Mon May 5 08:49:43 PDT 2008

Author: mturk
Date: Mon May  5 08:49:34 2008
New Revision: 439
URL: http://yt.spacepope.org/changeset/439

Log:
Document build, post-plane.  Still a lot to be done.



Added:
   trunk/doc/build/doctrees/cookbook/
   trunk/doc/build/doctrees/cookbook/index.doctree   (contents, props changed)
   trunk/doc/build/doctrees/modules/lagos/basedatatypes.doctree   (contents, props changed)
   trunk/doc/build/doctrees/tutorial/derived_quantities.doctree   (contents, props changed)
   trunk/doc/build/doctrees/tutorial/example_script.doctree   (contents, props changed)
   trunk/doc/build/html/_sources/cookbook/
   trunk/doc/build/html/_sources/cookbook/index.txt
   trunk/doc/build/html/_sources/modules/lagos/basedatatypes.txt
   trunk/doc/build/html/_sources/tutorial/derived_quantities.txt
   trunk/doc/build/html/_sources/tutorial/example_script.txt
   trunk/doc/build/html/cookbook/
   trunk/doc/build/html/cookbook/index.html
   trunk/doc/build/html/modules/lagos/basedatatypes.html
   trunk/doc/build/html/tutorial/derived_quantities.html
   trunk/doc/build/html/tutorial/example_script.html
   trunk/doc/source/.templates/layout.html
   trunk/doc/source/cookbook/
   trunk/doc/source/cookbook/index.rst
   trunk/doc/source/modules/lagos/basedatatypes.rst
   trunk/doc/source/tutorial/derived_quantities.rst
   trunk/doc/source/tutorial/example_script.rst
Removed:
   trunk/doc/.static/
   trunk/doc/.templates/
Modified:
   trunk/doc/build/doctrees/environment.pickle
   trunk/doc/build/doctrees/extending/index.doctree
   trunk/doc/build/doctrees/faq.doctree
   trunk/doc/build/doctrees/index.doctree
   trunk/doc/build/doctrees/intro.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/derived_fields.doctree
   trunk/doc/build/doctrees/tutorial/getting_started.doctree
   trunk/doc/build/doctrees/tutorial/index.doctree
   trunk/doc/build/doctrees/tutorial/profiles.doctree
   trunk/doc/build/doctrees/tutorial/projections.doctree
   trunk/doc/build/html/_sources/extending/index.txt
   trunk/doc/build/html/_sources/faq.txt
   trunk/doc/build/html/_sources/index.txt
   trunk/doc/build/html/_sources/intro.txt
   trunk/doc/build/html/_sources/modules/lagos/index.txt
   trunk/doc/build/html/_sources/tutorial/advanced_objects.txt
   trunk/doc/build/html/_sources/tutorial/automated_plotting.txt
   trunk/doc/build/html/_sources/tutorial/basic_objects.txt
   trunk/doc/build/html/_sources/tutorial/derived_fields.txt
   trunk/doc/build/html/_sources/tutorial/getting_started.txt
   trunk/doc/build/html/_sources/tutorial/index.txt
   trunk/doc/build/html/_sources/tutorial/profiles.txt
   trunk/doc/build/html/_sources/tutorial/projections.txt
   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/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/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/extending/index.rst
   trunk/doc/source/faq.rst
   trunk/doc/source/index.rst
   trunk/doc/source/intro.rst
   trunk/doc/source/modules/lagos/index.rst
   trunk/doc/source/tutorial/advanced_objects.rst
   trunk/doc/source/tutorial/automated_plotting.rst
   trunk/doc/source/tutorial/basic_objects.rst
   trunk/doc/source/tutorial/derived_fields.rst
   trunk/doc/source/tutorial/getting_started.rst
   trunk/doc/source/tutorial/index.rst
   trunk/doc/source/tutorial/profiles.rst
   trunk/doc/source/tutorial/projections.rst

Added: trunk/doc/build/doctrees/cookbook/index.doctree
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Modified: trunk/doc/build/doctrees/environment.pickle
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Modified: trunk/doc/build/doctrees/extending/index.doctree
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Modified: trunk/doc/build/doctrees/faq.doctree
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Modified: trunk/doc/build/doctrees/index.doctree
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Modified: trunk/doc/build/doctrees/intro.doctree
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Added: trunk/doc/build/doctrees/modules/lagos/basedatatypes.doctree
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Modified: trunk/doc/build/doctrees/modules/lagos/index.doctree
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Modified: trunk/doc/build/doctrees/tutorial/advanced_objects.doctree
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Modified: trunk/doc/build/doctrees/tutorial/automated_plotting.doctree
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Modified: trunk/doc/build/doctrees/tutorial/basic_objects.doctree
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Modified: trunk/doc/build/doctrees/tutorial/derived_fields.doctree
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Added: trunk/doc/build/doctrees/tutorial/derived_quantities.doctree
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Added: trunk/doc/build/doctrees/tutorial/example_script.doctree
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Modified: trunk/doc/build/doctrees/tutorial/getting_started.doctree
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Modified: trunk/doc/build/doctrees/tutorial/index.doctree
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Modified: trunk/doc/build/doctrees/tutorial/profiles.doctree
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Modified: trunk/doc/build/doctrees/tutorial/projections.doctree
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Added: trunk/doc/build/html/_sources/cookbook/index.txt
==============================================================================

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	Mon May  5 08:49:34 2008
@@ -18,3 +18,6 @@
 
 Analyzing in Parallel
 ---------------------
+
+Running Fortran Routines
+------------------------

Modified: trunk/doc/build/html/_sources/faq.txt
==============================================================================
--- trunk/doc/build/html/_sources/faq.txt	(original)
+++ trunk/doc/build/html/_sources/faq.txt	Mon May  5 08:49:34 2008
@@ -4,21 +4,66 @@
 Why Python?
 -----------
 
-What do I need to use yt?
--------------------------
+Well, the easiest answer is that I knew it, and it met the requirements.  The
+more interesting answer, though, is a combination of things.  Python right now
+has a lot of momentum behind it, particularly in the scientific community.
+It's easy to compile, portable across many architectures, relatively simple to
+write C-based exntesions for, and it's well-suited to rapid application
+development.  With access to an interpreter, new avenues of data-exploration
+are opened, and this can lead to much more rapid and interesting analysis.
+
+Where can I learn more about Python?
+------------------------------------
+
+There are several good, free books about Python available on the web.  The best
+place to start is with the `official tutorial <http://docs.python.org/tut/>`_,
+but there's also `Dive Into Python <http://www.diveintopython.org/>`_, an
+entire `collection of videos <http://showmedo.com/videos/python?topic=beginner_programming>`_ on 
+`ShowMeDo.com <http://showmedo.com/>`_, and a much more specific guide to using
+`NumPy <http://www.scipy.org/Tentative_NumPy_Tutorial>`_, which is the backend
+on which all the math done in yt is based.
+
+As far as books go, the only book I've found to be absolutely indispensible is
+the `Beazley Book <http://www.amazon.com/exec/obidos/ASIN/0735710910>`_.
 
 What's up with the names?
 -------------------------
 
+In the book `Snow Crash <http://en.wikipedia.org/wiki/Snow_Crash>`_, yt is
+Uncle Enzo's messenger.  Lagos is the keeper of the data, Raven is a master
+slicer, and so on.
+
 Are there any restrictions on my use of yt?
 -------------------------------------------
 
+yt has been released under Version 3 of the 
+`GNU General Public License <http://www.gnu.org/licenses/gpl.html>`_.
+
+If you found it useful, and have extended it in some meaningful way, of course
+I'd love to see your contributions so they can be shared with the community.
+Additionally, if you use yt in a paper, I'd love it if you'd drop me a line to
+let me know.
+
 How can I help?
 ---------------
 
+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. 
+
 Something has gone wrong.  What do I do?
 ----------------------------------------
 
+Well, first off, double check that you're giving the code what it needs, and
+not asking it for something it can't provide.  Use the ``help()`` command on
+an object or a method to get more information.
+
+If you can't figure out what's up, please go ahead and copy the resultant
+traceback information (the error message it prints out) along with any log
+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/>`_.  
+
 Where can I go for support?
 ---------------------------
 
+I've set up a ``yt-users`` mailing list.  There's more information about it
+at the `yt homepage <http://yt.spacepope.org>`_.

Modified: trunk/doc/build/html/_sources/index.txt
==============================================================================
--- trunk/doc/build/html/_sources/index.txt	(original)
+++ trunk/doc/build/html/_sources/index.txt	Mon May  5 08:49:34 2008
@@ -11,6 +11,7 @@
 
    intro
    tutorial/index
+   cookbook/index
    extending/index
    faq
    modules/lagos/index

Modified: trunk/doc/build/html/_sources/intro.txt
==============================================================================
--- trunk/doc/build/html/_sources/intro.txt	(original)
+++ trunk/doc/build/html/_sources/intro.txt	Mon May  5 08:49:34 2008
@@ -1,11 +1,92 @@
 Introduction
-===========
+============
 
-Adaptive Mesh Refinement Data
------------------------------
+History
+-------
+
+My name is Matthew Turk, and I am the primary author of yt.  I designed and
+implemented it during the course of my graduate studies working with Prof. Tom
+Abel at Stanford University, under the auspices of the Department of Energy
+through the Stanford Linear Accelerator Center and Los Alamos National Lab.  It
+has evolved from a simple data-reader and exporter into what I believe is a
+fully-featured toolkit.
+
+yt was designed to be a completely Free (as in beer *and* as in freedom)
+user-extensible framework for analyzing and visualizing adaptive mesh
+refinement data.  It relies on no proprietary software -- although it can be
+and has been extended to interface with proprietary software and libraries --
+and has been designed from the ground up to enable users to be as immersed in
+the data as they desire.
+
+Originally, yt was written as a frontend to HippoDraw, an extensible and
+comprehensive plotting package built at SLAC by Paul Kunz.  Over time, however,
+it has been generalized to rely on mostly commodity Python packages, and its
+dependencies reduced and ease of installation increased.
 
 What yt is and is not
 ---------------------
 
+In some sense, yt is also designed to be rather utilitarian.  By virtue of the
+fact that it has been written in an interpreted language, it can be somewhat
+slower than purely C-based analysis codes, although I believe that to be
+mitigated by a cleverness of algorithms and a substantially improved
+development time for the user in the case of a desire to expand the
+functionality.
+
+```EXPAND```
+
 Prerequisites for yt
 --------------------
+
+A driving factor in the development of yt over the months leading to release
+0.3 has been the reduction of dependencies.  To that extent, only a few
+packages are required for the base usage, and a GUI toolkit if you are going to use
+the graphical user interface, Reason.
+
+ * `Python <http://python.org/>`_, at least version 2.4, but preferably 2.5.
+ * `HDF5 <http://www.hdfgroup.org/>`_, the data storage backend used by Enzo
+   and yt (if you can run Enzo, this is already installed!)
+ * `NumPy <http://numpy.scipy.org/>`_, the fast numerical backend for Python
+ * `MatPlotLib <http://matplotlib.sf.net/>`_, the plotting package
+ * `wxPython <http://www.wxpython.org/>`_, the GUI toolkit
+
+(If you are only interested in manipulating data without any graphical plotting
+or interfaces, you only need to install NumPy and Python!)
+
+Installing the Necessary Packages
+---------------------------------
+
+Installing Python itself is usually quite simple, and often very fast.  Because
+we're setting up a small system of packages, even if you have a system-wide
+install of python2.5 it can be easier in some cases to create a local directory
+structure:
+
+.. code-block:: bash
+
+   $ tar xvf Python-2.5.2.tar.gz
+   $ cd Python-2.5.2
+   $ ./configure --prefix=$HOME/local/
+   $ make install
+
+This will create (if necessary) a directory named local in your home directory,
+along with the necessary subdirectories.  When the executable
+``$HOME/lcoal/bin/python2.4`` is used to install a package, it will install it
+to the ``$HOME/local/`` directory structure.
+
+The python packages are fairly straightforward to install.  The process of
+installing packages in python has been greatly simplified over the last few
+years with the addition of setuptools, but for these particular packages I
+typically recommend installing from source, which for Python packages consists
+of changing to the source directory and issues the command:
+
+.. code-block:: bash
+
+   $ tar xvfz $PKGNAME.tar.gz
+   $ cd $PKGNAME
+   $ python2.5 setup.py install
+
+This method works for NumPy, Matplotlib and yt itself, but for wxPython, I
+**strongly** suggest you seek binaries for your platform.  If they are not
+available, I recommend you read the ``INSTALL`` file and follow its directions
+closely.
+

Added: trunk/doc/build/html/_sources/modules/lagos/basedatatypes.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/modules/lagos/basedatatypes.txt	Mon May  5 08:49:34 2008
@@ -0,0 +1,15 @@
+:mod:`lagos.BaseDataTypes` -- Data Types
+===========================================
+
+.. module:: lagos.BaseDataTypes
+   :synopsis: Generate containers to hold AMR data
+.. moduleauthor:: Matthew Turk <mturk at stanford.edu>
+
+.. autoclass:: yt.lagos.EnzoData
+   :members:
+
+.. autoclass:: yt.lagos.Enzo3DData
+   :members:
+
+.. autoclass:: yt.lagos.EnzoSphereBase
+   :members:

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	Mon May  5 08:49:34 2008
@@ -0,0 +1,9 @@
+.. _lagos:
+
+yt.lagos
+======================
+
+.. toctree::
+   :maxdepth: 2
+
+   basedatatypes

Modified: trunk/doc/build/html/_sources/tutorial/advanced_objects.txt
==============================================================================
--- trunk/doc/build/html/_sources/tutorial/advanced_objects.txt	(original)
+++ trunk/doc/build/html/_sources/tutorial/advanced_objects.txt	Mon May  5 08:49:34 2008
@@ -1,5 +1,5 @@
 Advanced Objects
-----------------
+================
 
 So we've seen simple objects already -- sphere, profiles, and regions.
 There are two other types of objects that are fairly cool, as well, and
@@ -7,6 +7,11 @@
 profile them, all of that, right from the command line like you would a sphere
 or a region.
 
+.. index:: Cutting Plane, 2ddata;Cutting Plane
+
+Cutting Plane
+-------------
+
 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
@@ -25,6 +30,11 @@
 during the object instantiation.)  An appropriate 'up' vector is guessed at
 and then used to define the transformed coordinate system.
 
+.. index:: Extracted Regions, 3ddata;Extracted Regions
+
+Extracted Regions
+-----------------
+
 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 --
@@ -49,3 +59,8 @@
 everything, and we have been, too, when we've been using our data.  The 'where'
 command creates a list of indices, which can then get fed into an array accessor
 method, and that's the functionality we use here.
+
+.. index:: GridCollection, 3ddata;GridCollection
+
+Grid Collections
+----------------

Modified: trunk/doc/build/html/_sources/tutorial/automated_plotting.txt
==============================================================================
--- trunk/doc/build/html/_sources/tutorial/automated_plotting.txt	(original)
+++ trunk/doc/build/html/_sources/tutorial/automated_plotting.txt	Mon May  5 08:49:34 2008
@@ -1,9 +1,17 @@
+.. index:: Plotting
+
 Automated Plotting
-------------------
+==================
 
 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.
+
+.. index:: Raven, PlotCollections, Plotting;PlotCollections
+
+Collections of Plots
+--------------------
+
 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.
@@ -12,13 +20,21 @@
 
    >>> import yt.raven as raven
    >>> pc = raven.PlotCollection(a)
+
+.. index:: Plotting;Adding plots to PlotCollections, Raven, PlotCollections;Adding Plots
+
+Adding Plots
+------------
+
+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!::
+
    >>> pc.add_slice("Density", 0)
    >>> pc.add_slice("Density", 1)
    >>> pc.add_slice("Density", 2)
    >>> pc.set_width(15, 'kpc')
    >>> pc.save("somename_15kpc")
 
-
 There's a lot in that little block of text.  First I add a slice (note that while
 we can feed it a pre-existing slice, it will also grab one automatically if we
 don't!) along each axis (0,1,2) in the field "Density".  Each time we
@@ -34,6 +50,9 @@
 it takes care of adding some more information to the filename, so don't supply it
 a file suffix.  (It defaults to '.png')
 
+More Plots
+----------
+
 We have access to most of the interesting plots from the PlotCollection
 interface, including cutting planes and projections.  (More on those later!)::
 

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	Mon May  5 08:49:34 2008
@@ -1,58 +1,68 @@
 Basic Objects
--------------
+=============
 
 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.  ::
+pre-defined, but from within a script you can also define your own.
 
-   >>> print my_grid["Entropy"]
+.. index:: derivedfield, indices
+
+Derived Fields and Indices
+--------------------------
 
+Let's try out some of the derived fields.::
+
+   >>> print my_grid["Entropy"]
 
 Entropy is a derived field.  But how does it work?  Well, we have a built-in
 source-code inspector.  ::
 
    >>> print lagos.fieldInfo["Entropy"].get_source()
 
-
 But what if we only want a couple values?  We can directly grab indices.  ::
 
    >>> print my_grid["Density"][0,10,4] # 0-indexed!
 
-
 We can also slice, using the slice operator: ':' ::
 
    >>> print my_grid["Density"][0,:,4]
    >>> print my_grid["Density"][0,2:4,4]
 
-
 Okay, so now you've seen how to grab fields from a grid.  The thing about
 getting fields from a grid, though, is that it works the exact same way as
-all the other data types!  (Well, maybe not projection :)  So that raises the
+all the other data types!  (Well, maybe not projection.)  So that raises the
 question, how do we get more data objects?  Well, the hierarchy is our friend
 here.  We can get slices, projections, spheres, rectangular prisms,
 fixed-resolution grids and cutting planes from the herarchy.
 
+.. index:: Slices, 2ddata;Slices
+
+Slices
+------
+
 Let's start with a slice.  A slice needs some info, but how do we know what
 type?  Well, let's use 'help'!::
 
    >>> help(a.h.slice)
 
-
 Looks like we need to feed it an axis, a coordinate, and maybe some fields
 and a center.  Axes are always done as numbers, with 0 = x, 1 = y, 2 = z.::
 
    >>> my_slice = a.h.slice(0, 0.5, "Density")  # We don't really need to pass the field!
 
-
 Now let's test out getting new fields.::
 
    >>> print my_slice["Pressure"], my_slice["Density"]
 
-
 Okay, so enough of the slices.  (Although they can do some more stuff, like
-shift around inside the domain, and so on and so forth.)
+shift around inside the domain, and so on and so forth.)  Slices are typically
+used implicity with plotting (more on that later) and not very often from
+the interpreter.
+
+Data Regions
+------------
 
 Let's do a region.  This is a box with a left edge and a right edge, and a
 center.  (You need a center for some other calculations, not for getting the

Modified: trunk/doc/build/html/_sources/tutorial/derived_fields.txt
==============================================================================
--- trunk/doc/build/html/_sources/tutorial/derived_fields.txt	(original)
+++ trunk/doc/build/html/_sources/tutorial/derived_fields.txt	Mon May  5 08:49:34 2008
@@ -1,5 +1,5 @@
 Derived Fields
---------------
+==============
 
 Okay, now we have a region.  We can do stuff with this -- in fact, it has the
 same data-access protocol as a slice or a grid!  Plus, math on these things
@@ -16,6 +16,8 @@
 
    >>> print lagos.fieldInfo.keys()
 
+Defining Simple Fields
+----------------------
 
 There are LOTS!  Not only that, but you can set up your own fields, too,
 which then become available to all data-types. Here's a very simple example,
@@ -40,6 +42,9 @@
 we request "Density" from 'data' it is returned to us *already* in CGS, so we
 don't need to convert anything.
 
+More Complicated Fields
+-----------------------
+
 The last part, the call to add_field, is the most crucial.  It creates a
 DerivedField object which will control the behavior of the derived field in a
 couple crucial ways -- what you see here includes the string used for the

Added: trunk/doc/build/html/_sources/tutorial/derived_quantities.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/tutorial/derived_quantities.txt	Mon May  5 08:49:34 2008
@@ -0,0 +1,2 @@
+Derived Quantities
+==================

Added: trunk/doc/build/html/_sources/tutorial/example_script.txt
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/_sources/tutorial/example_script.txt	Mon May  5 08:49:34 2008
@@ -0,0 +1,37 @@
+A Demonstrative Example Script
+==============================
+
+During the course of my work, I often have to run a selection of data analysis
+tasks in order to keep tabs on my simulation as it runs.  I've included below a
+script that I run on each output as it is created.
+
+.. code-block:: python
+
+   import sys
+   import yt.lagos as lagos
+   import yt.raven as raven
+   
+   fn = sys.argv[-1]
+   pf = lagos.EnzoStaticOutput(fn)
+   pf.h.print_stats()
+
+   fields_to_plot = ["NumberDensity", "Density", "Temperature", "H2I_Fraction"]
+   
+   my_vals = [1000.0, 100.0, 10.0, 1.0]
+   my_units = ['au','rsun']
+   
+   my_widths = []
+   
+   for unit in my_units:
+       my_widths += [(v,units) for v in my_vals]
+   
+   pc = raven.PlotCollection(pf)
+   for i in range(3): pc.add_slice("NumberDensity", i)
+   
+   for field in fields_to_plot:
+       pc.switch_field(field)
+       for w, u in my_widths:
+           pc.set_width(w,u)
+           pc.save("%s" % pf)
+
+And that's it!

Modified: trunk/doc/build/html/_sources/tutorial/getting_started.txt
==============================================================================
--- trunk/doc/build/html/_sources/tutorial/getting_started.txt	(original)
+++ trunk/doc/build/html/_sources/tutorial/getting_started.txt	Mon May  5 08:49:34 2008
@@ -1,6 +1,8 @@
 Getting Started
 ===============
 
+.. index:: Starting yt
+
 Getting into yt
 ---------------
 
@@ -22,6 +24,8 @@
 
    >>> import yt.lagos as lagos
 
+.. index:: hierarchy
+
 The Hierarchy
 -------------
 
@@ -43,6 +47,8 @@
    >>> print v
    >>> print c
 
+.. index:: Grid, 3ddata;grid
+
 The Grids
 ---------
 

Modified: trunk/doc/build/html/_sources/tutorial/index.txt
==============================================================================
--- trunk/doc/build/html/_sources/tutorial/index.txt	(original)
+++ trunk/doc/build/html/_sources/tutorial/index.txt	Mon May  5 08:49:34 2008
@@ -1,7 +1,10 @@
 A Short Tutorial
 ================
 
-
+As with many interactive packages, getting started with yt can be a bit
+daunting.  Following this tutorial we'll walk through the intepreter, get used
+to some of the ways that yt works, and performing some common (and
+not-so-common) tasks.
 
 Contents:
 
@@ -15,3 +18,5 @@
    automated_plotting
    advanced_objects
    projections
+   derived_quantities
+   example_script

Modified: trunk/doc/build/html/_sources/tutorial/profiles.txt
==============================================================================
--- trunk/doc/build/html/_sources/tutorial/profiles.txt	(original)
+++ trunk/doc/build/html/_sources/tutorial/profiles.txt	Mon May  5 08:49:34 2008
@@ -1,5 +1,5 @@
 Profiles
---------
+========
 
 Profiles are one of the more interesting data types.  They are a binned average
 of one or more variables, along one or two different dimensions.  For example,
@@ -7,6 +7,9 @@
 Look at the distribution of Volume through Density and Temperature space.  Or you could
 take the spherically-averaged Number Density and see how it changes with radius.
 
+One Dimensional Profiles
+------------------------
+
 In order to make a profile, we first need a data object we want to get the profile
 *from*.  This can be a sphere, a region, or even an extracted region.  We'll
 first take a look at doing a spherically-average profile of Temperature with Radius.  ::
@@ -43,6 +46,8 @@
    >>> pylab.ylabel(r"$\rm{Density} (\rm{g}/\rm{cm}^3)$")
    >>> pylab.savefig("my_profile.png")
 
+Two-Dimensional Profiles
+------------------------
 
 Two-dimensional profiles are along the same lines.  ::
 

Modified: trunk/doc/build/html/_sources/tutorial/projections.txt
==============================================================================
--- trunk/doc/build/html/_sources/tutorial/projections.txt	(original)
+++ trunk/doc/build/html/_sources/tutorial/projections.txt	Mon May  5 08:49:34 2008
@@ -1,10 +1,13 @@
 Projections
------------
+===========
 
 Projections are the line integrals of a given quantity along a given access.
 These are useful in a wide variety of problems -- they can reveal morphologies
 that slicing cannot, in the simplest case.
 
+Simple Projections
+------------------
+
 There are several ways to generate projections in yt, and with the appropriate
 software package installed (mpi4py) one can even generate them in parallel,
 distributed across an arbitrary number of nodes.  However, I will deal here
@@ -24,3 +27,8 @@
 stored in an HDF5 file tied to the parameter file.  Then next time you ask
 for it, it is already available.  Zooming and panning is accomplished very
 simply.
+
+Parallel Projections
+--------------------
+
+

Added: trunk/doc/build/html/cookbook/index.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/cookbook/index.html	Mon May  5 08:49:34 2008
@@ -0,0 +1,87 @@
+<!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="next" title="Extending yt" href="../extending/index.html" />
+    <link rel="prev" title="A Short Tutorial" href="../tutorial/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="../extending/index.html" title="Extending yt" accesskey="N">next</a> |</li>
+          <li class="right"><a href="../tutorial/index.html" title="A Short Tutorial" 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>
+
+      </ul>
+    </div>
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  
+  
+
+          </div>
+        </div>
+      </div>
+      <div class="sidebar">
+        <div class="sidebarwrapper">
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="../tutorial/index.html" title="previous chapter">A Short Tutorial</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="../extending/index.html" title="next chapter">Extending yt</a></p>
+            <h3>This Page</h3>
+            <ul class="this-page-menu">
+              <li><a href="../_sources/cookbook/index.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="../extending/index.html" title="Extending yt" accesskey="N">next</a> |</li>
+          <li class="right"><a href="../tutorial/index.html" title="A Short Tutorial" 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>
+
+      </ul>
+    </div>
+    <div class="footer">
+      © Copyright 2008, Matthew Turk.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -19,7 +19,6 @@
     <link rel="search" title="Search" href="../search.html" />
     <link rel="top" title="yt v0.3 documentation" href="../index.html" />
     <link rel="next" title="FAQ" href="../faq.html" />
-    <link rel="prev" title="A Short Tutorial" href="../tutorial/index.html" />
   </head>
   <body>
     <div class="related">
@@ -28,8 +27,10 @@
         <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="../faq.html" title="FAQ" accesskey="N">next</a> |</li>
-          <li class="right"><a href="../tutorial/index.html" title="A Short Tutorial" 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>
+
       </ul>
     </div>
     <div class="document">
@@ -58,6 +59,9 @@
 <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>
 </div>
 
 
@@ -75,12 +79,11 @@
 <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>Previous topic</h4>
-            <p class="topless"><a href="../tutorial/index.html" title="previous chapter">A Short Tutorial</a></p>
             <h4>Next topic</h4>
             <p class="topless"><a href="../faq.html" title="next chapter">FAQ</a></p>
             <h3>This Page</h3>
@@ -103,13 +106,15 @@
         <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="../faq.html" title="FAQ" accesskey="N">next</a> |</li>
-          <li class="right"><a href="../tutorial/index.html" title="A Short Tutorial" 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>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -18,6 +18,7 @@
     <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="next" title="yt.lagos" href="modules/lagos/index.html" />
     <link rel="prev" title="Extending yt" href="extending/index.html" />
   </head>
   <body>
@@ -26,8 +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="modules/lagos/index.html" title="yt.lagos" accesskey="N">next</a> |</li>
           <li class="right"><a href="extending/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>
+
       </ul>
     </div>
     <div class="document">
@@ -40,24 +45,60 @@
 <h1 id="faq">FAQ<a class="headerlink" href="#faq" title="Permalink to this headline">¶</a></h1>
 <div class="section">
 <h2 id="why-python">Why Python?<a class="headerlink" href="#why-python" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section">
-<h2 id="what-do-i-need-to-use-yt">What do I need to use yt?<a class="headerlink" href="#what-do-i-need-to-use-yt" title="Permalink to this headline">¶</a></h2>
+<p>Well, the easiest answer is that I knew it, and it met the requirements.  The
+more interesting answer, though, is a combination of things.  Python right now
+has a lot of momentum behind it, particularly in the scientific community.
+It’s easy to compile, portable across many architectures, relatively simple to
+write C-based exntesions for, and it’s well-suited to rapid application
+development.  With access to an interpreter, new avenues of data-exploration
+are opened, and this can lead to much more rapid and interesting analysis.</p>
+</div>
+<div class="section">
+<h2 id="where-can-i-learn-more-about-python">Where can I learn more about Python?<a class="headerlink" href="#where-can-i-learn-more-about-python" title="Permalink to this headline">¶</a></h2>
+<p>There are several good, free books about Python available on the web.  The best
+place to start is with the <a class="reference" href="http://docs.python.org/tut/">official tutorial</a>,
+but there’s also <a class="reference" href="http://www.diveintopython.org/">Dive Into Python</a>, an
+entire <a class="reference" href="http://showmedo.com/videos/python?topic=beginner_programming">collection of videos</a> on
+<a class="reference" href="http://showmedo.com/">ShowMeDo.com</a>, and a much more specific guide to using
+<a class="reference" href="http://www.scipy.org/Tentative_NumPy_Tutorial">NumPy</a>, which is the backend
+on which all the math done in yt is based.</p>
+<p>As far as books go, the only book I’ve found to be absolutely indispensible is
+the <a class="reference" href="http://www.amazon.com/exec/obidos/ASIN/0735710910">Beazley Book</a>.</p>
 </div>
 <div class="section">
 <h2 id="what-s-up-with-the-names">What’s up with the names?<a class="headerlink" href="#what-s-up-with-the-names" title="Permalink to this headline">¶</a></h2>
+<p>In the book <a class="reference" href="http://en.wikipedia.org/wiki/Snow_Crash">Snow Crash</a>, yt is
+Uncle Enzo’s messenger.  Lagos is the keeper of the data, Raven is a master
+slicer, and so on.</p>
 </div>
 <div class="section">
 <h2 id="are-there-any-restrictions-on-my-use-of-yt">Are there any restrictions on my use of yt?<a class="headerlink" href="#are-there-any-restrictions-on-my-use-of-yt" title="Permalink to this headline">¶</a></h2>
+<p>yt has been released under Version 3 of the
+<a class="reference" href="http://www.gnu.org/licenses/gpl.html">GNU General Public License</a>.</p>
+<p>If you found it useful, and have extended it in some meaningful way, of course
+I’d love to see your contributions so they can be shared with the community.
+Additionally, if you use yt in a paper, I’d love it if you’d drop me a line to
+let me know.</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>
 </div>
 <div class="section">
 <h2 id="something-has-gone-wrong-what-do-i-do">Something has gone wrong.  What do I do?<a class="headerlink" href="#something-has-gone-wrong-what-do-i-do" title="Permalink to this headline">¶</a></h2>
+<p>Well, first off, double check that you’re giving the code what it needs, and
+not asking it for something it can’t provide.  Use the <tt class="docutils literal"><span class="pre">help()</span></tt> command on
+an object or a method to get more information.</p>
+<p>If you can’t figure out what’s up, please go ahead and copy the resultant
+traceback information (the error message it prints out) along with any log
+files, and either send an email to the <tt class="docutils literal"><span class="pre">yt-users</span></tt> mailing list (subscribe
+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="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>
 </div>
 </div>
 
@@ -71,7 +112,7 @@
             <ul>
 <li><a class="reference" href="">FAQ</a><ul>
 <li><a class="reference" href="#why-python">Why Python?</a></li>
-<li><a class="reference" href="#what-do-i-need-to-use-yt">What do I need to use yt?</a></li>
+<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="#how-can-i-help">How can I help?</a></li>
@@ -83,6 +124,8 @@
 
             <h4>Previous topic</h4>
             <p class="topless"><a href="extending/index.html" title="previous chapter">Extending yt</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="modules/lagos/index.html" title="next chapter">yt.lagos</a></p>
             <h3>This Page</h3>
             <ul class="this-page-menu">
               <li><a href="_sources/faq.txt">Show Source</a></li>
@@ -102,13 +145,17 @@
       <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="modules/lagos/index.html" title="yt.lagos" accesskey="N">next</a> |</li>
           <li class="right"><a href="extending/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>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -25,7 +25,10 @@
       <ul>
         <li class="right" style="margin-right: 10px"><a href="" 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><a href="http://yt.spacepope.org/">yt</a> »</li>
+    
         <li><a href="index.html">yt v0.3 documentation</a> »</li>
+
       </ul>
     </div>
     <div class="document">
@@ -36,11 +39,142 @@
 
    <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> 
 
    <hr />
 
    
+<h2 id="Symbols">Symbols</h2>
+<table width="100%" class="indextable"><tr><td width="33%" valign="top">
+<dl>
+
+<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>
+  </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>
+  </dl></dd></dl></td><td width="33%" valign="top"><dl>
+</dl></td></tr></table>
+
+<h2 id="C">C</h2>
+<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>
+  <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>
+</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>
+</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>
+  <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>
+  <dd><dl>
+    <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.extract_region">(lagos.BaseDataTypes.EnzoSphereBase method)</a></dt>
+  </dl></dd>
+<dt><a href="tutorial/advanced_objects.html#index-19">Extracted Regions</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>
+  <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>
+</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>
+</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>
+</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>
+  <dd><dl>
+    <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.paint_grids">(lagos.BaseDataTypes.EnzoSphereBase method)</a></dt>
+  </dl></dd>
+<dt><a href="tutorial/automated_plotting.html#index-34">PlotCollections</a></dt>
+  <dd><dl>
+    <dt><a href="tutorial/automated_plotting.html#index-35">Adding Plots</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>
+</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>
+</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>
+  <dd><dl>
+    <dt><a href="modules/lagos/basedatatypes.html#lagos.BaseDataTypes.EnzoSphereBase.select_grids">(lagos.BaseDataTypes.EnzoSphereBase 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>
+  <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>
+  </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>
+</dl></td></tr></table>
+
 
 
           </div>
@@ -63,12 +197,15 @@
       <ul>
         <li class="right" style="margin-right: 10px"><a href="" 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><a href="http://yt.spacepope.org/">yt</a> »</li>
+    
         <li><a href="index.html">yt v0.3 documentation</a> »</li>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -25,7 +25,10 @@
       <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><a href="http://yt.spacepope.org/">yt</a> »</li>
+    
         <li><a href="">yt v0.3 documentation</a> »</li>
+
       </ul>
     </div>
     <div class="document">
@@ -41,9 +44,10 @@
 <p>Contents:</p>
 <ul>
 <li><a class="reference" href="intro.html">Introduction</a><ul>
-<li><a class="reference" href="intro.html#adaptive-mesh-refinement-data">Adaptive Mesh Refinement Data</a></li>
+<li><a class="reference" href="intro.html#history">History</a></li>
 <li><a class="reference" href="intro.html#what-yt-is-and-is-not">What yt is and is not</a></li>
 <li><a class="reference" href="intro.html#prerequisites-for-yt">Prerequisites for yt</a></li>
+<li><a class="reference" href="intro.html#installing-the-necessary-packages">Installing the Necessary Packages</a></li>
 </ul>
 </li>
 </ul>
@@ -56,9 +60,13 @@
 <li><a class="reference" href="tutorial/automated_plotting.html">Automated Plotting</a></li>
 <li><a class="reference" href="tutorial/advanced_objects.html">Advanced Objects</a></li>
 <li><a class="reference" href="tutorial/projections.html">Projections</a></li>
+<li><a class="reference" href="tutorial/derived_quantities.html">Derived Quantities</a></li>
+<li><a class="reference" href="tutorial/example_script.html">A Demonstrative Example Script</a></li>
 </ul>
 </li>
 </ul>
+<ul class="simple">
+</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>
@@ -67,13 +75,14 @@
 <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>
 </ul>
 </li>
 </ul>
 <ul>
 <li><a class="reference" href="faq.html">FAQ</a><ul>
 <li><a class="reference" href="faq.html#why-python">Why Python?</a></li>
-<li><a class="reference" href="faq.html#what-do-i-need-to-use-yt">What do I need to use yt?</a></li>
+<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#how-can-i-help">How can I help?</a></li>
@@ -82,7 +91,11 @@
 </ul>
 </li>
 </ul>
-<ul class="simple">
+<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>
+</ul>
+</li>
 </ul>
 <ul class="simple">
 </ul>
@@ -131,12 +144,15 @@
       <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><a href="http://yt.spacepope.org/">yt</a> »</li>
+    
         <li><a href="">yt v0.3 documentation</a> »</li>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -29,7 +29,10 @@
         <li class="right"><a href="modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="tutorial/index.html" title="A Short Tutorial" accesskey="N">next</a> |</li>
           <li class="right"><a href="index.html" title="yt Overview" 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>
+
       </ul>
     </div>
     <div class="document">
@@ -40,20 +43,82 @@
   
   <div class="section">
 <h1 id="introduction">Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h1>
-<div class="system-message">
-<p class="system-message-title">System Message: WARNING/2 (<tt class="docutils">/Users/matthewturk/Development/yt/trunk/doc/source/intro.rst</tt>, line 2)</p>
-<p>Title underline too short.</p>
-<pre>Introduction
-===========</pre>
-</div>
 <div class="section">
-<h2 id="adaptive-mesh-refinement-data">Adaptive Mesh Refinement Data<a class="headerlink" href="#adaptive-mesh-refinement-data" title="Permalink to this headline">¶</a></h2>
+<h2 id="history">History<a class="headerlink" href="#history" title="Permalink to this headline">¶</a></h2>
+<p>My name is Matthew Turk, and I am the primary author of yt.  I designed and
+implemented it during the course of my graduate studies working with Prof. Tom
+Abel at Stanford University, under the auspices of the Department of Energy
+through the Stanford Linear Accelerator Center and Los Alamos National Lab.  It
+has evolved from a simple data-reader and exporter into what I believe is a
+fully-featured toolkit.</p>
+<p>yt was designed to be a completely Free (as in beer <em>and</em> as in freedom)
+user-extensible framework for analyzing and visualizing adaptive mesh
+refinement data.  It relies on no proprietary software – although it can be
+and has been extended to interface with proprietary software and libraries –
+and has been designed from the ground up to enable users to be as immersed in
+the data as they desire.</p>
+<p>Originally, yt was written as a frontend to HippoDraw, an extensible and
+comprehensive plotting package built at SLAC by Paul Kunz.  Over time, however,
+it has been generalized to rely on mostly commodity Python packages, and its
+dependencies reduced and ease of installation increased.</p>
 </div>
 <div class="section">
 <h2 id="what-yt-is-and-is-not">What yt is and is not<a class="headerlink" href="#what-yt-is-and-is-not" title="Permalink to this headline">¶</a></h2>
+<p>In some sense, yt is also designed to be rather utilitarian.  By virtue of the
+fact that it has been written in an interpreted language, it can be somewhat
+slower than purely C-based analysis codes, although I believe that to be
+mitigated by a cleverness of algorithms and a substantially improved
+development time for the user in the case of a desire to expand the
+functionality.</p>
+<p><tt class="docutils literal"><span class="pre">`EXPAND`</span></tt></p>
 </div>
 <div class="section">
 <h2 id="prerequisites-for-yt">Prerequisites for yt<a class="headerlink" href="#prerequisites-for-yt" title="Permalink to this headline">¶</a></h2>
+<p>A driving factor in the development of yt over the months leading to release
+0.3 has been the reduction of dependencies.  To that extent, only a few
+packages are required for the base usage, and a GUI toolkit if you are going to use
+the graphical user interface, Reason.</p>
+<blockquote>
+<ul class="simple">
+<li><a class="reference" href="http://python.org/">Python</a>, at least version 2.4, but preferably 2.5.</li>
+<li><a class="reference" href="http://www.hdfgroup.org/">HDF5</a>, the data storage backend used by Enzo
+and yt (if you can run Enzo, this is already installed!)</li>
+<li><a class="reference" href="http://numpy.scipy.org/">NumPy</a>, the fast numerical backend for Python</li>
+<li><a class="reference" href="http://matplotlib.sf.net/">MatPlotLib</a>, the plotting package</li>
+<li><a class="reference" href="http://www.wxpython.org/">wxPython</a>, the GUI toolkit</li>
+</ul>
+</blockquote>
+<p>(If you are only interested in manipulating data without any graphical plotting
+or interfaces, you only need to install NumPy and Python!)</p>
+</div>
+<div class="section">
+<h2 id="installing-the-necessary-packages">Installing the Necessary Packages<a class="headerlink" href="#installing-the-necessary-packages" title="Permalink to this headline">¶</a></h2>
+<p>Installing Python itself is usually quite simple, and often very fast.  Because
+we’re setting up a small system of packages, even if you have a system-wide
+install of python2.5 it can be easier in some cases to create a local directory
+structure:</p>
+<div class="highlight"><pre><span class="nv">$ </span>tar xvf Python-2.5.2.tar.gz
+<span class="nv">$ </span><span class="nb">cd </span>Python-2.5.2
+<span class="nv">$ </span>./configure --prefix<span class="o">=</span><span class="nv">$HOME</span>/local/
+<span class="nv">$ </span>make install
+</pre></div>
+<p>This will create (if necessary) a directory named local in your home directory,
+along with the necessary subdirectories.  When the executable
+<tt class="docutils literal"><span class="pre">$HOME/lcoal/bin/python2.4</span></tt> is used to install a package, it will install it
+to the <tt class="docutils literal"><span class="pre">$HOME/local/</span></tt> directory structure.</p>
+<p>The python packages are fairly straightforward to install.  The process of
+installing packages in python has been greatly simplified over the last few
+years with the addition of setuptools, but for these particular packages I
+typically recommend installing from source, which for Python packages consists
+of changing to the source directory and issues the command:</p>
+<div class="highlight"><pre><span class="nv">$ </span>tar xvfz <span class="nv">$PKGNAME</span>.tar.gz
+<span class="nv">$ </span><span class="nb">cd</span> <span class="nv">$PKGNAME</span>
+<span class="nv">$ </span>python2.5 setup.py install
+</pre></div>
+<p>This method works for NumPy, Matplotlib and yt itself, but for wxPython, I
+<strong>strongly</strong> suggest you seek binaries for your platform.  If they are not
+available, I recommend you read the <tt class="docutils literal"><span class="pre">INSTALL</span></tt> file and follow its directions
+closely.</p>
 </div>
 </div>
 
@@ -66,9 +131,10 @@
             <h3>Table Of Contents</h3>
             <ul>
 <li><a class="reference" href="">Introduction</a><ul>
-<li><a class="reference" href="#adaptive-mesh-refinement-data">Adaptive Mesh Refinement Data</a></li>
+<li><a class="reference" href="#history">History</a></li>
 <li><a class="reference" href="#what-yt-is-and-is-not">What yt is and is not</a></li>
 <li><a class="reference" href="#prerequisites-for-yt">Prerequisites for yt</a></li>
+<li><a class="reference" href="#installing-the-necessary-packages">Installing the Necessary Packages</a></li>
 </ul>
 </li>
 </ul>
@@ -98,12 +164,15 @@
         <li class="right"><a href="modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="tutorial/index.html" title="A Short Tutorial" accesskey="N">next</a> |</li>
           <li class="right"><a href="index.html" title="yt Overview" 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>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -25,7 +25,10 @@
       <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="" title="Global Module Index" accesskey="M">modules</a> |</li>
+    <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+    
         <li><a href="index.html">yt v0.3 documentation</a> »</li>
+
       </ul>
     </div>
     <div class="document">
@@ -38,7 +41,17 @@
 
 
 
-   <table width="100%" class="indextable" cellspacing="0" cellpadding="2">
+   <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>
+     <td><img src="_static/minus.png" id="toggle-1"
+            class="toggler" style="display: none" /></td>
+     <td>
+     <tt class="xref">lagos</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>
    </table>
 
 
@@ -62,12 +75,15 @@
       <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="" title="Global Module Index" accesskey="M">modules</a> |</li>
+    <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+    
         <li><a href="index.html">yt v0.3 documentation</a> »</li>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 2008.
     </div>
   </body>
 </html>
\ No newline at end of file

Added: trunk/doc/build/html/modules/lagos/basedatatypes.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/modules/lagos/basedatatypes.html	Mon May  5 08:49:34 2008
@@ -0,0 +1,239 @@
+<!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>lagos.BaseDataTypes – Data Types — 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" />
+    <link rel="prev" title="yt.lagos" 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="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><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">
+          <div class="body">
+            
+  
+  <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>
+<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>
+<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>
+<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>
+<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>
+<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>
+<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>
+<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>
+
+<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>
+</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>
+<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>
+
+<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>
+
+<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>
+<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>
+<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>
+<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>
+<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>
+
+<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>
+<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.
+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>
+
+<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>
+
+<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>
+<dd>Here we set up dictionaries that get passed up and down and ultimately
+to derived fields.</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="index.html" title="next chapter">yt.lagos</a></p>
+            <h3>This Page</h3>
+            <ul class="this-page-menu">
+              <li><a href="../../_sources/modules/lagos/basedatatypes.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="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><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 04, 2008.
+    </div>
+  </body>
+</html>
\ No newline at end of file

Modified: trunk/doc/build/html/modules/lagos/index.html
==============================================================================
--- trunk/doc/build/html/modules/lagos/index.html	(original)
+++ trunk/doc/build/html/modules/lagos/index.html	Mon May  5 08:49:34 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> — yt v0.3 documentation</title>
+    <title>yt.lagos — 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">
@@ -18,7 +18,7 @@
     <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="prev" title="A Short Tutorial on yt" href="../../tutorial/main.html" />
+    <link rel="prev" title="FAQ" href="../../faq.html" />
   </head>
   <body>
     <div class="related">
@@ -26,8 +26,11 @@
       <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="../../tutorial/main.html" title="A Short Tutorial on yt" accesskey="P">previous</a> |</li>
+          <li class="right"><a href="../../faq.html" title="FAQ" 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>
+
       </ul>
     </div>
     <div class="document">
@@ -36,7 +39,13 @@
           <div class="body">
             
   
-  
+  <div class="section">
+<h1 id="yt-lagos"><span id="lagos"></span>yt.lagos<a class="headerlink" href="#yt-lagos" title="Permalink to this headline">¶</a></h1>
+<ul>
+<li><a class="reference" href="basedatatypes.html"><tt class="docutils literal"><span class="pre">lagos.BaseDataTypes</span></tt> – Data Types</a></li>
+</ul>
+</div>
+
 
           </div>
         </div>
@@ -44,7 +53,7 @@
       <div class="sidebar">
         <div class="sidebarwrapper">
             <h4>Previous topic</h4>
-            <p class="topless"><a href="../../tutorial/main.html" title="previous chapter">A Short Tutorial on yt</a></p>
+            <p class="topless"><a href="../../faq.html" title="previous chapter">FAQ</a></p>
             <h3>This Page</h3>
             <ul class="this-page-menu">
               <li><a href="../../_sources/modules/lagos/index.txt">Show Source</a></li>
@@ -64,13 +73,16 @@
       <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="../../tutorial/main.html" title="A Short Tutorial on yt" accesskey="P">previous</a> |</li>
+          <li class="right"><a href="../../faq.html" title="FAQ" 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>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -18,7 +18,7 @@
     <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="next" title="Welcome to yt’s documentation!" href="../../index.html" />
+    <link rel="prev" title="yt.lagos" href="../lagos/index.html" />
   </head>
   <body>
     <div class="related">
@@ -26,8 +26,11 @@
       <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="Welcome to yt’s documentation!" accesskey="N">next</a> |</li>
+          <li class="right"><a href="../lagos/index.html" title="yt.lagos" 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>
+
       </ul>
     </div>
     <div class="document">
@@ -43,8 +46,8 @@
       </div>
       <div class="sidebar">
         <div class="sidebarwrapper">
-            <h4>Next topic</h4>
-            <p class="topless"><a href="../../index.html" title="next chapter">Welcome to yt’s documentation!</a></p>
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="../lagos/index.html" title="previous chapter">yt.lagos</a></p>
             <h3>This Page</h3>
             <ul class="this-page-menu">
               <li><a href="../../_sources/modules/raven/index.txt">Show Source</a></li>
@@ -64,13 +67,16 @@
       <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="Welcome to yt’s documentation!" accesskey="N">next</a> |</li>
+          <li class="right"><a href="../lagos/index.html" title="yt.lagos" 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>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -18,7 +18,7 @@
     <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="next" title="FAQ" href="../../faq.html" />
+    <link rel="next" title="yt Overview" href="../../index.html" />
   </head>
   <body>
     <div class="related">
@@ -26,8 +26,11 @@
       <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="../../faq.html" title="FAQ" accesskey="N">next</a> |</li>
+          <li class="right"><a href="../../index.html" title="yt Overview" 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>
+
       </ul>
     </div>
     <div class="document">
@@ -44,7 +47,7 @@
       <div class="sidebar">
         <div class="sidebarwrapper">
             <h4>Next topic</h4>
-            <p class="topless"><a href="../../faq.html" title="next chapter">FAQ</a></p>
+            <p class="topless"><a href="../../index.html" title="next chapter">yt Overview</a></p>
             <h3>This Page</h3>
             <ul class="this-page-menu">
               <li><a href="../../_sources/modules/reason/index.txt">Show Source</a></li>
@@ -64,13 +67,16 @@
       <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="../../faq.html" title="FAQ" accesskey="N">next</a> |</li>
+          <li class="right"><a href="../../index.html" title="yt Overview" 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>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -27,7 +27,10 @@
       <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><a href="http://yt.spacepope.org/">yt</a> »</li>
+    
         <li><a href="index.html">yt v0.3 documentation</a> »</li>
+
       </ul>
     </div>
     <div class="document">
@@ -65,12 +68,15 @@
       <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><a href="http://yt.spacepope.org/">yt</a> »</li>
+    
         <li><a href="index.html">yt v0.3 documentation</a> »</li>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -1 +1 @@
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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	Mon May  5 08:49:34 2008
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@@ -30,8 +30,11 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="projections.html" title="Projections" accesskey="N">next</a> |</li>
           <li class="right"><a href="automated_plotting.html" title="Automated Plotting" 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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="document">
@@ -47,6 +50,8 @@
 they behave the same way all the others do – you can get any field from them,
 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>
 <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
@@ -63,6 +68,9 @@
 (Note that the normal vector need not be a unit vector, as it will be normalized
 during the object instantiation.)  An appropriate ‘up’ vector is guessed at
 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>
 <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 –
@@ -86,6 +94,10 @@
 command creates a list of indices, which can then get fed into an array accessor
 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>
+</div>
+</div>
 
 
           </div>
@@ -93,6 +105,16 @@
       </div>
       <div class="sidebar">
         <div class="sidebarwrapper">
+            <h3>Table Of Contents</h3>
+            <ul>
+<li><a class="reference" href="">Advanced Objects</a><ul>
+<li><a class="reference" href="#cutting-plane">Cutting Plane</a></li>
+<li><a class="reference" href="#extracted-regions">Extracted Regions</a></li>
+<li><a class="reference" href="#grid-collections">Grid Collections</a></li>
+</ul>
+</li>
+</ul>
+
             <h4>Previous topic</h4>
             <p class="topless"><a href="automated_plotting.html" title="previous chapter">Automated Plotting</a></p>
             <h4>Next topic</h4>
@@ -118,13 +140,16 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="projections.html" title="Projections" accesskey="N">next</a> |</li>
           <li class="right"><a href="automated_plotting.html" title="Automated Plotting" 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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -18,7 +18,7 @@
     <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="A Short Tutorial on yt" href="main.html" />
+    <link rel="up" title="A Short Tutorial" href="index.html" />
     <link rel="next" title="Advanced Objects" href="advanced_objects.html" />
     <link rel="prev" title="Profiles" href="profiles.html" />
   </head>
@@ -30,8 +30,11 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="advanced_objects.html" title="Advanced Objects" accesskey="N">next</a> |</li>
           <li class="right"><a href="profiles.html" title="Profiles" 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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="document">
@@ -41,18 +44,26 @@
             
   
   <div class="section">
-<h1 id="automated-plotting">Automated Plotting<a class="headerlink" href="#automated-plotting" title="Permalink to this headline">¶</a></h1>
+<h1 id="automated-plotting"><span id="index-33"></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.
-The plotting tool is called ‘raven’ and it’s organized around the idea of
+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>
+<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.
 When you act on a PlotCollection, you act on all the plots that are part of that
 collection.  Each PlotCollection is associated with a single parameter file.</p>
 <div class="highlight"><pre><span class="gp">>>> </span><span class="k">import</span> <span class="nn">yt.raven</span> <span class="k">as</span> <span class="nn">raven</span>
 <span class="gp">>>> </span><span class="n">pc</span> <span class="o">=</span> <span class="n">raven</span><span class="o">.</span><span class="n">PlotCollection</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
-<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>
+</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>
+<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>
 <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">1</span><span class="p">)</span>
 <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">2</span><span class="p">)</span>
 <span class="gp">>>> </span><span class="n">pc</span><span class="o">.</span><span class="n">set_width</span><span class="p">(</span><span class="mf">15</span><span class="p">,</span> <span class="s">'kpc'</span><span class="p">)</span>
@@ -71,12 +82,16 @@
 can set to mpc, kpc, pc, au, km or cm.  Then we call save, and feed it a prefix –
 it takes care of adding some more information to the filename, so don’t supply it
 a file suffix.  (It defaults to ‘.png’)</p>
+</div>
+<div class="section">
+<h2 id="more-plots">More Plots<a class="headerlink" href="#more-plots" title="Permalink to this headline">¶</a></h2>
 <p>We have access to most of the interesting plots from the PlotCollection
 interface, including cutting planes and projections.  (More on those later!):</p>
 <div class="highlight"><pre><span class="gp">>>> </span><span class="n">pc</span><span class="o">.</span><span class="n">add_projection</span><span class="p">(</span><span class="s">"Temperature"</span><span class="p">,</span> <span class="mf">0</span><span class="p">,</span> <span class="n">weight_field</span><span class="o">=</span><span class="s">"CellMass"</span><span class="p">)</span>
 <span class="gp">>>> </span><span class="n">pc</span><span class="o">.</span><span class="n">add_threephase_sphere</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="s">'pc'</span><span class="p">,</span> <span class="p">[</span><span class="s">"Density"</span><span class="p">,</span><span class="s">"Temperature"</span><span class="p">,</span><span class="s">"H2I_Fraction"</span><span class="p">])</span>
 </pre></div>
 </div>
+</div>
 
 
           </div>
@@ -84,6 +99,16 @@
       </div>
       <div class="sidebar">
         <div class="sidebarwrapper">
+            <h3>Table Of Contents</h3>
+            <ul>
+<li><a class="reference" href="">Automated Plotting</a><ul>
+<li><a class="reference" href="#collections-of-plots">Collections of Plots</a></li>
+<li><a class="reference" href="#adding-plots">Adding Plots</a></li>
+<li><a class="reference" href="#more-plots">More Plots</a></li>
+</ul>
+</li>
+</ul>
+
             <h4>Previous topic</h4>
             <p class="topless"><a href="profiles.html" title="previous chapter">Profiles</a></p>
             <h4>Next topic</h4>
@@ -109,13 +134,16 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="advanced_objects.html" title="Advanced Objects" accesskey="N">next</a> |</li>
           <li class="right"><a href="profiles.html" title="Profiles" 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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -18,7 +18,7 @@
     <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="A Short Tutorial on yt" href="main.html" />
+    <link rel="up" title="A Short Tutorial" href="index.html" />
     <link rel="next" title="Derived Fields" href="derived_fields.html" />
     <link rel="prev" title="Getting Started" href="getting_started.html" />
   </head>
@@ -30,8 +30,11 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="derived_fields.html" title="Derived Fields" accesskey="N">next</a> |</li>
           <li class="right"><a href="getting_started.html" title="Getting Started" 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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="document">
@@ -47,6 +50,9 @@
 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>
+<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>
 <p>Entropy is a derived field.  But how does it work?  Well, we have a built-in
@@ -62,10 +68,13 @@
 </pre></div>
 <p>Okay, so now you’ve seen how to grab fields from a grid.  The thing about
 getting fields from a grid, though, is that it works the exact same way as
-all the other data types!  (Well, maybe not projection :)  So that raises the
+all the other data types!  (Well, maybe not projection.)  So that raises the
 question, how do we get more data objects?  Well, the hierarchy is our friend
 here.  We can get slices, projections, spheres, rectangular prisms,
 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>
 <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>
@@ -78,13 +87,19 @@
 <div class="highlight"><pre><span class="gp">>>> </span><span class="k">print</span> <span class="n">my_slice</span><span class="p">[</span><span class="s">"Pressure"</span><span class="p">],</span> <span class="n">my_slice</span><span class="p">[</span><span class="s">"Density"</span><span class="p">]</span>
 </pre></div>
 <p>Okay, so enough of the slices.  (Although they can do some more stuff, like
-shift around inside the domain, and so on and so forth.)</p>
+shift around inside the domain, and so on and so forth.)  Slices are typically
+used implicity with plotting (more on that later) and not very often from
+the interpreter.</p>
+</div>
+<div class="section">
+<h2 id="data-regions">Data Regions<a class="headerlink" href="#data-regions" title="Permalink to this headline">¶</a></h2>
 <p>Let’s do a region.  This is a box with a left edge and a right edge, and a
 center.  (You need a center for some other calculations, not for getting the
 region.)  Let’s get started by grabbing the ENTIRE domain.:</p>
 <div class="highlight"><pre><span class="gp">>>> </span><span class="n">my_region</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">region</span><span class="p">([</span><span class="mf">0.5</span><span class="p">,</span><span class="mf">0.5</span><span class="p">,</span><span class="mf">0.5</span><span class="p">],</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">0.0</span><span class="p">],</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span><span class="mf">1.0</span><span class="p">,</span><span class="mf">1.0</span><span class="p">])</span>
 </pre></div>
 </div>
+</div>
 
 
           </div>
@@ -92,6 +107,16 @@
       </div>
       <div class="sidebar">
         <div class="sidebarwrapper">
+            <h3>Table Of Contents</h3>
+            <ul>
+<li><a class="reference" href="">Basic Objects</a><ul>
+<li><a class="reference" href="#derived-fields-and-indices">Derived Fields and Indices</a></li>
+<li><a class="reference" href="#slices">Slices</a></li>
+<li><a class="reference" href="#data-regions">Data Regions</a></li>
+</ul>
+</li>
+</ul>
+
             <h4>Previous topic</h4>
             <p class="topless"><a href="getting_started.html" title="previous chapter">Getting Started</a></p>
             <h4>Next topic</h4>
@@ -117,13 +142,16 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="derived_fields.html" title="Derived Fields" accesskey="N">next</a> |</li>
           <li class="right"><a href="getting_started.html" title="Getting Started" 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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -18,7 +18,7 @@
     <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="A Short Tutorial on yt" href="main.html" />
+    <link rel="up" title="A Short Tutorial" href="index.html" />
     <link rel="next" title="Profiles" href="profiles.html" />
     <link rel="prev" title="Basic Objects" href="basic_objects.html" />
   </head>
@@ -30,8 +30,11 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="profiles.html" title="Profiles" accesskey="N">next</a> |</li>
           <li class="right"><a href="basic_objects.html" title="Basic Objects" 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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="document">
@@ -54,6 +57,8 @@
 But what other fields are available to us?:</p>
 <div class="highlight"><pre><span class="gp">>>> </span><span class="k">print</span> <span class="n">lagos</span><span class="o">.</span><span class="n">fieldInfo</span><span class="o">.</span><span class="n">keys</span><span class="p">()</span>
 </pre></div>
+<div class="section">
+<h2 id="defining-simple-fields">Defining Simple Fields<a class="headerlink" href="#defining-simple-fields" title="Permalink to this headline">¶</a></h2>
 <p>There are LOTS!  Not only that, but you can set up your own fields, too,
 which then become available to all data-types. Here’s a very simple example,
 where we just cube Density.:</p>
@@ -75,6 +80,9 @@
 returning fields – <em>everything is returned in cgs</em>!  This means that when
 we request “Density” from ‘data’ it is returned to us <em>already</em> in CGS, so we
 don’t need to convert anything.</p>
+</div>
+<div class="section">
+<h2 id="more-complicated-fields">More Complicated Fields<a class="headerlink" href="#more-complicated-fields" title="Permalink to this headline">¶</a></h2>
 <p>The last part, the call to add_field, is the most crucial.  It creates a
 DerivedField object which will control the behavior of the derived field in a
 couple crucial ways – what you see here includes the string used for the
@@ -85,6 +93,7 @@
 require ghost zones, which will be automatically generated.  Check the
 “AveragedDensity” and “DivV” fields in the source code for an example of this.</p>
 </div>
+</div>
 
 
           </div>
@@ -92,6 +101,15 @@
       </div>
       <div class="sidebar">
         <div class="sidebarwrapper">
+            <h3>Table Of Contents</h3>
+            <ul>
+<li><a class="reference" href="">Derived Fields</a><ul>
+<li><a class="reference" href="#defining-simple-fields">Defining Simple Fields</a></li>
+<li><a class="reference" href="#more-complicated-fields">More Complicated Fields</a></li>
+</ul>
+</li>
+</ul>
+
             <h4>Previous topic</h4>
             <p class="topless"><a href="basic_objects.html" title="previous chapter">Basic Objects</a></p>
             <h4>Next topic</h4>
@@ -117,13 +135,16 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="profiles.html" title="Profiles" accesskey="N">next</a> |</li>
           <li class="right"><a href="basic_objects.html" title="Basic Objects" 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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 2008.
     </div>
   </body>
 </html>
\ No newline at end of file

Added: trunk/doc/build/html/tutorial/derived_quantities.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/tutorial/derived_quantities.html	Mon May  5 08:49:34 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>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="A Short Tutorial" href="index.html" />
+    <link rel="next" title="A Demonstrative Example Script" href="example_script.html" />
+    <link rel="prev" title="Projections" href="projections.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="example_script.html" title="A Demonstrative Example Script" accesskey="N">next</a> |</li>
+          <li class="right"><a href="projections.html" title="Projections" 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">A Short Tutorial</a> »</li>
+      </ul>
+    </div>
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  
+  <div class="section">
+<h1 id="derived-quantities">Derived Quantities<a class="headerlink" href="#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="projections.html" title="previous chapter">Projections</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="example_script.html" title="next chapter">A Demonstrative Example Script</a></p>
+            <h3>This Page</h3>
+            <ul class="this-page-menu">
+              <li><a href="../_sources/tutorial/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="example_script.html" title="A Demonstrative Example Script" accesskey="N">next</a> |</li>
+          <li class="right"><a href="projections.html" title="Projections" 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">A Short Tutorial</a> »</li>
+      </ul>
+    </div>
+    <div class="footer">
+      © Copyright 2008, Matthew Turk.
+      Last updated on May 04, 2008.
+    </div>
+  </body>
+</html>
\ No newline at end of file

Added: trunk/doc/build/html/tutorial/example_script.html
==============================================================================
--- (empty file)
+++ trunk/doc/build/html/tutorial/example_script.html	Mon May  5 08:49:34 2008
@@ -0,0 +1,124 @@
+<!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>A Demonstrative Example Script — 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="A Short Tutorial" href="index.html" />
+    <link rel="next" title="A Short Tutorial" href="index.html" />
+    <link rel="prev" title="Derived Quantities" href="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="index.html" title="A Short Tutorial" accesskey="N">next</a> |</li>
+          <li class="right"><a href="derived_quantities.html" title="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">A Short Tutorial</a> »</li>
+      </ul>
+    </div>
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  
+  <div class="section">
+<h1 id="a-demonstrative-example-script">A Demonstrative Example Script<a class="headerlink" href="#a-demonstrative-example-script" title="Permalink to this headline">¶</a></h1>
+<p>During the course of my work, I often have to run a selection of data analysis
+tasks in order to keep tabs on my simulation as it runs.  I’ve included below a
+script that I run on each output as it is created.</p>
+<div class="highlight"><pre><span class="k">import</span> <span class="nn">sys</span>
+<span class="k">import</span> <span class="nn">yt.lagos</span> <span class="k">as</span> <span class="nn">lagos</span>
+<span class="k">import</span> <span class="nn">yt.raven</span> <span class="k">as</span> <span class="nn">raven</span>
+
+<span class="n">fn</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="o">-</span><span class="mf">1</span><span class="p">]</span>
+<span class="n">pf</span> <span class="o">=</span> <span class="n">lagos</span><span class="o">.</span><span class="n">EnzoStaticOutput</span><span class="p">(</span><span class="n">fn</span><span class="p">)</span>
+<span class="n">pf</span><span class="o">.</span><span class="n">h</span><span class="o">.</span><span class="n">print_stats</span><span class="p">()</span>
+
+<span class="n">fields_to_plot</span> <span class="o">=</span> <span class="p">[</span><span class="s">"NumberDensity"</span><span class="p">,</span> <span class="s">"Density"</span><span class="p">,</span> <span class="s">"Temperature"</span><span class="p">,</span> <span class="s">"H2I_Fraction"</span><span class="p">]</span>
+
+<span class="n">my_vals</span> <span class="o">=</span> <span class="p">[</span><span class="mf">1000.0</span><span class="p">,</span> <span class="mf">100.0</span><span class="p">,</span> <span class="mf">10.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">]</span>
+<span class="n">my_units</span> <span class="o">=</span> <span class="p">[</span><span class="s">'au'</span><span class="p">,</span><span class="s">'rsun'</span><span class="p">]</span>
+
+<span class="n">my_widths</span> <span class="o">=</span> <span class="p">[]</span>
+
+<span class="k">for</span> <span class="n">unit</span> <span class="ow">in</span> <span class="n">my_units</span><span class="p">:</span>
+    <span class="n">my_widths</span> <span class="o">+=</span> <span class="p">[(</span><span class="n">v</span><span class="p">,</span><span class="n">units</span><span class="p">)</span> <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">my_vals</span><span class="p">]</span>
+
+<span class="n">pc</span> <span class="o">=</span> <span class="n">raven</span><span class="o">.</span><span class="n">PlotCollection</span><span class="p">(</span><span class="n">pf</span><span class="p">)</span>
+<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mf">3</span><span class="p">):</span> <span class="n">pc</span><span class="o">.</span><span class="n">add_slice</span><span class="p">(</span><span class="s">"NumberDensity"</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span>
+
+<span class="k">for</span> <span class="n">field</span> <span class="ow">in</span> <span class="n">fields_to_plot</span><span class="p">:</span>
+    <span class="n">pc</span><span class="o">.</span><span class="n">switch_field</span><span class="p">(</span><span class="n">field</span><span class="p">)</span>
+    <span class="k">for</span> <span class="n">w</span><span class="p">,</span> <span class="n">u</span> <span class="ow">in</span> <span class="n">my_widths</span><span class="p">:</span>
+        <span class="n">pc</span><span class="o">.</span><span class="n">set_width</span><span class="p">(</span><span class="n">w</span><span class="p">,</span><span class="n">u</span><span class="p">)</span>
+        <span class="n">pc</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="s">"</span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">pf</span><span class="p">)</span>
+</pre></div>
+<p>And that’s it!</p>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sidebar">
+        <div class="sidebarwrapper">
+            <h4>Previous topic</h4>
+            <p class="topless"><a href="derived_quantities.html" title="previous chapter">Derived Quantities</a></p>
+            <h4>Next topic</h4>
+            <p class="topless"><a href="index.html" title="next chapter">A Short Tutorial</a></p>
+            <h3>This Page</h3>
+            <ul class="this-page-menu">
+              <li><a href="../_sources/tutorial/example_script.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="index.html" title="A Short Tutorial" accesskey="N">next</a> |</li>
+          <li class="right"><a href="derived_quantities.html" title="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">A Short Tutorial</a> »</li>
+      </ul>
+    </div>
+    <div class="footer">
+      © Copyright 2008, Matthew Turk.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -30,7 +30,10 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="basic_objects.html" title="Basic Objects" accesskey="N">next</a> |</li>
           <li class="right"><a href="index.html" title="A Short Tutorial" 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">A Short Tutorial</a> »</li>
       </ul>
     </div>
@@ -43,7 +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">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-21"></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>
@@ -59,7 +62,7 @@
 </pre></div>
 </div>
 <div class="section">
-<h2 id="the-hierarchy">The Hierarchy<a class="headerlink" href="#the-hierarchy" title="Permalink to this headline">¶</a></h2>
+<h2 id="the-hierarchy"><span id="index-22"></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>
@@ -77,7 +80,7 @@
 </pre></div>
 </div>
 <div class="section">
-<h2 id="the-grids">The Grids<a class="headerlink" href="#the-grids" title="Permalink to this headline">¶</a></h2>
+<h2 id="the-grids"><span id="index-23"></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>
@@ -138,13 +141,16 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="basic_objects.html" title="Basic Objects" accesskey="N">next</a> |</li>
           <li class="right"><a href="index.html" title="A Short Tutorial" 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">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -18,7 +18,7 @@
     <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="prev" title="FAQ" href="../intro.html" />
+    <link rel="prev" title="Introduction" href="../intro.html" />
   </head>
   <body>
     <div class="related">
@@ -26,8 +26,11 @@
       <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="../intro.html" title="FAQ" accesskey="P">previous</a> |</li>
+          <li class="right"><a href="../intro.html" title="Introduction" 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>
+
       </ul>
     </div>
     <div class="document">
@@ -38,6 +41,10 @@
   
   <div class="section">
 <h1 id="a-short-tutorial">A Short Tutorial<a class="headerlink" href="#a-short-tutorial" title="Permalink to this headline">¶</a></h1>
+<p>As with many interactive packages, getting started with yt can be a bit
+daunting.  Following this tutorial we’ll walk through the intepreter, get used
+to some of the ways that yt works, and performing some common (and
+not-so-common) tasks.</p>
 <p>Contents:</p>
 <ul>
 <li><a class="reference" href="getting_started.html">Getting Started</a><ul>
@@ -48,22 +55,55 @@
 </li>
 </ul>
 <ul>
-<li><a class="reference" href="basic_objects.html">Basic Objects</a></li>
+<li><a class="reference" href="basic_objects.html">Basic Objects</a><ul>
+<li><a class="reference" href="basic_objects.html#derived-fields-and-indices">Derived Fields and Indices</a></li>
+<li><a class="reference" href="basic_objects.html#slices">Slices</a></li>
+<li><a class="reference" href="basic_objects.html#data-regions">Data Regions</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li><a class="reference" href="derived_fields.html">Derived Fields</a><ul>
+<li><a class="reference" href="derived_fields.html#defining-simple-fields">Defining Simple Fields</a></li>
+<li><a class="reference" href="derived_fields.html#more-complicated-fields">More Complicated Fields</a></li>
+</ul>
+</li>
+</ul>
+<ul>
+<li><a class="reference" href="profiles.html">Profiles</a><ul>
+<li><a class="reference" href="profiles.html#one-dimensional-profiles">One Dimensional Profiles</a></li>
+<li><a class="reference" href="profiles.html#two-dimensional-profiles">Two-Dimensional Profiles</a></li>
+</ul>
+</li>
 </ul>
 <ul>
-<li><a class="reference" href="derived_fields.html">Derived Fields</a></li>
+<li><a class="reference" href="automated_plotting.html">Automated Plotting</a><ul>
+<li><a class="reference" href="automated_plotting.html#collections-of-plots">Collections of Plots</a></li>
+<li><a class="reference" href="automated_plotting.html#adding-plots">Adding Plots</a></li>
+<li><a class="reference" href="automated_plotting.html#more-plots">More Plots</a></li>
+</ul>
+</li>
 </ul>
 <ul>
-<li><a class="reference" href="profiles.html">Profiles</a></li>
+<li><a class="reference" href="advanced_objects.html">Advanced Objects</a><ul>
+<li><a class="reference" href="advanced_objects.html#cutting-plane">Cutting Plane</a></li>
+<li><a class="reference" href="advanced_objects.html#extracted-regions">Extracted Regions</a></li>
+<li><a class="reference" href="advanced_objects.html#grid-collections">Grid Collections</a></li>
+</ul>
+</li>
 </ul>
 <ul>
-<li><a class="reference" href="automated_plotting.html">Automated Plotting</a></li>
+<li><a class="reference" href="projections.html">Projections</a><ul>
+<li><a class="reference" href="projections.html#simple-projections">Simple Projections</a></li>
+<li><a class="reference" href="projections.html#parallel-projections">Parallel Projections</a></li>
+</ul>
+</li>
 </ul>
 <ul>
-<li><a class="reference" href="advanced_objects.html">Advanced Objects</a></li>
+<li><a class="reference" href="derived_quantities.html">Derived Quantities</a></li>
 </ul>
 <ul>
-<li><a class="reference" href="projections.html">Projections</a></li>
+<li><a class="reference" href="example_script.html">A Demonstrative Example Script</a></li>
 </ul>
 </div>
 
@@ -74,7 +114,7 @@
       <div class="sidebar">
         <div class="sidebarwrapper">
             <h4>Previous topic</h4>
-            <p class="topless"><a href="../intro.html" title="previous chapter">FAQ</a></p>
+            <p class="topless"><a href="../intro.html" title="previous chapter">Introduction</a></p>
             <h3>This Page</h3>
             <ul class="this-page-menu">
               <li><a href="../_sources/tutorial/index.txt">Show Source</a></li>
@@ -94,13 +134,16 @@
       <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="../intro.html" title="FAQ" accesskey="P">previous</a> |</li>
+          <li class="right"><a href="../intro.html" title="Introduction" 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>
+
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -18,7 +18,7 @@
     <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="A Short Tutorial on yt" href="main.html" />
+    <link rel="up" title="A Short Tutorial" href="index.html" />
     <link rel="next" title="Automated Plotting" href="automated_plotting.html" />
     <link rel="prev" title="Derived Fields" href="derived_fields.html" />
   </head>
@@ -30,8 +30,11 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="automated_plotting.html" title="Automated Plotting" accesskey="N">next</a> |</li>
           <li class="right"><a href="derived_fields.html" title="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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="document">
@@ -47,6 +50,8 @@
 you could get an average temperature in Density and H2 Fraction space.  Or you could
 Look at the distribution of Volume through Density and Temperature space.  Or you could
 take the spherically-averaged Number Density and see how it changes with radius.</p>
+<div class="section">
+<h2 id="one-dimensional-profiles">One Dimensional Profiles<a class="headerlink" href="#one-dimensional-profiles" title="Permalink to this headline">¶</a></h2>
 <p>In order to make a profile, we first need a data object we want to get the profile
 <em>from</em>.  This can be a sphere, a region, or even an extracted region.  We’ll
 first take a look at doing a spherically-average profile of Temperature with Radius.</p>
@@ -78,6 +83,9 @@
 <span class="gp">>>> </span><span class="n">pylab</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s">r"$\rm{Density} (\rm{g}/\rm{cm}^3)$"</span><span class="p">)</span>
 <span class="gp">>>> </span><span class="n">pylab</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s">"my_profile.png"</span><span class="p">)</span>
 </pre></div>
+</div>
+<div class="section">
+<h2 id="two-dimensional-profiles">Two-Dimensional Profiles<a class="headerlink" href="#two-dimensional-profiles" title="Permalink to this headline">¶</a></h2>
 <p>Two-dimensional profiles are along the same lines.</p>
 <div class="highlight"><pre><span class="gp">>>> </span><span class="n">prof2d</span> <span class="o">=</span> <span class="n">lagos</span><span class="o">.</span><span class="n">BinnedProfile2D</span><span class="p">(</span><span class="n">sphere</span><span class="p">,</span>
 <span class="gp">... </span>                <span class="mf">16</span><span class="p">,</span> <span class="s">"Density"</span><span class="p">,</span> <span class="mf">1e-32</span><span class="p">,</span> <span class="mf">1e-24</span><span class="p">,</span> <span class="bp">True</span><span class="p">,</span>
@@ -87,6 +95,7 @@
 <span class="gp">... </span>                 <span class="n">prof2d</span><span class="p">[</span><span class="s">"CellVolume"</span><span class="p">]</span><span class="o">.</span><span class="n">transpose</span><span class="p">())</span>
 </pre></div>
 </div>
+</div>
 
 
           </div>
@@ -94,6 +103,15 @@
       </div>
       <div class="sidebar">
         <div class="sidebarwrapper">
+            <h3>Table Of Contents</h3>
+            <ul>
+<li><a class="reference" href="">Profiles</a><ul>
+<li><a class="reference" href="#one-dimensional-profiles">One Dimensional Profiles</a></li>
+<li><a class="reference" href="#two-dimensional-profiles">Two-Dimensional Profiles</a></li>
+</ul>
+</li>
+</ul>
+
             <h4>Previous topic</h4>
             <p class="topless"><a href="derived_fields.html" title="previous chapter">Derived Fields</a></p>
             <h4>Next topic</h4>
@@ -119,13 +137,16 @@
         <li class="right"><a href="../modindex.html" title="Global Module Index" accesskey="M">modules</a> |</li>
           <li class="right"><a href="automated_plotting.html" title="Automated Plotting" accesskey="N">next</a> |</li>
           <li class="right"><a href="derived_fields.html" title="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="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 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	Mon May  5 08:49:34 2008
@@ -18,8 +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="A Short Tutorial on yt" href="main.html" />
-    <link rel="next" title="A Short Tutorial on yt" href="main.html" />
+    <link rel="up" title="A Short Tutorial" href="index.html" />
+    <link rel="next" title="A Short Tutorial" href="index.html" />
     <link rel="prev" title="Advanced Objects" href="advanced_objects.html" />
   </head>
   <body>
@@ -28,10 +28,13 @@
       <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="main.html" title="A Short Tutorial on yt" accesskey="N">next</a> |</li>
+          <li class="right"><a href="index.html" title="A Short Tutorial" 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>
+    
         <li><a href="../index.html">yt v0.3 documentation</a> »</li>
-          <li><a href="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="document">
@@ -45,6 +48,8 @@
 <p>Projections are the line integrals of a given quantity along a given access.
 These are useful in a wide variety of problems – they can reveal morphologies
 that slicing cannot, in the simplest case.</p>
+<div class="section">
+<h2 id="simple-projections">Simple Projections<a class="headerlink" href="#simple-projections" title="Permalink to this headline">¶</a></h2>
 <p>There are several ways to generate projections in yt, and with the appropriate
 software package installed (mpi4py) one can even generate them in parallel,
 distributed across an arbitrary number of nodes.  However, I will deal here
@@ -63,6 +68,10 @@
 for it, it is already available.  Zooming and panning is accomplished very
 simply.</p>
 </div>
+<div class="section">
+<h2 id="parallel-projections">Parallel Projections<a class="headerlink" href="#parallel-projections" title="Permalink to this headline">¶</a></h2>
+</div>
+</div>
 
 
           </div>
@@ -70,10 +79,19 @@
       </div>
       <div class="sidebar">
         <div class="sidebarwrapper">
+            <h3>Table Of Contents</h3>
+            <ul>
+<li><a class="reference" href="">Projections</a><ul>
+<li><a class="reference" href="#simple-projections">Simple Projections</a></li>
+<li><a class="reference" href="#parallel-projections">Parallel Projections</a></li>
+</ul>
+</li>
+</ul>
+
             <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="main.html" title="next chapter">A Short Tutorial on yt</a></p>
+            <p class="topless"><a href="index.html" title="next chapter">A Short Tutorial</a></p>
             <h3>This Page</h3>
             <ul class="this-page-menu">
               <li><a href="../_sources/tutorial/projections.txt">Show Source</a></li>
@@ -93,15 +111,18 @@
       <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="main.html" title="A Short Tutorial on yt" accesskey="N">next</a> |</li>
+          <li class="right"><a href="index.html" title="A Short Tutorial" 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>
+    
         <li><a href="../index.html">yt v0.3 documentation</a> »</li>
-          <li><a href="main.html" accesskey="U">A Short Tutorial on yt</a> »</li>
+
+          <li><a href="index.html" accesskey="U">A Short Tutorial</a> »</li>
       </ul>
     </div>
     <div class="footer">
       © Copyright 2008, Matthew Turk.
-      Last updated on May 03, 2008.
+      Last updated on May 04, 2008.
     </div>
   </body>
 </html>
\ No newline at end of file

Added: trunk/doc/source/.templates/layout.html
==============================================================================
--- (empty file)
+++ trunk/doc/source/.templates/layout.html	Mon May  5 08:49:34 2008
@@ -0,0 +1,5 @@
+{% extends "!layout.html" %}
+{% block rootrellink %}
+    <li><a href="http://yt.spacepope.org/">yt</a> »</li>
+    {{ super() }}
+{% endblock %}

Modified: trunk/doc/source/conf.py
==============================================================================
--- trunk/doc/source/conf.py	(original)
+++ trunk/doc/source/conf.py	Mon May  5 08:49:34 2008
@@ -23,7 +23,7 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-#extensions = []
+extensions = ['sphinx.ext.autodoc']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['.templates']

Added: trunk/doc/source/cookbook/index.rst
==============================================================================

Modified: trunk/doc/source/extending/index.rst
==============================================================================
--- trunk/doc/source/extending/index.rst	(original)
+++ trunk/doc/source/extending/index.rst	Mon May  5 08:49:34 2008
@@ -18,3 +18,6 @@
 
 Analyzing in Parallel
 ---------------------
+
+Running Fortran Routines
+------------------------

Modified: trunk/doc/source/faq.rst
==============================================================================
--- trunk/doc/source/faq.rst	(original)
+++ trunk/doc/source/faq.rst	Mon May  5 08:49:34 2008
@@ -4,21 +4,66 @@
 Why Python?
 -----------
 
-What do I need to use yt?
--------------------------
+Well, the easiest answer is that I knew it, and it met the requirements.  The
+more interesting answer, though, is a combination of things.  Python right now
+has a lot of momentum behind it, particularly in the scientific community.
+It's easy to compile, portable across many architectures, relatively simple to
+write C-based exntesions for, and it's well-suited to rapid application
+development.  With access to an interpreter, new avenues of data-exploration
+are opened, and this can lead to much more rapid and interesting analysis.
+
+Where can I learn more about Python?
+------------------------------------
+
+There are several good, free books about Python available on the web.  The best
+place to start is with the `official tutorial <http://docs.python.org/tut/>`_,
+but there's also `Dive Into Python <http://www.diveintopython.org/>`_, an
+entire `collection of videos <http://showmedo.com/videos/python?topic=beginner_programming>`_ on 
+`ShowMeDo.com <http://showmedo.com/>`_, and a much more specific guide to using
+`NumPy <http://www.scipy.org/Tentative_NumPy_Tutorial>`_, which is the backend
+on which all the math done in yt is based.
+
+As far as books go, the only book I've found to be absolutely indispensible is
+the `Beazley Book <http://www.amazon.com/exec/obidos/ASIN/0735710910>`_.
 
 What's up with the names?
 -------------------------
 
+In the book `Snow Crash <http://en.wikipedia.org/wiki/Snow_Crash>`_, yt is
+Uncle Enzo's messenger.  Lagos is the keeper of the data, Raven is a master
+slicer, and so on.
+
 Are there any restrictions on my use of yt?
 -------------------------------------------
 
+yt has been released under Version 3 of the 
+`GNU General Public License <http://www.gnu.org/licenses/gpl.html>`_.
+
+If you found it useful, and have extended it in some meaningful way, of course
+I'd love to see your contributions so they can be shared with the community.
+Additionally, if you use yt in a paper, I'd love it if you'd drop me a line to
+let me know.
+
 How can I help?
 ---------------
 
+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. 
+
 Something has gone wrong.  What do I do?
 ----------------------------------------
 
+Well, first off, double check that you're giving the code what it needs, and
+not asking it for something it can't provide.  Use the ``help()`` command on
+an object or a method to get more information.
+
+If you can't figure out what's up, please go ahead and copy the resultant
+traceback information (the error message it prints out) along with any log
+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/>`_.  
+
 Where can I go for support?
 ---------------------------
 
+I've set up a ``yt-users`` mailing list.  There's more information about it
+at the `yt homepage <http://yt.spacepope.org>`_.

Modified: trunk/doc/source/index.rst
==============================================================================
--- trunk/doc/source/index.rst	(original)
+++ trunk/doc/source/index.rst	Mon May  5 08:49:34 2008
@@ -11,6 +11,7 @@
 
    intro
    tutorial/index
+   cookbook/index
    extending/index
    faq
    modules/lagos/index

Modified: trunk/doc/source/intro.rst
==============================================================================
--- trunk/doc/source/intro.rst	(original)
+++ trunk/doc/source/intro.rst	Mon May  5 08:49:34 2008
@@ -1,11 +1,92 @@
 Introduction
 ============
 
-Adaptive Mesh Refinement Data
------------------------------
+History
+-------
+
+My name is Matthew Turk, and I am the primary author of yt.  I designed and
+implemented it during the course of my graduate studies working with Prof. Tom
+Abel at Stanford University, under the auspices of the Department of Energy
+through the Stanford Linear Accelerator Center and Los Alamos National Lab.  It
+has evolved from a simple data-reader and exporter into what I believe is a
+fully-featured toolkit.
+
+yt was designed to be a completely Free (as in beer *and* as in freedom)
+user-extensible framework for analyzing and visualizing adaptive mesh
+refinement data.  It relies on no proprietary software -- although it can be
+and has been extended to interface with proprietary software and libraries --
+and has been designed from the ground up to enable users to be as immersed in
+the data as they desire.
+
+Originally, yt was written as a frontend to HippoDraw, an extensible and
+comprehensive plotting package built at SLAC by Paul Kunz.  Over time, however,
+it has been generalized to rely on mostly commodity Python packages, and its
+dependencies reduced and ease of installation increased.
 
 What yt is and is not
 ---------------------
 
+In some sense, yt is also designed to be rather utilitarian.  By virtue of the
+fact that it has been written in an interpreted language, it can be somewhat
+slower than purely C-based analysis codes, although I believe that to be
+mitigated by a cleverness of algorithms and a substantially improved
+development time for the user in the case of a desire to expand the
+functionality.
+
+```EXPAND```
+
 Prerequisites for yt
 --------------------
+
+A driving factor in the development of yt over the months leading to release
+0.3 has been the reduction of dependencies.  To that extent, only a few
+packages are required for the base usage, and a GUI toolkit if you are going to use
+the graphical user interface, Reason.
+
+ * `Python <http://python.org/>`_, at least version 2.4, but preferably 2.5.
+ * `HDF5 <http://www.hdfgroup.org/>`_, the data storage backend used by Enzo
+   and yt (if you can run Enzo, this is already installed!)
+ * `NumPy <http://numpy.scipy.org/>`_, the fast numerical backend for Python
+ * `MatPlotLib <http://matplotlib.sf.net/>`_, the plotting package
+ * `wxPython <http://www.wxpython.org/>`_, the GUI toolkit
+
+(If you are only interested in manipulating data without any graphical plotting
+or interfaces, you only need to install NumPy and Python!)
+
+Installing the Necessary Packages
+---------------------------------
+
+Installing Python itself is usually quite simple, and often very fast.  Because
+we're setting up a small system of packages, even if you have a system-wide
+install of python2.5 it can be easier in some cases to create a local directory
+structure:
+
+.. code-block:: bash
+
+   $ tar xvf Python-2.5.2.tar.gz
+   $ cd Python-2.5.2
+   $ ./configure --prefix=$HOME/local/
+   $ make install
+
+This will create (if necessary) a directory named local in your home directory,
+along with the necessary subdirectories.  When the executable
+``$HOME/lcoal/bin/python2.4`` is used to install a package, it will install it
+to the ``$HOME/local/`` directory structure.
+
+The python packages are fairly straightforward to install.  The process of
+installing packages in python has been greatly simplified over the last few
+years with the addition of setuptools, but for these particular packages I
+typically recommend installing from source, which for Python packages consists
+of changing to the source directory and issues the command:
+
+.. code-block:: bash
+
+   $ tar xvfz $PKGNAME.tar.gz
+   $ cd $PKGNAME
+   $ python2.5 setup.py install
+
+This method works for NumPy, Matplotlib and yt itself, but for wxPython, I
+**strongly** suggest you seek binaries for your platform.  If they are not
+available, I recommend you read the ``INSTALL`` file and follow its directions
+closely.
+

Added: trunk/doc/source/modules/lagos/basedatatypes.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/modules/lagos/basedatatypes.rst	Mon May  5 08:49:34 2008
@@ -0,0 +1,15 @@
+:mod:`lagos.BaseDataTypes` -- Data Types
+===========================================
+
+.. module:: lagos.BaseDataTypes
+   :synopsis: Generate containers to hold AMR data
+.. moduleauthor:: Matthew Turk <mturk at stanford.edu>
+
+.. autoclass:: yt.lagos.EnzoData
+   :members:
+
+.. autoclass:: yt.lagos.Enzo3DData
+   :members:
+
+.. autoclass:: yt.lagos.EnzoSphereBase
+   :members:

Modified: trunk/doc/source/modules/lagos/index.rst
==============================================================================
--- trunk/doc/source/modules/lagos/index.rst	(original)
+++ trunk/doc/source/modules/lagos/index.rst	Mon May  5 08:49:34 2008
@@ -0,0 +1,9 @@
+.. _lagos:
+
+yt.lagos
+======================
+
+.. toctree::
+   :maxdepth: 2
+
+   basedatatypes

Modified: trunk/doc/source/tutorial/advanced_objects.rst
==============================================================================
--- trunk/doc/source/tutorial/advanced_objects.rst	(original)
+++ trunk/doc/source/tutorial/advanced_objects.rst	Mon May  5 08:49:34 2008
@@ -1,5 +1,5 @@
 Advanced Objects
-----------------
+================
 
 So we've seen simple objects already -- sphere, profiles, and regions.
 There are two other types of objects that are fairly cool, as well, and
@@ -7,6 +7,11 @@
 profile them, all of that, right from the command line like you would a sphere
 or a region.
 
+.. index:: Cutting Plane, 2ddata;Cutting Plane
+
+Cutting Plane
+-------------
+
 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
@@ -25,6 +30,11 @@
 during the object instantiation.)  An appropriate 'up' vector is guessed at
 and then used to define the transformed coordinate system.
 
+.. index:: Extracted Regions, 3ddata;Extracted Regions
+
+Extracted Regions
+-----------------
+
 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 --
@@ -49,3 +59,8 @@
 everything, and we have been, too, when we've been using our data.  The 'where'
 command creates a list of indices, which can then get fed into an array accessor
 method, and that's the functionality we use here.
+
+.. index:: GridCollection, 3ddata;GridCollection
+
+Grid Collections
+----------------

Modified: trunk/doc/source/tutorial/automated_plotting.rst
==============================================================================
--- trunk/doc/source/tutorial/automated_plotting.rst	(original)
+++ trunk/doc/source/tutorial/automated_plotting.rst	Mon May  5 08:49:34 2008
@@ -1,9 +1,17 @@
+.. index:: Plotting
+
 Automated Plotting
-------------------
+==================
 
 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.
+
+.. index:: Raven, PlotCollections, Plotting;PlotCollections
+
+Collections of Plots
+--------------------
+
 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.
@@ -12,13 +20,21 @@
 
    >>> import yt.raven as raven
    >>> pc = raven.PlotCollection(a)
+
+.. index:: Plotting;Adding plots to PlotCollections, Raven, PlotCollections;Adding Plots
+
+Adding Plots
+------------
+
+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!::
+
    >>> pc.add_slice("Density", 0)
    >>> pc.add_slice("Density", 1)
    >>> pc.add_slice("Density", 2)
    >>> pc.set_width(15, 'kpc')
    >>> pc.save("somename_15kpc")
 
-
 There's a lot in that little block of text.  First I add a slice (note that while
 we can feed it a pre-existing slice, it will also grab one automatically if we
 don't!) along each axis (0,1,2) in the field "Density".  Each time we
@@ -34,6 +50,9 @@
 it takes care of adding some more information to the filename, so don't supply it
 a file suffix.  (It defaults to '.png')
 
+More Plots
+----------
+
 We have access to most of the interesting plots from the PlotCollection
 interface, including cutting planes and projections.  (More on those later!)::
 

Modified: trunk/doc/source/tutorial/basic_objects.rst
==============================================================================
--- trunk/doc/source/tutorial/basic_objects.rst	(original)
+++ trunk/doc/source/tutorial/basic_objects.rst	Mon May  5 08:49:34 2008
@@ -1,58 +1,68 @@
 Basic Objects
--------------
+=============
 
 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.  ::
+pre-defined, but from within a script you can also define your own.
 
-   >>> print my_grid["Entropy"]
+.. index:: derivedfield, indices
+
+Derived Fields and Indices
+--------------------------
 
+Let's try out some of the derived fields.::
+
+   >>> print my_grid["Entropy"]
 
 Entropy is a derived field.  But how does it work?  Well, we have a built-in
 source-code inspector.  ::
 
    >>> print lagos.fieldInfo["Entropy"].get_source()
 
-
 But what if we only want a couple values?  We can directly grab indices.  ::
 
    >>> print my_grid["Density"][0,10,4] # 0-indexed!
 
-
 We can also slice, using the slice operator: ':' ::
 
    >>> print my_grid["Density"][0,:,4]
    >>> print my_grid["Density"][0,2:4,4]
 
-
 Okay, so now you've seen how to grab fields from a grid.  The thing about
 getting fields from a grid, though, is that it works the exact same way as
-all the other data types!  (Well, maybe not projection :)  So that raises the
+all the other data types!  (Well, maybe not projection.)  So that raises the
 question, how do we get more data objects?  Well, the hierarchy is our friend
 here.  We can get slices, projections, spheres, rectangular prisms,
 fixed-resolution grids and cutting planes from the herarchy.
 
+.. index:: Slices, 2ddata;Slices
+
+Slices
+------
+
 Let's start with a slice.  A slice needs some info, but how do we know what
 type?  Well, let's use 'help'!::
 
    >>> help(a.h.slice)
 
-
 Looks like we need to feed it an axis, a coordinate, and maybe some fields
 and a center.  Axes are always done as numbers, with 0 = x, 1 = y, 2 = z.::
 
    >>> my_slice = a.h.slice(0, 0.5, "Density")  # We don't really need to pass the field!
 
-
 Now let's test out getting new fields.::
 
    >>> print my_slice["Pressure"], my_slice["Density"]
 
-
 Okay, so enough of the slices.  (Although they can do some more stuff, like
-shift around inside the domain, and so on and so forth.)
+shift around inside the domain, and so on and so forth.)  Slices are typically
+used implicity with plotting (more on that later) and not very often from
+the interpreter.
+
+Data Regions
+------------
 
 Let's do a region.  This is a box with a left edge and a right edge, and a
 center.  (You need a center for some other calculations, not for getting the

Modified: trunk/doc/source/tutorial/derived_fields.rst
==============================================================================
--- trunk/doc/source/tutorial/derived_fields.rst	(original)
+++ trunk/doc/source/tutorial/derived_fields.rst	Mon May  5 08:49:34 2008
@@ -1,5 +1,5 @@
 Derived Fields
---------------
+==============
 
 Okay, now we have a region.  We can do stuff with this -- in fact, it has the
 same data-access protocol as a slice or a grid!  Plus, math on these things
@@ -16,6 +16,8 @@
 
    >>> print lagos.fieldInfo.keys()
 
+Defining Simple Fields
+----------------------
 
 There are LOTS!  Not only that, but you can set up your own fields, too,
 which then become available to all data-types. Here's a very simple example,
@@ -40,6 +42,9 @@
 we request "Density" from 'data' it is returned to us *already* in CGS, so we
 don't need to convert anything.
 
+More Complicated Fields
+-----------------------
+
 The last part, the call to add_field, is the most crucial.  It creates a
 DerivedField object which will control the behavior of the derived field in a
 couple crucial ways -- what you see here includes the string used for the

Added: trunk/doc/source/tutorial/derived_quantities.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/tutorial/derived_quantities.rst	Mon May  5 08:49:34 2008
@@ -0,0 +1,2 @@
+Derived Quantities
+==================

Added: trunk/doc/source/tutorial/example_script.rst
==============================================================================
--- (empty file)
+++ trunk/doc/source/tutorial/example_script.rst	Mon May  5 08:49:34 2008
@@ -0,0 +1,37 @@
+A Demonstrative Example Script
+==============================
+
+During the course of my work, I often have to run a selection of data analysis
+tasks in order to keep tabs on my simulation as it runs.  I've included below a
+script that I run on each output as it is created.
+
+.. code-block:: python
+
+   import sys
+   import yt.lagos as lagos
+   import yt.raven as raven
+   
+   fn = sys.argv[-1]
+   pf = lagos.EnzoStaticOutput(fn)
+   pf.h.print_stats()
+
+   fields_to_plot = ["NumberDensity", "Density", "Temperature", "H2I_Fraction"]
+   
+   my_vals = [1000.0, 100.0, 10.0, 1.0]
+   my_units = ['au','rsun']
+   
+   my_widths = []
+   
+   for unit in my_units:
+       my_widths += [(v,units) for v in my_vals]
+   
+   pc = raven.PlotCollection(pf)
+   for i in range(3): pc.add_slice("NumberDensity", i)
+   
+   for field in fields_to_plot:
+       pc.switch_field(field)
+       for w, u in my_widths:
+           pc.set_width(w,u)
+           pc.save("%s" % pf)
+
+And that's it!

Modified: trunk/doc/source/tutorial/getting_started.rst
==============================================================================
--- trunk/doc/source/tutorial/getting_started.rst	(original)
+++ trunk/doc/source/tutorial/getting_started.rst	Mon May  5 08:49:34 2008
@@ -1,6 +1,8 @@
 Getting Started
 ===============
 
+.. index:: Starting yt
+
 Getting into yt
 ---------------
 
@@ -22,6 +24,8 @@
 
    >>> import yt.lagos as lagos
 
+.. index:: hierarchy
+
 The Hierarchy
 -------------
 
@@ -43,6 +47,8 @@
    >>> print v
    >>> print c
 
+.. index:: Grid, 3ddata;grid
+
 The Grids
 ---------
 

Modified: trunk/doc/source/tutorial/index.rst
==============================================================================
--- trunk/doc/source/tutorial/index.rst	(original)
+++ trunk/doc/source/tutorial/index.rst	Mon May  5 08:49:34 2008
@@ -1,7 +1,10 @@
 A Short Tutorial
 ================
 
-
+As with many interactive packages, getting started with yt can be a bit
+daunting.  Following this tutorial we'll walk through the intepreter, get used
+to some of the ways that yt works, and performing some common (and
+not-so-common) tasks.
 
 Contents:
 
@@ -15,3 +18,5 @@
    automated_plotting
    advanced_objects
    projections
+   derived_quantities
+   example_script

Modified: trunk/doc/source/tutorial/profiles.rst
==============================================================================
--- trunk/doc/source/tutorial/profiles.rst	(original)
+++ trunk/doc/source/tutorial/profiles.rst	Mon May  5 08:49:34 2008
@@ -1,5 +1,5 @@
 Profiles
---------
+========
 
 Profiles are one of the more interesting data types.  They are a binned average
 of one or more variables, along one or two different dimensions.  For example,
@@ -7,6 +7,9 @@
 Look at the distribution of Volume through Density and Temperature space.  Or you could
 take the spherically-averaged Number Density and see how it changes with radius.
 
+One Dimensional Profiles
+------------------------
+
 In order to make a profile, we first need a data object we want to get the profile
 *from*.  This can be a sphere, a region, or even an extracted region.  We'll
 first take a look at doing a spherically-average profile of Temperature with Radius.  ::
@@ -43,6 +46,8 @@
    >>> pylab.ylabel(r"$\rm{Density} (\rm{g}/\rm{cm}^3)$")
    >>> pylab.savefig("my_profile.png")
 
+Two-Dimensional Profiles
+------------------------
 
 Two-dimensional profiles are along the same lines.  ::
 

Modified: trunk/doc/source/tutorial/projections.rst
==============================================================================
--- trunk/doc/source/tutorial/projections.rst	(original)
+++ trunk/doc/source/tutorial/projections.rst	Mon May  5 08:49:34 2008
@@ -1,10 +1,13 @@
 Projections
------------
+===========
 
 Projections are the line integrals of a given quantity along a given access.
 These are useful in a wide variety of problems -- they can reveal morphologies
 that slicing cannot, in the simplest case.
 
+Simple Projections
+------------------
+
 There are several ways to generate projections in yt, and with the appropriate
 software package installed (mpi4py) one can even generate them in parallel,
 distributed across an arbitrary number of nodes.  However, I will deal here
@@ -24,3 +27,8 @@
 stored in an HDF5 file tied to the parameter file.  Then next time you ask
 for it, it is already available.  Zooming and panning is accomplished very
 simply.
+
+Parallel Projections
+--------------------
+
+

