this means is that you can apply ‘cuts’ to the data –
@@ -95,7 +95,7 @@
method, and that’s the functionality we use here.</p>
</div>
<div class="section">
-<h2 id="grid-collections"><span id="index-20"></span>Grid Collections<a class="headerlink" href="#grid-collections" title="Permalink to this headline">¶</a></h2>
+<h2 id="grid-collections"><span id="index-40"></span>Grid Collections<a class="headerlink" href="#grid-collections" title="Permalink to this headline">¶</a></h2>
</div>
</div>
@@ -125,7 +125,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -149,7 +149,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/automated_plotting.html
==============================================================================
--- trunk/doc/build/html/tutorial/automated_plotting.html (original)
+++ trunk/doc/build/html/tutorial/automated_plotting.html Sat May 10 23:00:13 2008
@@ -44,12 +44,12 @@
<div class="section">
-<h1 id="automated-plotting"><span id="index-33"></span>Automated Plotting<a class="headerlink" href="#automated-plotting" title="Permalink to this headline">¶</a></h1>
+<h1 id="automated-plotting"><span id="index-41"></span>Automated Plotting<a class="headerlink" href="#automated-plotting" title="Permalink to this headline">¶</a></h1>
<p>So now we know how to get and manipulate most of the datatypes, but we
still have to go through some processes to plot them manually. However, yt has
facilities for plotting slices, projections and profiles in much easier ways.</p>
<div class="section">
-<h2 id="collections-of-plots"><span id="index-34"></span>Collections of Plots<a class="headerlink" href="#collections-of-plots" title="Permalink to this headline">¶</a></h2>
+<h2 id="collections-of-plots"><span id="index-42"></span>Collections of Plots<a class="headerlink" href="#collections-of-plots" title="Permalink to this headline">¶</a></h2>
<p>The plotting tool is called ‘raven’ and it’s organized around the idea of
PlotCollection objects. Each PlotCollection object is in some way thematically
associated – maybe they are all the same data, sliced along different axes, for instance.
@@ -60,7 +60,7 @@
</pre></div>
</div>
<div class="section">
-<h2 id="adding-plots"><span id="index-35"></span>Adding Plots<a class="headerlink" href="#adding-plots" title="Permalink to this headline">¶</a></h2>
+<h2 id="adding-plots"><span id="index-43"></span>Adding Plots<a class="headerlink" href="#adding-plots" title="Permalink to this headline">¶</a></h2>
<p>Now we’ve got a plot collection – a container for more plots that we can add
and then manipulate as a group. So, let’s try adding some plots to it!:</p>
<div class="highlight"><pre><span class="gp">>>> </span><span class="n">pc</span><span class="o">.</span><span class="n">add_slice</span><span class="p">(</span><span class="s">"Density"</span><span class="p">,</span> <span class="mf">0</span><span class="p">)</span>
@@ -119,7 +119,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -143,7 +143,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/basic_objects.html
==============================================================================
--- trunk/doc/build/html/tutorial/basic_objects.html (original)
+++ trunk/doc/build/html/tutorial/basic_objects.html Sat May 10 23:00:13 2008
@@ -44,14 +44,14 @@
<div class="section">
-<h1 id="basic-objects">Basic Objects<a class="headerlink" href="#basic-objects" title="Permalink to this headline">¶</a></h1>
+<h1 id="id1"><span id="basic-objects"></span>Basic Objects<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h1>
<p>What the code just did was access the grid files and then spit back the
results of the read operations. So we can access the fields pretty easily
this way, but what about generating new fields from our existing fields?
Well, that’s just as easy! And yt comes with many derived fields
pre-defined, but from within a script you can also define your own.</p>
<div class="section">
-<h2 id="derived-fields-and-indices"><span id="index-36"></span>Derived Fields and Indices<a class="headerlink" href="#derived-fields-and-indices" title="Permalink to this headline">¶</a></h2>
+<h2 id="derived-fields-and-indices"><span id="index-49"></span>Derived Fields and Indices<a class="headerlink" href="#derived-fields-and-indices" title="Permalink to this headline">¶</a></h2>
<p>Let’s try out some of the derived fields.:</p>
<div class="highlight"><pre><span class="gp">>>> </span><span class="k">print</span> <span class="n">my_grid</span><span class="p">[</span><span class="s">"Entropy"</span><span class="p">]</span>
</pre></div>
@@ -74,7 +74,7 @@
fixed-resolution grids and cutting planes from the herarchy.</p>
</div>
<div class="section">
-<h2 id="slices"><span id="index-37"></span>Slices<a class="headerlink" href="#slices" title="Permalink to this headline">¶</a></h2>
+<h2 id="slices"><span id="index-50"></span>Slices<a class="headerlink" href="#slices" title="Permalink to this headline">¶</a></h2>
<p>Let’s start with a slice. A slice needs some info, but how do we know what
type? Well, let’s use ‘help’!:</p>
<div class="highlight"><pre><span class="gp">>>> </span><span class="n">help</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">h</span><span class="o">.</span><span class="n">slice</span><span class="p">)</span>
@@ -127,7 +127,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -151,7 +151,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/derived_fields.html
==============================================================================
--- trunk/doc/build/html/tutorial/derived_fields.html (original)
+++ trunk/doc/build/html/tutorial/derived_fields.html Sat May 10 23:00:13 2008
@@ -120,7 +120,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -144,7 +144,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/derived_quantities.html
==============================================================================
--- trunk/doc/build/html/tutorial/derived_quantities.html (original)
+++ trunk/doc/build/html/tutorial/derived_quantities.html Sat May 10 23:00:13 2008
@@ -63,7 +63,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -87,7 +87,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/example_script.html
==============================================================================
--- trunk/doc/build/html/tutorial/example_script.html (original)
+++ trunk/doc/build/html/tutorial/example_script.html Sat May 10 23:00:13 2008
@@ -94,7 +94,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -118,7 +118,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/getting_started.html
==============================================================================
--- trunk/doc/build/html/tutorial/getting_started.html (original)
+++ trunk/doc/build/html/tutorial/getting_started.html Sat May 10 23:00:13 2008
@@ -46,7 +46,7 @@
<div class="section">
<h1 id="getting-started">Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
<div class="section">
-<h2 id="getting-into-yt"><span id="index-21"></span>Getting into yt<a class="headerlink" href="#getting-into-yt" title="Permalink to this headline">¶</a></h2>
+<h2 id="getting-into-yt"><span id="index-46"></span>Getting into yt<a class="headerlink" href="#getting-into-yt" title="Permalink to this headline">¶</a></h2>
<p>For the purposes of this tutorial, I’m going to assume that python is
installed, the prerequisites are installed and working, and that you know how
to launch a python interpreter. So first off, let’s start it up.</p>
@@ -62,7 +62,7 @@
</pre></div>
</div>
<div class="section">
-<h2 id="the-hierarchy"><span id="index-22"></span>The Hierarchy<a class="headerlink" href="#the-hierarchy" title="Permalink to this headline">¶</a></h2>
+<h2 id="the-hierarchy"><span id="index-47"></span>The Hierarchy<a class="headerlink" href="#the-hierarchy" title="Permalink to this headline">¶</a></h2>
<p>We first instantiate a StaticOutput. This is a pretty simple process - lagos
will grab the parameter file that you give it, parse it, set up some handy
units, and then return control to you.:</p>
@@ -80,7 +80,7 @@
</pre></div>
</div>
<div class="section">
-<h2 id="the-grids"><span id="index-23"></span>The Grids<a class="headerlink" href="#the-grids" title="Permalink to this headline">¶</a></h2>
+<h2 id="the-grids"><span id="index-48"></span>The Grids<a class="headerlink" href="#the-grids" title="Permalink to this headline">¶</a></h2>
<p>The hierarchy object has some interesting methods that let us access the data
in different ways. Let’s start by looking at the grids.</p>
<div class="highlight"><pre><span class="gp">>>> </span><span class="n">my_grid</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">h</span><span class="o">.</span><span class="n">grids</span><span class="p">[</span><span class="mf">0</span><span class="p">]</span> <span class="c"># The root grid</span>
@@ -126,7 +126,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -150,7 +150,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/index.html
==============================================================================
--- trunk/doc/build/html/tutorial/index.html (original)
+++ trunk/doc/build/html/tutorial/index.html Sat May 10 23:00:13 2008
@@ -121,7 +121,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -143,7 +143,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/profiles.html
==============================================================================
--- trunk/doc/build/html/tutorial/profiles.html (original)
+++ trunk/doc/build/html/tutorial/profiles.html Sat May 10 23:00:13 2008
@@ -122,7 +122,7 @@
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -146,7 +146,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/build/html/tutorial/projections.html
==============================================================================
--- trunk/doc/build/html/tutorial/projections.html (original)
+++ trunk/doc/build/html/tutorial/projections.html Sat May 10 23:00:13 2008
@@ -19,7 +19,7 @@
<link rel="search" title="Search" href="../search.html" />
<link rel="top" title="yt v0.3 documentation" href="../index.html" />
<link rel="up" title="A Short Tutorial" href="index.html" />
- <link rel="next" title="A Short Tutorial" href="index.html" />
+ <link rel="next" title="Derived Quantities" href="derived_quantities.html" />
<link rel="prev" title="Advanced Objects" href="advanced_objects.html" />
</head>
<body>
@@ -28,7 +28,7 @@
<ul>
<li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
- <li class="right"><a href="index.html" title="A Short Tutorial" accesskey="N">next</a> |</li>
+ <li class="right"><a href="derived_quantities.html" title="Derived Quantities" accesskey="N">next</a> |</li>
<li class="right"><a href="advanced_objects.html" title="Advanced Objects" accesskey="P">previous</a> |</li>
<li><a href="http://yt.spacepope.org/">yt</a> »</li>
@@ -91,14 +91,14 @@
<h4>Previous topic</h4>
<p class="topless"><a href="advanced_objects.html" title="previous chapter">Advanced Objects</a></p>
<h4>Next topic</h4>
- <p class="topless"><a href="index.html" title="next chapter">A Short Tutorial</a></p>
+ <p class="topless"><a href="derived_quantities.html" title="next chapter">Derived Quantities</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="../_sources/tutorial/projections.txt">Show Source</a></li>
</ul>
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" size="18"> <input type="submit" value="Go" />
+ <input type="text" name="q" size="18" /> <input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
@@ -111,7 +111,7 @@
<ul>
<li class="right" style="margin-right: 10px"><a href="../genindex.html" title="General Index" accesskey="I">index</a></li>
<li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
- <li class="right"><a href="index.html" title="A Short Tutorial" accesskey="N">next</a> |</li>
+ <li class="right"><a href="derived_quantities.html" title="Derived Quantities" accesskey="N">next</a> |</li>
<li class="right"><a href="advanced_objects.html" title="Advanced Objects" accesskey="P">previous</a> |</li>
<li><a href="http://yt.spacepope.org/">yt</a> »</li>
@@ -122,7 +122,7 @@
</div>
<div class="footer">
© Copyright 2008, Matthew Turk.
- Last updated on May 04, 2008.
+ Last updated on May 09, 2008.
</div>
</body>
</html>
\ No newline at end of file
Modified: trunk/doc/source/conf.py
==============================================================================
--- trunk/doc/source/conf.py (original)
+++ trunk/doc/source/conf.py Sat May 10 23:00:13 2008
@@ -26,6 +26,8 @@
extensions = ['sphinx.ext.autodoc']
autoclass_content = 'both'
+inherited_memers = 'true'
+
# Add any paths that contain templates here, relative to this directory.
templates_path = ['.templates']
Modified: trunk/doc/source/modules/lagos/basedatatypes.rst
==============================================================================
--- trunk/doc/source/modules/lagos/basedatatypes.rst (original)
+++ trunk/doc/source/modules/lagos/basedatatypes.rst Sat May 10 23:00:13 2008
@@ -1,11 +1,23 @@
-:mod:`yt.lagos.BaseDataTypes` -- Data Types
-===========================================
+Data Containers
+===============
-.. module:: yt.lagos.BaseDataTypes
- :synopsis: Generate containers to hold AMR data
-.. moduleauthor:: Matthew Turk <mturk at stanford.edu>
+yt provides a number of data containers, defined such that they satisfy a
+logical need. Each of these provides only the finest-resolution cells, unless
+an option is available to restrict the levels from which they draw, as is the
+case with :class:`~yt.lagos.EnzoCoveringGrid`.
-.. toctree::
+Each of these implements the same primary protocol - all data values can be
+access dictionary-style:
+
+.. code-block:: python
+
+ >>> object["Density"]
+ >>> object["Density"].max()
+
+And so on. For more information, see the
+:ref:`the tutorial topic <basic_objects>` on basic objects.
+
+.. currentmodule:: yt.lagos
Base Containers
---------------
@@ -18,16 +30,22 @@
.. autoclass:: yt.lagos.Enzo1DData
:members:
+ :inherited-members:
.. autoclass:: yt.lagos.Enzo2DData
:members:
+ :inherited-members:
.. autoclass:: yt.lagos.Enzo3DData
:members:
+ :inherited-members:
1D Data Containers
------------------
+Each of these inherits from :class:`~yt.lagos.Enzo1DData`, and so has all the
+member functions defined there.
+
.. autoclass:: yt.lagos.EnzoOrthoRayBase
:members:
Modified: trunk/doc/source/modules/lagos/index.rst
==============================================================================
--- trunk/doc/source/modules/lagos/index.rst (original)
+++ trunk/doc/source/modules/lagos/index.rst Sat May 10 23:00:13 2008
@@ -1,7 +1,12 @@
.. _lagos:
-yt.lagos
-======================
+yt.lagos - Data Handling and Analysis
+=====================================
+
+.. module:: yt.lagos
+ :synopsis: The data handling done with Enzo data
+.. moduleauthor:: Matthew Turk <mturk at stanford.edu>
+
.. toctree::
:maxdepth: 2
Modified: trunk/doc/source/modules/lagos/outputandhierarchy.rst
==============================================================================
--- trunk/doc/source/modules/lagos/outputandhierarchy.rst (original)
+++ trunk/doc/source/modules/lagos/outputandhierarchy.rst Sat May 10 23:00:13 2008
@@ -1,17 +1,13 @@
-:mod:`yt.lagos` -- Grid Type
-=========================================
+Native Enzo Data Structures
+===========================
-.. module:: yt.lagos.HierarchyType
- :synopsis: The various types of outputs from a simulation
-.. moduleauthor:: Matthew Turk <mturk at stanford.edu>
-
-.. autoclass:: yt.lagos.HierarchyType
- :members:
+.. currentmodule:: yt.lagos
.. autoclass:: yt.lagos.EnzoStaticOutput
:members:
-.. autoclass:: yt.lagos.BaseGridType
+.. autoclass:: yt.lagos.EnzoHierarchy
:members:
-
+.. autoclass:: yt.lagos.EnzoGridBase
+ :members:
Modified: trunk/doc/source/tutorial/basic_objects.rst
==============================================================================
--- trunk/doc/source/tutorial/basic_objects.rst (original)
+++ trunk/doc/source/tutorial/basic_objects.rst Sat May 10 23:00:13 2008
@@ -1,3 +1,5 @@
+.. _basic_objects:
+
Basic Objects
=============
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